bluuebunny/crossref_metadata_2025 huggingface dataset:
Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations
Authors: Panero Riccardo , Arigoni Maddalena , Olivero Martina , Cordero Francesca , Weisz Alessandro , Beccuti Marco , Renzo Mariaflavia Di , Calogero Raffaele A.
Published: April 2018

Background

RNA-seq represents an attractive methodology for the detection of functional genomic variants because it allows the integration of variant frequency and their expression. However, although specific statistic frameworks have been designed to detect SNVs/INDELS/gene fusions in RNA-seq data, very little has been done to understand the effect of library preparation protocols on transcript variant detection in RNA-seq data.

Results

Here, we compared RNA-seq results obtained on short reads sequencing platform with two protocols: one based on polyA+ RNA selection protocol (POLYA) and the other based on exonic regions capturing protocol (ACCESS). Our data indicate that ACCESS detects 10% more coding SNV/INDELs with respect to POLYA, making this protocol more suitable for this goal. Furthermore, ACCESS requires less reads for coding SNV detection with respect to POLYA. On the other hand, if the analysis aims at identifying SNV/INDELs also in the 5’and 3’ UTRs, POLYA is definitively the preferred method. No particular advantage comes from the usage of ACCESS or POLYA in the detection of fusion transcripts.

Conclusion

Data show that a careful selection of the “wet” protocol adds specific features that cannot be obtained with bioinformatics alone.
The Use of Visual Cues in Gravity Judgements on Parabolic Motion
Authors: Jörges Björn , Slupinski Lena , López-Moliner Joan
Published: April 2018

Evidence suggests that humans rely on an earth gravity prior for sensory-motor tasks like catching or reaching. Even under earth-discrepant conditions, this prior biases perception and action towards assuming a gravitational downwards acceleration of 9.81 m/s2. This can be particularly detrimental in interactions with virtual environments employing earth-discrepant gravity conditions for their visual presentation. The present study thus investigates how well humans discriminate visually presented gravities and which cues they use to extract gravity from the visual scene. To this end, we employed a Two-Interval Forced-Choice Design. In Experiment 1, participants had to judge which of two presented parabolas had the higher underlying gravity. We used two initial vertical velocities, two horizontal velocities and a constant target size. Experiment 2 added a manipulation of the reliability of the target size. Experiment 1 shows that participants have generally high discrimination thresholds for visually presented gravities, with weber fractions of 13 to beyond 30 %. We identified the rate of change of the elevation angle (ẏ) and the visual angle (θ) as major cues. Experiment 2 suggests furthermore that size variability has a small influence on discrimination thresholds, while at the same time larger size variability increases reliance on ẏ and decreases reliance on θ. All in all, even though we use all available information, humans display low precision when extracting the governing gravity from a visual scene, which might further impact our capabilities of adapting to earth-discrepant gravity conditions with visual information alone.
E proteins differentially co-operate with proneural bHLH transcription factors to sharpen neurogenesis
Authors: Dréau Gwenvael Le , Escalona René , Fueyo Raquel , Herrera Antonio , Martínez Juan D. , Usieto Susana , Menendez Anghara , Pons Sebastián , Martínez-Balbás Marian A. , Martí Elisa
Published: April 2018

Basic HLH proteins heterodimerize with class I HLH/E proteins to promote transcription. Here we show that E proteins differentially co-operate with proneural bHLH transcription factors sharpening their neurogeneic activity. We find that inhibiting BMP signaling or its target ID2, in the chick embryo spinal cord, impairs the neuronal production from progenitors expressing ATOH1/ASCL1, but less severely that from progenitors expressing NEUROG1/2/PTF1a. We define the mechanisms of this differential response as a dual co-operation of E proteins with proneural proteins. E proteins synergize with bHLH proteins when acting on CAGSTG motifs, thereby facilitating the neurogenic activity of ASCL1/ATOH1 which preferentially bind to such motifs. Conversely, E proteins restrict the strong neurogenic potential of NEUROG1/2 by directly inhibiting their preferential binding to CADATG motifs. Since we find this mechanism to be conserved in corticogenesis, we propose this dual co-operation of E proteins with bHLH proteins as a novel though general feature of their mechanism of action.
Epigenetic regulation of the circadian genePer1in the hippocampus mediates age-related changes in memory and synaptic plasticity
Authors: Kwapis Janine L. , Alaghband Yasaman , Kramár Enikö A. , López Alberto J. , Ciernia Annie Vogel , White André O. , Shu Guanhua , Rhee Diane , Michael Christina M. , Montellier Emilie , Liu Yu , Magnan Christophe N. , Sassone-Corsi Paolo , Baldi Pierre , Matheos Dina P. , Wood Marcelo A.
Published: April 2018

Aging is accompanied by impairments in both circadian rhythmicity and long-term memory. Although it is clear that memory performance is affected by circadian cycling, it is unknown whether age-related disruption of the circadian clock causes impaired hippocampal memory. Here, we show that the repressive histone deacetylase HDAC3 restricts long-term memory, synaptic plasticity, and learning-induced expression of the circadian genePer1in the aging hippocampus without affecting rhythmic circadian activity patterns. We also demonstrate that hippocampalPer1is critical for long-term memory formation. Together, our data challenge the traditional idea that alterations in the core circadian clock drive circadian-related changes in memory formation and instead argue for a more autonomous role for circadian clock gene function in hippocampal cells to gate the likelihood of long-term memory formation.
npphen: an R-package for non-parametric reconstruction of vegetation phenology and anomaly detection using remote sensing
Authors: Estay Sergio A. , Chávez Roberto O.
Published: April 2018

