Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates FSP34 and KS17. Multi-sample variant calling identified a total of 461683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. Variant density was higher on sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets affected by high impact variants. A core genome representing genomic elements conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements are present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help inform novel disease management strategies against the pathogen.

This paper presents a novel approach to decoding the Indus script, which was used by the Indus Valley Civilization (IVC) from approximately 3300 to 1900 BCE. The main focus of this research is the structural analysis of the signs within the Indus script. The central objective of the paper is to determine whether the Indus script can be classified as an alphabet, and it aims to provide compelling evidence regarding the number of primary signs. This includes establishing the actual count of Indus signs through the decomposition of compound signs, identifying diacritics and analyzing their consistent usage, as well as exploring the underlying concepts and implications associated with sign extraction. To comprehensively examine the Indus script, the paper analyzes over 400 signs, encompassing the entire script rather than a select subset of signs or texts. The visual decomposition of the signs employs a simple grid methodology. By summarizing the logical findings, the paper successfully identifies the primary signs and develops an understanding of their phonetic representation within the alphabet. The study recognizes the diverse writing styles used to combine the basic signs, The writing style of the Indus script incorporates variations in formation, composition, and combination, resulting in a significant number of signs. The research findings indicate that the Indus Script primarily consists of only 40 core signs.

The combination of micro- or nanofluidics and strong light–matter coupling has gained much interest in the past decade, which has led to the development of advanced systems and devices with numerous potential applications in different fields, such as chemistry, biosensing, and material science. Strong light–matter coupling is achieved by placing a dipole (e.g. an atom or a molecule) into a confined electromagnetic field, with molecular transitions being in resonance with the field and the coupling strength exceeding the average dissipation rate. Despite intense research and encouraging results in this field, some challenges still need to be overcome, related to the fabrication of nano- and microscale optical cavities, stability, scaling up and production, sensitivity, signal-to-noise ratio, and real-time control and monitoring. The goal of this paper is to summarize recent developments of micro- and nanofluidic systems employing strong light–matter coupling. An overview of various methods and techniques used to achieve strong light–matter coupling in micro- or nanofluidic systems is presented, preceded by a brief outline of the fundamentals of strong light–matter coupling and optofluidics operating in the strong coupling regime. The potential applications of these integrated systems in sensing, optofluidics, and quantum technologies are explored. The challenges and prospects in this rapidly developing field are discussed.

Summary Genome assembly projects have grown exponentially due to breakthroughs in sequencing technologies and assembly algorithms. Evaluating the quality of genome assemblies is critical to ensure the reliability of downstream analysis and interpretation. To fulfil this task, we have developed the AssemblyQC pipeline that performs file-format validation, contaminant checking, contiguity measurement, gene- and repeat-space completeness quantification, telomere inspection, taxonomic assignment, synteny alignment, scaffold examination through Hi-C contact-map visualisation, and assessments of completeness, consensus quality and phasing through K-mer analysis. It produces a comprehensive HTML report with method descriptions, tables, and visualisations. Availability and Implementation The pipeline uses NextFlow for workflow orchestration and adheres to the best-practice established by the nf-core community. This pipeline offers a reproducible, scalable, and portable method to assess the quality of genome assemblies – the code is available online.GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc Supplementary information Pipeline usage documentation, parameter descriptions and example outputs are available on GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc/tree/main/docs. A preview report is also hosted online: https://plant-food-research-open.github.io/assemblyqc

Nyssa yunnanensis is a deciduous tree species in the family Nyssaceae within the order Cornales. As only eight individual trees and two populations have been recorded in China’s Yunnan province, this species has been listed among China’s national Class I protection species since 1999 and also among 120 PSESP (Plant Species with Extremely Small Populations) in the Implementation Plan of Rescuing and Conserving China’s Plant Species with Extremely Small Populations(PSESP) (2011-2-15). Here, we present the draft genome assembly of N. yunnanensis. Using 10X Genomics linked-reads sequencing data, we carried out the de novo assembly and annotation analysis. The N. yunnanensis genome assembly is 1475 Mb in length, containing 288,519 scaffolds with a scaffold N50 length of 985.59 kb. Within the assembled genome, 799.51 Mb was identified as repetitive elements, accounting for 54.24% of the sequenced genome, and a total of 39,803 protein-coding genes were predicted. With the genomic characteristics of N. yunnanensis available, our study might facilitate future conservation biology studies to help protect this extremely threatened tree species.

The recent report that DNA extracted from ancient bone must have from the offspring of a female Neanderthal and a male Denisovan depends on the inference that the subject has a high level of heterozygosity for Neanderthal and Denisovan alleles across the genome. Here I point out that the relative frequencies of derived transversion polymorphisms varies markedly between the new specimen, Denisova 11, and two high-coverage Neanderthal genomes. In Denisova 11 the AC and CG polymorphisms are much commoner than the others and are almost twice as common as the AT polymorphism. In the high-coverage Neanderthal genomes the four types of transversion are about equally common, with the AT being slightly commoner than the others. These results suggest that allele-calling errors are frequent and that this may provide an alternative explanation for the observed heterozygosity.

To understand the mystery of final unification, in our earlier publications, we proposed that, 1) There exist three atomic gravitational constants associated with electroweak, strong and electromagnetic interactions; and 2) There exists a strong interaction elementary charge (e_s) in such a way that, it's squared ratio with normal elementary charge is close to inverse of the strong coupling constant. In this context, starting from lepton rest masses to stellar masses, we have developed many interesting and workable relations. We noticed that, electroweak field seems to be operated by a primordial massive fermion of rest energy 585 GeV. It can be considered as the zygote of all elementary particles and galactic dark matter. Proceeding further, with a characteristic fermion-boson mass ratio of 2.27, quarks can be classified into quark fermions and quark bosons. Considering strong charge conservation and electromagnetic charge conservation, fractional charge quark fermions and quark bosons can be understood. Quark fermions that generate observable massive baryons can be called as Fluons. Quark bosons that generate observable mesons can be called as Bluons. By considering a new hadronic fermion of rest energy 103.4 GeV, rest masses of fluons and bluons can be estimated and there by baryon masses and meson masses can be estimated.

Klebsiella pneumoniae is a leading cause of healthcare acquired infections. The severity of the infections is multifactorial including virulence and antimicrobial resistance properties. The objective of the study was to investigate the virulence determinants of K. pneumoniae strains colonizing patients hospitalized in the intensive care units (ICU) of a tertiary hospital in Uganda. A hospital based cross-sectional study involving 103 patients admitted in the ICU of Mulago National Referral hospital was conducted from January 2022 to April 2022. A total of 31 identified clinical strains of K. pneumoniae isolated from rectal swabs of the same number of patients were characterized. Susceptibility testing of colistin was performed by broth microdilution method, thereafter, 5 colistin resistant K. pneumoniae were purposefully selected for whole genome sequencing. Bioinformatics analysis was performed using established web-based tools to detect virulence genes, sequence type and other genomic features. Numerous virulence factor genes related to pathogenicity of K. pneumoniae were identified. They ranged from those related to colonization to those of persistence and dissemination including capsule genes (wzi), siderophore systems; yersiniabactin (ybt15), aerobactin (iutA), enterobactin (entC, entD, entF, entS, fepB, fepD, fepG, fes), and salmochelin (iroN), secretion systems; type II (T2SS) and type VI (T6SS-1). Furthermore, the isolates harbored outer membrane protein (ompA) gene, biofilm synthesis gene (fimH) and several adhesion genes. The results demonstrate the dual-risk of K. pneumoniae strains combining high level of virulence and colistin resistance which is a great concern as it leads to unmanageable infection outbreaks with high morbidity and mortality.

Ganoderma boninense is the major causal agent for the basal stem rot (BSR) disease in oil palm, causing the progressive rot of the basal part of the stem. Despite its prominence, key pathogenicity determinants for the aggressive nature of hemibiotrophic infection remain unknown. In this study, genome sequencing and annotation of G. boninense T10 were carried out using the Illumina sequencing platform and comparative genome analysis was performed with previously reported G. boninense strains (NJ3 and G3). The pan-secretome of G. boninense was constructed and comprised of 937 core orthogroups, 243 accessory orthogroups, and 84 strain-specific orthogroups. A set of core candidate effector proteins (CEPs) were found to be enriched with catalytic protein classified as the carbohydrate-active enzymes, hydrolases as well as non-catalytic proteins. Differential expression analysis revealed an upregulation of CEP genes which was linked to the suppression of PTI signaling cascade while the downregulation of CEP genes was linked to the inhibition of PTI by preventing host defense elicitation. Genome architecture analysis revealed the one-speed architecture of the G. boninense genome and the lack of preferential association of CEP genes to the transposable elements. The findings obtained from this study would aid in the characterization of pathogenicity determinants and molecular biomarkers of BSR disease.

Introduction: Flow-cytometry (FC) is a powerful tool that can assist in lymphoma diagnosis in lymph node (LN) specimens. Although lymphoma diagnosis and classification are mainly based on tumor cell characteristics, surrounding cells are less employed in this process.Methods: We retrospectively investigated alterations in the ploidy status, proliferative cell fraction (PF) and the percentages of surrounding immune cells in 62 consecutive LN specimens with B-Cell Non-Hodgkin Lymphoma (B-NHL) that were submitted for FC evaluation between 2019-2022.Results: Compared with indolent B-NHLs, aggressive B-NHLs show increased DNA aneuploidy and PF, increased monocytes, immature-granulocytes, mature granulocytes, CD8⁺ T-cells, Double-Negative-T-cells and Double-Positive-T-cells, and decreased total CD45⁺ cells, total lymphocytes, CD4⁺ T-cells and CD4/CD8 ratio. Receiver operating characteristic analysis determined PF > 6.8% and immature-granulocytes > 0.9% as optimal cutoffs with highest specificity and sensitivity in differentiating aggressive and indolent B-NHLs.Conclusions: These findings further strength the diagnostic value of DNA content analysis by FC and suggest the utilization of tumor surrounding immune cells in NHL diagnosis and classification.

Background: Thyroid nodules are common, affecting nearly 65% of the general population. While they are widespread, it's crucial to recognize that the majority of these nodules are not cancerous and can be effectively managed through careful monitoring. Thyroid ultrasound is commonly used to evaluate thyroid nodules owing to its low cost, wide availability and technical ease of application. In sonography, it's crucial to assess characteristics and vascular flow. Yet, conventional color and power Doppler ultrasound may not always effectively capture small vessels and low velocities due to their limitations. Superior Microvascular Imaging can display the blood flow of small vessels and low-velocity blood flow, which is difficult to visualize with conventional Doppler ultrasound. Meanwhile other thyroid scans, that utilize either [99mTc] pertechnetate or (18)F-fluorodeoxyglucose, can categorize nodules as hyperactive ('hot'), exhibiting normal activity ('warm'), or having reduced/no activity ('cold'). Thus, the main goal of screening and tracking thyroid nodules is to improve the management of potentially worrisome thyroid malignancies. Methodology: The study was conducted within the structural framework of a network meta-analysis, with the index tests being - SMI, Radionuclide Scanning and Color Doppler, and the general link between them being the reference gold standard. The data collection involved searching for all pertinent literature using PubMed, Google Scholar, and the Cochrane Library databases. The essential data was extracted following the application of specific inclusion and exclusion criteria.This meta-analysis included 7 RCTs with 1,152 patients for Radionuclide Scanning, 10 RCTs with 1,847 patients for SMI and 8 RCTs with 4,480 patients for Color Doppler. They were analyzed using the QualSyst tool and the risk of bias was evaluated by using QUADAS-2 analysis.The statistical software packages MetaDiSc 1.4, RevMan (Review Manager, version 5.3), SPSS (Statistical Package for the Social Sciences, version 20) and Excel in Stata 14 were used to perform the statistical analyses. Result: According to the findings, the sensitivity for Radionuclide Scanning is calculated as 0.79 (range: 0.76 to 0.81) and specificity as 0.55 (range: 0.50 to 0.60) with a 95% confidence interval. The overall diagnostic odds ratio (DOR) for Radionuclide Scanning Is 10.54.Additionally, with a 95% confidence interval, SMI exhibits a sensitivity of 0.82 (with a range of 0.79 to 0.84) and a specificity of 0.86 (with a range of 0.84 to 0.88), while the overall DOR is approximately 25.73. Color Doppler demonstrates a calculated sensitivity of 0.71 (ranging from 0.69 to 0.74) and specificity of 0.81 (ranging from 0.79 to 0.83) with a 95% confidence interval, while its DOR is 13.48.Conclusion: As evidenced by this meta-analysis, blood flow dependent imaging techniques are superior in their abilities to be used as diagnostic tests, especially in conjunction with their use in detecting thyroid nodules. This study offers a starting point for delving deeper into the utilization of Radionuclide Imaging, Superior Microvascular Imaging and Color Doppler in diagnosing thyroid nodules in a clinical setting. Key Words: - Thyroid Nodule, Radionuclide Scanning, Superior Microvascular Imaging, Color Doppler Diagnosis, Sensitivity, Specificity, Diagnostic imaging

