bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian estimation of gene constraint from an evolutionary model with gene features
Authors: Zeng Tony , Spence Jeffrey P. , Mostafavi Hakhamanesh , Pritchard Jonathan K.
Published: May 2023

Measures of selective constraint on genes have been used for many applications including clinical interpretation of rare coding variants, disease gene discovery, and studies of genome evolution. However, widely-used metrics are severely underpowered at detecting constraint for the shortest ~25% of genes, potentially causing important pathogenic mutations to be over-looked. We developed a framework combining a population genetics model with machine learning on gene features to enable accurate inference of an interpretable constraint metric,shet. Our estimates outperform existing metrics for prioritizing genes important for cell essentiality, human disease, and other phenotypes, especially for short genes. Our new estimates of selective constraint should have wide utility for characterizing genes relevant to human disease. Finally, our inference framework, GeneBayes, provides a flexible platform that can improve estimation of many gene-level properties, such as rare variant burden or gene expression differences.
Iron Memory inE. coli
Authors: Bhattacharyya Souvik , Bhattarai Nabin , Pfannenstiel Dylan M. , Wilkins Brady , Singh Abhyudai , Harshey Rasika M.
Published: May 2023

The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered whenE. coliencounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This memory pre-exists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, whether low or high, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We also demonstrate that iron memory can integrate multiple stimuli, impacting other bacterial behaviors such as biofilm formation and antibiotic tolerance.
Origin of biogeographically distinct ecotypes during laboratory evolution
Authors: Valenzuela Jacob J. , Christinal Immanuel Selva Rupa , Wilson James , Turkarslan Serdar , Ruiz Maryann , Gibbons Sean M. , Hunt Kristopher A. , Auer Manfred , Zemla Marcin , Stahl David A. , Baliga Nitin S.
Published: May 2023

Resource partitioning within microbial communities is central to their incredible productivity, including over 1 gigaton of annual methane emissions through syntrophic interactions1. Here, we show how isogenic strains of a sulfate reducing bacterium (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification over 300-1,000 generations in a purely planktonic environmental2–4context giving rise to coexisting ecotypes that could partition resources and improve overall stability, cooperativity, and productivity in a simulated subsurface environment. We discovered that mutations in just 15 Dv and 7 Mm genes gave rise to ecotypes within each species that were spatially enriched between sediment and planktonic phases over the course of only a few generations after transferring the evolved populations to a fluidized bed reactor (FBR). While lactate utilization by Dv in the attached community was significantly greater, the resulting H2was partially consumed by low affinity hydrogenases in Mm within the same attached phase. The unutilized H2was scavenged by high affinity hydrogenases in the planktonic phase Mm, generating copious amounts of methane and higher ratio of Mm to Dv. Our findings show how a handful of mutations that arise in one environmental context can drive resource partitioning by ecologically differentiated variants in another environmental context, whose interplay synergistically improves productivity of the entire mutualistic community.
Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs
Authors: Zhao Lan , Cunningham Christine M. , Andruska Adam M. , Schimmel Katharina , Ali Md Khadem , Kim Dongeon , Gu Shenbiao , Chang Jason L. , Spiekerkoetter Edda , Nicolls Mark R.
Published: May 2023

The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined a multi-tissue full lifespan microbial biogeography for healthy Fischer 344 rats. Microbial community profiling data was extracted and integrated with host transcriptomic data from the Sequencing Quality Control (SEQC) consortium. Unsupervised machine learning, Spearman’s correlation, taxonomic diversity, and abundance analyses were performed to determine and characterize the rat microbial biogeography and the identification of four inter-tissue microbial heterogeneity patterns (P1-P4). The 11 body habitats harbor a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundances progressively declined in lungs from breastfeed newborn to adolescence/adult and was below detectable levels in elderly rats. LAB’s presence and levels in lungs were further evaluated by PCR in the two validation datasets. The lung, testes, thymus, kidney, adrenal, and muscle niches were found to have age-dependent alterations in microbial abundance. P1 is dominated by lung samples. P2 contains the largest sample size and is enriched for environmental species. Liver and muscle samples were mostly classified into P3. Archaea species were exclusively enriched in P4. The 357 pattern-specific microbial signatures were positively correlated with host genes in cell migration and proliferation (P1), DNA damage repair and synaptic transmissions (P2), as well as DNA transcription and cell cycle in P3. Our study established a link between metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures would be useful for microbiome therapeutic approaches to human health and good quality of life.

Graphical Abstract
Myxococcus xanthus fruiting body morphology is important for spore recovery after exposure to environmental stress
Authors: Lall Dave , Glaser Maike M. , Higgs Penelope I.
Published: May 2023

Environmental microorganisms have evolved a variety of strategies to survive fluctuations in environmental conditions, including production of biofilms and differentiation into spores.Myxococcus xanthusare ubiquitous soil bacteria that produce starvation-induced multicellular fruiting bodies filled with environmentally resistant spores (a specialized biofilm). Fruiting bodies are thought to facilitate theM. xanthussocial life cycle by ensuring spores can germinateen masseinto a productive feeding community. Isolated spores have been shown to be more resistant than vegetative cells to heat, ultraviolet radiation, and desiccation, but it is unknown whether assembly of spores into a fruiting body provides additional protection from environmental insults. We developed a high-throughput method to compare the recovery (outgrowth) of distinct cell types (vegetative cells, free spores, and intact fruiting bodies) after exposure to ultraviolet radiation or desiccation. Our data indicate haystack-shaped fruiting bodies protect spores from extended UV radiation but do not provide additional protection from desiccation. Perturbation of fruiting body morphology strongly impedes recovery from both UV exposure and desiccation. These results hint that the distinctive fruiting bodies produced by different myxobacterial species may have evolved to optimize their persistence in distinct ecological niches.

