Cheng J, Liu C, Cai Y
… +4 more, Zhai H, Zhang W, Su M, Hao Q
Biology (Basel)
· 2026 Jun · PMID 42345761
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Phytoplankton primary production (PP) underpins marine ecosystems. In winter marginal seas, the magnitude and size structure of PP not only sustain overwintering zooplankton but also shape larval fish survival and fisher...Phytoplankton primary production (PP) underpins marine ecosystems. In winter marginal seas, the magnitude and size structure of PP not only sustain overwintering zooplankton but also shape larval fish survival and fishery resources in the following year. We conducted two cruises in the fish overwintering grounds of the East China Sea shelf to investigate the spatial distribution, size structure, and environmental controls of net primary production (NPP). Winter NPP was generally low relative to the annual range. Nutrient concentrations at most stations exceeded potential limitation thresholds, whereas the mixed-layer mean light exposure (LE) fell below the light-saturation threshold at most stations, indicating that insufficient light availability was primarily associated with sub-saturating light conditions of low winter productivity. Among size classes, the nano-sized fraction dominated NPP, followed by the pico-sized fraction, while the micro-sized fraction contributed least; however, the relative contribution of the micro-sized fraction increased in February. Measured values of two key parameters widely used in satellite-based NPP models-PBopt (optimal chlorophyll-specific carbon fixation rate) and F (a dimensionless light-related factor for the vertical distribution of primary production)-were both lower than model predictions, and the magnitude of deviation varied with water depth and mixing conditions. These findings refine our understanding of biogeochemical processes in overwintering grounds of winter marginal seas.
Wang Y, Lyu S, Wang Y
… +3 more, Li J, Liu X, Lei M
Biology (Basel)
· 2026 Jun · PMID 42345760
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INDETERMINATE DOMAIN (IDD) transcription factors are plant-specific regulators essential for plant development and stress adaptation. As a globally important staple crop, common wheat ( L.) is frequently threatened by fu...INDETERMINATE DOMAIN (IDD) transcription factors are plant-specific regulators essential for plant development and stress adaptation. As a globally important staple crop, common wheat ( L.) is frequently threatened by fungal diseases such as powdery mildew and stripe rust. To date, however, the gene family in wheat has not been systematically characterized, and its roles in biotic stress responses remain unclear. In this study, we performed genome-wide identification and a comprehensive analysis of the gene family. A total of 41 genes were identified, which were unevenly distributed across 15 chromosomes and divided into four phylogenetic groups. Synteny and selective pressure analyses demonstrated that segmental duplication was the main driver of family expansion and that genes underwent strong purifying selection during evolution. -acting element analysis revealed abundant hormone- and stress-related elements in their promoter regions. Transcriptome and RT-qPCR analyses indicated that genes exhibited distinct expression patterns under abiotic and biotic stress. Notably, , , and were significantly induced by multiple fungal pathogens, suggesting their potential involvement in stress-responsive pathways that may be related to disease resistance. Subcellular localization analysis further confirmed that TaIDD39 was exclusively localized in the nucleus, consistent with its function as a transcriptional regulator. Our findings provide insights into the evolutionary characteristics and stress-response mechanisms of genes and highlight and other potential candidates that may serve as valuable resources for wheat molecular breeding to enhance broad-spectrum disease resistance and stress tolerance.
Chen Y, Hu H, Li W
… +7 more, Wei X, Du L, Tian D, Qu M, Gong Z, Li X, Yao Y
Biology (Basel)
· 2026 Jun · PMID 42345759
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is a globally distributed soil-dwelling pest that poses a major threat to peanut cultivation in China. Neuropeptides, as critical signaling molecules, regulate multiple physiological and behavioral processes in insects a...is a globally distributed soil-dwelling pest that poses a major threat to peanut cultivation in China. Neuropeptides, as critical signaling molecules, regulate multiple physiological and behavioral processes in insects and represent highly promising targets for pest management. To date, the functional characteristics of neuropeptides in remain unreported. In this study, we isolated and cloned one and one gene, respectively. Bioinformatics analysis revealed that alternative splicing of the gene produces two transcript variants, NPFa (255 bp) and NPFb (369 bp). The gene spans a length of 1188 bp, encoding 395 amino acids that contain seven α-helical transmembrane domains, indicating that it belongs to the family A G protein-coupled receptor (GPCR) family. Spatiotemporal expression profiles demonstrated that was most abundant in the adult brain, whereas was highly enriched in the brain and antennae. expression peaked in second-to-third-instar larvae, while was highly expressed in eggs. Starvation stress significantly upregulated the expression of both genes. RNA interference (RNAi)-mediated silencing of and significantly reduced food intake, female fecundity, and glycogen content in adults. These findings enhance our understanding of insect neuropeptides signaling networks and support the development of behavior-based pest control strategies.