Harnessing the Remarkable Bio-Remediation Potential of Vernonia spp. for the Sustainable Restoration of Hydrocarbon-Polluted Clay Soil in Ogoni Land, Nigeria This study explores the potential of utilizing Vernonia spp. for eco-friendly bio-remediation of hydrocarbon-polluted clay soil in Ogoni Land, Nigeria. The aim is to find a sustainable and effective solution that promotes the restoration of the polluted soil while minimizing the use of external additives. The process of bio-remediation can occur naturally, through natural attenuation or intrinsic bio-remediation. However, it has been observed that in certain cases, the addition of fertilizers, oxygen, or organic matter is required to enhance the effectiveness of bio-remediation. In this research, we focus on the bio-remediation potential of Vernonia spp., a native plant species known for its strong phytoremediation abilities. By harnessing the remarkable bio-remediation properties of Vernonia spp., we seek to restore the hydrocarbon-polluted clay soil in Ogoni Land in an environmentally friendly and sustainable manner. Our methodology involves conducting greenhouse experiments to assess the bio-remediation efficiency of Vernonia spp. in different soil conditions. We will analyze the soil's physical and chemical properties, as well as the degradation of hydrocarbons over time. The experimental results will provide valuable insights into the effectiveness of Vernonia spp. in removing hydrocarbon pollutants from clay soil. Through this study, we aim to develop a cost-effective and sustainable approach to restore hydrocarbon-polluted clay soil in Ogoni Land. By leveraging the natural bio-remediation potential of Vernonia spp., we can potentially reduce the reliance on external additives, thus minimizing the environmental impact associated with traditional remediation methods. The research article explores methods to promote the growth of pollution-eating microbes in order to enhance bio-remediation. Bio-remediation refers to the use of naturally occurring organisms to break down harmful substances into less toxic or non-toxic forms. In situ bio-remediation involves treating the contaminated material directly at the site, while ex-situ bio-remediation involves removing the contaminated material for treatment elsewhere. This study specifically investigates ex-situ bio-remediation techniques for hydrocarbon-contaminated clay soil. The researchers found that the application of room dry and wet blended bitter leaf showed promising results in the bio-remediation of hydrocarbons in the clay soil. Using Vernonia galamensis, a concentration as high as 0.55 ug/ml was achieved, while Vernonia amygdalina yielded a concentration as high as 0.67 ug/ml when applied at 35g and 40g respectively, based on the wet blended approach. These findings highlight the effectiveness of wet blended Vernonia species in the bio-remediation process.During the remediation process of the clay soil, the pH levels showed a trend of increasing from acidic to normal to alkaline. This can be attributed to the remediation of excessive metals present in the soil. After 40 days, the pH of the clay soil reached 6.97 when treated with 40 grams of Vernonia galamensis, and 7.00 when treated with 40 grams of Vernonia amygdalina. Interestingly, while the remediation efficiency of HC (hydrocarbon) decreased with increasing mass of Vernonia galamensis, the remediation efficiency of HC increased when using Vernonia amygdalina. These observations highlight the varying effects of different Vernonia species on hydrocarbon remediation.The highest remediation values were observed when using Vernonia galamensis at 35g and Vernonia amygdalina at 40g. These particular amounts of these Vernonia species demonstrated effective remediation of the targeted pollutants. However, in comparison to other metals, the remediation effects were relatively lower for zinc (Zn), with only approximately 0.25 ug/ml being remediated. This suggests that the remediation potential of the Vernonia species may vary depending on the specific contaminant.The higher remediation effects observed for Zn metal in the soil can be attributed to the wet blended preparation method of the Vernonia species. In contrast, the room dried Vernonia species exhibited the lowest performance in remediating the soil, with approximately 0.17 ug/ml and 0.10 ug/ml remediation for galamensis and amygdalina, respectively. Both Vernonia leaf extracts achieved a remediation of 0.5 ug/ml for chromium. The sun dried and room dried methods also showed considerable remediation potential, with values above 0.4 ug/ml. The level of significance for the model was attained at 0.05, and the r2 value was appreciable. These findings indicate the effectiveness of different preparation methods and Vernonia species in soil remediation

With reference to our earlier published views on large nuclear gravitational constant , nuclear elementary charge and strong coupling constant , in this paper, we present simple relations for nuclear stability range, binding energy of isotopes and magic proton numbers.

High-quality optical Fano resonances, which exist in a spherical dielectric microparticle in the spatial configurations of the "whispering-gallery modes" (WGMs) and recently are referred to as the “super-resonances”, possess extremal sensitivity not only to the micro-cavity size and shape but also to the optical properties of the particulate material. The increase in the power of light radiation coupling into a super-resonance can lead to the manifestation of strong optical nonlinearity of the resonator material due to the cubic nonlinearity (optical Kerr effect) and generation of free electron plasma in certain regions of the spherical microcavity. In fact, an optically linear medium of the resonance cavity transforms into a Drude-Kerr-type medium with a strong dependence on input laser intensity. With the help of the finite-elements numerical simulations, we theoretically analyze the transformations of the resonant contour for a number of high-quality WGMs excited in a lanthanum-glass microsphere exposed to an optical radiation of different intensity. We show that in a certain input intensity range, the competition of Kerr and plasma optical nonlinearities can stop and even reverse the Stokes shift of the super-resonance observed in a pure Kerr medium. Additionally, optical ionization and plasma generation within the mode volume significantly reduce the strength of the magnetic super-resonance and lead to its spoiling and frequency splitting.

Current artificial intelligence (AI) technology is still considered weak AI. However, the progression towards strong AI unavoidably involves grappling with concerns surrounding consciousness, the mind, and creativity. This paper focuses on analyzing consciousness, creativity, and the generation of emotions to explore the possibility of machine-based consciousness, creativity, and emotion. We believe that the emergence of consciousness relies on the complex interplay at different layers within a complex system, rather than wholly relying on the underlying substrates of the system. Thus, it is plausible to consider the existence of machine-based consciousness, creativity, and emotion. Furthermore, swarm intelligence should be recognized as a distinct form of intelligence. Human individuals serve as the foundational substrate enabling the realization of swarm intelligence, with individual intelligence reflecting the projection of swarm intelligence at the individual level. The advanced state of human civilization is primarily attributable to the effect of swarm intelligence. Building upon basic emotions to adapt to environmental conditions, advanced human emotions are a product of the evolutionary process by swarm intelligence. Emotions serve as a pivotal impetus for the formation and development of societies grounded in swarm intelligence. In pursuit of super-AI that surpasses human civilization in the future, nurturing swarm intelligence represents an inevitable trajectory.

The overcrowding of high-rise buildings in the city adversely affects the wind environment by changing the air currents in the surrounding areas. In particular, extreme climate phenomena caused by climate change are stronger and more frequent, causing social damages in cities. To comprehensively better understand the wind properties around high-rise buildings, actual filed measurement is necessary to determine the environment assessment of wind effect. We performed the on-site measurement on LCT residential complex regions (411.6m tall) with highly concentrated high-rise buildings in coastal city Busan, South Korea under extreme weather conditions such as typhoon invasions to determine wind fluid characteristics. In the field monitoring, five anemometers were installed to analyze the wind environment around high-rise buildings when typhoon 'Hinnamnor' invaded. Compared to the nearby weather station operated by KMA(Korea Meteorological Administration), the gust was 3.7 times stronger and the max 1 min-mean wind speed was 3.1 times stronger, and the characteristics of the downward wind and the canyon wind were shown depending on the location characteristics of the point. Turbulence intensity decreased as the wind speed increased and converged to a certain value. Likewise, the gust factor also decreased as the wind speed increased and converged to 2.0, which is considered to be the parameter that best represents the intensity of the instantaneous gust caused by the skyscraper wind effect.

BackgroundLiving donor liver transplantation offers comparable long-term results to cadaveric donor transplantation. This study analyzes the selection process of living liver donors at a Western transplant center that utilizes both donation forms. MethodsThis retrospective analysis examined potential living donors, collecting medical data and reasons for refusal, and divided patients by indication and urgency for transplantation. ResultsFrom January 2013 to December 2023, 594 potential living donors were assessed at Jena University Hospital. Of these, 124 living donor transplants were performed. During outpatient evaluation, 357 potential donors were excluded. Subsequently, 238 individuals underwent inpatient assessment, with 100 more being excluded. Main reasons for donor refusal included medical or psychological issues (n=160), disease progression in recipients (n=90), and recipient refusal or donor withdrawal (n=54). The evaluation process showed a trend towards considering more distant relatives and acquaintances as donor candidates with increasing severity of the recipient's disease.

This article describes a novel electrochemical on-chip biosensor that utilizes anti-PSA antibody (Ab) and silver nanoparticles (AgNPs) to enhance the sensing and detection capability of prostate specific antigen (PSA) in the blood. The AgNPs are prepared, characterized, and applied onto a silicon photonic on-chip biosensing receptor platform designed to enhance the accurate detection of PSA. The AgNPs were synthesized by a chemical reduction method using silver nitrate (AgNO₃) as the precursor. Transmission electron microscopy (TEM), selected area electron diffraction (SAED), energy dispersion X-ray spectroscopy (EDS), small angle X-ray scattering (SAXS), X-ray diffraction (XRD), and light microscopy were among the methods used in the characterization and analysis of the AgNPs. Each stage of the immunosensor fabrication was characterized using cyclic voltammetry. The proposed immunosensor was applied in the detection of PSA, a prostate cancer biomarker, with a high sensitivity and a limit of detection of 0.17 ng/mL over a linear concentration range of 2.5 to 11.0 ng/mL. The immunosensor displayed good stability and was selective in the presence of interfering species like immunoglobulin (Ig) in human serum, ascorbic acid (AA), and diclofenac (Dic). The detectivity and sensitivity are significantly higher than previous reports on similar or related technologies.

Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains - Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198 - previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbors, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.

The genus Lirianthe in the family Magnoliaceae includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and protected due to their endangered status. The limited knowledge of species within this genus and the absence of research on its chloroplast genome have greatly impeded studies on the relationship between its evolution and systematics. In this study, the chloroplast genomes of 8 species from the genus Lirianthe were sequenced and analyzed, their phylogenetic relationships with other genera of the family Magnoliaceae are also elucidated. The results showed that the chloroplast genome sizes of the 8 Lirianthe species ranged from 159,548 to 159,833 bp. The genomes consisted of a large single copy region, a small single copy region, and a pair of inverted repeat sequences. The GC content was very similar across species. Gene annotation revealed that the chloroplast genomes contained 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, totaling 130 genes. Codon usage analysis indicated that codon usage was highly conserved among the 8 Lirianthe species. Repeat sequence analysis identified 42-49 microsatellite sequences, 16-18 tandem repeats, and 50 dispersed repeats, with microsatellite sequences being predominantly single nucleotide repeats. DNA polymorphism analysis revealed 10 highly variable regions located in the large single copy and small single copy regions, among which rpl32-trnL, petA-psbJ and trnH-psbA are recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. Phylogenetic tree analysis confirmed the monophyly of the genus Lirianthe and its closest relationship with the genera, Talauma and Dugandiodendron. Morphological studies found noticeable differences between Lirianthe species in aspects including leaf indumentum, stipule scars, floral orientation, tepal number, tepal texture, and fruit dehiscence. In summary, this study elucidated the chloroplast genome evolution within Lirianthe and laid a foundation for further systematic and taxonomic research of this genus.

