bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering precise adenine base editor with infinitesimal rates of bystander mutations and off-target editing
Authors: Chen Liang , Zhang Shun , Xue Niannian , Hong Mengjia , Zhang Xiaohui , Zhang Dan , Yang Jing , Bai Sijia , Huang Yifan , Meng Haowei , Wu Hao , Luan Changming , Zhu Biyun , Ru Gaomeng , Liu Meizhen , Liu Mingyao , Cheng Yiyun , Yi Chengqi , Song Gaojie , Wang Liren , Li Dali 
Published: August 2022

AbstractAdenine base editors (ABEs) catalyze A-to-G transitions showing broad applications, but their bystander mutations and off-target editing effects raise the concerns of safety issues. Through structure-guided engineering, we found ABE8e with an N108Q mutation reduced both adenine and cytosine bystander editing, and introduction of an additional L145T mutation (ABE9), further refined the editing window to 1-2nt with eliminated cytosine editing. Importantly, ABE9 induced very minimal RNA and undetectable Cas9-independent DNA off-target effects, which mainly installed desired single A-to-G conversion in mouse and rat embryos to efficiently generate disease models. Moreover, ABE9 accurately edited A5 position of the protospacer sequence in pathogenic homopolymeric adenosine sites (up to 342.5-fold precision than ABE8e) and was further confirmed through a library of guide RNA-target sequence pairs. Due to the minimized editing window, ABE9 could further broaden the targeting scope for precise correction of pathogenic SNVs when fused to Cas9 variants with expanded PAM compatibility.
Evolution of constitutive bacteriocin production and release
Authors: Bhattacharya Amrita , Lively Curtis M 
Published: August 2022

AbstractThe production of the bacterial anti-competitor toxins, called bacteriocins, is widely described as spite, because the production of the toxins is costly and often requires cell death for release. Given these costs, it reasonable to think that bacteriocin production should be induced by the presence of unrelated competitor strains. Nonetheless, recent evidence in the insect-pathogenic bacteriumXenorhabdus koppenhoeffrishowed that bacteriocin production occurs regardless of the presence of unrelated competitors. Could the constitutive production of bacteriocins be favored by natural selection? Here we use a mathematical model to examine this question, both within and between subpopulations. The model assumes that bacteriocin production is constitutive and costly, and that toxin release only occurs during natural cell death. We found that constitutive bacteriocin producers can outcompete non-producer sensitive strains within populations, and that it can spread in a metapopulation provided there is local competition for patches. Hence, the evolution of bacteriocin production does not require the detection of competitors or “suicidal” release of toxins.
Elements of divergence in germline determination in closely related species
Authors: Morita Shumpei , Oulhen Nathalie , Foster Stephany , Wessel Gary M. 
Published: August 2022

AbstractEvolutionary transitions enable the wide diversity in life histories of plants and animals. This is particularly germane in the development of the germ line in which fitness is a direct readout of evolutionary change. Here, we focused on the gem line of two distinct sea urchin species who shared a common ancestor 50 million years ago. Even though they both rely on inherited mechanisms to specify their germ line, the integration of stage-matched single cell RNA-seq (scRNA-seq) datasets from these two sea urchins revealed a variety of differences in gene expression, including a broader expression of the germ line factor Nanos2 in Lytechinus variegatus (Lv) compared to Strongylocentrotus purpuratus (Sp). In Sp, Nanos2 mRNA expression is highly restricted to the primordial germ cells (PGCs) by a lability element in its 3’UTR. This element is lacking in the mRNA of Lv Nanos2, explaining how this mRNA more broadly accumulates in the Lv embryos. We discovered that the Lv Nanos2 3’UTR instead leads to a germline specific translation of the protein. The results emphasize that regulatory mechanisms resulting in germline diversity rely less on transcriptional regulation and more on post-transcriptional and post-translational restrictions of key gene products, such as Nanos2.Highlights-The first integration of scRNA-seq datasets comparing two echinoderm species.-We find Nanos2 positive cells in the embryonic soma of Lytechinus variegatus, an unusual occurrence, but not in Strongylocentrous purpuratus.-We discovered that this somatic Nanos2 mRNA is lacking an important regulatory element (GNARLE) in its 3’UTR-Instead, in Lv, the 3’UTR of Nanos2 leads to its specific translation in the germ cells.
Dancing with the ions: symport and antiport mechanisms of human glutamate transporters
Authors: Qiu Biao , Boudker Olga 
Published: August 2022