For ecologists, the challenge at using remote sensing tools is to convert spectral data into ecologically relevant information like abundance, productivity or traits distribution. Among these features, plant phenology is one of the most used variables in any study applying remote sensing to plant ecology and it has formally considered as one of the Essential Biodiversity Variables. Currently, satellite imagery make possible cost-efficient monitoring of land surface phenology (LSP), but methods applicable to different ecosystems are not available. Here, we introduce the ‘npphen’ R-package developed for remote sensing LSP reconstruction and anomaly detection using non-parametric techniques. The package implements basic and high-level functions for manipulating vector and raster data to obtain high resolution spatial and temporal LSP reconstructions. Advantages of ‘npphen’ are: its flexibility to describe any LSP pattern (suitable for any ecosystem), it handles time series or raster stacks with and without gaps, and it provides confidence interval for the expected LSP at yearly basis, useful to judge anomaly magnitudes. We present two study cases to show how ‘npphen’ can successfully reconstruct and map LSP and anomalies for contrasting ecosystems.
Searching Algorithm for Type IV Effector proteins (S4TE) 2.0: improved tools for type IV effector prediction, analysis and comparison
Authors: Noroy Christophe , Lefrançois Thierry , Meyer Damien F.
Published: April 2018

Bacterial pathogens have evolved numerous strategies to corrupt, hijack or mimic cellular processes in order to survive and proliferate. Among those strategies, Type IV effectors (T4Es) are proteins secreted by pathogenic bacteria to manipulate host cell processes during infection. They are delivered into eukaryotic cells in an ATP-dependent manner via the type IV secretion system, a specialized multiprotein complex. T4Es contain a wide spectrum of features including eukaryotic-like domains, localization signals or a C-terminal translocation signal. A combination of these features enables prediction of T4Es in a given bacterial genome. In this study, we developed a web-based comprehensive suite of tools with a user-friendly graphical interface. This version 2.0 of S4TE (Searching Algorithm for Type IV Effector Proteins; http://sate.cirad.fr) enables accurate prediction and comparison of T4Es. Search parameters and threshold can be customized by the user to work with any genome sequence, whether publicly available or not. Applications range from characterizing effector features and identifying potential T4Es to analyzing the effectors based on the genome G+C composition and local gene density. S4TE 2.0 allows the comparison of putative T4E repertoires of up to four bacterial strains at the same time. The software identifies T4E orthologs among strains and provides a Venn diagram and lists of genes for each intersection. New interactive features offer the best visualization of the location of candidate T4Es and hyperlinks to NCBI and Pfam databases. S4TE 2.0 is designed to evolve rapidly with the publication of new experimentally validated T4Es, which will reinforce the predictive power of the algorithm. The computational methodology can be used to identify a wide spectrum of candidate bacterial effectors that lack sequence conservation but have similar amino acid characteristics. This approach will provide very valuable information about bacterial host-specificity and virulence factors, and help identify host targets for the development of new anti-bacterial molecules.
Schizophrenia-related cognitive dysfunction in the Cyclin-D2 knockout mouse model of ventral hippocampal hyperactivity
Authors: Grimm Christina M. , Aksamaz Sonat , Schulz Stefanie , Teutsch Jasper , Sicinski Piotr , Liss Birgit , Kätzel Dennis
Published: April 2018

Elevated activity at the output stage of the anterior hippocampus has been described as a physiological endophenotype of schizophrenia, and its development maps onto the transition from its prodromal to its psychotic state. Interventions that halt the spreading glutamatergic over-activity in this region and thereby the development of overt schizophrenia could be promising therapies. However, animal models with high construct validity to support such pre-clinical development are scarce. The Cyclin-D2 knockout (CD2-KO) mouse model shows a hippocampal Parvalbumin-interneuron dysfunction and its pattern of hippocampal over-activity shares similarities with that seen in prodromal patients. In a comprehensive phenotyping of CD2-KO mice, we found that they displayed novelty-induced hyperlocomotion (a correlate in the positive symptom domain), that was largely resistant against D1- and D2-dopamine receptor antagonism, but responsive to the mGluR2/3-agonist LY379268. In the negative symptom domain, CD2-KO mice showed transiently reduced sucrose-preference (anhedonia), but enhanced interaction with novel mice and objects, as well as normal nest building and incentive motivation. Also, unconditioned anxiety, perseveration, and motor impulsivity were unaltered. However, in the cognitive domain, CD2-knockouts showed reduced executive function in assays of rule-shift and rule-reversal learning, but also an impairment in working memory, that was resistant against LY379268. In contrast, sustained attention and forms of spatial and object-related memory that are mediated by short-term habituation of stimulus-specific attention were intact. Our results suggest, that CD2-KO mice are a valuable model in translational research targeted at the pharmacoresistant cognitive symptom domain in causal relation to hippocampal over-activity in the prodrome-to-psychosis transition.
Intrinsic cooperativity potentiates parallel cis-regulatory evolution
Authors: Sorrells Trevor R , Johnson Amanda N , Howard Conor J , Britton Candace S , Fowler Kyle R , Feigerle Jordan T , Weil P Anthony , Johnson Alexander D
Published: April 2018