The ZIPs (ZRT/IRT-like proteins) play critical roles in the absorption, transport, and intracellular balance of metal ions essential for various physiological processes in plants. However, little is known about the pan-genomic characteristics and properties of ZIP genes in cucumber (Cucumis sativus L.). In this study, we identified 10 CsZIP genes from the pan-genome of 13 C. sativus accessions. Among them, only CsZIP10 showed no variation in protein sequence length. We analyzed the gene structure, conserved domains, promoter cis-elements, and phylogenetic relationships of these 10 CsZIP genes derived from "9930". Based on phylogenetic analysis, the CsZIP genes were classified into three branches. Amino acid sequence comparison revealed the presence of conserved histidine residues in the ZIP proteins. Analysis of promoter cis-elements showed that most promoters contained elements responsive to plant hormones. Expression profiling in different tissues showed that most CsZIP genes were expressed at relatively low levels in C. sativus leave, stem, and tendril, and CsZIP7 and CsZIP10 were specifically expressed in root, indicating their potential involvement in the absorption and transport of metal ions. Transcriptomic data indicated that these 10 ZIP genes displayed responses to both downy mildew and powdery mildew, and CsZIP1 were significantly downregulated after both salt and heat treatments. In conclusion, this study deepens our understanding of the ZIP gene family and enhances our knowledge of the biological functions of CsZIP genes in C. sativus.

In the rapidly evolving landscape of genetic engineering, the advent of CRISPR-Cas technologies has catalyzed a paradigm shift, empowering scientists to manipulate the genetic code with unprece-dented accuracy and efficiency. Despite the remarkable capabilities inherent to CRISPR-Cas sys-tems, recent advancements have witnessed the integration of small molecule to augment their functionality, introducing new dimensions to the precision and versatility of gene editing applica-tions. This review delves into the synergy between CRISPR-Cas technologies and small molecule drugs, elucidating the pivotal role of chemicals in optimizing target specificity and editing efficiency. By examining a diverse array of applications, ranging from therapeutic interventions to agricultural advancements, we explore how the judicious use of chemicals enhances the precision of CRISPR-Cas-mediated genetic modifications. In this review we emphasize the significance of small molecule drugs in fine-tuning the CRISPR-Cas machinery, which allows researchers to exert meticulous con-trol over the editing process. We delve into the mechanisms through which these chemicals bolster target specificity, mitigate off-target effects, and contribute to the overall refinement of gene edit-ing outcomes. Additionally, we discuss the potential of chemical integration in expanding the scope of CRISPR-Cas technologies, enabling tailored solutions for diverse genetic manipulation challenges. As CRISPR-Cas technologies continue to evolve, the integration of small molecule drugs emerges as a crucial avenue for advancing the precision and applicability of gene editing techniques. This re-view not only synthesizes current knowledge but also highlights future prospects, paving the way for a deeper understanding of the synergistic interplay between CRISPR-Cas systems and chemical modulators in the pursuit of more controlled and efficient genetic modifications.

The Peruvian creole cattle (PCC) is a neglected breed, and is an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of the PCC using a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. The obtained genome size of the PCC was 2.77 Gb with a contig N50 of 108Mb and 92.59% complete BUSCOs. Also, we identified 40.22% of repetitive DNA of the genome assembly, of which retroelements occupy 32.39% of the total genome. A total of 19,803 protein-coding genes were annotated in the PCC genome. We downloaded proteomes and genomes of the Bovinae subfamily, and conducted a comparative analysis with our draft genome. Phylogenomic analysis showed that PCC is related to Bos indicus. Also, we identified 7,746 family genes shared among the Bovinae subfamily. This first PCC genome is expected to contribute to a better understanding of its genetics to adapt to the tough conditions of the Andean ecosystem, and evolution.

Escherichia coli phage Eco_BIFF was isolated from several laboratory stocks of E. coli K-12 MG1655 derivatives. The source of the contamination is unknown. Eco_BIFF is a lytic phage that shows effective growth inhibition of E. coli K-12. Here, we announce the complete genome sequence of Eco_BIFF, and major findings from its genome annotation.

Hox gene clusters are crucial in Embryogenesis. It was observed that some Hox genes are located in order along the telomeric to centromeric direction of the DNA sequence: Hox1, Hox2, Hox3…. These genes are expressed in the same order in the ontogenetic units of the Drosophila embryo along the Anterior-Posterior axis. The two entities (genome and embryo) differ significantly in linear size and in-between distance. This strange phenomenon was named Spatial Collinearity (SP). Later, it was observed that, particularly in the Vertebrates, a Temporal Collinearity (TC) coexists: first is Hox1 expressed, later Hox2 and even later Hox3,…,. According to a Biophysical Model (BM), pulling forces act at the anterior end of the cluster while a cluster fastening applies at the posterior end. Hox clusters are irreversibly elongated along the force direction. During Evolution, the elongated Hox clusters are broken at variable lengths thus split clusters may be created. An Empirical Rule was formulated distinguishing development due to a complete Hox cluster from development due to split Hox clusters. BM can ‘explain’ this Empirical Rule. In a spontaneous mutation where the cluster fastening is dismantled, a weak pulling force automatically shifts the cluster inside the Hox activation domain. This cluster translocation can probably explain the absence of Temporal Collinearity in Drosophila.

The inherited ‘EIA’ process at Brexit is based on a ‘Project’ period from Inception tothe start of construction works. The ‘Incompleteness’ of the process covers andidentifies stages that will impact on the environmental cycle: construction period,operational life, de-commissioning and a return to acceptable environmental footprint.A master environment structure-plan framework is required to commence with theupgrading of the complete ‘EIA’ process, embracing separate limbs for the UK’spriority environmental targets for climate change, and other major adverse effectswhich result in serious ‘harm’ to the UK environment. The identification of the processfor ‘incompleteness’ requires effective sustainability, and inclusion of effectivemanagement tools, for the essential ‘monitoring/control/recording’ proceduresthroughout the project life and the natural environmental cycle. This will allow theopportunity for a new approach to a structured ‘Suite of EIAR Directives’, to enable a‘EIAR’ regime that ‘will remain fit and proper for UK purpose’.

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. Aim of the study was to identify the antimicrobial resistance and accessory genes, the clonal relatedness and the evolution dynamics of selected CRKP isolates recovered in an adult and a pediatric intensive care unit of a tertiary hospital in Greece. Methods: Twenty-four CRKP isolates recovered during 2018-2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed applying various bioinformatics software. Results: The isolates belonged to eight sequence types 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16 and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323 and ST39 were classified in distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs. Conclusion: The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates.

Here we analyze three well-known conjectures: (i) the existence of infinitely-many twin primes, (ii) Goldbach’s strong conjecture, and (iii) Polignac’s conjecture. We show that the three conjectures are related to each other. In particular, we see that in analysing the validity of the Goldbach’s strong conjecture, one must consider also the existence of an infinite number of twin primes. As a consequence of how we approach this analysis, we also observe that if this conjecture is true, then so is Polignac’s conjecture. Our first step is an analysis of the existence of infinitely-many twin primes numbers. For this, using the formula 4((n−1)!+1) ≡ −n (mod n(n + 2)) – satisfied if and only if (n, n + 2) are twin primes –, together with Wilson’s theorem, we obtain conditions that must be met for two numbers to be twin primes. Our results, obtained from an analytic and functional study, lead us to conclude that there may exist infinitely-many twin primes. Next, we consider the validity of the Goldbach’s strong conjecture. After showing that the conjecture is true for the first even numbers, we notice a pattern that we analyze for any even number, reducing it to three cases: (i) when the even number 2n is two times a prime number n; (ii) when the even number 2n is such that n = 2m, with 2m − 1 and 2m + 1 twin primes; (iii) all other cases, i.e., for any 2n even number ∀n ∈ N with n > 1, n prime or not, with independence of n = 2m being 2m−1 and 2m+1 twin primes or not. In this last case we show that one can always find a certain r ∈ N such that 1 < r < n satisfying that n−r and n+r are primes, so that their sum is 2n. In this case we use the reduction to absurd method, and our results lead us to conclude that Goldbach’s strong conjecture is true to the best of our calculations, as well as the Polignac’s conjecture.

We construct a repeated quantum game with public goods by the quantum entanglement and strong reciprocity. By using the paradigm of quantum game analysis, we obtain that both the quantum entanglement and strong reciprocity are helpful to intensify cooperation and achieving Pareto optimality. In addition, under an example which is greenhouse green viable planting industry, we verify that the quantum entanglement and strong reciprocity have a positive role in cooperation.

A physical scrutiny of experimental results published in Physical Review Letters (December 2015, M. Giustina, et al., Phys. Rev. Lett. 115, 250401, and L. K. Shalm et al., Phys. Rev. Lett. 115, 250402) is undertaken. These articles reported that measured outcomes were fitted with quantum states possessing a dominant component of non-entangled photons, thereby contradicting their own claim of quantum nonlocality. With probabilities of photon detections lower than 0.1 %, the alleged quantum nonlocality cannot be classified as a resource for developing quantum computing devices, despite recent publicity. Experimental evidence of a feasible process for quantum-strong correlations has been identified (M. Iannuzzi, et al., Phys. Lett. A, 384 (9), 126200, 2020) in terms of correlations between independent and multi-photon states evaluated as Stokes vectors on the Poincaré sphere. As single-photon sources are not needed, the design and implementation of quantum computing operations will be significantly streamlined.

Physics of high-Tc superconducting cuprates is obscured by the effect of strong electronic correlations. One way to overcome the problem is to seek for an exact solution at least within the small cluster and expand it to the whole crystal. Such an approach is in the heart of the cluster perturbation theory (CPT). Here we develop CPT for the dynamic charge and spin susceptibilities (spin-CPT), within which the correlation effects are explicitly taken into account by the exact diagonalization. We apply spin-CPT to the effective two-band Hubbard model for the cuprates obtained from the three-band Emery model and calculate one- and two-particle correlation functions, namely, spectral function and spin and charge susceptibilities. Doping dependence of the spin susceptibility was studied within spin-CPT and CPT-RPA that is the CPT generalization of the random phase approximation (RPA). Both methods produce the low energy response at four incommensurate wave vectors in qualitative agreement to the results of the inelastic neutron scattering on overdoped cuprates.

New setting is introduced to study the global powerful alliance. Global powerful alliance is about a set of vertices which are applied into the setting of neutrosophic graphs. Neighborhood has the key role to define this notion. Also, neighborhood is defined based on strong edges. Strong edge gets a framework as neighborhood and after that, too close vertices have key role to define global powerful alliance based on strong edges. The structure of set is studied and general results are obtained. Also, some classes of neutrosophic graphs excluding empty, path, star, and wheel and containing complete, cycle and r-regular-strong are investigated in the terms of set, minimal set, number, and neutrosophic number. Neutrosophic number is used in this way. It’s applied to use the type of neutrosophic number in the way that, three values of a vertex are used and they’ve same share to construct this number. It’s called “modified neutrosophic number”. Summation of three values of vertex makes one number and applying it to a set makes neutrosophic number of set. This approach facilitates identifying minimal set and optimal set which forms minimal-global-powerful-alliance number and minimal-global-powerful-alliance-neutrosophic number. Two different types of sets namely global-powerful alliance and minimal-global-powerful alliance are defined. Global-powerful alliance identifies the sets in general vision but minimal-global-powerful alliance takes focus on the sets which deleting a vertex is impossible. Minimal-global-powerful-alliance number is about minimum cardinality amid the cardinalities of all minimal-global-powerful alliances in a given neutrosophic graph. New notions are applied in the settings both individual and family. Family of neutrosophic graphs has an open avenue, in the way that, the family only contains same classes of neutrosophic graphs. The results are about minimal-global-powerful alliance, minimal-global-powerful-alliance number and its corresponded sets, minimal-global-powerful-alliance-neutrosophic number and its corresponded sets, and characterizing all minimal-global-powerful alliances, minimal-t-powerful alliance, minimal-t-powerful-alliance number and its corresponded sets, minimal-t-powerful-alliance-neutrosophic number and its corresponded sets, and characterizing all minimal-t-powerful alliances. The connections amid t-powerful-alliances are obtained. The number of connected components has some relations with this new concept and it gets some results. Some classes of neutrosophic graphs behave differently when the parity of vertices are different and in this case, cycle, and complete illustrate these behaviors. Two applications concerning complete model as individual and family, under the titles of time table and scheduling conclude the results and they give more clarifications and closing remarks. In this study, there’s an open way to extend these results into the family of these classes of neutrosophic graphs. The family of neutrosophic graphs aren’t study deeply and with more results but it seems that analogous results are determined. Slight progress is obtained in the family of these models but there are open avenues to study family of other models as same models and different models. There’s a question. How can be related to each other, two sets partitioning the vertex set of a graph? The ideas of neighborhood and neighbors based on strong edges illustrate open way to get results. A set is global powerful alliance when two sets partitioning vertex set have uniform structure. All members of set have more amount of neighbors in the set than out of set and reversely for non-members of set with less members in the way that the set is simultaneously t-offensive and(t-2)-defensive. A set is global if t=0. It leads us to the notion of global powerful alliance. Different edges make different neighborhoods but it’s used one style edge titled strong edge. These notions are applied into neutrosophic graphs as individuals and family of them. Independent set as an alliance is a special set which has no neighbor inside and it implies some drawbacks for these notions. Finding special sets which are well-known, is an open way to purse this study. Special set which its members have only one neighbor inside, characterize the connected components where the cardinality of its complement is the number of connected components. Some problems are proposed to pursue this study. Basic familiarities with graph theory and neutrosophic graph theory are proposed for this article.