SummaryExcitatory amino acid transporters (EAATs) pump glutamate into glial cells and neurons. EAATs achieve million-fold transmitter gradients by symporting it with three sodium ions and a proton and counter-transporting a potassium ion via an elevator mechanism. Despite the availability of structures, the symport and antiport mechanisms remain unclear. We report high-resolution Cryo-EM structures of human EAAT3 bound to the neurotransmitter glutamate with symported ions, potassium ions, sodium ions alone, or in the absence of ligands. We show that an evolutionarily conserved occluded translocation intermediate has a dramatically higher affinity for the neurotransmitter and the counter-transported potassium ion than outward- or inward-facing transporters and plays a crucial role in ion coupling. We propose a comprehensive ion coupling mechanism involving a choreographed interplay between bound solutes, conformations of conserved amino acid motifs, and movements of the gating hairpin and the substrate-binding domain.
Changes in behavioral priority influence the accessibility but not the quality of working memory content
Authors: Ester Edward F. , Pytel Paige 
Published: August 2022

AbstractEvolving behavioral goals require the existence of selection mechanisms that prioritize task-relevant working memory (WM) content for action. Selecting an item stored in WM is known to blunt and/or reverse information loss in stimulus-specific representations of that item reconstructed from human brain activity, but extant studies have focused on all-or-none circumstances that allow or disallow an agent to select one of several items stored in WM. Conversely, behavioral studies suggest that humans can flexibly assign different levels of priority to different items stored in WM, but how doing so influences neural representations of WM content is unclear. One possibility is that assigning different levels of priority to items in WM influences the quality of those representations, resulting in more robust neural representations of high- vs. low-priority WM content. A second – and non-exclusive – possibility is that asymmetries in behavioral priority influence how rapidly neural representations of high- vs. low-priority WM content can be selected and reported. We tested these possibilities in two experiments by decoding high- and low-priority WM content from EEG recordings obtained while human volunteers performed a retrospectively cued WM task. Probabilistic changes in the behavioral relevance of a remembered item had no effect on our ability to decode it from EEG signals; instead, these changes influenced the latency at which above-chance decoding performance was reached. Thus, our results indicate that probabilistic changes in the behavioral relevance of WM content influence the ease with which memories can be accessed and retrieved independently of their strength.
Genetic architecture and evolution of color variation in American black bears
Authors: Puckett Emily E. , Davis Isis S. , Harper Dawn C. , Wakamatsu Kazumasa , Battu Gopal , Belant Jerrold L. , Beyer Dean E. , Carpenter Colin , Crupi Anthony P. , Davidson Maria , DePerno Christopher S. , Forman Nicholas , Fowler Nicholas L. , Garshelis David L. , Gould Nicholas , Gunther Kerry , Haroldson Mark , Ito Shosuke , Kocka David , Lackey Carl , Leahy Ryan , Lee-Roney Caitlin , Lewis Tania , Lutto Ashley , McGowan Kelly , Olfenbuttel Colleen , Orlando Mike , Platt Alexander , Pollard Matthew D. , Ramaker Megan , Reich Heather , Sajecki Jaime L. , Sell Stephanie K. , Strules Jennifer , Thompson Seth , van Manen Frank , Whitman Craig , Williamson Ryan , Winslow Frederic , Kaelin Christopher B. , Marks Michael S. , Barsh Gregory S. 
Published: August 2022