IMPORTANCE

The myxobacteria are environmentally ubiquitous social bacteria that influence the local microbial community composition. Understanding how these bacteria are affected by environmental insults is important in predicting how microbial biogeochemical cycling is affected by climate change. When starved, myxobacteria produce multicellular fruiting bodies filled with spores. As spores are resistant to a variety of environmental insults, it has long been held that the fruiting body evolved to ensure group germination into a productive feeding community. Using the model myxobacterium,Myxococcus xanthus, we demonstrate that the haystack-shaped fruiting body morphology enables significantly more resistance to UV exposure than the free spores. In contrast, fruiting bodies are slightly detrimental to recovery from extended desiccation, an effect that is strongly exaggerated if fruiting body morphology is perturbed. These results suggest the variety of fruiting body morphologies observed in the myxobacteria may dictate their relative resistance to changing climate conditions.
Flagellin is essential for initial attachment to mucosal surfacesby Clostridioides difficile
Authors: Sidner Ben , Lerma Armando , Biswas Baishakhi , Ronish Leslie A. , McCullough Hugh , Auchtung Jennifer M. , Piepenbrink Kurt H.
Published: May 2023

Mucins are glycoproteins which can be found in host cell membranes and as a gelatinous surface formed from secreted mucins. Mucosal surfaces in mammals form a barrier to invasive microbes, particularly bacteria, but are a point of attachment for others.Clostridioides difficileis anaerobic bacterium which colonizes the mammalian GI tract and is a common cause of acute GI inflammation leading to a variety of negative outcomes. AlthoughC. difficiletoxicity stems from secreted toxins, colonization is a prerequisite forC. difficiledisease. WhileC. difficileis known to associate with the mucus layer and underlying epithelium, the mechanisms underlying these interactions that facilitate colonization are less well-understood. To understand the molecular mechanisms by whichC. difficileinteracts with mucins, we usedex vivomucosal surfaces to test the ability ofC. difficileto bind to mucins from different mammalian tissues. We found significant differences inC. difficileadhesion based upon the source of mucins, with highest levels of binding observed to mucins purified from the human colonic adenocarcinoma line LS174T and lowest levels of binding to porcine gastric mucin. We also observed that defects in adhesion by mutants deficient in flagella, but not type IV pili. These results imply that interactions between host mucins andC. difficileflagella facilitate the initial host attachment ofC. difficileto host cells and secreted mucus.
The regulation of Insulin/IGF-1 signaling by miR-142-3p associated with human longevity
Authors: Wang Xifan , Jung Hwa Jin , Milholland Brandon , Cui Jinhua , Tazearslan Cagdas , Atzmon Gil , Wang Xizhe , Yang Jiping , Guo Qinghua , Barzilai Nir , Robbins Paul D. , Suh Yousin
Published: May 2023

MicroRNAs (miRNAs) have been demonstrated to modulate life span in the invertebratesC. elegansandDrosophilaby targeting conserved pathways of aging, such as insulin/IGF-1 signaling (IIS). However, a role for miRNAs in modulating human longevity has not been fully explored. Here we investigated novel roles of miRNAs as a major epigenetic component of exceptional longevity in humans. By profiling the miRNAs in B-cells from Ashkenazi Jewish centenarians and 70-year-old controls without a longevity history, we found that the majority of differentially expressed miRNAs were upregulated in centenarians and predicted to modulate the IIS pathway. Notably, decreased IIS activity was found in B cells from centenarians who harbored these upregulated miRNAs. miR-142-3p, the top upregulated miRNA, was verified to dampen the IIS pathway by targeting multiple genes includingGNB2, AKT1S1, RHEBandFURIN. Overexpression of miR-142-3p improved the stress resistance under genotoxicity and induced the impairment of cell cycle progression in IMR90 cells. Furthermore, mice injected with a miR-142-3p mimic showed reduced IIS signaling and improved longevity-associated phenotypes including enhanced stress resistance, improved diet/aging-induced glucose intolerance, and longevity-associated change of metabolic profile. These data suggest that miR-142-3p is involved in human longevity through regulating IIS-mediated pro-longevity effects. This study provides strong support for the use of miR-142-3p as a novel therapeutic to promote longevity or prevent aging/aging-related diseases in human.
Allele-specific epigenetic regulation ofFURINexpression at a coronary artery disease susceptibility locus
Authors: Yang Wei , Cao Junjun , McVey David G. , Ye Shu
Published: May 2023

Background

Genome-wide association studies have revealed an association between the genetic variant rs17514846 on chromosome 15q26.1 and coronary artery disease susceptibility. Studies have shown that rs17514846 influences the expression of the FES Upstream Region (FURIN) gene located at this locus in monocytes. We investigated the mechanism through which rs17514846 modulatesFURINexpression.

