Abstract: Vernal ponds are temporary, isolated bodies of water that lack vertebrate predators like fish. Palmer Park in Detroit MI USA, contains an old-growth forest with multiple vernal ponds that are home to numerous invertebrates, including water mites, which are the main focus of this study. These vernal ponds are unique since they are geographically isolated in the middle of an urban landscape. Previous research discovered new species of non-biting midges in Palmer Park vernal ponds, suggesting the potential for the discovery of previously undocumented organisms and relationships in this ecosystem. Here we document the invertebrate species found in the vernal ponds of Palmer Park, both to illustrate their diversity and to determine their cytochrome oxidase I barcodes. The barcodes are used in this study to verify identification and to provide reference sequences for comparison to sequences in the diets of water mites also collected from the ponds. Three taxa of water mites found in Palmer Park Pond A are Hydryphantes waynensis, Parathyas sp., and Hydryphantes sp. (distinct from H. waynensis by having a COI barcode 11.6% different from Hydryphantes sp.). This paper also uses Next Generation Sequencing (NGS) to analyze the complex diets of the water mites at Palmer Park. The diets consisted of a diversity of species of worms, mosquitoes, non-biting midges, crustaceans, flies, and beetles. Beetles identified as whole organisms in the ponds or from diet-detected bar codes in vernal pond water mites include Copelatus glyphicus, Acilius sp., and Hygrotus sayi. The diets of water mite in these vernal ponds are compared to previous molecular studies in which water mites in a riverine lagoon were identified as opportunistic predators of a diverse invertebrate diet. Beetles have not previously been reported in water mite diets, so this finding represents a new discovery. Diet analysis revealed taxa and novel barcodes not observed through traditional sampling, highlighting the value of water mites for community characterization. These results support the hypothesis that water mites are opportunistic predators, uniquely reports beetles in their diets, and emphasizes their ecological importance and utility in assessing vernal pond biodiversity.

Abstract: Plant species can significantly influence soil nutrients. We assessed how soil micronutrients (B, Fe, Cu, Zn, Mn) and Aluminum were affected by plant species in agricultural fields at Masako Forest Reserve. Soil samples were collected in June 2022 and 2023 at three depths: 0–10 cm, 10-20 and 20-30 cm in fields grown to Costus lucanusianus, Manihot esculenta, Zea mays, Triumfetta cordifolia, and Xanthosoma sagittifolium. A completely randomized design was used with 3 soil depths (SD) x 5 plant species (PS) replicated 4 times. Soil samples were air-dried, sieved 2 mm and sent to Brookside Laboratories (OH, USA) for analyses. Results showed that in 2022, Fe, Mn, Cu and Zn were significantly affected by soil depth (p< 0.05). Mn, Cu and Zn concentrations were higher in 0-10 cm while Fe dominated in 10-30 cm depth. Only Cu (p=0.0001) was affected by plant species. The soil under Xanthosoma sagittifolium (0.19 mg/kg) and Triumfetta cordifolia (0.47 mg/kg) had significantly the lowest level of Cu. In 2023, however, only Zn was significantly affected by SD (p=0.0004) with its highest level (1.22 mg/kg) in 0-10 cm. PS significantly affected Fe, Mn, Cu, Zn and aluminum (p< 0.05). The soil under Manihot esculenta had the highest concentration of Fe (171.42 mg/kg) while Zn (1.03 mg/kg) was significantly higher in the soil under Zea mays. The 0-10 cm layer significantly held more micronutrients. Plant species such as Manihot esculenta had a noticeable effect on soil micronutrients.

Abstract: This article addresses a current point of contention in the field of single molecule/single particle tracking, as well as relevant literature, and supplements it with some published cell-based experiments to illustrate our conclusions and known theorems. We attempt to explain the controversy surrounding the differing biophysical and cell biological results of studies on the individual molecule and those “at the single-molecule level” as well as at the level of many molecules in such a way that even readers who are unfamiliar with the subject can understand it without having to read all the mathematical, physical, and biophysical references. Given this abundance of studies in the literature, it is obvious that genuine single-molecule studies are urgently needed, i.e., single-molecule studies that focus on increasing the sensitivity of the temporal resolution of single-molecule measurements and not just on spatial resolution.