SUMMARYColor variation is a frequent evolutionary substrate for camouflage in small mammals but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus, exhibits a range of colors including the cinnamon morph which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (P < 10−13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that impaired protein localization and decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos, but is not fixed across the range.HIGHLIGHTSThe cinnamon morph of American black bears and brown bears have different missense mutations in TYRP1 that account for their similar colorationTYRP1 variants in American black bears and brown bears are loss-of-function alleles associated with impaired protein localization to melanosomesIn American black bears, the variant causing the cinnamon morph arose 9,360 years ago in the western lineage where it provides an adaptive advantage, and has spread northwards and eastwards by migration
A comprehensive model of Drosophila epithelium reveals the role of embryo geometry and cell topology in mechanical responses
Authors: Cheikh Mohamad Ibrahim , Tchoufag Joel , Osterfield Miriam , Dean Kevin , Bhaduri Swayamdipta , Chuzhong Zhang , Mandadapu Kranthi Kiran , Doubrovinski Konstantin 
Published: August 2022

AbstractIn order to understand morphogenesis, it is necessary to know the material properties or forces shaping the living tissue. In spite of this need, very fewin vivomeasurements are currently available. Here, using the early Drosophila embryo as a model, we describe a novel cantilever-based technique which allows for the simultaneous quantification of applied force and tissue displacement in a living embryo. By analyzing data from a series of experiments in which embryonic epithelium is subjected to developmentally relevant perturbations, we conclude that the response to applied force is adiabatic and is dominated by elastic forces and geometric constraints, or system size effects. Crucially, computational modeling of the experimental data indicated that the apical surface of the epithelium must be softer than the basal surface, a result which we confirmed experimentally. Further, we used the combination of experimental data and comprehensive computational model to estimate the elastic modulus of the apical surface and set a lower bound on the elastic modulus of the basal surface. More generally, our investigations revealed important general features that we believe should be more widely addressed when quantitatively modeling tissue mechanics in any system. Specifically, different compartments of the same cell can have very different mechanical properties; when they do, they can contribute differently to different mechanical stimuli and cannot be merely averaged together. Additionally, tissue geometry can play a substantial role in mechanical response, and cannot be neglected.
Direct conversion of somatic cells into ‘insulin-producing-cells’ by user-defined multiplex-epigenetic-engineering vector (MEEV-β)
Authors: Naqvi Raza Ali , Naqvi Afsar R , Priyadarshini Medha 
Published: August 2022

AbstractWe demonstrate here a single-step and user-friendly approach to generate insulin producing cells by gRNA driven specific-activation of PDX1, NKX6.1, MAFA, Insulin and Glut2 genes in somatic cells via multiplex-epigenetic-engineering-vector (MEEV-β) containing dCas9.P300core developed by us. Sorted Glut2+ cells could secrete insulin in response to glucose challenge and showed expression of β-cell specific transcription factors: NKX2.2, and aforementioned genes. Expression of Cav1.3, GSK3β,, KJNC11, and SLC30A8 genes substantiated the functional insulin secreting machinery genes in these Glut2+ cells. Also, absence of ARX and GCG expression in these cells highlighted the specificity of the conversion.
mtFociCounter for automated single-cell mitochondrial nucleoid quantification and reproducible foci analysis
Authors: Rey Timo , Tábara Luis Carlos , Prudent Julien , Minczuk Michal 
Published: August 2022