Starting from the model of a slow-rolling missile with six degrees of freedom (6 DOF) in the body frame, a 6 DOF model in the Resal frame is obtained, which is used to linearize the coupled commanded motion. Based on the linearized model, we obtain the structural scheme of the commanded object and define the quality parameters. The obtained parameters have a complex representation (with real and imaginary parts) due to the coupling between longitudinal channels. Then, the kinematic guidance equations, the seeker equations and the actuator specific to the slow-rolling single-channel missile are defined using a switching function. The guidance kinematic equations, the seeker equations and the actuator model are linearized in the Resal frame, and the structural diagram of the homing missile is constructed. Starting from this, the characteristic polynomial having complex coefficients is determined and then analyzed with the Frank-Wall stability criterion. Based on the analysis, a stability range is determined for the navigation constant and a minimum and possibly a maximum limit for the time to hit the target is obtained. The stability range defined for the navigation constant on the linear model is finally validated on the nonlinear model in the body frame.

In the realm of metal steel and iron manufacturing, there is a constant drive to optimize production efficiency and enhance the quality of the final products. This abstract explores a paradigm shift in this industry through the utilization of Computational Fluid Dynamics (CFD) as a powerful tool for achieving these goals .The study focuses on various critical aspects of the manufacturing process. Firstly, it delves into three-phase processes such as slag and gas entrainment in liquid steel, which have a significant impact on the overall product quality. Understanding and optimizing these processes is crucial to ensure the desired chemical composition and physical properties of the final metal.The abstract investigates the role of CFD in vacuum degassing, a process that plays a pivotal role in removing impurities, such as hydrogen and oxygen, from the liquid steel. By leveraging CFD to simulate and analyze the fluid flow patterns, researchers and engineers can design more efficient vacuum degassing systems, leading to improved product purity and reduced waste.Another crucial aspect explored in this abstract is the alloy melt and mixing process. By employing CFD simulations, researchers can gain insights into the movement of different alloy components and optimize their distribution within the melt. This aids in achieving the desired alloy composition, ensuring uniformity, and enhancing the mechanical properties of the final product.In addition, the study delves into the movement and flotation of inclusions, which are unwanted impurities present in the metal. CFD can be utilized to model and analyze the behavior of these inclusions, enabling engineers to design efficient strategies for their removal, thereby enhancing the purity and integrity of the final product.Moreover, the abstract considers the impact of melt temperature losses, which can occur during different stages of the manufacturing process. By employing CFD, it becomes possible to understand and mitigate these temperature losses, leading to improved energy efficiency and better control over the manufacturing parameters.Part 1 of this abstract critically evaluates the use of CFD in iron making, analyzing its benefits and limitations. It highlights how CFD can aid in process optimization, improving the understanding of complex phenomena involved in iron making, and ultimately leading to enhanced production efficiency.Part 2 focuses on the application of CFD in steel making and steel operation. It explores the fluid flow dynamics during different stages of steel production, including refining, casting, and rolling. By leveraging CFD, engineers can optimize these processes, leading to improved product quality, reduced defects, and increased productivity.This abstract demonstrates the transformative potential of Computational Fluid Dynamics in metal, steel, and iron manufacturing. By utilizing CFD as a tool to model and analyze complex fluid flow phenomena, researchers and engineers can revolutionize the production process, maximizing efficiency, and ensuring high-quality end products.

Transient receptor potential melastatin-8 (TRPM8) is a cation channel that is activated by cold and “cooling agents” such as menthol and icilin, which induce a cold sensation. Stimulation of TRPM8 activates an intracellular signaling cascade that ultimately leads to a change in the gene expression pattern of the cells. Here, we investigated the TRPM8-induced signaling pathway that links TRPM8 channel activation to gene transcription. Using a pharmacological approach, we show that inhibition of phosphatidylinositol 4-phosphate 5 kinase alpha (PIP5K), an enzyme essential for the biosynthesis of phosphatidylinositol 4,5-bisphosphate, attenuated TRPM8-induced gene transcription. Analyzing the link between TRPM8 and Gq proteins, we show that pharmacological inhibition of the beta gamma subunits impairs TRPM8 signaling. In addition, genetic studies showed that TRPM8 requires an activated Galpha subunit for signaling. In the nucleus, the TRPM8-induced signaling cascade triggers an activation of the transcription factor AP-1, a complex consisting of a dimer of basic region leucine zipper (bZIP) transcription factors. Here, we identified the bZIP protein c-Jun as an essential component of AP-1 within the TRPM8-induced signling cscade. In summary, with PIP5K, Gq subunits and c-Jun we have identified key molecules in the TRPM8-induced signaling from the plasma membrane to the nucleus.

The 2022-2023 Mpox multi-country outbreak, identified in over 110 WHO Member States, revealed a predominant impact on cisgender men, particularly those engaging in sex with men, while less frequently affecting women. This disparity prompted a focused investigation into the gender-specific characteristics of Mpox infections, particularly among women, to address a notable knowledge gap. This review systematically gathers and analyzes scientific literature and case reports concerning Mpox infections in women, covering a broad geographical spectrum including regions such as Buenos Aires, Brazil, Northern California, Colombia, Nigeria, Europe, Vietnam, Spain, Switzerland, and the United States. The analysis delves into various aspects of Mpox in women, including clinical features, epidemiology, psychological impacts, preparedness strategies, and case studies, with particular attention to pregnant women and those with underlying health conditions. Empirical data from multiple studies underscore the unique epidemiological and clinical patterns of Mpox in women. In the United States, a small percentage of Mpox cases were reported among cisgender women, with a notable portion involving non-Hispanic Black or African American, non-Hispanic White, and Hispanic or Latino ethnicities. The primary transmission route was identified as sexual or close intimate contact, with the virus predominantly manifesting on the legs, arms, and genital areas. Further, a study in Spain highlighted significant disparities in diagnosis delays, transmission modes, and clinical manifestations between genders, indicating a different risk profile and disease progression in women. Additionally, a case from Vietnam linked to a new Mpox sublineage in women emphasizes the role of women in the transmission dynamics and the importance of genomic monitoring. This review emphasizes the necessity for inclusive surveillance and research to fully understand Mpox dynamics across diverse population groups, including women. Highlighting gender and sexual orientation in public health responses is crucial for an effective approach to managing the spread and impact of the disease. The findings advocate for a gender-diverse assessment in health services and further research to explore the nuances of Mpox transmission, behavior, and progression among different groups, thereby enhancing the global response to Mpox and similar public health challenges.

Infertility is affecting around 20 % of couples in the age of procreation but however in some societies as many as one-third of all couples are unable to conceive. Different factors are contributing to male fertility declining such us endocrine disruptors environmental and professional exposures, oxidative stress and life style changes with risks of de novo epigenetics dysregulation. Since the fantastic development of new technologies of Omes and Omics , the contribution of inherited or de novo genomes and epigenome disorders contributions in male infertility are more elucidated and relevant. More than somatic genome investigation of infertile men (from chromosome to single or multiple gene point mutations) many others techniques become available in molecular andrology laboratory to investigate the genome and epigenome integrity, the maturation and the competency of the spermatozoa and its physiological environment. All those new methods of assessment are demonstrating the role of genetics and epigenetics disorders contribution on reproductive pathology and are helping the professional of assisted reproductive technology to propose different management strategy of male infertility to improve the clinical outcomes and minimize the risk of genetics or metabolic disorders at birth.

Dendrobium Sw have multiple photosynthetic pathways but due to the lack of identification, the influence of CAM pathway on the plastid genomic evolution of Dendrobium and the origin of CAM pathway are still poorly understood. In this study, based on the results of δ13C, net photosynthetic rates (Pn) and titratable acid value, we identified Dendrobium species into three photosynthetic pathways. Then the chloroplast whole genome characteristics of 10 Dendrobium species were analyzed with next-generation sequencing technology. The quadripartite-structure plastomes ranged from 151,673 bp to 160,375 bp and included 127 to 132 genes. Five noncoding mutational hotspots (rbcL-accD, atpB-rbcL, rbcL, trnLUAA, accD, Pi &gt; 0.10) were identified. A total of 41–60 SSRs were recognized, the average trinucleotide content was only about 4%, which is probably due to a more conserved SSR. Among multiple photosynthetic pathways, the apparent differences in IR junctions of SSC/IRB junctions (JSBs) were measured within chloroplast genomes, and the chloroplast genome size of constitutive CAM plants is shorter because of their ndh gene loss or pseudogenization, and this phenomenon accounts for a decreasing proportion of constitutive CAM, facultative CAM, and obligate C3 plants, so that the loss of the ndh gene may be speculated to be closely related to the CAM pathway. Phylogenetic analyses showed that there are multiple independent CAM origins in selected Dendrobium species, and the ancestral Dendrobium plastome possessed full ORFs for all ndh genes. The study aims to clarify the chloroplast genomic features of different photosynthetic pathways, enrich the genomic data of CAM plants, and provide genetic information from different perspectives for further systematic study of Dendrobium.

Malaxidinae is one of the confusing groups with classification in Orchidaceae. Previous phylogenetic analysis reveals that the relationships among the taxa in Malaxidinae have not yet been reliably established using a few plastome regions or nuclear ribosomal internal transcribed spacer (nrITS). In the present study, the complete plastomes of Oberonia integerrima and Crepidium purpureum were assembled using high-throughput sequencing. Combined with publicly available complete plastome data, this resulted in a data set of 19 plastomes, including 17 species of Malaxidinae. The plastome feature and phylogenetic relationship were compared and analyzed. The results showed that: (1) The plastomes of Malaxidinae species possessed the quadripartite structure of typical angiosperms, with sizes ranging from 142,996 bp to 158,787 bp and encoding from 125 to 133 genes. The ndh genes were lost or pseudogenized with varying degrees in six species. An unusal inversion was detected in the Large Single-Copy region (LSC) of Oberonioides microtatantha. (2) A total of 8 regions, including ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trn-FGAA-ndhJ, and trnSGCU-trnGUCC, were identified as mutational hotspots. (3) Based on complete plastomes, 68 protein-coding genes and 51 intergenic regions, respectively, the phylogenetic analyses resolved genera-level relationships in this subtribe with strong support. The Liparis was supported as polyphyletic.

Legume plants enter symbiosis with soil nitrogen-fixing bacteria (rhizobia), thereby gaining access to the assimilable atmospheric nitrogen. This symbiosis is important for agriculture, thus, biofertilizers with effective strains of rhizobia are created for crop legumes to increase their yield and minimize the amounts of mineral fertilizers used. In this work, we sequenced and characterized the genome of Rhizobium leguminosarum bv. viciae strain RCAM1022, a component of the ‘Rhizotorfin’ biofertilizer produced in Russia and used for pea (Pisum sativum L.).

MADS-box genes play a crucial role in fruit ripening, yet limited research has been conducted on mango. Based on the conserved domains of this gene family, 84 MADS-box genes were identified in the mango genome, including 22 type I and 62 type II MADS-box genes. Gene duplication analysis revealed that both tandem duplication and segmental replication significantly contributed to the expansion of MADS-box genes in the mango genome, with purifying selection playing a vital role in the segmental duplication events within the MiMADS gene family. Cis-acting element analysis demonstrated that most MiMADS genes were hormonally regulated and participated in the growth, development, and stress resistance of mango fruit. Moreover, through expression pattern analysis and phylogenetic tree construction, we identified six MiMADS genes belonging to the SEP1 subfamily and two belonging to the AG subfamily as potential candidates involved in mango ripening regulation. Notably, Mi08g17750 and Mi04g18430 from the SEP1 subfamily were identified as key regulators inhibiting mango fruit maturation; their interaction network was also analyzed. These findings provide a foundation for further investigation into the regulatory mechanisms underlying mango ripening.

