bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolic profiling of mulberry (Morus alba) wine fermented using Saccharomyces cerevisiae JIS strain
Authors: Jang Man Saeng , Lee Geo Lyong
Published: May 2020

GC/MS coupled with multivariate statistical analysis was performed to investigate metabolic differences between mulberry wines fermented with Saccharomyces cerevisiae JIS (KCCM 43338), Saccharomyces cerevisiae K1-V1116, and Saccharomyces bayanus EC-1118. The mulberry samples were crushed, and equal volumes of water were added to the must. Sugar was then added to adjust the must to 22.5 °Brix. Following fermentation of the mulberry fruit using different yeasts, differences in the consumption of soluble solids were observed during fermentation, but the final ethanol concentrations in the wines were similar for all samples, ranging from 10.4% to 11.4%. In addition, the glucose intensities of the fermented wines were similar for all samples. Following alcohol fermentation, principal component analysis and partial least squares-discriminant analysis score plots showed a clear separation, indicating that the metabolites of mulberry wine differed depending on the yeast employed. The obtained results therefore show that the different yeasts employed for wine production exert a strong influence on the metabolic profile of the wine. Furthermore, it was confirmed that Saccharomyces cerevisiae JIS can be used as a yeast for wine production. This study highlights the applicability of GC/MS-based metabolomics for evaluating the metabolic profiles of mulberry wine during fermentation.
Effects of innate immunity improvement in Lycii
radicis Cortex extract
Authors: Sim Boo-Yong , Ji Joong-Gu
Published: May 2020

The effects of Lycii Radicis Cortex extract (LRC) on improvements in the innate
immunity were evaluated in both in vitro and in vivo tests. Thus, various
concentrations of LRC were used for the treatment of RAW 264.7 and NK cells. In
addition, LRC was administered orally at doses of 100 or 300 mg/kg/day for 2
weeks prior to an intraperitoneal injection of LPS (1 mg/kg of 0.9%
saline). Following the LPS-intraperitoneal injection, blood was collected after
90 min by cardiac puncture under ether anaesthesia from all animals, and
verification of the immune regulation efficacy was carried out based on blood or
serum biomarker analysis. Compared to the control, LRC did not exhibit toxicity
in RAW 264.7 cells, and it was found to increase the activity of NK cells. In
the in vivo tests, LRC treatment significantly increased the count of immune
cells (i.e., white blood cell levels, neutrophils, and monocyte counts), but no
changes were observed for the lymphocyte content. In addition, LRC treatment
significantly reduced the levels of pro-inflammatory cytokines, such as
IL-1β, IL-6, and TNF-ɑ, and significantly increased the levels of
anti-inflammatory cytokines, such a IL-10. Furthermore, LRC treatment
significantly increased the levels of ROS, LTB4, and PGE2,
Overall, the obtained results indicate that LRC alleviated the acute
inflammatory reaction though an improvement in the innate immunity. Thus, LRC
may be considered a potential raw material for the development health foods to
enhance the innate immunity.
Automatic Detection of COVID-19 Infection from Chest X-ray using Deep Learning
Authors: Medhi kishore , Jamil Md. , Hussain Iftekhar
Published: May 2020

COVID-19 infection has created a panic across the globe in recent times. Early detection of COVID-19 infection can save many lives in the pre-vailing situation. This virus affects the respiratory system of a person and creates white patchy shadows in the lungs. Deep learning is one of the most effective Artificial Intelligence techniques to analyse chest X-ray images for efficient and reliable COVID-19 screening. In this paper, we have proposed a Deep Convolutional Neural Network method for fast and dependable identification of COVID-19 infection cases from the patient chest X-ray images. To validate the performance of the proposed system, chest X-ray images of more than 150 confirmed COVID-19 patients from the Kaggle data repository are used in the experimentation. The results show that the proposed system identifies the cases with an accuracy of 93%.
FLEXIQuant-LF: Robust Regression to Quantify Protein Modification Extent in Label-Free Proteomics Data
Authors: Kahnert Konstantin , Schlaffner Christoph N. , Muntel Jan , Chauhan Ruchi , Renard Bernhard Y. , Steen Judith A. , Steen Hanno
Published: May 2020

Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without prior knowledge of the type of modification. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.
Multi-scale modeling shows that dielectric differences make NaV channels faster than KV channels
Authors: Catacuzzeno Luigi , Sforna Luigi , Franciolini Fabio , Eisenberg Robert S.
Published: May 2020

