Sequence analysis of sub-genotype D hepatitis B surface antigens isolated from Jeddah,Saudi Arabia

Little is known about the prevalence of HBV genotypes/sub-genotypes in Jeddah province, although the hepatitis B virus (HBV) was identified as the most predominant type of hepatitis in Saudi Arabia. To characterize HBV genotypes/sub-genotypes, serum samples from 15 patients with chronic HBV were collected and subjected to HBsAg gene amplification and sequence analysis. Phylogenetic analysis of the HBsAg gene sequences revealed that 11 (48%) isolates belonged to HBV/D while 4 (18%) were associated with HBV/C. Notably, a HBV/D sub-genotype phylogenetic tree identified that eight current isolates (72%) belonged to HBV/D1, whereas three isolates (28%) appeared to be more closely related to HBV/D5, although they formed a novel cluster supported by a branch with 99% bootstrap value. Isolates belonging to D1 were grouped in one branch and seemed to be more closely related to various strains isolated from different countries. For further determination of whether the three current isolates belonged to HBV/D5 or represented a novel sub-genotype, HBV/DA, whole HBV genome sequences would be required. In the present study, we verified that HBV/D1 is the most prevalent HBV sub-genotype in Jeddah, and identified novel variant mutations suggesting that an additional sub-genotype designated HBV/DA should be proposed. Overall, the results of the present HBsAg sequence analyses provide us with insights regarding the nucleotide differences between the present HBsAg/D isolates identified in the populace of Jeddah, Saudi Arabia and those previously isolated worldwide. Additional studies with large numbers of subjects in other areas might lead to the discovery of the specific HBV strain genotypes or even additional new sub-genotypes that are circulating in Saudi Arabia.     

IDENTIFYING ASSESSOR DIFFERENCES IN WEIGHTING THE UNDERLYING SENSORY DIMENSIONS

In a previous paper Kunert and Qannari (1999) discussed a simple alternative to Generalized Procrustes Analysis to analyze data derived from a sensory profiling study. After simple pretreatments of the individual data matrices, they propose to merge the data sets together and undergo Principal Components Analysis of the matrix thus formed. On the basis of two data sets, it was shown that the results slightly differ from those obtained by means of Generalized Procrustes Analysis.
In this paper we give a mathematical justification to this approach by relating it to a statistical regression model. Furthermore, we obtain additional information from this method concerning the dimensions used by the assessors as well as the contribution of each assessor to the determination of these dimensions. This information may be useful to characterize the performance of the assessors and single out those assessors who downweight or overweight some dimensions. In particular, those assessors who overweight the last dimensions should arouse suspicion regarding their performance as, in general, the last dimensions in a principal components analysis are deemed to reflect random fluctuations.     

Response of plant species richness and primary productivity in shrublands along a north–south gradient in Europe to seven years of experimental warming and drought: reductions in primary productivity in the heat and drought year of 2003