Convergent evolutionary events in independent lineages provide an opportunity to understand why evolution favors certain outcomes over others. We studied such a case, where a large set of genes—those coding for the ribosomal proteins—gained cis-regulatory sequences for a particular transcription regulator (Mcm1) in independent fungal lineages. We present evidence that these gains occurred because Mcm1 shares a mechanism of transcriptional activation with an ancestral regulator of the ribosomal protein genes, Rap1. Specifically, we show that Mcm1 and Rap1 have the inherent ability to cooperatively activate transcription through contacts with the general transcription factor TFIID. Because the two regulatory proteins share a common interaction partner, the presence of one ancestral cis-regulatory sequence can “channel” random mutations into functional sites for the second regulator. At a genomic scale, this type of intrinsic cooperativity can account for a pattern of parallel evolution involving the fixation of hundreds of substitutions.
Learning and Imputation for Mass-spec Bias Reduction (LIMBR)
Authors: Crowell Alexander M , Greene Casey S , Loros Jennifer J. , Dunlap Jay C
Published: April 2018

Motivation

Decreasing costs are making it feasible to perform time series proteomics and genomics experiments with more replicates and higher resolution than ever before. With more replicates and time points, proteome and genome-wide patterns of expression are more readily discernible. These larger experiments require more batches exacerbating batch effects and increasing the number of bias trends. In the case of proteomics, where methods frequently result in missing data this increasing scale is also decreasing the number of peptides observed in all samples. The sources of batch effects and missing data are incompletely understood necessitating novel techniques.

Results

Here we show that by exploiting the structure of time series experiments, it is possible to accurately and reproducibly model and remove batch effects. We implement Learning and Imputation for Mass-spec Bias Reduction (LIMBR) software, which builds on previous block based models of batch effects and includes features specific to time series and circadian studies. To aid in the analysis of time series proteomics experiments, which are often plagued with missing data points, we also integrate an imputation system. By building LIMBR for imputation and time series tailored bias modeling into one straightforward software package, we expect that the quality and ease of large-scale proteomics and genomics time series experiments will be significantly increased.

Contact

alexander.m.crowell@gmail.com, jay.c.dunlap@dartmouth.edu
Effects of duplicated mapped read PCR artifacts on RNA-seq differential expression analysis based on qRNA-seq
Authors: Salzberg Anna C. , Hu Jiafen , Conroy Elizabeth J. , Cladel Nancy M. , Brucklacher Robert M. , Bixler Georgina V. , Kawasawa Yuka Imamura
Published: April 2018

Best practices to handling duplicated mapped reads in RNA-seq analyses has long been discussed but a gold standard method has yet to be established, as such duplicates could originate from valid biological transcripts or they could be PCR-related artifacts. Here we used the NEXTflex™qRNA-SeqTM(aka Molecular Indexing™) technology to identify PCR duplicates via the random attachment of unique molecular labels to each cDNA molecule prior to PCR amplification. We found that up to 64.3% of the single end and 19.3% of the mouse paired end duplicates originated from valid biological transcripts rather than PCR artifacts. For single end reads, either removing or retaining all duplicates resulted in a substantial number of false positives (up to 47.0%) and false negatives (up to 12.1%) in the sets of significantly differentially expressed genes. For paired end reads, only the alignment retaining all duplicates resulted in a substantial number of false positives. This is the first effort to evaluate the performance of qRNA-seq using ‘real-world’ biomedical samples, and we found that PCR duplicate identification provided minor benefits for paired end reads but greatly improved the sensitivity and specificity in the determination of the significantly differentially expressed genes for single end reads.
Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT
Authors: Harvey Samuel E. , Xu Yilin , Lin Xiaodan , Gao Xin D. , Qiu Yushan , Ahn Jaegyoon , Xiao Xinshu , Cheng Chonghui
Published: April 2018

The epithelial-mesenchymal transition (EMT) is a fundamental developmental process that is abnormally activated in cancer metastasis. Dynamic changes in alternative splicing occur during EMT. ESRP1 and hnRNPM are splicing regulators that promote an epithelial splicing program and a mesenchymal splicing program, respectively. The functional relationships between these splicing factors in the genome-scale remain elusive. Comparing alternative splicing targets of hnRNPM and ESRP1 revealed that they co-regulate a set of cassette exon events, with the majority showing discordant splicing regulation. hnRNPM discordantly regulated splicing events show a positive correlation with splicing during EMT while concordant splicing events do not, highlighting the antagonistic role of hnRNPM and ESRP1 during EMT. Motif enrichment analysis near co-regulated exons identifies guanine-uridine rich motifs downstream of hnRNPM-repressed and ESRP1-enhanced exons, supporting a model of competitive binding to these cis-elements to antagonize alternative splicing. The set of co-regulated exons are enriched in genes associated with cell-migration and cytoskeletal reorganization, which are pathways associated with EMT. Splicing levels of co-regulated exons are associated with breast cancer patient survival and correlate with gene sets involved in EMT and breast cancer subtypes. These data identify complex modes of interaction between hnRNPM and ESRP1 in regulation of splicing in disease-relevant contexts.
The E3 ubiquitin ligase MIB-1 is necessary to form the nuclear halo inC. eleganssperm
Authors: Herrera Leslie A. , Starr Daniel A.
Published: April 2018