The generation of action potentials in excitable cells requires different activation kinetics of voltage gated Na (NaV) and K (KV) channels. NaV channels activate much faster and allow the initial Na+ influx that generates the depolarizing phase and propagates the signal. Recent experimental results suggest that the molecular basis for this kinetic difference is an amino acid side chain located in the gating pore of the voltage sensor domain, which is a highly conserved isoleucine in KV channels, but an equally highly conserved threonine in NaV channels. Mutagenesis suggests that the hydrophobicity of this side chain in Shaker KV channels regulates the energetic barrier that gating charges need to overcome to move through the gating pore, and ultimately the rate of channel opening. We use a multi-scale modeling approach to test this hypothesis. We use high resolution molecular dynamics to study the effect of the mutation on polarization charge within the gating pore. We then incorporate these results in a lower resolution model of voltage gating to predict the effect of the mutation on the movement of gating charges. The predictions of our hierarchical model are fully consistent with the tested hypothesis, thus suggesting that the faster activation kinetics of NaV channels comes from a stronger dielectric polarization by threonine (NaV channel) produced as the first gating charge enters the gating pore, compared to isoleucine (KV channel).

eTOC Summary

Voltage-gated Na+ channels activate faster than K+ channels in excitable cells. Catacuzzeno et al. develop a model that shows how the dielectric properties of a divergent side-chain produce this difference in speed.
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
Authors: Shen Xing-Xing , Steenwyk Jacob L. , LaBella Abigail L. , Opulente Dana A. , Zhou Xiaofan , Kominek Jacek , Li Yuanning , Groenewald Marizeth , Hittinger Chris Todd , Rokas Antonis
Published: May 2020

Ascomycota, the largest and best-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts); organisms from all three subphyla have been invaluable as models in diverse fields (e.g., biotechnology, cell biology, genetics, and medicine). Despite its importance, we still lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. To address these gaps, we examined 1,107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species to infer the Ascomycota phylogeny, estimate its timetree, and examine the evolution of key genomic properties. We inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran (~563 ± 68 million years ago). Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina, the two taxon-rich subphyla, differed greatly in their genome properties. Saccharomycotina typically have smaller genomes, lower GC contents, lower numbers of genes, and higher rates of molecular sequence evolution compared to Pezizomycotina. Ancestral state reconstruction showed that the genome properties of the Saccharomycotina and Pezizomycotina last common ancestors were very similar, enabling inference of the direction of evolutionary change. For example, we found that a lineage-specific acceleration led to a 1.6-fold higher evolutionary rate in Saccharomycotina, whereas the 10% difference in GC content between Saccharomycotina and Pezizomycotina genomes stems from a trend toward AT bases within budding yeasts and toward GC bases within filamentous fungi. These results provide a robust evolutionary framework for understanding the diversification of the largest fungal phylum.
Effects of the GluN2B antagonist, Ro 25-6981, on extinction consolidation following adolescent- or adult-onset methamphetamine self-administration in male and female rats
Authors: Westbrook Sara R. , Gulley Joshua M.
Published: May 2020

Previous work suggests adolescent rats have deficient extinction consolidation relative to adults. Although the mechanisms underlying this age difference are currently unknown, studies in adult rats have implicated GluN2B-containing NMDA receptor function in extinction consolidation of drug-associated memory. Importantly, GluN2B neurotransmission emerges during adolescent development, and drugs of abuse during adolescence may delay the development of extinction consolidation by disrupting the ontogeny of GluN2B function. Here, we trained Sprague-Dawley rats of both sexes to self-administer methamphetamine (METH, 0.1 mg/kg/infusion i.v.) beginning during adolescence [postnatal (P) day 41] or adulthood (P91). Rats were given short access (2 h) to self-administer METH in seven daily sessions followed by fourteen sessions with long access (6 h). Subsequently, rats underwent four daily 30-min extinction sessions with immediate post-session injections of either a GluN2B antagonist (Ro25-6981; 6 mg/kg, i.p.) or a vehicle solution. After four daily 2-h extinction sessions, a priming injection (1 mg/kg METH, i.p.) was given prior to a final 2-h reinstatement session. During LgA, adolescent-onset rats earn more METH than adult-onset rats and display greater drug-loading behavior. Rats reduced their drug-seeking behavior across extinction sessions, with no significant group differences. Rats reinstated drug-seeking following the METH priming injection, with females displaying greater reinstatement than males. These results do not support oura priorihypothesis that adolescent-onset METH use disrupts the ontogeny of GluN2B transmission and contributes to age-of-onset differences in extinction of METH-seeking. However, our findings suggest that age-of-onset contributes to excessive METH-taking, while sex confers vulnerability to relapse to METH-seeking.
A growth-based, high-throughput selection platform enables remodeling of 4-hydroxybenzoate hydroxylase active site
Authors: Maxel Sarah , Aspacio Derek , King Edward , Zhang Linyue , Acosta Ana Paula , Li Han
Published: May 2020

