The microbial food web along salinity gradients

The microbial food web was studied along a gradient of salinity in two solar salterns used for the commercial production of salt. The different ponds in the salterns provide a wide range of ecosystems with food webs of different complexities. Abundance of prokaryotes, cell volume, prokaryotic heterotrophic production, chlorophyll a, abundance of heterotrophic flagellates, ciliates and phytoplankton were determined in several ponds in each saltern. Increases in salinity resulted in a progressive reduction in the abundance and number of different groups of eukaryotic microorganisms present, but an increase in biomass of prokaryotes. Maximal activity of both phyto- and bacterioplankton was found at a salinity of around 100 per thousand, where there was also a maximum in chlorophyll a concentration. Growth rates of heterotrophic prokaryotes decreased with increasing salinity. Bacterivory disappeared above 250 per thousand salinity, whereas other loss factors such as viral lysis appeared to be of minor importance throughout the gradient [Guixa-Boixereu et al. (1996) Aquat. Microb. Ecol. 11, 215-227].     

Semiautomated clone verification by real-time PCR using molecular beacons

Conventional, high-throughput PCR analysis of common elements utilizing numerous primer sets and template DNA requires multiple rounds of PCR to ensure optimal conditions. Laborious gel electrophoresis and staining is then necessary to visualize amplification products. We propose novel multicolor molecular beacons, to establish a high-throughput, PCR-based sequence tagged site (STS) detection system that swiftly and accurately confirms marker content in template containing common repeat elements. A simple, one-tube, real-time PCR assay system was developed to specifically detect regions containing CA and GATA repeats. Ninety-six samples can be confirmed for marker content in a closed-tube format in 3 h, eliminating product confirmation on agarose gels and avoiding crossover contamination. Multiple STSs can be detected simultaneously in the same reaction tube by utilizing molecular beacons labeled with multicolor fluorophores. Template DNA from 260 RPCI-11 bacterial artificial chromosome (BAC) clones was examined for the presence of CA and/or GATA repeats using molecular beacon PCR and compared with conventional PCR results of the same clones. Of the 205 clones containing CA and GATA repeats, we were able to identify 129 clones (CA, n = 99; GATA, n = 30) by using molecular beacons and only 121 clones (CA, n = 92; GATA, n = 29) by conventional PCR amplification. As anticipated, 55 clones that contained sequences other than CA or GATA failed molecular beacon detection. Molecular beacon PCR, employing beacons specific for tandem repeat elements, provides a fast, accurate, and sensitive multiplex detection assay that will expedite verification of marker content in a multitude of template containing these repeats.     

Marsupials and monotremes sort genome treasures from junk

A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species.     

Novel monoclonal antibody-based Helicobacter pylori stool antigen test

BACKGROUND: A number of noninvasive tests have been developed to establish the presence of Helicobacter pylori infection. Although polyclonal antibody-based stool antigen testing has a good sensitivity and specificity, it is less accurate than urea breath testing. Recently, a monoclonal antibody-based stool antigen test demonstrated an excellent performance in diagnosing H. pylori infection in adults and in pediatric populations. AIM: To evaluate the diagnostic accuracy of a novel stool test based on monoclonal antibodies to detect H. pylori antigens in frozen human stool in the pretreatment setting. PATIENTS AND METHODS: Stool specimens were prospectively collected from 78 patients undergoing gastroscopy and stored at -20 degrees C until tested. Helicobacter pylori infection was evaluated by histology, rapid urease testing and urea breath tests ((13)C-UBT). Positivity of the three tests was considered the gold standard for H. pylori active infection. Patients with no positive test were considered negative. The gold standard was compare to the results of the monoclonal antibody stool antigen test. Frozen stool specimens were tested using a novel monoclonal-antibody-based enzyme immunoassay (HePy-Stool, Biolife-Italiana, Milan, Italy). RESULTS: The sensitivity and specificity of the monoclonal stool antigen test were 97%[95% confidence interval, (CI) 86-100] and 94% (95% CI: 81-99), respectively. Negative and positive predictive values were 97% (95% CI: 85-99), and 95% (95% CI: 83-99), respectively. The diagnostic accuracy was 96% (95% CI: 88-99). The likelihood ratio for a positive test was 17 and for a negative test was 0. CONCLUSIONS: Although the (13)C-UBT is the most accurate among the available noninvasive tests, our results show that an H. pylori stool test using monoclonal antibody might be an excellent alternative.     