Methods and Results

An analysis of isogenic monocytic cell lines with either the rs17514846 C/C or A/A genotype showed that the cells of the A/A genotype expressed higher levels ofFURINthan cells of the C/C genotype. A pyrosequencing methylation analysis showed that the cytosine (in a CpG motif) at the rs17514846 position on the C allele was methylated. Treatment with the DNA methylation inhibitor 5-aza-2’-deoxycytidine increasedFURINexpression. A bioinformatic analysis indicated that the rs17514846 site might interact with the transcription factor MeCP2 that often functions as a gene repressor by binding to methylated CpG sites. An electrophoretic mobility super-shift assay with a probe corresponding to the DNA sequence at and around the rs17514846 position of the C allele detected two DNA-protein complex bands, which were altered by the addition of an anti-MeCP2 antibody in the assay, whilst these DNA-protein complexes were barely detectable with a probe for the A allele. A chromatin immunoprecipitation assay showed an enrichment of the DNA sequence containing the rs17514846 site in chromatin precipitates pulled down by an anti-MeCP2 antibody. siRNA-mediated knockdown of MeCP2 caused an increase inFURINexpression. Furthermore, MeCP2 knockdown increased monocyte migration and proliferation, and this effect was diminished by a FURIN inhibitor.

Conclusions

The results of our study suggest that DNA methylation inhibitsFURINexpression and that the coronary artery disease predisposing variant rs17514846 modulatesFURINexpression and monocyte migration via an allele-specific effect on DNA methylation.
Species composition of Culicidae (Diptera) in Bromeliads in rural and urban areas of Londrina, Brazil
Authors: Silva Bianca Piraccini , Arcos Adriano Nobre , Ferreira Francisco Augusto da Silva , Medri Cristiano , Zequi João Antonio Cyrino
Published: May 2023

Bromeliaceae, has 82 genera and 3,719 species found throughout the Neotropical region, from the southern United States to central Argentina and Chile. These plants are present in environments with different characteristics and have high endemism in the Atlantic Forest in Brazil. Tank bromeliads stand out for their morphology, which forms permanent water-accumulating compartments called phytotelmata, rich in organic detritus and living organisms. Culicidae use phytotelma as a breeding ground, and some species of Wyeomyia are highly dependent on these tanks. Research on the importance of bromeliads as water reservoirs that may favor the reproduction of mosquitoes that carry pathogens are controversial. Some studies indicate that these plants are potential breeding grounds forAedes, while others suggest that they are not preferential foci for synanthropic mosquitoes, as is the case forA. aegypti. This work aimed at verifying the presence ofAedesand other Culicidae in native bromeliads in natural habitat and under ornamental cultivation in an urban environment, comparing the incidence of larvae in these possible breeding sites and contrasting with the luminosity and accumulated water volumes. Differences in species composition were observed between rural and urban environments. In the rural environment, four species of Culicidae were collected, the most abundant beingWyeomyia galvaoi-19 specimens, followed byCulex(Microculex)imitator- five specimens, whileAedes aegyptiandToxorhynchitessp 1, were the least abundant, with two individuals each. In the urban environment, five species were found, with greater abundance ofAedes aegypti(461 individuals), followed byAedes albopictus(45),Toxorhynchitessp. 01 (3),Wyeomyiasp1 (02), andWyeomyia galvaoi(01) In addition, these phytotelma showed great diversity of other organisms, such as: mites, nematodes, protists, rotifers, ostracods, and insect larvae of the Chironomidae, Syrphidae and Tachinidae families. The study concluded that the incidence of mosquito larvae in native bromeliads is low, and that luminosity and accumulated water volumes can influence the presence of larvae. The authors emphasize that the importance of bromeliads in mosquito reproduction may vary according to several factors.
Multiplexed volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex
Authors: Han Xiaomeng , Lu Xiaotang , Li Peter H. , Wang Shuohong , Schalek Richard , Meirovitch Yaron , Lin Zudi , Adhinarta Jason , Berger Daniel , Wu Yuelong , Fang Tao , Meral Elif Sevde , Asraf Shadnan , Ploegh Hidde , Pfister Hanspeter , Wei Donglai , Jain Viren , Trimmer James S. , Lichtman Jeff W.
Published: May 2023