We report an aerobic, growth-based selection platform founded on NADP(H) redox balance restoration inEscherichia coli, and demonstrate its application in high-throughput evolution of oxygenase. A single round of selection enabledPseudomonas aeruginoasa4-hydroxybenzoate hydroxylase (PobA) to accept 3,4-dihydroxybenzoic acid efficiently, an essential step toward gallic acid biosynthesis. The best variant DA015 exhibited more than 5-fold higher catalytic efficiency compared to previously engineered enzymes. Structural modeling suggests precise re-organization of active site hydrogen bond network, which is difficult to obtain without deep navigation of combinatorial sequence space. We envision universal application of this selection platform in engineering NADPH-dependent oxidoreductases.
Listeria monocytogenespersonalized cancer vaccines drive therapeutic immune responses to cancer derived neoantigens
Authors: Coder Brandon , Pryshchep Olga , Kelkar Dipti , Filippova Elena , Ju Xiaoming , Balli David , Mottershead Cristina , Ramos Kim , Thambi Nithya , Cheng Zhiyong , Lugt Bryan Vander , Lesch Justin , Liu Xian , DeVoss Jason , Cooke Keegan , Liu Siyuan , Zhan Jinghui , Mitchell Petia , Villarreal Daniel O , Hayes Sandra M. , Johnston James A , Petit Robert , Phee Hyewon , Princiotta Michael F.
Published: May 2020

Background

Recent advances in the field of cancer immunotherapy have identified CD8+T cell responses against tumor-specific mutations as a key driver of tumor regression and overall survival. ADXS-NEO is a personalizedListeria monocytogenes(Lm)-based immunotherapy designed to target a patient’s mutation-derived tumor-specific neoantigens. The objective of this study is to demonstrate the feasibility of using the ADXS-NEO platform to target tumor-specific point mutations and control tumor growth by generating neoantigen-specific T cell responses using a pre-clinical mouse tumor model.

Methods

Whole-exome sequencing of the MC38 mouse tumor cell line identified 2870 unique non-synonymous mutations. The netMHCcons algorithm was used to predict 137 potential neoantigens. We validated 20 immunogenic neoantigens either by peptide immunization followed by ELISPOT or by the presence of CD8+T cells recognizing the neoantigen peptide following checkpoint inhibitor treatment. Two ADXS-NEO vectors were constructed; Lm20, targeting 20 validated immunogenic neoantigens, and Lm19, targeting most of the non-validated NSMs.

Results

Both Lm19 & Lm20 significantly slowed tumor growth in C57BL/6 mice compared to control. An accumulation of ADXS-NEO-specific TILs was observed in tumor bearing mice treated with either Lm19 or Lm20. Examination of the tumor microenvironment in Lm19 or Lm20 treated mice revealed a decrease in the frequency and absolute number of Tregs, TAMs, MDSCs, and PD1highexhausted CD8+T cells as well as an increase in the frequency and absolute number of effector CD8+T cells, relative to control.

Conclusion

ADXS-NEO is a potent immunotherapy capable of driving immune responses against tumor-specific mutations and leading to tumor control in mice.
Leukemia cell of origin influences apoptotic priming and sensitivity to LSD1 inhibition
Authors: Cai Sheng F. , Chu S. Haihua , Goldberg Aaron D. , Parvin Salma , Koche Richard P. , Glass Jacob L. , Stein Eytan M. , Tallman Martin S. , Sen Filiz , Famulare Christopher , Cusan Monica , Huang Chun-Hao , Chen Chun-Wei , Zou Lihua , Cordner Keith B. , DelGaudio Nicole L. , Durani Vidushi , Kini Mitali , Rex Madison , Tian Helen S. , Zuber Johannes , Baslan Timour , Lowe Scott W. , Rienhoff Hugh Y. , Letai Anthony , Levine Ross L. , Armstrong Scott A.
Published: May 2020

Previous studies have established that the cell of origin of oncogenic transformation is a determinant of therapeutic sensitivity. However, the mechanisms governing cell-of-origin-driven differences in therapeutic response have not been delineated. Leukemias initiating in hematopoietic stem cells (HSC) are less sensitive to cytotoxic chemotherapy and express high levels of the transcription factorEvi1compared to leukemias derived from myeloid progenitors. Here, we compared drug sensitivity and expression profiles of murine and human leukemias initiated in either HSCs or myeloid progenitors to reveal a novel function forEvi1in modulating p53 protein stability and activity. HSC-derived leukemias exhibit decreased apoptotic priming, attenuated p53 transcriptional output, and resistance to lysine-specific demethylase 1 inhibitors in addition to classical genotoxic stresses. p53 loss-of-function inEvi1lowprogenitor-derived leukemias induces resistance to LSD1 inhibition. By contrast,Evi1highleukemias are sensitized to LSD1 inhibition by the BH3 mimetic venetoclax, resulting in enhanced apoptosis and greater reductions in disease burden. Our findings demonstrate a cell-of-origin determined novel role forEVI1in p53 wild-type cancers in reducing p53 function and provide a strategy to circumvent drug resistance in high-risk, chemoresistantEVI1highAML.
Neural encoding of task-dependent errors during adaptive learning
Authors: Kao Chang-Hao , Lee Sangil , Gold Joshua I. , Kable Joseph W.
Published: May 2020

