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At least 19 recordsLinked to original sources

PubMed2025

Migration strategies, connectivity and corridor features of the partial migrant little bustard (Tetrax tetrax) across the Iberian Peninsula.

The study of migration ecology is crucial for understanding the factors and pressures affecting migratory species. Here, we studied the migratory ecology of the little bustard (Tetrax tetrax), a steppe bird that has suffered a sharp decline over recent decades, mainly due to agricultural intensification. Using 105 adult birds tagged across the main Iberian regions where the species is present (Alentejo, Extremadura, Ebro Valley, Northern Plateau, Southern Plateau and Guadalquivir Valley), we analysed the ratio of migratory and resident birds in each population and assessed their connectivity during the three main migratory periods (summer, winter and pre-breeding). Additionally, we describe the features of the migrations recorded in terms of length, duration and day period. Our results corroborate that little bustards can be considered partial migrants across Iberia, although the proportion of residents versus migrants varied between populations: the Alentejo (94.74%) and Northern Plateau (93.75%) had the highest proportion of migrants, followed by Guadalquivir Valley (81.82%), Extremadura (65.38%), Southern Plateau (55.56%) and Ebro Valley (25.93%). Migratory connectivity varied between periods: the pre-breeding and summering migrations showed a trend to move northwards, while birds moved southwards for winter. Regarding the migratory corridors obtained from the 253 migrations identified, we found three main routes: one corridor that connects the Northern Plateau with the western part of the Southern Plateau and Extremadura, another one that connects the Southern Plateau, Extremadura, Alentejo and Guadalquivir Valley, and one corridor that concentrates migrations within the Ebro Valley, and between the Ebro Valley and the Southern Plateau. Finally, analyses showed that little bustards migrate at night through areas dominated by herbaceous cover (avoiding tree-covered land and water bodies) and of low elevation and terrain roughness. Our results highlight the importance of developing an international and inter-regional conservation strategy to protect not only the breeding and wintering quarters, but also this endangered species' migratory corridors, thus supporting the viability of the metapopulation.

Brownian bridge kernel↗

PubMed2026

Large-scale benchmarking of prokaryotic annotation tools across thousands of species.

BACKGROUND: Genome annotation is an important step in deriving functional meaning from prokaryotic sequencing data, yet systematic evaluations guiding tool selection are lacking. We present the first large-scale investigation of four prominent open-source annotation tools (Prokka, Bakta, EggNOG-mapper, and PGAP) across 156,033 diverse genomes. This includes Escherichia coli strains for baseline performance, thousands of archaea and bacteria genomes, as well as frameshifted and metagenome-assembled genomes. RESULTS: Bakta excels in annotating high-quality bacterial genomes, while PGAP was better for archaeal genomes and challenging bacterial assemblies, including metagenome-assembled, fragmented, or contaminated samples. For Gene Ontology annotation, PGAP consistently provides broader term coverage, whereas EggNOG-mapper offers more terms per feature. CONCLUSIONS: Our findings highlight tool-specific strengths crucial for selecting optimal solutions based on genome quality, taxonomy, and origin (e.g. MAGs). This study provides an evidence-based guide for users and informs future tool development.

Molecular Sequence Annotation↗

PubMed1976

Sudden potential drop in bullfrog gastric mucosa.

The previously reported sudden potential drop (SPD), which occurs under anoxia in 10% CO2, has been further explored. We find several conditions necessary for this effect: 1) anoxia; 2) serosal pH less than 7.1;3) presence of chloride; and 4) a PD, either spontaneous or voltage clamped, which changes across the region of 10 mV, serosal positive. With the first three conditions satisfied, a reversible decrease in measured resistance can be produced at will by changing the clamp voltage. In the anoxic, low-resistance state, changes in K+ or C1- concentration give little change in voltage, showing that the increased conductivity is not selective for either ion. A model is proposed containing a shunt-resistance element whose resistance is a step function of PD. This model can mimic the responses of the tissue and provides a working model for the SPD.

Animals↗

PubMed1976

Radiologic evaluation of the function of the cervical spine.

Cervical functional examinations initiated in 1965 suggested the need of a correlated, multifactorial expression of the cervical sagittal movement function, allowing comparative evaluations of physiologic-diagnostic significance. Technical aspects of the successive steps of investigation, together with the final morphologic-functional formula are described. The significance of the normal and abnormal functional patterns, identified in a selected series of 300 cases, is finally discussed.

Adult↗

PubMed2025

Multi-step genomics on single cells and live cultures in sub-nanoliter capsules.

Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes and reagents. Capsules enable high-throughput multi-step assays combining live-cell culture with genome-wide readouts. We establish methods for barcoding CAGE DNA libraries, and apply them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extension to live-cell assays.

Journal Article↗

PubMed2024

Lineage-specific splicing regulation of MAPT gene in the primate brain.

Divergence of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is widespread in mammals, including primates, but the underlying mechanisms and functional impact are poorly understood. Here, we modeled cassette exon inclusion in primate brains as a quantitative trait and identified 1,170 (∼3%) exons with lineage-specific splicing shifts under stabilizing selection. Among them, microtubule-associated protein tau (MAPT) exons 2 and 10 underwent anticorrelated, two-step evolutionary shifts in the catarrhine and hominoid lineages, leading to their present inclusion levels in humans. The developmental-stage-specific divergence of exon 10 splicing, whose dysregulation can cause frontotemporal lobar degeneration (FTLD), is mediated by divergent distal intronic MBNL-binding sites. Competitive binding of these sites by CRISPR-dCas13d/gRNAs effectively reduces exon 10 inclusion, potentially providing a therapeutically compatible approach to modulate tau isoform expression. Our data suggest adaptation of MAPT function and, more generally, a role for AS in the evolutionary expansion of the primate brain.

tau Proteins↗

PubMed2023

Proteomics from compartment-specific APEX2 labeling in Mycobacterium tuberculosis reveals Type VII secretion substrates in the cell wall.

The cell wall of mycobacteria plays a key role in interactions with the environment. Its ability to act as a selective filter is crucial to bacterial survival. Proteins in the cell wall enable this function by mediating the import and export of diverse metabolites, from ions to lipids to proteins. Identifying cell wall proteins is an important step in assigning function, especially as many mycobacterial proteins lack functionally characterized homologues. Current methods for protein localization have inherent limitations that reduce accuracy. Here we showed that although chemical labeling of live cells did not exclusively label surface proteins, protein tagging by the engineered peroxidase APEX2 within live Mycobacterium tuberculosis accurately identified the cytosolic and cell wall proteomes. Our data indicate that substrates of the virulence-associated Type VII ESX secretion system are exposed to the periplasm, providing insight into the currently unknown mechanism by which these proteins cross the mycobacterial cell envelope.

Mycobacterium tuberculosis↗

PubMed1978

Experimental evolution of a new enzymatic function. II. Evolution of multiple functions for ebg enzyme in E. coli.

The evolution of ebgo enzyme of Escherichia coli, an enzyme which is unable to hydrolyze lactose, lactulose, lactobionate, or galactose-arabinoside effectively, has been directed in successive steps so that the evolved enzyme is able to hydrolyze these galactosides effectively. I show that in order for a strain of E. coli with a lacZ deletion to evolve the ability to use lactobionate as a carbon source, a series of mutations must occur in the ebg genes, and that these mutations must be selected in a particular order. The ordered series of mutations constitutes an obligatory evolutionary pathway for the acquisition of a new function for ebgo enzyme. A comparison of newly evolved strains with parental strains shows that when ebg enzyme acquires a new function, its old functions often suffer; but that in several cases old functions are either unaffected or are improved. I conclude that divergence of functions catalyzed by an enzyme need not require gene duplication.

Biological Evolution↗

PubMed1976

A spin label study of the thermal unfolding of secondary and tertiary structure in E. colic transfer RNAs.

The molecular mechanism of thermal unfolding of E. coli tRNAGlu, tRNAfMet and tRNAPhe (in 0.02M Tris-HC1, pH 7.5. 10 MM Mg C12) has been examined by the spin-labeling technique. The rate of tumbling of the spin label has been measured as a function of temperature for ten different selectively spin-labeled tRNAs. Only spin labels at position s4U-8 were able to probe the tertiary structure. Evidences are presented which support the hypothesis that the thermal denaturation of the three species of tRNAs studied is sequential. The unfolding process occurs in three discrete stages. The first step (30 degrees-32 degrees) could either be assigned to a localized reorganization of the cold-denatured structure or to a "transient" melting, followed by the simultaneous disruption of the tertiary structure and part of the hU helix. This transition is observed even in the absence of magnesium. The second step (50 degrees-54 degrees) involves the melting of the anticodon and miniloop regions. The last step occurs above 65 degrees where the t psi c and amino acid acceptor stems, forming one continuous double helix, melt. A simple dynamic model is considered for tRNA function in protein biosynthesis.

Binding Sites↗

PubMed2026

Generation of spCAS9 expressing human mesenchymal stem cell line to study gene function during osteoblast differentiation.

