bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliable inference of phylogenomic relationship via assembly-based strategy accommodating raw reads and proteins
Authors: Li Yunlong , Liu Xu , Chen Chong , Qiu Jian-Wen , Kocot Kevin , Sun Jin 
Published: July 2024

AbstractPhylogenomics has emerged as a transformative approach in systematics, conservation biology, and biomedicine, enabling the inference of evolutionary relationships by leveraging hundreds to thousands of genes from genomic or transcriptomic data. However, acquiring high-quality genomes and transcriptomes necessitates samples with intact DNA and RNA, substantial sequencing investments, and extensive bioinformatic processing, such as genome/transcriptome assembly and annotation. This challenge is particularly pronounced for rare or difficult-to-collect species, such as those inhabiting the deep sea, where only fragmented DNA reads are often available due to environmental degradation or suboptimal preservation conditions. To address these limitations, we introduce VEHoP (Versatile, Easy-to-use Homology-based Phylogenomic pipeline), a tool designed to infer protein-coding regions from diverse inputs, including raw reads (short and long), draft genomes, transcriptomes, and annotated genomes. VEHoP automates the generation of orthologous sequence alignments, concatenated matrices, and phylogenetic trees, streamlining phylogenomic analyses for researchers across disciplines. The tool aims to (1) expand taxonomic sampling by accommodating a wide range of input data types and (2) simplify phylogenomic workflows, making them accessible to researchers with varying levels of bioinformatic expertise. We evaluated VEHoP’s performance using datasets from oysters, catfish, and insects, demonstrating its ability to produce robust phylogenetic trees with strong bootstrap support, outperforming assembly-free methods. Additionally, we applied VEHoP to reconstruct the phylogeny of the enigmatic deep-sea gastropod order Neomphalida, successfully resolving a well-supported phylogenetic backbone for this poorly understood group. VEHoP is freely available on GitHub (https://github.com/ylify/VEHoP), with dependencies easily installable via Bioconda.
Structural diversity and distribution of NMCP-class nuclear lamina proteins in streptophytic algae
Authors: Kosztyo Brendan S. , Richards Eric J. 
Published: July 2024

ABSTRACTNuclear Matrix Constituent Proteins (NMCPs) in plants function like animal lamins, providing the structural foundation of the nuclear lamina and regulating nuclear organization and morphology. Although they are well-characterized in angiosperms, the presence and structure of NMCPs in more distantly related species, such as streptophytic algae, are relatively unknown. The rapid evolution of NMCPs throughout the plant lineage has caused a divergence in protein sequence that makes similarity-based searches less effective. Structural features are more likely to be conserved compared to primary amino acid sequence; therefore, we developed a filtration protocol to search for diverged NMCPs based on four physical characteristics: intrinsically disordered content, isoelectric point, number of amino acids, and the presence of a central coiled-coil domain. By setting parameters to recognize the properties of bona fide NMCP proteins in angiosperms, we filtered eight complete proteomes from streptophytic algae species and identified strong NMCP candidates in six taxa in the Classes Zygnematophyceae, Charophyceae, and Klebsormidophyceae. Through analysis of these proteins, we observed structural variance in domain size between NMCPs in algae and land plants, as well as a single block of amino acid conservation. Our analysis indicates that NMCPs are absent in the Mesostigmatophyceae. The presence versus absence of NMCP proteins does not correlate with the distribution of different forms of mitosis (e.g., closed/semi-closed/open) but does correspond to the transition from unicellularity to multicellularity in the streptophytic algae, suggesting that an NMCP-based nucleoskeleton plays important roles in supporting cell-to-cell interactions.SIGNIFICANCE STATEMENTAll eukaryotic organisms contain a membrane-bound nucleus, which holds a cell’s DNA, but plants and animals have distinct sets of proteins that make up the mesh-like scaffold inside the nucleus (i.e., nuclear lamina) that is essential for structural integrity and organization. Nonetheless, the major nuclear lamina proteins in plants and animals share structural features, and we exploited these characteristics to identify a key class of nuclear lamina proteins in streptophytic algae, allowing us to chart the distribution of these proteins across photosynthetic organisms and to gain insight into the evolution of nuclear organization. Our results indicate that the major class of nuclear lamina protein in plants evolved independently from structurally similar nuclear lamina proteins in animals.
Flooding patterns shape microbial community in mangrove sediments
Authors: Vázquez-Rosas-Landa Mirna , Pérez-Ceballos Rosela , Zaldívar-Jiménez Arturo , Hereira-Pacheco Stephanie E , Pérez-González Leonardo D. , Prieto‑Davó Alejandra , Celis-Hernández Omar , Canales-Delgadillo Julio C. 
Published: July 2024