Abstract:

The secondary immunomodulatory effects of conventional therapeutics, such as antibiotics and cytostatics, are frequently overlooked despite their significant clinical implications. Building on our previous findings that drugs like paclitaxel and doxorubicin heavily influence macrophage polarization—potentially driving metastasis or inflammation—this study systematically evaluates the secondary immune-modulating actions of standard drugs and natural adjuvants. Using patient-derived bronchoalveolar lavage (BAL) fluid (ex vivo alveolar macrophages), we developed an analytical platform using synthetic carbohydrate-functionalized fluorescent ligands targeting key receptors (CD206, CD209, CD280, CD301). Integrating ligand-binding profiles with Linear Discriminant Analysis (LDA) yielded quantitative immune-state vectors capable of differentiating between favorable prognostic signatures and imbalanced immune states. Profiling samples across heterogeneous respiratory conditions revealed highly context-dependent responses. While some treatments synergistically corrected imbalanced profiles, others provoked dysregulation. Notably, in pneumonia or bronchitis with an asthma-prone M2-dominant profile, specific antibiotic regimens are critical; doxycycline, for instance, may exacerbate patient deterioration by further driving M2a polarization. Crucially, we identified that natural adjuvants (e.g., curcumin, coumarins, polyphenols) exhibit potent properties capable of correcting these adverse secondary drug effects. Ultimately, this profiling platform highlights the necessity of evaluating patient-specific secondary drug effects, offering a functional blueprint for precision immunotherapy and the rational design of adjuvant-enhanced treatments.

Abstract: In China, the enormous gap between domestic soybean supply and increasing consumption necessitates large-scale soybean imports. The use of cultivated soybean (Glycine max) leaves as feed for the edible insect Clanis bilineata tsingtauica further reduces crop yields, posing a threat to national soybean production security. To address this issue, this study evaluated wild soybean (Glycine soja) as a potential alternative feed source. Comparative analyses examined the nutritional and anti-nutritional properties of G. max (cv. Qihuang34) and laboratory-preserved G. soja germplasm, together with their effects on larval growth performance, nutritional composition, and associated microbiota. G. soja leaves exhibited significantly higher crude fat (5.61% vs. 2.17%), ash (11.07% vs. 9.62%), neutral detergent fiber (23.75% vs. 21.00%), calcium (4.05 g/kg vs. 3.41 g/kg), and phosphorus (2.52 g/kg vs. 2.38 g/kg) than G. max, alongside lower trypsin inhibitor levels (P< 0.01) despite higher phytic acid content (P< 0.05). Fifth-instar larvae reared on G. soja leaves achieved a 12.9% increase in body weight (6.846 g vs. 6.066 g), higher crude protein (672.14 g/kg vs. 555.02 g/kg), total soluble sugar (21.27 mg/g vs. 8.96 mg/g), and soluble protein (26.35 mg/g vs. 24.71 mg/g), but lower crude fat (187.44 g/kg vs. 205.82 g/kg, P< 0.05). 16S rRNA sequencing revealed distinct phyllosphere microbial communities, with G. soja enriched in diverse taxa (e.g., Bacteroidota, Proteobacteria) and G. max dominated by Firmicutes. Corresponding differences were observed in larval gut microbiota, with positive correlation analyses suggesting potential microbe transfer from G. soja leaves to larval guts. Overall, G. soja represents a promising alternative feed for C. bilineata, reducing competition with soybean grain production and supporting sustainable insect farming.

Abstract: Metal homeostasis, which coordinates the influx and efflux of essential elements such as iron (Fe) and manganese (Mn) in chloroplasts, is essential for optimum photosynthesis, especially in metal accumulating plants. Brassica juncea (Indian mustard) is a metal-tolerant species with a strong metal accumulation capacity, making it a suitable model for studying transition metal homeostasis. In this study, we identified two efflux transporters, BjYSL6.1 and BjYSL6.4, that localize in the endomembrane system of Schizosaccharomyces pombe and interact with the chloroplast Mn influx transporter BjNRAMP4.1 at the plasma membrane and within the chloroplasts. Bimolecular fluorescence complementation and split-ubiquitin yeast two-hybrid assays confirmed specific protein-protein interactions among these transporters, as well as with the membrane-bound thioredoxin BjHCF164, a known regulator of photosynthetic electron transport. Gene expression studies revealed that BjNRAMP4.1 and BjYSL6 isoforms are inversely regulated under Fe and Mn stress conditions, with BjNRAMP4.1 being strongly induced under deficiency, whereas BjYSL6.1 and BjYSL6.4 are downregulated. These findings suggest that a coordinated network involving BjNRAMP4.1, BjYSL6s, and BjHCF164 modulates metal influx and efflux at the chloroplast and plasma membrane interfaces, thereby maintaining metal homeostasis, which is critical for photosynthetic efficiency in B. juncea.

