The evolution and structure of snake venom phosphodiesterase (svPDE) highlight its importance in venom actions.

For decades, studies of snake venoms focused on the venom-ome-specific toxins (VSTs). VSTs are dominant soluble proteins believed to contribute to the main venomous effects and emerged into gene clusters for fast adaptation and diversification of snake venoms. However, the conserved minor venom components, such as snake venom phosphodiesterase (svPDE), remain largely unexplored.

A genome-wide association study (GWAS) of the personality constructs in CPAI-2 in Taiwanese Hakka populations.

Here in this study we adopted genome-wide association studies (GWAS) to investigate the genetic components of the personality constructs in the Chinese Personality Assessment Inventory 2 (CPAI-2) in Taiwanese Hakka populations, who are likely the descendants of a recent admixture between a group of Chinese immigrants with high emigration intention and a group of the Taiwanese aboriginal population generally without it. A total of 279 qualified participants were examined and genotyped by an Illumina array with 547,644 SNPs to perform the GWAS. Although our sample size is small and that unavoidably limits our statistical power (Type 2 error but not Type 1 error), we still found three genomic regions showing strong association with Enterprise, Diversity, and Logical vs.

MicroRNA retrocopies generated via L1-mediated retrotransposition in placental mammals help to reveal how their parental genes were transcribed.

In mammalian genomes, most retrocopies emerged via the L1 retrotransposition machinery. The hallmarks of an L1-mediated retrocopy, i.e.

Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase.

The discriminator base N73 is a key identity element of tRNA. In eukaryotes, N73 is an "A" in cytoplasmic tRNA and a "C" in mitochondrial tRNA. We present evidence herein that yeast histidyl-tRNA synthetase (HisRS) recognizes both A73 and C73, but somewhat prefers A73 even within the context of mitochondrial tRNA.

Triple-layer dissection of the lung adenocarcinoma transcriptome: regulation at the gene, transcript, and exon levels.

Lung adenocarcinoma is one of the most deadly human diseases. However, the molecular mechanisms underlying this disease, particularly RNA splicing, have remained underexplored. Here, we report a triple-level (gene-, transcript-, and exon-level) analysis of lung adenocarcinoma transcriptomes from 77 paired tumor and normal tissues, as well as an analysis pipeline to overcome genetic variability for accurate differentiation between tumor and normal tissues.

Differentiation of visual spectra and nuptial colorations of two subspecies (Cyprinoidea: Acheilognathidae) in response to the distinct photic conditions of their habitats.

Background: Vision, an important sensory modality of many animals, exhibits plasticity in that it adapts to environmental conditions to maintain its sensory efficiency. Nuptial coloration is used to attract mates and hence should be tightly coupled to vision. In Taiwan, two closely related bitterlings ( and ) with different male nuptial colorations reside in different habitats.

Divergent Alanyl-tRNA Synthetase Genes of Vanderwaltozyma polyspora Descended from a Common Ancestor through Whole-Genome Duplication Followed by Asymmetric Evolution.

Cytoplasmic and mitochondrial forms of a eukaryotic aminoacyl-tRNA synthetase (aaRS) are generally encoded by two distinct nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. However, in most known yeasts, only the mitochondrial-origin alanyl-tRNA synthetase (AlaRS) gene is retained and plays a dual-functional role. Here, we present a novel scenario of AlaRS evolution in the yeast Vanderwaltozyma polyspora.

The complete mitochondrial genome of the crocodile shark, Pseudocarcharias kamoharai (Chondrichthyes, Lamnidae).

The complete mitochondrial genome of the crocodile shark consists of 16,688 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 replication origin region, and 1 control region. The mitochondrial gene arrangement of the crocodile shark is the same as that of most vertebrates. Base composition of the genome is A (32.

Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species.

Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships.

Complete mitochondrial genome of the longfin mako shark, Isurus paucus (Chondrichthyes, Lamnidae).

Here we describe the complete mitochondrial genome sequence of the longfin mako, Isurus paucus, which is a pelagic shark found in temperate and tropical waters. The circle genome (16,704 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.

The complete mitochondrial genome of the salmon shark, Lamna ditropis (Chondrichthyes, Lamnidae).

The complete mitochondrial genome of the salmon shark consists of 16,699 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the salmon shark is the same as that of most vertebrates. Base composition of the genome is A (29.

