bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-driven prediction of colonization outcomes for complex microbial communities
Authors: Wu Lu , Wang Xu-Wen , Tao Zining , Wang Tong , Zuo Wenlong , Zeng Yu , Liu Yang-Yu , Dai Lei 
Published: April 2023

AbstractComplex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. Here, we proposed a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validated this approach using synthetic data, finding that machine learning models (including Random Forest and neural ODE) can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conducted colonization experiments for two commensal gut bacteria speciesEnterococcus faeciumandAkkermansia muciniphilain hundreds of human stool-derivedin vitromicrobial communities, confirming that the data-driven approach can successfully predict the colonization outcomes. Furthermore, we found that while most resident species were predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., the presence ofEnterococcus faecalisinhibits the invasion ofE. faecium. The presented results suggest that the data-driven approach is a powerful tool to inform the ecology and management of complex microbial communities.
Previous breeding success and carrion substrate together influence subsequent carrion choice by adultNicrophorus vespilloides
Authors: Park Hyun Woo , Issar Swastika , Kilner Rebecca M. 
Published: April 2023

AbstractInsects can adjust their behaviour in relation to experience in a wide range of contexts including foraging, mate selection, and choice of oviposition site. Here we investigate whether burying beetles modulate their choice of carrion in relation to the outcome of their past breeding experience. Burying beetles require small vertebrate carrion to reproduce. Beetle parents convert carrion into an edible nursery for their larvae, whom they typically care for throughout larval development. We tested whether a beetle’s past breeding experience influenced its subsequent choice of carrion, when presented simultaneously with either a dead mouse or a dead chick. We found that both male and female beetles favoured the same carrion as used in their first breeding attempt – but only if they had produced many larvae and only if they had previously bred on a mouse. Beetles that had produced fewer larvae on a dead mouse switched to favouring dead chicks in their second breeding attempt. Those that had bred on a dead chick chose carrion at random subsequently, regardless of their previous breeding success. Our general conclusion is that burying beetles can integrate different sources of information about their past breeding experience with current cues when selecting carrion for reproduction.
Comparison of three quantitative approaches for estimating time-since-deposition from autofluorescence and morphological profiles of cell populations from forensic biological samples
Authors: Gentry Amanda Elswick , Ingram Sarah , Philpott M. Katherine , Archer Kellie J. , Ehrhardt Christopher J. 
Published: April 2023

AbstractDetermining when DNA recovered from a crime scene transferred from its biological source, i.e., a sample’s ‘time-since-deposition’ (TSD), can provide critical context for biological evidence. Yet, there remains no analytical techniques for TSD that are validated for forensic casework. In this study, we investigate whether morphological and autofluorescence measurements of forensically-relevant cell populations generated with Imaging Flow Cytometry (IFC) can be used to predict the TSD of ‘touch’ or trace biological samples. To this end, three different prediction frameworks for estimating the number of day(s) for TSD were evaluated: the elastic net, gradient boosting machines (GBM), and generalized linear mixed model (GLMM) LASSO. Additionally, we transformed these continuous predictions into a series of binary classifiers to evaluate the potential utility for forensic casework. Results showed that GBM and GLMM-LASSO showed the highest accuracy, with mean absolute error estimates in a hold-out test set of 29 and 21 days, respectively. Binary classifiers for these models correctly binned 94-96% and 98-99% of the age estimates as over/under 7 or 180 days, respectively. This suggests that predicted TSD using IFC measurements coupled to one or, possibly, a combination binary classification decision rules, may provide probative information for trace biological samples encountered during forensic casework.
GSR-DB: a manually curated and optimised taxonomical database for 16S rRNA amplicon analysis
Authors: Molano Leidy-Alejandra G. , Vega-Abellaneda Sara , Manichanh Chaysavanh 
Published: April 2023