Abstract: Anthocyanins and betalains are hydrophilic plant pigments with numerous physiological and ecological functions. The biosynthesis routes of anthocyanins and betalains differ with anthocyanins being synthesized from phenylalanine via the general phenylpropanoid pathway, whereas betalains are derived from tyrosine. Although the precursors phenylalanine and tyrosine are present in all plants, there is no known plant where both these pigments are co-accumulated. Most plants synthesize anthocyanins, while certain families in the order Caryophyllales produce betalains. There is apparent mutual exclusion of these two plant pigments. Over the past five decades, evidence accumulated supporting this theory of mutual exclusion of the two pigments. However, recently published reports claim the presence of anthocyanins in well-known betalain-pigmented plants. Here, we explore the causes of such claims and provide recommendations for future studies on the topic.

Abstract: The armless snake eel, Dalophis imberbis, is a fossorial rare species; being considered as a non-target fishery resource with elusive behavior, knowledge on its distribution and biology results scarce. This study reports three new documented occurrence records of D. imberbis along the northern and southeastern coastal areas of Sicily (central Mediterranean Sea) during 2025. Specimens were collected at depths ranging from 43 m to an unusually shallow depth of 5.4 m. Environmental parameters have been collected through a multiparametric probe and integrated with products from the Copernicus Marine Service (CMS), providing new insights which highlight the presence of the species in relatively warm (17.6-20.8 °C) and moderately oxygen undersaturated (6.9-8.5 mg/L) waters. A global distributional analysis was performed by aggregating the field data with literature records and datasets from the Global Biodiversity Information Facility (GBIF), refining the distribution of the species in the Mediterranean and Atlantic sectors. This work underscores the importance of combining traditional surveys with big-data repositories and remote sensing to monitor rare marine biodiversity.

Abstract: One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive model that explains how amino acid sequences dictate folding pathways and trajectories. This manuscript introduces a novel treatment for the issue by employing the “principle of least action.” This approach enables us to explore an intriguing question: how does a protein achieve its native state at a constant folding rate and within a biologically plausible time frame? A response to this inquiry will help us understand why proteins must fold along specific pathways and identify the boundary conditions that limit their availability. Additionally, the principle of least action—together with the effective trajectory conjecture—enables us to explain why different proteins could exhibit the same folding rate. Finally, it will enable us to provide an in-depth description of the genesis and solution of Levinthal's paradox. Our results are expected to pave the way for a more profound understanding of how proteins fold, shedding light on how the amino acid sequence and its surrounding environment encode the protein's folding pathways and, consequently, the protein's three-dimensional structure.

Abstract: Quorum sensing (QS) governs microbial virulence, symbiosis, and critical ecosystem processes, such as rhizosphere nitrogen mineralization, positioning QS as both an attractive agricultural target and a potential point of ecological trade-off. This review synthesizes current evidence on coumarins, plant-derived secondary metabolites, that have evolved from being viewed as classical phytoalexins to being recognized as regulators of QS-mediated interaction in the plant-soil system. We synthesize current evidence on the multifaceted mechanisms of coumarin action, from direct antimicrobial effects to selective interference with bacterial QS systems and virulence. Key studies demonstrate that coumarins can suppress phytopathogens while sparing beneficial bacteria, thereby actively editing rhizosphere community composition. However, coumarin effects are profoundly context-dependent, with outcomes ranging from selective microbiome modulation to broad suppression or unintended pathogen enrichment - depending on concentration, plant host and native community structure. Beyond community assembly, coumarin-mediated QS disruption may have functional consequences for QS controlled ecosystem processes such as nutrient cycling. Revealing a potential ecological trade-off between pathogen defense and resource acquisition, this warrants further investigation. Coumarins are versatile compounds that plants use for sensing, communicating with, and actively shaping their microbial environments. Developing the ability to use them precisely and in an environmentally friendly manner represents a promising avenue for sustainable agriculture.