Unlike the classical nuclear envelope with two membranes found in other eukaryotic cells, most nematode sperm nuclei are not encapsulated by membranes. Instead, they are surrounded by a nuclear halo of unknown composition. How the halo is formed and regulated is unknown. We used forward genetics to identify molecular lesions behind three classicalfer(fertilization defective) mutations that disrupt the ultrastructure of theC. eleganssperm nuclear halo. We foundfer-2andfer-4alleles to be nonsense mutations inmib-1.fer-3was caused by a nonsense mutation ineri-3. GFP::MIB-1 was expressed in the germline during early spermatogenesis, but not in mature sperm.mib-1encodes a conserved E3 ubiquitin ligase homologous to vertebrate Mib1 and Mib2, which function in Notch signaling. However,C. elegans mib-1has no Notch-related phenotypes. Thus,mib-1has been co-opted to regulate the formation of the nuclear halo during nematode spermatogenesis.
Loss of charge at solvent exposed Lys residues does not induce the aggregation of superoxide dismutase 1
Authors: Crosby Keith , Crown Anthony M. , Roberts Brittany L. , Brown Hilda , Ayers Jacob I. , Borchelt David R.
Published: April 2018

Mutations in superoxide dismutase 1 (SOD1) associated with familial amyotrophic lateral sclerosis (fALS) induce the protein to misfold and aggregate. To date, missense mutations at more than 80 different amino acid positions have been associated with disease. How these mutations perturb native structure to heighten the propensity to misfold and aggregate is unclear. One potential mechanism that has been suggested is that when mutations occur at positions occupied by charged amino acids, then repulsive forces that would inhibit aberrant protein:protein interactions would be reduced. Mutations at twenty-one charged residues in SOD1 have been associated with fALS. Here, we examined whether loss of positively charged surface Lys residues would induce the misfolding and aggregation of SOD1. We randomly mutated four different Lys residues (K30, K36, K75, K91) in SOD1 and expressed these variants as fusion proteins with yellow fluorescent protein (YFP). We also assessed whether these mutations induced binding to a conformation-restricted SOD1 antibody, designated C4F6, which recognizes non-natively folded protein. Our findings indicate that SOD1 generally tolerates mutations at surface exposed lysine residues, and that loss of positive charge is insufficient to induce aggregation. Our findings may explain why mutations at these Lys residues have not been identified in ALS patients.
Vms1p is a release factor for the Ribosome-associated Quality control Complex
Authors: Rendón Olga Zurita , Fredrickson Eric K. , Howard Conor J. , Van Vranken Jonathan , Fogarty Sarah , Tolley Neal D. , Kalia Raghav , Osuna Beatriz A. , Shen Peter S. , Hill Christopher P. , Frost Adam , Rutter Jared
Published: April 2018

Eukaryotic cells employ the Ribosome-associated Quality control Complex (RQC) to maintain homeostasis despite defects that cause ribosomes to stall. The RQC comprises the E3 ubiquitin ligase Ltn1p, the ATPase Cdc48p, and the novel proteins Rqc1p and Rqc2p1–3. Following recognition and subunit splitting of stalled ribosomes, the RQC detects and assembles on 60S subunits that hold incomplete polypeptides linked to a tRNA (60S:peptidyl–tRNA)4–8. Ltn1p cooperates with Rqc1p to facilitate ubiquitination of the incomplete nascent chain, marking it for degradation7,9,10. Rqc2p stabilizes Ltn1p on the 60S3–5,8 and recruits charged tRNAs to the 60S to catalyze elongation of the nascent protein with Carboxy-terminal Alanine and Threonine extensions, or CAT tails, via a mechanism that is distinct from canonical translation4,10. CAT-tailing mobilizes and exposes lysine residues in the nascent chain, especially those stalled within the exit tunnel, thereby supporting efficient ubiquitination10,11. If the ubiquitin-proteasome system is overwhelmed or unavailable, CAT-tailed nascent chains aggregate in the cytosol or within organelles like the mitochondria12–14. Here we identify Vms1p as the tRNA hydrolase that releases nascent polypeptides for extraction and degradation in the RQC pathway.
MGDb: An analyzed database and a genomic resource of mango (Mangifera Indica L.) cultivars for mango research
Authors: Qamar-ul-Islam Tayyaba , Khan M. Ahmed , Faizan Rabia , Mahmood Uzma
Published: April 2018

Mango is one of the famous and fifth most important subtropical/tropical fruit crops worldwide with the production centered in India and South-East Asia. Recently, there has been a worldwide interest in mango genomics to produce tools for Marker Assisted Selection and trait association. There are no web-based analyzed genomic resources available for mango particularly. Hence a complete mango genomic resource was required for improvement in research and management of mango germplasm. In this project, we have done comparative transcriptome analysis of four mango cultivars i.e. cv. Langra, cv. Zill, cv. Shelly and cv. Kent from Pakistan, China, Israel, and Mexico respectively. The raw data is obtained through De-novo sequence assembly which generated 30,953-85,036 unigenes from RNA-Seq datasets of mango cultivars. The project is aimed to provide the scientific community and general public a mango genomic resource and allow the user to examine their data against our analyzed mango genome databases of four cultivars (cv. Langra, cv. Zill, cv. Shelly and cv. Kent). A mango web genomic resource MGdb, is based on 3-tier architecture, developed using Python, flat file database, and JavaScript. It contains the information of predicted genes of the whole genome, the unigenes annotated by homologous genes in other species, and GO (Gene Ontology) terms which provide a glimpse of the traits in which they are involved. This web genomic resource can be of immense use in the assessment of the research, development of the medicines, understanding genetics and provides useful bioinformatics solution for analysis of nucleotide sequence data. We report here world’s first web-based genomic resource particularly of mango for genetic improvement and management of mango genome.
Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates
Authors: Deatherage Daniel E. , Leon Dacia , Rodriguez Álvaro E. , Omar Salma K. , Barrick Jeffrey E.
Published: April 2018