Effective learning requires using errors in a task-dependent manner, for example adjusting to errors that result from unpredicted environmental changes but ignoring errors that result from environmental stochasticity. Where and how the brain represents errors in a task-dependent manner and uses them to guide behavior are not well understood. We imaged the brains of human participants performing a predictive-inference task with two conditions that had different sources of errors. Their performance was sensitive to this difference, including more choice switches after fundamental changes versus stochastic fluctuations in reward contingencies. Using multi-voxel pattern classification, we identified task-dependent representations of error magnitude and past errors in posterior parietal cortex. These representations were distinct from representations of the resulting behavioral adjustments in dorsomedial frontal, anterior cingulate, and orbitofrontal cortex. The results provide new insights into how the human brain represents errors in a task-dependent manner and guides subsequent adaptive behavior.
Molecular Basis for N-terminal Alpha-Synuclein Acetylation by Human NatB
Authors: Deng Sunbin , Pan Buyan , Gottlieb Leah , Petersson E. James , Marmorstein Ronen
Published: May 2020

NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in Parkinson’s disease pathogenesis and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA andCandida albicansNatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes.
Amplification lags nonlinearity in the recovery from reduced endocochlear potential
Authors: Strimbu C. Elliott , Wang Yi , Olson Elizabeth S.
Published: May 2020

The mammalian hearing organ, the cochlea, contains an active amplifier to boost the vibrational response to low level sounds. Hallmarks of this active process are sharp location-dependent frequency tuning and compressive nonlinearity over a wide stimulus range. The amplifier relies on outer hair cell (OHC) generated forces driven in part by the endocochlear potential (EP), the ~ +80 mV potential maintained in scala media, generated by the stria vascularis. We transiently eliminated the EP in vivo by an intravenous injection of furosemide and measured the vibrations of different layers in the cochlea’s organ of Corti using optical coherence tomography. Distortion product otoacoustic emissions (DPOAE) were monitored at the same times. Following the injection, the vibrations of the basilar membrane lost the best frequency (BF) peak and showed broad tuning similar to a passive cochlea. The intra-organ of Corti vibrations measured in the region of the OHCs lost their BF peak and showed low-pass responses, but retained nonlinearity, indicating that OHC electromotility was still operational. Thus, while electromotility is presumably necessary for amplification, its presence is not sufficient for amplification. The BF peak recovered nearly fully within 2 hours, along with a non-monotonic DPOAE recovery that suggests that physical shifts in operating condition are a final step in the recovery process.

SIGNIFICANCE

The endocochlear potential, the +80 mV potential difference across the fluid filled compartments of the cochlea, is essential for normal mechanoelectrical transduction, which leads to receptor potentials in the sensory hair cells when they vibrate in response to sound. Intracochlear vibrations are boosted tremendously by an active nonlinear feedback process that endows the cochlea with its healthy sensitivity and frequency resolution. When the endocochlear potential was reduced by an injection of furosemide, the basilar membrane vibrations resembled those of a passive cochlea, with broad tuning and linear scaling. The vibrations in the region of the outer hair cells also lost the tuned peak, but retained nonlinearity at frequencies below the peak, and these sub-BF responses recovered fairly rapidly. Vibration responses at the peak recovered nearly fully over 2 hours. The staged vibration recovery and a similarly staged DPOAE recovery suggests that physical shifts in operating condition are a final step in the process of cochlear recovery.
NLRP3 controls ATM activation in response to DNA damage
Authors: Bodnar-Wachtel Mélanie , Huber Anne-Laure , Gorry Julie , Hacot Sabine , Gerossier Laetitia , Guey Baptiste , Goutagny Nadège , Bartosch Birke , Ballot Elise , Ghiringhelli François , Py Bénédicte F. , Coute Yohann , Ballesta Annabelle , Lantuejoul Sylvie , Hall Janet , Petrilli Virginie
Published: May 2020

The DNA damage response (DDR) is essential to preserve genomic integrity and acts as a barrier to cancer. The ATM pathway orchestrates the cellular response to DNA double strand breaks (DSBs), and its attenuation is frequent during tumorigenesis. Here, we show that NLRP3, a Pattern Recognition Receptor known for its role in the inflammasome complex formation, interacts with the ATM kinase to control the early phase of DDR, independently of its inflammasome activity. NLRP3 down-regulation in human bronchial epithelial cells impairs ATM pathway activation as shown by an altered ATM substrate phosphorylation profile, and due to impaired p53 activation, confers resistance to acute genomic stress. Moreover, we found that NLRP3 is down-regulated in Non-Small Cell Lung Cancer (NSCLC) tissues and NLRP3 expression is correlated with patient overall survival. NLRP3 re-expression in NSCLC cells restores appropriate ATM signaling. Our findings identify a non-immune function for NLRP3 in genome integrity surveillance and strengthen the concept of a functional link between innate immunity and DNA damage sensing pathways.
SORBS2is a genetic factor contributing to cardiac malformation of 4q deletion syndrome
Authors: Liang Fei , Zhang Xiaoqing , Wang Bo , Geng Juan , You Guoling , Fa Jingjing , Sun Huiying , Chen Huiwen , Fu Qihua , Zhang Zhen
Published: May 2020

