Articles

The role of cell location and spatial gradients in the evolutionary dynamics of colon and intestinal crypts

Colon and intestinal crypts serve as an important model system for adult stem cell proliferation and differentiation. We develop a spatial stochastic model to study the rate of somatic evolution in a normal cr...

Authors: Leili Shahriyari, Natalia L. Komarova and Alexandra Jilkine

Optimal treatment and stochastic modeling of heterogeneous tumors

In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how hetero...

Authors: Hamidreza Badri and Kevin Leder

Primary and metastatic tumor dormancy as a result of population heterogeneity

Existence of tumor dormancy, or cancer without disease, is supported both by autopsy studies that indicate presence of microscopic tumors in men and women who die of trauma (primary dormancy), and by long peri...

Authors: Irina Kareva

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics

For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have per...

Authors: Johann-Mattis List, Jananan Sylvestre Pathmanathan, Philippe Lopez and Eric Bapteste

Compartmentalization in PVC super-phylum: evolution and impact

The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomy...

Authors: Sandrine Pinos, Pierre Pontarotti, Didier Raoult, Jean Pierre Baudoin and Isabelle Pagnier

The multiple evolutionary origins of the eukaryotic N-glycosylation pathway

The N-glycosylation is an essential protein modification taking place in the membranes of the endoplasmic reticulum (ER) in eukaryotes and the plasma membranes in archaea. It shares mechanistic similarities based...

Authors: Jonathan Lombard

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not...

Authors: Marcin Jąkalski, Kazutaka Takeshita, Mathieu Deblieck, Kanako O. Koyanagi, Izabela Makałowska, Hidemi Watanabe and Wojciech Makałowski

Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α p...

Authors: Mauro Degli Esposti, Diego Cortez, Luis Lozano, Simon Rasmussen, Henrik Bjørn Nielsen and Esperanza Martinez Romero

Stem-like features of cancer cells on their way to metastasis

More than 90 % of cancer-related deaths are due to the development of a systemic metastatic disease. Clearly, much remains to be understood about the biological principles that govern human cancer metastasis, ...

Authors: Sofia Gkountela and Nicola Aceto

The evolutionary scope and neurological disease linkage of yeast-prion-like proteins in humans

Prions are proteinaceous particles that propagate alternative protein conformations/states to further copies of the same proteins, and are transmitted from cell-to-cell, and organism-to-organism. Prions are us...

Authors: Lu An and Paul M. Harrison

Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable

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...

Authors: Alena Orlenko, Ashley I. Teufel, Peter B. Chi and David A. Liberles

Intrinsic protein disorder in histone lysine methylation

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...

Authors: Tamas Lazar, Eva Schad, Beata Szabo, Tamas Horvath, Attila Meszaros, Peter Tompa and Agnes Tantos

Erratum to: What can ecosystems learn? Expanding evolutionary ecology with learning theory

Authors: Daniel A. Power, Richard A. Watson, Eörs Szathmáry, Rob Mills, Simon T. Powers, C. Patrick Doncaster and Błazej Czapp

Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis

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)...

Authors: Alexander V. Markov and Ilya S. Kaznacheev

Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria

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...

Authors: Gayatri Ramakrishnan, Abha Jain, Nagasuma Chandra and Narayanaswamy Srinivasan

Gene overlapping and size constraints in the viral world

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...

Authors: Nadav Brandes and Michal Linial

Biochemical and biophysical characterization of cell-free synthesized Rift Valley fever virus nucleoprotein capsids enables in vitro screening to identify novel antivirals

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...

Authors: Sean Broce, Lisa Hensley, Tomoharu Sato, Joshua Lehrer-Graiwer, Christian Essrich, Katie J. Edwards, Jacqueline Pajda, Christopher J. Davis, Rami Bhadresh, Clarence R. Hurt, Beverly Freeman, Vishwanath R. Lingappa, Colm A. Kelleher and Marcela V. Karpuj

Estimation of ribosome profiling performance and reproducibility at various levels of resolution

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.

Authors: Alon Diament and Tamir Tuller

Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development

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 ...

Authors: Bálint Mészáros, András Zeke, Attila Reményi, István Simon and Zsuzsanna Dosztányi

Beyond Turing: mechanochemical pattern formation in biological tissues

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...

Authors: Moritz Mercker, Felix Brinkmann, Anna Marciniak-Czochra and Thomas Richter

The cyclin D1 carboxyl regulatory domain controls the division and differentiation of hematopoietic cells

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...

Authors: Miguel Chaves-Ferreira, Gerald Krenn, Florence Vasseur, Aleksandr Barinov, Pedro Gonçalves, Orly Azogui, Ana Cumano, Zhi Li, Sandra Pellegrini, Benedita Rocha and Diego Laderach

Ribosome reinitiation at leader peptides increases translation of bacterial proteins

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...