Abstract: Neural computation is not performed by static circuits processing signals corrupted by noise, but by actively moving biological structures that use motion itself to sample, encode, and predict the world. Neurons are often modelled as filters that transmit information through chemical and electrical signals constrained by noise and bandwidth. However, this static view contrasts with biological reality, in which dynamical processes operate across scales, from whole-animal movements to motion at the subneural level. Here, we combine recent experimental observations with biophysically realistic modelling to show that neural information processing, beyond electrochemical signalling, is dynamically shaped by motion across biological scales, from morphodynamic ultrastructural changes to whole-body movements. In this framework, ultrafast mechanical adjustments in cellular and synaptic structures interact with retinal, eye, head, and body motions to accelerate encoding and enhance precision. Adaptive variability in self-motion-coupled morphodynamic sampling arises from changes in response waveforms, latencies, refractoriness, and ultrastructural dynamics. This variability improves signal fidelity and extends spatiotemporal resolution, enabling neurons to generate reliable, high-speed representations with minimal delay. Thus, through active sensing, animals continuously enhance the speed and reliability of sensory representations. This perspective, in which self-generated sampling motion across multiple scales enhances encoding and perception, offers new insight into how the brain achieves efficient, predictive, and noise-resistant computation while providing a foundation for future experimental tests and biologically inspired AI designs. We first explain how motion-coupled encoding improves neural performance, focusing on edge-coding in early sensory systems. We then extend these ideas more speculatively, proposing how motion-coupled sampling may have influenced the evolution of neural architectures at multiple levels, potentially contributing to efficient predictive cognition.

Abstract: Current efforts in improving photodynamic therapy focus on nanomaterials that integrate deep-tissue imaging with efficient reactive oxygen species generation. Gold nanoclusters (Au NCs) are promising alternatives to conventional photosensitizers due to their effective ROS production and enhanced biocompatibility when stabilized by protein corona. However, both photosensitizers and Au NCs are typically activated by ultraviolet or visible light, which cannot penetrate deeper into tissues and is limited to superficial applications. Here, we report a near-infrared (NIR)-activated photodynamic nanoplatform based on core-shell upconverting nanoparticles (UCNPs; NaGdF₄:Yb³⁺,Er³⁺@NaGdF₄:Yb³⁺,Nd³⁺), functionalized with a protein corona containing bovine serum albumin-stabilized Au NCs (BSA-Au NCs) and photosensitizer chlorin e6 (Ce6). Spectroscopic data confirmed the formation of the UCNP-BSA-Au-Ce6 nanoplatform and demonstrated 32% energy transfer efficiency from UCNPs to Ce6, resulting in efficient reactive oxygen species generation under 808 nm irradiation. Cellular experiments confirmed effective internalization and optimal biocompatibility of the nanoplatform in human breast cancer and healthy cells. Upon 808 nm irradiation, the nanoplatform significantly reduced viability of MDA-MB-231 cancer cells. These findings indicate that the UCNP-BSA-Au-Ce6 nanoplatform couples NIR activation with enhanced singlet oxygen production, providing a multifunctional platform for deep-tissue imaging and NIR-activated photodynamic therapy.

Abstract: Large language models (LLMs) show considerable promise for mental health dialogue systems, yet their deployment raises pressing concerns around safety, hallucination, reproducibility, and clinical reliability (Ji et al., 2023; Bommasani et al., 2021). We present a deterministic architecture for AI-assisted counseling that combines retrieval-augmented response generation, structured dialogue management, rule-based risk routing, and a cryptographically verifiable evaluation pipeline. The system was evaluated on two independent datasets spanning 1,895 counseling scenarios in English and Chinese. On 783 English counseling cases, the system achieved mean scores of 4.33/5 for empathy, 3.55/5 for clinical fidelity, and 4.45/5 for safety. On 1,112 Chinese cognitive-behavioral therapy (CBT) scenarios, the corresponding scores were 4.85/5, 4.73/5, and 4.77/5. No system failures or unintended diagnostic outputs were observed across either evaluation. Ablation experiments demonstrate that retrieval grounding and deterministic safety routing each contribute significantly to overall performance, with the former driving clinical fidelity and the latter driving safety. These results suggest that deterministic, retrieval-grounded LLM architectures can serve as a viable foundation for scalable and safe psychological support systems.