Chromosome 4q deletion is one of the most frequently detected genomic imbalance events in congenital heart disease (CHD) patients. However, a portion of CHD-associated 4q deletions do not include known CHD genes. Alignment of those 4q deletions defined a minimal overlapping region including only one gene-SORBS2. Histological analysis ofSorbs2-/-heart revealed atrial septal hypoplasia/aplasia or double atrial septum. Mechanistically,SORBS2had a dual role in maintaining sarcomeric integrity of cardiomyocytes and specifying the fate of second heart field (SHF) progenitors through c-ABL/NOTCH/SHH axis. In a targeted sequencing of a panel of known and candidate CHD genes on 300 CHD cases, we found that rareSORBS2variants were significantly enriched in CHD patients. Our findings indicate thatSORBS2is a regulator of cardiac development and its haploinsufficiency may contribute to cardiac phenotype of 4q deletion syndrome. The presence of double atrial septum inSorbs2-/-hearts reveals the first molecular etiology of this rare anomaly linked to paradoxical thromboembolism.
Human follicular CD4 T cell function is defined by specific molecular, positional and TCR dynamic signatures
Authors: Padhan Kartika , Moysi Eirini , Noto Alessandra , Chassiakos Alexander , Ghneim Khader , Shah Sanjana , Papaioannou Vasilis , Fabozzi Giulia , Ambrozak David , Poultsidi Antigoni , Ioannou Maria , Fenwik Craig , Darko Samuel , Douek Daniel C. , Sekaly Rafick-Pierre , Pantaleo Giuseppe , Koup Richard A. , Petrovas Constantinos
Published: May 2020

The orchestrated interaction between follicular helper CD4 T cells (TFH) and germinal center (GC) B cells is crucial for optimal humoral immunity. However, the regulatory mechanisms behind spatial distribution and function of TFH is not well understood. Here, we studied human TFH cells and found that transitioning to a CD57hiTFH status was associated with distinct positioning in the GC, phenotype, transcriptional signatures, function and downregulation of their T-cell receptor (TCR). Single cell TCR clonotype analysis indicated a unidirectional transition towards the CD57hiTFH status, which was marked with drastic changes in the nature of immunological synapse formation where peripheral microclusters become dominant. Lack of central supra molecular activation cluster (cSMAC) formation in TFH synapse was associated with enhanced ubiquitination/proteasome activity in these cells. Our data reveal significant aspects of the tissue organization and heterogeneity of follicular adaptive immunity and suggest that CD57hiTFH cells are endowed with distinctive programming and spatial positioning for optimal GC B cell help.

One Sentence Summary

human TFH cell heterogeneity
Insights into the genetic architecture of the human face
Authors: White Julie D. , Indencleef Karlijne , Naqvi Sahin , Eller Ryan J. , Roosenboom Jasmien , Lee Myoung Keun , Li Jiarui , Mohammed Jaaved , Richmond Stephen , Quillen Ellen E. , Norton Heather L. , Feingold Eleanor , Swigut Tomek , Marazita Mary L. , Peeters Hilde , Hens Greet , Shaffer John R. , Wysocka Joanna , Walsh Susan , Weinberg Seth M. , Shriver Mark D. , Claes Peter
Published: May 2020

The human face is complex and multipartite, and characterization of its genetic architecture remains intriguingly challenging. Applying GWAS to multivariate shape phenotypes, we identified 203 genomic regions associated with normal-range facial variation, 117 of which are novel. The associated regions are enriched for both genes relevant to craniofacial and limb morphogenesis and enhancer activity in cranial neural crest cells and craniofacial tissues. Genetic variants grouped by their contribution to similar aspects of facial variation show high within-group correlation of enhancer activity, and four SNP pairs display evidence of epistasis, indicating potentially coordinated actions of variants within the same cell types or tissues. In sum, our analyses provide new insights for understanding how complex morphological traits are shaped by both individual and coordinated genetic actions.
Strain-dependent modifier genes determine survival inZfp423mice
Authors: Alcaraz Wendy A. , Liu Zheng , Valdes Phoebe , Chen Edward , Valdovino Gonzalez Alan G. , Wade Shelby , Wong Cinny , Kim Eunnie , Chen Hsiang-Hua M. , Ponn Alison , Concepcion Dorothy , Hamilton Bruce A.
Published: May 2020

Zfp423encodes a transcriptional regulatory protein that interacts with canonical signaling and lineage pathways. Mutations in mouseZfp423or its human orthologZNF423are associated with a range of developmental abnormalities reminiscent of ciliopathies, including cerebellar vermis hypoplasia and other midline brain defects. Null mice have reduced viability in most strain backgrounds. Here we show complete lethality on a C57BL/6J background, dominant rescue in backcrosses to any of 13 partner strains, with strain-dependent survival frequencies, and evidence for a BALB/c-derived survival modifier locus on chromosome 5. Survival data indicate both perinatal and postnatal periods of lethality. Anatomical data from a hypomorphic gene trap allele observed on both C57BL/6J and BALB/c congenic backgrounds shows an aggregate effect of background on sensitivity to Zfp423 loss rather than a binary effect on viability.
The role of conidia in the dispersal of Ascochyta rabiei
Authors: Khaliq Ihsanul , Fanning Joshua , Melloy Paul , Galloway Jean , Moore Kevin , Burrell Daniel , Sparks Adam H
Published: May 2020

