bluuebunny/crossref_metadata_2025 huggingface dataset:
Parental Population Range Expansion Before Secondary Contact Promotes Heterosis
Authors: MacPherson Ailene , Wang Silu , Yamaguchi Ryo , Rieseberg Loren H. , Otto Sarah P.
Published: April 2020

Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele surfing where neutral or slightly deleterious mutations drift to high frequency at the expansion front. If these surfed deleterious alleles are recessive, they can contribute to substantial heterosis in hybrids produced at secondary contact, counteracting negative effects of Bateson-Dobzhansky-Muller incompatibilities (BDMIs) hence weakening reproductive isolation. When BDMIs are linked to such recessive deleterious alleles the fitness benefit of introgression at these loci can facilitate introgression at the BDMIs. The extent to which this occurs depends on the strength of selection against the linked deleterious alleles and the distribution of recombination across the chromosome. Finally, surfing of neutral loci can alter the expected pattern of population ancestry, thus accounting for historical population expansion is necessary to develop accurate null genomic models of secondary-contact hybrid zones.
Empirical lognormality of biological variation: implications for the ‘zero-force evolutionary law’
Authors: Gingerich Philip D.
Published: April 2020

The zero-force evolutionary law (ZFEL) of McShea et al. states that independently evolving entities, with no forces or constraints acting on them, will tend to accumulate differences and therefore diverge from each other. McShea et al. quantified the law by assuming normality on an additive arithmetic scale and reflecting negative differences as absolute values, systematically augmenting perceived divergence. The appropriate analytical framework is not additive but proportional, where logarithmic transformation is required to achieve normality. Logarithms and logarithmic differences can be negative but the proportions they represent cannot be negative. Reformulation of ZFEL in a proportional or geometric reference frame indicates that when entities evolve randomly and independently, differences smaller than any initial difference are balanced by differences larger than the initial difference. Total variance increases with each step of a random walk, but there is no statistical expectation of divergence between random-walk lineages.
PD-1 blockade-driven anti-tumor CD8+T cell immunity requires XCR1+dendritic cells
Authors: Mao Tianyang , Song Eric , Iwasaki Akiko
Published: April 2020

CD8+T cells are required for effective anti-PD-1 (αPD-1) cancer immunotherapy. Type 1 conventional dendritic cells (cDC1s) bearing XCR1 critically mediate the initiation of protective anti-tumor CD8+T cell responses in mice and humans. However, whether cDC1s contribute to evoking the effector function of CD8+T cells during αPD-1 antibody therapy remains unclear. Here, by deleting cDC1s at the effector phase of αPD-1 therapy, we identify these cells as a crucial innate determinant for effective αPD-1 immunotherapy. αPD-1 treatment unleashed cDC1s to promote anti-tumor CD8+T cell immunity, through the expansion of TCF1+precursors and generation of TIM3+terminally differentiated effectors. Furthermore, tumor cDC1 abundance was predictive of enhanced CD8+T cell infiltration, higher survival, and improved clinical responses to αPD-1 therapy in human cancer patients. Together, this study reveals the requirement for cDC1s in PD-1 blockade therapy, through their ability to elicit CD8+T cell effector responses that mediate tumor control, and highlight cDC1s as an attractive cellular target to be harnessed for novel immunotherapeutics.
Establishment of a stablezg6pdM118-144transgenic zebrafish model of glucose-6-phosphate dehydrogenase deficiency
Authors: Xia Hai-Xiong , Zhou Yan-Hua , Tuo Yuan-Yuan , Ren Ping-Ping , Song Jin , Shang Lu-Jun , Jin Jiao , He Zhi-Xu , Shu Li-Ping
Published: April 2020

Glucose-6-phosphate dehydrogenase (G6PD) deficiency, the most common genetic defect and enzymopathy with a wide distribution and increased public health concern, predisposes subjects succumb to oxidative stress. G6PD deficiency has been associated with hemolysis. Clinically, G6PD deficiency is asymptomatic and the clinical manifestations occur with the exposure to certain agents. Due to the lack of suitable animal models that can predict the clinical hemolytic potential of drugs, it needs an appropriate research model to fully recapitulate the manifestations of G6PD deficiency in clinic, to optimize the malaria therapy and promote anti-malarias development. The present study has displayed a stable transgenicTg(zgata1-g6pdM118-144-egfp) zebrafish model with G6PD deficiency which mimics the clinical features of G6PD deficiency phenotypically and functionally. The findings showed that there was an inadequate level of reduced GSH in the transgenicTg(zgata1-g6pdM118-144-egfp) zebrafish line in the presence or absence of α-naphthol, compared to the wildtype zebrafish, indicating an attenuation of g6pd activity in the transgenic zebrafish line. In addition, the observations show that there is a less abundance of g6pd in the transgenicTg(zgata1-g6pdM118-144-egfp) zebrafish line. On the other hand, there is no morphological abnormality in the transgenicTg(zgata1-g6pdM118-144-egfp) zebrafish line. Taken together, our work has delivered a novel stable transgenic zebrafish model of G6PD deficiency that will facilitate the mechanistic and functional elucidation for the role of G6PD in erythrocytic pathophysiology. This model will promote the translational research for the drug development, in particular, for anti-malarias development.
Gromov-Wasserstein optimal transport to align single-cell multi-omics data
Authors: Demetci Pinar , Santorella Rebecca , Sandstede Björn , Noble William Stafford , Singh Ritambhara
Published: April 2020