Human bone marrow-derived stromal cells (hMSCs) are a great resource for studying how genes influence cell fate and differentiation into various cell types like osteoblasts, adipocytes, and chondrocytes, among other cell types. However, genetic manipulation of primary hMSCs has been challenging due to their short lifespan and cellular senescence after limited passaging. Their low and unstable transfection efficiency also complicates gene delivery or inactivation, hindering long-term functional studies. The limited lifespan has been effectively solved by immortalizing hMSCs with telomerase reverse transcriptase (hMSCs-TERT). The use of these cells is ideal for functional studies of osteoblast and adipocyte differentiation through genetic manipulation, providing a stable and reliable model. Here, we have engineered a stable CAS9 expressing hMSC-TERT cell line (hMSC-TERTCAS9) via lentiviral transduction. The constitutive expression of spCas9 enables efficient and reproducible gene editing. We demonstrate the potential of these hMSC-TERTCAS9 cells for generating gene disruptions using plasmid delivery of guide RNAs as a fast and efficient strategy for targeted genome editing. The edited cells can be sorted and expanded as single cells to obtain homogenous clonal cell lines with mono- as well as bi-allelic gene deletions, a crucial step for producing reliable experimental results. We further validate this cell line as a powerful tool for studying gene function during hMSC proliferation and differentiation, providing 3 distinct examples of its utility. Through the generation of indels, single-cell sorting, and clonal selection, we have efficiently inactivated the vitamin D receptor and created both larger (256 nucleotides) gene disruptions in Forkhead box protein O1 and precise removals of a small genomic sequence (73 nucleotides) coding for microRNA MIR675. This novel hMSC-TERTCAS9 cell line represents a significant advancement, offering a stable, efficient, and versatile platform for advanced genetic studies, high-throughput screening, and the creation of reliable cellular disease models.

CRISPR-Cas9↗

PubMed1975

Gene duplication as a mechanism of genetic adaptation in Saccharomyces cerevisiae.

It has been shown that specific mutations of the gene that codes for the general acid monophophatase (Aphtase) of S. cerevisiae can increase the affinity of this enzyme for beta-glycerophosphate (BGP) and thereby provide this organism with the capacity to exploit extremely low concentrations of this organic phosphate (Francis and Hansche 1973). In this report two additional avenues are demonstrated to be available to this organism for increasing its capacity to exploit low concentrations of organic phosphates. One avenue is through mutations that increase the amount of Aphtase that associates with the cell wall, where it catalizes the hydrolysis of exogenous organic phosphates. The other avenue is through duplication of the gene that codes for Aphtase, doubling the amount of Aphtase synthesized.--The spontaneous duplication of the structural gene of Aphtase and the incorporation of the duplicate into this experimental population as a means of exploiting low concentrations of exogenous organic phosphates provides direct support for the first step of the mechanism through which new metabolic functions are postulated to evolve.

Acid Phosphatase↗

PubMed2026

Graph neural network-based risk stratification of prostate cancer using gene expression and SHAP interpretability.

Accurate risk stratification is essential for guiding treatment decisions and preventing over treatment of prostate cancer, which remains one of the most prevalent cancers among adult men. While the Gleason score, obtained from prostate biopsies, is routinely used to assess tumor aggressiveness, the biopsy procedure carries risks such as pain, infection, and, in some cases, serious complications such as sepsis. In this study, we proposed an artificial intelligence-based framework that integrates mRNA expression profiles with functional interaction networks to classify prostate cancer patients into low-, medium-, and high-risk groups defined by Gleason scores. The pipeline comprised five steps: (1) data collection from The Cancer Genome Atlas (TCGA), (2) preprocessing of gene expression data, (3) two-stage feature selection to identify informative biomarkers, (4) risk classification using a dual-branch graph neural network (GNN) that combines gene-gene interaction graphs with sample-level expression features, and (5) model interpretation using SHAP to quantify feature contributions. Differentially expressed genes were identified in the High (ASPN, GMNN, PEBP4, C2, KNCK17), Medium (C2, IGSF1, ASPN, CDKN3, AMH), and Low (TNMD, VWA5B2, ST6GALNAC5, CYP3A5, PHGR1) risk groups, underscoring the molecular heterogeneity of disease progression. On an independent held-out test set, the model achieved AUCs of 0.86, 0.88, and 0.95 for the low-, medium-, and high-risk groups, respectively, with an overall accuracy of 80%. These results suggest that combining GNN-based modeling with explainable AI can capture both global and local molecular patterns relevant to tumor aggressiveness. However, as the model was developed and evaluated solely on the TCGA cohort, the findings should be regarded as exploratory, and external validation will be required to establish generalizability. Within these limitations, the proposed framework highlights the potential of molecular profiling and graph-based deep learning to support more precise, potentially less invasive, risk assessment and individualized treatment planning in prostate cancer.

