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Biology Direct

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https://www.readbyqxmd.com/read/29789016/unraveling-bacterial-fingerprints-of-city-subways-from-microbiome-16s-gene-profiles
#1
Alejandro R Walker, Tyler L Grimes, Somnath Datta, Susmita Datta
BACKGROUND: Microbial communities can be location specific, and the abundance of species within locations can influence our ability to determine whether a sample belongs to one city or another. As part of the 2017 CAMDA MetaSUB Inter-City Challenge, next generation sequencing (NGS) data was generated from swipe samples collected from subway stations in Boston, New York City hereafter New York, and Sacramento. DNA was extracted and Illumina sequenced. Sequencing data was provided for all cities as part of 2017 CAMDA contest challenge dataset...
May 22, 2018: Biology Direct
https://www.readbyqxmd.com/read/29776380/use-of-designed-sequences-in-protein-structure-recognition
#2
Gayatri Kumar, Richa Mudgal, Narayanaswamy Srinivasan, Sankaran Sandhya
BACKGROUND: Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold...
May 9, 2018: Biology Direct
https://www.readbyqxmd.com/read/29743119/profiling-microbial-strains-in-urban-environments-using-metagenomic-sequencing-data
#3
Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett, Nicola Segata
BACKGROUND: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context...
May 9, 2018: Biology Direct
https://www.readbyqxmd.com/read/29703221/conservation-of-the-separase-regulatory-domain
#4
Michael Melesse, Joshua N Bembenek, Igor B Zhulin
ᅟ: We report a protein sequence analysis of the cell cycle regulatory protease, separase. The sequence and structural conservation of the C-terminal protease domain has long been recognized, whereas the N-terminal regulatory domain of separase was reported to lack detectable sequence similarity. Here we reveal significant sequence conservation of the separase regulatory domain and report a discovery of a cysteine motif (CxCxxC) conserved in major lineages of Metazoa including nematodes and vertebrates. This motif is found in a solvent exposed linker region connecting two TPR-like helical motifs...
April 27, 2018: Biology Direct
https://www.readbyqxmd.com/read/29678199/megan-lr-new-algorithms-allow-accurate-binning-and-easy-interactive-exploration-of-metagenomic-long-reads-and-contigs
#5
Daniel H Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic, Rohan B H Williams
BACKGROUND: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets...
April 20, 2018: Biology Direct
https://www.readbyqxmd.com/read/29615097/multi-omics-integration-for-neuroblastoma-clinical-endpoint-prediction
#6
Margherita Francescatto, Marco Chierici, Setareh Rezvan Dezfooli, Alessandro Zandonà, Giuseppe Jurman, Cesare Furlanello
BACKGROUND: High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data could provide a broader insight into the mechanisms of cancer biology, helping researchers and clinicians to develop personalized therapies. RESULTS: In the context of CAMDA 2017 Neuroblastoma Data Integration challenge, we explore the use of Integrative Network Fusion (INF), a bioinformatics framework combining a similarity network fusion with machine learning for the integration of multiple omics data...
April 3, 2018: Biology Direct
https://www.readbyqxmd.com/read/29499764/prevalence-of-loss-of-function-alleles-does-not-correlate-with-lifetime-fecundity-and-other-life-history-traits-in-metazoans
#7
Aleksandra V Bezmenova, Georgii A Bazykin, Alexey S Kondrashov
BACKGROUND: Natural selection is possible only because all species produce more offsprings than what is needed to maintain the population. Still, the lifetime number of offspring varies widely across species. One may expect natural selection to be stronger in high-fecundity species. Alternatively, natural selection could be stronger in species where a female invests more into an individual offspring. This issue needed to be addressed empirically. RESULTS: We analyzed the prevalence of loss-of-function alleles in 35 metazoan species and have found that the strength of negative selection does not correlate with lifetime fecundity or other life-history traits...
March 2, 2018: Biology Direct
https://www.readbyqxmd.com/read/29467011/genes-sharing-the-protein-family-domain-decrease-the-performance-of-classification-with-rna-seq-genomic-signatures
#8
Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska-Beręsewicz, Michal J Okoniewski
BACKGROUND: The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis and selection of genes used for classification. This paper aims in pointing out several factors that may influence the downstream machine learning analysis. In particular those factors are: type of the primary analysis, type of the classifier and increased correlation between the genes sharing a protein domain...
February 21, 2018: Biology Direct
https://www.readbyqxmd.com/read/29433547/finite-size-effects-in-transcript-sequencing-count-distribution-its-power-law-correction-necessarily-precedes-downstream-normalization-and-comparative-analysis
#9
Wing-Cheong Wong, Hong-Kiat Ng, Erwin Tantoso, Richie Soong, Frank Eisenhaber
BACKGROUND: Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i...
February 12, 2018: Biology Direct
https://www.readbyqxmd.com/read/29409513/efficient-differentially-private-learning-improves-drug-sensitivity-prediction
#10
Antti Honkela, Mrinal Das, Arttu Nieminen, Onur Dikmen, Samuel Kaski
BACKGROUND: Users of a personalised recommendation system face a dilemma: recommendations can be improved by learning from data, but only if other users are willing to share their private information. Good personalised predictions are vitally important in precision medicine, but genomic information on which the predictions are based is also particularly sensitive, as it directly identifies the patients and hence cannot easily be anonymised. Differential privacy has emerged as a potentially promising solution: privacy is considered sufficient if presence of individual patients cannot be distinguished...
