bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D imaging reveals apical stem cell responses to ambient temperature
Authors: Wenzl Christian , Lohmann Jan U. 
Published: May 2023

AbstractPlant growth is driven by apical meristems at the shoot and root growth points, which comprise continuously active stem cell populations. While many of the key factors involved in homeostasis of the shoot apical meristem (SAM) have been extensively studied under artificial constant growth conditions, only little is known how variations in the environment affect the underlying regulatory network. To shed light on the responses of the SAM to ambient temperature, we combined 3D live imaging of fluorescent reporter lines that allowed us to monitor the activity of two key regulators of stem cell homeostasis in the SAM namelyCLAVATA3(CLV3)andWUSCHEL (WUS),with computational image analysis to derive morphological and cellular parameters of the SAM. WhereasCLV3expression marks the stem cell population,WUSpromoter activity is confined to the organizing center (OC), the niche cells adjacent to the stem cells, hence allowing us to record on the two central cell populations of the SAM. Applying an integrated computational analysis of our data we found that variations in ambient temperature not only led to specific changes in spatial expression patterns of key regulators of SAM homeostasis, but also correlated with modifications in overall cellular organization and shoot meristem morphology.
Novel regulatory variant in ABO intronic RUNX1 binding site inducing A3phenotype
Authors: Thun Gian Andri , Gueuning Morgan , Sigurdardottir Sonja , Meyer Eduardo , Gourri Elise , Schneider Linda , Merki Yvonne , Trost Nadine , Neuenschwander Kathrin , Engström Charlotte , Frey Beat M. , Meyer Stefan , Mattle-Greminger Maja P. 
Published: May 2023

AbstractBackground and ObjectivesMixed-field agglutination in ABO phenotyping (A3, B3) has been linked to genetically different blood cell populations like in chimerism, or to rare variants in eitherABOexon 7 or regulatory regions. Clarification of such cases is challenging and would greatly benefit from sequencing technologies that allow resolving full-gene haplotypes at high resolution.Materials and MethodsWe used long-read sequencing by Oxford Nanopore Technologies to sequence the entireABOgene, amplified in two overlapping long-range PCR fragments, in a blood donor presented with A3B phenotype. Confirmation analyses were carried out by Sanger sequencing and included samples from other family members.ResultsOur data revealed a novel heterozygous g.10924C>A variant on theABO*A-allele located in the transcription factor binding site for RUNX1 in intron 1 (+5.8 kb site). Inheritance was shown by the results of the donor’s mother, who shared the novel variant and the anti-A specific mixed-field agglutination.ConclusionWe discovered a regulatory variant in the 8-bp RUNX1 motif ofABO, which extends current knowledge of three other variants affecting the same motif and also leading to A3or B3phenotypes. Overall, long-range PCR combined with nanopore sequencing proved powerful and showed great potential as emerging strategy for resolving cases with cryptic ABO phenotypes.
JLOH: Inferring Loss of Heterozygosity Blocks from Sequencing Data
Authors: Schiavinato Matteo , del Olmo Valentina , Muya Victor Njenga , Gabaldón Toni 
Published: May 2023

AbstractHeterozygosity is a genetic condition in which two or more alleles are found at a genomic locus. Among the organisms that are more prone to heterozygosity are hybrids, i.e. organisms that are the offspring of genetically divergent yet still interfertile individuals. One of the most studied aspects is the loss of heterozygosity (LOH) within genomes, where multi-allelic sites lose one of their two alleles by converting it to the other, or by remaining hemizygous at that site. LOH is deeply interconnected with adaptation, especially in hybrids, but thein silicotechniques to infer LOH blocks are hardly standardized, and a general tool to infer and analyse them in most genomic contexts and species is missing. Here, we present JLOH, a computational toolkit for the inference and exploration of LOH blocks which only requires commonly available genomic data as input. Starting from mapped reads, called variants and a reference genome sequence, JLOH infers candidate LOH blocks based on single-nucleotide polymorphism density (SNPs/kbp) and read coverage per position. If working with a hybrid organism of known parentals, JLOH is also able to assign each LOH block to its subgenome of origin.
Intercellular interaction between FAP fibroblasts and CD150 inflammatory monocytes mediates fibro-stenosis in Crohn’s disease
Authors: Ke Bo-Jun , Abdurahiman Saeed , Biscu Francesca , Dragoni Gabriele , Santhosh Sneha , De Simone Veronica , Zouzaf Anissa , van Baarle Lies , Stakenborg Michelle , Bosáková Veronika , Van Rymenant Yentl , Verhulst Emile , Verstockt Sare , Bislenghi Gabriele , Wolthuis Albert , Frič Jan , Breynaert Christine , D’Hoore Andre , Van Der Veken Pieter , De Meester Ingrid , Verstockt Bram , de Hertogh Gert , Vermeire Séverine , Matteoli Gianluca 
Published: May 2023

