Elevated male European and female African contributions to the genomes of African American individuals

The differential relative contribution of males and females from Africa and Europe to individual African American genomes is relevant to mapping genes utilizing admixture analysis. The assessment of ancestral population contributions to the four types of genomic DNA (autosomes, X and Y chromosomes, and mitochondrial) with their differing modes of inheritance is most easily addressed in males. A thorough evaluation of 93 African American males for 2,018 autosomal single nucleotide polymorphic (SNP) markers, 121 X chromosome SNPs, 10 Y chromosome haplogroups specified by SNPs, and six haplogroup defining mtDNA SNPs is presented. A distinct lack of correlation observed between the X chromosome and the autosomal admixture fractions supports separate treatment of these chromosomes in admixture-based gene mapping applications. The European genetic contributions were highest (and African lowest) for the Y chromosome (28.46%), followed by the autosomes (19.99%), then the X chromosome (12.11%), and the mtDNA (8.51%). The relative order of admixture fractions in the genomic compartments validates previous studies that suggested sex-biased gene flow with elevated European male and African female contributions. There is a threefold higher European male contribution compared with European females (Y chromosome vs. mtDNA) to the genomes of African American individuals meaning that admixture-based gene discovery will have the most power for the autosomes and will be more limited for X chromosome analysis. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Responses of a eutrophic pond community to separate and combined effects of N:P supply and planktivorous fish: a mesocosm experiment

We conducted an outdoor mesocosm experiment of factorial design consisting of three levels of nutrient supply (no nutrient addition and additions of nitrogen and phosphorus in ratios of 10:1 and 45:1) cross-classified with two levels of bluegill (Lepomis macrochirus) (presence and absence). Nutrient supply significantly affected total phosphorus (TP), total nitrogen (TN), TN: TP ratio, turbidity, Secchi depth, phytoplankton chlorophyll, filamentous blue-green algae, periphyton chlorophyll, Asplanchna and non-predatory rotifers. The presence of bluegill significantly increased TP, turbidity, diatoms, unicellular green algae, colonial blue-green algae, filamentous blue-green algae, periphyton chlorophyll, Asplanchna and non-predatory rotifers, and decreased Secchi depth, cladocerans, cyclopoid copepodids, copepod nauplii and chironomid tube densities. Nutrient supply and fish effects were not independent of each other as shown by significant nutrient × fish interaction effects for TP, Secchi depth, filamentous blue-green algae, periphyton chlorophyll, Asplanchna and non-predatory rotifers.     

4号染色体短臂微卫星多态性与鼻咽癌相关性的研究

鼻咽癌（NPC）是一种多因素复杂疾病。其发病过程涉及EB病毒慢性感染、环境致癌因素及宿主基因之间的相互作用。在这一过程中,那些宿主基因在EB病毒感染及鼻咽癌的发生发展中起了关键作用仍不清楚。 本研究的目的是发现与鼻咽癌发生发展中两个关键步骤相关的遗传变异,即EB病毒持续性感染鼻咽部上皮细胞和鼻咽癌的形成。我们在广西梧州市及苍梧县鼻咽癌高发区收集汉族鼻咽癌患者350例、EB病毒壳抗原IgA抗体阳性者(IgA/VCA+)288例和EB病毒壳抗原IgA抗体阴性者(IgA/VCA-)346例。对先前鼻咽癌家系研究显示的鼻咽癌易感区4号染色体短臂（4p15.1-q12）进行了微卫星精细扫描,在 18 Mb的范围内选择34个微卫星标记,包括319个等位基因,对其进行基因分型。比较分析NPC 组和IgA/VCA+组等位基因频率结果显示,9个等位基因与鼻咽癌呈相关,其中5个为易感等位基因（OR=1.51-5.36, p=0.01-0.03）,4个为限制性等位基因（OR值为0.3-0.71, p值为0.02-0.045）。比较分析IgA/VCA+组和IgA/VCA-组及比较所有IgA/VCA+者（包括NPC患者）和IgA/VCA-者等位基因频率的结果显示,12个等位基因与EB病毒壳抗原IgA抗体持续存在相关,其中3个在两组比较中均呈显著相关。等位基因 D4S3241-136 (p=0.004, OR=1.9, 95%CI=1.2-3.0) 和D4S3347-213 (p=0.001, OR=1.6, 95%CI=1.2-2.1) 可增加EB病毒 IgA/VCA抗体形成的危险,为易感基因;而等位基因D4S174-202 (p=0.001, OR=0.5, 95%CI=0.3-0.7) 可限制IgA/VCA抗体的形成。 但上述结果经多因素比较校正后,均失去相关性。我们的研究结果不能 确定该区域与鼻咽癌的形成相关,而另一个家系研究的结果也未得出相关的结果,但本研究却提供了进一步发现鼻咽癌相关基因的研究模式。有关4号染色体短臂 与EB病毒慢性持续感染及鼻咽癌的形成仍值得进一步深入研究。     

Characterization of Tn916S, a Tn916-like element containing the tetracycline resistance determinant tet(S)

We have characterized a transferable tetracycline resistance (Tcr) element from a Streptococcus intermedius isolate. The gene responsible for this resistance was identified by PCR and Southern hybridization as tet(S). Furthermore, the genetic support for this determinant was shown to be a conjugative transposon closely related to Tn916. This element has been designated Tn916S.     