Mapping neuronal networks that underlie behavior has become a central focus in neuroscience. While serial section electron microscopy (ssEM) can reveal the fine structure of neuronal networks (connectomics), it does not provide the molecular information that helps identify cell types or their functional properties. Volumetric correlated light and electron microscopy (vCLEM) combines ssEM and volumetric fluorescence microscopy to incorporate molecular labeling into ssEM datasets. We developed an approach that uses small fluorescent single-chain variable fragment (scFv) immuno-probes to perform multiplexed detergent-free immuno-labeling and ssEM on the same samples. We generated eight such fluorescent scFvs that targeted useful markers for brain studies (green fluorescent protein, glial fibrillary acidic protein, calbindin, parvalbumin, voltage-gated potassium channel subfamily A member 2, vesicular glutamate transporter 1, postsynaptic density protein 95, and neuropeptide Y). To test the vCLEM approach, six different fluorescent probes were imaged in a sample of the cortex of a cerebellar lobule (Crus 1), using confocal microscopy with spectral unmixing, followed by ssEM imaging of the same sample. The results show excellent ultrastructure with superimposition of the multiple fluorescence channels. Using this approach we could document a poorly described cell type in the cerebellum, two types of mossy fiber terminals, and the subcellular localization of one type of ion channel. Because scFvs can be derived from existing monoclonal antibodies, hundreds of such probes can be generated to enable molecular overlays for connectomic studies.
Enhancer status in the primitive endoderm supports unrestricted lineage plasticity in regulative development
Authors: Linneberg-Agerholm Madeleine , Sell Annika Charlotte , Redo-Riveiro Alba , Proks Martin , Knudsen Teresa E. , Perera Marta , Brickman Joshua M.
Published: May 2023

Mammalian blastocyst formation involves the specification of trophectoderm followed by the differentiation of the inner cell mass into either epiblast or primitive endoderm. During this time, the embryo maintains a window of plasticity and can redirect its cellular fate when challenged experimentally. In this context, we found that the primitive endoderm alone was sufficient to regenerate a complete blastocyst and continue normal postimplantation development to term. We identify anin vitropopulation similar to the early primitive endodermin vivo, that exhibits the same embryonic and extra-embryonic potency, forming three dimensional embryoid structures. Commitment in early primitive endoderm is suppressed by JAK/STAT signalling, collaborating with OCT4 to safeguard enhancer status enabling multi-lineage differentiation. Our observations support the notion that transcription factor persistence underlies plasticity in regulative development and highlights the importance of primitive endoderm in perturbed development.
SRC-1 controls growth cone polarity and protrusion with the UNC-6/Netrin receptor UNC-5 inCaenorhabditis elegans
Authors: Mahadik Snehal S. , Burt Emily K. , Lundquist Erik A.
Published: May 2023

In the Polarity/Protusion model of growth cone migration away from the guidance cue UNC-6/Netrin, the UNC-5 receptor polarizes the VD growth cone such that filopodial protrusions are biased to the dorsal leading edge of the growth cone. UNC-5 also inhibits growth cone protrusion ventrally based upon this polarity. The SRC-1 tyrosine kinase has been previously shown to physically interact with and phosphorylate UNC-5, and to act with UNC-5 in axon guidance and cell migration. Here, the role of SRC-1 in VD growth cone polarity and protrusion is investigated. A precise deletion ofsrc-1was generated, and mutants displayed unpolarized growth cones with increased size, similar tounc-5mutants. Transgenic expression ofsrc-1(+)in VD/DD neurons resulted in smaller growth cones, and rescued growth cone polarity defects ofsrc-1mutants, indicating cell-autonomous function. Transgenic expression of a putative kinase-deadsrc-1(D831A)mutant caused a phenotype similar tosrc-1loss-of-function, suggesting that this is a dominant negative mutation. The D381A mutation was introduced into the endogenoussrc-1gene by genome editing, which also had a dominant-negative effect. Genetic interactions ofsrc-1andunc-5suggest they act in the same pathway on growth cone polarity and protrusion, but might have overlapping, parallel functions in other aspects of axon guidance.src-1function was not required for the effects of activatedmyr::unc-5, suggesting that SRC-1 might be involved in UNC-5 dimerization and activation by UNC-6, of whichmyr::unc-5is independent. In sum, these results show that SRC-1 acts with UNC-5 in growth cone polarity and inhibition of protrusion.
Distinct brain network features predict internalizing and externalizing traits in children and adults
Authors: Qu Yueyue Lydia , Chen Jianzhong , Tam Angela , Ooi Leon Qi Rong , Dhamala Elvisha , Cocuzza Carrisa , Lawhead Connor , Yeo B. T. Thomas , Holmes Avram J.
Published: May 2023

Internalizing and externalizing traits are two distinct classes of behaviors in psychiatry. However, whether shared or unique brain network features predict internalizing and externalizing behaviors in children and adults remain poorly understood. Using a sample of 2262 children from the Adolescent Brain Cognitive Development (ABCD) study and 752 adults from the Human Connectome Project (HCP), we show that network features predicting internalizing and externalizing behavior are, at least in part, dissociable in children, but not in adults. In ABCD children, traits within internalizing and externalizing behavioral categories are predicted by more similar network features concatenated across task and resting states than those between different categories. We did not observe this pattern in HCP adults. Distinct network features predict internalizing and externalizing behaviors in ABCD children and HCP adults. These data reveal shared and unique brain network features accounting for individual variation within broad internalizing and externalizing categories across developmental stages.
Transcriptome mining of RNA viruses (familyTotiviridae) inEimeria necatrixandEimeria stiedai
Authors: Nibert Max L. , Xie Yue , Xiao Jie , Gao Yang , Liu Dandan , Yang Guangyou , Tao Jianping
Published: May 2023