We used a nonintrusive field experiment carried out at six sites – Wales (UK), Denmark (DK), the Netherlands (NL), Hungary (HU), Sardinia (Italy – IT), and Catalonia (Spain – SP) – along a climatic and latitudinal gradient to examine the response of plant species richness and primary productivity to warming and drought in shrubland ecosystems. The warming treatment raised the plot daily temperature by ca. 1 °C, while the drought treatment led to a reduction in soil moisture at the peak of the growing season that ranged from 26% at the SP site to 82% in the NL site. During the 7 years the experiment lasted (1999–2005), we used the pin‐point method to measure the species composition of plant communities and plant biomass, litterfall, and shoot growth of the dominant plant species at each site. A significantly lower increase in the number of species pin‐pointed per transect was found in the drought plots at the SP site, where the plant community was still in a process of recovering from a forest fire in 1994. No changes in species richness were found at the other sites, which were at a more mature and stable state of succession and, thus less liable to recruitment of new species. The relationship between annual biomass accumulation and temperature of the growing season was positive at the coldest site and negative at the warmest site. The warming treatment tended to increase the aboveground net primary productivity (ANPP) at the northern sites. The relationship between annual biomass accumulation and soil moisture during the growing season was not significant at the wettest sites, but was positive at the driest sites. The drought treatment tended to reduce the ANPP in the NL, HU, IT, and SP sites. The responses to warming were very strongly related to the Gaussen aridity index (stronger responses the lower the aridity), whereas the responses to drought were not. Changes in the annual aboveground biomass accumulation, litterfall, and, thus, the ANPP, mirrored the interannual variation in climate conditions: the most outstanding change was a decrease in biomass accumulation and an increase in litterfall at most sites during the abnormally hot year of 2003. Species richness also tended to decrease in 2003 at all sites except the cold and wet UK site. Species‐specific responses to warming were found in shoot growth: at the SP site, Globularia alypum was not affected, while the other dominant species, Erica multiflora, grew 30% more; at the UK site, Calluna vulgaris tended to grow more in the warming plots, while Empetrum nigrum tended to grow less. Drought treatment decreased plant growth in several studied species, although there were some species such as Pinus halepensis at the SP site or C. vulgaris at the UK site that were not affected. The magnitude of responses to warming and drought thus depended greatly on the differences between sites, years, and species and these multiple plant responses may be expected to have consequences at ecosystem and community level. Decreases in biodiversity and the increase in E. multiflora growth at the SP site as a response to warming challenge the assumption that sensitivity to warming may be less well developed at more southerly latitudes; likewise, the fact that one of the studied shrublands presented negative ANPP as a response to the 2003 heat wave also challenges the hypothesis that future climate warming will lead to an enhancement of plant growth and carbon sequestration in temperate ecosystems. Extreme events may thus change the general trend of increased productivity in response to warming in the colder sites.     

The tobacco Ntann12 gene, encoding an annexin, is induced upon Rhodoccocus fascians infection and during leafy gall development

Annexins are calcium-binding proteins that have been associated in plants with different biological processes such as responses to abiotic stress and early nodulation stages. Until now, the implication of annexins during plant–pathogen interactions has not been reported. Here, a novel plant annexin gene induced in tobacco BY-2 cell suspension cultures infected with the phytopathogenic bacterium Rhodococcus fascians (strain D188) has been identified . Expression of this gene, called Ntann12 , is also induced, but to a lower extent, by a strain (D188-5) that is unable to induce leafy gall formation. This gene was also induced in BY-2 cells infected with Pseudomonas syringae but not in cells infected with Agrobacterium tumefaciens or Escherichia coli. Ntann12 expression was also found to be stimulated by abiotic stress, including NaCl and abscissic acid, confirming a putative role in stress signal transduction pathways. In addition, promoter- GUS analyses using homozygous transgenic tobacco seedlings showed that the developmentally controlled expression of Ntann12 is altered upon R. fascians infection. Finally, up-regulation of Ntann12 during leafy gall ontogenesis was confirmed by RT-qPCR. Discussion is focused on the potential role of Ntann12 in biotic and abiotic stress responses and in plant development, both processes that may involve Ca²⁺-dependent signalling.     

Inhibition of Germination in Kochia indica

Seeds of Kochia indica Wight germinate rapidly in shallow water,but their germination is retarded on moist filter-paper. Theretardation is traced to a surface-active, saponin-like inhibitor,which is readily leached away in water and is adsorbed by charcoalor soil. Excised embryos may also remain dormant on filter-paper,but if rinsed in water quickly become active. Inhibition isfavoured by higher temperature (30°C. as against 20°or less), especially in an atmosphere of oxygen, although onceactive the embryos grow rapidly in such conditions. When theoxygen concentration is reduced to 5 per cent., germinationand growth are markedly retarded, but 5 per cent. CO₂ has littleor no retarding effect.     

Intracommunity relationships, dispersal pattern and paternity success in a wild living community of Bonobos (Pan paniscus) determined from DNA analysis of faecal samples.