SUMMARYCrohn’s disease (CD) is marked by recurring intestinal inflammation and tissue injury, often resulting in fibro-stenosis and bowel obstruction, necessitating surgical intervention with high recurrence rates. To elucidate complex intercellular interactions leading to fibro-stenosis in CD, we analysed the transcriptome of cells isolated from the transmural ileum of CD patients, including a trio of lesions from each patient: non-affected, inflamed, and stenotic ileum samples, and compared them with samples from non-CD patients. Our computational analysis revealed that pro-fibrotic signals from a subset of monocyte-derived cells expressing CD150 induce a disease-specific fibroblast population, resulting in chronic inflammation and tissue fibrosis. The transcription factor TWIST1 was identified as a key modulator of fibroblast activation and extracellular matrix (ECM) production. Therapeutic inhibition of TWIST1 inhibits fibroblast activation, reducing ECM production and deposition. These findings suggest that the myeloid-stromal axis may offer a promising therapeutic target to prevent fibro-stenosis in CD.
Genetic control of the error-prone repair of a chromosomal double-strand break with 5’ overhangs in yeast
Authors: Shaltz Samantha , Jinks-Robertson Sue 
Published: May 2023

ABSTRACTA targeted double-strand break introduced into the genome ofSaccharomyces cerevisiaeis repaired by the relatively error-prone nonhomologous-end joining (NHEJ) pathway when homologous recombination is not an option. A ZFN cleavage site was inserted out-of-frame into theLYS2locus of a haploid yeast strain to study the genetic control of NHEJ when the ends contain 5′ overhangs. Repair events that destroyed the cleavage site were identified either as Lys+colonies on selective medium or as surviving colonies on rich medium. Junction sequences in Lys+events solely reflected NHEJ and were influenced by the nuclease activity of Mre11 as well as by the presence/absence of the NHEJ-specific polymerase Pol4 and the translesion-synthesis DNA polymerases Pol σ and Pol 11. Although most NHEJ events were dependent on Pol4, a 29-bp deletion with endpoints in 3-bp repeats was an exception. The Pol4-independent deletion required TLS polymerases as well as the exonuclease activity of the replicative Pol DNA polymerase. Survivors were equally split between NHEJ events and 1 kb or 11 kb deletions that reflected microhomology-mediated end joining (MMEJ). MMEJ events required the processive resection activity of Exo1/Sgs1, but there unexpectedly was no dependence on the Rad1-Rad10 endonuclease for the removal of presumptive 3′ tails. Finally, NHEJ was more efficient in non-growing than in growing cells and was most efficient in G0 cells. These studies provide novel insight into the flexibility and complexity of error-prone DSB repair in yeast.
VERY LONG-CHAIN ACYL-CoA SYNTHETASE-3 (ACSVL3) PROMOTES THE MALIGNANT GROWTH BEHAVIOR OF U87 GLIOMA CELLS VIA CHANGES IN CELL CYCLE WITHOUT AFFECTING APOPTOSIS
Authors: Yang Haiyan , Shi Xiaohai , Kolar Elizabeth A. , Clay Emily M. , Xia Shuli , Pei Zhengtong , Watkins Paul A. 
Published: May 2023

ABSTRACTDecreasing the expression of very long-chain acyl-CoA synthetase 3 (ACSVL3) in U87MG glioblastoma cells by either RNA interference or genomic knockout (KO) significantly decreased their growth rate in culture, as well as their ability to form rapidly growing tumors in mice. U87-KO cells grew at a 9-fold slower rate than U87MG cells. When injected subcutaneously in nude mice, the tumor initiation frequency of U87-KO cells was 70% of that of U87MG cells, and the average growth rate of tumors that did form was decreased by 9-fold. Two hypotheses to explain the decreased growth rate of KO cells were investigated. Lack of ACSVL3 could reduce cell growth either by increasing apoptosis, or via effects on the cell cycle. We examined intrinsic, extrinsic, and caspase-independent apoptosis pathways; none were affected by lack of ACSVL3. However, significant differences in the cell cycle were seen in KO cells, suggesting arrest in S-phase. Levels of cyclin-dependent kinases 1, 2, and 4 were elevated in U87-KO cells, as were regulatory proteins p21 and p53 that promote cell cycle arrest. In contrast, lack of ACSVL3 reduced the level of the inhibitory regulatory protein p27. γ-H2AX, a marker of DNA double strand breaks, was elevated in U87-KO cells, while pH3, a mitotic index marker, was reduced. Previously reported alterations in sphingolipid metabolism in ACSVL3-depleted U87 cells may explain the effect of KO on cell cycle. These studies reinforce the notion that ACSVL3 is a promising therapeutic target in glioblastoma.
Local Genetic Sex Differences in Quantitative Traits
Authors: Uffelmann Emil , de Leeuw Christiaan , Posthuma Danielle 
Published: May 2023

