Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia.

The genetic variation in Northern Asian populations is currently undersampled. To address this, we generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The cataloged variation in the panel shows strong population stratification among these tribes, which correlates with the diverse demographic histories in the region.

Functional and phylogenetic characterization of noncanonical vitamin B-binding proteins in zebrafish suggests involvement in cobalamin transport.

In humans, transport of food-derived cobalamin (vitamin B) from the digestive system into the bloodstream involves three paralogous proteins: transcobalamin (TC), haptocorrin (HC), and intrinsic factor (IF). Each of these proteins contains two domains, an α-domain and a β-domain, which together form a cleft in which cobalamin binds. Zebrafish () are thought to possess only a single cobalamin transport protein, referred to as Tcn2, which is a transcobalamin homolog.

Multiple non-catalytic ADAMs are novel integrin α4 ligands.

The ADAM (a disintegrin and metalloprotease) protein family uniquely exhibits both catalytic and adhesive properties. In the well-defined process of ectodomain shedding, ADAMs transform latent, cell-bound substrates into soluble, biologically active derivatives to regulate a spectrum of normal and pathological processes. In contrast, the integrin ligand properties of ADAMs are not fully understood.

BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees.

The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on hand. BuddySuite is a collection of four independent yet interrelated command-line toolkits that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction.

Pannexin 3 is required for late stage bone growth but not for initiation of ossification in avian embryos.

Background: Pannexin 3 (PANX3) is a channel-forming protein capable of stimulating osteogenesis in vitro. Here, we studied the in vivo roles of PANX3 in the chicken embryo using the RCAS retroviral system to over-express and knockdown expression during endochondral bone formation.

Results: In the limbs, PANX3 RNA was first detected in the cartilage condensations and became restricted to the prehypertrophic cartilage of the epiphyses, diaphysis, and perichondrium.

The pannexins: past and present.

The pannexins (Panxs) are a family of chordate proteins homologous to the invertebrate gap junction forming proteins named innexins. Three distinct Panx paralogs (Panx1, Panx2, and Panx3) are shared among the major vertebrate phyla, but they appear to have suppressed (or even lost) their ability to directly couple adjacent cells. Connecting the intracellular and extracellular compartments is now widely accepted as Panx's primary function, facilitating the passive movement of ions and small molecules along electrochemical gradients.

Pannexin 1 ohnologs in the teleost lineage.

Advances in genomic analysis indicate that the early chordate lineage underwent two whole-genome duplication events in fairly rapid succession around 400-600 million years ago, and that a third duplication event punctuated the radiation of ray-finned fishes (teleosts) around 320-350 million years ago. Connexin ohnologs have been disproportionately well maintained in the teleost genome following this third event, implying that gap junction proteins are amenable to neofunctionalization. A second family of gap junction-like proteins, the pannexins, is also present in chordates, but expansion of this family following the teleost whole-genome duplication has not been addressed in the literature.

RF-Cloning.org: an online tool for the design of restriction-free cloning projects.

Restriction-free cloning (RF-cloning) is a PCR-based technology that expands on the QuikChange™ mutagenesis process originally popularized by Stratagene in the mid-1990s, and allows the insertion of essentially any sequence into any plasmid at any location. While RF-cloning is a powerful tool for the design of custom plasmids when restriction sites are not conveniently situated, manually designing the requisite primers can be tedious and error prone. We present here a web-service that automates the primer design process, along with a user interface that includes a number of useful tools for managing both the input sequences and the resulting outputs.

Pannexin 3 is a novel target for Runx2, expressed by osteoblasts and mature growth plate chondrocytes.

Pannexins are a class of chordate channel proteins identified by their homology to insect gap junction proteins. The pannexin family consists of three members, Panx1, Panx2, and Panx3, and the role each of these proteins plays in cellular processes is still under investigation. Previous reports of Panx3 expression indicate enrichment in skeletal tissues, so we have further investigated this distribution by surveying the developing mouse embryo with immunofluorescence.

Stress and interpopulation variation in glycolytic enzyme activity and expression in a teleost fish Fundulus heteroclitus.

Northern populations of Fundulus heteroclitus have twofold greater activity of lactate dehydrogenase-B (LDH-B) than southern populations, but exposure to stress increases LDH-B in southern populations, abolishing this difference. To test whether differences in the activity of other hepatic glycolytic enzymes between populations are sensitive to stress, we injected fish with a pharmacological dose of cortisol in coconut oil (400 microg g(-1)) or exposed them to handling stress and measured the activities of all the glycolytic enzymes. At rest, liver phosphofructokinase (PFK) and aldolase (ALD) activities were greater in southern fish, whereas LDH-B activity was greater in northern fish.