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Biochemical Genetics (v.41, #11-12)
Detection of Genetic Variability in Pearl Millet Downy Mildew (Sclerospora graminicola) by AFLP by R. Singru; S. Sivaramakrishnan; R. P. Thakur; V. S. Gupta; P. K. Ranjekar (pp. 361-374).
Downy mildew, caused by Sclerospora graminicola, is an economically important disease of pearl millet in the semiarid regions of Asia and Africa. Amplified restriction fragment length polymorphism (AFLP) was used to detect the extent of genomic variation among 19 fungal isolates from different cultivars of pearl millet grown in various regions of India. Fourteen AFLP primer combinations produced 184 polymorphic bands. An unweighted pair-group method of averages cluster analysis represented by dendrogram and principal coordinate analysis separated the mildew collections into four distinct groups. Isolates having characteristic opposite mating abilities, geographic relatedness, virulence, common host cultivars, and changes through asexual generations reflected heterogeneity of the pathogen. The use of AFLP to detect genetic variation is particularly important in selecting mildew isolates to screen breeding material for identification of resistant millet and monitoring changes in S. graminicola in relation to changes in host for effective disease management.
Keywords: AFLP; DNA fingerprinting; downy mildew fungus; pearl millet
The Bovine Mx1 Gene: Characterization of the Gene Structure, Alternative Splicing, and Promoter Region by Takatoshi Kojima; Kazunaga Oshima; Hiroko Watanabe; Masanori Komatsu (pp. 375-390).
The Mx gene encodes an antiviral protein and is induced by type I interferons (IFNs). In this study, a new bovine Mx gene (designated Mx1B) was isolated from the endometrial cDNA library of the early pregnant cow. Although the Mx1B cDNA contained a single open reading frame (ORF) the same as the known Mx1, the 5′ untranslated region (UTR) and 5′ coding region of Mx1B were rather different from the corresponding regions of Mx1 Genomic structure analysis revealed that bovine Mx1B was an alternative splicing variant of Mx1 and had transcription regulatory sequences in the upstream region. RT-PCR and its sequencing identified another Mx1 splicing variant and demonstrated that these bovine Mx1 splicing variants were ubiquitously expressed in various tissues. Furthermore, it was found that all the bovine breeds investigated had identical splice sites of Mx1 and Mx1B. It is speculated that cattle have at least two functional Mx isoforms that might provide strong natural resistance to specific viruses.
Keywords: bovine Mx1 ; DNA sequence; alternative splicing; gene expression
Biochemical and Population Genetics of the Rabbit, Oryctolagus cuniculus, Carbonic Anhydrases I and II, from the Iberian Peninsula and France by M. Branco; N. Ferrand (pp. 391-404).
Available studies on the biochemical and electrophoretic characterization of European rabbit (Oryctolagus cuniculus) carbonic anhydrases I and II (CAI, CAII) show contradictory results about their relative electrophoretic mobility and substrate specificity. After positive identification of carbonic anhydrase activity by CO2 hydration, the differential esterase activity of CAI and CAII toward β-napththyI acetate and flourescein diacetate,respectively, were used to identify the banding patterns corresponding to each locus. Electrophoretic and hybrid isoelectric focusing analyses of the CAI and CAII loci in 1 domestic and 19 wild rabbit populations led to the recognition of genetic polymorphism at the CAI locus and of extensive variability at the CAII locus. Four and nine alleles at the CAI and CAII loci, respectively, are described. The geographic distribution of genetic variability is consistent with the existence of two evolutionary groups within O. cuniculus.
Keywords: carbonic anhydrases; genetic polymorphism; specific enzyme detection; European rabbit; Oryctolagus cuniculus ; hybrid isoelectric focusing
A Rapid Method of Screening for N-Acetyltransferase (NAT2) Phenotype by Use of the WAVE DNA Fragment Analysis System by Aileen Osborne; Christine Bell; Faye Grant; Finlay Dick; Anthony Seaton; Neva Haites (pp. 405-411).
