The XbaI-BlnI-CeuI genomic cleavage map of Salmonella enteritidis shows an inversion relative to Salmonella typhimurium LT2

We have established the genomic cleavage map of Salmonella enteritidis strain SSU7998 using pulsed-field gel electrophoresis. The chromosome of 4600kb was analysed by XbaI (16 fragments), I-CeuI (7 fragments) and BlnI (12 fragments); the genome also contains a plasmid of 60 kb. Cleavage sites of I-CeuI, in the large subunit ribosomal RNA gene, are conserved from Salmonella typhimurium and Escherichia coli K-12, and the XbaI and BinI sites in glt-tRNA are also conserved, but other sites are less conserved. Transposon Tn10, located at 60 different positions in the chromosome of S. typhimurium, was transduced by bacteriophage P22 into S. enteritidis and the insertion mapped using the XbaI and BlnI sites on Tn10. Gene order in S. enteritidis is identical to S. typhimurium LT2 and similar to E. coli K-12 except for an inversion of 815 kb, which covers the terminus region including T1 and T2. Endpoints are in the NDZs, or non-divisible zones, in which inversion endpoints were not detected in experiments in E. coli K-12 and S. typhimurium LT2. This inversion resembles the inversion between S. typhimurium and E. coli, but is longer at both ends.     

A method for the interpretation of signals in afferent nerves from muscle spindles

A method is proposed for the interpretation of the signals in sensory nerve fibres. It is applicable to systems in which the transfer function between the input to a sense organ and the action potential firing frequency is known. In the present case, the chelonian muscle spindle is considered since its output to ramphold-relase and sinusoidal stretches can be rather accurately simulated.     

Rapid Copper Acquisition by Developing Murine Mesothelioma: Decreasing Bioavailable Copper Slows Tumor Growth,Normalizes Vessels and Promotes T Cell Infiltration

Copper, an essential trace element acquired through nutrition, is an important co-factor for pro-angiogenic factors including vascular endothelial growth factor (VEGF). Decreasing bioavailable copper has been used as an anti-angiogenic and anti-cancer strategy with promising results. However, the role of copper and its potential as a therapy in mesothelioma is not yet well understood. Therefore, we monitored copper levels in progressing murine mesothelioma tumors and analyzed the effects of lowering bioavailable copper. Copper levels in tumors and organs were assayed using atomic absorption spectrophotometry. Mesothelioma tumors rapidly sequestered copper at early stages of development, the copper was then dispersed throughout growing tumor tissues. These data imply that copper uptake may play an important role in early tumor development. Lowering bioavailable copper using the copper chelators, penicillamine, trientine or tetrathiomolybdate, slowed in vivo mesothelioma growth but did not provide any cures similar to using cisplatin chemotherapy or anti-VEGF receptor antibody therapy. The impact of copper lowering on tumor blood vessels and tumor infiltrating T cells was measured using flow cytometry and confocal microscopy. Copper lowering was associated with reduced tumor vessel diameter, reduced endothelial cell proliferation (reduced Ki67 expression) and lower surface ICAM/CD54 expression implying reduced endothelial cell activation, in a process similar to endothelial normalization. Copper lowering was also associated with a CD4⁺ T cell infiltrate. In conclusion, these data suggest copper lowering is a potentially useful anti-mesothelioma treatment strategy that slows tumor growth to provide a window of opportunity for inclusion of other treatment modalities to improve patient outcomes.     

Macroevolutionary insights into sedges (Carex: Cyperaceae): The effects of rapid chromosome number evolution on lineage diversification

Changes in holocentric chromosome number due to fission and fusion have direct and immediate effects on genome structure and recombination rates. These, in turn, may influence ecology and evolutionary trajectories profoundly. Sedges of the genus Carex (Cyperaceae) comprise ca. 2000 species with holocentric chromosomes. The genus exhibits a phenomenal range in the chromosome number (2n = 10 − 132) with almost not polyploidy. In this study, we integrated the most comprehensive cytogenetic and phylogenetic data for sedges with associated climatic and morphological data to investigate the hypothesis that high recombination rates are selected when evolutionary innovation is required, using chromosome number evolution as a proxy for recombination rate. We evaluated Ornstein–Uhlenbeck models to infer shifts in chromosome number equilibrium and selective regime. We also tested the relationship between chromosome number and diversification rates. Our analyses demonstrate significant correlations between morphology and climatic niche and chromosome number in Carex. Nevertheless, the amount of chromosomal variation that we are able to explain is very small. We recognized a large number of shifts in mean chromosome number, but a significantly lower number in climatic niche and morphology. We also detected a peak in diversification rates near intermediate recombination rates. In combination, these analyses point toward the importance of chromosome evolution to the evolutionary history of Carex. Our work suggests that the effect of chromosome evolution on recombination rates, not just on reproductive isolation, may be central to the evolutionary history of sedges.     