ABSTRACTAmplicon-based 16S ribosomal RNA sequencing remains the most widely used method to profile microbial communities, as a low-cost and low-complexity approach. Reference databases are a mainstay for taxonomic assignments, which typically rely on popular databases such as SILVA, Greengenes, GTDB, or RDP. However, the inconsistency of the nomenclature across databases, and the presence of shortcomings in the annotation of these databases are limiting the resolution of the analysis. To overcome these limitations, we created the GSR database (Greengenes, SILVA, and RDP database), an integrated and manually curated database for bacterial and archaeal 16S amplicon taxonomy analysis. Unlike previous integration approaches, this database creation pipeline includes a taxonomy unification step to ensure consistency in taxonomical annotations. The database was validated with three mock communities and two real datasets and compared with existing 16S databases such as Greengenes, GTDB, ITGDB, SILVA, RDP, and MetaSquare. Results showed that the GSR database enhances taxonomical annotations of 16S sequences, outperforming current 16S databases at the species level. The GSR database is available for full-length 16S sequences and the most commonly used hypervariable regions: V4, V1-V3, V3-V4, and V3-V5.IMPORTANCETaxonomic assignments of microorganisms have long been hindered by inconsistent nomenclature and annotation issues in existing databases like SILVA, Greengenes, GTDB, or RDP. To overcome these issues, we created GSR-DB, accurate and comprehensive taxonomic annotations of 16S amplicon data. Unlike previous approaches, our innovative pipeline includes a unique taxonomy unification step, ensuring consistent and reliable annotations. Validated with mock communities and real datasets, GSR-DB outperforms existing databases in providing species-level resolution, making it a game-changer for microbiome studies. Moreover, GSR-DB is designed to be accessible to researchers with limited computational resources, making it a powerful tool for scientists across the board. Available for full-length 16S sequences and commonly used hypervariable regions, including V4, V1-V3, V3-V4, and V3-V5, GSR-DB is a go-to database for robust and accurate microbial taxonomy analysis.
Annotating Metagenomically Assembled Bacteriophage from a Unique Ecological System using Protein Structure Prediction and Structure Homology Search
Authors: Say Henry , Joris Ben , Giguere Daniel , Gloor Gregory B. 
Published: April 2023

ABSTRACTEmergent long read sequencing technologies such as Oxford’s Nanopore platform are invaluable in constructing high quality and complete genomes from a metagenome, and are needed investigate unique ecosystems on a genetic level. However, generating informative functional annotations from sequences which are highly divergent to existing nucleotide and protein sequence databases is a major challenge. In this study, we present wet and dry lab techniques which allowed us to generate 5432 high quality sub-genomic sized metagenomic circular contigs from 10 samples of microbial communities. This unique ecological system exists in an environment enriched with naphthenic acid (NA), which is a major toxic byproduct in crude oil refining and the major carbon source to this community. Annotation by sequence homology alone was insufficient to characterize the community, so as proof of principle we took a subset of 227 putative bacteriophage and greatly improved our existing annotations by predicting the structures of hypothetical proteins with ColabFold and using structural homology searching with Foldseek. The proportion of proteins for each bacteriophage that were highly similar to known proteins increased from approximately 10% to about 50%, while the number of annotations with KEGG or GO terms increased from essentially 0% to 15%. Therefore, protein structure prediction and homology searches can produce more informative annotations for microbes in unique ecological systems. The characterization of novel microbial ecosystems involved in the bioremediation of crude oil-process-affected wastewater can be greatly improved and this method opens the door to the discovery of novel NA degrading pathways.IMPORTANCEFunctional annotation of metagenomic assembled sequences from novel or unique microbial communities is challenging when the sequences are highly dissimilar to organisms or proteins in the known databases. This is a major obstacle for researchers attempting to characterize the functional capabilities of unique ecosystems. In this study, we demonstrate that including protein structure prediction and homology search based methods vastly improves the annotation of predicted genes identified in novel putative bacteriophage in a bacterial community that degrades naphthenic acids the major toxic component of oil refinery wastewater. This method can be extended to similar genomics studies of unique, uncharacterized ecosystems, to improve their annotations.Please read theInstructions to Authorscarefully, or browse theFAQsfor further details.
Heat stress impairs centromere structure and segregation of meiotic chromosomes in Arabidopsis
Authors: Khaitova Lucie Crhak , Mikulkova Pavlina , Pecinkova Jana , Kalidass Manikandan , Heckmann Stefan , Lermontova Inna , Riha Karel 
Published: April 2023