Data integration of single-cell measurements is critical for understanding cell development and disease, but the lack of correspondence between different types of measurements makes such efforts challenging. Several unsupervised algorithms can align heterogeneous single-cell measurements in a shared space, enabling the creation of mappings between single cells in different data domains. However, these algorithms require hyperparameter tuning for high-quality alignments, which is difficult in an unsupervised setting without correspondence information for validation. We present Single-Cell alignment using Optimal Transport (SCOT), an unsupervised learning algorithm that uses Gromov Wasserstein-based optimal transport to align single-cell multi-omics datasets. We compare the alignment performance of SCOT with state-of-the-art algorithms on four simulated and two real-world datasets. SCOT performs on par with state-of-the-art methods but is faster and requires tuning fewer hyperparameters. Furthermore, we provide an algorithm for SCOT to use Gromov Wasserstein distance to guide the parameter selection. Thus, unlike previous methods, SCOT aligns well without using any orthogonal correspondence information to pick the hyperparameters. Our source code and scripts for replicating the results are available athttps://github.com/rsinghlab/SCOT.
Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world
Authors: Phelan Jody , Deelder Wouter , Ward Daniel , Campino Susana , Hibberd Martin L. , Clark Taane G
Published: April 2020

Background

SARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines.

Methods

We used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure.

Results

We used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades.

Conclusion

The worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.
The CRISPR-Cas9 crATIC HeLa transcriptome: Characterization of a novel cellular model of ATIC deficiency and ZMP accumulation
Authors: Mazzarino Randall C , Baresova Veronika , Zikánová Marie , Duval Nathan , Wilkinson Terry G. , Patterson David , Vacano Guido N.
Published: April 2020

Inde novopurine biosynthesis (DNPS), 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (2.1.2.3) / inosine monophosphate cyclohydrolase (3.5.4.10) (ATIC) catalyzes the last two reactions of the pathway: conversion of 5-aminoimidazole-4-carboxamide ribonucleotide [aka Z-nucleotide monophosphate (ZMP)] to 5-formamido-4-imidazolecarboxamide ribonucleotide (FAICAR) then to inosine monophosphate (IMP). ZMP is an adenosine monophosphate (AMP) mimetic and a known activator of AMP-activated protein kinase (AMPK). Recently, a HeLa cell line null mutant for ATIC was constructed via CRISPR-Cas9 mutagenesis. This mutant, crATIC, accumulates ZMP during purine starvation. Given that the mutant can accumulate ZMP in the absence of treatment with exogenous compounds, crATIC is likely an important cellular model of DNPS inactivation and ZMP accumulation. In the current study, we characterize the crATIC transcriptome versus the HeLa transcriptome in purine-supplemented and purine-depleted growth conditions. We report and discuss transcriptome changes with particular relevance to Alzheimer’s disease and in genes relevant to lipid and fatty acid synthesis, neurodevelopment, embryogenesis, cell cycle maintenance and progression, extracellular matrix, immune function, TGFβ and other cellular processes.
Investigation of the anti-TB potential of selected alkaloid constituents using molecular docking approach
Authors: Siam Mohammad Kawsar Sharif , Shohan Mohammad Umer Sharif , Zafroon Zaira
Published: April 2020

Mycobacterium tuberculosis, the leading bacterial killer disease worldwide, causes Human tuberculosis (TB). Due to the growing problem of drug resistantMycobacterium tuberculosisstrains, new anti-TB drugs are urgently needed. Natural sources such as plant extracts have long played an important role in tuberculosis management and can be used as a template to design new drugs. A wide screening of natural sources is time consuming but the process can be significantly sped up using molecular docking. In this study, we used a molecular docking approach to investigate the interactions between selected natural constituents and three proteins MtPanK, MtDprE1 and MtKasA involved in the physiological functions of Mycobacterium tuberculosis which are necessary for the bacteria to survive and cause disease. The molecular docking score, a score that accounts for the binding affinity between a ligand and a target protein, for each protein was calculated against 150 chemical constituents of different classes to estimate the binding free energy. The docking scores represent the binding free energy. The best docking scores indicates the highest ligand protein binding which is indicated by the lowest energy value. Among the natural constituents, Shermilamine B showed a docking score of - 8.5kcal/mol, Brachystamide B showed a docking score of −8.6 kcal/mol with MtPanK, Monoamphilectine A showed a score of −9.8kcal/mol with MtDprE1.These three compounds showed docking scores which were superior to the control inhibitors and represent the opportunity of in vitro biological evaluation and anti-TB drug design. Consequently, all these compounds belonged to the alkaloid class. Specific interactions were studied to further understand the nature of intermolecular bonds between the most active ligands and the protein binding site residues which proved that among the constituents monoamphilectine A and Shermilamine B show more promise as Anti-TB drugs. Furthermore, the ADMET properties of these compounds or ligands showed that they have no corrosive or carcinogenic parameters.

