Positive Darwinian selection on crustacean hyperglycemic hormone (CHH) of the green shore crab, Carcinus maenas

The tissue-specific expression and differential function of the crustacean hyperglycemic hormone (CHH) in Carcinus maenas indicate an interesting evolutionary history. Previous studies have shown that CHH from the sinus gland X-organ (XO-type) has hyperglycemic activity, whereas the CHH from the pericardial organ (PO-type) neither shows hyperglycemic activity nor it inhibits Y-organ ecdysteroid synthesis. Here we examined the types of selective pressures operating on the variants of CHH in Carcinus maenas. Maximum likelihood-based codon substitution analyses revealed that the variants of this neuropeptide in C. maenas have been subjected to positive Darwinian selection indicating adaptive evolution and functional divergence among the CHH variants leading to two unique groups (PO and XO-type). Although the average ratio of nonsynonymous to synonymous substitution (omega) for the entire coding region is 0.5096, few codon sites showed significantly higher omega (10.95). Comparison of models that incorporate positive selection (omega > 1) with models not incorporating positive selection (omega <1) at certain codon sites failed to reject (p=0) evidence of positive Darwinian selection.     

Insights into the role of d-amino acid oxidase mutations in amyotrophic lateral sclerosis

Missense mutations in the coding region of d -amino acid oxidase (DAO) have been found in patients suffering from amyotrophic lateral sclerosis (ALS). Mutations primarily impair the enzymatic activity of DAO and cause neurodegeneration due to an abnormal accumulation of d -serine in the spinal cord. However, the structural and dynamic changes that lead to impaired enzymatic activity are not fully understood. We present here extensive molecular dynamics simulations of wild-type, and all reported ALS-associated DAO mutants to elucidate the plausible mechanisms of impaired enzymatic activity, a critical function needed for neuroprotection. Simulation results show that DAO mutations disrupt several key interactions with the active site residues and decrease the conformational flexibility of active site loop comprising 216 to 228 residues, necessary for substrate binding and product release. This conformational restriction of the active site loop in the mutants is mainly due to the distortion of critical salt bridge and hydrogen bond interactions compared with wild-type. Furthermore, binding free energy calculations show that DAO mutants have a lower binding affinity toward cofactor flavin adenine dinucleotide and substrate imino-serine than the wild-type. A closer look at the cofactor and substrate interaction profiles further show that DAO mutants have lost several critical interactions with the neighboring residues as compared with wild-type. Taken together, this study provides first-hand explanation of crucial structural features that lead to the loss of enzymatic function in DAO mutants and highlights the need of further genomic scans of patients with ALS to map the association of novel DAO variants in ALS pathophysiology.     

RMND5 from Xenopus laevis Is an E3 Ubiquitin-Ligase and Functions in Early Embryonic Forebrain Development

In Saccharomyces cerevisiae the Gid-complex functions as an ubiquitin-ligase complex that regulates the metabolic switch between glycolysis and gluconeogenesis. In higher organisms six conserved Gid proteins form the CTLH protein-complex with unknown function. Here we show that Rmnd5, the Gid2 orthologue from Xenopus laevis, is an ubiquitin-ligase embedded in a high molecular weight complex. Expression of rmnd5 is strongest in neuronal ectoderm, prospective brain, eyes and ciliated cells of the skin and its suppression results in malformations of the fore- and midbrain. We therefore suggest that Xenopus laevis Rmnd5, as a subunit of the CTLH complex, is a ubiquitin-ligase targeting an unknown factor for polyubiquitination and subsequent proteasomal degradation for proper fore- and midbrain development.     

Protonated 4′-(2-pyridyl)-2,2′:6′,2″-terpyridine and its Fe(II) bischelates: Syntheses and molecular structures

Compounds of the molecular formulae, [LH₃](NO₃)₃ (1), [Fe(LH)₂](PF₆)₄·5H₂O (2), [Fe(L)₂][Fe(L)(LH)](PF₆)₅·H₂O (3), [Fe(L)₂][Fe(L)(LH)](BF₄)₅·2H₂O (4) and [Fe(L)₂](Cr₂O₇)·6H₂O (5) have been synthesized using 4′-(2-pyridyl)-2,2′:6′,2″-terpyridine (L). The molecular structures of all the compounds were determined. The Fe(II) complexes are high spin in nature at room temperature and upon cooling a gradual spin-transition is observed. Among 1-5, hydrogen-bonding, π···π, and anion···π interactions as well as water tetramer and pentamer are present in the molecular packing.     