Prostatic Neoplasms↗

PubMedDate not supplied

Use of a symmetry condition to compute the conformation of gramicidin S1.

Using an improved method for computing conformations of closed rings with symmetry, in conjunction with an improved empirical energy function, the conformational space of Gramicidin S is reexamined. The search for minimum energy conformations is confined to the subspace containing closed symmetric rings. A large number of initial conformations selected from that subspace is subjected to energy minimization or is eliminated in a sequence of steps designed to locate the global minimum-energy conformation. One conformation having distinctly low energy is found and is judged to be the global minimum-energy conformation. This conformation is of the beta-pleated sheet type and is in complete agreement with experimental data. Similar structures with beta-pleated sheet-type conformations have been proposed previously on the basis of less extensive examiniations of the conformational space; the condition of exact ring closure, and the extensive examination of conformational space, used here, establish this structure on a firm basis.

Computers↗

PubMed2026

Alternatively spliced killer-protector system confers S19-mediated hybrid male sterility in rice.

Hybrid sterility limits the use of strong interspecific heterosis and S19 is a major locus that confers hybrid sterility between Oryza sativa (Asian cultivated rice) and Oryza glaberrima (African cultivated rice). However, the S19 is not yet cloned and its underlying mechanism remains elusive. In this study, we identify two closely linked genes (S19A1 and S19A7) specific to African rice allele that encode a killer-protector module at the S19 locus. Two alternatively spliced transcripts expressed from the killer gene S19A1 (S19A1.1 and S19A1.2) encode mitochondria-targeted cytotoxic proteins that cause toxicity diversity for somatic and/or gametic cell death, respectively. However, S19A7 interacts with S19A1.1 and S19A1.2, blocking their cytotoxic effect. Because the Asian rice S19 allele lacks S19A1 and S19A7, male gametes that carry this allele are selectively aborted in Asian-African F1 hybrids. Knockout of S19A1 can overcome S19-mediated hybrid sterility. Haplotype analysis reveals that the functional S19 allele is absent in non-AA-genome Oryza species and likely emerged in the O. barthii-O. glaberrima lineage through a multi-step evolutionary process. Our findings provide insight into the genetic mechanisms responsible for hybrid sterility between Asian and African rice and suggest genetic and biotechnological strategies for the use of interspecific heterosis in rice.

Oryza↗

PubMed2026

plinkQC: an integrated tool for ancestry inference, sample selection, and quality control in population genetics.

MOTIVATION: Population genetic analyses rely on high quality datasets that pass rigorous controls for sample and marker quality. Many analyses also require additional processing including identification of ancestry and sample relatedness. A software package that addresses all these common, yet crucial tasks is missing. RESULTS: We have developed plinkQC, an R/CRAN package that combines these functionalities into a single software package with detailed vignettes for example applications. plinkQC determines the ancestry of study samples via a pre-trained random forest classifier that reaches 98% performance accuracy with just 5% of marker overlap between reference and user data. To obtain the maximal set of unrelated study samples, we developed a graph-based pruning method, taking both relationship estimates and sample quality into account. We demonstrate optimal sample selection on the 1000 Genomes project, where we retain an additional 71 samples compared to publicly available exclusion lists. Finally, plinkQC bundles these results together with per-individual and per-marker quality control checks into three simple functions and returns both the quality controlled dataset and quality control report about each step of the analysis. AVAILABILITY AND IMPLEMENTATION: plinkQC is available as an R/CRAN package. The documentation and code are available on github: https://meyer-lab-cshl.github.io/plinkQC/ and https://github.com/meyer-lab-cshl/plinkQC_manuscript.

Software↗

PubMed2026

Mapping the Molecular Evolution and Role of Wild Rice GLYIII Protein-Encoding Genes in Abiotic Stress Response.