Graphical Abstract
Proteasome activator PA200 maintains stability of histone marks during transcription and aging
Authors: Jiang Tian-Xia , Ma Shuang , Han Xia , Luo Zi-Yu , Zhu Qian-Qian , Chiba Tomoki , Xie Wei , Chen Su-Ren , Lin Kui , Qiu Xiao-Bo
Published: April 2020

The epigenetic inheritance relies on stability of histone marks, but various diseases, including aging-related diseases, are usually associated with alterations of histone marks. How the stability of histone marks is maintained still remains unclear. The core histones can be degraded by the atypical proteasome, which contains the proteasome activator PA200, in an acetylation-dependent manner during somatic DNA damage response and spermiogenesis. Here we show that PA200 promotes the transcription-coupled degradation of the core histones, and plays an important role in maintaining the stability of histone marks. Degradation of the histone variant H3.3, which is incorporated into chromatin during transcription, was much faster than that of its canonical form H3.1, which is incorporated during DNA replication. This degradation of the core histones could be suppressed by the transcription inhibitor, the proteasome inhibitor or deletion of PA200. The histone deacetylase inhibitor accelerated the degradation rates of H3 in general, especially its variant H3.3, while the mutations of the putative acetyl-lysine-binding region of PA200 abolished histone degradation in the G1-arrested cells, supporting that acetylation is involved in the degradation of the core histones. Deletion of PA200 dramatically altered deposition of the active transcriptional hallmarks (H3K4me3 and H3K56ac) and transcription, especially during cellular aging. Furthermore, deletion of PA200 or its yeast ortholog Blm10 accelerated cellular aging. Notably, the PA200-deficient mice displayed a range of aging-related deteriorations, including immune malfunction, anxiety-like behaviors and shorter lifespan. Thus, the proteasome activator PA200 is critical to the maintenance of the stability of histone marks during transcription and aging.
Cell culture NAIL-MS allows insight into human RNA modification dynamicsin vivo
Authors: Heiss Matthias , Hagelskamp Felix , Kellner Stefanie
Published: April 2020

In the last years, studies about the dynamics of RNA modifications are among the most controversially discussed. As the main reason, we have identified the unavailability of a technique which allows to follow the temporal dynamics of RNA transcripts in human cell culture. Here, we present a NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) scheme for efficient stable isotope labeling in both RNA and DNA (>95% within 7 days) in common human cell lines and growth media. Validation experiments reveal that the labeling procedure itself does neither interfere with the isotope dilution MS quantification nor with RNA modification density. We design pulse chase NAIL-MS experiments and apply the new tool to study the temporal placement of modified nucleosides ine.g.tRNAPheand 18S rRNA. In existing RNAs, we observe a constant loss of modified nucleosides over time which is masked by a post-transcriptional methylation mechanism and thus not detectable without NAIL-MS. During alkylation stress, NAIL-MS reveals an adaptation of tRNA modifications in new transcripts but not existing transcripts.

Overall, we present a fast and reliable stable isotope labeling strategy which allows a more detailed study of RNA modification dynamics in human cell culture. With cell culture NAIL-MS it is finally possible to study the speed of both modification and demethylation reactions inside human cells. Thus it will be possible to study the impact of external stimuli and stress on human RNA modification kinetics and processing of mature RNA.
Adaptations accumulated under prolonged resource exhaustion are highly transient
Authors: Avrani Sarit , Katz Sophia , Hershberg Ruth
Published: April 2020

