Diversity and Abundance of the Planktonic Rotifers in Different Environments of the Upper Paraná River Floodplain (Paraná State – Mato Grosso do Sul State,Brazil)

This study proposes that diversity and abundance of rotifers show spatial and temporal variations in the Upper Paraná River floodplain due to heterogeneity of the environment and hydrological level fluctuations of the main river. The structure and dynamics of rotifer assemblages were investigated by samplings carried out during the rainy (February) and dry period (August) of the year 2000, in 36 environments (rivers, channels, backwaters, open and isolated floodplain lakes). The influence of phytoplankton biomass on rotifer diversity and abundance was also investigated. 104 taxa of rotifers were identified. The highest species richness was found in rivers and open floodplain lakes, the highest abundances in the isolated floodplain lakes, and the highest values of species diversity in the channels, especially during the rainy period. β₂-diversity values were higher in the channels, especially during the dry period. Flow differences and food availability were predominant factors influencing the structure and dynamics of the rotifer communities.     

DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA)1

Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well‐supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1–3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter‐clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella, and Erythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, and Rufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera).     

Phylogeographic structure and regional history of Lemniscomys striatus (Rodentia: Muridae) in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Lemniscomys striatus and to evaluate the relative roles of ecological change, habitat patchiness, rivers and geological barriers in structuring patterns of diversity. Location Sub‐Saharan Africa. Methods The extent of phylogeographic patterns and molecular genetic diversity (cytochrome b gene) were addressed in a survey of 128 individuals of L. striatus from 42 localities. Using maximum parsimony, maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intraspecific relationships and tested hypotheses for historical patterns of gene flow within L. striatus. Results Our results identified four major geographical clades within L. striatus: a West African clade, a Benin‐Nigeria clade, a Central African clade, and an East African clade. Several subclades were identified within these four major clades. Restricted gene flow with isolation by distance was recorded, which is congruent with the low dispersal ability of such a small murid rodent. No clear signal of population expansion was detected within clades or subclades. Main conclusions The western rift system and the Volta and Niger rivers may have acted as long‐term extrinsic barriers to gene flow, resulting in the emergence of the four main clades of L. striatus. The observed pattern of mitochondrial variation observed within each clade probably results from late Pleistocene climatic and vegetation changes: during adverse conditions (forest expansion), L. striatus may have survived only in refugia, and then experienced range expansion under favourable conditions (savanna expansion).     

True pedigree errors more frequent than apparent errors for single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs) are currently being developed for use in disequilibrium analyses. These SNPs consist of two alleles with varying degrees of polymorphism. A natural design for use with SNPs is the 'haplotype relative risk' sampling design in which a father, mother, and child are typed at an SNP locus. Given such a trio of genotypes, we ask: what is the probability that a pedigree error (a change from one allele to the other) at an SNP locus will be detected using only Mendel's laws as a check? We calculate the probability of detecting such errors for a hypothetical SNP locus with varying degrees of polymorphism and for various true error rates. For the sets of allele frequencies considered, we find that the detection rates range between 25 and 30%, the detection rate being lowest when the two alleles have equal frequencies and the highest when one allele has a frequency of 10%. Based on this detection rate, we determine that the true error rate is roughly 3.3-4 times that of the apparent error rate at an SNP locus. The greatest discrepancy between true and apparent error rates occurs when allele frequencies are equal.     

Insights into the oligomeric states, conformational changes, and helicase activities of SV40 large tumor antigen

The large T (LT) antigen encoded by SV40 virus is a multi-domain, multi-functional protein that can not only transform cells but can also function as an efficient molecular machine to unwind duplex DNA for DNA replication. Here we report our findings on the oligomeric forms, domain interactions, and ATPase and helicase activities of various LT constructs. For the LT constructs that hexamerize, only two oligomeric forms, hexameric and monomeric, were detected in the absence of ATP/ADP. However, the presence of ATP/ADP stabilizes LT in the hexameric form. The LT constructs lacking the N- and C-terminal domains, but still retaining hexamerization ability, have ATPase as well as helicase activities at a level comparable to the full-length LT, suggesting the importance of hexamerization for these activities. The domain structures and the possible interactions between different LT fragments were probed with limited protease (trypsin) digestion. Such protease digestion generated a distinct pattern in the presence and absence of ATP/ADP and Mg(2+). The most C-terminal fragment (residues 628-708, containing the host-range domain), which was thought to be completely unstructured, was somewhat trypsin-resistant despite the presence of multiple Arg and Lys, possibly due to a rather structured C terminus. Furthermore, the N- and C-terminal fragments cleaved by trypsin were associated with other parts of the molecule, suggesting the interdomain interactions for the fragments at both ends.     