Jiang C, Huang R, Luo R
… +3 more, Wang T, Qiu HJ, Sun Y
Biology (Basel)
· 2026 Jun · PMID 42345758
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African swine fever (ASF), caused by African swine fever virus (ASFV), is a devastating swine disease. To date, no commercial ASF vaccine has been authorized for global marketing except in Vietnam, and emerging genotype...African swine fever (ASF), caused by African swine fever virus (ASFV), is a devastating swine disease. To date, no commercial ASF vaccine has been authorized for global marketing except in Vietnam, and emerging genotype I/II recombinant ASFV strains pose severe new challenges to ASF control. Live-attenuated vaccines (LAVs) are widely recognized as the most promising strategy for ASF control. This review systematically summarizes three conventional development strategies for ASF LAVs, dissects the molecular mechanisms of two core bottlenecks-intergenotypic ASFV recombination and vaccine strain reversion to virulence-and elaborates rational design strategies for next-generation LAVs based on cutting-edge technologies. These strategies can fundamentally mitigate the aforementioned risks, offering promising solutions for addressing the major limitations of conventional ASF LAVs.
Biology (Basel)
· 2026 Jun · PMID 42345757
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Plant pests pose a severe threat to global agricultural productivity and ecosystem stability [...].Plant pests pose a severe threat to global agricultural productivity and ecosystem stability [...].
Biology (Basel)
· 2026 Jun · PMID 42345756
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Imaging-based spatial transcriptomics has advanced from low-plex single-molecule fluorescence in situ hybridization to a diverse set of highly multiplexed platforms, with recent multimodal and pathology-compatible capabi...Imaging-based spatial transcriptomics has advanced from low-plex single-molecule fluorescence in situ hybridization to a diverse set of highly multiplexed platforms, with recent multimodal and pathology-compatible capabilities. Despite major differences in chemistry, coding, and imaging strategies across different platforms, their biological interpretation often converges on a few notable computational biology problems. This review examines imaging-based spatial transcriptomics through the lens of data interpretation and applications, focusing on the analytical framework that converts raw fluorescence signals or accompanying in situ sequencing data into molecule-, cell-, and tissue-level representations. We discuss the key challenges in preprocessing, registration, restoration, feature detection, barcode decoding, molecule calling, cell segmentation, transcript assignment, probabilistic cell typing, spatial-domain inference, and atlas integration. We also highlight how optical crowding, tissue thickness, panel bias, and multimodal complexity increase computational difficulty. Finally, we summarize applications of imaging-based spatial transcriptomics techniques, ranging from subcellular RNA localization to atlas-scale and pathology-aware spatial analysis.
Biology (Basel)
· 2026 Jun · PMID 42345755
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The efficiency of converting ripe fruits into processed beans is an economically relevant component of production systems, yet its genetic parameters remain poorly characterized in studies that do not partition the geno...The efficiency of converting ripe fruits into processed beans is an economically relevant component of production systems, yet its genetic parameters remain poorly characterized in studies that do not partition the genotype × year (G×Y) interaction. This study estimated genetic parameters for five processing efficiency traits, namely grain proportion (% grain), husk proportion (% husk), fruit fresh mass per grain mass (FWM/GW), fruit fresh mass per bag (FWM/bag), and fruit volume per bag (FVol/bag), in 48 genotypes (40 Robusta, 8 Conilon) evaluated over two crop years (2023-2024) in Jaguaré, Espírito Santo, Brazil. Bayesian inference via MCMC (brms) revealed that the genotype × year variance component exceeded the genotypic variance in 79-97% of posterior samples across the 48 genotypes evaluated over two crop years, a result that should be interpreted within the context of this restricted temporal window, with median heritabilities of 0.27-0.50 (95% credible intervals spanning up to 0.66 units, reflecting the uncertainty inherent to the two-year evaluation window) and genotypic correlations of 0.19-0.38 between years, indicating low consistency of genetic merit across crop seasons. Bayesian probability of consistent superiority identified Z21 as the genotype with the highest predictability for FWM/bag (prob. =0.846 at 20% selection intensity), while VR3 showed a favorable profile across four traits simultaneously. The multi-trait model with unstructured covariance estimated a negative genetic correlation between % grain and FWM/bag (r^g=-0.87), suggesting potential for indirect selection. UPGMA clustering based on Mahalanobis distance (CCC =0.813) yielded six divergence groups that did not coincide with the botanical classification Conilon/Robusta. In this single-location, two-year study, temporal instability was the predominant source of uncertainty in the selection for processing efficiency in under restricted evaluation windows. under restricted evaluation windows. Accordingly, the highlighted genotypes should be interpreted as priority candidates for validation in multi-environment, multi-year networks, rather than as definitive cultivar recommendations, given that the short evaluation window limits the generalizability of genotypic rankings.