Many non-sproulating bacterial species can survive for years within exhausted growth media in a state termed long-term stationary phase (LTSP). We have been carrying out evolutionary experiments aimed at elucidating the dynamics of genetic adaptation under LTSP. We showed thatEscherichia coliadapts to prolonged resource exhaustion through the highly convergent acquisition of mutations. In the most striking example of such convergent adaptation, we observed that across all independently evolving LTSP populations, over 90% ofE. colicells carry mutations to one of three specific sites of the RNA polymerase core enzyme (RNAPC). These LTSP adaptations reduce the ability of the cells carrying them to grow once fresh resources are again provided. Here, we examine how LTSP populations recover from costs associated with their adaptation, once resources are again provided to them. We demonstrate that due to the ability of LTSP populations to maintain high levels of standing genetic variation during adaptation, costly adaptations are very rapidly purged from the population once they are provided with fresh resources. We further demonstrate that recovery from costs acquired during adaptation under LTSP occurs much more rapidly than would be possible if LTSP adaptations had fixed during the time populations spent under resource exhaustion. Finally, we previously reported that under LTSP, some clones develop a mutator phenotype, greatly increasing their mutation accumulation rates. Here, we show that the mechanisms, by which populations recover from costs associated with fixed adaptations, may depend on mutator status.
Validation of a single-step, single-tube reverse transcription-loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA
Authors: Lee Jean Y. H. , Best Nickala , McAuley Julie , Porter Jessica L. , Seemann Torsten , Schultz Mark B. , Sait Michelle , Orlando Nicole , Mercoulia Karolina , Ballard Susan A. , Druce Julian , Tran Thomas , Catton Mike G. , Pryor Melinda J. , Cui Huanhuan L. , Luttick Angela , McDonald Sean , Greenhalgh Arran , Kwong Jason C. , Sherry Norelle L. , Graham Maryza , Hoang Tuyet , Herisse Marion , Pidot Sacha J. , Williamson Deborah A. , Howden Benjamin P. , Monk Ian R. , Stinear Timothy P.
Published: April 2020

2.

Introduction

The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues.

Aim

To establish and validate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs.

Methodology

We used a commercial RT-LAMP mastermix from OptiGene Ltd in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby as little as 1 μL of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65°C for 30 minutes and measure fluorescence in the FAM channel at one-minute intervals.

Results

Assay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87% and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 minutes (SD ±7 minutes). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50mL−1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay.

Conclusion

With a simplified workflow, N1-STOP-LAMP is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19.

3.

Data summary

The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Imaging translation dynamics in live embryos reveals spatial heterogeneities
Authors: Dufourt Jeremy , Bellec Maelle , Trullo Antonio , Dejean Matthieu , De Rossi Sylvain , Lagha Mounia
Published: April 2020

The translation of individual mRNA molecules is a key biological process, yet this multi-step process has never been imaged in living multicellular organisms. Here we deploy the recently developed Suntag method to visualize and quantify translation dynamics of single mRNAs in livingDrosophilaembryos. By focusing on the translation of the conserved major epithelial-mesenchymal transition (EMT)-inducing transcription factor Twist, we identified spatial heterogeneity in mRNA translation efficiency and reveal the existence of translation factories, where clustered mRNAs are co-translated preferentially at basal perinuclear regions. Simultaneous visualization of transcription and translation dynamics in a living multicellular organism opens exciting new avenues for understanding of gene regulation during development.
Investigating DNA methylation as a potential mediator between pigmentation genes, pigmentary traits and skin cancer
Authors: Bonilla Carolina , Bertoni Bernardo , Min Josine L , Hemani Gibran ,   Genetics of DNA Methylation Consortium, Elliott Hannah R
Published: April 2020

Background

Incidence rates for melanoma and non-melanoma skin cancer (NMSC), which includes basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), have been steadily increasing in all populations. Populations of European ancestry exhibit the highest rates and therefore, have been widely studied. Pigmentation characteristics are well-known risk factors for skin cancer, particularly fair skin, red hair, blue eyes and the inability to tan. Polymorphisms in established pigmentation-related genes have been associated with these traits and with an increased risk of malignancy. However, the functional relationship between genetic variation and disease is still unclear, with the exception of red hair colour variants in the melanocortin 1 receptor (MC1R) gene.

Objectives

The aim of this study was to explore the possibility that non-coding pigmentation SNPs are associated with pigmentary traits and skin cancer via DNA methylation (DNAm).

Methods and Results

Using a meta-GWAS of whole blood DNAm from 36 European cohorts (N=27,750; the Genetics of DNA Methylation Consortium, GoDMC), we found that 19 out of 27 pigmentation-associated SNPs distributed within 10 genes (ASIP, BNC2, IRF4, HERC2, MC1R, OCA2, SLC24A4, SLC24A5, SLC45A2, TYR) were associated with 391 DNAm sites across 30 genomic regions. We selected 25 DNAm sites for further analysis.

We examined the effect of the chosen DNAm sites on pigmentation traits, sun exposure phenotypes, and skin cancer, and on gene expression in whole blood. We found an association of decreased DNAm at cg07402062 with red hair in the Avon Longitudinal Study of Parents and Children (ALSPAC), and a strong positive association of DNAm at this and correlated sites with higher expression ofSPIRE2. Additionally, we investigated the association of gene expression in skin with pigmentation traits and skin cancer. The expression ofASIP,FAM83C,NCOA6,CDK10, andEXOC2was associated with hair colour, whilst that ofASIPandCDK10also had an effect on melanoma and BCC.