Several genetic tools have been developed for Clostridium acetobutylicum utilizing 5-fluorouracil (5FU) or 5-fluorocytosine (5FC) resistance as a selection method. A method based on the integration, by single crossing-over, of a suicide plasmid (pCat-upp) followed by selection for the second crossing-over using a counter-selectable marker (the upp gene and 5FU resistance) was recently developed for genome editing in C. acetobutylicum. This method allows the modification of the genome without any marker or scar left in a strain of C. acetobutylicum that is ∆upp. Unfortunately, 5FU has strong mutagenic properties inducing mutations in the strain’s genome. After numerous applications of the pCat-upp/5FU system for genome modification in C. acetobutylicum, the bacteria became completely resistant to 5FU in the presence of the upp gene, resulting in failure in the selection for the second crossing-over. It was found that the potential repressor of the pyrimidine operon, PyrR, was mutated at position A115, leading to the 5FU resistance of the strain. We developed two plasmids, one overexpressing the native pyrR gene and a suicide plasmid carrying a non-mutated and optimized pyrR gene (pyrR*) and upp, which allowed us to restore the 5FU sensitivity of the strain. We also improved the pCat-upp/5FU system by reducing the concentration of 5FU from 1mM to 5 µM using a define synthetic medium.

For a significant period, conventional breeding and genetic modification were the key techniques that were effective in managing biotic and abiotic stresses in crops and adding desirable traits. However, the recent appearance of novel diseases and unexpected climatic changes that have substantial implications for agriculture worldwide have urged scientists to look for alternative methods to quickly manage seasonal crises. The primary emphasis of this chapter is on the obstacles and diverse biotechnological methods employed to enhance crop resilience against a range of biotic and abiotic stressors in plants. Furthermore, we consider gene transformation, omics techniques, genome editing, and other sophisticated biotechnological tools that utilize transcriptomic, proteomic, metabolomic, phenomics, RNA interference, and epigenome modifications for enhancing plant resilience. Lastly, we examine the potential of merging these eco-friendly and innovative methods with conventional breeding to promote modern agriculture and aid in enhancing tolerance to different biotic, abiotic stresses and growth promotion.

Bats are of significant interest as reservoirs for various zoonotic viruses with high diversity. During the past two decades, many herpesviruses have been identified in various bats worldwide by genetic approaches, whereas there have been few reports on the isolation of infectious herpesviruses. Herein, we report the prevalence of herpesvirus infection of bats captured in Zambia and genetic characterization of novel gammaherpesviruses isolated from Macronycteris vittatus bats. By our PCR screening, herpesvirus genomes were detected in 29.2% (7/24) of Rousettus aegyptiacus, 78.1% (82/105) of Macronycteris vittatus, and 100% (1/1) of Hipposideros caffer bats in Zambia. Phylogenetic analyses of the detected herpesvirus genomes revealed that the Zambian bat herpesviruses were divided into seven betaherpesvirus groups and five gammaherpesvirus groups. Two infectious strains of a novel gammaherpesvirus, tentatively named Macronycteris gammaherpesvirus 1 (MaGHV1), were successfully isolated from Macronycteris vittatus bats, and their complete genomes were sequenced. The genome of MaGHV1 encoded 79 open reading frames, and phylogenic analyses of the DNA polymerase and glycoprotein B demonstrated that MaGHV1 formed an independent lineage sharing a common origin with other bat-derived gammaherpesviruses. Our findings provide new information regarding the genetic diversity of herpesviruses maintained in African bats.

Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: 1) informing breeding programmes by adding a priori information about the genome, 2) providing tools such as pangenomes for characterising and conserving genetic diversity, and 3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

The newly established virus family Phenuiviridae in Bunyavirales harbors viruses infecting three kingdoms of host organisms (animals, plants, and fungi), which is rare in known virus families. Many phenuiviruses are arboviruses and replicate in two distinct hosts (e.g., insects and humans or rice). Multiple phenuiviruses, such as Dabie bandavirus, Rift Valley fever phlebovirus, and Rice stripe tenuivirus, are highly pathogenic to humans, animals, or plants. They impose heavy global burdens on human health, livestock industry, and agriculture and are research hotspots. In recent years the taxonomy of Phenuiviridae has been expanded greatly, and researches on phenuiviruses have made significant progress. With these advances, this review drew a novel panorama regarding the biomedical significance, distribution, morphology, genomics, taxonomy, evolution, replication, transmission, pathogenesis, and control of phenuiviruses, to aid researchers in various fields to recognize this highly adaptive and very important virus family.

The origin of the nucleus remains a great mystery in life science, although nearly two centuries have passed since the discovery of nuclei. To date, studies of eukaryogenesis have focused largely on micro-evolutionary explanations. Here, we examined macro-patterns of C-values (the total amount of DNA within the haploid chromosome set of an organism) for over 110,000 species and the chromosome numbers for over 11,000 species and their potential links with the state of atmospheric oxidation over geological time. Eukaryogenesis was in sync with an over 2.5 order-of-magnitude increase in genome size from prokaryote to eukaryote, and also with a rapid rise of atmospheric oxidation, suggesting that eukaryogenesis would have resulted from a regime shift of genomes driven by the oxidation-driven complexification and structuralization (e.g. chromatin packing).

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It also has been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler— SMARTdenovo, which is an SMS assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a fast assembler that did not require highly accurate raw reads for error correction, unlike other, contemporaneous SMS assemblers. It has performed well for evaluating congeneric assemblers and has been successful for a variety of assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015, and here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

Background: Transposable elements (TEs) constitute the vast majority of all eukaryotic DNA, and display extreme diversity, with thousands of families. Given their abundance and diversity, TEs discovery and annotation becomes challengeable. At present, tools and databases have built libraries to mask TEs in genomes based on de novo- and homology-based identification strategies, but no consensus criteria about which tools should be used have been proposed. Results: In the de novo-based strategy, we compared performances of TE libraries developed by four commonly used tools, including RepeatModeler, LTR_FINDER, LTRharvest, and MITE_Hunter, by using a simulated genome as a standard control. The results showed that the performance of RepeatModeler decreased as it was combined with either LTR_FINDER or LTRharvest. Combination of RepeatModeler and MITE_Hunter showed better performance than RepeatModeler and MITE_Hunter alone. In the homology-based strategy, we evaluated different sources from a taxonomic point of view to build an accurate TE library. When we selected a library from databases to identify TEs for Arabidopsis thaliana genome, the library from a genus genetically closer to Arabidopsis achieved better performance than other genera with further genetic distance. Without the Arabidopsis, combination of top three genera closer to Arabidopsis showed better performance than combination of all genera. Conclusion: This study proposes a series of recommendations to perform an accurate TE annotation: 1) For de novo-based strategy, RepeatModeler and MITE_Hunter are suggested to build a TE library; 2) For homology-based strategy, it is recommended to use library of genus genetically close to the species rather than use combined library from all genera.

A previous study involving whole genome sequencing of the white shark suggested unique molecular evolution accounting for gigantism and the enhanced longevity of sharks including positive selection of dozens of protein-coding genes potentially involved in genome stability. We performed a reanalysis on some of the genes and identified serious flaws in their results. In this short article, we scrutinize one of the serious problems we identified, report other concerns, and point out a potential bias in analyzing iconic shark species in general.

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of the apomictic species Boechera divaricarpa. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. 27048 protein-coding genes were predicted using a hybrid approach that combines homology-based and de novo methods. Also repeats, tRNA and rRNA genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. Also, a detailed analysis of evolution of the APOLLO apomixis-associated locus was performed. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species such as B. divaricarpa.

Objective: To evaluate audiological outcomes, quality of life, and complications in patients implanted with Active middle ear implants (AMEI). The secondary objective is to investigate the required duration after implantation to reach satisfactory outcomes. Methods: This retrospective study included 31 patients implanted with Active middle ear implants (AMEI) with different methods of floating mass transducer attachment. Patients with incomplete medical records and those who did not respond to postoperative follow-up were excluded. Patients were assessed preoperatively, and at one, three, and six months postoperatively. The assessment included Pure Tone Average (PTA4), Speech Reception Threshold (SRT) and Speech Discrimination Score (SDS). The Speech Spatial and Qualities of Hearing scale (SSQ12) was also used to evaluate levels of satisfaction. Result: There are no significant differences found in PTA and SRT between the 3-, 6-, and 12-month visits. The speech reception threshold (SRT) showed a statistically significant improvement at 3, 6, and 12 months post-operative measures compared to pre-operative. Additionally, the SDS exhibited a significant increase only after 12 months, compared to the 3-month time point. However, satisfaction levels did not significantly differ between the 6-month and 12-month measurements following surgery. Conclusion: Vibrant Sound bridge improves subjective satisfaction scores and audiological test scores in patients with different types of hearing loss. AMEI has a low risk of medical or surgical complications, the ease of using a hearing implant, and the social benefits of good hearing and communication.

Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand for scientists with a combined background in both fields, the education in dry lab and wet lab is often separated. This work describes an example of integrated education with focus on genomics and transcriptomics. Participants learn computational and molecular biology methods in the same practical course. Peer-review is applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. Evaluation results indicate acceptance and appreciation of this approach.

Nondipole terms in the atom-laser interaction arising due to the presence of a magnetic component in an electromagnetic wave and its inhomogeneity lead to nonseparability of the center-of-mass (CM) and electron variables in the neutral atom and, as a consequence, to its acceleration. We investigate this effect as well as the accompanying excitation and ionization processes for the hydrogen atom in strong (1012 - 2×1014 W/cm2) linearly polarized short-wavelength (5eV ≲ℏω≲ 27 eV) electromagnetic pulses of about 8 fs duration. The study has been carried out within the framework of a hybrid quantum-quasiclassical approach in which the coupled time-dependent Schrödinger equation for an electron and the classical Hamilton equations for the CM of an atom are simultaneously integrated. Optimal conditions with respect to the frequency and intensity of the electromagnetic wave for the acceleration of atoms without their noticeable ionization are found in the analyzed region.

We introduce a new variation on the domination theme which we call vertex domination as reducing waste of time in transportation planning and optimization of transport routes. We determine the vertex domination number $\gamma_v$ for several classes of fuzzy graphs. The bounds is obtained for it. In fuzzy graphs, monotone decreasing property and monotone increasing property are introduced. We prove both of the vizing's conjecture and the Grarier-Khelladi's conjecture are monotone decreasing fuzzy graph property for vertex domination. We obtain Nordhaus-Gaddum (NG) type results for these parameters. The relationship between several classes of operations on fuzzy graphs with the vertex domination number of them is studied. Finally, we discuss about vertex dominating set of a fuzzy tree by using the bridges and $\alpha$-strong edges equivalence.

The aim of this expository article is to present recent developments in the centuries-old discussion on the interrelations between several types of domination in graphs. However, the novelty even more prominent in the newly discovered simplified presentations of several older results. Domination can be seen as arising from real-world application and extracting classical results as first described by this article.The main part of this article, concerning a new domination and older one, is presented in a narrative that answers two classical questions: (i) To what extend must closing set be dominating? (ii) How strong is the assumption of domination of a closing set? In a addition, we give an overview of the results concerning domination. The problem asks how small can a subset of vertices be and contain no edges or, more generally how can small a subset of vertices be and contain other ones. Our work was as elegant as it was unexpected being a departure from the tried and true methods of this theory that had dominated the field for one fifth a century. This expository article covers all previous definitions. The inability of previous definitions in solving even one case of real-world problems due to the lack of simultaneous attentions to the worthy both of vertices and edges causing us to make the new one. The concept of domination in a variety of graphs models such as crisp, weighted and fuzzy, has been in a spotlight. We turn our attention to sets of vertices in a fuzzy graph that are so close to all vertices, in a variety of ways, and study minimum such sets and their cardinality. A natural way to introduce and motivate our subject is to view it as a real-world problem. In its most elementary form, we consider the problem of reducing waste of time in transport planning. Our goal here is to first describe the previous definitions and the results, and then to provide an overview of the flows ideas in their articles. The final outcome of this article is twofold: (i) Solving the problem of reducing waste of time in transport planning at static state; (ii) Solving and having a gentle discussions on problem of reducing waste of time in transport planning at dynamic state. Finally, we discuss the results concerning holding domination that are independent of fuzzy graphs. We close with a list of currently open problems related to this subject. Most of our exposition assumes only familiarity with basic linear algebra, polynomials, fuzzy graph theory and graph theory.

