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New Window Opens on the Secret Life of Microbes: Scientists Develop First Microbial Profiles of Ecosystems
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Biochemical Genetics (v.45, #5-6)
Adaptive Evolution of the First Extra Exon in the Murid Rodent Prolactin Gene Family by Ying Li; Jing-Fei Huang; Ya-Ping Zhang (pp. 397-408).
The prolactin gene family in rodents consists of multiple members that coordinate the processes of reproduction and pregnancy. Some members of this family acquired one or two additional exons between exon 2 and exon 3 of the prototypical 5-exon, 4-intron structure, but the evolutionary importance of this insertion is unclear. Here, we focus on those members and survey this question by molecular evolutionary methods. Phylogenetic analysis shows that those members cluster into two distinct groups. Further analysis shows that the two groups of genes originated before the divergence of mouse and rat but after that of rodents from other mammals. We compared the d N/d S values for each branch of the gene tree but found no evidence to support positive selection for any branch. We found strong evidence, however, that one site (11E) of the 13 sites of the first extra exon underwent positive selection by the site-specific models of the maximum-likelihood method. Combining our molecular evolutionary analysis with other known functional evidence, we believe that the insertion of the extra exon implies some functional adaptation.
Keywords: adaptive evolution; gene family; prolactin; rodent
Population Genetic Analysis of Serbian Red Foxes (Vulpes vulpes) by Means of Mitochondrial Control Region Sequences by Julia Kirschning; Frank E. Zachos; Dusko Cirovic; Ivica T. Radovic; San San Hmwe; Günther B. Hartl (pp. 409-420).
A population genetic analysis based on sequences of the mitochondrial control region in 110 red foxes from five sampling localities in northern Serbia was carried out. The analysis yielded nine different haplotypes. Neither haplotype phylogeny nor their distribution was in accordance with the geographic location of the populations. In particular, the data failed to detect an unequivocal influence of the two big rivers, the Danube and the Tisza, separating the populations studied. Population differentiation was altogether low, without any relationship to the rivers as possible migration barriers. Although the possibility of foxes crossing the rivers over bridges or by swimming, thus keeping up gene flow, cannot be ruled out, it is most probable that the control region sequences are not sensitive enough to resolve small-scale population relationships but rather show patterns determined by stochastic processes such as genetic drift or lineage sorting.
Keywords: red fox; Vulpes vulpes ; Serbia; mitochondrial control region
Novel Mutations Found in Two Genes of Thai Patients with Isolated Methylmalonic Acidemia by Siriporn Keeratichamroen; James R. Ketudat Cairns; Phannee Sawangareetrakul; Somporn Liammongkolkul; Voraratt Champattanachai; Chantragan Srisomsap; Mahattana Kamolsilp; Pornswan Wasant; Jisnuson Svasti (pp. 421-430).
Molecular genetic analysis of three patients diagnosed with isolated methylmalonic acidemia (MMA) revealed that one was mut 0 MMA, with a mutation in the MUT gene encoding the l-methylmalonyl-CoA mutase (MCM), and two were cblB MMA, with mutations in the MMAB gene required for synthesizing the deoxyadenosylcobalamin cofactor of MCM. The mut 0 patient was homozygous for a novel nonsense mutation in MUT, p.R31X (c.167C → T), and heterozygous for three previously described polymorphisms, p.K212K (c.712A → G), p.H532R (c.1671A → G), and p.V671I (c.2087G → A). The new MMAB mutation, p.E152X (c.454G → T), was found to be homozygous in one cblB patient and heterozygous in the other patient, who also had four intron polymorphisms in this gene.
Keywords: methylmalonic acidemia; methylmalonyl-CoA mutase; cblB; mutation
Decreased total carbonic anhydrase esterase activity and decreased levels of carbonic anhydrase 1 isozyme in erythrocytes of type II diabetic patients by Kanwal K. Gambhir; Jehan Ornasir; Verle Headings; Adolphus Bonar (pp. 431-439).
In this exploratory study, we investigated total erythrocyte carbonic anhydrase (CA) estrase activity as well as CA I isozyme concentration in patients with diabetes mellitus type II (DM) and healthy individuals of Howard University Hospital community. Total estrase activity of CA was measured spectrophotometrically using p-nitrophenol acetate before and after inhibition with acetazolamide. CA I isozyme was measured by radial immunodiffusion using monoclonal antibody (CA I) in agarose plates. The study involved 20 consented participants; 10 normal (N) and 10 (DM), 21 to 84 years of age. The study was approved by the Howard University Institution Review Board. The CA activity was measured following lysis of cells as U/min/mL and CA I concentration as mg/l. We observed CA activity as 46.3±4(N) and 25±2.1 (DM) whereas CA I concentration as 1896±125 (N) and 1104 ±63 (DM). We speculate that the change in the CA activity may of fundamental importance in the regulation of intracellular; pHi for the basic control of metabolism in diabetes mellitus. Further, we propose that CA activity is a good candidate for a biomarker of diabetes mellitus for the early detection of insulin resistance because the CA activity variation was proportional to the severity of the diabetes.