Coccidian protozoa from the genusEimeriaare widespread parasites of vertebrates, causing serious disease (coccidiosis) and economic loss most notably in poultry. Several species ofEimeriaare themselves infected with small RNA viruses assigned to the familyTotiviridae. In this study, the sequences of two such viruses were newly determined, one of which represents the first complete protein-coding sequence of a virus fromE. necatrix, an important pathogen of chickens, and the other of which is fromE. stiedai, an important pathogen of rabbits. Sequence features of the newly identified viruses, compared with those of ones reported previously, provide several insights. Phylogenetic analyses suggest that these eimerian viruses constitute a well-demarcated clade, probably deserving of recognition as a distinct genus.
Comprehensive structural and interactome analysis reveals novel interactions and protein binding sites in miR-675: a non-coding RNA critically involved in multiple diseases
Authors: Dey Abhishek
Published: May 2023

miR-675 is a microRNA expressed from exon 1 of H19 long non-coding RNA. H19 lncRNA is temporally expressed in humans and atypical expression of miR-675 has been linked with several diseases and disorders. To execute its function inside the cell, miR-675 is folded into a particular conformation which aids in its interaction with several other biological molecules. However, the exact folding dynamics of miR-675 and its complete interaction map are currently unknown. Moreover, how H19 lncRNA and miR-675 crosstalk and modulate each other’s activities is also unclear. Detailed structural analysis of miR-675 in this study determines its conformation and identifies novel protein binding sites on miR-675 which can make it an excellent therapeutic target against numerous diseases. Mapping of the interactome identified some of known and unknown interactors of miR-675 which aid in expanding our repertoire of miR-675 involved pathways in the cell. This analysis also identified some of the previously unknown and yet to be characterised proteins as probable interactors of miR-675. Structural and base pair conservation analysis between H19 lncRNA and miR-675 results in structural transformations in miR-675 thus describing the earlier unknown mechanism of interaction between these two molecules. Comprehensively, this study details the conformation of miR-675, its interacting biological partners and explains its relationship with H19 lncRNA which can be interpreted to understand the role of miR-675 in the development and progression of various diseases.
Self-driving laboratories to autonomously navigate the protein fitness landscape
Authors: Rapp Jacob T. , Bremer Bennett J. , Romero Philip A.
Published: May 2023

Protein engineering has nearly limitless applications across chemistry, energy, and medicine, but creating new proteins with improved or novel functions remains slow, labor-intensive, and inefficient. In this work, we present theSelf-driving Autonomous Machines for Protein Landscape Exploration(SAMPLE) platform for fully autonomous protein engineering. SAMPLE is driven by an intelligent agent that learns protein sequence-function relationships, designs new proteins, and sends designs to a fully automated robotic system that experimentally tests designed proteins and provides feedback to improve the agent’s understanding of the system. We deployed four SAMPLE agents with the goal of engineering glycoside hydrolase enzymes with enhanced thermal tolerance. Despite showing individual differences in their search behavior, all four agents quickly converged on thermostable enzymes that were at least 12 °C more stable than the starting sequences. Self-driving laboratories automate and accelerate the scientific discovery process and hold great potential for the fields of protein engineering and synthetic biology.
Epitranscriptomics m6A analyses reveal distinct m6A marks under tumor necrosis factor α (TNF-α)-induced apoptotic conditions in HeLa cells
Authors: Akçaöz-Alasar Azime , Tüncel Özge , Sağlam Buket , Gazaloğlu Yasemin , Atbinek Melis , Cagiral Umut , Iscan Evin , Ozhan Gunes , Akgül Bünyamin
Published: May 2023

TNF-α is a ligand that induces both intrinsic and extrinsic apoptotic pathways in HeLa cells by modulating complex gene regulatory mechanisms. However, the full spectrum of TNF-α-modulated epitranscriptomic m6A marks is unknown. We employed a genomewide approach to examine the extent of m6A RNA modifications under TNF-α-modulated apoptotic conditions in HeLa cells. miCLIP-seq analyses revealed a plethora of m6A marks on 632 target mRNAs with an enrichment on 99 mRNAs associated with apoptosis. Interestingly, the m6A RNA modification patterns were quite different under cisplatin- and TNF-α-mediated apoptotic conditions. We then examined the abundance and translational efficiencies of several mRNAs under METTL3 knockdown and/or TNF-α treatment conditions. Our analyses showed changes in the translational efficiency ofTP53INP1mRNA based on the polysome profile analyses. Additionally, TP53INP1 protein amount was modulated by METTL3 knockdown upon TNF-α treatment but not CP treatment, suggesting the existence of a pathway-specific METTL3-TP53INP1 axis. Congruently, METLL3 knockdown sensitized HeLa cells to TNF-α-mediated apoptosis, which was also validated in a zebrafish larval xenograft model. These results suggest that apoptotic pathway-specific m6A methylation marks exist in cells and TNF-α-METTL3-TP53INP1 axis modulates TNF-α-mediated apoptosis in HeLa cells.
SF3B1-dependent alternative splicing is critical for maintaining endometrial homeostasis and the establishment of pregnancy
Authors: Popli Pooja , Chadchan Sangappa B. , Dias Michelle , Deng Xinchao , Gunderson Stephanie J. , Jimenez Patricia , Yalamanchili Hari , Kommagani Ramakrishna
Published: May 2023