Intra-Host Diversity and Emergence of Unique GBV-C Viral Lineages in HIV Infected Subjects in Central China

GB virus C (GBV-C), which is highly prevalent among HIV/AIDS, seemed to slow the HIV disease progression. The HIV/GBV-C co-infected individuals may represent an interesting model for the investigation of the role played by HIV infection and/or the immune system in driving the evolution of the GBV-C viral populations. The present study investigated the prevalence and population dynamics of GB virus C in HIV infected individuals representing 13 geographic regions of Hubei Province of China. Approximately 37% of HIV-1 infected individuals were infected with GBV-C and genotype 3 is appeared to be predominant. Utilizing the 196 complete E2 nucleotide sequence data from 10 HIV/GBV-C infected individuals and employing coalescence based phylogenetic approaches; the present study has investigated the intra-host dynamics of GBV-C. The results revealed patient-specific unique GBV-C viral lineages and each viral lineage showed the evidence of rapid population expansion in respective HIV-1 infected patients, thus suggesting HIV-1 was unlikely to have been inhibiting effect on the GBV-C viral replication. GBV-C in all patients has experienced intense purifying selection, suggesting the GBV-C viral invasion and subsequent expansion within the HIV-1 infected hosts without any modification of the functional epitopes at their membrane protein. The finding of within host GBV-C recombinant sequences indicated recombination was one of the significant forces in the evolution and divergence of GBV-C.     

FHL5, a novel actin-binding protein, is highly expressed in eel gill pillar cells and responds to wall tension

Supporting evidence for the contractile nature of fish branchial pillar cells was provided by demonstrating the presence of actin fibers and a novel four-and-a-half LIM (FHL) protein in which expression is specific for contractile tissues and sensitive to the tension applied to the pillar cell. When eel gill sections were stained with rhodamine-phalloidin, a selective fluorescent probe for fibrous actin, a strong bundle-like staining was observed around collagen columns in pillar cells, suggesting the presence of abundant actin fibers. A cDNA clone encoding a novel member of the actin-binding FHL family, FHL5, was isolated from a subtracted cDNA library of eel gill. Northern analysis revealed that FHL5 mRNA is highly expressed only in gills, heart, and skeletal muscle. In gills, FHL5 was found to be confined to pillar cells by immunohistochemistry. Confocal fluorescence microscopy showed that FHL5 is present in both cytosol and nucleus; within the cytosol, a large portion of FHL5 is colocalized with the phalloidin-positive actin bundles. Furthermore, transfection of myogenic C2C12 cells with FHL5 cDNA demonstrated, in addition to its interaction with actin stress fibers, a nuclear shuttling activity of FHL5. The mRNA and protein levels were found to be elevated on 1) transfer of eels from seawater to freshwater, 2) volume expansion by infusion of isotonic dextran-saline, and 3) constriction of gill vasculature by bolus injection of endothelin-1. These results suggest contractile nature of pillar cells and a role of FHL5 in maintaining the integrity and regulating the dynamics of pillar cells.     

Sequence Polymorphism of GroEL Gene in Natural Population of Bacillus and Brevibacillus spp. that Showed Variation in Thermal Tolerance Capacity and mRNA Expression

GroEL, a class I chaperonin, plays an important role in the thermal adaptation of the cell and helps to maintain the viability of the cell under heat shock condition. Function of groEL in vivo depends on the maintenance of proper structure of the protein which in turn depends on the nucleotide and amino acid sequence of the gene. In this study, we investigated the changes in nucleotide and amino acid sequences of the partial groEL gene that may affect the thermotolerance capacity as well as mRNA expression of bacterial isolates. Sequences among the same species having differences in the amino acid level were identified as different alleles. The effect of allelic variation on the groEL gene expression was analyzed by comparison and relative quantification in each allele under thermal shock condition by RT-PCR. Evaluation of K _a/K _s ratio among the strains of same species showed that the groEL gene of all the species had undergone similar functional constrain during evolution. The strains showing similar thermotolerance capacity was found to carry same allele of groEL gene. The isolates carrying allele having amino acid substitution inside the highly ATP/ADP or Mg²⁺-binding region could not tolerate thermal stress and showed lower expression of the groEL gene. Our results indicate that during evolution of these bacterial species the groEL gene has undergone the process of natural selection, and the isolates have evolved with the groEL allelic sequences that help them to withstand the thermal stress during their interaction with the environment.     

Geographic variation within a tandemly repeated mitochondrial DNA D-loop region of a North American freshwater fish, Pylodictis olivaris

The present study reports the distribution of a 35-bp mitochondrial DNA (mtDNA) D-loop tandemly repeated sequence in the populations of a North American freshwater catfish, Pylodictis olivaris, and the important role of a past geological event in the phylogeographic pattern of this species. A total of 330 individuals of flathead catfish, representing 34 drainages throughout the species' native range in the United States, were collected. While more than 70% of individuals sampled from the Southeastern Gulf Coast drainages were characterized by the presence of a 35-bp mtDNA D-loop tandem repeat proximal to the 5′ end, more than 95% of samples from the Mississippi River and its tributaries, as well as from the drainages of the Southwest Gulf Coast region, lack this tandem repeat. Concomitantly, phylogenetic analyses revealed the existence of two distinct matrilineal lineages (lineage I and II) of P. olivaris, which were estimated to have diverged from a common ancestor sometime between 0.70 and 2.05 myr ago. While one lineage is comprised of samples from the Mississippi River and its tributaries and rivers draining to the Southwest Gulf Coast, the other lineage is comprised of samples from the Southeastern Gulf Coast drainages. Each lineage also has two sub-lineages, which also showed geographic specificity.