N-Acetyltransferase 2 (NAT2) is involved in Phase II biotransformation of a variety of toxicants. Polymorphisms in the NAT2gene result in a slow acetylator phenotype, which has been associated with various cancers and neurodegenerative diseases. To date most studies investigating NAT2 genotype/phenotype have adopted an RFLP approach, which is both expensive and time-consuming. Using the Wave DNA fragment analysis system, we have developed a fast and robust method of identifying two polymorphisms (C282T and T341C) of the NAT2 gene which allows identification of the most common slow acetylator alleles found in Caucasian populations: NAT2*5, NAT2*6, NAT2*7, and NAT2*14. This was done by comparing phenotype status in 126 samples genotyped by RFLP analysis and also by Wave analysis for the polymorphisms C282T and T341C. All 126 samples analyzed by both RFLP and Wave analysis gave consistent phenotype results and 100% correlation was achieved between the two methods.
Keywords: NAT2 ; WAVE DNA fragment analysis; genotyping; RFLP analysis
Induction of Suppressed ADH Activity in Drosophila pachea Exposed to Different Alcohols by Edward Pfeiler; Therese A. Markow (pp. 413-426).
Laboratory-reared males of the cactophilic Drosophila pachea exhibit a spontaneous and sex-specific suppression of alcohol dehydrogenase (ADH) activity within 4 days after eclosion. A lack of ADH activity also is usually seen in wild-caught males, although relatively high activity is always seen in female flies. In the present study we examined the effectiveness of different alcohols and related compounds, including several found naturally in necroses of the host cactus, to induce suppressed ADH activity in wild males of D. pachea and to serve as enzyme substrates. The primary alcohols (methanol, ethanol, 1-propanol, 1-butanol, and 1-pentanol), and the secondary alcohols (2-propanol and 2-butanol), each induced activity after 24 h exposure, although to different degrees. 1,2-Propanediol was usually effective as an inducer, but 2,3-butanediol usually was ineffective. Little or no induction was seen with 1-octanol, 2-pentanol, 3-methyl-1-butanol, 3-hydroxy-2-butanone, or acetaldehyde. Although the compounds tested varied in their ability to function as ADH substrates, methanol was the only alcohol that showed no activity staining. Ethanol induction of ADH activity was apparent after 3–6 h exposure and induced activity decreased dramatically within 1 week of flies being placed in an alcohol-free environment. Ethanol exposure did not induce ADH in adult female D. pachea, or in adult males and females of D. acutilabella in which control males show reduced ADH activity compared to females. The implications of the loss of ADH activity in adult males of D. pachea, as they relate to feeding ecology and fitness, are discussed.
Keywords: alcohol dehydrogenase; alcohol induction; Drosophila pachea ; fitness
Mitochondrial DNA Sequence-Based Population Genetic Structure of the Firefly, Pyrocoelia rufa (Coleoptera: Lampyridae) by Sang-Chul Lee; Jin-Sik Bae; Iksoo Kim; Hirobumi Suzuki; Seong-Ryul Kim; Jong-Gill Kim; Keun-Young Kim; Won-Jin Yang; Sang-Mong Lee; Hung-Dae Sohn; Byung-Rae Jin (pp. 427-452).
The genetic divergence, population genetic structure, and possible speciation of the Korean firefly, Pyrocoelia rufa, were investigated on the midsouthern Korean mainland, coastal islets, a remote offshore island, Jedu-do, and Tsushima Island in Japan. Analysis of DNA sequences from the mitochondrial COI protein-coding gene revealed 20 mtDNA-sequence-based haplotypes with a maximum divergence of 5.5%. Phylogenetic analyses using PAUP, PHYLIP, and networks subdivided the P. rufa into two clades (termed clade A and B) and the minimum nucleotide divergence between them was 3.7%. Clade A occurred throughout the Korean mainland and the coastal islets and Tsushima Island in Japan, whereas clade B was exclusively found on Jeju-do Island. In the analysis of the population genetic structure, clade B formed an independent phylogeographic group, but clade A was further subdivided into three groups: two covering western and eastern parts of the Korean peninsula, respectively, and the other occupying one eastern coastal islet and Japanese Tsushima Island. Considering both phylogeny and population structure of P. rufa, the Jeju-do Island population is obviously differentiated from other P. rufa populations, but the Tsushima Island population was a subset of the Korean coastal islet, Geoje. We interpreted the isolation of the Jeju-do population and the grouping of Tsushima Island with Korean coastal islets in terms of Late Pleistocene–Holocene events. The eastern–western subdivision on the Korean mainland was interpreted partially by the presence of a large major mountain range, which bisects the midpart of the Korean peninsula into western and eastern parts.
Keywords: firefly; Pyrocoelia rufa ; mitochondrial DNA; COI gene; population genetic structure; genetic diversity; speciation