The remarkable potential of human endometrium to undergo spontaneous remodeling is shaped by controlled spatiotemporal gene expression patterns. Although hormone-driven transcription shown to govern these patterns, the post-transcriptional processing of these mRNA transcripts, including the mRNA splicing in the endometrium is not studied yet. Here, we report that the splicing factor, SF3B1 is central in driving alternative splicing (AS) events that are vital for physiological responses of the endometrium. We show that loss of SF3B1 splicing activity impairs stromal cell decidualization as well as embryo implantation. Transcriptomic analysis revealed that SF3B1 depletion decidualizing stromal cells led to differential mRNA splicing. Specifically, a significant upregulation in mutually exclusive AS events (MXEs) with SF3B1 loss resulted in the generation of aberrant transcripts. Further, we found that some of these candidate genes phenocopy SF3B1 function in decidualization. Importantly, we identify progesterone as a potential upstream regulator of SF3B1-mediated functions in endometrium possibly via maintaining its persistently high levels, in coordination with deubiquitinating enzymes. Collectively, our data suggest that SF3B1-driven alternative splicing plays a critical role in mediating the endometrial-specific transcriptional paradigms. Thus, the identification of novel mRNA variants associated with successful pregnancy establishment may help to develop new strategies to diagnose or prevent early pregnancy loss.
Neuronal Branching is Increasingly Asymmetric Near Synapses, Potentially Enabling Plasticity While Minimizing Energy Dissipation and Conduction Time
Authors: Desai-Chowdhry Paheli , Brummer Alexander B. , Mallavarapu Samhita , Savage Van M
Published: May 2023

Neurons’ primary function is to encode and transmit information in the brain and body. The branching architecture of axons and dendrites must compute, respond, and make decisions while obeying the rules of the substrate in which they are enmeshed. Thus, it is important to delineate and understand the principles that govern these branching patterns. Here, we present evidence that asymmetric branching is a key factor in understanding the functional properties of neurons. First, we derive novel predictions for asymmetric scaling exponents that encapsulate branching architecture associated with crucial principles such as conduction time, power minimization, and material costs. We compare our predictions with extensive data extracted from images to associate specific principles with specific biophysical functions and cell types. Notably, we find that asymmetric branching models lead to predictions and empirical findings that correspond to different weightings of the importance of maximum, minimum, or total path lengths from the soma to the synapses. These different path lengths quantitatively and qualitatively affect energy, time, and materials. Moreover, we generally observe that higher degrees of asymmetric branching— potentially arising from extrinsic environmental cues and synaptic plasticity in response to activity— occur closer to the tips than the soma (cell body).
Focusing attention in human working memory and long-term memory: benefits through dissociable processes
Authors: Gong Dongyu , Draschkow Dejan , Nobre Anna C.
Published: May 2023

We developed a new experimental approach to compare how attentional orienting facilitates retrieval from working memory (WM) and long-term memory (LTM), and how selective attention within these two memory types impacts incoming sensory information processing. In three experiments with healthy young adults, retrospective attention cues prioritized an item represented in WM or LTM. Participants then retrieved a memory item or performed a perceptual task. The retrocue was informative for the retrieval task but not for the perceptual task. Attentional orienting benefited performance for both WM and LTM, with stronger effects for WM. Eye-tracking revealed significant gaze shifts and microsaccades correlated with attention in WM but not LTM. Visual discrimination of unrelated visual stimuli was consistently improved for items matching attended WM locations. Similar effects occurred at LTM locations but less consistently. The findings suggest potent and at least partly dissociable attention-orienting processes for different memory types.
Hijacking of internal calcium dynamics by intracellularly residing rhodopsins
Authors: Eria-Oliveira Ana-Sofia , Folacci Mathilde , Chassot Anne Amandine , Fedou Sandrine , Thézé Nadine , Zabelskii Dmitrii , Alekseev Alexey , Bamberg Ernst , Gordeliy Valentin , Sandoz Guillaume , Vivaudou Michel
Published: May 2023

Rhodopsins are ubiquitous light-driven membrane proteins with diverse functions, including ion transport. Widely distributed, they are also coded in the genomes of giant viruses infecting phytoplankton where their function is not settled. We examined the properties of three type 1 viral channelrhodopsins (VCR1s), and, unexpectedly, found that VCR1s accumulate exclusively intracellularly, and, upon illumination, induced calcium release from intracellular IP3-dependent stores. In vivo, this light-induced calcium release was sufficient to remote control muscle contraction and behavior in VCR1-expressing tadpoles. VCR1s are the first rhodopsins shown to natively confer light-induced Ca2+release, suggesting an original mechanism for reshaping the response to light of virus-infected algae. The ability of VCR1s to photorelease calcium without altering plasma membrane electrical properties marks them as precursors for novel optogenetics tools, with potential applications in basic research and medicine.
Eighteen‐year nitrogen addition does not increase plant phosphorus demand in a nitrogen‐saturated tropical forest
Authors: Yu Guangcan , Chen Jing , Yu Mengxiao , Li Andi , Wang Ying‐Ping , He Xinhua , Tang Xuli , Liu Hui , Jiang Jun , Mo Jiangming , Zhang Shuo , Yan Junhua , Zheng Mianhai
Published: May 2023

Nitrogen (N) deposition usually increases plant tissue N concentrations and thus phosphorus (P) demand in young and/or N‐limited forests, but the N deposition effect on plant P demand has rarely been assessed in N‐saturated forests.