Introductory ParagraphRecently, large-scale sex-stratified Genome-Wide Association Studies (GWASs) have been conducted that compare heritabilities and estimate global genetic correlations between males and females1–5. These studies have identified a small number of traits that show genetic sex differences on a global level. However, such global analyses cannot elucidate the local architecture of genetic sex differences6. To address this gap and gain insight into local (dis-)similarities in genetic signal between males and females, we estimated local genetic correlations and tested whether these differ from one, compared local heritability estimates, and tested for equality of local genetic effects in 157 quantitative traits. While the vast majority of loci do not significantly differ between males and females, almost every trait we studied had at least one locus that did. We show that these loci can highlight trait-relevant biology and may partly explain observed phenotypic sex differences.
Self-assembly of DNA nanostructures in different cations
Authors: Rodriguez Arlin , Gandavadi Dhanush , Mathivanan Johnsi , Song Tingjie , Madhanagopal Bharath Raj , Talbot Hannah , Sheng Jia , Wang Xing , Chandrasekaran Arun Richard 
Published: May 2023

ABSTRACTThe programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg2+and Na+). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (∼134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca2+, Ba2+, Na+, K+and Li+and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na+, K+and Li+) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg2+, Ca2+and Ba2+). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.
Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller
Authors: Wang Shuxin , Sass Mikaila I. , Kwon Yujin , Ludlam W. Grant , Smith Theresa M. , Carter Ethan J. , Gladden Nathan E. , Riggi Margot , Iwasa Janet H. , Willardson Barry M. , Shen Peter S. 
Published: May 2023

SUMMARYThe cytosolic Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β- propeller domains. Here, we determined structures of CCT in complex with its accessory co chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ5, a component of Regulator of G protein Signaling (RGS) complexes. Cryo-EM and image processing revealed an ensemble of distinct snapshots that represent the folding trajectory of Gβ5from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ5folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β-sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT directs folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
Ab initioprediction of specific phospholipid complexes and membrane association of HIV-1 MPER antibodies by multi-scale simulations
Authors: Maillie Colleen , Golden Jay , Wilson Ian A. , Ward Andrew B. , Mravic Marco 
Published: May 2023

SummaryA potent class of HIV-1 broadly neutralizing antibodies (bnAbs) targets the envelope glycoprotein’s membrane proximal exposed region (MPER) through a proposed mechanism where hypervariable loops embed into lipid bilayers and engage headgroup moieties alongside the epitope. We address the feasibility and determinant molecular features of this mechanism using multi-scale modeling. All-atom simulations of 4E10, PGZL1, 10E8 and LN01 docked onto HIV-like membranes consistently form phospholipid complexes at key complementarity-determining region loop sites, solidifying that stable and specific lipid interactions anchor bnAbs to membrane surfaces. Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. Coarse-grained simulations effectively capture antibodies embedding into membranes. Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. The modeling demonstrated here uncovers insights into lipid participation in antibodies’ recognition of membrane proteins and highlights antibody features to prioritize in vaccine design.
Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall
Authors: Harvey William T. , Ebert Peter , Ebler Jana , Audano Peter A. , Munson Katherine M. , Hoekzema Kendra , Porubsky David , Beck Christine R. , Marschall Tobias , Garimella Kiran , Eichler Evan E. 
Published: May 2023

