Y chromosome lineage- and village-specific genes on chromosomes 1p22 and 6q27 control visceral leishmaniasis in Sudan

Familial clustering and ethnic differences suggest that visceral leishmaniasis caused by Leishmania donovani is under genetic control. A recent genome scan provided evidence for a major susceptibility gene on Chromosome 22q12 in the Aringa ethnic group in Sudan. We now report a genome-wide scan using 69 families with 173 affected relatives from two villages occupied by the related Masalit ethnic group. A primary ten-centimorgan scan followed by refined mapping provided evidence for major loci at 1p22 (LOD score 5.65; nominal p = 1.72 × 10⁻⁷; empirical p < 1 × 10⁻⁵; λ_S = 5.1) and 6q27 (LOD score 3.74; nominal p = 1.68 × 10⁻⁵; empirical p < 1 × 10⁻⁴; λ_S = 2.3) that were Y chromosome–lineage and village-specific. Neither village supported a visceral leishmaniasis susceptibility gene on 22q12. The results suggest strong lineage-specific genes due to founder effect and consanguinity in these recently immigrant populations. These chance events in ethnically uniform African populations provide a powerful resource in the search for genes and mechanisms that regulate this complex disease.     

Combined use of Monte Carlo DNA damage simulations and deterministic repair models to examine putative mechanisms of cell killing

A kinetic repair-misrepair-fixation (RMF) model is developed to better link double-strand break (DSB) induction to reproductive cell death. Formulas linking linear-quadratic (LQ) model radiosensitivity parameters to DSB induction and repair explicitly account for the contribution to cell killing of unrejoinable DSBs, misrepaired and fixed DSBs, and exchanges formed through intra- and intertrack DSB interactions. Information from Monte Carlo simulations is used to determine the initial yields and complexity of DSBs formed by low- and high-LET radiations. Our analysis of published survival data for human kidney cells suggests that intratrack DSB interactions are negligible for low-LET radiations but increase rapidly with increasing LET. The analysis suggests that no class of DSB is intrinsically unrejoinable or that DSB reparability is not strictly determined by the number of lesions forming the DSB. For radiations with LET >110 keV/mum, the model predicts that the relative cell killing efficiency, per unit absorbed dose, should continue to increase, whereas data from published experiments indicate a reduced cell killing efficiency. This observation suggests that the Monte Carlo simulation overestimates the DSB yield beyond 110 keV/microm or that other biological phenomena not included in the model, such as proximity effects, are important. For 200-250 kVp X rays ( approximately 1.9 keV/microm), only about 1% of the one-track killing is attributed to intratrack binary misrepair interactions. The analysis indicates that the remaining 99% of the lethal damage is due to other types of one-track damage, including possible unrepairable, misrepaired and fixed damage. Compared to the analysis of the X-ray results, 48% of the one-track lethal damage caused by 5.1 MeV alpha particles (approximately 88 keV/microm) is due to intratrack DSB interactions while the remainder is due to other forms of one-track damage.     

The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria

The gene Rv0813c from Mycobacterium tuberculosis, which codes for a hypothetical protein of unknown function, is conserved within the order Actinomycetales but absent elsewhere. The crystal structure of Rv0813c reveals a new family of proteins that resemble the fatty acid-binding proteins (FABPs) found in eukaryotes. Rv0813c adopts the 10-stranded beta-barrel fold typical of FABPs but lacks the double-helix insert that covers the entry to the binding site in the eukaryotic proteins. The barrel encloses a deep cavity, at the bottom of which a small cyclic ligand was found to bind to the hydroxyl group of Tyr192. This residue is part of a conserved Arg-X-Tyr motif much like the triad that binds the carboxylate group of fatty acids in FABPs. Most of the residues forming the internal surface of the cavity are conserved in homologous protein sequences found in CG-rich prokaryotes, strongly suggesting that Rv0813c is a member of a new family of bacterial FABP-like proteins that may have roles in the recognition, transport, and/or storage of small molecules in the bacterial cytosol.     

ALFRED: An allele frequency database for anthropology

The deluge of data from the human genome project (HGP) presents new opportunities for molecular anthropologists to study human variation through the promise of vast numbers of new polymorphisms (e.g., single nucleotide polymorphisms or SNPs). Collecting the resulting data into a single, easily accessible resource will be important to facilitate this research. We created a prototype Web-accessible database named ALFRED (ALelle FREquency Database, http://alfred.med.yale.edu/alfred/) to store and make publicly available allele frequency data on diverse polymorphic sites for many populations. In constructing this database, we considered many different concerns relating to the types of information needed for anthropology, population genetics, molecular genetics, and statistics, as well as issues of data integrity and ease of access to data. We also developed links to other Web-based databases as well as procedures for others to make links to the data in ALFRED. Here we present an overview of the issues considered and provisional solutions, as well as an example of data already available. It is our hope that this database will be useful for research and teaching in a wide range of fields, and that colleagues from various fields will contribute to making ALFRED an important resource for many studies as yet unforeseen.     

Overexpression of the human insulinlike growth factor I receptor promotes ligand-dependent neoplastic transformation.