Zhang J, Wang Z, Xiao Q
… +6 more, Fu X, Li S, Chen S, Cao Y, Zhao X, Zhang Y
Biology (Basel)
· 2026 Jun · PMID 42345754
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The northern pike () is an economically important cold-water fish species in northern China. It exhibits pronounced sexual dimorphism, yet the molecular mechanism underlying its sex differentiation remains unclear, which...The northern pike () is an economically important cold-water fish species in northern China. It exhibits pronounced sexual dimorphism, yet the molecular mechanism underlying its sex differentiation remains unclear, which hinders the development of aquaculture. Whole-transcriptome sequencing is a powerful approach for screening sex-related genes; however, no such study has been reported for this species to date. In this study, gonadal tissues from three female and three male were collected for whole-transcriptome sequencing. A total of 14,941 differentially expressed messengerRNAs, 119 differentially expressed microRNAs, 229 differentially expressed circularRNAs, and 2055 differentially expressed long non-codingRNAs were identified. Functional enrichment analysis revealed that the differentially expressed genes were significantly enriched in pathways closely associated with sex differentiation, such as steroid hormone biosynthesis and oocyte meiosis. Several key sex-biased genes were identified, including female-biased genes (, , ) and male-biased genes (, , ). Furthermore, a competing endogenous RNA (ceRNA) regulatory network involving dre-miR-107b was constructed, which may represent a candidate for further investigation into sex differentiation in . This study provides the first comprehensive whole-transcriptome dataset of female and male gonads in , identifies key sex-biased genes and core pathways involved in its sex differentiation, and thereby identifies the dre-miR-107b-centered ceRNA network and key sex-biased genes (, , , , , ) as core molecular players in sex differentiation of this species.
Ma Y, Guo W, Wang H
… +5 more, Zhang J, Wei M, Shi C, Ji K, Yu Q
Biology (Basel)
· 2026 Jun · PMID 42345753
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mA is an important RNA modification involved in post-transcriptional regulation in plants. However, putative mA writers and erasers in remain poorly characterized. In this study, a total of 17 candidate mA regulatory ge...mA is an important RNA modification involved in post-transcriptional regulation in plants. However, putative mA writers and erasers in remain poorly characterized. In this study, a total of 17 candidate mA regulatory genes, including 8 writers and 9 erasers, were identified through genome-wide analysis. Phylogenetic and structural analyses indicated that these proteins are generally conserved, with some members showing potential functional divergence. Promoter analysis revealed abundant hormone- and stress-responsive cis-elements, and expression profiling showed tissue-specific patterns and dynamic responses to ABA, MeJA, and NaCl treatments, with erasers exhibiting greater transcriptional responsiveness than writers. In addition, protein interaction network and phase separation predictions suggested potential roles in RNA methylation-related processes. These results provide a foundation for further functional studies of mA regulation in .