Authors: Semen A. Korolev, Oleg A. Zverkov, Alexandr V. Seliverstov and Vassily A. Lyubetsky

Infinitely long branches and an informal test of common ancestry

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...

Authors: Leonardo de Oliveira Martins and David Posada

Conservation and divergence of the histone code in nucleomorphs

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...

Authors: Georgi K. Marinov and Michael Lynch

The Columbian Exchange as a source of adaptive introgression in human populations

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...

Authors: I. King Jordan

Nucleic acids delivery methods for genome editing in zygotes and embryos: the old, the new, and the old-new

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...

Authors: Masahiro Sato, Masato Ohtsuka, Satoshi Watanabe and Channabasavaiah B. Gurumurthy

Viroids: “living fossils” of primordial RNAs?

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...

Authors: Theodor O. Diener

A web server for analysis, comparison and prediction of protein ligand binding sites

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...

Authors: Harinder Singh, Hemant Kumar Srivastava and Gajendra P. S. Raghava

Onset, timing, and exposure therapy of stress disorders: mechanistic insight from a mathematical model of oscillating neuroendocrine dynamics

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...

Authors: Lae U. Kim, Maria R. D’Orsogna and Tom Chou

Numerical simulation of vascular tumour growth under antiangiogenic treatment: addressing the paradigm of single-agent bevacizumab therapy with the use of experimental data

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...

Authors: Katerina D. Argyri, Dimitra D. Dionysiou, Fay D. Misichroni and Georgios S. Stamatakos

Preservation of methylated CpG dinucleotides in human CpG islands

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...

Authors: Alexander Y. Panchin, Vsevolod J. Makeev and Yulia A. Medvedeva

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data

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, ...

Authors: Yeongjun Jang, Namhee Yu, Jihae Seo, Sun Kim and Sanghyuk Lee

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms

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...

Authors: Eugene V. Koonin and Yuri I. Wolf

Altools: a user friendly NGS data analyser

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 ...

Authors: Salvatore Camiolo, Gaurav Sablok and Andrea Porceddu

Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology

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...

Authors: Angelo Vianello and Sabina Passamonti

Characterizing exons and introns by regularity of nucleotide strings

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...

Authors: Tonya Woods, Thanawadee Preeprem, Kichun Lee, Woojin Chang and Brani Vidakovic

A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution

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 ...

Authors: Marek Eliáš, Vladimír Klimeš, Romain Derelle, Romana Petrželková and Jan Tachezy

BLAST-based structural annotation of protein residues using Protein Data Bank

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...

Authors: Harinder Singh and Gajendra P. S. Raghava

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

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 ...

Authors: Dingchen Li, Zongwei Li, Zhe Zhou, Zhen Li, Xinyan Qu, Peisong Xu, Pingkun Zhou, Xiaochen Bo and Ming Ni

The mysterious orphans of Mycoplasmataceae

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...

Authors: Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky and Alexander Bolshoy

A mathematical approach to virus therapy of glioblastomas

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...

Authors: Victor Lopez de Rioja, Neus Isern and Joaquim Fort

Evolutionary loss of peroxisomes – not limited to parasites

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...

Authors: Vojtěch Žárský and Jan Tachezy

PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues

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...

Authors: Sandeep Singh, Harinder Singh, Abhishek Tuknait, Kumardeep Chaudhary, Balvinder Singh, S. Kumaran and Gajendra P. S. Raghava

Horizontally transferred genes cluster spatially and metabolically

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...

Authors: Alexander Dilthey and Martin J. Lercher

Quantitative proteomics signature profiling based on network contextualization

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...

Authors: Wilson Wen Bin Goh, Tiannan Guo, Ruedi Aebersold and Limsoon Wong

A novel RING finger in the C-terminal domain of the coatomer protein α-COP

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...

Authors: Gurmeet Kaur and Srikrishna Subramanian

What can ecosystems learn? Expanding evolutionary ecology with learning theory

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...

Authors: Daniel A. Power, Richard A. Watson, Eörs Szathmáry, Rob Mills, Simon T. Powers, C. Patrick Doncaster and BłaŻej Czapp

A principle of organization which facilitates broad Lamarckian-like adaptations by improvisation

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...

Authors: Yoav Soen, Maor Knafo and Michael Elgart

The progene hypothesis: the nucleoprotein world and how life began

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...

Authors: Anatoly D. Altstein

Bacterial calpains and the evolution of the calpain (C2) family of peptidases

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...

Authors: Neil D. Rawlings