bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective Plane Illumination Microscopy and Computing Reveal Differential Obliteration of Retinal Vascular Plexuses
Authors: Chang Chih-Chiang , Chu Alison , Meyer Scott , Sun Michel M. , Abiri Parinaz , In Baek Kyung , Gudapati Varun , Ding Xili , Guihard Pierre , Ding Yichen , Bostrom Kristina I. , Li Song , Gordon Lynn K. , Zheng Jie J. , Hsiai Tzung K. 
Published: May 2020

ABSTRACTMurine models of visual impairment provide micro-vascular insights into the 3-D network disarray in retinopathy. Current imaging and analysis tend to be confined to the 2-D retinal vasculature. We hereby integrated selective plane illumination imaging or known as light-sheet fluorescence microscopy (LSFM) with dual-illumination, followed by computational analyses, to reveal the topological network of vertical sprouts bridging the primary and secondary plexuses in a postnatal mouse model of oxygen-induced retinopathy (OIR). We revealed a preferential obliteration of the secondary plexus and bridging vessels despite a relatively unscathed primary plexus. We compared the local versus global vascular connectivity using clustering coefficients and Euler numbers, respectively. The global vascular connectivity in hyperoxia-exposed retinas was significantly reduced (p< 0.05, n = 5 vs. normoxia), whereas the local connectivity was preserved (p> 0.05, n = 5 vs. normoxia). We further applied principal component analysis (PCA) to automatically segment the vertical sprouts, corroborating the preferential obliteration of the interconnection between vertical sprouts and secondary plexuses that were accompanied with impaired vascular branching and connectivity, and reduced vessel volumes and lengths (p< 0.05, n=5 vs. normoxia). Thus, integration of 3-D selective plane illumination with computational analyses allows for early detection of global and spatially-specific vaso-obliteration, but preserved local reticular structure in response to hyperoxia-induced retinopathy.
pegFinder: A pegRNA designer for CRISPR prime editing
Authors: Chow Ryan D. , Chen Jennifer S. , Shen Johanna , Chen Sidi 
Published: May 2020

To the EditorCRISPR technologies have been widely adopted as powerful tools for targeted genomic manipulation1. Recently, a new CRISPR-based strategy for precision genome editing was developed that enables diverse genomic alterations to be directly written into target sites without requiring double-strand breaks (DSBs) or donor templates2. Termed prime editing, this approach involves two key components: 1) a catalytically impaired Cas9 nickase fused to a reverse transcriptase (PE2), and 2) a multifunctional prime editing guide RNA (pegRNA) that specifies the target site and further acts as a template for reverse transcription (RT). pegRNAs are similar to standard single-guide RNAs (sgRNAs), but additionally have a customizable extension on the 3’ end. The 3’ extension is composed of a RT template that encodes the desired edit and a primer binding site (PBS) that anneals to the target genomic site to prime the RT reaction2. These additional components considerably increase the complexity of pegRNA design compared to standard sgRNAs. While many tools have been developed for identifying candidate sgRNAs in a target DNA sequence3–8, no user-friendly web application currently exists for designing pegRNAs. We therefore developed pegFinder, a streamlined web tool that rapidly designs candidate pegRNAs (Figure 1). The pegFinder web portal is freely available athttp://pegfinder.sidichenlab.org/(Supplementary Figure 1).
Characterization Of Ancestral Origin Of Cystic Fibrosis Of Patients With New Reported Mutations In CFTR
Authors: Paz-y-Miño César , Zambrano Ana Karina , Ruiz-Cabezas Juan Carlos , Armendáriz-Castillo Isaac , García-Cárdenas Jennyfer M. , Guerrero Santiago , López-Cortés Andrés , Pérez-Villa Andy , Guevara-Ramírez Patricia , Yumiceba Verónica , Leone Paola E. 
Published: May 2020

AbstractThe incidence of Cystic fibrosis (CF) and the frequency of the variants for CFTR depend on the population; furthermore, CF symptomatology is characterized by obstructive lung disease, pancreatic insufficiency among others, reliant on the individual genotype. Ecuadorian population is a mixture of Native Americans, Europeans, and Africans. That population admixture could be the reason for the new mutations reported in a previous study by Ruiz et al. (2019). A panel of 46 Ancestry Informative Markers was used to estimate the ancestral proportions of each available sample (12 samples in total). As a result, the Native American ancestry proportion was the most prevalent in almost all individuals, except for three patients from Guayaquil with the mutation[c.757G>A:p.Gly253Arg; c.1352G>T:p.Gly451Val]who had the highest European composition.
DNA extraction and sequencing of the Mawangdui ancient cadaver protected by formalin
Authors: Huang Hua-Lin , Yin Shikui , Zhao Huifang , Tian Chao , Huang Jufang , Deng Sihao , Li Zhiyuan 
Published: May 2020

