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Several prokaryotic plasmids maintain themselves in their hosts by means of diverse post-segregational cell killing systems. Recent findings suggest that chromosomally encoded copies of toxins and antitoxins o...
Mammalian microRNAs (miRNAs) are sometimes subject to adenosine-to-inosine RNA editing, which can lead to dramatic changes in miRNA target specificity or expression levels. However, although a few miRNAs are k...
Amino acid repeats (AARs) are common features of protein sequences. They often evolve rapidly and are involved in a number of human diseases. They also show significant associations with particular Gene Ontolo...
Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish operon' hypothesis, operons are viewed as mobile g...
The ability of grass species to adapt to various habitats is attributed to the dynamic nature of their genomes, which have been shaped by multiple rounds of ancient and recent polyploidization. To gain a bette...
In mammals, splice-regulatory domains impose marked trends on the relative abundance of certain amino acids near exon-intron boundaries. Is this a mammalian particularity or symptomatic of exonic splicing regu...
Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes ...
MicroRNAs (miRNAs) are a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity. Most miRNAs were identified by direct cloning of small RNAs, an approach that f...
Alu elements are primate-specific repeats and comprise 11% of the human genome. They have wide-ranging influences on gene expression. Their contribution to genome evolution, gene regulation and disease is reviewe...
We evaluated the evolutionary conservation of glycine myristoylation within eukaryotic sequences. Our large-scale cross-genome analyses, available as MYRbase, show that the functional spectrum of myristoylated...
Sorghum is the first C4 plant and the second grass with a full genome sequence available. This makes it possible to perform a whole-genome-level exploration of C4 pathway evolution by comparing key photosynthe...
The basic helix-loop-helix (bHLH) proteins are a large and complex multigene family of transcription factors with important roles in animal development, including that of fruitflies, nematodes and vertebrates....
Aberrant CpG island promoter DNA hypermethylation is frequently observed in cancer and is believed to contribute to tumor progression by silencing the expression of tumor suppressor genes. Previously, we obser...
Understanding the molecular mechanisms plants have evolved to adapt their biological activities to a constantly changing environment is an intriguing question and one that requires a systems biology approach. ...
Mounting evidence suggests a major role for epigenetic feedback in Plasmodium falciparum transcriptional regulation. Long non-coding RNAs (lncRNAs) have recently emerged as a new paradigm in epigenetic remodeling...
The formin family of proteins has been implicated in signaling pathways of cellular morphogenesis in both animals and fungi; in the latter case, at least, they participate in communication between the actin cy...
Several long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has grea...
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their flexible organization and functional redundancies make deciphering their sequence-function relationships challenging. This a...
Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute t...
A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented. The method is based on two novel diagrams - the highway plot and the ...
Rhomboid proteases are the largest family of enzymes that hydrolyze peptide bonds within the cell membrane. Although discovered to be serine proteases only a decade ago, rhomboid proteases are already consider...
Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location...
Genetic code alterations have been reported in mitochondrial, prokaryotic, and eukaryotic cytoplasmic translation systems, but their evolution and how organisms cope and survive such dramatic genetic events ar...
The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk ce...
The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are mu...
The completion of the Arabidopsis thaliana (mustard weed) genome sequence constitutes a major breakthrough in plant biology. It will revolutionize how we answer questions about the biology and evolution of plants...
Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined be...
A comparison of transcriptional profiles derived from different tissues in a given species or among different species assumes that commonalities reflect evolutionarily conserved programs and that differences r...
Infection with the bacterium Wolbachia is sufficient to establish a reproductive barrier between two otherwise compatible species of wasp, making Wolbachia a potential driving force in evolution.
A report from Microbial Genomes, a joint conference of the American Society for Microbiology and the Institute for Genomic Research, Monterey, California, USA, 28-31 January, 2001.
The germ cell nuclear factor (GCNF, also known as retinoid acid receptor-related testis-associated receptor, neuronal cell nuclear receptor or NR6A1) is an orphan receptor in the nuclear receptor superfamily f...
Invertebrate retroelements have borrowed diverse viral envelopes for infection.
An excellent candidate for the master sex-determining gene on the Y chromosome of the medaka fish is not related to the mammalian SRY gene
Recent work in the silkworm Bombyx mori has uncovered a novel Piwi-interacting RNA regulator of the sex determination switch doublesex.
Comparative genomics using the pufferfish genome will help with identifying and characterizing human genes
This article is part of a Supplement: Volume 12 Supplement 1
The 1000 Genomes Project Consortium has recently published an important early contribution to a new generation of systematic surveys of rare human genetic variation.
Ring-type polymerases consist of a DNA polymerase, a ring-shaped sliding clamp protein and a clamp-loading complex. Sliding clamp proteins are found in all organisms and are called proliferating cell nuclear a...
A report on the 19th Whitehead Institute Symposium, Cambridge, USA, 14-16 October 2001.
Antibiotics alter the abundance and types of bacteriophage-associated genes in the mouse gut, suggesting that phage help bacterial communities during times of stress.
The Blocks server allows access to multiply aligned ungapped sequence segments corresponding to the most highly conserved regions of proteins, and aids detection and verification of protein sequence homologies...
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