AbstractHeat stress is a major threat to global crop production, and understanding its impact on plant fertility is crucial for developing climate-resilient crops. Despite the known negative effects of heat stress on plant reproduction, the underlying molecular mechanisms remain poorly understood. Here, we investigated the impact of elevated temperature on centromere structure and chromosome segregation during meiosis inArabidopsis thaliana. Consistent with previous studies, heat stress leads to a decline in fertility and micronuclei formation in pollen mother cells. Our results reveal that elevated temperature causes a decrease in the amount of centromeric histone and the kinetochore protein BMF1 at meiotic centromeres with increasing temperature. Furthermore, we show that heat stress increases the duration of meiotic divisions and prolongs the activity of the spindle assembly checkpoint during meiosis I, indicating an impaired efficiency of the kinetochore attachments to spindle microtubules. Our analysis of mutants with reduced levels of centromeric histone suggests that weakened centromeres sensitize plants to elevated temperature, resulting in meiotic defects and reduced fertility even at moderate temperatures. These results indicate that the structure and functionality of meiotic centromeres inArabidopsisare highly sensitive to heat stress, and suggest that centromeres and kinetochores may represent a critical bottleneck in plant adaptation to increasing temperatures.
Transcription promotes the restoration of chromatin following DNA replication
Authors: Bandau Susanne , Alvarez Vanesa , Jiang Hao , Graff Sarah , Sundaramoorthy Ramasubramanian , Toman Matt , Owen-Hughes Tom , Sidoli Simone , Lamond Angus , Alabert Constance 
Published: April 2023

AbstractDNA replication results in the transient eviction of nucleosomes, RNAPII and transcription regulators. How chromatin organization is duplicated on the two daughter strands is a central question in epigenetics. In mammals, transcription restarts on newly replicated DNA within a couple of hours, promoting chromatin accessibility. However, the role of transcription in the restoration of other chromatin determinants following DNA replication remains unclear. Here we have monitored protein re-association to newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription restart. However, upon transcription inhibition, the re-association of many proteins was altered, including ATP-dependent remodellers, transcription regulators, the histone variant H2A.Z, histone modifiers as well as the restoration of H3.3K36me2. Finally, transcription also provoked the recruitment of several DNA repair proteins, revealing that transcription promotes chromatin reestablishment post-replication but is also a potential source of genotoxic stress.
A chromosome scale genome assembly and evaluation of mtDNA variation in the willow leaf beetleChrysomela aeneicollis
Authors: Bracewell Ryan R. , Stillman Jonathon H. , Dahlhoff Elizabeth P. , Smeds Elliott , Chatla Kamalakar , Bachtrog Doris , Williams Caroline , Rank Nathan E. 
Published: April 2023

ABSTRACTThe leaf beetleChrysomela aeneicollishas a broad geographic range across Western North America, but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2900-3450 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here we report a chromosome-scale genome assembly alongside a complete mitochondrial genome, and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology withTribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.
OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates
Authors: Liu Shuming , Wang Cong , Latham Andrew , Ding Xinqiang , Zhang Bin 
Published: April 2023

AbstractBiomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performances on a single GPU that rival the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that Open-ABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates. Open-ABC is available athttps://github.com/ZhangGroup-MITChemistry/OpenABC
Identifying antisense oligonucleotides to disrupt small RNA regulated antibiotic resistance via a cell-free transcription-translation platform
Authors: Tsai Min Jen , Zambrano Raphael Angelo I. , Susas Jeremiah Lyn , Silva Lizette , Takahashi Melissa K. 
Published: April 2023

ABSTRACTBacterial small RNAs (sRNAs) regulate many important physiological processes in cells including antibiotic resistance and virulence genes through base pairing interactions with mRNAs. Antisense oligonucleotides (ASOs) have great potential as therapeutics against bacterial pathogens by targeting sRNAs such as MicF, which regulates outer membrane protein OmpF expression and limits permeability of antibiotics. Here, we devise a cell-free transcription-translation (TX-TL) assay to identify ASO designs that sufficiently sequester MicF. ASOs were then ordered as peptide nucleic acids conjugated to cell-penetrating peptides (CPP-PNA) to allow for effective delivery into bacteria. Subsequent minimum inhibitory concentration (MIC) assays demonstrated that simultaneously targeting the regions of MicF responsible for sequestering the start codon and the Shine-Dalgarno sequence ofompFwith two different CPP-PNAs synergistically reduced the MIC for a set of antibiotics. This investigation offers a TX-TL based approach to identify novel therapeutic candidates to combat intrinsic sRNA-mediated antibiotic resistance mechanisms.
Genomic markers of drug resistance inMycobacterium tuberculosispopulations with minority variants
Authors: Zhang Xiaomei , Lam Connie , Martinez Elena , Sim Eby , Crighton Taryn , Marais Ben J , Sintchenko Vitali 
Published: April 2023