AbstractMawangdui ancient Cadaver is the first wet corpse found in the world, which is famous for being immortal for over two thousands of years. After being unearthed, the female corpse was immersed in the formalin protective solution for more than 40 years. We used magnetic bead method and formalin fixed paraffing (FFPE) method to extract the DNA of the female corpse, respectively. PCR amplification, sanger sequencing, library building, high throughput sequencing (testing) and data processing were carried out on the DNA samples, and about 0.5% of the whole genome coverage sequencing data was obtained. Comparing the results of DNA trough two extraction and sequencing methods. We found that the FFPE and high throughput sequencing methods is better than others for DNA extraction of the ancient samples which were preserved in formalin, providing a guidance for dealing with formalin preserved ancient samples in the future.
Reclassification of seven honey bee symbiont strains asBombella apis
Authors: Smith Eric A. , Anderson Kirk E. , Corby-Harris Vanessa , McFrederick Quinn S. , Parish Audrey J. , Rice Danny W. , Newton Irene L. G. 
Published: May 2020

AbstractHoney bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture’s most important pollinator. One factor that may influence colony health is the microbial community. Although honey bee worker guts have a characteristic community of bee-specific microbes, the honey bee queen digestive tracts are colonized predominantly by a single acetic acid bacterium tentatively named “Parasaccharibacter apium”. This bacterium is related to flower-associated microbes such asSaccharibacter floricola, and initial phylogenetic analyses placed it as sister to these environmental bacteria. We used a combination of phylogenetic and sequence identity methods to better resolve evolutionary relationships among “P. apium”, strains in the genusSaccharibacter, and strains in the closely related genusBombella. Interestingly, measures of genome-wide average nucleotide identity and aligned fraction, coupled with phylogenetic placement, indicate that many strains labeled as “P. apium” andSaccharibactersp. are all the same species asBombella apis. We propose reclassifying these strains asBombella apisand outline the data supporting that classification below.
In situ detection of protein interactions for recombinant therapeutic enzymes
Authors: Samoudi Mojtaba , Kuo Chih-Chung , Robinson Caressa M. , Shams-Ud-Doha Km , Schinn Song-Min , Kol Stefan , Weiss Linus , Bjorn Sara Petersen , Voldborg Bjorn G. , Campos Alexandre Rosa , Lewis Nathan E. 
Published: May 2020

AbstractDespite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and post-translational modifications (PTMs). Here we aimed to identify the machinery supporting recombinant protein secretion by measuring the protein-protein interaction (PPI) networks of four different recombinant proteins (SERPINA1, SERPINC1, SERPING1 and SeAP) with various PTMs and structural motifs using the proximity-dependent biotin identification (BioID) method. We identified PPIs associated with specific features of the secreted proteins using a Bayesian statistical model, and found proteins involved in protein folding, disulfide bond formation and N-glycosylation were positively correlated with the corresponding features of the four model proteins. Among others, oxidative folding enzymes showed the strongest association with disulfide bond formation, supporting their critical roles in proper folding and maintaining the ER stability. Knockdown of disulfide-isomerase PDIA4, a measured interactor with significance for SERPINC1 but not SERPINA1, led to the decreased secretion of SERPINC1, which relies on its extensive disulfide bonds, compared to SERPINA1, which has no disulfide bonds. Proximity-dependent labeling successfully identified the transient interactions supporting synthesis of secreted recombinant proteins and refined our understanding of key molecular mechanisms of the secretory pathway during recombinant protein production.
A Pipeline for Precise and Efficient Genome Editing by sgRNA-Cas9 RNPs inDrosophila
Authors: Nyberg Kevin G. , Nguyen Joseph Q. , Kwon Yong-Jae , Blythe Shelby , Beitel Greg J. , Carthew Richard W. 
Published: May 2020