Unwanted evolution of designed DNA sequences limits metabolic and genome engineering efforts. Engineered functions that are burdensome to host cells and slow their replication are rapidly inactivated by mutations, and unplanned mutations with unpredictable effects often accumulate alongside designed changes in large-scale genome editing projects. We developed a directed evolution strategy, Periodic Reselection for Evolutionarily Reliable Variants (PResERV), to discover mutations that prolong the function of a burdensome DNA sequence in an engineered organism. Here, we used PResERV to isolate E. coli cells that replicate ColE1 plasmids with higher fidelity. We found mutations in DNA polymerases I and IV and in RNase E that reduce plasmid mutation rates by 6-to 30-fold. The PResERV method implicitly selects to maintain the growth rate of host cells, and high plasmid copy numbers and gene expression levels are maintained in some of the evolved E. coli strains, indicating that it is possible to improve the genetic stability of cellular chassis without encountering trade-offs in other desirable performance characteristics. Utilizing these new antimutator E. coli and applying PResERV to other organisms in the future promises to prevent evolutionary failures and unpredictability to provide a more stable genetic foundation for synthetic biology.
Integrated proteogenomic analysis of metastatic thoracic tumors identifies APOBEC mutagenesis and copy number alterations as drivers of proteogenomic tumor evolution and heterogeneity
Authors: Roper Nitin , Gao Shaojian , Maity Tapan K. , Banday A. Rouf , Zhang Xu , Venugopalan Abhilash , Cultraro Constance M. , Patidar Rajesh , Sindiri Sivasish , Goncearenco Alexandr , Panchenko Anna R. , Biswas Romi , Thomas Anish , Rajan Arun , Carter Corey A. , Kleiner David , Hewitt Stephen , Khan Javed , Prokunina-Olsson Ludmila , Guha Udayan
Published: April 2018

Elucidation of the proteogenomic evolution of metastatic tumors may offer insight into the poor prognosis of patients harboring metastatic disease. We performed whole-exome and transcriptome sequencing, copy number alterations (CNA) and mass spectrometry-based quantitative proteomics of 37 lung adenocarcinoma (LUAD) and thymic carcinoma (TC) metastases obtained by rapid autopsy and found evidence of patient-specific, multi-dimensional heterogeneity. Extreme mutational heterogeneity was evident in a subset of patients whose tumors showed increased APOBEC-signature mutations and expression of APOBEC3 region transcripts compared to patients with lesser mutational heterogeneity. TP53 mutation status was associated with APOBEC hypermutators in our cohort and in three independent LUAD datasets. In a thymic carcinoma patient, extreme heterogeneity and increased APOBEC3AB expression was associated with a high-risk germline APOBEC3AB variant allele. Patients with CNA occurring late in tumor evolution had corresponding changes in gene expression and protein abundance indicating genomic instability as a mechanism of downstream transcriptomic and proteomic heterogeneity between metastases. Across all tumors, proteomic heterogeneity was greater than copy number and transcriptomic heterogeneity. Enrichment of interferon pathways was evident both in the transcriptome and proteome of the tumors enriched for APOBEC mutagenesis despite a heterogeneous immune microenvironment across metastases suggesting a role for the immune microenvironment in the expression of APOBEC transcripts and generation of mutational heterogeneity. The evolving, heterogeneous nature of LUAD and TC, through APOBEC-mutagenesis and CNA illustrate the challenges facing treatment outcomes.
Microevolution of aquaticStreptococcus agalactiaeST-261 from Australia indicates dissemination via imported tilapia and ongoing adaptation to marine hosts or environment
Authors: Kawasaki Minami , Delamare-Deboutteville Jerome , Bowater Rachel O , Walker Mark J , Beatson Scott , Zakour Nouri L Ben , Barnes Andrew C
Published: April 2018

Streptococcus agalactiae(GBS) causes disease in a wide range of animals. The serotype 1b lineage is highly adapted to aquatic hosts, exhibiting substantial genome reduction compared with terrestrial con-specifics. Here we sequence genomes from 40 GBS isolates including 25 from wild fish and captive stingrays in Australia, six local veterinary or human clinical isolates, and nine isolates from farmed tilapia in Honduras and compare with 42 genomes from public databases. Phylogenetic analysis based on non-recombinant core genome SNPs indicated that aquatic serotype Ib isolates from Queensland were distantly related to local veterinary and human clinical isolates. In contrast, Australian aquatic isolates are most closely related to a tilapia isolate from Israel, differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on core genome SNPs indicates dissemination of ST-261 from an ancestral tilapia strain, which is congruent with several introductions of tilapia into Australia from Israel during the 1970s and 1980s. Pan-genome analysis identified 1,440 genes as core with the majority being dispensable or strain-specific with non-protein-coding intergenic regions (IGRs) divided amongst core and strain-specific genes. Aquatic serotype Ib strains have lost many virulence factors during adaptation, but six adhesins were well conserved across the aquatic isolates and might be critical for virulence in fish and targets for vaccine development. The close relationship amongst recent ST-261 isolates from Ghana, USA and China with the Israeli tilapia isolate from 1988 implicates the global trade in tilapia seed for aquaculture in the widespread dissemination of serotype Ib fish-adapted GBS.