Impacts of 18‐year external N additions (Control: 0, Low N: 50, Moderate N:100 and High N: 150 kg N ha−1 year−1) on leaf P of four plant life‐forms (tree, shrub, herb and liana), P fractions of bulk and rhizosphere soils were examined in a N‐saturated mature tropical forest in southern China.

Leaf N, P and N: P ratios of all plant life‐forms remained stable under three N additions. Among soil P fractions, moderate labile organic P increased by 25%–33% across three N additions; and soil total P was increased by 11.76% under Low N, and 8.87% under High N, compared with the control. The PLS‐PM results showed that path coefficient of microbial community to available P significantly increased and of inorganic P to available P significantly decreased under N additions than control. N additions improved soil P availability through microbe‐mediated P transformation: Low N significantly increased soil microbial taxonomic diversity, and a higher microbial diversity could enlarge the sources of nutrient acquisition and stimulate decomposition of recalcitrant organic matters; while High N significantly decreased soil microbial taxonomic diversity, the remaining microorganisms that were screened by N‐rich environments had the characteristics of resisting the N addition effects and maintained efficient P acquisition.

Synthesis. Our findings provide a novel line of evidence that long‐term N deposition did not increase plant P demand in a N‐saturated mature tropical forest. The underlying mechanism is that plants did not increase N uptakes therefore nor increase P uptakes (a stable leaf N: P stoichiometry) in an already N‐saturated ecosystem. Different N addition rates regulated soil P transformation via microbial community transition. These findings help improve the understanding of plant P acquisition and modelling of biogeochemical N–P cycling and vegetation productivity in N‐rich forest ecosystems, particularly considering the fact that chronic N deposition may likely lead to soil N richness and even saturation of many forests in the future.
Enoxaparin initiation after chronic subdural haematoma evacuation: a randomized clinical trial on timing and outcomes
Authors: Shafiei Mehdi , Sabouri Masih , Aminmansour Bahram , Mahmoodkhani Mehdi , Sourani Arman , Salehi Iman , Foroughi Mina
Published: May 2023

Aim

Patients with chronic subdural haematoma (CSDH) are at a significant risk for venous thromboembolism (VTE). Surgeons should weigh the advantages versus disadvantages of anticoagulants in the postoperative period.

Patients and Methods

This study was a randomized clinical trial conducted in Isfahan, Iran, from May 2016 to April 2021. Patients with CSDH eligible for bur‐hole craniostomy were primarily enrolled. All of them underwent bilateral lower limb Doppler ultrasonography (DUS) for deep venous thrombosis (DVT) screening. The patients were randomized into the case (n = 66, enoxaparin initiation 24 h after operation) and control (n = 70, enoxaparin initiation 72 h after operation) groups. Routine postoperative brain computed tomography scans were obtained 1 and 3 days after surgery. A second DUS was performed 96 h after operation to screen newly developed venous thrombosis; P value <.05 was defined significant.

Results

A total of 73 patients (59.8%) were female and 49 (40.2%) were male. The mean age was 65.1 ± 10.19 years; 9.9% of the patients had previously used antiplatelets. One patient had asymptomatic preoperative DVT. The mean values for enoxaparin dosage were 40.4918 ± 5.43 mg/day. Postoperative DVT or rebleeding prevalence was 0% in both groups. The mean follow‐up duration was 19.139 ± 2.2 months. Long‐term recurrence rate was 2.4% (n = 3). Postoperative pneumocephalus was associated with a higher recurrence rate (P = .031).

Conclusion

In terms of VTE chemoprophylaxis, following bur‐hole craniostomy for CSDH, enoxaparin will effectively prevent VTE development without any clinically significant rebleeding.
Segment 3 cholangiojejunostomy for unresectable peri‐hilar cholangiocarcinoma: A case report and literature review
Authors: Tidjane Anisse , Boudjenan Nabil , Ikhlef Nacim , Bengueddach Aicha , Meharzi Sif‐Elislem , Larbi Hakim , Ourabah Anissa , Tabeti Benali
Published: May 2023

Surgical management of unresectable perihilar cholangiocarcinoma is no longer relevant. Often these patients benefit from less invasive endoscopic or radiological management, but in the event of failure of these techniques, and in selected patients, cholangiojejunostomy in segment 3 can be an effective option. We describe the case of a 48‐year‐old patient presenting with an unresectable perihilar cholangiocarcinoma, in whom palliative endoscopic management failed two times and an open segment 3 intrahepatic cholangiojejunostomy was performed. The patient was discharged on the 7th day, has a complete resolution of jaundice at 2 months and is alive at 6 months without any readmission.
AMPK activation alleviated dextran sulfate sodium‐induced colitis by inhibiting ferroptosis
Authors: Sun Shao Peng , Lu Yi Fan , Li Heng , Weng Chun Yan , Chen Jia Jia , Lou Yi Jie , Lyu Dong , Lyu Bin
Published: May 2023

Objectives

Ferroptosis is a newly discovered cell death mode that has been confirmed to occur in the intestinal epithelial cells in ulcerative colitis (UC). In this study we aimed to elucidate the mechanism of ferroptosis and its association with adenosine monophosphate‐activated protein kinase (AMPK) in UC.