ABSTRACTGenome editing via homology-directed repair (HDR) has made possible precise and deliberate modifications to gene sequences. CRISPR/Cas9-mediated HDR is the simplest means to carry this out. However, technical challenges remain to improve efficiency and broaden applicability to any genetic background ofDrosophila melanogasteras well as to otherDrosophilaspecies. To address these issues, we developed a two-stage marker-assisted strategy in which embryos are injected with RNPs and pre-screened using T7EI. Using sgRNA in complex with recombinant Cas9 protein, we assayed each sgRNA for genome-cutting efficiency. We then conducted HDR using sgRNAs that efficiently cut target genes and the application of a transformation marker that generates RNAi againsteyes absent. This allows for screening based on eye morphology rather than color. These new tools can be used to make a single change or a series of allelic substitutions in a region of interest, or to create additional genetic tools such as balancer chromosomes.
Plasmids shape the diverse accessory resistomes ofEscherichia coliST131
Authors: Decano Arun Gonzales , Tran Nghia , Al-Foori Hawriya , Al-Awadi Buthaina , Campbell Leigh , Ellison Kevin , Mirabueno Louisse Paola , Nelson Maddy , Power Shane , Smith Genevieve , Smyth Cian , Vance Zoe , Woods Caitriona , Rahm Alexander , Downing Tim 
Published: May 2020

AbstractThe human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes that exchange these predominantly through conjugative plasmids.Escherichia coliis a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenicE. coli(ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensalE. coliand uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and here we examined this using a preterm infant resistome. Here, individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrialpiloperon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.Data SummaryThe following files are available on the FigShare project “Plasmids_ST131_resistome_2020” :The set of 794 AMR genes derived from [74] are available (with their protein sequence translation) at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961402.The AMR gene profiles per sample determined by their BLAST sequence similarity results against CARD are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961612. This dataset includes the PlasmidFinder results. It also includes other AMR database comparisons (ARG-ANNOT, ResFinder, MegaRes, VFDB and VirulenceFinder).The BLAST sequence similarity results for thefim, pil, papanducloperons’ genes versus 4,071E. coliST131 assemblies from Decano & Downing (2019) are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961711.The genome sequences and annotation files for reference genomes NCTC13441, EC958 and SE15, along with the assembled contigs for 83972 and 3_2_53FAA are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961813.The 4,071E. coliST131 genome assemblies from Decano & Downing (2019) are available at FigShare at doi: 10.6084/m9.figshare.11962278 (the first 1,680 assemblies) and at doi: dx.doi.org/10.6084/m9.figshare.11962557 (the second 2,391 assemblies).
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution
Authors: Li Qiuyi , Scornavacca Celine , Galtier Nicolas , Chan Yao-Ban 
Published: May 2020

AbstractIncomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, themultilocus multispecies coalescent(MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.
3D single cell migration driven by temporal correlation between oscillating force dipoles
Authors: Godeau A.L. , Leoni M. , Comelles J. , Guyomar T. , Lieb M. , Delanoë-Ayari H. , Ott A. , Harlepp S. , Sens P. , Riveline D. 
Published: May 2020

AbstractDirectional cell locomotion requires symmetry breaking between the front and rear of the cell. In some cells, symmetry breaking manifests itself in a directional flow of actin from the front to the rear of the cell. Many cells, especially in physiological 3D matrices do not show such coherent actin dynamics and present seemingly competing protrusion/retraction dynamics at their front and back. How symmetry breaking manifests itself for such cells is therefore elusive. We take inspiration from the scallop theorem proposed by Purcell for micro-swimmers in Newtonian fluids: self-propelled objects undergoing persistent motion at low Reynolds number must follow a cycle of shape changes that breaks temporal symmetry. We report similar observations for cells crawling in 3D. We quantified cell motion using a combination of 3D live cell imaging, visualization of the matrix displacement and a minimal model with multipolar expansion. We show that our cells embedded in a 3D matrix form myosin-driven force dipoles at both sides of the nucleus, that locally and periodically pinch the matrix. The existence of a phase shift between the two dipoles is required for directed cell motion which manifests itself as cycles with finite area in the dipole-quadrupole diagram, a formal equivalence to the Purcell cycle. We confirm this mechanism by triggering local dipolar contractions with a laser. This leads to directed motion. Our study reveals that these cells control their motility by synchronizing dipolar forces distributed at front and back. This result opens new strategies to externally control cell motion as well as for the design of micro-crawlers.
AI-based identification of grain cultivars via non-target mass spectrometry
Authors: Nichani Kapil , Uhlig Steffen , Colson Bertrand , Hettwer Karina , Simon Kirsten , Bönick Josephine , Uhlig Carsten , Rawel Harshadrai M. , Stoyke Manfred , Gowik Petra , Huschek Gerd 
Published: May 2020

