Dissecting the Conformational Dynamics of the Bile Acid Transporter Homologue ASBTNM

Apical sodium-dependent bile acid transporter (ASBT) catalyses uphill transport of bile acids using the electrochemical gradient of Na⁺ as the driving force. The crystal structures of two bacterial homologues ASBT_NM and ASBT_Yf have previously been determined, with the former showing an inward-facing conformation, and the latter adopting an outward-facing conformation accomplished by the substitution of the critical Na⁺-binding residue glutamate-254 with an alanine residue. While the two crystal structures suggested an elevator-like movement to afford alternating access to the substrate binding site, the mechanistic role of Na⁺ and substrate in the conformational isomerization remains unclear. In this study, we utilized site-directed alkylation monitored by in-gel fluorescence (SDAF) to probe the solvent accessibility of the residues lining the substrate permeation pathway of ASBT_NM under different Na⁺ and substrate conditions, and interpreted the conformational states inferred from the crystal structures. Unexpectedly, the crosslinking experiments demonstrated that ASBT_NM is a monomer protein, unlike the other elevator-type transporters, usually forming a homodimer or a homotrimer. The conformational dynamics observed by the biochemical experiments were further validated using DEER measuring the distance between the spin-labelled pairs. Our results revealed that Na⁺ ions shift the conformational equilibrium of ASBT_NM toward the inward-facing state thereby facilitating cytoplasmic uptake of substrate. The current findings provide a novel perspective on the conformational equilibrium of secondary active transporters.     

The effect of costs associated with toxin production in a competitive system

In this paper, we study a two-species competitive system where both the species produce toxin against each other at some cost to their growth rates. A much wider set of outcomes is possible for our system. These outcomes are important contrasts to competitive exclusion or bistable attractors that are often the outcomes for competitive systems. We show that toxin helps to gain an advantage in competition for toxic species whenever the cost of toxin production remains within some moderate value; otherwise it may result in the extinction of the species itself.     

The trophic impact of small mammals in successional grasslands

The habitat use and diets of small mammals inhabiting grassland plots of different successional ages were investigated by live-trapping and faecal analysis over a period of 16 months. The contribution of the major plant life forms and the structural profile of the vegetation of each plot and the availability of insect prey were assessed. The dominant species of small mammal found on each plot were Sorex araneus, S. minutus, Apodemus sylvaticus and Microtus agrestis . Small mammals were most commonly found in the late and mid-successional stages, reflecting the habitat structure and food availability. A wide range of insects and other invertebrates were eaten by all four species and insects formed 50–62% of the animal prey taken. The incidence of certain prey in the diets differed between plots. The daily consumption rate of invertebrates by shrews and mice was estimated at some 6800 prey per ha. The greatest predatory impact came from shews but A. sylvaticus showed increased consumption of invertebrates in spring. The combined predatory impact of the grassland small mammal community on insect populations alone was estimated to average 0.01% per day and is predicted to be greatest in the mid-successional stages.     

DNA “fingerprints” and paternity ascertainment in chimpanzees (Pan troglodytes)

Highly variable regions of DNA are found in a wide diversity of organisms and are typically composed of alleles consisting of a variable number of tandem repeats (VNTRs) of a short core sequence. DNA fingerprinting probes are VNTR probes that simultaneously detect a large number of similar VNTRs in the target DNA. The highly polymorphic pattern observed in a DNA fingerprint allows resolution of questions concerning individual identification. M13 phage was used to fingerprint captive chimpanzees for paternity ascertainment. Although the probability of band sharing among captive chimps appears to be higher than among some other reported captive and feral animal populations, the probe is highly useful and can be expected to become more widely used in the genetic management of captive populations.     

Correlation of physical maps and some genetic functions in the genomes of the kappa-theta phage family of Bacillus licheniformis

Summary Natural recombinant genomes between several, phenotypically distinct forms of phages and were isolated and characterized by DNA restriction fragment mapping and electron microscopic heteroduplex analysis. The phenotypes of the recombinants were correlated with the physical maps of the genomes, and several genetic functions were therfore defined and mapped. All genes necessary for the assembly of infectious virus particles map in a contiguous tract of DNA comprising about 20 kb, or nearly one third of the genome length. No DNA homology occurs within these domains of the two genomes, so that homologous recombination does not take place here and phenotypic mixing of the phages is eo ipso excluded. Other regions of heterology contain regulatory genes responsible for the lytic or temperate character of the phages, and for exclusion of phage by .     