The complete mitochondrial genome of the sand tiger shark, Carcharias taurus (Chondrichthyes, Odontaspididae).

The complete mitochondrial genome of the sand tiger shark consists of 16,773 bp and including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the sand tiger shark is the same as the one observed in most vertebrates. Base composition of the genome is A (31.

The complete mitochondrial genome of the shortfin mako, Isurus oxyrinchus (Chondrichthyes, Lamnidae).

The complete mitochondrial genome of the shortfin mako (Isurus oxyrinchus) was determined by using a PCR-based method. The total length of mitochondrial DNA is 16,701 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region, and 1 control region. The mitochondrial gene arrangement of the tiger tail seahorse is also matching the one observed in the most vertebrate creatures.

The complete mitochondrial genome of the Rhodeus shitaiensis (Teleostei, Cypriniformes, Acheilognathidae).

The complete mitochondrial genome of the Rhodeus shitaiensis was determined by using a PCR-based method. The total length of mitochondrial DNA of this bitterling is 16,774 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the R.

The complete mitochondrial genome of the great white shark, Carcharodon carcharias (Chondrichthyes, Lamnidae).

The complete mitochondrial genome of the great white shark having 16,744 bp and including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the great white shark is the same as the one observed in the most vertebrates. Base composition of the genome is A (30.

Complete mitochondrial genome of the megamouth shark Megachasma pelagios (Chondrichthyes, Megachasmidae).

Here we describe the complete mitochondrial genome sequence of the megamouth shark, Megachasma pelagios, which is an extremely rare species of deepwater shark. The circle genome (16,694 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.

The complete mitochondrial genome of the big-eye thresher shark, Alopias superciliosus (Chondrichthyes, Alopiidae).

The complete mitochondrial genome of the big-eye thresher shark was sequenced using a polymerase chain reaction (PCR)-based method. The total length of mitochondrial DNA is 16,719 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the big-eye thresher shark is the same as the one observed in the most vertebrates.

The complete mitochondrial genome of the three-spot seahorse, Hippocampus trimaculatus (Teleostei, Syngnathidae).

The complete mitochondrial genome of the three-spot seahorse was sequenced using a polymerase chain reaction-based method. The total length of mitochondrial DNA is 16,535 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The mitochondrial gene order of the three-spot seahorse also conforms to the distinctive vertebrate mitochondrial gene order.

The complete mitochondrial genome of the tiger tail seahorse, Hippocampus comes (Teleostei, Syngnathidae).

The complete mitochondrial genome of the tiger tail seahorse was sequenced using a polymerase chain reaction-based method. The total length of mitochondrial DNA is 16,525 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of the tiger tail seahorse is also matching the one observed in the most vertebrate creatures.

Evolutionary information hidden in a single protein structure.

The knowledge of conserved sequences in proteins is valuable in identifying functionally or structurally important residues. Generating the conservation profile of a sequence requires aligning families of homologous sequences and having knowledge of their evolutionary relationships. Here, we report that the conservation profile at the residue level can be quantitatively derived from a single protein structure with only backbone information.

A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples.

A practical way to reduce the cost of surveying single-nucleotide polymorphism (SNP) in a large number of individuals is to measure the allele frequencies in pooled DNA samples. Pyrosequencing(TM) has been frequently used for this application because signals generated by this approach are proportional to the amount of DNA templates. The Pyrosequencing(TM) pyrogram is determined by the dispensing order of dNTPs, which is usually designed based on the known SNPs to avoid asynchronistic extensions of heterozygous sequences.

Using a strategy based on the concept of convergent evolution to identify residue substitutions responsible for thermal adaptation.

Factors that are related to thermostability of proteins have been extensively studied in recent years, especially by comparing thermophiles and mesophiles. However, most of them are global characters. It is still not clear how to identify specific residues or fragments which may be more relevant to protein thermostability.

Fast evolution of core promoters in primate genomes.

Despite much interest in regulatory evolution, how promoters have evolved remains poorly studied, mainly owing to paucity of data on promoter regions. Using a new set of high-quality experimentally determined core promoters of the human genome, we conducted a comparative analysis of 2,492 human and rhesus macaque promoters and their neighboring nearly neutral regions. We found that the core promoters have an average rate of nucleotide substitution substantially higher than that at 4-fold degenerate sites and only slightly lower than that for the assumed neutral controls of neighboring noncoding regions, suggesting that core promoters are subject to very weak selective constraints.