Importance

Streptococcus agalactiae(GBS) is a significant pathogen of humans and animals. Some lineages have become adapted to particular hosts and serotype Ib is highly specialized to fish. Here we show that this lineage is likely to have been distributed widely by the global trade in tilapia for aquaculture, with probable introduction into Australia in the 1970s and subsequent dissemination in wild fish populations. We report variability in the polysaccharide capsule amongst this lineage, but identify a cohort common surface proteins that may be a focus of future vaccine development to reduce the biosecurity risk in international fish trade.
Whole genome sequence analysis of 91SalmonellaEnteritidis isolates from mice caught on poultry farms in the mid 1990s
Authors: Guard Jean , Cao Guojie , Luo Yan , Baugher Joseph D. , Davison Sherrill , Yao Kuan , Hoffmann Maria , Zhang Guodong , Bell Rebecca , Zheng Jie , Brown Eric , Allard Marc
Published: April 2018

Salmonella entericaserovar Enteritidis (SE), the most commonly reported serovar of human salmonellosis, has been frequently associated with poultry farms, eggs and egg products. Mice are known vectors of SE contamination in these facilities. The objective of this study was to use whole-genome sequencing (WGS) to analyze SE from mice obtained at poultry farms in Pennsylvania. Documenting pathogen diversity can identify reliable biomarkers for rapid detection and speed up outbreak investigations. We sequenced 91 SE isolates from 83 mice (62 spleen isolates, 29 intestinal isolates) caught at 15 poultry farms between 1995-1998 using an Illumina NextSeq 500. We identified 742 single nucleotide polymorphisms (SNPs) capable of distinguishing each isolate from one another. Isolates were divided into two major clades: there were more SNPs differences within Clade B than counterparts in Clade A. All isolates containing antimicrobial resistance genes belong to Subgroup B2. Clade-defining SNPs provided biomarkers distinguishing isolates from 12 individual subgroups, which were separated by farm location or year of collection. Nonsynonymous changes from the clade-defining SNPs proffered a better understanding of possible genetic variations among these isolates. For a broader view of SE diversity, we included data from NCBI Pathogen Detection Isolates Browser, in which subgroups in Clade B formed new SNP Clusters.

Importance

WGS and SNPs analyses are excellent and powerful tools for investigating SE phylogenies. Identifying the evolutionary relationships among SE isolates from mouse, poultry, environmental, and clinical isolates, along with patterns of genetic diversity, advances understanding of SE and the role mice may play in SE contamination and spread among poultry population. Our data was able to identify SE isolates from different farms or years of collection. Moreover, the annotations of clade-defining SNPs provided information about possible protein functions among these SE isolates from each subgroup. Clade-defining or farm-unique biomarkers were useful for rapid detection and outbreak investigations.
BrucellaPeptide Cross-Reactive MHC I Presentation Activates SIINFEKL-Specific TCR Expressing T Cells
Authors: Harms Jerome S. , Khan Mike , Hall Cherisse , Splitter Gary A. , Homan E. Jane , Bremel Robert D. , Smith Judith A.
Published: April 2018

Brucella sppare intracellular pathogenic bacteria remarkable in their ability to escape immune surveillance and therefore inflict a state of chronic disease within the host. To enable further immune response studies,Brucellawere engineered to express the well characterized chicken ovalbumin (OVA). Surprisingly, we found that CD8 T cells bearing T cell receptors (TCR) nominally specific for the OVA peptide SIINFEKL (OT-1) reacted to parentalBrucella-infected targets as well as OVA-expressingBrucellavariants in cytotoxicity assays. Furthermore, splenocytes fromBrucellaimmunized mice produced IFN-γ and exhibited cytotoxicity in response to SIINFEKL-pulsed target cells. To determine if the SIINFEKL-reactive OT-1 TCR could be cross-reacting toBrucellapeptides, we searched theBrucellaproteome using an algorithm to generate a list of near-neighbor nonamer peptides that would bind to H2Kb. Selecting fiveBrucellapeptide candidates, along with controls, we verified that several of these peptides mimicked SIINFEKL resulting in T cell activation through the “SIINFEKL-specific” TCR. Activation was dependent on peptide concentration as well as sequence. Our results underscore the complexity and ubiquity of cross-reactivity in T cell recognition. This cross-reactivity may enable microbes such asBrucellato escape immune surveillance by presenting peptides similar to the host, and may also lead to the activation of autoreactive T cells.
Vitexin altersStaphylococcus aureussurface hydrophobicity to interfere with biofilm formation
Authors: Das Manash C. , Das Antu , Samaddar Sourabh , Daware Akshay Vishnu , Ghosh Chinmoy , Acharjee Shukdeb , Sandhu Padmani , Jawed Junaid Jibran , De Utpal C. , Majumdar Subrata , Gupta Sujoy K. Das , Akhter Yusuf , Bhattacharjee Surajit
Published: April 2018