ABSTRACTDetection of food fraud and geographical traceability of ingredients is a continually sought goal for government institutions, producers, and consumers. Herein we explore the use of non-target high-resolution mass spectrometry approaches and demonstrate its utility through a particularly challenging case study – to distinguish wheat and spelt cultivars. By employing a data-independent acquisition (DIA) approach for sample measurement, the spectra are of considerable size and complexity. We utilize artificial intelligence (AI) algorithms (artificial neural networks) to evaluate the extensive proteomic footprint of several wheat and spelt cultivars. The AI model thus obtained is used to classify newer varieties of spelt, processed flour, and bread samples. Additionally, we discuss the validation of such a method coupling DIA and AI approaches. The novel framework for method validation enables calculation of precision parameters for facile comparison of the discriminatory power of the method and in the development of a reliable decision rule.
A Modified ACE2 peptide mimic to block SARS-CoV2 entry
Authors: Saurabh Suman , Purohit Shubh Sanket 
Published: May 2020

AbstractA 23-residue peptide fragment that forms a part of theα-1 helix of the ACE2 peptidase domain, the recognition domain for SARS-CoV2 on the ACE2 receptor, holds the potential as a drug to block the viral receptor binding domain (RBD) from forming a complex with ACE2. The peptide has recently been shown to bind the viral RBD with good efficiency. Here, we present a detailed analysis of the energetics of binding of the peptide to the SARS-CoV2 RBD. We use equilibrium molecular dynamics simulation to study the dynamics of the complex. We perform end-state binding energy calculations to gain a residue-level insight into the binding process and use the information to incorporate point mutations into the peptide. We demonstrate using binding energy calculations that the peptide with certain point mutations, especially E17L, shows a stronger binding to the RBD as compared to the wild type peptide. We propose that the modified peptide will thus be more efficient in blocking RBD-ACE2 binding.
Haldane’s rule in the placenta: sex-biased misregulation of theKcnq1imprinting cluster in hybrid mice
Authors: Arévalo Lena , Gardner Sarah , Campbell Polly 
Published: May 2020

ABSTRACTMammalian hybrids often show striking asymmetries in their phenotypes both between reciprocal crosses, and between sexes in accordance with Haldane’s rule. Hybrid inviability is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted genes is a strong candidate mechanism. However, direct evidence for the involvement of abnormal imprinting and the mechanisms behind this proposed misregulation is limited. We used transcriptome and reduced representation bisulfite sequencing to evaluate the contribution of imprinted genes to a long-standing example of parent-of-origin placental growth dysplasia in the cross between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus). We found little evidence for loss of imprinting and imprinted genes with biallelic expression were not misexpressed. Instead, imprinted genes with transgressive expression and methylation were concentrated in theKcnq1cluster, which contains causal genes for prenatal growth abnormalities in both mice and humans. Hypermethylation of the cluster’s imprinting control region, and consequent misexpression of the genesPhlda2andAscl2, is a strong candidate mechanism for hybrid placental undergrowth. Transgressive placental and gene regulatory phenotypes, including expression and methylation in the Kcnq1 cluster, were more extreme in hybrid males. While consistent with Haldane’s rule, male-biased defects are not expected in rodent placenta because the maternal X chromosome is effectively hemizygous in both sexes. In search of an explanation we found evidence of leaky imprinted X-chromosome inactivation in hybrid females. Supplementary expression from the paternal X-chromosome may buffer the females from the effects of X-linked incompatibilities to which males are fully exposed. Sex differences in chromatin structure on the X and sex-biased maternal effects are non-mutually exclusive alternative explanations for adherence to Haldane’s rule in hybrid placenta. The results of this study contribute to understanding of the genetic basis of hybrid inviability in mammals, and the role of imprinted genes in speciation.
ampir: an R package for fast genome-wide prediction of antimicrobial peptides
Authors: Fingerhut Legana C.H.W , Miller David J. , Strugnell Jan M. , Daly Norelle L. , Cooke Ira R. 
Published: May 2020

AbstractSummaryAntimicrobial peptides (AMPs) are key components of the innate immune system that protect against pathogens, regulate the microbiome, and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ampir. ampir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data.Availability and Implementationampir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained athttps://github.com/legana/ampirContactlegana.fingerhut@my.jcu.edu.au;ira.cooke@jcu.edu.auSupplementary informationSupplementary data are available athttps://github.com/legana/amp_pub