Keywords: Carbonic anhydrase; carbonic anhydrase I isozyme; diabetes mellitus; erythrocyte; human red blood cell
Quality of Seeds Produced by Psychotria tenuinervis (Rubiaceae): Distance from Anthropogenic and Natural Edges of Atlantic Forest Fragment by Flavio Nunes Ramos; Juliana José; Vera Nisaka Solferini; Flavio A. M. Santos (pp. 441-458).
The aim of this study was to investigate whether there were differences in the genetic variability and rate and velocity of the seed germination produced by Psychotria tenuinervis located at anthropogenic edges, natural edges, and in the forest interior. The populations of P. tenuinervis showed no differences in genetic variability or structure among the three habitats. There was, however, an indication of inbreeding, which was significantly higher in natural edges than in anthropogenic edges and the forest interior. Within-habitat variation was considerable, but there were no differences in seed mass or rate and velocity of germination among the three habitats. These results suggest that seed characteristics were not influenced by the genetic pattern of P. tenuinervis and that other characteristics of the forest fragment, such as gaps, edge age, and type of matrix exert more influence on seed mass and germination than the distance from the edges.
Keywords: allozymes; edges; fragmentation; genetic variability; germination
Molecular cloning, mapping, and tissue expression of the porcine cluster of differentiation 14 (CD14) gene by Xiao-Tian Qiu; Yu-Hua Li; HeJun Li; Ying Yu; Qin Zhang (pp. 459-468).
CD14 plays an important role in initiating the innate response to lipopolysaccharide from Gram-negative bacteria. The gene and corresponding cDNA of porcine CD14 were sequenced and characterized. The porcine CD14 gene consists of two exons and a short intron (80 bp) located immediately after the ATG translation start codon. This structure is very similar to the CD14 gene of human, rat, mouse, rabbit, horse, and cow. The sequence of the porcine CD14 protein is 59–76% identical to that of rat, mouse, rabbit, human, horse, and cow CD14 protein. A highly conserved structure of the CD14 protein with respect to the leucine-rich repeats domain and the N-glycosylation sites was observed between species. Porcine CD14 was assigned to porcine chromosome 2q21 by a radiation hybrid panel. Using RT-PCR analysis, porcine CD14 transcripts were detected in liver, spleen, thymus, white matter, and skeletal muscle.
Keywords: CD14; Innate immunity; Leucine-rich repeats; Radiation hybrid panel; Gene expression
Isolation and sequence analysis of wheat NBS-LRR type disease resistance gene analogs using degenerate PCR primers by O. Bozkurt; E. E. Hakki; M. S. Akkaya (pp. 469-486).
Isolation of disease resistance gene analogs (RGAs) using the conserved motifs of the resistance genes has attracted considerable attention since it was first reported more than a decade ago. In this study, RGAs are isolated using homology-based PCR to target the nucleotide binding site (NBS) conserved regions from hexaploid wheat varieties and a few accessions of wild types. Based on sequence similarity analysis, 83 of the sequenced clones were clustered as groups. Of these RGAs, 40 were in the NBS-LLR class, containing kinase-1a (GGVGKTT or GGVGKTA), kinase-2 (KRFLIVLDDXW), kinase-3a (GSXIVVITTR or GCXVLATTR), and the GLPL motif of the NBS-spanning region. Among these, 15 contained possible intron regions, similar to Avena sativa O2 NBS-LLR type disease resistance gene (AF078874), and one to Rpm1 of rice and Yr10 and Lr10 of wheat. To our knowledge, this is the first observation of an intronic site within the P-loop domain of wheat RGAs. We detected an unspecified motif (VMVCVS) between the kinase-1a and kinase-2 domains within our clones. Additionally, one of the clones showed replacement with the kinase-3a motif with an undefined sequence.
Keywords: Resistance gene analog (RGA); Nucleotide binding site (NBS); Kinase2 and kinase3 motifs; Wheat
Genetic diversity and population differentiation of chestnut blight fungus, Cryphonectria parasitica, in China as revealed by RAPD by Boqian Yan; Zuozhou Li; Hongwen Huang; Ling Qin (pp. 487-506).
Seventeen Cryphonectria parasitica populations sampled from six regions in China were investigated using RAPD. Across all 169 isolates from the 17 populations evaluated, 52 of the 71 markers (73%) were polymorphic, total genetic diversity (h) was 0.1463, and Shannon’s index was 0.2312. Diversity within populations accounted for 74% of total genetic diversity, and genetic differentiation among populations was 0.26 (G ST = 0.26). Gene flow was 1.4 among the populations; higher gene flow was found among populations within regions and among regions [N m (G SR) = 2.8 and N m (G RT) = 3.5]. The unweighted pair group mean analysis (UPGMA) dendrogram revealed two distinct clusters: the northern China group and the southern China group. The spatial autocorrelation analysis revealed that the variation at most loci was randomly distributed and lacked spatial structure, but several loci and closer distances were spatially structured. Human activity and habitat could also be important factors affecting genetic structure among C. parasitica populations in China. Genetic diversity was highest in Southwest China, descending in an orderly fashion to Northeast China. This pattern indicated that Southwest China might be the center of origin of C. parasitica in China. The present study provides useful information for understanding the origin and spread of chestnut blight fungus in China and valuable data for formulating relevant strategies for controlling the disease in China.
Keywords: Cryphonectria parasitica ; Genetic diversity; Population genetic structure; Gene flow; Spatial autocorrelation