Pathogenicity of many bacteria including Bacillus cereus and Staphylococcus aureus depends on pore-forming toxins (PFTs), which cause lysis of host cells by forming pores in membranes of eukaryotic cells. Bioinformatic analysis revealed in over 600 PFTs a region homologous to the Lys171-Gly250 sequence in hemolysin II (HlyII) from B. cereus, which we designated as “homologous peptide”. Three β-barrel PFTs were used for a detailed comparative analysis. Two of them –HlyII and cytotoxin K2 (CytK2), – are synthesized in Bacillus cereus sensu lato; the third – S. aureus α-toxin (Hla) – is the most investigated representative of the family. Protein modeling showed certain amino acids of homologous peptide to be located on the surface of the monomeric forms of these β-barrel PFTs. We obtained monoclonal antibodies against both a cloned homologous peptide and a 14-membered synthetic peptide DSFNTFYGNQLFMK as part of homologous peptide. The HlyII, CytK2 and Hla regions recognized by the obtained antibodies, as well as an antibody capable of suppressing the hemolytic activity of CytK2, were identified in the course of the work. Antibodies capable of recognizing PFTs of various origins can be useful tools for both identification and suppression of the cytolytic activity of PFTs.

This article is devoted to the problem of genetically coding of inherited cyclic structures in biological bodies, whose life activity is based on a great inherited set of mutually coordinated cyclic processes. The author puts forward and arguments the idea that the genetic coding system is capable of encoding inherited cyclic processes because it itself is a system of cyclic codes connected with Boolean algebra of logic. In other words, the physiological processes in question are cyclical because they are genetically encoded by cyclic codes. In support of this idea, the author presents a set of his results on the connection of the genetic coding system with cyclic Gray codes, which are one of many known types of cyclic codes. This opens up the possibility of using for modeling inherited cyclic biostructures those algebraic and logical theories and constructions that are associated with Gray codes and have long been used in engineering technologies: Karnaugh maps, Hilbert curve, Hadamard matrices, Walsh functions, dyadic analysis, etc. Additionally, the connections of these constructions with statistical rules of genomic DNAs and binary-genomic numbers are considered.

The Ylistrum japonicum is a commercially valuable scallop known for its long-distance swimming abilities. Despite its economic importance, genetic and genomic research on this species is limited. This study presents the first complete mitochondrial genome of Y. japonicum. The mitochondrial genome is 19,475 bp long and encompasses 13 protein-coding genes, 3 ribosomal RNA genes, and 23 transfer RNA genes. By selecting 15 Pectinidae species and additional outgroup taxa, we have constructed phylogenetic trees to elucidate the evolutionary placement of Ylistrum within the family Pectinidae. Our analysis reveals that Ylistrum is a basal lineage to the Pectininae clade, distinct from its previously assigned tribe, Amusiini. This study offers critical insights into the genetic makeup and evolutionary history of Y. japonicum, enhancing our knowledge of this economically vital species.

We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, we designated Lineage 1, Lineage 2 and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50-440 kbp. The transfer of a 186 kbp region from Lineage 1 to Lineage 2 appears to have generated Lineage 3. Human-associated isolates appear to be limited to Lineages 2 and 3 but Lineage 2 appears to contain a higher number of human pathogenic isolates. The chicken isolates from our lameness trials included genomically diverse isolates from both Lineage 1 and 2, and isolates from both lineages were obtained from osteomyelitis lesions of individual birds. Our results expand the diversity of Staphylococci associated with osteomyelitis in poultry and suggest a high diversity in the microbiome of day-old chicks. Our data also support a reevaluation and unification of the taxonomic classifications of S. cohnii and S. urealyticus.

Jujube (Ziziphus jujuba Mill.) stands as a pivotal fruit tree with significant economic, ecological, and social value. Recent years have witnessed remarkable strides in multi-omics-based biological re-search on jujube. This review began by summarizing advancements in jujube genomics. Subse-quently, we provided a comprehensive overview of the integrated application of genomics, tran-scriptomics, and metabolomics to explore pivotal genes governing jujube domestication traits, quality attributes (including sugar synthesis, terpenoids, and flavonoids), and responses to abiotic stress, and discussed the transcriptional regulatory mechanisms underlying these traits. Further-more, challenges in multi-omics research on jujube biological traits were outlined, and we pro-posed the integration of resources such as pan-genomics and sRNAome to unearth key molecules and regulatory networks influencing diverse biological traits. Incorporating these molecules into practical breeding strategies, including gene editing, transgenic approaches, and progressive breeding, holds the potential for achieving molecular-design breeding and efficient genetic en-hancement of jujube.

Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations on our study. Here, we reported the complete cp genomes of seven Bulbophyllum species, including B. ambrosia, B. crassipes, B. farreri, B. hamatum, B. shanicum, B. triste and B. violaceolabellum, and compared with related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. A total of 28 Bulbophyllum cp genomes exhibit typical quadripartite structures with lengths ranging from 145,092 bp to 165,812 bp and GC content of 36.60% to 38.04%. Each genome contained 125–132 genes, encompassing 74–86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The genome arrangements, gene contents and length were similar with differences observed in ndh gene composition. A total of 18–49 long repeats and 38–80 simple sequence repeats (SSRs) were detected and the single-nucleotide (A/T) was dominant in Bulbophyllum cp genomes, with an obvious A/T preference. An analysis of relative synonymous codon usage (RSCU) revealed Leucine (Leu) was the most frequently used codon, while cysteine (Cys) was the least used. Six highly variable regions including ndhF-trnLUAG, trnTUGU-trnLUAA, trnFGAA-ndhJ, rps15-trnNGUU, rbcL-accD and psbI-trnSGCU were identified based on the ranking of the Pi values, had the potential to serve as DNA markers for species identification and phylogeny of the genus Bulbophyllum. Phylogenetic analysis based on the complete cp genome sequences and 68 protein-coding genes strongly supported 28 Bulbophyllum species can be divided into four branches and sects. Brachyantha, Cirrhopetalum, Leopardinae defined by morphology were non-monophyly. Our results enriched the genetic resources of Bulbophyllum species, providing valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the genus.

Machine learning, including deep learning, reinforcement learning, and generative artificial intelligence are revolutionising every area of our lives when data is made available. With the help of these methods, we can decipher information from larger datasets while addressing the complex nature of biological systems in a more efficient way. Although machine learning methods have been introduced to human genetic epidemiological research as early as 2004, those were never used to their full capacity. In this review, we outline some of the main applications of machine learning to assigning human genetic loci to health outcomes. We summarise widely used methods and discuss their advantages and challenges. We also identify several tools, such as Combi, GenNet and GMSTool, specifically designed to integrate these methods for hypothesis-free analysis of genetic variation data. We elaborate on the additional value and limitations of these tools from a geneticist’s perspective. Finally, we discuss the fast-moving field of foundation models and large multi-modal omics biobank initiatives.

Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for the beginners as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detections including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes the transposon classification and explains why the terms of ‘autonomous’ and ‘non-autonomous’ cannot be used to classify the superfamilies of transposons. Last, this review also discusses how to identify misannotated transposons and improve the quality of transposon database. This review provides helpful information about plant transposons and a beginner’s guide on annotating these repetitive sequences.

Elongate loach (Leptobotia elongata) is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition, and the phylogenetic relationships of L. elongata inferred using protein-coding genes (PCGs). However, the detailed information about is limited. Therefore, in this study, we sequenced the complete mitochondrial genome of L. elongata and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis respectively. The complete mitochondrial genome of the L. elongata, together with those of 36 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and two non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, L. elongata shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other 5 Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with L. elongata forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobititdae species.

Littoraria melanostoma (Gray, 1839) is a most common species of gastropods in mangroves. They quickly respond during the early stage of mangrove restoration and usually form a dominant community within a certain period. We characterized the complete mitochondrial genome of the species. The whole mitogenome of L. melanostoma was 16,149 bp in length and its nucleotide composition showed high AT-content of 64.16%. It had 37 genes, including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, one control region between tRNA-Phe and COX3. The A/T compositions in the control region is 74.7%, respectively, and are much higher than the overall A/T composition of the mitochondrial genomes. The amino acid composition and codon usage of the mitochondrial genomes of from eight superfamilies of Littorinimorpha were analyzed, and the results showed that CUU (Leu), GCU (Ala), AUU (Ile), UCU (Ser), UUA (Leu), GUU (Gly) and UUU (Phe) are the commonly used codons in this order. The results of phylogenetic analysis were roughly consistent with morphological classification, which showed that L. melanostoma is closely related to L. sinensis, a rock-dwelling species that is widespread in the coastal intertidal zone of China. These results may provide a basis to understand the phylogeny and evolution of the Littorinimorpha.

Histoplasmosis is one of the most underdiagnosed and underreported endemic mycoses in the United States. Histoplasma capsulatum is the causative agent of this disease. To date, molecular epidemiologic studies detailing the phylogeographic structure of H. capsulatum in the United States have been limited. We conducted genomic sequencing using isolates from histoplasmosis cases reported in the United States. We identified North American Clade 2 (NAm2) as the most prevalent clade in the country. Despite high intra-clade diversity, isolates from Minnesota and Michigan cases predominately clustered by state. Future work incorporating environmental sampling and veterinary surveillance may further elucidate the molecular epidemiology of H. capsulatum in the United States and how genomic sequencing can be applied for surveillance and outbreak investigation of histoplasmosis.

Plesiomonas shigelloides is the only species in the genus and has zoonotic importance due to its serious implications resulting from the consumption of contaminated seafood. This is the first report on the genomic features of the whole-genome sequence (WGS) of P. shigelloides strain V-78 recovered from diseased rainbow trout, Oncorhynchus mykiss. The genome of P. shigelloides V-78 consists of 4,478,098 base pairs (bp), which encode 3730 proteins and has a G+C content of 51.1%. The bioinformatics analysis of WGS of V-78 confirmed the presence of 121 tRNA genes and 42 rRNA genes (15 genes for 5S rRNA, 13 genes for 16S rRNA and 14 genes for 23S rRNA). Comprehensive genome analyses revealed that the strain encodes for secondary metabolites, antimicrobial resistance, and virulence genes. The strain V-78 has 31 known antibiotic resistance models, which encode many antimicrobial resistances. Also, strain V-78 has 42 different virulence genes such as adhesion, secretion system, and motility. The digital DNA-DNA hybridization value against P. shigelloides NCTC 10360 was 74.2%, while the average nucleotide identity value was 97.1%. Based on the scrutinized analysis of genomic data, strain V-78 should be considered a novel subspecies of P. shigelloides, for which Plesiomonas shigelloides subsp. oncorhynchi is proposed.

Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the section Vetrix are interesting for comparative studies of sex determination systems, yet genomic resources for these species are still quite limited. Only a few annotated reference genome assemblies are available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of 11 shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism, and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance.

Background. Mitochondrial dysfunction has been identified as a pathophysiological hallmark of disease onset and progression in patients with Parkinsonian disorders. Besides the overall emergence of gene therapies in treating these patients, this highly relevant molecular concept has not yet been defined as a target for gene therapeutic approaches. Methods. This narrative review will discuss the experimental evidence suggesting mitochondrial dysfunction as a viable treatment target in patients with monogenic and idiopathic Parkinson’s disease. In addition, we will focus on general treatment strategies and crucial challenges which need to be overcome. Results. Our current understanding of mitochondrial biology in parkinsonian disorders opens up the avenue for viable treatment strategies in Parkinsonian disorders. Insights can be obtained from primary mitochondrial diseases. However, substantial knowledge gaps and unique challenges of mitochondria-targeted gene therapies need to be addressed to provide innovative treatments in the future. Conclusions. Mitochondria-targeted gene therapies are a potential strategy to improve an important primary disease mechanism in Parkinsonian disorders. However, further studies are needed to address the unique design challenges for mitochondria-targeted gene therapies.

