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Biology Direct

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https://www.readbyqxmd.com/read/29202832/inevitability-of-the-emergence-and-persistence-of-genetic-parasites-caused-by-evolutionary-instability-of-parasite-free-states
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28886750/evidence-based-gene-models-for-structural-and-functional-annotations-of-the-oil-palm-genome
#11
Kuang-Lim Chan, Tatiana V Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Nagappan Jayanthi, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Eng-Ti Leslie Low
BACKGROUND: Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited...
September 8, 2017: Biology Direct
https://www.readbyqxmd.com/read/28851439/on-the-global-crispr-array-behavior-in-class-i-systems
#12
Alice Toms, Rodolphe Barrangou
BACKGROUND: Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes...
August 29, 2017: Biology Direct
https://www.readbyqxmd.com/read/28806979/breath-giving-cooperation-critical-review-of-origin-of-mitochondria-hypotheses-major-unanswered-questions-point-to-the-importance-of-early-ecology
#13
REVIEW
István Zachar, Eörs Szathmáry
The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address...
August 14, 2017: Biology Direct
https://www.readbyqxmd.com/read/28800767/cell-adhesion-heterogeneity-reinforces-tumour-cell-dissemination-novel-insights-from-a-mathematical-model
#14
David Reher, Barbara Klink, Andreas Deutsch, Anja Voss-Böhme
BACKGROUND: Cancer cell invasion, dissemination, and metastasis have been linked to an epithelial-mesenchymal transition (EMT) of individual tumour cells. During EMT, adhesion molecules like E-cadherin are downregulated and the decrease of cell-cell adhesion allows tumour cells to dissociate from the primary tumour mass. This complex process depends on intracellular cues that are subject to genetic and epigenetic variability, as well as extrinsic cues from the local environment resulting in a spatial heterogeneity in the adhesive phenotype of individual tumour cells...
August 11, 2017: Biology Direct
https://www.readbyqxmd.com/read/28764727/emqit-a-machine-learning-approach-for-energy-based-pwm-matrix-quality-improvement
#15
Karolina Smolinska, Marcin Pacholczyk
BACKGROUND: Transcription factor binding affinities to DNA play a key role for the gene regulation. Learning the specificity of the mechanisms of binding TFs to DNA is important both to experimentalists and theoreticians. With the development of high-throughput methods such as, e.g., ChiP-seq the need to provide unbiased models of binding events has been made apparent. We present EMQIT a modification to the approach introduced by Alamanova et al. and later implemented as 3DTF server. We observed that tuning of Boltzmann factor weights, used for conversion of calculated energies to nucleotide probabilities, has a significant impact on the quality of the associated PWM matrix...
August 1, 2017: Biology Direct
https://www.readbyqxmd.com/read/28738827/bacterial-tail-anchors-can-target-to-the-mitochondrial-outer-membrane
#16
Güleycan Lutfullahoğlu-Bal, Abdurrahman Keskin, Ayşe Bengisu Seferoğlu, Cory D Dunn
BACKGROUND: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria...
July 24, 2017: Biology Direct
https://www.readbyqxmd.com/read/28595592/computational-prediction-of-lncrna-mrna-interactionsby-integrating-tissue-specificity-in-human-transcriptome
#17
Junichi Iwakiri, Goro Terai, Michiaki Hamada
Long noncoding RNAs (lncRNAs) play a key role in normal tissue differentiation and cancer development through their tissue-specific expression in the human transcriptome. Recent investigations of macromolecular interactions have shown that tissue-specific lncRNAs form base-pairing interactions with various mRNAs associated with tissue-differentiation, suggesting that tissue specificity is an important factor controlling human lncRNA-mRNA interactions.Here, we report investigations of the tissue specificities of lncRNAs and mRNAs by using RNA-seq data across various human tissues as well as computational predictions of tissue-specific lncRNA-mRNA interactions inferred by integrating the tissue specificity of lncRNAs and mRNAs into our comprehensive prediction of human lncRNA-RNA interactions...
June 8, 2017: Biology Direct
https://www.readbyqxmd.com/read/28569180/rotational-restriction-of-nascent-peptides-as-an-essential-element-of-co-translational-protein-folding-possible-molecular-players-and-structural-consequences
#18
Irina Sorokina, Arcady Mushegian
BACKGROUND: A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in protein folding in vivo. Recently, we hypothesized that energy-dependent twisting of the protein backbone is an unappreciated essential factor guiding the protein folding process in vivo...
May 31, 2017: Biology Direct
https://www.readbyqxmd.com/read/28545555/the-complex-domain-architecture-of-samd9-family-proteins-predicted-stand-like-ntpases-suggests-new-links-to-inflammation-and-apoptosis
#19
Sergei L Mekhedov, Kira S Makarova, Eugene V Koonin
We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family is represented in most animals and also, unexpectedly, in bacteria, in particular actinomycetes. From the N to C terminus, the core SAMD9 family architecture includes DNA/RNA-binding AlbA domain, a variant Sir2-like domain, a STAND-like P-loop NTPase, an array of TPR repeats and an OB-fold domain with predicted RNA-binding properties...
May 25, 2017: Biology Direct
https://www.readbyqxmd.com/read/28526057/recognition-of-a-structural-domain-rwdbd-in-gcn1-proteins-that-interacts-with-the-rwd-domain-containing-proteins
#20
Ramachandran Rakesh, Rangachari Krishnan, Evelyn Sattlegger, Narayanaswamy Srinivasan
The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for its importance for cells to sense and overcome amino acid starvation. Gcn1 directly binds to the RWD (RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases) domain of the protein kinase Gcn2, and this is essential for delivering the starvation signal to Gcn2...
May 19, 2017: Biology Direct
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