AbstractMitochondrial DNA (mtDNA) encodes the core subunits for OXPHOS and is essential in eukaryotes. mtDNA is packed into distinct foci (nucleoids) inside mitochondria, and the number of mtDNA differs between cell-types, and is affected in several human diseases. Today, common protocols estimate per-cell mtDNA-molecule numbers by sequencing or qPCR from bulk samples. However, this does not allow insight into cell-to-cell heterogeneity and can mask phenotypical sub-populations. Here, we presentmtFociCounter, a single-cell image-analysis tool for reproducible quantification of nucleoids and other foci.mtFociCounteris a light-weight, open-source freeware and overcomes current limitations to reproducible single-cell analysis of mitochondrial foci. We demonstrate its use by analysing 2165 single fibroblasts, and observe a large cell-to-cell heterogeneity in nucleoid numbers. In addition,mtFociCounterquantifies mitochondrial content and our results show good correlation (R=0.90) between nucleoid number and mitochondrial area, and we find nucleoid density is less variable than nucleoid numbers in wild-type cells. Finally, we demonstratemtFociCounterreadily detects differences in foci numbers upon sample-treatment, and applies to superresolution microscopy. Together, we presentmtFociCounteras a solution to reproducibly quantify cellular foci in single cells and our results highlight the importance of accounting for cell-to-cell variance and mitochondrial context in mitochondrial nucleoid analysis.
Viruses Diversity and Interactions with Hosts in Deep-Sea Hydrothermal Vents
Authors: Cheng Ruolin , Li Xiaofeng , Jiang Lijing , Gong Linfeng , Geslin Claire , Shao Zongze 
Published: August 2022

AbstractBackgroundDeep-sea harbor enormous viruses, yet their diversity and interactions with hosts in hydrothermal ecosystem are largely unknown. Here, we analyzed the viral composition, distribution, host preference and metabolic potential in different inhabits of global hydrothermal vents.ResultsFrom 34 samples of eight vent sites, a total of 4,662 viral populations were recovered from the metagenome assemblies, encompassing diverse phylogenetic groups and defining many novel lineages. Apart for the abundant unclassified viruses, tailed phages are most predominant across the global hydrothermal vents, while single-stranded DNA viruses including Microviridae and small eukaryotic viruses also constitute a significant part of the viromes. These viral populations were grouped into 1,138 genus-level clusters by protein-sharing network analysis. More than half were exclusively of hydrothermal origin, reflecting the remarkable novelty of hydrothermal viruses. Among the typical niches, vent plumes own the largest number of viral clusters compared to diffuse flows and sediments. Moreover, merely 11% of the viral populations can be linked to specific hosts, which are the key microbial taxa of hydrothermal habitats, such as Gammaproteobacteria and Campylobacteraeota. Intriguingly, vent viromes shared some metabolic features in common that they encode auxiliary genes extensively involved in metabolisms of carbohydrate, amino acid, cofactors and vitamins. Specifically in plume viruses, various auxiliary genes related with the methane, nitrogen and sulfur metabolisms were observed, indicating their contribution to host’s energy conservation. Moreover, the prevalence of sulfur relay pathway genes notified the significant role of vent virus in stabilizing tRNA structure, which promotes host’s adaptation to the steep environmental gradients.ConclusionsThe deep-sea hydrothermal systems reserve an untapped viral diversity with novelty. They may affect both vent prokaryotic and eukaryotic communities, and modulate host metabolisms related to vent adaptability. More explorations are needed to depict global vent virus diversity and their role in the unique ecosystem.
Conserved and divergent peptide substrate binding properties of bacterial Hsp70
Authors: Sun Yiyue , Xu Hongke , Li Jiong , Zhu Hanmo , Ma Hongwei , Ma Yiming , Yang Jiao 
Published: August 2022

AbstractThe 70-kDa heat shock protein (Hsp70) interacts with the polypeptide segments of abundant native proteins to fulfill various cellular activities in both stress and normal conditions. However, a non-native linear polypeptide NR (NRLLLTG) is widely used for the study of Hsp70 substrate binding properties, which is too simple to reflect the complex status of Hsp70 substrates in living organisms. To further broaden our knowledge in this area, we screened 2645 polypeptides derived from 78 biologically relevant proteins and identified eight native peptide substrates (named VP1∼VP8) for bacterial Hsp70 DnaK. Consistent with previous findings, the amino acid distribution in VP1∼VP8 were enriched in aliphatic and basic residues, and most of their residues were buried in folded proteins as well. Besides, the substrate binding properties for seven polypeptides were largely the same as observed in NR, suggesting their conserved binding mode to DnaK. However, VP5, which contains more percentage of positively charged residues, demonstrates divergent substrate binding properties during in-vitro biochemical studies. Moreover, VP5 efficiently inhibits the refolding activity of DnaK and bacterial viability, implying its potential to be a good lead peptide for antibacterial drug development.
The ChlorON Series: Turn-on Fluorescent Protein Sensors for Imaging Labile Chloride in Living Cells
Authors: Tutol Jasmine N. , Ong Whitney S. Y. , Phelps Shelby M. , Peng Weicheng , Goenawan Helen , Dodani Sheel C. 
Published: August 2022