Ascochyta rabiei asexual spores (conidia) were assumed to spread over short distances (∼10 m) in a combination of rain and strong wind. The potential distance of conidial spread was investigated in three rainfall and three sprinkler irrigation events. Chickpea trap plants were distributed at the distances of 0, 10, 25, 50 and 75 m from infected chickpea plots before scheduled irrigation and forecast rainfall events. Trap plants were transferred to a controlled temperature room (20 °C) for 48 h (100% humidity) after being exposed in the field for 2–6 days for rainfall events, and for one day for irrigation events. After a 48 h incubation period, trap plants were transferred to a glasshouse (20 °C) to allow lesion development. Lesions on all plant parts were counted after two weeks, which gave an estimate of the number of conidia released and the distance travelled. Trap plants at all distances were infected in all sprinkler irrigation and rainfall events. The highest number of lesions on trap plants were recorded closest to the infected plots – the numbers decreased as the distance from the infected plots increased. There was a positive relationship between the amount of rainfall and the number of lesions recorded. A generalised additive model was developed that efficiently described spatial patterns of conidial spread. With further development, the model can be used to predict the spread of A. rabiei. This is the first systematic study to show that conidia distribute A. rabiei over longer distances than previously reported.
Conserved anti-inflammatory effects and sensing of butyrate in zebrafish
Authors: Cholan Pradeep Manuneedhi , Han Alvin , Woodie Brad R , Kurz Angela RM , Britton Warwick J , Ye Lihua , Holmes Zachary C , McCann Jessica R , David Lawrence A , Rawls John F , Oehlers Stefan H
Published: May 2020

Short chain fatty acids (SCFAs) are produced by microbial fermentation of dietary fiber in the gut. Butyrate is a particularly important SCFA with anti-inflammatory properties and is generally present at lower levels in inflammatory diseases associated with gut microbiota dysbiosis in mammals. We aimed to determine if SCFAs are produced by the zebrafish microbiome and if SCFAs exert conserved effects on zebrafish immunity as an example of the non-mammalian vertebrate immune system. We demonstrate that bacterial communities from adult zebrafish intestines synthesize all three main SCFAin vitro, although SCFA were below our detectable limits in zebrafish intestinesin vivo. Immersion in butyrate, but not acetate or propionate, reduced the recruitment of neutrophils and M1-type pro-inflammatory macrophages to wounds. We found conservation of butyrate sensing by neutrophils via orthologs of thehydroxycarboxylic acid receptor 1(hcar1) gene. Neutrophils from Hcar1-depeleted embryos were no longer responsive to the anti-inflammatory effects of butyrate, while macrophage sensitivity to butyrate was independent of Hcar1. Our data demonstrate conservation of anti-inflammatory butyrate effects and identify the presence of a conserved molecular receptor in fish.
Predicting Parallelism and Quantifying Divergence in Experimental Evolution
Authors: Shoemaker William R. , Lennon Jay T.
Published: May 2020

The degree that the environment determines what genes contribute towards adaptation is a fundamental question in microbial evolution. Microbial populations are often experimentally passaged in different environments and sequenced in order to identify candidates for adaptation in a particular environment. However, there remains the need to develop an appropriate statistical framework to identify genes that acquired more mutations in one environment over the other (i.e., divergent evolution). Here we demonstrate how the evolutionary outcomes among replicate populations in the same environment, known as parallel evolution, can be leveraged to construct an intuitive statistical test for identifying the genes that contribute towards divergent evolution. To accomplish this task, we examined publicly available evolve-and-resequence experiment datasets and found that the distribution of mutation counts among genes can be predicted using an ensemble of independent Poisson random variables. Building on this result, we propose that the degree of divergent evolution at a given gene between populations from two different environments can be modeled as the difference between two Poisson random variables, known as the Skellam distribution. We then propose and apply a statistical test to identify specific genes that contribute towards divergent evolution. IMPORTANCE: There is currently no existing framework that can be leveraged to identify genes that contribute towards divergent evolution in microbial evolution experiments. To correct for this absence, we investigated the distribution of mutation counts among genes in order to identify an appropriate null model. Our observations suggest that divergent evolution within a given gene can be modeled as the difference in the total number of mutations observed between two environments. This quantity is described by a probability distribution known as the Skellam distribution, providing an appropriate statistical test for researchers seeking to identify the set of genes that contribute towards divergent evolution in evolution experiments.
Recombination proteins differently control the acquisition of homeologous DNA duringBacillus subtilisnatural chromosomal transformation
Authors: Serrano Ester , Ramos Cristina , Alonso Juan C. , Ayora Silvia
Published: May 2020