Conclusions

Our results indicate that DNAm and expression of genes in the 16q24.3 and 20q11.22 regions, deserve to be further investigated as potential mediators of the relationship between genetic variants, pigmentation/sun exposure phenotypes, and some types of skin cancer.
Unequivocal mapping of molecular ether lipid species by LC-MS/MS in plasmalogen-deficient mice
Authors: Koch Jakob , Lackner Katharina , Wohlfarter Yvonne , Sailer Sabrina , Zschocke Johannes , Werner Ernst R. , Watschinger Katrin , Keller Markus A.
Published: April 2020

Deficient ether lipid biosynthesis in rhizomelic chondrodysplasia punctata and other disorders is associated with a wide range of severe symptoms including small stature with proximal shortening of the limbs, contractures, facial dysmorphism, congenital cataracts, ichthyosis, spasticity, microcephaly, and mental disability. Mouse models are available but show less severe symptoms. In both humans and mice it has remained elusive which of the symptoms can be attributed to lack of plasmanyl or plasmenyl ether lipids. The latter compounds, better known as plasmalogens, harbor a vinyl ether double bond conferring special chemical and physical properties. Discrimination between plasmanyl and plasmenyl ether lipids is a major analytical challenge, especially in complex lipid extracts with many isobaric species. Consequently, these lipids are often neglected also in recent lipidomic studies. Here we present a comprehensive LC-MS/MS based approach that allows unequivocal distinction of these two lipid subclasses based on their chromatographic properties. The method was validated using a novel plasmalogen-deficient mouse model which lacks plasmanylethanolamine desaturase and therefore cannot form plasmenyl ether lipids. We demonstrate that plasmanylethanolamine desaturase deficiency causes an accumulation of plasmanyl species, a little studied but biologically important substance class.
Biochemically diverse CRISPR-Cas9 orthologs
Authors: Gasiunas Giedrius , Young Joshua K. , Karvelis Tautvydas , Kazlauskas Darius , Urbaitis Tomas , Jasnauskaite Monika , Grusyte Mantvyda , Paulraj Sushmitha , Wang Po-Hao , Hou Zhenglin , Dooley Shane K. , Cigan Mark , Alarcon Clara , Chilcoat N. Doane , Bigelyte Greta , Curcuru Jennifer L. , Mabuchi Megumu , Sun Zhiyi , Fuchs Ryan T. , Schildkraut Ezra , Weigele Peter R. , Jack William E. , Robb G. Brett , Venclovas Česlovas , Siksnys Virginijus
Published: April 2020

CRISPR-Cas9 nucleases are abundant in microbes. To explore this largely uncharacterized diversity, we applied cell-free biochemical screens to rapidly assess the protospacer adjacent motif (PAM) and guide RNA (gRNA) requirements of novel Cas9 proteins. This approach permitted the characterization of 79 Cas9 orthologs with at least 7 distinct classes of gRNAs and 50 different PAM sequence requirements. PAM recognition spanned the entire spectrum of T-, A-, C-, and G-rich nucleotides ranging from simple di-nucleotide recognition to complex sequence strings longer than 4. Computational analyses indicated that most of this diversity came from 4 groups of interrelated sequences providing new insight into Cas9 evolution and efforts to engineer PAM recognition. A subset of Cas9 orthologs were purified and their activities examined further exposing additional biochemical diversity. This constituted both narrow and broad ranges of temperature dependence, staggered-end DNA target cleavage, and a requirement for longer stretches of homology between gRNA and DNA target to function robustly. In all, the diverse collection of Cas9 orthologs presented here sheds light on Cas9 evolution and provides a rich source of PAM recognition and other potentially desirable properties that may be mined to expand the genome editing toolbox with new RNA-programmable nucleases.
Fluorogenic probe for fast 3D whole-cell DNA-PAINT
Authors: Chung Kenny KH , Zhang Zhao , Kidd Phylicia , Zhang Yongdeng , Williams Nathan D , Rollins Bennett , Yang Yang , Lin Chenxiang , Baddeley David , Bewersdorf Joerg
Published: April 2020

DNA-PAINT is an increasingly popular super-resolution microscopy method that can acquire high-fidelity images at nanometer resolution. It suffers, however, from high background and very slow imaging speed, both of which can be attributed to the presence of unbound fluorophores in solution. We present a fluorogenic DNA-PAINT probe that solves these problems and demonstrate 3D imaging without the need for optical sectioning and a 26-fold increase in imaging speed over regular DNA-PAINT.
Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax
Authors: Daron J. , Boissière A. , Boundenga L. , Ngoubangoye B. , Houze S. , Arnathau C. , Sidobre C. , Trape J.-F. , Durant P. , Renaud F. , Fontaine M.C. , Prugnolle F. , Rougeron V.
Published: April 2020