To address the need for sustainable food production amid rapid global climate change, developing rice varieties that grow optimally even under harsh conditions is essential. An effective approach in this direction would be to harness the stress resilience traits of the crop wild relatives (CWRs) of rice. Among the various crucial stress-responsive genes, the Glyoxalase III (GLYIII) gene family is of utmost importance for its ability to detoxify the toxic glycolytic byproduct, methylglyoxal (MG), in a less energy-intensive, single-step process, as well as for its multifaceted cytoprotective role. In our study, a comprehensive genome-wide search across the Oryza genus revealed that GLYIII genes are conserved across wild rice genotypes. Their number has expanded during domestication, driven by gene duplications. Interestingly, only a few orthologous pairs showed positive selection, suggesting that the functions of most others need to be constrained and or conserved.We found that higher GLYIII activity, Total Antioxidant Capacity, endogenous glutathione (GSH) levels, and free radical scavenging activity contributes to the stress resilience of wild rices O. punctata, O. meridionalis, and O. nivara, in addition to other factors. , , . , . Our qRT-PCR analysis revealed differential expression of the OpGLYIII, OmGLYIII, and OnGLYIII genes across different developmental stages and in response to various abiotic stresses. Furthermore, we report that wild rice GLYIII proteins, specifically OpGLYIII-3, OmGLYIII-3, and OnGLYIII-5, exhibit high catalytic efficiency over a broad pH range and at higher temperatures under in vitro assay conditions. Overexpression of these proteins was found to impart substantial stress resilience to the transformed E. coli cells. These findings collectively suggest that GLYIII proteins constitute a key component of the abiotic stress response machinery in wild rice.

Oryza↗

PubMed2026

The function of Mgs1/WRNIP1 in genome maintenance.

Preservation of genomic integrity during replication is challenging, because replication forks are often stalled by several forms of DNA damage or stable secondary DNA structures. Prolonged stalling of the replication fork can lead to incomplete replication, which may induce double strand breaks, genome rearrangements and cell death. Therefore, several DNA repair mechanisms evolved to rescue stalled replication forks, which can elaborate in error-free or error-prone manners. The pathway selection and the fine tuning of the collaboration between different DNA repair proteins involved in the rescue of the stalled replication fork are very important. Based on our recent knowledge, yeast Mgs1 and its human homologue WRNIP1 proteins can be excellent candidates for this fine-tuning regulator function. In this review we summarize our current knowledge about them and try to point out the most important future steps to prove this hypothesis.

DNA repair↗

PubMed1975

Functional deacylases of pigeon liver fatty acid synthetase complex.

Fatty acid synthetase complex (Mr = 500,000) purified from pigeon liver homogenates is inactivated by phenylmethylsulfonyl fluoride. A well characterized inhibitor of serine esterases. Pseudounimolecular kinetics are followed at all inhibitor concentrations studied (0.05 to 1.0 mM). The second order rate constant obtained at pH 7.0, 30 degrees in 0.05 M potassium phosphate, 1 mM EDTA is 250 plus or minus 10 M-1 min-1 and appears to be independent of pH between 6 and 7.9. The inactivation of the enzyme complex appears to be selective since only one of the several component enzymes of fatty acid synthesis, palmityl-CoA deacylase, is inhibited. Acetyl- and malonyl-CoA-pantetheine transacylase activities as well as the kinetics of the reduction and dehydration steps are nearly identical for the native and the modified enzymes. The rate of approach of the condensation-CO2 exchange reaction (substrates: hexanoyl-CoA, malonyl-CoA, CoA, and H14CO3-) is slightly slower in the modified enzyme, though this change is not large enough to account for total loss of activity for fatty acid synthesis. The rate of loss of palmityl-CoA deacylase activity at a constant inhibitor concentration follows biphasic kinetics. Complete inactivation is achieved only after 2 mol of the inhibitor are bound per mol of the enzyme complex. Acetyl-, butyryl-, and hexanoyl-CoA thioesters (at 1.0 mM concentrations) protect the enzyme complex against inactivation by phenylmethylsulfonyl fluoride whereas CoA has no effect. Malonyl-CoA on the other hand, promotes inhibitor-mediated inactivation. Of the N-acetyl cysteamine derivatives tested, S-acetyl-N-acetyl cysteamine (at 10 mM) gives almost complete protection against inactivation whereas S-acetoacetyl-, S-beta-hydroxybutyryl-, and S-crotonyl-N-acetyl cysteamine thioesters exhibit either slight or no protection. These data demonstrate that phenylmethylsulfonyl fluoride is a selective reagent for the inactivation of functional fatty acyl deacylase component(s) of the pigeon liver fatty acid synthetase complex, and that it has no effect on malonyl or acetyl transacylases. The data are also in accord with the postulation that the inhibitor interacts at two catalytic centers of the enzyme complex. Furthermore, the patterns of protective effects shown by saturated acyl-CoA asters and malonyl-CoA point to different mechanisms of deacylation for these esters.

Acetyl Coenzyme A↗