Ma L, Tian Y, Che X
… +4 more, Ouyang W, Bi R, Zhao M, Cui D
Biology (Basel)
· 2026 Jun · PMID 42345752
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In the present study, FeO@hydrothermal carbon was prepared successfully using rice straw waste. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) analysis confirmed that the material had rich and s...In the present study, FeO@hydrothermal carbon was prepared successfully using rice straw waste. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) analysis confirmed that the material had rich and strong redox-active centers on its surface, indicating that it has potential to be used as a redox mediator for electron transfer. FeO@hydrothermal carbon was added into the anaerobic sludge treatment system for the collaboration of dye decolorization. The results showed that azo dye decolorization efficiency reached the maximum value (98.3%) with the presence of FeO@hydrothermal carbon, which was 16.6% higher than control reactor (without FeO@hydrothermal carbon added). In addition, FeO@hydrothermal carbon exhibits good reusability and the dye decolorization rates in the "anaerobic sludge-material" combining system were significantly higher than that in the "sludge-alone" system during the semi-continuous wastewater treatment process. Mechanistic investigations revealed that the enhanced decolorization is driven by a synergistically constructed interspecies electron transfer pathway. Specifically, the addition of FeO@hydrothermal carbon improved the formation of the extracellular polymeric substance (EPS), which had positive effects on sludge stability and its interaction with the material. CV and electron transport system (ETS) activity analysis showed that the sludge exhibited high electrochemical activities with the support of the material, which led to a high electron transfer efficiency between the electron-donating and accepting microbial pairs in the treatment system. The high-throughput sequencing analysis showed that the structure of the microbial community changed during the semi-continuous treatment process; and accounted for more than 87.5% of the total abundance of the bacterial community in the anaerobic sludge with material addition. Driven by the material-mediated process, these enriched functional taxa exhibited a high electron transfer efficiency between electron-donating and accepting pairs, accelerating the catalytic cleavage of azo bonds and ultimately improving the overall anaerobic treatment performance.
Chen Y, Qiu J, Liu J
… +5 more, Lin H, Kan L, Zheng Y, Wei J, Zhang L
Biology (Basel)
· 2026 Jun · PMID 42345751
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The cellulose synthase gene superfamily encompasses two major groups, and , which are vital for synthesizing cellulose and hemicellulose in plant cell walls and fundamental to plant growth and developmental regulation....The cellulose synthase gene superfamily encompasses two major groups, and , which are vital for synthesizing cellulose and hemicellulose in plant cell walls and fundamental to plant growth and developmental regulation. is a rare tree with high timber value. Currently, there is no relevant report on the identification and characterization of the / gene family in . In this study, based on the high-quality genome of , 47 members of the / superfamily were identified and classified into seven subfamilies, including , , , , , and . Cis-acting elements were identified via analysis of the 2000 bp upstream sequences of , suggesting extensive involvement in biotic and abiotic stress regulation. Based on the transcriptome data of five growth periods, the expression of the / family was analyzed. Combined with phylogenetic information, it is inferred that /// may regulate the secondary wall, while // may regulate the primary wall. Protein-protein interaction showed that // were in the core site. Finally, we constructed the cellulose synthase complex (//) model using AlphaFold3, which suggests that // may form a complex on the plasma membrane to carry out cellulose synthesis. This study has a limitation in that the complex and its expression lack experimental validation, and only data analysis is provided as a reference, offering some directions for future research. In summary, the systematic characterization of the / gene family provides important insights into cell wall formation, genetic enhancement, and future biotechnological applications of this species.
Zhang D, Liu P, Lu X
… +4 more, Hao H, Sun H, Nie Z, Ren S
Biology (Basel)
· 2026 Jun · PMID 42345750
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To test the performance of -based DNA barcoding in species delimitation, we amplified and sequenced the mitochondrial gene from six Schizothoracine fishes endemic to Xinjiang, China. We then characterized the gene data...To test the performance of -based DNA barcoding in species delimitation, we amplified and sequenced the mitochondrial gene from six Schizothoracine fishes endemic to Xinjiang, China. We then characterized the gene dataset, quantified genetic divergence, and inferred phylogenetic relationships using distance-based approaches. Morphological examination supported clear phenotypic differentiation among taxa. In particular, can be readily distinguished from the densely scaled species by having a single pair of barbels and relatively sparse scales. The gene sequences showed an evident AT bias (55.1%), consistent with patterns reported for teleost mitochondrial genomes. Across all samples, 11 haplotypes were identified. Pairwise comparisons indicated a maximum interspecific divergence of 15.296%, whereas the smallest interspecific distance (0.262%) occurred between and . Species-delimitation analyses and phylogenetic reconstruction supported and as distinct mitochondrial lineages, whereas , , , and were not fully resolved by gene. The shared haplotypes and low genetic distances among the four species may reflect recent divergence, incomplete lineage sorting, or historical gene flow. Overall, gene barcoding is effective for distinguishing the major lineages in this dataset, especially and .