AbstractBeyond its role as the queen electrolyte, chloride can also serve as an allosteric regulator or even a signaling ion. To illuminate this essential anion across such a spectrum of biological processes, researchers have relied on fluorescence imaging with genetically encoded sensors. In large part, these have been derived from the green fluorescent protein found in the jellyfishAequorea victoria. However, a standalone sensor with a turn-on intensiometric response at physiological pH has yet to be reported. Here, we address this technology gap by building on our discovery of mNeonGreen (mNG) derived from lanYFP found in the cephalochordateBranchiostoma lanceolatum. Targeted engineering of two non-coordinating residues in the chloride binding pocket of mNG unlocks the ChlorON series.In vitrospectroscopy reveals that the binding of chloride tunes the chromophore environment to give rise to the turn-on response. We further showcase how this unique sensing mechanism can be exploited for directly imaging labile chloride in living cells with spatial and temporal resolution, accelerating the path forward for fundamental and translational aspects of chloride biology.Abstract Figure
Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes
Authors: Grevesse Thomas , Guéguen Céline , Onana Vera E. , Walsh David A. 
Published: August 2022

AbstractBackgroundThe Arctic Ocean receives massive freshwater input and a correspondingly large amount of humic-rich organic matter of terrestrial origin. Global warming, permafrost melt, and a changing hydrological cycle will contribute to an intensification of terrestrial organic matter release to the Arctic Ocean. Although considered recalcitrant to degradation due to complex aromatic structures, humic substances can serve as substrate for microbial growth in terrestrial environments. However, the capacity of marine microbiomes to process aromatic-rich humic substances, and how this processing may contribute to carbon and nutrient cycling in a changing Arctic Ocean, is relatively unexplored. Here, we used a combination of metagenomics and metatranscriptomics to assess the prevalence and diversity of metabolic pathways and bacterial taxa involved in aromatic compound degradation in the salinity-stratified summer waters of the Canada Basin in the western Arctic Ocean.ResultsCommunity-scale meta-omics profiling revealed that 22 complete pathways for processing aromatic compounds were present and expressed in the Canada Basin, including those for aromatic ring fission and upstream funnelling pathways to access diverse aromatic compounds of terrestrial origin. A phylogenetically diverse set of functional marker genes and transcripts were associated with fluorescent dissolved organic matter, a component of which is of terrestrial origin. Pathways were common throughout global ocean microbiomes, but were more abundant in the Canada Basin. Genome-resolved analyses identified 12 clades ofAlphaproteobacteria, includingRhodospirillales, as central contributors to aromatic compound processing. These genomes were mostly restricted in their biogeographical distribution to the Arctic Ocean, and were enriched in aromatic compound processing genes compared to their closest relatives from other oceans.ConclusionOverall, the detection of a phylogenetically diverse set of genes and transcripts implicated in aromatic compound processing supports the view that Arctic Ocean microbiomes have the capacity to metabolize humic substances of terrestrial origin. In addition, the demonstration that bacterial genomes replete with aromatic compound degradation genes exhibit a limited distribution outside of the Arctic Ocean suggests that processing humic substances is an adaptive trait of the Arctic Ocean microbiome. Future increases in terrestrial organic matter input to the Arctic Ocean may increase the prominence of aromatic compound processing bacteria and their contribution to Arctic carbon and nutrient cycles.