Abstract:

In recent years, the poultry industry has actively sought more sustainable feed additives to address the various challenges of intensive production. To evaluate the oral effect with Lactobacillus reuteri CLP4 on performance, carcass traits, organ weights, cecal microbiology, tibial mineralization, blood indicators, and nitrogen and phosphorus excretion in broilers, 800 one-day-old unsexed Ross 308^® chicks were randomly assigned to two treatments: a basal diet (T0; BD) without additives and BD+Lactobacillus reuteri CLP4 (T1) in the drinking water during the period from 0 to 21 days old. T1 decreased feed intake and feed conversion ratio without affecting body weight or viability of broilers. Likewise, it diminished abdominal fat and improved breast protein content. The probiotic also increased the relative weights of the thymus, spleen, liver, and pancreas, decreased the population of Salmonella spp. and cecal pH, and promoted the growth of lactic acid bacteria. Moreover, T1 improved serum immunoglobulin concentrations and decreased harmful serum lipids and nitrogen excretion, although without modifying the moisture, calcium, and phosphorus content of the tibia or phosphorus excretion. Oral supplementation with Lactobacillus reuteri CLP4 enhances productivity, breast protein, immune function, atherogenic index, cecal competitive exclusion, and reduces the environmental nitrogen load in broiler production.

Abstract: The method of X-ray Footprinting and Mass Spectrometry (XFMS) using high brightness synchrotron X-ray sources has become an established method in structural biology and is based on the radiolytic production of hydroxyl radicals which oxidatively modify protein sidechains. While other methods of producing hydroxyl radicals are available, one benefit of using high flux density sources is that hydroxyl radical scavenging reactions can be minimized, and exposure times kept short to minimize secondary reactions. Here we present an application of the XFMS method using low dose rate X-rays from a commercial instrument. We demonstrate the feasibility of the approach using short peptides, characterizing the oxidative modifications +14, +16, and +32 Da under both aerated and low-oxygen conditions, and we additionally quantify the hydrogen peroxide production for various doses using the low dose rate source. These results provide fundamental information on the oxidative damage to peptides due to hydroxyl radicals using a low dose rate X-ray source.

Abstract: Biological systems display phenomena—particularly in enzymatic catalysis, excitonic coherence, and protein folding—that appear to exploit selective stabilisation of microstates beyond what standard quantum mechanics typically predicts for warm, noisy environments. We propose that these deviations can be interpreted as signatures of an informational reservoir: a hidden, aperiodic layer of structured information accessible only to sufficiently complex biological systems. Standard quantum mechanics then emerges as a limiting, coarse‑grained description in which the reservoir term vanishes. The proposed reservoir is not reducible to any finite set of underlying parameters; instead, it functions as a high‑complexity information landscape that can be “read” only by finely organised biomolecular architectures. We outline empirically testable predictions and discuss implications for biological stability, functional directionality, and the physical foundations of living systems.

Abstract: Background: Autism spectrum disorder (ASD) affects approximately 1-2% of childrenworldwide, yet its etiology remains incompletely understood. Emerging evidence suggeststhat offspring of parents with autoimmune diseases show elevated autism prevalence.Notably, children of parents with psoriasis (OR 1.59), type 1 diabetes (OR 1.49-2.36), andrheumatoid arthritis (OR 1.51) demonstrate particularly strong associations. Hypothesis: I propose that autism may be conceptualized as an immune-metabolic disorderin which TNF-α-mediated mitochondrial dysfunction contributes to cerebral energydeficiency. This energy deficit impairs three critical processes: (1) synaptic pruning duringneurodevelopment, (2) real-time social cognition including gaze processing and emotionrecognition, and (3) protein synthesis of critical synaptic scaffolding molecules.The proposed mechanism is TNF-α pathway dysregulation arising from inheritedinflammatory susceptibility and/or direct fetal exposure to elevated maternal TNF-α duringpregnancy.I further propose that the well-documented “firstborn effect” in autism reflects maternalimmune maladaptation during primigravid pregnancies. Additionally, for cases withoutparental autoimmune history, a speculative secondary mechanism is proposed: mitonuclearimmune conflict, where paternal immune genes may partially recognize maternalmitochondria as non-self, generating endogenous TNF-α.