Choanoflagellates, the closest living relatives of animals, have the potential to reveal the genetic and cell biological foundations of complex multicellular development in animals. Here we describe the history of research on the choanoflagellate Salpingoeca rosetta. From its original isolation in 2000 to the establishment of CRISPR-mediated genome editing in 2020, S. rosetta provides an instructive case study in the establishment of a new model organism.

The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.

The development of CRISPR associated proteins, such as Cas9, has led to increased accessibility and ease of use in genome editing. However, additional tools are needed to quantify and identify successful genome editing events in living animals. We developed a method to rapidly and quantitatively monitor gene editing activity non-invasively in living animals that also facilitates confocal microscopy and nucleotide level analyses at the end of study. Here we report a new CRISPR “footprinting” approach to activate luciferase and fluorescent proteins in mice as a function of gene editing. This system is based on experience with our prior Cre-detector system and is designed for Cas editors able to target LoxP including gRNAs including SaCas9 and ErCas12a [1, 2]. These CRISPRs cut specifically within LoxP, an approach that is a departure from previous gene editing in vivo activity detection techniques that targeted adjacent stop sequences. In this sensor paradigm, CRISPR activity was monitored non-invasively in living Cre reporter mice (FVB.129S6(B6)-Gt(ROSA)26Sortm1(Luc)Kael/J and Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J, which will be referred to as LSL and mT/mG throughout the paper) after intramuscular or intravenous hydrodynamic plasmid injections, demonstrating utility in two diverse organ systems. The same genome-editing event was examined at the cellular level in specific tissues by confocal microscopy to determine the identity and frequency of successfully genome-edited cells. Further, SaCas9 induced targeted editing at efficiencies that were comparable to Cre recombinase demonstrating high effective delivery and activity in a whole animal. This work establishes genome editing tools and models to track CRISPR editing in vivo non-invasively and to fingerprint the identity of targeted cells. This approach also enables similar utility for any of the thousands of previously generated LoxP animal models.

Entamoeba histolytica, like other Organismes, is characterized by diversity and heterogeneity in its genetic content, which is one of the most important reasons for survival, and the increase in susceptibility to infection.Non-condensation of chromosomes during the process of cell division and the ambiguity of the chromosomal ploidy makes predicting the exact chromosomal number difficult. Genes distributed across 14 chromosomes as well as many extra-chromosome elements. Most Genes composed of one axon only, with Introns in 25% of Genes. This genome is characterized by the presence of Polymorphic internal repeat regions, and several gene families, one of these large families encoding Transmembrane kinas, Cysteine protease (CP), SREHP protein, and others.

Human metapneumovirus (HMPV) is an important cause of upper and lower respiratory tract disease in individuals of all ages. It is estimated that most individuals will be infected by HMPV by the age of 5 years old. Despite this burden of disease, there remains caveats in our knowledge of virus global genetic diversity due to a lack of HMPV sequencing, particularly at whole genome scale. The purpose of this study was to create a simple and robust approach for HMPV whole genome sequencing to be used for genomic epidemiological studies. To design our assay, all available HMPV full length genome sequences were downloaded from the NCBI GenBank database and used to design four primer sets to amplify long, overlapping amplicons spanning the viral genome and, importantly, specific to all known HMPV subtypes. These amplicons were then pooled and sequenced on an Illumina iSeq; however the approach is suitable to other common NGS platforms. We demonstrate the utility of this method using a representative subset of clinical samples and examine these sequences using a phylogenetic approach. Here we present an amplicon-based method for the whole genome sequencing of HMPV from clinical extracts that can be used to better inform genomic studies of HMPV epidemiology and evolution.

The constitutively active tyrosine kinase BCR/ABL1 oncogene plays a key role in human chronic myeloid leukemia development and disease maintenance, and determines most of the features of this leukemia. For this reason, tyrosine kinase inhibitors are the first-line treatment, offering most patients a life expectancy like that of an equivalent healthy person. However, since the oncogene is not destroyed, lifelong oral medication is essential, even though this trigger adverse effects in many patients. Furthermore, leukemic stem cells remain quiescent and resistance is observed in approximately 25% of patients. Thus, new therapeutic alternatives are still needed. In this scenario, the emergence of CRISPR technology can offer a definitive treatment based on its capacity to disrupt coding sequences. This review describes CML disease and the main advances in the genome-editing field by which it may be treated in the future.

Recently the polyvalent bacteriophage FP01, isolated from wastewater in Valparaiso, Chile, was described to have lytic activity across species against Escherichia coli and Salmonella enterica serovars. Due to it polyvalent nature the bacteriophage FP01 could have potential application in food and agri-industry. Also, fundamental aspects of polyvalent bacteriophage biology are not well known. In this study we sequenced and describe the complete genome of the polyvalent phage FP01 (MH745368) using the nanopore technology. The bacteriophage FP01 genome has a 44,900 bp, double-stranded DNA with an average G+C content of 49.41% and 90 coding sequences (CDSs). We found that the phage FP01 critically depends on host factors for replication and transcription. Also, it has a critical lysogenic repressor pseudogene. Phylogenetic analyses indicated that the phage FP01 is closely related to phages lambda and P22. These results suggest that the phage FP01 could be a lytic variant of a lysogenic phage or acquired genes from lysogenic phages during host infection.

Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with diverse chemical structures and potent biological activities and toxicities. The chemical identification of these compounds remains a major bottleneck. Strategies that can prioritize the most prolific strains and novel compounds are of great interest. Here, we combine chemical analysis and genomics to investigate the chemodiversity of secondary metabolites based on their pattern of distribution within some cyanobacteria. Planktothrix being a cyanobacterial genus known to form blooms worldwide and to produce a broad spectrum of toxins and other bioactive compounds, we applied this combined approach on four closely related strains of Planktothrix. The chemical diversity of the metabolites produced by the four strains was evaluated using an untargeted metabolomics strategy with high-resolution LC-MS. Metabolite profiles were correlated with the potential of metabolite production identified by genomics for the different strains. Although, the Planktothrix strains present a global similarity in term biosynthetic cluster gene for microcystin, aeruginosin and prenylagaramide for example, we found remarkable strain-specific chemo-diversity. Only few of the chemical features were common to the four studied strains. Additionally, the MS/MS data were analyzed using Global Natural Products Social Molecular Networking (GNPS) to identify molecular families of the same biosynthetic origin. In conclusion, we present an efficient integrative strategy for elucidating the chemical diversity of a given genus and link the data obtained from analytical chemistry to biosynthetic genes of cyanobacteria.

We propose and experimentally realize a scheme of the optical nonreciprocity (ONR) using degenerate two-level atoms embedded in an optical ring cavity. For the degenerate transition Fg=4→Fe=3, we first study the cavity-transmission property in different coupling field, and verify that within the strong-coupling regime, the single-dark-state peak formed by electromagnetically induced transparency (EIT) shows ONR. Qualitative theoretical analysis shows that the stable ground-state Zeeman coherence is necessary for intracavity EIT. However, due to the frequency degeneracy, the large Rabi frequency of counter-propagating coupling field can reduce the number of effective atoms and weaken the strong-coupling of the atom-cavity, which determines that ONR based on intracavity EIT occurs only at weaker probe intensity. Furthermore, the ONR transmission with high contrast, linewidth-narrowed and broadband is experimentally demonstrated.

The idea of strong and weak adjacencies between vertices has been generalized into fuzzy graphs and intuitionistic fuzzy graphs (IFGs) and it is an important part of making decisions. However, one or two membership degrees are not always sufficient for making decisions on real-world problems that need an answer of types “yes, neutral, and no". Consequently, in previous work, we generalized the concept into picture fuzzy graphs (PFGs) where each element in the PFG has membership, neutral, and non-membership degrees. Moreover, we constructed the notion of the coloring of PFGs based on strong and weak adjacencies between vertices. In this paper, we investigate some properties of the chromatic number of PFGs based on the concept of strong and weak adjacencies between vertices. According to the properties, we construct an algorithm to find the chromatic number of PFGs. The algorithm is usefull when we work with large PFGs. Further, we improve the method to implement the PFG’s coloring for determining traffic signal phasing at an intersection. A case study has also been done to evaluate the method.

In this work we report recent theoretical calculations of a superconducting island in a strong vortex confinement regime. The obtained results reveal the evolution of superconducting condensate as a function of electron mean-free path (l) with the evolution of an applied magnetic field H0. The results of this study provide an insight about the emergent superconducting properties under such conditions, using the Ginzburg-Landau numerical simulations where spatial variation of thickness d on island, omnipresent in these kind of structures grown on Si (111), is taken into account. These results offer a new route to tailor superconducting circuits by using the controlled bombardment, in order to explore the impact on vortex distribution, phase of order parameter, number of vortices, free energy and the first H1 and second critical field H2.

We present simple relations for nuclear stability and nuclear binding energy with respect to three gravitational constants associated with electroweak, strong and electromagnetic interactions.

Natural Gas (NG) processing is a prominent industrial separation process. Among the available techniques, the innovative membrane process shows potential for efficient removal of impurities, including carbon dioxide (CO₂). This study focuses on utilizing breakthroughs in membrane separation to drive sustainable CO₂ extraction from natural gas. Through comprehensive research and analysis, we explore the effectiveness and feasibility of membrane-based systems in removing CO₂ impurities from NG, thus promoting greener and more sustainable industrial practices. Our findings underscore the transformative nature of membrane separation technology, presenting new possibilities for a more environmentally-friendly and sustainable approach to CO₂ extraction from natural gas.Natural Gas (NG) processing utilizes various techniques for impurity removal, with the membrane process emerging as a promising option for efficient carbon dioxide (CO₂) extraction. This research proposes the integration of a simple mathematical model into ASPEN HYSYS to design a membrane system for CO₂/CH₄ separation. The study also investigates parameter sensitivities by altering operating conditions, such as feed composition and pressure, as well as membrane properties, including selectivity. By analyzing these variables, we aim to optimize the performance and efficiency of the membrane system, facilitating the sustainable extraction of CO₂ from NG. The findings contribute to advancing the design and operation of membrane-based processes for CO₂ separation, paving the way for greener and more sustainable industrial practices. In addition, this study explores various configurations for optimizing the design of the membrane system, including single-stage with and without recycling as well as double-stage configurations. The investigation demonstrates that methane recovery can be enhanced through the recycling of the permeate stream and by implementing a double stage membrane system. These findings highlight the potential for improving the efficiency and performance of the membrane system, enabling higher methane recovery rates. By considering different configurations, this research contributes to the development of more effective and sustainable CO₂ extraction processes from natural gas.

Immune checkpoint receptors play a crucial role in steering tumor progression, prompting a focused investigation into the role of TIM3 in breast cancer. Analysis of TCGA BRCA data unveiled diverse correlations between TIM-3 expression and immune cell infiltration across subtypes. In our in-house cohort studied through IHC, significant changes in TIM3 expression with tumor grades were observed. Higher TIM3 expression correlated with increased disease-free survival in pan breast cancer, marking the first revelation of TIM3's positive role in pan BC prognosis. The study indicates that alluring TIM3 response, rather than suppression, may enhance breast cancer prognosis.

Biotic stressors pose serious threats to crop yield, jeopardizing food security and resulting in over US$220 billion per year losses to the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements of plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have provided new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel frontiers to disrupt the molecular compatibility of pathogens and introduce durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R gene-based plant genome engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems.

The flowering period of rice significantly impacts variety adaptability and yield formation. Properly shortening the reproductive period of rice varieties can expand their ecological range without significant yield reduction. Targeted genome editing, like CRISPR/Cas9, is an ideal tool to fine-tune rice growth stages and boost yield synergistically. In this study, we developed a CRISPR/Cas9-mediated multiplex genome editing vector containing five genes related to three traits: Hd2, Ghd7, and DTH8 (flowering stage genes), along with the recessive rice blast resistance gene Pi21 and the aromatic gene BADH2. This vector was introduced into the high-quality Geng rice variety in Zhejiang province, Jiahe212 (JH212), resulting in 34 T0 plants with various effective mutations. Among the 17 mutant T1 lines, several displayed diverse flowering dates, but most exhibited undesirable agronomic traits. Notably, three homozygous mutant lines (JH-C15, JH-C18, and JH-C31) showed slightly earlier flowering dates without significant differences in yield-related traits compared to JH212. Through special Hyg and Cas marker selection of T2 plants, we identified 7, 6, and 2 fragrant glutinous plants devoid of transgenic components, respectively. These single plants will serve as sib lines of JH212 and potential resources for breeding applications, including maintenance lines for Xian-Geng interspecific three-line hybrid rice. In summary, our research offers practical insights and potential resources for targeted improvement of Geng rice varieties, and would also promote the Geng rice varieties expending from the southward to the northward.

