Single nucleotide polymorphisms,haplotypes and combined genotypes of lactoferrin gene and their associations with mastitis in Chinese Holstein cattle

Lactoferrin (Lf) is naturally produced by the mammary gland, having biological functions of antibacterial and anti-inflammatory activities. To investigate whether the Lf gene is associated with mastitis in dairy cattle, a DNA sequencing approach was used to identify single nucleotide polymorphisms (SNPs) in the gene. Three previously reported SNPs in the 5′ flanking region and one novel SNP in exon1 of Lf gene were identified. A total of 353 individuals from Holstein cattle populations were genotyped for their SNPs using Created Restriction Site PCR (CRS-PCR) and PCR-RFLP methods. Twenty-two and nineteen combinations of three SNPs (g.3440T>G, g.3879_3880insG, and g.4432T>C) and another three SNPs (g.3429G>A, g.3440T>G, g.3879_3880insG) were observed, respectively. The result of haplotype analysis of four SNPs showed that fourteen different haplotypes were identified. Two major haplotypes (GECB and GECA) occurred with a frequency of 22.5 and 18.5% in the study population, respectively. Statistical analyses revealed no significant association between one single SNP of Lf gene and SCS, whereas significant associations between their combined genotypes of three SNPs, haplotype and SCS. Combined genotype EFCDBB and GGEFDD with the lowest SCS were favorable for the mastitis resistance. They may be used as a possible candidate for marker-assisted selection in dairy cattle breeding program.     

Biodegradation of <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis> diethylaniline in a contaminated aquifer: laboratory- and field-scale evidences

The effectiveness of biosparging to mitigate N,N diethylaniline in aquifer was evaluated by measuring the time course of decrease in concentration of the aforementioned compound in aerobic microcosm experiments. The first-order kinetic constant for N,N diethylaniline aerobic biodegradation was estimated from microcosm data (0.037 ± 0.004 d⁻¹), and the value was consistent with the best-fitting value in the transport and reaction model of the aquifer (0.020 d⁻¹). Furthermore, the biodegradability of the compound was evaluated under anaerobic condition in microcosm experiments, which was supported by field modelling. There was no significant degradation in the anaerobic microcosm experiments, confirming the recalcitrance of N,N diethyl aniline under the aforementioned aquifer condition.     

Identifying hybridizing taxa within the <Emphasis Type="Italic">Daphnia longispina</Emphasis> species complex: a comparison of genetic methods and phenotypic approaches

Daphnia galeata Sars, D. longispina O. F. Müller and D. cucullata Sars (Crustacea: Cladocera) are closely related species which often produce interspecific hybrids in natural populations. Several marker systems are available for taxon determination in this hybridizing complex, but their performance and reliability has not been systematically assessed. We compared results from identifications by three molecular methods. More than 1,200 individuals from 10 localities in the Czech Republic were identified as parental species or hybrids by allozyme electrophoresis and the analysis of the restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP); over 440 of them were additionally analyzed and identified by 12 microsatellite loci. Identification by microsatellite markers corresponded well with allozyme analyses. However, consistent discrepancies between ITS-RFLP and other markers were observed in two out of 10 studied localities. Although some marker discrepancies may have been caused by occasional recent introgression, consistent deviations between ITS-RFLP and other markers suggest a long-term maintenance of introgressed alleles. These results warn against its use as a sole identification method in field studies. Additionally, we quantitatively evaluated the discriminatory power of geometric morphometric (elliptic Fourier) analysis of body shapes based on photos of over 1,300 individuals pre-classified by allozyme markers. Furthermore, a randomly selected subset of 240 individuals was independently determined from photos by several experts. Despite a tendency for morphological divergence among parental Daphnia species, some taxa (especially D. galeata, D. longispina, and their hybrids) substantially overlapped in their body shapes. This was reflected in different determination success for particular species and hybrids in discriminant analysis based on shape data as well as from photographs.     

