Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

Background  

In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once.     

Estimation of divergence time between two sibling species of the <Emphasis Type="Italic">Anopheles (Kerteszia) cruzii</Emphasis>complex using a multilocus approach

Background  

Anopheles cruzii is the primary human Plasmodium vector in southern and southeastern Brazil. The distribution of this mosquito follows the coast of the Brazilian Atlantic Forest. Previous studies indicated that An. cruzii is a complex of cryptic species.     

Gene regulatory divergence among species estimated by altered developmental patterns in interspecific hybrids

Disturbances in the schedules of gene expression in developing interspecific fish hybrids have been used to draw inferences about the extent of gene regulatory divergence between species and about the degree to which this gene regulatory divergence is correlated with structural gene divergence, as estimated by genetic distance. Sperm from each of 10 different species representing six genera within the family Centrarchidae was used to fertilize eggs of the Florida largemouth bass (Micropterus salmoides floridanus). The genetic distances (D; Nei 1978) between the parental species used to form the hybrids ranged from 0.133 to 0.974. The developmental success and temporal patterns of gene expression of each of the hybrids were compared with those of the Florida largemouth bass. As the genetic distance between the paternal species and the Florida largemouth bass increased, there was a general decline in developmental success in the hybrid embryos as demonstrated by the observed reductions in the percentage of hatching and by progressively earlier and more extensive morphological abnormalities. Concomitantly, progressively more marked alterations in developmental schedules of expression of 15 enzyme loci occurred in the hybrids as the genetic distance between parental species increased. However, observed deviations from this trend for a few species may represent an uncoupling of the rates and modes of evolution of structural genes from those for genes regulating developmental processes.      

Mesozooplankton community structure changes in the Mfolozi–Msunduzi estuarine system,South Africa,during contrasting river flow conditions

The Mfolozi–Msunduzi estuarine system is subject to periodic dry and wet cycles, with subsequent changes in the abiotic and biotic characteristics of the system. The aim of the current study was to compare its mesozooplankton composition during relatively dry and wet periods. Mesozooplankton samples were collected between 2007 and 2010 in both the Mfolozi and the Msunduzi, covering a dry period between 2007 and 2008 and a period of relatively high freshwater inputs during 2009 and 2010. High flows during the wet period reduced the densities of most of the dominant estuarine mesozooplankton taxa in the Mfolozi Estuary, such as estuarine calanoids Pseudodiaptomus stuhlmanni (Poppe & Mrázek, 1895) and Acartiella natalensis (Connell & Grindley, 1974). The Msunduzi Estuary functioned as a reservoir from which recolonisation by estuarine taxa would quickly take place after the Mfolozi was scoured by floodwaters. Densities of dominant meroplankton taxa, such as zoeae of the crab Paratylodiplax blephariskios and Macrobrachium spp., were not noticeably different in the Mfolozi–Msunduzi system between the low- and high-flow periods.     

A Mutation Altering Auxin Homeostasis and Plant Morphology in Arabidopsis

Many aspects of plant development are associated with changing concentrations of the phytohormone auxin. Several stages of root formation exhibit extreme sensitivities to exogenous auxin and are correlated with shifts in endogenous auxin concentration. In an effort to elucidate mechanisms regulating development of adventitious roots, an ethyl methanesulfonate-mutagenized M2 population of Arabidopsis was screened for mutants altered in this process. A recessive nuclear mutant, rooty (rty), displayed extreme proliferation of roots, inhibition of shoot growth, and other alterations suggesting elevated responses to auxin or ethylene. Wild-type Arabidopsis seedlings grown on auxin-containing media phenocopied rty, whereas rty seedlings were partially rescued on cytokinin-containing media. Analysis by gas chromatography-selected ion monitoring-mass spectrometry showed endogenous indole-3-acetic acid concentrations to be two to 17 times higher in rty than in the wild type. Dose-response assays with exogenous indole-3-acetic acid indicated equal sensitivities to auxin in tissues of the wild type and rty. Combining rty with mutations conferring resistance to auxin (axr1-3) or ethylene (etr1-1) suggested that root proliferation and restricted shoot growth are auxin effects, whereas other phenotypic alterations are due to ethylene. Four mutant alleles from independently mutagenized populations were identified, and the locus was mapped using morphological and restriction fragment length polymorphism markers to 3.9 centimorgans distal to marker m605 on chromosome 2. The wild-type RTY gene product may serve a critical role in regulating auxin concentrations and thereby facilitating normal plant growth and development.     