Bacterial surface hydrophobicity is one of the determinant biophysical parameters of bacterial aggregation for being networked to form biofilm. Phytoconstituents like vitexin have long been in use for their antibacterial effect. The present work is aimed to characterise the effect of vitexin onS. aureussurface hydrophobicity and corresponding aggregation to form biofilm. We have found that vitexin shows minimum inhibitory concentration at 252 μg/ml againstS. aureus.Vitexin reduces cell surface hydrophobicity and membrane permeability at sub-MIC dose of 126 μg/ml. Thein silicobinding analysis showed higher binding affinity of vitexin with surface proteins ofS. aureus.Down regulation ofdltA,icaAB and reduction in membrane potential under sub-MIC dose of vitexin, explains reducedS. aureussurface hydrophobicity. Vitexin has substantially reduced the intracellular adhesion of planktonic cells to form biofilm through interference of EPS formation, motility and subsequent execution of virulence. This was supported by the observation that vitexin down regulates the expression oficaAB andagrAC genes ofS. aureus.In addition, vitexin also found to potentiate antibiofilm activity of sub-MIC dose of gentamicin and azithromycin. Furthermore, CFU count, histological examination of mouse tissue and immunomodulatory study justifies thein vivoprotective effect of vitexin fromS. aureusbiofilm associated infection. Finally it can be inferred that, vitexin has the ability to modulateS. aureuscell surface hydrophobicity which can further interfere biofilm formation of the bacteria.

Importance

There has been substantial information known about role of bacterial surface hydrophobicity during attachment of single planktonic bacterial cells to any surface and the subsequent development of mature biofilm. This study presents the effect of flavone phytoconstituent vitexin on modulation of cell surface hydrophobicity in reducing formation of biofilm. Our findings also highlight the ability of vitexin in reducingin vivo S. aureusbiofilm which will eventually outcompete the correspondingin vitroantibiofilm effect. Synergistic effect of vitexin on azithromycin and gentamicin point to a regime where development of drug tolerance may be addressed. Our findings explore one probable way of overcoming drug tolerance through application of vitexin in addressing the issue ofS. aureusbiofilm through modulation of cell surface hydrophobicity.
TP53I11 Suppresses Extracellular Matrix-independent Survival and Mesenchymal Transition in Mammary Epithelial Cells
Authors: Xiao Tongqian , Zhang Hai , Zhou Yuanshuai , Geng Junsa , Xu Zhongjuan , Liang Yu , Qiao Hong , Suo Guangli
Published: April 2018

Extracellular matrix (ECM)-independent survival is an essential prerequisite for tumor metastasis and a hallmark of epithelial cancer stem cells and epithelial-mesenchymal transition (EMT). We found that, in MCF10A and MDA-MB-231 cells, loss of TP53I11 (Tumor Protein P53 Inducible Protein 11) enhanced the ECM-independent survival and suppressed glucose starvation induced cell death by increasing the activation of AMPK that confer cells metabolic flexibility to survive under stress conditions. We show here that, TP53I11 enhanced glycolysis and promoted proliferation of MCF10A and MDA-MB-231 cells in normal culture, but exerted negative effect on EMT, cell migration and invasion, and its overexpression suppressed tumor progression and metastasis of MDA-MB-231 cells in vivo. Considering cancer cells also are confronted with the hostile environment such as nutrient scarcity during tumorigenesis and metastasis, our findings suggested that the disruption of metabolic flexibility by TP53I11 through inhibiting AMPK activation resulted in the suppression of tumorigenesis and metastasis of breast cancer.
MicroRNA-205 affects mouse granulosa cell apoptosis and estradiol synthesis by targeting CREB1
Authors: Zhang Pengju , Wang Jun , Lang Hongyan , Wang Weixia , Liu Xiaohui , Liu Haiyan , Tan Chengcheng , Li Xintao , Zhao Yumin , Wu Xinghong
Published: April 2018

MicroRNAs-205 (miR-205), were reportedly to be involved in various physiological and pathological processes, but its biological function in follicular atresia remain unknown. In this study, we investigated the expression of miR-205 in mouse granulosa cells (mGCs), and explored its functions in primary mGCs using a serial of in vitro experiments. The result of qRT-PCR demonstrated that miR-205 expression was significantly increased in early atretic follicles (EAF), and progressively atretic follicles (PAF) compared to healthy follicles (HF). Our results also revealed that overexpression of miR-205 in mGCs significantly promoted apoptosis, caspas-3/9 activities, and inhibited estrogen E2 release, and cytochrome P450 family 19 subfamily A polypeptide 1 (CYP19A1, a key gene in E2 production) expression. Bioinformatics and luciferase reporter assays revealed that the gene of cyclic AMP response element (CRE)-binding protein 1 (CREB1) was a potential target of miR-205. qRT-PCR and western blot assays revealed that overexpression of miR-205 inhibited the expression of CREB1 in mGCs. Importantly, CREB1 upregulation partially rescued the effects of miR-205 on apoptosis, caspase-3/9 activities, E2 production and CYP19A1 expression in mGCs. Our results indicate that miR-205 may play an important role in ovarian follicular development and provide new insights into follicular atresia.
Computational assessment of blood flow heterogeneity in dialysis patients’ cardiac ventricles
Authors: Kharche Sanjay R , So Aaron , Salerno Fabio , Lee Ting-Yim , Ellis Chris , Goldman Daniel , McIntyre C W
Published: April 2018

Dialysis prolongs life but augments cardiovascular mortality. Imaging data suggests that dialysis increases myocardial blood flow (BF) heterogeneity, but its causes remain poorly understood. A biophysical model of human coronary vasculature was used to explain the imaging observations, and highlight causes of coronary BF heterogeneity.