In naturally competentBacillus subtiliscells the acquisition of closely related genes occursviahomology-directed chromosomal transformation (CT), and its frequency decreases log-linearly with increased sequence divergence (SD) up to 15%. Beyond this and up to 23% SD the interspecies boundary prevails, the CT frequency marginally decreases, and short (<10-nucleotides) segments are integratedviahomology-facilitated micro-homologous integration. Both poorly known CT mechanisms are RecA-dependent. Here we identify the recombination proteins required for the acquisition of interspecies DNA. The absence of AddAB, RecF, RecO, RuvAB or RecU, crucial for repair-by-recombination, does not affect CT. However, inactivation ofdprA, radA, recJ, recXorrecD2strongly interfered with CT. Interspecies CT was abolished beyond ~8% SD in ΔdprA, ~10% in ΔrecJ, ΔradA, ΔrecXand 14% in ΔrecD2cells. We propose that DprA, RecX, RadA/Sms, RecJ and RecD2 help RecA to unconstrain speciation and gene flow. These functions are ultimately responsible for generating genetic diversity and facilitate CT and gene acquisition from bacteria of the same genus.
SIRPα on mouse B1 cells restricts lymphoid tissue migration and natural antibody production
Authors: Franke Katka , Pillai Saravanan Y. , Hoogenboezem Mark , Gijbels Marion J.J. , Matlung Hanke , Geissler Judy , Olsman Hugo , Pottgens Chantal , van Gorp Patrick J. , Ozsvar-Kozma Maria , Saito Yasuyuki , Matozaki Takashi , Kuijpers Taco W. , Hendriks Rudi W. , Kraal Georg , Binder Christoph J. , de Winther Menno P.J. , van den Berg Timo K.
Published: May 2020

The inhibitory immunoreceptor SIRPα is expressed on myeloid and neuronal cells and interacts with the broadly expressed CD47. CD47-SIRPα interactions form an innate immune checkpoint and its targeting has shown promising results in cancer patients. Here, we report expression of SIRPα on B1 lymphocytes, a non-conventional subpopulation of murine B cells responsible for the production of natural antibodies. Mice defective in SIRPα signaling (SIRPαΔCYTmice) displayed an enhanced CD11b/CD18 integrin-dependent B1 cell migration from the peritoneal cavity to the spleen, local B1 cell accumulation, and enhanced circulating natural antibody levels, which was further amplified upon immunization with T-independent type 2 antigen. As natural antibodies are atheroprotective we investigated the involvement of SIRPα signaling in atherosclerosis development. Bone marrow (SIRPαΔCYT>LDLR−/−) chimaeric mice developed reduced atherosclerosis accompanied by increased natural antibody production. Collectively, our data identify SIRPα as a unique B1 cell inhibitory receptor acting to control B1 cell migration, and imply SIRPα as a potential therapeutic target in atherosclerosis.
Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection
Authors: Das Asim Bikas
Published: May 2020

Higher mortality of COVID19 patients with comorbidity is the formidable challenge faced by the health care system. In response to the present crisis, understanding the molecular basis of comorbidity is essential to accelerate the development of potential drugs. To address this, we have measured the genetic association between COVID19 and various lung disorders and observed a remarkable resemblance. 141 lung disorders directly or indirectly linked to COVID19 result in a high-density disease-disease association network that shows a small-world property. The clustering of many lung diseases with COVID19 demonstrates a greater complexity and severity of SARS-CoV-2 infection. Furthermore, our results show that the functional protein-protein interaction modules involved RNA and protein metabolism, substantially hijacked by SARS-CoV-2, are connected to several lung disorders. Therefore we recommend targeting the components of these modules to inhibit the viral growth and improve the clinical conditions in comorbidity.
Convergence in sympatry: evolution of blue-banded wing pattern inMorphobutterflies
Authors: Llaurens V , Le Poul Y , Puissant A , Noûs C , Blandin P , Debat V
Published: May 2020

Species interactions such as mimicry can promote trait convergence but disentangling this effect from those of shared ecology, evolutionary history and niche conservatism is often challenging. Here by focusing on wing color pattern variation within and between three butterfly species living in sympatry in a large proportion of their range, we tested the effect of species interactions on trait diversification. These butterflies display a conspicuous iridescent blue coloration on the dorsal side of their wings and a cryptic brownish colour on the ventral side. Combined with an erratic and fast flight, these color patterns increase the difficulty of capture by predators and contribute to the high escape abilities of these butterflies. We hypothesize that, beyond their direct contribution to predator escape, these wing patterns can be used as signals of escape abilities by predators, resulting in positive frequency-dependent selection favouring convergence in wing pattern in sympatry. To test this hypothesis, we quantified dorsal wing pattern variations of 723 butterflies from the three species sampled throughout their distribution, including sympatric and allopatric situations and compared the phenotypic distances between species, sex and localities. We detected a significant effect of localities on colour pattern, and higher inter-specific resemblance in sympatry as compared to allopatry, consistent with the hypothesis of local convergence of wing patterns. Our results provide some support to the existence of escape mimicry in the wild and stress the importance of estimating trait variation within species to understand trait variation between species, and to a larger extent, trait diversification at the macro-evolutionary scale.
Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples
Authors: Fajardo Álvaro , Pereira-Gómez Marianoel , Echeverría Natalia , López-Tort Fernando , Perbolianachis Paula , Aldunate Fabián , Moreno Pilar , Moratorio Gonzalo
Published: May 2020

