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While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily sta...
Histone lysine methyltransferases (HKMTs), catalyze mono-, di- and trimethylation of lysine residues, resulting in a regulatory pattern that controls gene expression. Their involvement in many different cellul...
The original article was published in Biology Direct 2015 10:69
The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis)...
Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed...
Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified evolutionary explanation that accounts for...
Viral capsid assembly involves the oligomerization of the capsid nucleoprotein (NP), which is an essential step in viral replication and may represent a potential antiviral target. An in vitro transcription-tr...
Ribosome profiling (or Ribo-seq) is currently the most popular methodology for studying translation; it has been employed in recent years to decipher various fundamental gene expression regulation aspects.
Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights ...
During embryogenesis, chemical (morphogen) and mechanical patterns develop within tissues in a self-organized way. More than 60 years ago, Turing proposed his famous reaction-diffusion model for such processes...
The family of D cyclins has a fundamental role in cell cycle progression, but its members (D1, D2, D3) are believed to have redundant functions. However, there is some evidence that contradicts the notion of m...
Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation re...
The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison betwee...
Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved in...
The term “Columbian Exchange” refers to the massive transfer of life between the Afro-Eurasian and American hemispheres that was precipitated by Columbus’ voyage to the New World. The Columbian Exchange is wid...
In the recent years, sequence-specific nucleases such as ZFNs, TALENs, and CRISPR/Cas9 have revolutionzed the fields of animal genome editing and transgenesis. However, these new techniques require microinject...
The discovery of the viroid in 1971, which initiated the third major expansion of the biosphere towards smaller living entities—after discovery of the “subvisual” microorganisms in 1675 and that of the “submic...
One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites i...
The hypothalamic-pituitary-adrenal (HPA) axis is a neuroendocrine system that regulates numerous physiological processes. Disruptions in the activity of the HPA axis are correlated with stress-related diseases...
Antiangiogenic agents have been recently added to the oncological armamentarium with bevacizumab probably being the most popular representative in current clinical practice. The elucidation of the mode of acti...
CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cyto...
Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, ...
The CRISPR-Cas system of prokaryotic adaptive immunity displays features of a mechanism for directional, Lamarckian evolution. Indeed, this system modifies a specific locus in a bacterial or archaeal genome by...
Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to ...
Functional biologists, like Claude Bernard, ask “How?”, meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Char...
Translation of nucleotides into a numeric form has been approached in many ways and has allowed researchers to investigate the properties of protein-coding sequences and noncoding sequences. Typically, more pr...
The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their ...
In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of th...
Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and ...
The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in t...
It is widely believed that the treatment of glioblastomas (GBM) could benefit from oncolytic virus therapy. Clinical research has shown that Vesicular Stomatitis Virus (VSV) has strong oncolytic properties. In...
Peroxisomes are ubiquitous eukaryotic organelles that compartmentalize a variety of metabolic pathways that are primarily related to the oxidative metabolism of lipids and the detoxification of reactive oxygen...
In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated...
Genomic uptake of DNA by prokaryotes often encompasses more than a single gene. In many cases, several horizontally transferred genes may be acquired together. Accordingly, we expect that horizontally transfer...
We present a network-based method, namely quantitative proteomic signature profiling (qPSP) that improves the biological content of proteomic data by converting protein expressions into hit-rates in protein co...
The C-terminal domain of α-COP, an essential subunit of the COPI coatomer complex, is composed of an all α-helical region and a small β-sheet domain. We show that this β-sheet domain is a Really Interesting Ne...
The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have sh...
The Erratum to this article has been published in Biology Direct 2016 11:29
During the lifetime of an organism, every individual encounters many combinations of diverse changes in the somatic genome, epigenome and microbiome. This gives rise to many novel combinations of internal fail...
In this article, I review the results of studies on the origin of life distinct from the popular RNA world hypothesis. The alternate scenario postulates the origin of the first bimolecular genetic system (a po...
Homologues of calpain, often thought to be an essential, cytoplasmic, calcium-dependent cysteine endopeptidase found exclusively in eukaryotes, have been found in bacterial proteomes. The homologues lack calci...
Many proteins of viruses infecting hyperthermophilic Crenarchaeota have no detectable homologs in current databases, hampering our understanding of viral evolution. We used sensitive database search methods an...
Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenet...
Microbial rhodopsins and G-protein coupled receptors (GPCRs, which include animal rhodopsins) are two distinct (super) families of heptahelical (7TM) membrane proteins that share obvious structural similaritie...
The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalow...
Transposable elements (TEs) play an important role in genome function and evolution. It has been shown that TEs are a considerable source of adaptive changes in the genome of Drosophila melanogaster. Specifically...
Epigenetic regulation contributes to many important processes in biological cells. Examples include developmental processes, differentiation and maturation of stem cells, evolution of malignancy and other. Cel...
Genomic studies have greatly expanded our knowledge of structural non-coding RNAs (ncRNAs). These RNAs fold into characteristic secondary structures and perform specific-structure dependent biological function...
Elucidation of human disease similarities has emerged as an active research area, which is highly relevant to etiology, disease classification, and drug repositioning. In pioneer studies, disease similarity wa...
While hundreds of genes have been implicated already in the etiology of schizophrenia, the exact cause is not known or the disease is considered multigenic in origin. Recent discoveries of new types of RNAs an...
Synthetic lethality (SL) refers to the genetic interaction between two or more genes where only their co-alteration (e.g. by mutations, amplifications or deletions) results in cell dea...
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