Plasmodium vivaxis the most prevalent and widespread human malaria parasite, with almost three billion people living at risk of infection. With the discovery of its closest genetic relatives in African great apes (Plasmodium vivax-like), the origin ofP. vivaxhas been proposed to be located in the sub-Saharan African area. However, the limited number of genetic markers and samples investigated questioned the robustness of this result. Here, we examined the population genomic variation of 447 humanP. vivaxstrains and 19 apeP. vivax-likestrains originating from 24 different countries across the world. We identified 2,005,455 high quality single-nucleotide polymorphism loci allowing us to conduct an extensive characterization to date ofP. vivaxworldwide genetic variation. Phylogenetic relationships between human and apePlasmodiumrevealed thatP. vivaxis a sister clade ofP. vivax-like, not included within the radiation ofP. vivax-like. By investigating a variety of aspects ofP. vivaxvariation, we identified several striking geographical patterns in summary statistics as function of increasing geographic distance from Southeast Asia, suggesting thatP. vivaxmay derived from serial founder effects from a single origin located in Asia.
InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes
Authors: Karpe Snehal D. , Tiwari Vikas , Ramanathan Sowdhamini
Published: April 2020

Insect Olfactory Receptors (ORs) are diverse family of membrane protein receptors responsible for most of the insect olfactory perception and communication, and hence they are of utmost importance for developing repellents or pesticides. Hence, accurate gene prediction of insect ORs from newly sequenced genomes is an important but challenging task. We have developed a dedicated web-server, ‘insectOR’, to predict and validate insect OR genes using multiple gene prediction algorithms, accompanied by relevant validations. It is possible to employ this sever nearly automatically and perform rapid prediction of the OR gene loci from thousands of OR-protein-to-genome alignments, resolve gene boundaries for tandem OR genes and refine them further to provide more complete OR gene models. InsectOR outperformed the popular genome annotation pipelines (MAKER and NCBI eukaryotic genome annotation) in terms of overall sensitivity at base, exon and locus level, when tested on two distantly related insect genomes. It displayed more than 95% nucleotide level precision in both tests. Finally, given the same input data and parameters, InsectOR missed less than 2% gene loci, in contrast to 55% loci missed by MAKER forDrosophila melanogaster. The web-server is freely available on the web athttp://caps.ncbs.res.in/insectOR/. All major browsers are supported. Website is implemented in Python with Jinja2 for templating and bootstrap framework which uses HTML, CSS and JavaScript/Ajax. The core pipeline is written in Perl.
Empowering Virus Sequences Research through Conceptual Modeling
Authors: Bernasconi Anna , Canakoglu Arif , Pinoli Pietro , Ceri Stefano
Published: April 2020

The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology).

VCM is inspired by GCM, our previously developed Genomic Conceptual Model, but it introduces many novel concepts, as viral sequences significantly differ from human genomes. When applied to SARS-CoV2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research.

In addition to VCM, we also illustrate the data dictionary for patient’s phenotype used by the COVID-19 Host Genetic Initiative. Our effort is part of a broad vision: availability of conceptual models for both human genomics and viruses will provide important opportunities for research, especially if interconnected by the same human being, playing the role of virus host as well as provider of genomic and phenotype information.
Cryo-EM of mammalian PA28αβ-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28αβ
Authors: Chen Jinhuan , Wang Yifan , Xu Cong , Peng Chao , Ding Zhanyu , Cong Yao
Published: April 2020

The proteasome activator PA28αβ affects MHC class-I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, how PA28αβ regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αβ-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determined the spatial arrangement between PA28αβ and iCP through XL-MS. Our structures revealed a slight leaning of PA28αβ towards the α3-α4 side of iCP, disturbing the allosteric network of the gate-keeper α2/3/4 subunits, resulting in a partial open iCP gate. We found that the binding and activation mechanism of iCP by PA28αβ is distinct from those of constitutive CP by the homoheptamericTbPA26 orPfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αβ-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response.
MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data
Authors: Gatto Laurent , Gibb Sebastian , Rainer Johannes
Published: April 2020

We present version 2 of theMSnbaseR/Bioconductor package.MSnbaseprovides infrastructure for the manipulation, processing and visualisation of mass spectrometry data. We focus on the newon-diskinfrastructure, that allows the handling of large raw mass spectrometry experiments on commodity hardware and illustrate how the package is used for elegant data processing, method development, and visualisation.
Persistent thermal input controls steering behavior inCaenorhabditis elegans
Authors: Ikeda Muneki , Matsumoto Hirotaka , Izquierdo Eduardo J.
Published: April 2020

Motile organisms actively detect environmental signals and migrate to a preferable environment. Especially, small-size animals convert subtle difference in sensory input into orientation behavioral output for directly steering toward a destination, but the neural mechanisms underlying steering behavior remain elusive. Here, we analyze aC. elegansthermotactic behavior in which a small number of neurons are shown to mediate steering toward a destination temperature. We construct a neuroanatomical model and use an evolutionary algorithm to find configurations of the model that reproduce empirical thermotactic behavior. We find that, in all the evolved models, steering rates are modulated by persistent thermal signals sensed through forward locomotion. Persistent temperature increment lessens steering rates resulting in straight movement of model worms, whereas temperature decrement enlarges steering rates resulting in curvy movement. This relationship between temperature change and steering rates reproduces the empirical thermotactic migration up thermal gradients and steering bias toward higher temperature. Further, spectrum decomposition of neural activities in model worms show that thermal signals are transmitted from a sensory neuron to motor neurons on the longer time scale than sinusoidal locomotion ofC. elegans. Our results suggest that employments of persistent sensory signals enable small-size animals to steer toward a destination in natural environment with variable, noisy, and subtle cues.