Predator-induced behavioral defense and its ecological consequences for two calanoid copepods

Summary We used an automated technique for the observation and quantification of zooplankton swimming behavior to study the behavioral responses of two congeneric, herbivorous, freshwater copepod prey to a copepod predator (Limnocalanus macrurus). One prey, Diaptomus sicilis, often co-occurs with Limnocalanus, while previous studies indicated that the zoogeographic distribution of the second prey, Diaptomus oregonensis, was independent of the predator. We found that in the presence of Limnocalanus, D. sicilis swims more slowly and with less hopping and jumping than D. oregonensis. Diaptomus sicilis is also attacked and consumed by the predator Limnocalanus macrurus less frequently than D. oregonensis. We suggest that the faster, noisier swimming of D. oregonensis increases its vulnerability to Limnocalanus. The behavioral defenses to both prey are induced by the presence of the predator, and may represent two different anti-predator strategies, crypsis and avoidance for D. sicilis and D. oregonensis respectively. In a zoogeographical analysis D. oregonensis occurs at densities below D. sicilis in lakes where Limnocalanus is at elevated abundances, while in low-predator lakes the opposite is true. This distribution pattern supports our experimental results, and suggests that D. sicilis is adapted to survive with Limnocalanus, while D. oregonensis is not.     

Molecular basis for the special properties of proteins and enzymes from Halobacterium marismortui

Abstract Three proteins from Halobacterium marismortui , malate dehydrogenase (hMDH), glutamate dehydrogenase (hGDH) and ferredoxin (hFD) were purified and characterized with respect to their molecular masses, amino acid composition and, for hFD only, primary structure. Striking features of halophilic proteins are: the high excess of acidic over basic residues; acidic clusters in the sequence. Low-salt concentration causes inactivation and changes in structural parameters of hMDH and hGDH. Reactivation of hMDH involves long-lived stable intermediates. The salt concentration optimum of enzymic activity is independent of salt nature. The high capacity of halophilic proteins to retain water and salt is due to unique molecular properties, studied by physico-chemical techniques.     

Interactions of lens proteins. Self-association and mixed-association studies of bovine alpha-crystallin and gamma-crystallin

Concentrated solutions of calf alpha-crystallin (up to 45 g/l) and gamma-crystallin (up to 67 g/l) were subjected to frontal exclusion chromatography at pH 7.3, ionic strength 0.17 and 20 degrees C. The experimental concentration dependence of the weight-average partition coefficient was compared with theoretical expressions, which include considerations of thermodynamic non-ideality effects, for the concentration dependence of a single solute and of a solute undergoing reversible self-association. Two types of association pattern were examined, discrete dimerization and indefinite self-association. The partition chromatography results are consistent with an indefinite self-association of gamma-crystallin, governed by an isodesmic association constant of 6.7 X 10(-3) l/g. alpha-Crystallin appears to self-associate either very weakly, with a maximal association constant of 0.9 X 10(-3) l/g, or not at all; the distinction depends on the assessment of the non-ideality coefficients. The consequences of excluded volume effects on these self-association equilibria at high total protein concentration are discussed. Mixtures of alpha-crystallin and gamma-crystallin were analyzed by frontal exclusion chromatography (up to 14 g/l) and sedimentation velocity (up to 115 g/l): no interaction was observed.     

Temperature-related distributions of Metadiaptomus and Tropodiaptomus (Copepoda: Calanoida), particularly in southern Africa

Updated locality records of species of Metadiaptomus and Tropodiaptomus on the African continent confirm the generally disjunct distribution of these two taxa as recognised by Dumont (1980) in North Africa. Distributional data for southern Africa reveal little range overlap between these two genera. Apart from two south western Cape taxa, species of Metadiaptomus are largely confined to upland, higher latitude, semi-arid or arid warm subtemperate regions, while species of Tropodiaptomus generally occupy moist, lower-lying, lower latitude subtropical regions. Separation along latitudinal and/or altitudinal axes implicates temperature as a controlling factor, while separation on the precipitation axis suggests the importance of habitat permanence. Using a multiple regression equation derived for African waters to predict water temperature from latitude and altitude, it is shown that the two genera tend to separate around the 20 °C mean annual temperature isotherm. Additional factors influencing distribution (habitat permanence, water quality, competition and predation) are discussed.     

Exclusion cage studies on the impact of predation on Helicoverpa armigera in cotton

The impact of predation on Helicoverpa armigera was studied in four field cage exclusion trials on cotton in Kenya. H. armigera egg cohorts were introduced inside predator‐free and open control cages, and the impact of local predator populations on the cohort was examined. Fourteen days after inoculation, exclusion cages had four times more larvae than controls, indicating a strong impact of predation. Ants and Anthocoridae were the predominant predator groups. Exclusion cages had more damaged fruiting plant parts (squares, flowers and bolls) than the control. In the absence of predators, natural mortality of H. armigera was greater as cotton matured, and is likely to be linked to the host plant condition.