Mapping the Naked Neck (NA) and Polydactyly (PO) mutants of the chicken with microsatellite molecular markers

The bulked segregant analysis methodology has been used to map, with microsatellite markers, two morphological mutations in the chicken: polydactyly (PO) and naked neck (NA). These autosomal mutations show partial dominance for NA, and dominance with incomplete penetrance for PO. They were mapped previously to different linkage groups of the classical map, PO to the linkage group IV and NA being linked to the erythrocyte antigen CPPP. An informative family of 70 offspring was produced by mating a sire, heterozygous for each of the mutations, to 7 dams homozygous recessive for each locus. Three DNA pools were prepared, pool PO included 20 chicks exhibiting at least one extra-toe, pool NA included 20 non-polydactyly chicks showing the typical phenotype associated with heterozygosity for the naked neck mutation, and pool NP included 20 chicks exhibiting neither of the mutant phenotypes. Typings were done on an ABI-373 automatic sequencer with 147 microsatellite markers covering most of the genome. An unbalanced distribution of sire marker alleles were detected between pool PO, and pools NA and NP, for two markers of chromosome 2p, MCW0082 and MCW0247. A linkage analysis taking into account the incomplete penetrance of polydactyly (80%) was performed with additional markers of this region and showed that the closest marker to the PO locus was MCW0071 (5 cM, lod score = 9). MCW0071 lies within the engrailed gene EN2 in the chicken. In the mouse, the homologous gene maps on chromosome 5, close to the hemimelic extra-toes mutation Hx. In the case of the NA locus, markers of chromosome 3 were selected because CPPP was mapped on this chromosome. Analysis of individual typings showed a linkage of 5.7 cM (lod score = 13) between the NA locus and ADL0237 in the distal region of chromosome 3q. These results contribute to connecting the former classical map to the molecular genetic map of the chicken, and open the way to the identification of the molecular nature of two developmental mutations of the chicken that are known to occur in many breeds of chickens.     

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.     

A new species of Macquaridrilus (Annelida: Clitellata: Naididae) from subantarctic Campbell Island

Macquaridrilus mcmurtrieae n. sp. is described from Campbell Island. This resembles the only other species in the genus, Macquaridrilus bennettae Jamieson, 1968, in most aspects, but shows significant differences in the anatomy of its genitalia. In particular, the spermathecal pores are dorsal rather than lateral, the spermathecae lack diverticulae, the ejaculatory duct is more stout and muscular, the vas deferens is shorter relative to other organs and the anterior prostate is compact rather than elongate. The presence of a cuticular sperm canal appears to be an apomorphy for the genus. The new species was collected from streams and tarns across the island.

http://zoobank.org/urn:lsid:zoobank.org:pub:652AF61D-CFB2-4D07-94C8-59E6FB549D5F

http://zoobank.org/urn:lsid:zoobank.org:act:984F2456-768D-48A1-87AD-4453768BAB8A     

Effect of fertilizer levels on grain yield,incidence and severity of downy mildew in pearl millet

The effect of various levels of nitrogen (0.0, 30.0, 60.0, 120.0) and phosphorus (0.0, 6.5, 13.0, 36.0) on the incidence and severity of downy mildew of pearl millet and yield of two pearl millet varieties (Zango and GB8375) were studied under field conditions in 2000 and 2001 respectively. Both nitrogen and phosphorus significantly increased incidence and severity of the disease in the two varieties. Grain yield and 1000 grain weight of the varieties also increased with nitrogen and phosphorus levels.