Author summary

A free-living nematodeCaenorhabditis elegansmemorizes an environmental temperature and steers toward the remembered temperature on a thermal gradient. How does theC. elegansbrain, consisting of 302 neurons, achieve this thermotactic steering behavior? Here, we address this question through neuroanatomical modeling and simulation analyses. We find that persistent thermal input modulates steering rates of model worms; worms run straight when they move up to a destination temperature, whereas run crookedly when move away from the destination. As a result, worms steer toward the destination temperature as observed in experiments. Our analysis also shows that persistent thermal signals are transmitted from a thermosensory neuron to dorsal and ventral neck motor neurons, regulating the balance of dorsoventral muscle contractions of model worms and generating steering behavior. This study indicates thatC. eleganscan steer toward a destination temperature without processing acute thermal input that informs to which direction it should steer. Such indirect mechanism of steering behavior is potentially employed in other motile organisms.
A Model Selection Approach to Hierarchical Shape Clustering with an Application to Cell Shapes
Authors: Mirshahi Mina , Partovi-Nia Vahid , Asgharian Masoud
Published: April 2020

Shape is an important phenotype of living species that contain different environmental and genetic information. Clustering living cells using their shape information can provide a preliminary guide to their functionality and evolution. Hierarchical clustering and dendrograms, as a visualization tool for hierarchical clustering, are commonly used by practitioners for classification and clustering. The existing hierarchical shape clustering methods are distance based. Such methods often lack a proper statistical foundation to allow for making inference on important parameters such as the number of clusters, often of prime interest to practitioners. We take a model selection perspective to clustering and propose a shape clustering method through linear models defined on Spherical Harmonics expansions of shapes. We introduce a BIC-type criterion, called CLUSBIC, and study consistency of the criterion. Special attention is paid to the notions of over- and under-specified models, important in studying model selection criteria and naturally defined in model selection literature. These notions do not automatically extend to shape clustering when a model selection perspective is adopted for clustering. To this end we take a novel approach using hypothesis testing. We apply our proposed criterion to cluster a set of real 3D images from HeLa cell line.
Toward the pathogenicity of the SLC26A4 p.C565Y variant using a genetically driven mouse model
Authors: Hu Chin-Ju , Lu Ying-Chang , Yang Ting-Hua , Chan Yen-Hui , Tsai Cheng-Yu , Yu I-Shing , Lin Shu-Wha , Liu Tien-Chen , Cheng Yen-Fu , Wu Chen-Chi , Hsu Chuan-Jen
Published: April 2020

Recessive variants of the SLC26A4 gene are a common cause of hearing impairment worldwide. In the past, cell lines and transgenic mice have been widely used to investigate the pathogenicity associated with the SLC26A4 variants. However, discrepancies in the pathogenicity between humans and cell lines or transgenic mice have been documented for some of the SLC26A4 variants. For instance, the p.C565Y variant, which has been reported to be pathogenic in humans, did not exhibit functional pathogenic consequences in cell lines. To address the pathogenicity of p.C565Y, we used a genotype-based approach in which we generated knock-in mice heterozygous (Slc26a4+/C565Y), homozygous (Slc26a4C565Y/C565Y), and compound heterozygous (Slc26a4919-2A>G/C565Y) for this variant. Subsequent phenotypic characterization revealed that mice segregating these genotypes demonstrated normal auditory and vestibular functions and normal inner ear morphology and expression of pendrin. These findings indicate that the p.C565Y variant is non-pathogenic for mice and that a single p.C565Y allele is sufficient to maintain normal inner ear physiology in mice. Our results highlight the differences in the pathogenicity associated with certain SLC26A4 variants between transgenic mice and humans, which should be taken into consideration while interpreting the results of animal studies for SLC26A4-related deafness.
Scarless removal of large resistance island AbaR results in antibiotic susceptibility and increased natural transformability inAcinetobacter baumannii
Authors: Godeux Anne-Sophie , Svedholm Elin , Lupo Agnese , Haenni Marisa , Laaberki Maria-Halima , Charpentier Xavier
Published: April 2020