AbstractBackgroundMangrove ecosystems located in the tropics and subtropics, are crucial for regulating global weather patterns and sequestering carbon. However, they face threats from human activities like altered water flow and deforestation. While the symbiotic relationship between mangrove trees and surrounding microbes are essential for their survival, the impact of human activity on these microbial communities remains incompletely understood. We investigated how microbial communities change in degraded mangrove ecosystems due to loss of hydrologic connectivity, aiming to elucidate consequences and inform restoration strategies.MethodsEmploying 16S rRNA sequencing, we analyzed samples of sediment cores from conserved, moderately degraded, and degraded mangrove sites across dry and flood seasons at three sediment depths.ResultsOur analysis identified 11,469 Amplicon Single Variant (ASVs), revealing diversity loss correlated with degradation levels. Notably, we observed shifts in microbial diversity within sediment layers, with conserved sites dominated by Vibrionaceae in upper layers, potentially indicating urban contamination. In moderate-degradation sites, seasonal patterns emerged, with Halomonas and Marinomonas dominating the dry season and Exiguobacterium thriving during flooding. Interestingly, a community mainly composed of Firmicutes persisted across all degradation scenarios in deeper sediment layers, suggesting potential for ecosystem restoration. Our findings provide insights into microbial responses to human-induced stressors and highlight the role of core microbial communities in guiding restoration efforts for degraded mangrove ecosystems.
Illuminating microbial mat assembly: Cyanobacteria and Chloroflexota cooperate to structure light-responsive biofilms
Authors: Bunbury Freddy , Rivas Carlos , Calatrava Victoria , Malkovskiy Andrey , Joubert Lydia-Marie , Parvate Amar D. , Evans James E. , Grossman Arthur , Bhaya Devaki 
Published: July 2024

AbstractMicrobial mats are stratified communities often dominated by unicellular and filamentous phototrophs within an exopolymer matrix. It is challenging to quantify the dynamic responses of community membersin situas they experience steep gradients and rapid fluctuations of light. To address this, we developed a binary consortium using two representative isolates from hot spring mats: the unicellular oxygenic phototrophic cyanobacteriumSynechococcusOS-B’ (Syn OS-B’) and the filamentous anoxygenic phototrophChloroflexusMS-CIW-1 (Chfl MS-1). We quantified the motility of individual cells and entire colonies and demonstrated that Chfl MS-1 formed bundles of filaments that moved in all directions with no directional bias to light. Syn OS- B’ was slightly less motile but exhibited positive phototaxis. This binary consortium displayed cooperative behavior by moving further than either species alone and formed ordered arrays where both species aligned with the light source. No cooperative motility was observed when a non-motilepilBmutant of Syn OS-B’ was used instead of Syn OS-B’. The binary consortium also produced more adherent biofilm than individual species, consistent with the close interspecies association revealed by electron microscopy. We propose that cyanobacteria and Chloroflexota cooperate in forming natural microbial mats, by colonizing new niches and building robust biofilms.SignificanceMicrobial mats are dense, layered communities with ancient origins and widespread occurrence, but how they assemble is not well understood. To investigate how microbial motility, physical interactions, and responses to light affect mat assembly, we developed a binary consortium from representative hot spring mat isolates. Individually, the Cyanobacteria and Chloroflexota isolates displayed significant differences in motility and biofilm formation. When combined, the consortium exhibited enhanced motility towards light and formed more robust biofilms. This model consortium approach complementsin situstudies by directly testing the role of motility and physical cooperation in shaping microbial mats, and could inform biofilm applications in industrial settings.
Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae
Authors: Duenas Marco A. , Craig Rory J. , Gallaher Sean D. , Moseley Jeffrey L. , Merchant Sabeeha S. 
Published: July 2024