Epoxidation of C-branched glycals: unexpected stereochemical results and their theoretical rationale

This paper describes the synthesis of C-3 methyl-branched glycosides by epoxidation of partially unblocked L-configured glycals. The stereochemical result depends on the orientation of the allylic hydroxyl group. A theoretical explanation is presented, based on the conformational preferences of the respective glycal half-chair conformations that were estimated by applying the BP density functional and a valence triple-zeta basis set.     

Early pregnancy diagnosis in sheep by progesterone and pregnancy-associated glycoprotein tests

The aim of this study was to compare the accuracy of the progesterone (P4) and pregnancy associated glycoprotein (PAG) tests for determination of early pregnancy in sheep. Estrus was synchronized in 182 Awassi x Merino ewes and blood samples were collected at Days 0 (day of the insemination), 18, 22, 29, 36, and 50 after artificial insemination (AI). Plasma P4 concentrations at Days 0 and 18 were determined by double antibody radioimmunoassay, while PAG concentrations at Days 22, 29, 36 and 50 were determined by a heterologous, double-antibody radioimmunoassay (RIA) using the bovine PAG 67 kDa subunit as tracer and standard and rabbit antiserum raised against a mixture of caprine 55 and 59 kDa PAG subunits as the first antibody. The discriminatory value for diagnosis of pregnancy by the P4 and the PAG-RIA tests was > or = 1 ng/ml. Based on lambing data, the accuracy for diagnosing pregnant (sensitivity) and non-pregnant ewes (specificity) and predictivity of both tests were calculated. The sensitivity, specificity, positive and negative predictive values for P4 and PAG tests were 100, 95.4, 81.6, and 100% at Day 18 (P4) and 93.5, 100, 100 and 98.7% at Day 22 (PAG), respectively. For diagnosis of non-pregnant ewes the PAG test had significantly higher specificity than the P4 test (P < 0.05). It is concluded that ovine pregnancy can be reliably diagnosed at Day 22 after AI by using a heterologous radioimmunoassay of PAG.     

Low-shear modeled microgravity: a global environmental regulatory signal affecting bacterial gene expression,physiology, and pathogenesis

Bacteria inhabit an impressive variety of ecological niches and must adapt constantly to changing environmental conditions. While numerous environmental signals have been examined for their effect on bacteria, the effects of mechanical forces such as shear stress and gravity have only been investigated to a limited extent. However, several important studies have demonstrated a key role for the environmental signals of low shear and/or microgravity in the regulation of bacterial gene expression, physiology, and pathogenesis [Chem. Rec. 1 (2001) 333; Appl. Microbiol. Biotechnol. 54 (2000) 33; Appl. Environ. Microbiol. 63 (1997) 4090; J. Ind. Microbiol. 18 (1997) 22; Curr. Microbiol. 34(4) (1997) 199; Appl. Microbiol. Biotechnol. 56(3-4) (2001) 384; Infect Immun. 68(6) (2000) 3147; Cell 109(7) (2002) 913; Appl. Environ. Microbiol. 68(11) (2002) 5408; Proc. Natl. Acad. Sci. U. S. A. 99(21) (2002) 13807]. The response of bacteria to these environmental signals, which are similar to those encountered during prokaryotic life cycles, may provide insight into bacterial adaptations to physiologically relevant conditions. This review focuses on the current and potential future research trends aimed at understanding the effect of the mechanical forces of low shear and microgravity analogues on different bacterial parameters. In addition, this review also discusses the use of microgravity technology to generate physiologically relevant human tissue models for research in bacterial pathogenesis.