February 6, 2018: Biology Direct
https://www.readbyqxmd.com/read/29202832/inevitability-of-the-emergence-and-persistence-of-genetic-parasites-caused-by-evolutionary-instability-of-parasite-free-states
#11
Eugene V Koonin, Yuri I Wolf, Mikhail I Katsnelson
Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic diversity. Here we examine simple thought experiments to demonstrate that both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable. REVIEWERS: This article has been reviewed by Yitzhak Pilpel, Bojan Zagrovic, and Eric van Nimwegen...
December 4, 2017: Biology Direct
https://www.readbyqxmd.com/read/29191215/domestication-of-self-splicing-introns-during-eukaryogenesis-the-rise-of-the-complex-spliceosomal-machinery
#12
REVIEW
Julian Vosseberg, Berend Snel
ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated...
December 1, 2017: Biology Direct
https://www.readbyqxmd.com/read/29187234/cogcollator-a-web-server-for-analysis-of-distant-relationships-between-homologous-protein-families
#13
Daria V Dibrova, Kirill A Konovalov, Vadim V Perekhvatov, Konstantin V Skulachev, Armen Y Mulkidjanian
BACKGROUND: The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs. AIM: We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server. RESULTS: Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis...
November 29, 2017: Biology Direct
https://www.readbyqxmd.com/read/29178964/over-expression-of-mir-146b-and-its-regulatory-role-in-intestinal-epithelial-cell-viability-proliferation-and-apoptosis-in-piglets
#14
Xin Tao, Shujie Liu, Xiaoming Men, Ziwei Xu
BACKGROUND: Weaning stress affects the small intestine of piglets. MiR-146b is differentially expressed in suckling and weaned piglets. In this study, we evaluated the effects of miR-146b on cell viability, proliferation, and apoptosis in IPEC-J2 cells. RESULTS: Transfection with miR-146b mimics successfully increased miR-146b levels by 1000× (P < 0.001). The over-expression of miR-146b significantly promoted the apoptosis (P < 0.01) of IPEC-J2 cells, with no significant effects on cell viability or proliferation...
November 25, 2017: Biology Direct
https://www.readbyqxmd.com/read/29178959/sugar-lego-gene-composition-of-bacterial-carbohydrate-metabolism-genomic-loci
#15
Anna Kaznadzey, Pavel Shelyakin, Mikhail S Gelfand
BACKGROUND: Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. This study focuses on a large-scale analysis of bacterial genomic loci related to the carbohydrate metabolism. RESULTS: We demonstrate that only 53% of 148,000 studied genes from over six hundred bacterial genomes are co-localized in bacterial genomes with other carbohydrate metabolism genes, which points to a significant role of singleton genes...
November 25, 2017: Biology Direct
https://www.readbyqxmd.com/read/29166914/cognat-a-web-server-for-comparative-analysis-of-genomic-neighborhoods
#16
Olesya I Klimchuk, Kirill A Konovalov, Vadim V Perekhvatov, Konstantin V Skulachev, Daria V Dibrova, Armen Y Mulkidjanian
BACKGROUND: In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts...
November 22, 2017: Biology Direct
https://www.readbyqxmd.com/read/29132422/cellular-origin-of-the-viral-capsid-like-bacterial-microcompartments
#17
Mart Krupovic, Eugene V Koonin
ᅟ: Bacterial microcompartments (BMC) are proteinaceous organelles that structurally resemble viral capsids, but encapsulate enzymes that perform various specialized biochemical reactions in the cell cytoplasm. The BMC are constructed from two major shell proteins, BMC-H and BMC-P, which form the facets and vertices of the icosahedral assembly, and are functionally equivalent to the major and minor capsid proteins of viruses, respectively. This equivalence notwithstanding, neither of the BMC proteins displays structural similarity to known capsid proteins, rendering the origins of the BMC enigmatic...
November 13, 2017: Biology Direct
https://www.readbyqxmd.com/read/29037253/asxl-gain-of-function-truncation-mutants-defective-and-dysregulated-forms-of-a-natural-ribosomal-frameshifting-product
#18
Adam M Dinan, John F Atkins, Andrew E Firth
BACKGROUND: Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses utilize PRF to control or regulate gene expression, but very few phylogenetically conserved examples are known in vertebrate genes. Additional sex combs-like (ASXL) genes 1 and 2 encode important epigenetic and transcriptional regulatory proteins that control the expression of homeotic genes during key developmental stages...
October 16, 2017: Biology Direct
https://www.readbyqxmd.com/read/28969666/why-we-don-t-want-another-synthesis
#19
Arlin Stoltzfus
High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory. The OMS held that evolution can be adequately understood as a process of smooth adaptive change by shifting the frequencies of small-effect alleles at many loci simultaneously, without the direct involvement of new mutations...
October 2, 2017: Biology Direct
https://www.readbyqxmd.com/read/28915909/differential-signal-sensitivities-can-contribute-to-the-stability-of-multispecies-bacterial-communities
#20
János Juhász, Dóra Bihary, Attila Jády, Sándor Pongor, Balázs Ligeti
BACKGROUND: Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to the same signal molecule has been well documented in quorum sensing which is one of the best studied inter-cellular signalling mechanisms in bacteria. The biological significance of this phenomenon is still poorly understood, and cannot be easily studied in nature or in laboratory models...
September 15, 2017: Biology Direct
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