A comparison of the macrobenthic faunas of permanently open and temporarily open/closed South African estuaries

Thirteen estuaries in the Eastern Cape Province, South Africa, were broadly categorised according to size and salinity distribution and were assigned to one of the following categories: permanently open estuaries having a strong salinity gradient between mouth and upper estuary, freshwater-deprived permanently open estuaries, medium-sized temporarily open/closed estuaries, and small, temporarily open/closed estuaries. The macrobenthos collected during surveys was then compared in terms of the following parameters: species composition, salinity, sediment mud content, density of macrobenthic animals, Hill's N0 (species richness), and Hill's N1 (diversity). Mud content was found to be the most important environmental variable responsible for biotic patterns found, and sites were consequently assigned to either a sand zone fauna, or a mud zone fauna. Both types of fauna are present in all estuaries sampled, with upper sites of river dominated estuaries having an additional oligohaline fauna, and freshwater-deprived estuaries providing habitat for many marine species. Small, temporarily open/closed estuaries have the highest macrobenthic density, whereas N0 and N1 are highest in freshwater-deprived permanently open systems. River-dominated permanently open estuaries tend to have lower macrobenthic densities, species richness, and diversities compared to estuaries in the other categories. No seasonal differences in these ecological indices were found within any of the estuarine categories.     

The biological background of a recurrently emerging infectious disease: prevalence,diversity and host specificity of Avipoxvirus in wild Neotropical birds

Understanding which factors promote disease emergence and transmission remains a major challenge of epidemiology. A problem with research on emerging diseases is that we seldom know to what extent pathogens circulate in natural populations before emergence is already occurring. Moreover, it is critical to determine which pathogen characteristics are key to predict their emergence and invasion potential. We examined the prevalence, host specificity and evolutionary relationships of Avipoxvirus causing skin lesions in birds in two megadiverse and unexplored geographical regions of South America: an elevational gradient in the south Ecuadorian Andes, and a lowland Amazon rainforest in French Guiana. Next, we analyzed the host specificity and distribution of the worldwide Avipoxvirus diversity in order to understand their invasion potential. In French Guiana Avipoxvirus prevalence was 0% (n = 889, 94 bird species). In Ecuador, prevalence was 0.3% (n = 941, 132 bird species), with cases spanning the range of elevations between 1500 and 2500 m. These were caused by two newly described strains, one of which belonged to an American clade of Avipoxvirus shared by different bird families, and another one closely related to a strain recovered from a different family of birds in Madeira. An analysis of the host specificity and geographic distribution of all Avipoxvirus strains known worldwide finds that these viruses are usually host generalists (particularly those in the fowlpox clade), and that many closely related strains are found on multiple continents. Our study at the community level suggests that distantly related Avipoxvirus strains circulate at very low prevalence in continental tropical South America. Avipoxvirus assemblages are composed of generalist strains with different ancestry and widespread distribution, a combination of characteristics which may make these typically scarce viruses perfect candidates to emerge under favorable ecological conditions.     

The CD8 T cell coreceptor exhibits disproportionate biological activity at extremely low binding affinities

T lymphocytes recognize peptides presented in the context of major histocompatibility complex (MHC) molecules on the surface of antigen presenting cells. Recognition specificity is determined by the alphabeta T cell receptor (TCR). The T lymphocyte surface glycoproteins CD8 and CD4 enhance T cell antigen recognition by binding to MHC class I and class II molecules, respectively. Biophysical measurements have determined that equilibrium binding of the TCR with natural agonist peptide-MHC (pMHC) complexes occurs with KD values of 1-50 microm. The pMHCI/CD8 and pMHCII/CD4 interactions are significantly weaker than this (KD >100 microm), and the relative roles of TCR/pMHC and pMHC/coreceptor affinity in T cell activation remain controversial. Here, we engineer mutations in the MHCI heavy chain and beta2-microglobulin that further reduce or abolish the pMHCI/CD8 interaction to probe the significance of pMHC/coreceptor affinity in T cell activation. We demonstrate that the pMHCI/CD8 coreceptor interaction retains the vast majority of its biological activity at affinities that are reduced by over 15-fold (KD > 2 mm). In contrast to previous reports, we observe that the weak interaction between HLA A68 and CD8, which falls within this spectrum of reduced affinities, retains substantial functional activity. These findings are discussed in the context of current concepts of coreceptor dependence and the mechanism by which TCR coreceptors facilitate T cell activation.     