Post-dialysis CT images from patients under control, pharmacological stress (adenosine), therapy (cooled dialysate), and adenosine and cooled dialysate conditions were obtained. The data presented disparate phenotypes. To dissect vascular mechanisms, a 3D human coronary vasculature model was implemented. Simulations were performed to investigate the effects of altered aortic pressure and blood vessel diameters on myocardial BF heterogeneity which was quantified using relative dispersion, fractal dimension, and transmural BF distribution.

Imaging showed that stress and therapy potentially increased mean and total BF, while reducing heterogeneity. BF histograms of one patient showed multi-modality. Using the model, it was found that total coronary BF increased as coronary perfusion pressure (CPP) was increased. BF heterogeneity was differentially affected by large or small vessel blocking. BF heterogeneity was found to be inversely related to small blood vessel diameters. Simulation of large artery stenosis indicates that BF became heterogeneous (increase relative dispersion) and gave multi-modal histograms. The total transmural BF as well as transmural BF heterogeneity reduced due to large artery stenosis, generating large patches of very low BF regions downstream. Blocking of arteries at various orders showed that blocking larger arteries results in multi-modal BF histograms and large patches of low BF, whereas smaller artery blocking results in augmented relative dispersion and fractal dimension. Transmural heterogeneity was also affected. Finally, the effects of augmented aortic pressure in the presence of blood vessel blocking shows differential effects on BF heterogeneity as well as transmural BF.

Improved aortic blood pressure may lead to improved BF. Stress and therapy may be effective if they dilate small vessels. A potential cause for the observed complex BF distributions (multi-modal BF histograms) may indicate existing large vessel stenosis.

The intuitive BF heterogeneity methods used can be readily used in clinical studies. Further development of the model and methods will permit personalised assessment of patient BF status.
A population-based human enCYCLOPedia for circadian medicine
Authors: Ruben Marc D. , Wu Gang , Smith David F. , Schmidt Robert E. , Francey Lauren J. , Anafi Ron C. , Hogenesch John B.
Published: April 2018

The discovery that half of the mammalian protein-coding genome is clock-regulated has clear implications for medicine. Indeed, recent studies demonstrate time-of-day impact on therapeutic outcomes in human heart disease and cancer. Yet biological time is rarely given clinical consideration. A key barrier is the absence of information on thewhatandwhereof molecular rhythms in the human body. Here, we have applied CYCLOPS, an algorithm designed to reconstruct sample order in the absence of time-of-day information, to the GTEx collection of 632 human donors contributing 4,292 RNA-seq samples from 13 distinct human tissue types. We identify rhythms in expression across the body that persist at the population-level. This includes a set of ‘ubiquitous cyclers’ comprised of well-established circadian clock factors but also many genes without prior circadian context. Among thousands of tissue-divergent rhythms, we discover a set of genes robustly oscillating in cardiovascular tissue, including key drug targets relevant to heart disease. These results also have implications for genetic studies where circadian variability may have masked genetic influence. It is our hope that the human enCYCLOPedia helps drive the translation of circadian biology into prospective clinical trials in cardiology and many other therapeutic areas.

One Sentence Summary

Bioinformatic analyses on thousands of human tissue samples reveals an enCYCLOPedia of rhythmic gene expression across the body and identifies key translational opportunities for circadian medicine in cardiovascular disease.
The polar localization hub protein PopZ restrains adaptor dependent ClpXP proteolysis inCaulobacter crescentus
Authors: Joshi Kamal Kishore , Chien Peter
Published: April 2018

InCaulobacter crescentus, timely degradation of several proteins by the ClpXP protease is critical for proper cell cycle progression. During the cell cycle, the ClpXP protease, the substrate CtrA and many other proteins are localized to the stalked pole dependent on a polar interaction hub composed of PopZ protein oligomers. Prior work suggests that the localization of ClpXP, protease substrates, and cofactors is needed for recognition of substrates such as CtrA by ClpXP. Here, we formally test this hypothesis by examining the role of PopZ in ClpXP activity and find surprisingly that CtrA degradation is enhanced in cells lacking polar localization due to loss of PopZ. The ClpXP adaptor CpdR is required for this enhanced degradation of CtrA and other adaptor-dependent substrates, but adaptor-independent substrate degradation is not affected upon loss of PopZ. We find that overexpression of PopZ also leads to faster degradation of CtrA, but is likely due to nonphysiologically relevant recognition of CtrA by ClpXP alone as loss of CpdR does not affect this enhancement. Our main conclusion is that loss of PopZ, and therefore loss of polar localization, does not result in the loss of ClpXP regulated proteolysis, as would be predicted from a model which requires polar localization of ClpXP for its activation. Rather, our data point to a model where PopZ normally restrains ClpXP proteolysis by promoting the inactivation of the CpdR adaptor, likely through the phosphorylation activity of the CckA kinase.