Scientists can use the Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) protein 9 system, which is a powerful and flexible tool for changing the genome, to change only certain parts of the genome. This has helped researchers figure out how target genes work in biology and disease. CRISPR/Cas9 is made up of a sequence-specific CRISPR RNA (crRNA) set and a generic Cas9 nuclease. The crRNA set tells Cas9 where to cut DNA and cause double-strand breaks. In the next step of cellular DNA repair, insertions, deletions, and swaps are made at specific spots. For CRISPR/Cas9-mediated DNA cleavage to be specific, the target sequences must match the crRNA, and a protospacer nearby motif must be placed after the target sequences. In this article, we talk about how CRISPR/Cas9 works at the molecular level, what it can be used for, what it can't do, and what its future clinical treatment promise might be.

The purpose of this study was to identify candidate novel species performing beneficial ecological functions from soil. The hypothesis was that novel culturable species with antibiotic production potential could be readily found from soil in the Nature Canyon at Los Angeles Pierce College. 137 bacterial isolates from soil were grown on nutrient agar, ISP-6 medium, or LB agar and partial 16S was ascertained using the Sanger platform for regions V1-V4. One of the potentially novel isolates, Pseudomonas sp. 21-C3-ER, was isolated on nutrient agar from fallow soil in an agricultural nature preserve in Los Angeles. The soil conditions were 3.7% moisture, clay texture by touch, 13.37% organic matter, pH=6.63, TDS=638, 150 ppm nitrogen, 114 ppm phosphate, and 42 ppm potash. Whole genome sequencing was performed on the DNBseq platform and species identification was performed with TRUEBacID; the closest relative was Pseudomonas brassicacearum subsp. neoaurantiaca which was 92.05% similar by genomic evidence. 197 virulence factors were identified including flagellar biosynthesis, motor proteins, Beta-lactamase, Fosfomycin, copper, and sulfur drug resistance. Gram stain of strain 21-C3-ER revealed gram negative rods. Rods were visualized with scanning electron microscopy, revealing individuals approximately 1 µm in length. Secondary metabolite analysis using antiSMASH showed a variety of post-translationally modified proteins and a promysalin analog. The qualitative test for pyoverdine siderophore production using UV light was positive. Metabolic analysis using RAST indicated genes were present for pyoverdine production, antimicrobial resistance, and ammonification. The nitrate reduction test was positive. Denitrifying bacteria may prevent leaching of nitrates from soil, since ammonia has a higher affinity to soil and organic matter than nitrate. We propose Pseudomonas fernandeno as a novel species. The type stain is 21-C3-ER.

Fecal Microbial Transplant (FMT) has been emerging as a prominent therapeutics in the modern science to modulate and correct the dysbiotic state of gut microbiome that leads to various metabolic and gastro-enteric diseases. A similar concept called as “panchagavya prasahan” exists in Ayurveda. This technique unlike the FMT involves the use of Cive by- products of cow viz. Cow dung, urine, milk, curd, ghee mixed in a copper vessel. In this study we assess the microbial composition of this preparation before and after the mixing in the copper vessel. We used the 16S rRNA gene based amplicon sequencing approach to understand the bacterial composition in the panchagavya preparation. We observed signiCicant decrease in the abundance of genera Pseudomonas and Streptococcus (p

Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Optical genome mapping (OGM) is an emerging technology that enables genome-wide detection of all classes of SVs at a high resolution and sensitivity. Identification of cryptic SVs leading to gene disruption or predicted novel gene fusions could be important drivers for cancer development and/or portend a prognostic relevance, which could be used to modify the treatment plan. A cohort of 106 consented cases that had a successful OGM analysis performed were included in the study. Demographic, clinical, laboratory and treatment data were collected. Routine diagnostic and prognostic testing were done on the peripheral blood and bone marrow aspirate as indicated. Additional samples of peripheral blood and/or bone marrow were sent for OGM testing. OGM led to a change in risk stratification in 17/66 (25.75%) of patients with hematological malignancies, the majority of these patients (15/66, 22.72%), having their risk stratification upgraded with a resulting change in treatment of 14 patients. This study highlights the ability of OGM to detect rare, cryptic and clinically relevant variants that potentially impact disease diagnosis, risk stratification and actionable treatment targets.

Metabolites are at the end of the gene-transcript-protein-metabolism cascade. As such, metabo-lomics is the omic approach that offers the most direct correlation with phenotype. This allows that, where genomics, transcriptomics and proteomics fail to explain a trait, metabolomics might give an answer. Complex phenotypes, which are determined by the influence of multiple small effect alleles, are an example of these situations. Consequently, the interest in metabolomics has increased ex-ponentially in the last years. As a newer discipline, the metabolomics bioinformatics analysis pipe-lines are not as standardized as in the other omic approaches. In this review we synthesized the different steps that need to be carried out to obtain biological insight from the annotated metabolite abundance raw data. These steps were grouped in three different modules: preprocessing, statistical analyses and metabolic pathway enrichment. We included within each one of them the different state-of-the art procedures and tools that can be used depending on the characteristics of the study, providing details about the characteristics of each method has, as well as the issues the reader might encounter. Finally, we introduce genome scale metabolic modeling as a tool for obtaining pseu-do-metabolomic data in situations where its acquisition is difficult, being possible to analyze the resulting data with the modules of the described workflow.

Background and objectives: TSC1 is a crucial component of the mTOR pathway, impacting cell growth, proliferation, and autophagy, while TSC2 is a tumor suppressor gene that regulates cell growth and is associated with the mTOR signaling pathway. In the present study, we analyzed TSC1 and TSC2 mRNA expression levels in rectal cancer, and evaluated the clinicopathological and prognostic characteristics of TSC1 and TSC2. Materials and Methods: TSC1 and TSC2 mRNA expression was examined in various cancer types. We further evaluated survival to determine the prognostic significance of TSC1 and TSC2 mRNA in CRC using The Cancer Genome Atlas (TCGA) data. Results: The study focused on rectal cancer, as it exhibited the most promising results. The patients were split into two subgroups, each comprising 50% of the total, based on the TSC gene expression levels. This division was made to assess the clinical characteristics associated with the expression of TSC1 and TSC2 genes. In the study, lower TSC1 expression was linked to venous invasion in rectal cancer patients, and there was also a related trend with lymphatic invasion, although it didn't reach statistical significance. Lower TSC2 expression was observed in younger patients and had some associations with sex and M stage, but these correlations were not statistically significant. When it came to survival analysis, TSC1 expression did not significantly impact overall survival, while higher TSC2 expression was associated with a poorer prognosis in rectal cancer. To enhance our comprehension, additional research, especially in larger case studies, is needed to explore the molecular mechanisms and clinical characteristics of TSC genes in colorectal cancer.

Objective: To identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. Methods: nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which have been considered mild, moderate and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. Results: it was determined that during the period December 2020 and January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, B.1.111 circulated, lineage C.14 the most predominant with 76.7% (n=23/30), these lineages were classified in clade 20D mainly and also within clade 20B and 20A. On the contrary, the variants found in the second batch of samples of the period September – October 2021 were Delta Variant (72.7%), Gamma (13.6%), Mu (4.6%), Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J and 21I. Conclusions: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.

In our article in Genome Biology Ecology six years ago, one complete plastid genome of Belian was assembled for comparative analyses of the plastomes in Lauraceae. However, Ariati et al. (2023) concluded that our sequenced Belian individual could be located in the clade of Myristicaceae instead of that of Lauraceae. Here, we performed re-analyses of additional two Belian plastomes, along with 42 plastomes from plants spanning ten families of the Magnoliids. The plastomes of the three Belian individuals range from 157,535 to 157,577 bp in length. Comparative genomic analysis revealed 170 mutation sites in their plastomes, which include 111 substitutions, 53 indels, and six microinversions. Phylogeny was reconstructed using maximum likelihood and Bayesian approaches for 44 magnoliids species indicated that our three Belian individuals are nested among the species in the family Lauraceae rather than Myristicaceae.

The aim of this work is the study of genome organization and metabolic potential of Streptomyces carpaticus strain SCPM-O-B-9993, promising plant-protecting and plant-stimulating strain isolated from brown semi-desert soils with a very high degree of salinity. The genome of the strain contains of a linear chromosome of 5,968,715 bp and has no plasmids. Gene clusters of production of secondary metabolites with antimicrobial properties (ohmyungsamycin, pellasoren, naringenin, ansamycin) were identified in the genome. The strain SCPM-O-B-9993 has antiviral activity against cucumber mosaic virus on tomatoes under laboratory conditions.

Cycas (family Cycadaceae), spread throughout tropical and subtropical regions, is crucial in con-servation biology. Due to the subtle morphological variations between species, a solid spe-cies-level phylogeny for Cycas is lacking. Because of the rapid progress in high-throughput se-quencing technology, it has become feasible to acquire complete chloroplast (cp) genome se-quences, which provide a molecular foundation for phylogenetic research. In the present study, we employed next-generation sequencing technology to assemble and analyze the chloroplast genomes of six Cycas plants, including their genome structure, GC content, and nucleotide di-versity. The Cycas chloroplast genome spans 162,038 to 162,159 bp and contains 131 genes, in-cluding 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Through a comparative analysis, we found that the chloroplast genome of Cycas was highly conserved, as indicated by the contraction and expansion of the inverted repeat (IR) re-gions and sequence polymorphisms. In addition, several non-coding sites (psbK-psbI, petN-psbM, trnE-UUC-psbD, ndhC-trnM-CAU, and rpl32-trnP-GGG) showed significant varia-tion. The utilization of phylogenetic analysis relying on protein-coding genes has substantiated the division of Cycas primarily into four groups. The application of these findings will prove valuable in evaluating genetic diversity and the phylogenetic connections among closely related species. Moreover, it will provide essential support for the advancement of wild germplasm re-sources.

The non-pharmaceutical interventions implemented to prevent the spread of COVID-19 have affected the epidemiology of other respiratory viruses. In South Korea, Human metapneumovirus (HMPV) typically occurs from winter to the following spring; however, it was not detected for two years during the COVID-19 pandemic and re-emerged in the fall of 2022, which is a non-epidemic season. To examine the molecular genetic characteristics of HMPV before and after the COVID-19 pandemic, we analyzed 427 HMPV-positive samples collected in the Gwangju area from 2018 to 2022. Among these, 24 samples were subjected to whole-genome sequencing. The results showed a shift in the predominant genotype from A2b2 before the COVID-19 pandemic to A2b1 in 2022. Furthermore, a significant increase in HMPV cases was observed in the 6–10-year age group. Since the onset of the COVID-19 pandemic, social distancing have reduced the possibility of HMPV exposure and herd immunity due to non-transmission, resulting in the introduction of new HMPV genotypes in different seasons.

Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research of molecular breeding and genetic evolution has been severely restricted, due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (Mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibit many presence/absence variants. Moreover, a large inversion at the 7,588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protecting, developing, and utilizing P. tenella germplasm resources.

Bean common mosaic virus from the genus Potyvirus has a wide range of hosts and a very negative impact on cultivated crops from the genus Phaseolus. The risk of viral infection of economically important crops increases even if the carriers of the virus are related plant species growing on agroecological interfaces. Such plant species have emerged as new hosts for BCMV, usually harboring novel genetic variants of the virus. A novel genetic variant of BCMV was isolated from a symptomatic crownvetch plant, where the presence of this virus was confirmed by Western-blotting analysis and by amino acid identities in peptide fragments of CI, HC-pro, and CP proteins using the nanoLC-ESI-Q-TOF. The novel BCMV SVK isolate differed from the most genetically similar one in 0.91% of nucleotides and 1.55% of amino acids. The highest number of amino acid substitutions (8.8% of amino acids) was in the P1 protein, followed by CP (2.44% of amino acids). Minor substitutions were in Hc-pro, CI, and Nib proteins. The symptomatic crownvetch plant was confirmed as a new host and carrier of the novel BCMV isolate.