AbstractMinority variants ofMycobacterium tuberculosisharbouring mutations conferring resistance can become dominant populations during tuberculosis (TB) treatment, leading to treatment failure. Our understanding of drug resistant within-host sub-populations and the frequency of resistance conferring mutations in minority variants remains limited.M. tuberculosissequences recovered from liquid cultures of culture-confirmed TB cases notified between January 2017 and December 2021 in New South Wales, Australia were examined. Potential drug resistance conferring minority variants were identified using LoFreq, and mixed populations of differentM. tuberculosisstrains (≥100 SNPs apart) were examined using QuantTB.A total of 1831 routinely sequencedM. tuberculosisstrains were included in the analysis. Drug resistance conferring minority variants were detected in 3.5% (65/1831) of sequenced cultures; 84.6% (55/65) had majority strains that were drug susceptible and 15.4% (10/65) had majority strains that were drug resistant. Minority variants with high confidence drug resistance conferring mutations were 1.5 times more common when the majority strains were drug resistant. MixedM. tuberculosisstrain populations were documented in 10.0% (183/1831) of specimens. Minority variants with high confidence drug resistance conferring mutations were more frequently detected in mixedM. tuberculosisstrain populations (2.7%, 5/183) than in single strain populations (0.6%, 10/1648; p=0.01).Drug resistant minority variants require careful monitoring in settings that implement routineM. tuberculosissequencing. The frequency with which drug resistant minority variants are detected is influenced by selective culture methods and culture-independent sequencing should provide a more accurate picture.
Nuclear growth and import can be uncoupled
Authors: Chen Pan , Mishra Sampada , Levy Daniel L. 
Published: April 2023

ABSTRACTWhat drives nuclear growth? Studying nuclei assembled inXenopusegg extract and focusing on importin α/β–mediated nuclear import, we show that, while nuclear growth depends on nuclear import, nuclear growth and import can be uncoupled. Nuclei containing fragmented DNA grew slowly despite exhibiting normal import rates, suggesting nuclear import itself is insufficient to drive nuclear growth. Nuclei containing more DNA grew larger but imported more slowly. Altering chromatin modifications caused nuclei to grow less while still importing to the same extent or to grow larger without increasing nuclear import. Increasing heterochromatin in vivo in sea urchin embryos increased nuclear growth but not import. These data suggest that nuclear import is not the primary driving force for nuclear growth. Instead, live imaging showed that nuclear growth preferentially occurred at sites of high chromatin density and lamin addition, whereas small nuclei lacking DNA exhibited less lamin incorporation. Our hypothesized model is that lamin incorporation and nuclear growth are driven by chromatin mechanical properties, which depend on and can be tuned by nuclear import.
Contrasting walking styles map to discrete neural substrates in the mouse brainstem
Authors: Worley Audrey , Kirby Alana , Luks Sophie , Samardzic Tamara , Ellison Brian , Broom Lauren , Latremoliere Alban , VanderHorst Veronique G 
Published: April 2023

AbstractWalking is a slow gait which is particularly adaptable to meet internal or external needs and is prone to maladaptive alterations that lead to gait disorders. Alterations can affect speed, but also style (the way one walks). While slowed speed may signify the presence of a problem, style represents the hallmark essential for clinical classification of gait disorders. However, it has been challenging to objectively capture key stylistic features while uncovering neural substrates driving these features. Here we revealed brainstem hotspots that drive strikingly different walking styles by employing an unbiased mapping assay that combines quantitative walking signatures with focal, cell type specific activation. We found that activation of inhibitory neurons that mapped to the ventromedial caudal pons induced slow motion-like style. Activation of excitatory neurons that mapped to the ventromedial upper medulla induced shuffle-like style. Contrasting shifts in walking signatures distinguished these styles. Activation of inhibitory and excitatory neurons outside these territories or of serotonergic neurons modulated walking speed, but without walking signature shifts. Consistent with their contrasting modulatory actions, hotspots for slow-motion and shuffle-like gaits preferentially innervated different substrates. These findings lay the basis for new avenues to study mechanisms underlying (mal)adaptive walking styles and gait disorders.Graphical abstract