Methods

Gene expression profiles of colonic mucosa (GSE87473) were downloaded. Both human colonic samples and dextran sodium sulfate (DSS)‐induced colitis murine model were used. The molecular markers of ferroptosis were detected using western blot and immunohistochemistry. Symptoms, iron abundance, and lipid peroxidation level of the mouse model were measured to evaluate the role of AMPK activation in ferroptosis.

Results

Both gene and protein expressions of GPX4 and FTH1 were decreased in UC patients compared with the healthy controls. An increased iron abundance and lipid peroxidation level in colon tissues and damaged mitochondria were found in DSS‐induced colitis. AMPK expression was decreased in UC patients and correlated with FTH1 and GPX4. Activation of AMPK with metformin inhibited ferroptosis in the colon, improved symptoms, and prolonged the lifespan in DSS‐induced colitis mice.

Conclusions

Ferroptosis can be observed in colonic tissues in UC. AMPK activation inhibits ferroptosis in murine colitis model, which may act as a potential target for the treatment of colitis.
Clinical importance of tumor rupture in gastrointestinal stromal tumor
Authors: Nishida Toshirou , Gotouda Naoto , Takahashi Tsuyoshi , Cao Hui
Published: May 2023

Risk factors of gastrointestinal stromal tumors (GISTs) include tumor size, location, mitosis, and tumor rupture. Although the first three are commonly recognized as independent prognostic factors, tumor rupture is not a consistent finding. Indeed, tumor rupture may be subjectively diagnosed and is rarely observed. Moreover, the criteria used for diagnosis differ among oncologists, which may result in inconsistent outcomes. Based on these conditions, a universal definition of tumor rupture was proposed in 2019 and consists of six scenarios: tumor fracture, blood‐stained ascites, gastrointestinal perforation at the tumor site, histologically proven invasion, piecemeal resection, and open incisional biopsy. Although the definition is considered appropriate for selection of GISTs with worse prognostic outcomes, each scenario lacks a high level of evidence and there is yet no consensus for some, including histological invasion and incisional biopsy. It may be, however, important to have common criteria for clinical decision‐making, which may facilitate reliability, external validity, and comparability of clinical studies in rare GISTs. After the definition, several retrospective reports indicated that even with adjuvant therapy, tumor rupture was associated with high recurrence rates and poor prognostic outcomes. The prognosis of patients with ruptured GISTs is improved by 5‐year adjuvant therapy compared with 3‐year therapy. Nevertheless, the universal definition requires further evidence, and prospective clinical studies based on the definition are warranted.
Efficacy of new hemostatic techniques in nonvariceal gastrointestinal bleeding: A systematic review and network meta‐analysis
Authors: Liu Kai , Gao Li , Bai Jia Wei , Wang Lu Lu , Zhu Shao Hua , Zhao Xin , Han Ying , Liu Zhi Guo
Published: May 2023

Objectives

Nonvariceal gastrointestinal bleeding (NVGIB) is a common medical condition with significant mortality and morbidity. Several types of hemostatic modalities are currently available in clinical setting. This systematic review and network meta‐analysis aimed to assess the efficacy of these modalities in treating NVGIB.

Methods

PubMed, EMBASE, and the Cochrane Library databases were searched for studies that compared the efficacy of different hemostatic techniques (over‐the‐scope clip [OTSC], hemostatic powder [HP] and conventional endoscopic treatment [CET]) for NVGIB published up to June 2022. The 30‐day rebleeding rate was regarded as the primary outcome. We performed pairwise and network meta‐analyses for all treatments. The heterogeneity and transitivity were evaluated.

Results

Twenty‐two studies were included. Regarding the 30‐day rebleeding rate, OTSC and HP plus CET showed superior efficacy in treating NVGIB compared with CET (OTSC vs CET: relative risk [RR] 0.42, 95% confidence interval [CI] 0.28–0.60; HP plus CET vs CET: RR 0.40, 95% CI 0.17–0.87), while OTSC and HP plus CET had comparable efficacy (RR 0.95, 95% CI 0.38–2.31). HP plus CET ranked the highest in the network ranking estimate. The sensitivity analysis showed that it was not robust that OTSC was superior to CET regarding the short‐term rebleeding rate and the initial hemostasis rate. While all‐cause mortality, bleeding‐related mortality and necessity of surgical or angiographic salvage therapy showed no statistically significant difference.

Conclusion

OTSC and HP plus CET significantly reduced 30‐day rebleeding rate compared to CET and had comparable efficacy in the treatment of NVGIB.