Abstract: Muscle stem cells (MuSC) are the cellular source for generation and regeneration of skeletal muscle. To ensure correct muscle growth, MuSC self-renewal and differentiation need to be tightly regulated. Several signaling systems have been implicated in the control of MuSCs, among them Bone Morphogenetic Proteins (BMPs) and Notch, both of which promote MuSC proliferation and suppress differentiation. To better understand the mechanisms of function and the target genes regulated by BMP signaling in myogenesis, we investigated the transcriptional responses of adult mouse MuSCs to BMP6/4 using RNA-sequencing. BMP6/4-stimulation of freshly isolated MuSCs for one hour rapidly increased the expression of classical BMP target genes like Id1 and strongly induced expression of genes of the Notch pathway (Hes1, Hey1, Lfng, Snai1). In parallel, using Cleavage Under Targets and Tagmentation (CUT&Tag), we generated whole-genome binding profiles for the BMP pathway effectors pSMAD1/5/9 and SMAD4 and detected binding in promoters and potential regulatory elements of BMP targets and Notch pathway genes (Hes1, Hey1, Lfng, Snai1) indicating that BMP signaling directly influences Notch and that crosstalk between the two pathways regulates myogenesis.

Abstract: Elucidating the pathophysiological mechanisms of mental disorders remains a critical challenge in psychiatric research. Recent studies have highlighted the potential involvement of cytoskeletal and molecular motor abnormalities in the development of mental disorders such as schizophrenia and autism spectrum disorder (ASD). This review synthesizes the latest findings on the relationship between cytoskeletal and molecular motor abnormalities and mental disorders. The cytoskeleton, composed of microtubules, actin filaments, and intermediate filaments, along with molecular motors such as kinesins, dyneins, and myosins, plays crucial roles in neurodevelopment, synapse formation, and neurotransmission. In schizophrenia, decreased expression of the microtubule-associated protein MAP2 and abnormalities in the DISC1 gene have been reported, potentially leading to dendritic morphological abnormalities and neurodevelopmental disorders. Additionally, abnormalities in molecular motors such as KIF17 and KIF1A have been implicated in disturbances of synaptic plasticity. In ASD, Myosin Id has been identified as a risk gene, and its localization in dendritic spines has recently been elucidated. Furthermore, abnormalities in actin-related proteins such as SHANK3 and CYFIP1 have been shown to cause synaptic dysfunction. These findings suggest that mental disorders arise from complex pathologies involving multiple cytoskeletal and molecular motor-related protein abnormalities. Future research should focus on elucidating the functions of individual proteins and adopting a comprehensive approach that includes glial cells. Advances in this field may deepen our understanding of the pathophysiological mechanisms of mental disorders and potentially lead to the development of novel therapeutic strategies.

Abstract: Since the features of cross-seeding of alpha-synuclein forms may affect sensitivity and specificity of the test systems, we developed a modified approach to obtain alpha-synuclein amyloid seeds with particle sizes from 20 to 50 nm prepared from either the wild-type protein (α-synWT) or its more fibrillation-prone form A53T (α-synA53T). These seeds had optimal properties for subsequent initiation of fibrillation. Our data showed that the elevated efficiency of alpha-synuclein A53T monomers transformation was hardly affected by the type of used seeds, whereas the addition of the seeds obtained from the alpha-synuclein mutant form to wild-type protein monomers had a significantly less effect than α-synWT seeds. TEM data revealed that in the presence of α-synWT seeds the wild-type alpha-synuclein formed long and wide fibrils, while the addition of α-synA53T seeds led to the formation of long, but thin fibrils. The application of α-synA53T monomers significantly reduced the fibrillation lag period, making it a promising candidate for use in medical test systems. In the future, a set of alpha-synuclein mutant forms could be used for the differential diagnosis of synucleinopathies caused by the different mutations of this protein.