With a great diversity in gene composition including multiple putative antibiotic-resistance genes, AbaR islands are potential contributors to multi-drug resistance inAcinetobacter baumannii. However, the effective contribution of AbaR to antibiotic resistance and bacterial physiology remains elusive. To address this, we sought to accurately remove AbaR islands and restore the integrity of their insertion site. To this end, we devised a versatile scarless genome editing strategy. We performed this genetic modification in two recentA. baumanniiclinical strains: the strain AB5075 and the nosocomial strain AYE which carry AbaR11 and AbaR1 islands of 19.7 kbp and 86.2 kbp, respectively. Antibiotic susceptibilities were then compared between the parental strains and their AbaR-cured derivatives. As anticipated by the predicted function of the ORF of this island, the antibiotic resistance profiles were identical between the wild type and the AbaR11-cured AB5075 strains. In contrast, AbaR1 carries 25 ORFs with a predicted resistance to several classes of antibiotics and the AYE AbaR1-cured derivative showed restored susceptibility to multiple classes of antibiotics. Moreover, curing of AbaRs restored high levels of natural transformability. Indeed, most AbaR islands are inserted into thecomMgene involved in natural transformation. Our data indicate that AbaR insertion effectively inactivatescomMand that the restoredcomMis functional. Curing of AbaR consistently resulted in highly transformable, and therefore, easily genetically tractable strains. Emendation of AbaR provides insight into the functional consequences of AbaR acquisition.
Polyploidy of semi-cloned embryos generated from parthenogenetic haploid embryonic stem cells
Authors: Aizawa Eishi , Dumeau Charles-Etienne , Freimann Remo , Di Minin Giulio , Wutz Anton
Published: April 2020

In mammals, the fusion of two gametes, an oocyte and a spermatozoon, during fertilization forms a totipotent zygote. There has been no reported case of natural parthenogenesis, in which embryos develop from unfertilized oocytes. The genome and epigenetic information of haploid gametes are crucial for the proper development of embryos. Haploid embryonic stem cells (haESCs) are unique stem cells established from uniparental blastocysts and possess only one set of chromosomes. Previous studies have shown that sperm or oocyte genome can be replaced by haESCs with or without manipulation of genomic imprinting for generation of mice. Recently, these remarkable semi-cloning methods have been applied for screening of key factors of mouse embryonic development. While haESCs have been applied as substitute of gametic genome, the fundamental mechanism how haESCs contribute to the genome of totipotent embryos is unclear. Here, we show the generation of fertile semi-cloned mice by injection of parthenogenetic haESCs (phaESCs) into oocytes after deletions of two differentially methylated regions (DMRs), theIG-DMR andH19-DMR. For characterizing the genome of semi-cloned embryos further we establish ESC lines from semi-cloned blastocysts. We report that polyploid karyotypes are observed frequently in semi-cloned ESCs (scESCs). Our results confirm that mitotically arrested phaESCs provide high efficiency for semi-cloning when theIG-DMR andH19-DMR are deleted. In addition, we highlight the occurrence of polyploidy that needs to be considered for further improvement for development of semi-cloned embryos derived by haESC injection.
Hyperiid amphipods from the Gulf of Ulloa and offshore region, Baja California: Intermittent use of the coastal shelf
Authors: Lavaniegos Bertha E.
Published: April 2020

Hyperiid amphipod species from the Gulf of Ulloa, Baja California, and the adjacent region (from shelf break to 200 km offshore) were analyzed in order to evaluate diversity and abundances in this productive area that supports small-scale commercial fisheries such as barred sand bass (Paralabrax nebulifer), California spiny lobster (Panulirus interruptus), abalones, clams, and others. Strong coastal upwelling events were observed during summer seasons of the period 2002-2008 between Punta Eugenia and Punta Abreojos. The upwelling plumes at Punta Abreojos are projected southward in slope waters bordering the coastal shelf of the Gulf of Ulloa, contributing to the separation of coastal and oceanic regions, and explain differences in amphipod diversity and abundances. In the offshore region, the most abundant species wereVibilia armata, Lestrigonus schizogeneios, Primno brevidens, andEupronoe minuta, similar to previous findings in northern regions of Baja California and southern California. However, their abundances were lower (between 10 and 30 individuals/1000 m3), only reaching 20-50% of abundance levels reported off northern Baja California. In the coastal shelf of the Gulf of Ulloa, amphipods were virtually absent during 2002, 2003 and 2006. However, during 2004 and 2005, abundances ofP. brevidensincreased (54 and 20 ind/1000 m3, respectively). Moreover, during 2007, abundances ofL. schizogeneios, P. brevidens, Lycaea nasuta, Lycaea pulex, andSimorhynchotus antennariusincreased considerably (261, 39, 31, 68, 416 ind/1000 m3, respectively), indicating occasional utilization of the coastal shelf by pelagic amphipods. Gelatinous organisms paralleled changes in hyperiid populations and were particularly abundant in 2007 in the coastal shelf. Significant correlations of 17 amphipod species with gelatinous taxa, which are often used as host organisms by hyperiid amphipods, suggest that those organisms enhanced hyperiid abundance and promoted the progression onto the coastal shelf during some years of the 2002-2008 period.