A new study in PLOS Biology shows that neuronal firing is selectively tuned to oscillatory frequency in human intracranial recordings, complementary to phase tuning, suggesting an additional dimension in how brain rhythm...A new study in PLOS Biology shows that neuronal firing is selectively tuned to oscillatory frequency in human intracranial recordings, complementary to phase tuning, suggesting an additional dimension in how brain rhythms may organize neural activity.
Understanding and predicting how communities assemble is a paramount challenge in ecology. Here we address these questions normatively by comparing the observed species abundance distribution to a game-theoretically fair...Understanding and predicting how communities assemble is a paramount challenge in ecology. Here we address these questions normatively by comparing the observed species abundance distribution to a game-theoretically fair distribution based on each species' Shapley value. By analyzing in total 56 distinct community outcomes, we assess how fairly biomass is distributed in microbial communities displaying both competitive and cooperative interactions in different growth conditions. We find examples of fair communities that closely follow their Shapley value across all environments as well as counterexamples where the true abundances deviate from the species' objective contribution to community biomass. Next, we develop a fair assembly rule based on the recursive definition of Shapley value and show that also unfair community compositions are consistent with the principles of fair assembly after the lower-level competitive outcomes are known. Our results give unique empirical insights into the distributive function of ecological dynamics and lay down the theoretical foundations of what might become a normative community assembly theory.
The dynamics of stem cell maintenance and proliferative patterns are key determinants of tissue aging in multicellular organisms. Leveraging our previously developed SMALT system with enhanced sequencing compatibility, w...The dynamics of stem cell maintenance and proliferative patterns are key determinants of tissue aging in multicellular organisms. Leveraging our previously developed SMALT system with enhanced sequencing compatibility, we performed longitudinal lineage tracing of the adult Drosophila melanogaster midgut across different developmental stages. Using ubiquitous Tubulin-GAL4-driven labeling, we first profiled midgut-wide clonal dynamics during early adulthood (3-33 days post-eclosion). Phylogenetic reconstruction revealed that clonal diversity peaked immediately after eclosion and began to decline earlier than anticipated, accompanied by a reduction in effective population size. To further investigate stem cell-specific dynamics during late adulthood, we employed intestinal stem cell (ISC)-specific Dl-GAL4-driven labeling (33-63 days post-eclosion) and observed sustained clonal attrition in the posterior midgut. This progressive loss of diversity was consistent with an age-associated change in effective proliferative behavior and reduced lineage maintenance capacity, as reflected by a decline in net proliferative output inferred from lineage topology. Remarkably, ISC lineages emerging within the first 10 days post-eclosion exhibited sustained clonal dominance in aging populations, with a single lineage comprising over 63% of sampled cells by Day 63. Bayesian survival modeling confirmed that these early-origin lineages have the highest probabilities of long-term persistence, while a graph neural network model accurately predicted their structural evolution across successive stages. Together, we delineate a timeline for clonal attrition and deliver topology-driven predictors of clone survival and structural change, enabling prospective identification of dominant and failing clones during aging.
Web-based modeling platforms can enhance collaboration between modelers and experimentalists during early model development. Drawing on two interdisciplinary case studies, we provide guiding principles on how to build in...Web-based modeling platforms can enhance collaboration between modelers and experimentalists during early model development. Drawing on two interdisciplinary case studies, we provide guiding principles on how to build interactive agile modeling tools.