ABSTRACTAdvances in long-read sequencing (LRS) technology continue to make whole-genome sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phasedde novogenome assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs) associated with disease. Limitations remain with respect to cost, scalability, and platform-dependent read accuracy and the tradeoffs between sequence coverage and sensitivity of variant discovery are important experimental considerations for the application of LRS. We compare the genetic variant calling precision and recall of Oxford Nanopore Technologies (ONT) and PacBio HiFi platforms over a range of sequence coverages. For read-based applications, LRS sensitivity begins to plateau around 12-fold coverage with a majority of variants called with reasonable accuracy (F1 score above 0.5), and both platforms perform well for SV detection. Genome assembly increases variant calling precision and recall of SVs and indels in HiFi datasets with HiFi outperforming ONT in quality as measured by the F1 score of assembly-based variant callsets. While both technologies continue to evolve, our work offers guidance to design cost-effective experimental strategies that do not compromise on discovering novel biology.
The microbiota ofAmblyomma americanumreflects known westward expansion
Authors: Martinez-Villegas Luis , Lado Paula , Klompen Hans , Wang Selena , Cummings Caleb , Pesapane Risa , Short Sarah M. 
Published: May 2023

AbstractAmblyomma americanum, a known vector of multiple tick-borne pathogens, has expanded its geographic distribution across the United States in the past decades. Tick microbiomes may play a role shaping their host’s life history and vectorial capacity. Bacterial communities associated withA. americanummay reflect, or enable, geographic expansion and studying the microbiota will improve understanding of tick- borne disease ecology. We examined the microbiota structure of 189 adult ticks collected in four regions encompassing their historical and current geographic distribution. Both geographic region of origin and sex were significant predictors of alpha diversity. As in other tick models, within-sample diversity was low and uneven given the presence of dominant endosymbionts. Beta diversity analyses revealed that bacterial profiles of ticks of both sexes collected in the West were significantly different from those of the Historic range. Biomarkers were identified for all regions except the historical range. In addition, Bray-Curtis dissimilarities overall increased with distance between sites. Relative quantification of ecological processes showed that, for females and males, respectively, drift and dispersal limitation were the primary drivers of community assembly. Collectively, our findings highlight how microbiota structural variance discriminates the western-expanded populations ofA. americanumticks from the Historical range. Spatial autocorrelation, and particularly the detection of non- selective ecological processes, are indicative of geographic isolation. Our conclusions demonstrate the value of synergistic analysis of biogeographic and microbial ecology data in investigating range expansion inA. americanumand potentially other tick vectors as well.ImportanceThe incidence of tick-borne diseases is on the rise worldwide, including in the United States. This increase in cases is in large part due to the geographic expansion of tick vectors. Among them is the Lone Star tick,Amblyomma americanum, and understanding the factors driving its recent expansion is important for risk assessment and tick population control. Climate change and human activities have previously been posited to be main driving forces for their expansion. New sources of relevant biological data can further our understanding of this phenomenon. Microbial communities associated with ticks include bacteria that affect pathogen transmission and tick behaviors. Here, we investigated whether bacterial community and geographic location data could be combined to better understand the expansion ofA. americanumpopulations. It’s not clear whether differences in the microbiota are reflective of or facilitating expansion, but our findings suggest this approach is promising and warrants further investigation.
Graded and sharp transitions in semantic function in left temporal lobe
Authors: Krieger-Redwood Katya , Wang Xiuyi , Souter Nicholas , Alam Tirso Rene del Jesus Gonzalez , Smallwood Jonathan , Jackson Rebecca L. , Jefferies Elizabeth 
Published: May 2023

AbstractRecent work has focussed on how patterns of functional change within the temporal lobe relate to whole-brain dimensions of intrinsic connectivity variation (Margulies et al., 2016). We examined two such ‘connectivity gradients’ reflecting the separation of (i) unimodal versus heteromodal and (ii) visual versus auditory-motor cortex, examining visually presented verbal associative and feature judgments, plus picture-based context and emotion generation. Functional responses along the first dimension sometimes showed graded change between modality-tuned and heteromodal cortex (in the verbal matching task), and other times showed sharp functional transitions, with deactivation at the extremes and activation in the middle of this gradient (internal generation). The second gradient revealed more visual than auditory-motor activation, regardless of content (associative, feature, context, emotion) or task process (matching/generation). We also uncovered subtle differences across each gradient for content type, which predominantly manifested as differences in relative magnitude of activation or deactivation.
Atomistic ensemble of active SHP2 phosphatase
Authors: Anselmi Massimiliano , Hub Jochen S. 
Published: May 2023

ABSTRACTSHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2 domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, non-stimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known for two decades, its active, open structure still represents a conundrum. Since the oncogenic mutant SHP2E76Kalmost completely populates the active, open state, this mutant has been extensively studied as a model for activated SHP2. By molecular dynamics simulations and accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic ensemble of constitutively active SHP2E76Kin solution, encompassing a set of conformational arrangements and radii of gyration in agreement with experimental SAXS data.