Resistance against various fungal pathogens and reniform nematode in transgenic cotton plants expressing Arabidopsis <Emphasis Type="Italic">NPR1</Emphasis>

Cotton is an economically important crop worldwide that suffers severe losses due to a wide range of fungal/bacterial pathogens and nematodes. Given its susceptibility to various pathogens, it is important to obtain a broad-spectrum resistance in cotton. Resistance to several fungal and bacterial diseases has been obtained by overexpressing the Non-expressor of Pathogenesis-Related genes-1 (NPR1) in various plant species with apparently minimal or no pleiotropic effects. We examined the efficacy of this approach in cotton by constitutive expression of the Arabidopsis (Arabidopsis thaliana) NPR1 gene. The results show that NPR1-expressing lines exhibited significant resistance to Verticillium dahliae isolate TS2, Fusarium oxysporum f. sp. vasinfectum, Rhizoctonia solani, and Alternaria alternata. Interestingly, the transformants also showed significant resistance to reniform nematodes. Analysis of defense-related, biochemical and molecular responses suggest that when challenged with pathogens or certain systemic acquired resistance-inducing chemicals, the transgenic lines respond to a greater degree compared to the wild-type plants. Importantly, the basal activities of the defense-related genes and enzymes in uninduced transformants were no different than those in their non-transgenic counterparts. The results provide additional evidence supporting the role of NPR1 as an important part of the plant defense system and suggest a means to achieve broad-spectrum resistance to pathogens via genetic engineering.     

Development of acaricide resistance in Pacific spider mite (<Emphasis Type="Italic">Tetranychus pacificus</Emphasis>) from California vineyards

In recent years, grape growers in California reported failures of acaricides against Tetranychus pacificus McGregor. We collected T. pacificus populations from four vineyards and tested them for resistance to bifenazate, propargite and pyridaben. In addition, we sequenced part of the cytochrome b gene of bifenazate-resistant and -susceptible T. pacificus to test for the presence of mutations reported to confer resistance to the congeneric T. urticae. None of the mutations conferring resistance to bifenazate in T. urticae were present in resistant T. pacificus. Resistance levels ranged from full susceptibility to statistically significant 11-fold resistance to pyridaben, sevenfold resistance to bifenazate and fourfold resistance to propargite compared to a susceptible population. Despite the relatively low levels of resistance detected, we estimated that under the conditions of our study the highest field rates of bifenazate and pyridaben application would cause less than 58 and 66% mortality of adult females in the most resistant populations, respectively. In contrast, field rates of propargite application would cause close to 100% mortality in the least susceptible population. These results highlight a potential link between resistance development and reduced field effectiveness for bifenazate and pyridaben. Finally, T. pacificus may be more tolerant to bifenazate and propargite than T. urticae, since the LC₅₀ values for the susceptible population of T. pacificus were several times higher than LC₅₀’s reported for susceptible T. urticae.     

WaveletQuant,an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis

Background  

Quantitative proteomics technologies have been developed to comprehensively identify and quantify proteins in two or more complex samples. Quantitative proteomics based on differential stable isotope labeling is one of the proteomics quantification technologies. Mass spectrometric data generated for peptide quantification are often noisy, and peak detection and definition require various smoothing filters to remove noise in order to achieve accurate peptide quantification. Many traditional smoothing filters, such as the moving average filter, Savitzky-Golay filter and Gaussian filter, have been used to reduce noise in MS peaks. However, limitations of these filtering approaches often result in inaccurate peptide quantification. Here we present the WaveletQuant program, based on wavelet theory, for better or alternative MS-based proteomic quantification.     

Antibiotic susceptibility profiles of some <Emphasis Type="Italic">Vibrio</Emphasis> strains isolated from wastewater final effluents in a rural community of the Eastern Cape Province of South Africa

Background  

To evaluate the antibiogram and antibiotic resistance genes of some Vibrio strains isolated from wastewater final effluents in a rural community of South Africa. V. vulnificus (18), V. metschnikovii (3), V. fluvialis (19) and V. parahaemolyticus (12) strains were isolated from final effluents of a wastewater treatment plant (WWTP) located in a rural community of South Africa. The disk diffusion method was used for the characterization of the antibiogram of the isolates. Polymerase chain reaction (PCR) was employed to evaluate the presence of established antibiotic resistance genes using specific primer sets.     

A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase

Background  

Meiotic prophase is a critical stage in sexual reproduction. Aberrant chromosome recombination during this stage is a leading cause of human miscarriages and birth defects. However, due to the experimental intractability of mammalian gonads, only a very limited number of meiotic genes have been characterized. Here we aim to identify novel meiotic genes important in human reproduction through computational mining of cross-species and cross-sex time-series expression data from budding yeast, mouse postnatal testis, mouse embryonic ovary, and human fetal ovary.