AbstractAdvances in sequencing technology have unveiled examples of nucleus-encoded polycistronic genes, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for polycistronic expression in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae,Chlamydomonas reinhardtiiandAuxenochlorella protothecoides, revealed 1) a preference for weak Kozak-like sequences for ORF 1 and 2) an underrepresentation of potential initiation codons before ORF 2, which are suitable conditions for leaky scanning to allow ORF 2 translation. We used mutational analysis inAuxenochlorella protothecoidesto test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky ribosome scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames found across eukaryotic genomes and for transgene expression in synthetic biology applications.Significance StatementTextbook dogma states that nucleus-encoded genes are monocistronic, producing transcripts with a single translated open reading frame. However, highly conserved bicistronic loci are pervasive in green algae that are separated by several hundred million years of evolution, speaking to their ancestral origins and functions within the Chlorophyte lineage. A combination of bioinformatic analysis and in vivo gene manipulation supports leaky ribosomal scanning as the primary mechanism for translation of multiple ORFs from bicistronic transcripts. We have successfully tuned synthesis levels of two proteins encoded on one mRNA by modifying the ORF 1 Kozak-like sequence. These findings may have broad applications in synthetic biology.
Does early-life food shortage alter the effect of elevated temperature on female life history?
Authors: Chung Meng-Han Joseph , Zang Chenke , Moura-Campos Diego , Jennions Michael D. , Head Megan L. 
Published: July 2024

AbstractGlobal warming is reducing prey availability in many aquatic systems, raising questions about the combined effects of higher temperatures and lower food availability on fish life histories and reproductive output.In ectotherms, higher temperatures accelerate growth and promote an earlier onset of reproduction. However, when fish have less food during development, resource depletion might constrain these temperature-driven processes.We manipulated water temperature (24 or 28°C) and early-life food availability (control or restricted) for female guppies (Poecilia reticulata). We measured how both factors affected key life history traits (growth, reproduction, survival, self-maintenance).Higher temperature significantly affected female life histories. Females at 28°C matured at a larger size, but then grew more slowly and produced fewer, smaller offspring than females at 24°C. The effect of temperature on reproduction persisted even after controlling for body size, suggesting there was a shift in the fecundity-size relationship.Adult mortality was greater at 28°C. Higher temperature also resulted in a longer gut, potentially enhancing resource acquisition, but a higher temperature did not affect immunity or telomere length of the surviving females.Early-life food shortage affected very few traits, except for a weak interaction with temperature that affected total fecundity. At 28°C, females that experienced early-life food restriction produced fewer offspring than females with continual food supply. No such diet effect occurred at 24°C.Our results suggest that tropical fish may be severely impacted by increased temperatures (i.e., decreased reproduction with increased morality), but are likely to be resilient to brief periods of food limitations during early development.Interestingly, early-life food shortage caused a reduction in total offspring number but only at 28°C, suggesting that global prey decline might exacerbate the negative effects of a warming climate on stock recruitment of tropical fish.
Self-Assembled Chambered Cardiac Organoids for Modeling Cardiac Chamber Formation and Cardiotoxicity Assessment
Authors: Zou Xinle , Wang Fanwen , Zheng Huilin , Kong Tianci , Pei Duanqing 
Published: July 2024