Differences in social relationships among community members are often explained by differences in genetic relationships. The current techniques of DNA analysis allow explicit testing of such a hypothesis. Here, we have analysed the genetic relationships for a community of wild bonobos (Pan paniscus) using nuclear and mitochondrial DNA markers extracted from faecal samples. Bonobos show an opportunistic and promiscuous mating behaviour, even with mates from outside the community. Nonetheless, we find that most infants were sired by resident males and that two dominant males together attained the highest paternity success. Intriguingly, the latter males are the sons of high-ranking females, suggesting an important influence of mothers on the paternity success of their sons. The molecular data support previous inferences on female dispersal and male philopatry. We find a total of five different mitochondrial haplotypes among 15 adult females, suggesting a frequent migration of females. Moreover, for most adult and subadult males in the group we find a matching mother, while this is not the case for most females, indicating that these leave the community during adolescence. Our study demonstrates that faecal samples can be a useful source for the determination of kinship in a whole community.     

Sexually dimorphic responses to neonatal basal forebrain lesions in mice: II. Cortical morphology

Previous studies in the mouse have shown that neonatal lesions to the cholinergic basal forebrain (nBM) areas result in transient cholinergic depletion of neocortex and precipitate altered cortical morphogenesis. Lesion-induced morphological alterations in cortex persist into adulthood and are accompanied by behavioral changes, including spatial memory deficits. The current study investigated whether neonatal nBM lesions affect male and female mice differently in adulthood. Quantitative morphometry of cortical layer width was employed to assess alterations in cytoarchitecture in neonatally nBM-lesioned and littermate control mice of both sexes following behavioral testing. Our results showed significant decreases in cortical layer IV and V widths across somato/motor cortex in neonatally nBM lesioned mice of both sexes. Sexually dimorphic responses were observed in cortical layer II/III and total cortical width, limited to the area containing the “barrel cortex” representation of the whisker hairs. In lesioned females, layer II/III and total cortical width were decreased relative to female controls, and in lesioned males, layer II/III was increased relative to controls, whereas total cortical width was unchanged. In male but not female mice we observed significant correlations between decreased widths in layer IV and V and impaired performance on a spatial memory task. The current data further support a role of developing cholinergic cortical afferents in the modulation of cortical morphogenesis and cortical circuits involved in cognitive behaviors. In addition, our observations provide further evidence for sexually dimorphic development and function in cognitive centers of the rodent brain. © 1998 John Wiley & Sons, Inc. J Neurobiol 37: 595–606, 1998     

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools

Tandem mass spectrometry (MS/MS) is frequently used in the identification of peptides and proteins. Typical proteomic experiments rely on algorithms such as SEQUEST and MASCOT to compare thousands of tandem mass spectra against the theoretical fragment ion spectra of peptides in a database. The probabilities that these spectrum-to-sequence assignments are correct can be determined by statistical software such as PeptideProphet or through estimations based on reverse or decoy databases. However, many of the software applications that assign probabilities for MS/MS spectra to sequence matches were developed using training data sets from 3D ion-trap mass spectrometers. Given the variety of types of mass spectrometers that have become commercially available over the last 5 years, we sought to generate a data set of reference data covering multiple instrumentation platforms to facilitate both the refinement of existing computational approaches and the development of novel software tools. We analyzed the proteolytic peptides in a mixture of tryptic digests of 18 proteins, named the "ISB standard protein mix", using 8 different mass spectrometers. These include linear and 3D ion traps, two quadrupole time-of-flight platforms (qq-TOF), and two MALDI-TOF-TOF platforms. The resulting data set, which has been named the Standard Protein Mix Database, consists of over 1.1 million spectra in 150+ replicate runs on the mass spectrometers. The data were inspected for quality of separation and searched using SEQUEST. All data, including the native raw instrument and mzXML formats and the PeptideProphet validated peptide assignments, are available at http://regis-web.systemsbiology.net/PublicDatasets/.