Geographical vs. ecological diversification in Carex section Phacocystis (Cyperaceae): Patterns hidden behind a twisted taxonomy

Carex section Phacocystis (Cyperaceae) is one of the most diverse and taxonomically complex groups of sedges (between 116 and 147 species), with a worldwide distribution in a wide array of biomes. It has a very complicated taxonomic history, with numerous disagreements among different treatments. We studied the biogeography and niche evolution in a phylogenetic framework to unveil the relative contribution of geographical and ecological drivers to diversification of the group. We used a large species sampling of the section (82% of extant species) to build a phylogeny based on four DNA regions, constrained with a phylogenomic HybSeq tree and dated with six fossil calibrations. Our phylogenetic results recovered section Phacocystis s.s. (core Phacocystis) as sister to section Praelongae. Ancestral area reconstruction points toward the N Pacific as the cradle for the crown diversification of section Phacocystis during the Middle Miocene. Wide distributions were recurrently inferred across deep nodes. Large Northern Hemisphere lineages with geographical congruence were retrieved, pointing toward the importance of allopatric divergence at deep phylogenetic levels, whereas within-area speciation emerges as the predominant pattern at shallow phylogenetic level. The Southern Hemisphere (Neotropics, SW Pacific) was colonized several times from the Northern Hemisphere. The global expansion of Carex section Phacocystis did not entail major ecological changes along the inner branches of the phylogeny. Nevertheless, ecological differentiation seems to gain importance toward recent times.     

The effect of the elongation of the proximal aorta on the estimation of the aortic wall distensibility

The compliance of the proximal aortic wall is a major determinant of cardiac afterload. Aortic compliance is often estimated based on cross-sectional area changes over the pulse pressure, under the assumption of a negligible longitudinal stretch during the pulse. However, the proximal aorta is subjected to significant axial stretch during cardiac contraction. In the present study, we sought to evaluate the importance of axial stretch on compliance estimation by undertaking both an in silico and an in vivo approach. In the computational analysis, we developed a 3-D finite element model of the proximal aorta and investigated the discrepancy between the actual wall compliance to the value estimated after neglecting the longitudinal stretch of the aorta. A parameter sensitivity analysis was further conducted to show how increased material stiffness and increased aortic root motion might amplify the estimation errors (discrepancies between actual and estimated distensibility ranging from − 20 to − 62%). Axial and circumferential aortic deformation during ventricular contraction was also evaluated in vivo based on MR images of the aorta of 3 healthy young volunteers. The in vivo results were in good qualitative agreement with the computational analysis (underestimation errors ranging from − 26 to − 44%, with increased errors reflecting higher aortic root displacement). Both the in silico and in vivo findings suggest that neglecting the longitudinal strain during contraction might lead to severe underestimation of local aortic compliance, particularly in the case of women who tend to have higher aortic root motion or in subjects with stiff aortas.

     

Human Germline Antibody Gene Segments Encode Polyspecific Antibodies

Structural flexibility in germline gene-encoded antibodies allows promiscuous binding to diverse antigens. The binding affinity and specificity for a particular epitope typically increase as antibody genes acquire somatic mutations in antigen-stimulated B cells. In this work, we investigated whether germline gene-encoded antibodies are optimal for polyspecificity by determining the basis for recognition of diverse antigens by antibodies encoded by three V_H gene segments. Panels of somatically mutated antibodies encoded by a common V_H gene, but each binding to a different antigen, were computationally redesigned to predict antibodies that could engage multiple antigens at once. The Rosetta multi-state design process predicted antibody sequences for the entire heavy chain variable region, including framework, CDR1, and CDR2 mutations. The predicted sequences matched the germline gene sequences to a remarkable degree, revealing by computational design the residues that are predicted to enable polyspecificity, i.e., binding of many unrelated antigens with a common sequence. The process thereby reverses antibody maturation in silico. In contrast, when designing antibodies to bind a single antigen, a sequence similar to that of the mature antibody sequence was returned, mimicking natural antibody maturation in silico. We demonstrated that the Rosetta computational design algorithm captures important aspects of antibody/antigen recognition. While the hypervariable region CDR3 often mediates much of the specificity of mature antibodies, we identified key positions in the V_H gene encoding CDR1, CDR2, and the immunoglobulin framework that are critical contributors for polyspecificity in germline antibodies. Computational design of antibodies capable of binding multiple antigens may allow the rational design of antibodies that retain polyspecificity for diverse epitope binding.     