A new species of Gastrosaccus (Crustacea,Mysidacea) from Algoa Bay (South Africa)

The effect of temperature on growth rate, shell size and shell shape in Krithe praetexta praetexta (Sars) was studied in four thermocultures. From July 1995 to June 1996, the cultures were kept in a continuously flowing open system pumping water from the intermediate watermass of the Gullmarn fjord, west coast of Sweden. Three cultures were kept at constant temperatures of 5, 10 and 14 °C, respectively. The fourth (reference) culture largely followed the natural variation in temperature. At the termination of the experiment, all living ostracods from a 125 m sieve were sampled from the cultures. Population age structures were analysed for the various thermocultures of K. praetexta praetexta. These were more shifted towards later ontogenetic stages with higher temperature, i.e. the ontogenetic development was more rapid in the warmer cultures. An alternative explanation is due to diapause causing cohorts to accumulate in some ontogenetic stages only when the temperature is constant. The differences in shell size of K. praetexta praetexta among the thermoconstant cultures were not statistically significant.     

An Investigation of the Diversity of Strains of Enteroaggregative Escherichia coli Isolated from Cases Associated with a Large Multi-Pathogen Foodborne Outbreak in the UK

Following a large outbreak of foodborne gastrointestinal (GI) disease, a multiplex PCR approach was used retrospectively to investigate faecal specimens from 88 of the 413 reported cases. Gene targets from a range of bacterial GI pathogens were detected, including Salmonella species, Shigella species and Shiga toxin-producing Escherichia coli, with the majority (75%) of faecal specimens being PCR positive for aggR associated with the Enteroaggregative E. coli (EAEC) group. The 20 isolates of EAEC recovered from the outbreak specimens exhibited a range of serotypes, the most frequent being O104:H4 and O131:H27. None of the EAEC isolates had the Shiga toxin (stx) genes. Multilocus sequence typing and single nucleotide polymorphism analysis of the core genome confirmed the diverse phylogeny of the strains. The analysis also revealed a close phylogenetic relationship between the EAEC O104:H4 strains in this outbreak and the strain of E. coli O104:H4 associated with a large outbreak of haemolytic ureamic syndrome in Germany in 2011. Further analysis of the EAEC plasmids, encoding the key enteroaggregative virulence genes, showed diversity with respect to FIB/FII type, gene content and genomic architecture. Known EAEC virulence genes, such as aggR, aat and aap, were present in all but one of the strains. A variety of fimbrial genes were observed, including genes encoding all five known fimbrial types, AAF/1 to AAF/V. The AAI operon was present in its entirety in 15 of the EAEC strains, absent in three and present, but incomplete, in two isolates. EAEC is known to be a diverse pathotype and this study demonstrates that a high level of diversity in strains recovered from cases associated with a single outbreak. Although the EAEC in this study did not carry the stx genes, this outbreak provides further evidence of the pathogenic potential of the EAEC O104:H4 serotype.     

The role of glyceraldehyde 3-phosphate dehydrogenase (GapA-1) in <Emphasis Type="Italic">Neisseria meningitidis</Emphasis> adherence to human cells

Background  

Glyceraldehyde 3-phosphate dehydrogenases (GAPDHs) are cytoplasmic glycolytic enzymes, which although lacking identifiable secretion signals, have also been found localized to the surface of several bacteria (and some eukaryotic organisms); where in some cases they have been shown to contribute to the colonization and invasion of host tissues. Neisseria meningitidis is an obligate human nasopharyngeal commensal which can cause life-threatening infections including septicaemia and meningitis. N. meningitidis has two genes, gapA-1 and gapA-2, encoding GAPDH enzymes. GapA-1 has previously been shown to be up-regulated on bacterial contact with host epithelial cells and is accessible to antibodies on the surface of capsule-permeabilized meningococcal cells. The aims of this study were: 1) to determine whether GapA-1 was expressed across different strains of N. meningitidis; 2) to determine whether GapA-1 surface accessibility to antibodies was dependant on the presence of capsule; 3) to determine whether GapA-1 can influence the interaction of meningococci and host cells, particularly in the key stages of adhesion and invasion.     

Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain

Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize (Zea mays) is a food staple. Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percentage of phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide an in-depth genome-level understanding of the genetic and molecular control of carotenoids in plants. In addition, these findings provide a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals.

Eleven genes were identified for grain carotenoids by integrating joint-linkage, genome-wide association, RNA-seq, pleiotropy, and epistasis analyses of the US maize nested association mapping panel.