AbstractThe human heart, crucial for health and longevity, is a primary focus of medical research. Despite advancements in cardiac organoid technology, replicating early cardiac chamber formation stages remains challenging. Here, we develop chambered cardiac organoids (CCOs) by orchestrating cardiac signaling pathways, including the synergistic modulation of FGF and Wnt signaling via the HAND1 transcription factor. These CCOs exhibit stable chambers with self-organized outer myocardial and inner endocardial layers, and express developmental markers such as NKX2.5, TNNT2, and NAPPA, demonstrating physiological functionality including spontaneous contractions and calcium transients. Immunofluorescence and single-cell RNA sequencing confirmed the presence and stability of cardiomyocytes within CCOs. Further validation showed CCOs’ involvement in critical processes like endothelial-mesenchymal transition (EndoMT) and valvulogenesis. Ultrastructural and electrophysiological analysis revealed organized myofibrils and atrial-like action potentials. Importantly, CCOs proved effective in assessing cardiotoxicity through observable morphological changes, demonstrating specific cellular responses to established cardiotoxic compounds, thereby highlighting their potential for drug testing and safety evaluations. Our findings offer insights into cardiac chamber formation mechanisms and establish a robust platform for drug testing, disease modeling, and personalized medicine, representing a significant advancement in functional cardiac organoid development for both basic research and translational applications.
How to reward animals based on their subjective percepts: A Bayesian approach to online estimation of perceptual biases
Authors: Dong Yelin , Lengyel Gabor , Shivkumar Sabyasachi , Anzai Akiyuki , DiRisio Grace F. , Haefner Ralf M. , DeAngelis Gregory C. 
Published: July 2024

1AbstractElucidating the neural basis of perceptual biases, such as those produced by visual illusions, can provide powerful insights into the neural mechanisms of perceptual inference. However, studying the subjective percepts of animals poses a fundamental challenge: unlike human participants, animals cannot be verbally instructed to report what they see, hear, or feel. Instead, they must be trained to perform a task for reward, and researchers must infer from their responses what the animal perceived. However, animals’ responses are shaped by reward feedback, thus raising the major concern that the reward regimen may alter the animal’s decision strategy or even intrinsic perceptual biases. We developed a method that estimates perceptual bias during task performance and then computes the reward for each trial based on the evolving estimate of the animal’s perceptual bias. Our approach makes use of multiple stimulus contexts to dissociate perceptual biases from decision-related biases. Starting with an informative prior, our Bayesian method updates a posterior over the perceptual bias after each trial. The prior can be specified based on data from past sessions, thus reducing the variability of the online estimates and allowing it to converge to a stable estimate over a small number of trials. After validating our method on synthetic data, we apply it to estimate perceptual biases of monkeys in a motion direction discrimination task in which varying background optic flow induces robust perceptual biases. This method overcomes an important challenge to understanding the neural basis of subjective percepts.
Co-recognition of histone acetylation and H3K4 trimethylation by GTE4-EML complex in Arabidopsis
Authors: Qian Feng , Zhao Qiang-Qiang , Zhou Jin-Xing , Yuan Dan-Yang , Su Yin-Na , Li Lin , Chen She , He Xin-Jian 
Published: July 2024

AbstractAlthough histone acetylation and H3K4 trimethylation (H3K4me3) are well-known histone marks associated with active transcription, how they cooperate to regulate transcription remains largely unclear in plants. Our study revealed that the Bromodomain and Extra-terminal (BET) protein GTE4 binds to acetylated histone and forms a complex with the redundant H3K4me3-binding EMSY-Likeproteins EML1 or EML2 (EML1/2) inArabidopsis thaliana. Theeml1 eml2(eml1/2) double mutant exhibited a morphological phenotype similar to thegte4mutant, and most of thegte4-mediated differentially expressed genes were co-regulated in theeml1/2mutant. Through chromatin immunoprecipitation followed by deep sequencing (ChIP-seq), we found that GTE4 and EML2 co-occupy protein-coding genes enriched with both histone acetylation and H3K4me3, exhibiting a synergistic effect on the association of the GTE4-EML complex with chromatin. The association of GTE4 with chromatin requires both the Bromodomain and the EML-interacting domain. This study identified a previously uncharacterized complex and uncovered how it cooperatively recognizes histone acetylation and H3K4me3 to facilitate gene transcription at the whole-genome level in Arabidopsis.
Characterization of radiations-induced genomic structural variations inArabidopsis thaliana
Authors: Sall Salimata Ousmane , Alioua Abdelmalek , Staerck Sébastien , Graindorge Stéfanie , Pellicioli Michel , Schuler Jacky , Raffy Quentin , Rousseau Marc , Molinier Jean 
Published: July 2024