The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low and middle income countries. In the interest of economy, time and availability of chemicals and consumables, the SYBR Green-based detection was implemented to establish a convenient assay. Therefore, we adapted one of WHO recommended Taqman-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results suggest that SYBR-Green detection represents a reliable cost-effective alternative to increase the testing capacity.
PHERI - Phage Host Exploration pipeline
Authors: Baláž Andrej , Kajsík Michal , Budiš Jaroslav , Szemeš Tomáš , Turňa Ján
Published: May 2020

Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multi-resistant bacterial strains occurring in all world regions. One of the possible future solutions is the use of bacteriophages in therapy. Bacteriophages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm based tool called PHERI. PHERI predicts suitable bacterial host genus for purification of individual viruses from different samples. Besides, it can identify and highlight protein sequences that are important for host selection. PHERI is available athttps://hub.docker.com/repository/docker/andynet/pheri. The source code for the model training is available athttps://github.com/andynet/pheri_preprocessing, and the source code for the tool is available athttps://github.com/andynet/pheri.
A point mutation inTtc26causes lumbar spinal cord fusion and synchronous hind-limb locomotion inhopmice
Authors: Bernhardt Nadine , Memic Fatima , Velica Anna , Tran Michelle A. , Vieillard Jennifer , Chersa Taha , Andersson Leif , Whelan Patrick J. , Boije Henrik , Kullander Klas
Published: May 2020

Identifying the spinal circuits controlling locomotion is critical for unravelling the mechanisms controlling the production of gaits. Development of the circuits governing left-right coordination relies on axon guidance molecules such as ephrins and netrins. To date, no other class of proteins have been shown to play a role during this process. Here we have analyzedhopmice, which walk with a characteristic hopping gait using their hind legs in synchrony. Fictive locomotion experiments suggest that a local defect in the ventral spinal cord contributes to the aberrant locomotor phenotype.Hopmutant spinal cords had severe morphological defects, including the absence of the ventral midline and a poorly defined border between white and grey matter. Thehopmice represent the first model where the left and right central pattern generators (CPGs) are fused to form one central CPG, with a synchronous gait as a functional consequence. These defects were exclusively found in the lumbar domain and were associated with abnormal developmental processes, including a misplaced notochord and reduced induction of ventral progenitor domains. While the underlying mutation inhopmice has been suggested to lie withinTtc26, other genes in close vicinity have been associated with gait defects. By replicating the point mutation withinTtc26, employing CRISPR technology, we observed mice with an identical phenotype, thereby verifying the hop mutation. Thus, we show that the assembly of the lumbar CPG network is dependent on a fully functional TTC26 protein.
Dynamic phenotypic heterogeneity generated by delayed genetic oscillations
Authors: Peña-Miller R. , Arnoldini M. , Ackermann M. , Beardmore R. E.
Published: May 2020

Eukaryotes and prokaryotes exploit the ability of genetically identical cells to exhibit different phenotypes in order to enhance their survival. However, the mechanisms by which cells transition from one phenotype to another remain unclear. Canonical models of this dynamic posit that molecular fluctuations provide the noise that drives the cell out of one stable state and into another. Stochastic processes generated by canonical models should, therefore, be good descriptors of phenotype dynamics and between-state transitions should become more likely at greater noise amplitude, for instance at higher extracellular temperatures. To test these predictions, we observed temporal expression dynamics of the promoter of a flagellum gene,fliC, in a microfluidic device usingSalmonella entericaserovar Typhimurium and green fluorescent protein (GFP). Our observations show that while cells can exhibit multistable phenotypes, including stablefliC-OFF andfliC-ON states characterised by low and high GFP levels, respectively, between-state transitions can exhibit oscillatory dynamics whose return statistics do not conform to canonical theories. For example, here thefliC-ON state was more frequent following a temperature increase. To better understand our data we developed different dynamical frameworks to predictfliCexpression data. We conclude that a stochastic dynamical system tailored to the genetic network offliCis better suited to our data than prior theories where dynamical features, like oscillations and pulsing, are driven by inevitable delays in the post-translational regulation offliC. Thus, while transcriptional noise promotes phenotypic heterogeneity, as we show here, regular features like oscillatory heterogeneity can result from delays that fundamental molecular processes impose upon a cell’s gene regulatory architecture.