UNLABELLED: Sleep is essential for synaptic homeostasis, a proposed mechanism whereby wakefulness leads to synaptic potentiation and sleep facilitates synaptic down-selection. Synaptic vesicle glycoprotein 2A (SV2A), who...UNLABELLED: Sleep is essential for synaptic homeostasis, a proposed mechanism whereby wakefulness leads to synaptic potentiation and sleep facilitates synaptic down-selection. Synaptic vesicle glycoprotein 2A (SV2A), whose availability is quantifiable by [¹⁸F]SynVesT-1 positron emission tomography (PET), is commonly interpreted as a proxy for synaptic density. In this randomized study, we examined 40 healthy adults (mean age 27.5 ± 6.5 years) who underwent two [¹⁸F]SynVesT-1 PET scans on consecutive days. Half of the participants were assigned to the normal sleep (i.e., control) condition and half to the sleep deprivation condition. Scans were performed at the same circadian time point, approximately 4 h after awakening in the control group and during baseline in the sleep deprivation group or after ~28 h of continuous wakefulness in the sleep deprivation group after sleep deprivation. Sleep deprivation led to significant increases in synaptic vesicle glycoprotein 2A binding in multiple brain regions, including the thalamus (+4.6%), hippocampus (+5.6%), and parietal cortex (+3.2%), whereas no changes were observed in controls. The degree of increase in synaptic vesicle glycoprotein 2A positively correlated with elevated slow wave activity during recovery sleep, a physiological marker of sleep pressure. These findings provide in vivo support for the synaptic homeostasis hypothesis in humans and suggest that synaptic vesicle glycoprotein 2A PET imaging is sensitive to sleep-wake dependent synaptic plasticity. TRIAL REGISTRATION: The study was prospectively registered on 19.01.2022 here: German Clinical Trials Registry: DRKS # DRKS00027867, https://drks.de/search/en/trial/DRKS00027867.
Neural oscillations play a critical role in shaping neuronal firing patterns. While phase-locked neuronal firing ("phase tuning") has been extensively studied in animal models and human invasive recordings, much less is...Neural oscillations play a critical role in shaping neuronal firing patterns. While phase-locked neuronal firing ("phase tuning") has been extensively studied in animal models and human invasive recordings, much less is known about whether neurons show preferential firing at specific oscillatory frequencies, termed frequency tuning. Here, we employ human intracranial recordings across several brain regions including hippocampus, entorhinal cortex, anterior and posterior cingulate cortex, and orbitofrontal cortex to test the hypothesis that neurons exhibit frequency-specific firing. We analyzed 357 single units recorded simultaneously with local field potentials in 19 neurosurgical patients during awake resting. We estimated the instantaneous frequency of the LFP using adaptive spectral decomposition and assessed frequency tuning of each neuron while controlling for changes in firing rate unrelated to frequency changes. We found 27% of neurons exhibited increased or decreased firing within specific frequencies, most commonly within the low-frequency range (<10 Hz). Neurons exhibiting frequency tuning were distinct from those displaying phase tuning, and both types of tuning were observed across multiple brain regions with no anatomical preference. Together, our results demonstrate that the instantaneous frequency of neural oscillations modulates neuronal firing which may serve as an additional mechanism for information processing in the human brain, opening new avenues for frequency-targeted neural stimulation.
BACKGROUND: Fanconi anemia is a rare genomic instability syndrome associated with congenital abnormalities and cancer predisposition. These alterations are mainly due to deficiencies in DNA repair mechanisms. The Fanconi...BACKGROUND: Fanconi anemia is a rare genomic instability syndrome associated with congenital abnormalities and cancer predisposition. These alterations are mainly due to deficiencies in DNA repair mechanisms. The Fanconi anemia pathway is evolutionarily conserved, allowing functional studies in model organisms like Caenorhabditis elegans, where it promotes and executes error-free homologous-recombination over the mutagenic non-homologous-end-joining pathway; fcd-2 (FANCD2 ortholog) plays a key role in this regulation to preserve genome stability. In this study, we report that the choice of DNA repair pathway for resolving double-strand breaks is influenced by absence of the RAD-51 long isoform, a key component of the Fanconi anemia pathway that plays a central role in homologous strand exchange during recombination. RESULTS: In C. elegans, which is predicted to encode three RAD-51 isoforms, we find that loss of RAD-51 isoform A enhances homologous recombination efficiency. Additionally, RAD-51 isoform A depletion decreases developmental and meiotic defects in fcd-2 mutants as well as reduces chromosome aggregation in fcd-2-deficient germ cells. CONCLUSIONS: Together, these findings reveal a novel role for RAD-51 C. elegans, suggesting that the pattern of RAD-51 isoform expression modulates the balance between homologous recombination and non-homologous-end-joining, thereby preserving genome stability.