ABSTRACTDNA, is assaulted by endogenous and exogenous agents that lead to the formation of damage. In order to maintain genome integrity DNA repair pathways must be efficiently activated to prevent mutations and deleterious chromosomal rearrangements. Conversely, genome flexibility is also necessary to allow genetic diversity and evolution. The antagonist interaction between maintenance of genome integrity and flexibility determines genome shape and organization. Therefore, it is of great interest to understand how the whole linear genome structure behaves upon formation and repair of DNA damage. For this, we used long reads sequencing technology to identify and to characterize genomic structural variations (SV) of wild-typeArabidopsis thalianasomatic cells exposed either to UV-B, to UV-C or to protons irradiations. We found that genomic regions located in heterochromatin a more prone to form SVs than those located in euchromatin, highlighting that genome stability and flexibility differs along the chromosome. This holds true in Arabidopsis plants deficient for the expression of master regulators of the DNA Damage Response (DDR), ATM and ATR, suggesting that independent and alternative surveillance processes exist to maintain integrity in genic regions. Finally, the analysis of the radiations-induced deleted regions allowed determining that exposure UV-B, UV-C and protons induced the Microhomology-mediated end joining mechanism (MMEJ) and that both ATM and ATR repress this repair pathway.
The deubiquitinating enzyme CYLD impairs NF-κB- and STAT1-dependent macrophage intrinsic immunity toStaphylococcus aureus
Authors: Schmidt Christina , Harit Kunjan , Traidl Stephan , Werfel Thomas , Rösner Lennart , Nishanth Gopala , Schlüter Dirk 
Published: July 2024

AbstractIn atopic dermatitis (AD), lesional skin is frequently colonized byStaphylococcus(S.)aureus, contributing to the severity and clinical symptoms of the disease. The inflammatory milieu in the skin is characterized by a type 2 inflammatory signature, including M2 macrophages, which cannot eradicate S. aureus. Since S. aureus is effectively controlled in macrophages activated by pattern recognition receptor (PRR)-induced NF-κB and interferon (IFN)-γ-induced STAT1 stimulation, we hypothesized that pre-treatment with LPS as a PRR/TLR4-activating agent and IFN-γ would induce effective control of S. aureus in monocyte-derived macrophages (MDMs) of AD patients. Our data show that the deubiquitinating enzyme CYLD is strongly expressed in skin macrophages and MDMs from AD patients compared to healthy controls and impairs the anti-staphylococcal activity of PRR-activated and IFN-treated MDMs. Functionally, CYLD impaired M1 macrophage polarization, as evidenced by reduced expression of CD80, TNF, and IL-6 upon LPS- and IFN-γ treatment in CYLD-deficient as compared to wild-type (WT) MDM/THP1 macrophages. Mechanistically, CYLD inhibited IFN-γ-induced STAT1 phosphorylation and activation by binding to STAT1 and inducing its K63 deubiquitination. CYLD also interacted with TRAF6 and NEMO/IKKγ in the MYD88 signaling pathway and with RIPK2 in the NOD2 pathway, leading to impaired activation of NF-κB. Inhibition of both STAT1 by siRNA and NF-κB by IKK inhibitor treatment, respectively, independently abolished the control ofS. aureusin both CYLD-deficient and WT THP1 macrophages, which harbored identical high numbers of the pathogen. The in vivo inhibitory function of CYLD on the control ofS. aureuswas also observed upon infection ofCyld-deficient and WT mice. Collectively, these data illustrate that the increased expression of CYLD in macrophages of AD patients is a factor contributing to the ineffective control ofS. aureus, diminishes M1 macrophage polarization, and that CYLD deletion unleashes the break on effective STAT1 and NF-κB-dependent control ofS. aureus.