Ecology and genetics of hybrid zones in the southern African Pycnonotus bulbul species complex

Lloyd, P., Craig, A.J.F.K., Hulley, P.E., Essop, M.F., Bloomer, P. & Crowe, T.M. 1997. Ecology and genetics of hybrid zones in the southern African Pycnonotus bulbul species complex. Ostrich 68 (2–4): 90–96.

The closely related Blackeyed Bulbul Pycnonotus barbatus, Cape Bulbul P. capensis and Redeyed Bulbul P. nigricans have parapatric to locally sympatric distributions within southern Africa. Extensive hybridization along narrow transition zones between each of the three species pairs is described in a region of the Eastern Cape province, South Africa. The transition zones coincide with ecotones between different vegetation types, which in turn follow escarpments or mountain ranges. The lack of population density depressions within the hybrid zones, together with the variability of the hybrids, suggests the hybrids are viable. Sharp step clines in various phenotypic characters are described across the P. barbatus/P. nigricans hybrid zone. A mtDNA analysis found evidence of possible introgression between P. barbatus and P. capensis. All eight P. barbatus x P. nigricans hybrids analysed possessed P. barbatus mtDNA, suggesting the existence of either positive assortative mating or strong directional selection, but our data are unable to distinguish which. Our results do not support the dynamic-equilibrium model, but are compatible with the bounded-hybrid-superiority model. We conclude that the maintenance of the parapatric distributions of the different taxa is due mainly to differences in environmentally-associated fitness between parental phenotypes or among parental and hybrid phenotypes along an ecotone, with the narrowness of the hybrid zones maintained by the steepness of the environmental gradients crossing them.     

A preliminary assessment of congruence between biodiversity patterns in Afrotropical forest birds and forest mammals

Burgess, N., de Klerk, H., Fjeldsá, J., Crowe, T. & Rahbek, R. 2000. A preliminary assessment of congruence between biodiversity patterns in Afrotropical forest birds and forest mammals. Ostrich 71 (1 & 2): 286–291.

Databases compiled for forest birds and forest mammals in the Afrotropics were tested for congruence of overall patterns and hotspots of species richness and endemism. We also looked at how well a near-minimum set of priority areas for one taxon catered for the second taxon. Overall species richness and richness hotspots of forest birds were significantly correlated with those of forest mammals, as was the case for overall endemism. Endemism hotspots for forest birds and mammals were not significantly correlated. The near-minimum set for forest birds represented 136 (76.5%) forest mammal species. The near-minimum set for forest mammals represented 350 (93.62%) forest bird species. However, to represent all forest mammals three times each, 51 grids were needed in addition to the 78 chosen as a near-minimum set for forest birds, and to represent all forest birds three times each, 43 more grids were needed in addition to the 80 selected for forest mammals. There is some congruence between the patterns of richness, endemism and near-minimum sets for forest birds and mammals in the Afrotropics, but the one taxon does not provide the ideal conservation solution for the other. Further refinement of the databases used in this paper would allow for more rigorous testing of congruence between these two groups.     

SEASONAL AND DEMOGRAPHICAL VARIATION IN INTESTINAL HELMINTH INFECTION OF GREYWING FRANCOLIN

Little, R.M., Verster, A. & Crowe, T.M. 1993. Seasonal and demographical variation in intestinal helminth infection of Greywing Francolin. Ostrich 64:178-181.

The proportion of the population carrying intestinal parasites (prevalence of infection) and the mean number of parasites per host within the host population (worm burden) for 312 Greywing Francolin Fran-colinus africanus were recorded on the Stormberg Plateau, eastern Cape Province, during April 1989-De-cember 1990. Most Greywing (86%) had helminths in their small intestine or caeca. Variation in levels of helminth infection (i.e. both prevalence and burdens) was independent of host sex. Nematodes were confined to the caeca where they were present in high numbers throughout the year with two peaks during June-August and November-January. The prevalence and worm burdens of nematodes were independent of host age Nematodes were more prevalent than cestodes. The prevalence and number of cestodes in the small intestine were highest during September-February and Faked during November-December. Levels of prevalence of cestodes were significantly higher in juvenile Greywing than in adults during the austral winter (May-July). The number of cestodes was consistently, but not significantly, higher in juveniles than in adults. Greywing body mass and population density were not significantly correlated with worm burdens.