The human insulinlike growth factor I receptor was overexpressed in NIH 3T3 cells as well as human and rat primary fibroblast strains. The NIH 3T3 cells displayed a ligand-dependent, highly transformed phenotype. When exposed to insulinlike growth factor I or supraphysiologic levels of insulin, NIH 3T3 cells that expressed high levels of receptors formed aggregates in tissue culture dishes, colonies in soft agar, and tumors in nude mice. Expression of 1 million receptors per cell, a 40-fold increase above the base-line level, was required for anchorage-independent growth. Primary fibroblasts that expressed high levels of receptors displayed a ligand-dependent change in morphology and an increase in saturation density but did not acquire a fully transformed phenotype. The results demonstrate that when amplified, this ubiquitous growth factor receptor behaves like an oncogenic protein and is capable of promoting neoplastic growth in vivo.     

Egg size and emergence timing affect morphology and behavior in juvenile Chinook Salmon,Oncorhynchus tshawytscha

Variation in early life history traits often leads to differentially expressed morphological and behavioral phenotypes. We investigated whether variation in egg size and emergence timing influence subsequent morphology associated with migration timing in juvenile spring Chinook Salmon, Oncorhynchus tshawytscha. Based on evidence for a positive relationship between growth rate and migration timing, we predicted that fish from small eggs and fish that emerged earlier would have similar morphology to fall migrants, while fish from large eggs and individuals that emerged later would be more similar to older spring yearling migrants. We sorted eyed embryos within females into two size categories: small and large. We collected early and late‐emerging juveniles from each egg size category. We used landmark‐based geometric morphometrics and found that egg size appears to drive morphological differences. Egg size shows evidence for an absolute rather than relative effect on body morphology. Fish from small eggs were morphologically more similar to fall migrants, while fish from large eggs were morphologically more similar to older spring yearling migrants. Previous research has shown that the body morphology of fish that prefer the surface or bottom location in a tank soon after emergence also correlates with the morphological variations between wild fall and spring migrants, respectively. We found that late‐emerging fish spent more time near the surface. Our study shows that subtle differences in early life history characteristics may correlate with a diversity of future phenotypes.     

Kinetic analysis of nanoparticle‐protein interactions using a plasmon waveguide resonance

A plasmon waveguide resonance (PWR) sensor is proposed for studying the interaction between gold nanoparticles and proteins. The ability of the PWR sensor to operate in both TM and TE Polarizations, i.e. its polarization diversity, facilitates the simultaneous spectroscopy of the nanoparticles surface reactions using both polarizations. The response of each polarization to streptavidin‐biotin binding at the surface of gold nanoparticles is investigated in real time. Finally, using the principles of multimode spectroscopy, the nanoparticle's surface reactions are decoupled from the bulk solution refractive index variations.

Schematic diagram of the NP‐modified PWR sensor     

Drought stress and recovery of riparian cottonwoods due to water table alteration along Willow Creek,Alberta

A 5-m-deep gravel pit was excavated from 1996 to 1998 in the floodplain between Willow Creek, Alberta, and a grove of balsam poplars ('cottonwoods', Populus balsamifera L.) and water level at the pit was lowered 2.5 m through pumping. This interrupted the infiltration of stream water into the riparian groundwater and imposed drought stress on the cottonwoods. Trees in the drought-affected grove displayed extensive leaf senescence and abscission in late August 1998, while trees in nearby control groves remained green until autumnal senescence in late September. The precocious senescence was accompanied by a two-thirds reduction in leaf stomatal conductance (g _s) but mid-day leaf xylem water potentials (ψ_l) were only slightly reduced (?1.55 vs 1.42 MPa). Pumping ceased in 1999, the pit was partially refilled, and the hydraulic linkage between the stream and the riparian zone recovered. Subsequently in August 1999, g _s and ψ_l were similar for trees in the affected and control groves and senescence phenologies were similar in 1999 and 2000. Annual branch growth increments varied 3-fold across years between 1994 and 1999, but there was no reduction in these growth increments in the drought-affected trees in 1998 or 1999. This study supports the hydraulic linkage between a stream and the adjacent riparian zone in a semi-arid region and demonstrates the vulnerability of riparian cottonwoods to drought due to water table depletion. It also indicates rapid physiological recovery of cottonwoods following restoration of water availability.     

Ethanol Inhibits Basic Fibroblast Growth Factor-Mediated Proliferation of C6 Astrocytoma Cells

Abstract: Early ethanol exposure alters the proliferative activity of glial and neuronal precursors in the developing CNS. The present study tests the hypothesis that ethanol-induced alterations in cell proliferation result from interference with growth factors. An in vitro model of astroglia (C6 astrocytoma cells) was used to study the effects of ethanol on proliferation mediated by basic fibroblast growth factor (bFGF). bFGF stimulated the proliferation of C6 cells. This bFGF-enhanced proliferation was evident by increases in total cell number, DNA synthesis (as measured by [³H]thymidine incorporation), and the number of cells that took up bromodeoxyuridine. A synthetic peptide that specifically blocked the binding of bFGF to its high-affinity receptor completely abolished the proliferation-promoting effect of bFGF. The action of another mitogen for C6 cells, insulin-like growth factor-1, was not affected by this peptide. Therefore, the bFGF-stimulated proliferation was mediated through a specific bFGF receptor. Ethanol inhibited bFGF-mediated proliferation in a concentration-dependent manner. Ethanol concentrations of 100 and 200 mg/dl partially inhibited bFGF-mediated proliferation (by 58 and 74%, respectively), whereas concentrations of ≥400 mg/dl completely abolished the growth-stimulating effect of bFGF. Our data show that ethanol alters proliferative activity of C6 cells by disrupting the action of bFGF. The target of ethanol neurotoxicity is a receptor-mediated activity. bFGF can affect cell proliferation by a non-receptor-mediated intracellular pathway, but ethanol does not have an impact on this pathway.