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Clonorchis sinensis is a carcinogenic human liver fluke that is widespread in Asian countries. Increasing infection rates of this neglected tropical disease are leading to negative economic and public health cons...
The in vivo validation of cancer mutations and genes identified in cancer genomics is resource-intensive because of the low throughput of animal experiments. We describe a mouse model that allows multiple cancer ...
Recent work on the circadian clock of the unicellular green alga Chlamydomonas reinhardtii strengthens its standing as a convenient model system for circadian study. It was shown to be amenable to molecular engin...
Cis-acting RNA elements control the accurate expression of human multi-exon protein coding genes. Single nucleotide variants altering the fidelity of this regulatory code and, consequently, pre-mRNA splicing are ...
It has been long thought that the stop codon in a gene is followed by another stop codon that acts as a backup if the real one is read through by a near-cognate tRNA. The existence of such 'tandem stop codons'...
Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation.
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase catalyzes the conversion of HMG-CoA to mevalonate, a four-electron oxidoreduction that is the rate-limiting step in the synthesis of cholest...
Protein fold recognition using sequence profile searches frequently allows prediction of the structure and biochemical mechanisms of proteins with an important biological function but unknown biochemical activ...
Nuclear pore complexes, the conduits for information exchange between the nucleus and cytoplasm, appear broadly similar in eukaryotes from yeast to human. Precisely how nuclear pore complexes regulate macromol...
Identification of orthologous relationships between genes from widely divergent taxa allows partial reconstruction of the gene complement of ancestral genomes. C2H2 zinc-finger genes are one of the largest and...
RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNA processing from single-cell RNA sequencing data are limited by reliance...
Sox proteins encompass an evolutionarily conserved family of transcription factors with critical roles in animal development and stem cell biology. In common with vertebrates, the Drosophila group B proteins SoxN...
The extensive polymorphism revealed in non-coding gene-regulatory sequences, particularly in the immune system, suggests that this type of genetic variation is functionally and evolutionarily far more importan...
In most eukaryotes, histones, which are the major structural components of chromatin, are expressed as a family of sequence variants encoded by multiple genes. Because different histone variants can contribute...
The serine hydroxymethyltransferase processed pseudogene SHMT-ps1 has been suggested to be unique to the order Primates because of the failure to amplify this sequence by PCR from genomic DNAs of any non-primate ...
Genomic segments that do not code for proteins yet show high conservation among vertebrates have recently been identified by various computational methodologies. We refer to them as ANCORs (ancestral non-codin...
It has recently been shown that the detection of gene fusion events across genomes can be used for predicting functional associations of proteins, including physical interaction or complex formation. To obtain...
Frizzled genes encode integral membrane proteins that function in multiple signal transduction pathways. They have been identified in diverse animals, from sponges to humans. The family is defined by conserved st...
Recent genomic studies showing abnormalities in the fibroblast growth factor system in the postmortem brains of people with major depressive disorder support previous indications of a role for growth factors i...
A report on the fourth International Meeting on Single Nucleotide Polymorphisms and Complex Genome Analysis, Stockholm, Sweden, 10-13 October 2001.
Genome sequence comparisons reveal that some sets of genes are in similar linkage groups in different organisms while other sets are dispersed. Are some linkage groups maintained by chance, or is there an adva...
The photosensitive molecule rhodopsin and its relatives consist of a protein moiety - an opsin - and a non-protein moiety - the chromophore retinal. Opsins, which are G-protein-coupled receptors (GPCRs), are f...
Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is tha...
The reovirus λ2 protein catalyzes mRNA capping, that is, addition of a guanosine to the 5' end of each transcript in a 5'-to-5' orientation, as well as transfer of a methyl group from S-adenosyl-L-methionine (Ado...
Granzymes, a family of serine proteases, are expressed exclusively by cytotoxic T lymphocytes and natural killer (NK) cells, components of the immune system that protect higher organisms against viral infectio...
A report on the Third Genetic Effects on Aging Meeting, The Jackson Laboratory, Bar Harbor, Maine, August 4-8, 2000.
Water is the major component of all living cells, and efficient regulation of water homeostasis is essential for many biological processes. The mechanism by which water passes through biological membranes was ...
We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via...
With the advent of gene-expression profiling, a large number of genes can now be investigated simultaneously during critical stages of development. This approach will be particularly informative in studies of ...
At the ends of eukaryotic chromosomes are telomeres, specialized structures with unusual properties. The repetitive structure of telomere regions makes them difficult to deal with in general genome-sequencing ...
DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress in this ...
This article is part of a Supplement: Volume 8 Supplement 1
The polarization of views on how best to exploit new information from the Human Genome Project for medicine reflects our ignorance of the genetic architecture underlying common diseases: are susceptibility all...
Planarian stem cells, or neoblasts, drive the almost unlimited regeneration capacities of freshwater planarians. Neoblasts are traditionally described by their morphological features and by the fact that they ...
A report on the first European Keystone symposium 'Multi-protein complexes involved in cell regulation', Cambridge, UK, 18-23 August 2006.
Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nemat...
From among a plethora of various gene delivery methods, the researcher must choose the right one according to availability for a given species and the precise application the transgenic animal is intended for....
This article is part of a Supplement: Volume 8 Supplement 1
The genomes of the malaria parasite, its vector and its host are now sequenced. This has been a tremendous scientific achievement. But will it offer hope to the millions who die from malaria each year? Yes, bu...
The recognition of microbe-associated molecular patterns during infection is central to the mounting of an effective immune response. In spite of their importance, it remains difficult to identify these molecu...
Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. Th...
Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a ...
Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We i...
In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adapta...
Proteome-wide sampling of function can be used to shed light on complex biological systems. Protein microarrays have now been used to investigate the substrate specificities of essentially all the protein kina...
Transcriptional analysis of all the genes expressed by breast tumors has provided the first steps towards defining a molecular signature for the disease, and might ultimately make conventional diagnostic techn...
Population metagenomics reveals the reduced metabolic capacities of a marine nitrogen-fixing cyanobacterium that lacks many of the signature features of typical cyanobacteria.
Surprising correlations between human disease phenotypes are emerging. Recent work now reveals startling phenotype connections between species, which could provide new disease models.
A report on the 35th Annual Lorne Genome Conference 2014 held in Lorne, Victoria, Australia, February 16–18, 2014.
The usual BLAST-based methods for assessing gene presence and absence lead to systematic overestimation of within-species gene gain by lateral transfer.
Immediately after a gene duplication event, the duplicate genes have redundant functions. Is natural selection therefore completely relaxed after duplication? Does one gene evolve more rapidly than the other? ...
A report on the joint Cold Spring Harbor/Wellcome Trust Meeting 'Interactome Networks', Hinxton, UK, 31 August-4 September 2005.
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