Penaeid and carid community changes in the St Lucia estuarine lake system,South Africa,under low water level,extended closed periods and marine reconnection conditions

Penaeid and carid communities were assessed in St Lucia over a wide range of saline conditions, water level conditions and mouth states, including a six-month marine connection and various connections to the Mfolozi Estuary. Samples were collected biannually in spring and autumn from November 2004 to May 2012 using seine nets. Seven penaeid and seven carid species were recorded, of which Palaemon pacificus, P. peringueyi, Penaeus indicus and Metapenaeus monoceros were the most abundant. The decline from 2004 to 2007 in both species recorded and densities of freshwater, estuarine and marine species during the initial closed period was linked to increased salinity, lack of recruitment and reduced estuarine surface area. Increased wave action and high seas following Cyclone Gamede opened the mouth in March 2007 after a 57-month closed period, resulting in recruitment of marine species, predominantly P. indicus, followed by a decline in densities after reclosure in August 2007. Increases in marine and freshwater species were evident after Mfolozi flood connections during 2008, 2009 and 2010. Highest densities were recorded after breaching in 2007 and after flood connections, highlighting the importance of a marine link to maintain the recruitment of penaeid species.     

Influence of Zinnia angustifolia HBK genotype on embryonic and vegetative development of Z. angustifolia x Z. elegans Jacq. interspecific hybrids

Summary Interspecific crosses between Zinnia angustifolia clones (maternal parents) and Z. elegans lines (paternal parents) were performed to investigate postzygotic barriers among Z. angustifolia X Z. elegans hybrids and to determine influence of parental genotype on embryonic and vegetative development of interspecific hybrids. Variation in percentage of emerged seedlings (PES) and percentage of morphologically normal hybrids (PNH) was attributable to Z. angustifolia clones with minor or no effect attributable to Z. elegans lines. Heterogeneity in PES values among Z. angustifolia clones was due to differences in amount of hybrid embryo breakdown and ungerminable seed. Cytological observations of normal and abnormal interspecific hybrids revealed similar chromosome numbers (2n=23) but indicated a low mitotic index for abnormal hybrids. Genetic analysis of PES and PNH suggested control by multiple genes inherited from the Z. angustifolia genome. Adequate sampling of the Z. angustifolia gene pool would permit exploitation of genetic variability present within the species and allow improvements in PES and PNH for interspecific hybrids.Scientific Article No. A-4479, Contribution No. 7472 of the Maryland Agricultural Experiment Station, Department of Horticulture     

Traditional zootherapeutic studies in India: a review

Background

The objective of the present study was to reveal patterns in the treatment of health conditions in a Quechua-speaking community in the Bolivian Andes based on plant use data from traditional healers and patient data from a primary health care (PHC) service, and to demonstrate similarities and differences between the type of illnesses treated with traditional and biomedical health care, respectively.

Methods

A secondary analysis of plant use data from semi-structured interviews with eight healers was conducted and diagnostic data was collected from 324 patients in the community PHC service. Health conditions were ranked according to: (A) the percentage of patients in the PHC service diagnosed with these conditions; and (B) the citation frequency of plant use reports to treat these conditions by healers. Healers were also queried about the payment modalities they offer to their patients.

Results

Plant use reports from healers yielded 1166 responses about 181 medicinal plant species, which are used to treat 67 different health conditions, ranging from general symptoms (e.g. fever and body pain), to more specific ailments, such as arthritis, biliary colic and pneumonia. The results show that treatment offered by traditional medicine overlaps with biomedical health care in the case of respiratory infections, wounds and bruises, fever and biliary colic/cholecystitis. Furthermore, traditional health care appears to be complementary to biomedical health care for chronic illnesses, especially arthritis, and for folk illnesses that are particularly relevant within the local cultural context. Payment from patients to healers included flexible, outcome contingent and non-monetary options.

Conclusion

Traditional medicine in the study area is adaptive because it corresponds well with local patterns of morbidity, health care needs in relation to chronic illnesses, cultural perceptions of health conditions and socio-economic aspects of health care. The quantitative analysis of plant use reports and patient data represents a novel approach to compare the contribution of traditional and biomedical health care to treatment of particular health conditions.     

Song learning with audiovisual compound stimuli in zebra finches

We investigated the effects of audiovisual compound training on song learning in zebra finches, Taeniopygia guttata. In the first experiment, presentation of a stuffed adult zebra finch male was found to be reinforcing to zebra finch males in an operant task. In a separate experiment, zebra finch males were reared without their father from day 7 after hatching onwards. Between 35 and 76 days, they were placed in isolation and exposed to taped songs of a zebra finch male, according to a random schedule (20 presentations/h). For half of the birds, presentation of the song coincided with presentation of a stuffed zebra finch male. For the remaining birds, each presentation of the song was followed by presentation of a stuffed male. The birds were subsequently isolated until day 142, when their own songs were recorded and analysed. Birds in both groups shared significantly more song elements with their tutor songs than with an unfamiliar song. There was no significant difference in song learning between the groups. These results confirm that zebra finches can learn part of their songs from taped tutor songs. Furthermore, simultaneous presentation of the tutor song and a relevant, salient visual stimulus is not superior to sequential presentation. Copyright 1999 The Association for the Study of Animal Behaviour.