The Case for Selection at CCR5-Δ32

The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the past 1,000 y and rose to its present high frequency (5%–14%) in Europe as a result of strong positive selection, perhaps by such selective agents as the bubonic plague or smallpox during the Middle Ages. This hypothesis was based on several lines of evidence, including the absence of the allele outside of Europe and long-range linkage disequilibrium at the locus. We reevaluated this evidence with the benefit of much denser genetic maps and extensive control data. We find that the pattern of genetic variation at CCR5-Δ32 does not stand out as exceptional relative to other loci across the genome. Moreover using newer genetic maps, we estimated that the CCR5-Δ32 allele is likely to have arisen more than 5,000 y ago. While such results can not rule out the possibility that some selection may have occurred at C-C chemokine receptor 5 (CCR5), they imply that the pattern of genetic variation seen atCCR5-Δ32 is consistent with neutral evolution. More broadly, the results have general implications for the design of future studies to detect the signs of positive selection in the human genome.     

CFTR drives Na+-nHCO-3 cotransport in pancreatic duct cells: a basis for defective HCO-3 secretion in CF

Pancreatic dysfunction in patients with cystic fibrosis (CF) isfelt to result primarily from impairment of ductalHCO₃ secretion. We provide molecularevidence for the expression of NBC-1, an electrogenicNa⁺-HCO₃cotransporter (NBC) in cultured human pancreatic ductcells exhibiting physiological features prototypical of CF ductfragments (CFPAC-1 cells) or normal duct fragments [CAPAN-1 cellsand CFPAC-1 cells transfected with wild-type CF transmembraneconductance regulator (CFTR)]. We further demonstrate that1)HCO₃ uptake across the basolateralmembranes of pancreatic duct cells is mediated via NBC and2) cAMP potentiates NBC activitythrough activation of CFTR-mediatedCl secretion. We proposethat the defect in agonist-stimulated ductal HCO₃ secretion in patients with CF ispredominantly due to decreased NBC-drivenHCO₃ entry at the basolateralmembrane, secondary to the lack of sufficient electrogenic drivingforce in the absence of functional CFTR.

     

CFTR upregulates the expression of the basolateral Na+-K+-2Cl- cotransporter in cultured pancreatic duct cells

The purpose ofthe current experiments was 1) toassess basolateralNa⁺-K⁺-2Clcotransporter (NKCC1) expression and2) to ascertain the role of cysticfibrosis transmembrane conductance regulator (CFTR) in the regulationof this transporter in a prototypical pancreatic duct epithelial cellline. Previously validated human pancreatic duct celllines (CFPAC-1), which exhibit physiological features prototypical ofcystic fibrosis, and normal pancreatic duct epithelia (stablerecombinant CFTR-bearing CFPAC-1 cells, termed CFPAC-WT) were grown toconfluence before molecular and functional studies. High-stringencyNorthern blot hybridization, utilizing specific cDNA probes, confirmedthat NKCC1 was expressed in both cell lines and its mRNA levels weretwofold higher in CFPAC-WT cells than in CFPAC-1 cells(P < 0.01, n = 3).Na⁺-K⁺-2Clcotransporter activity, assayed as the bumetanide-sensitive, Na⁺- andCl-dependentNH⁺₄ entry into the cell (withNH⁺₄ acting as a substitute forK⁺), increased by ~115% inCFPAC-WT cells compared with CFPAC-1 cells(P < 0.01, n = 6). Reducing the intracellularCl by incubating the cellsin a Cl-free mediumincreasedNa⁺-K⁺-2Clcotransporter activity by twofold (P < 0.01, n = 4) only in CFPAC-WT cells. We concluded that NKCC1 is expressed in pancreatic duct cellsand mediates the entry ofCl. NKCC1 activity isenhanced in the presence of an inwardCl gradient. The resultsfurther indicate that the presence of functional CFTR enhances theexpression of NKCC1. We speculate that CFTR regulates this process in aCl-dependent manner.

     

Visualization of protein interactions in living Caenorhabditis elegans using bimolecular fluorescence complementation analysis

The bimolecular fluorescence complementation (BiFC) assay is a powerful tool for visualizing and identifying protein interactions in living cells. This assay is based on the principle of protein-fragment complementation, using two nonfluorescent fragments derived from fluorescent proteins. When two fragments are brought together in living cells by tethering each to one of a pair of interacting proteins, fluorescence is restored. Here, we provide a protocol for a Venus-based BiFC assay to visualize protein interactions in the living nematode, Caenorhabditis elegans. We discuss how to design appropriate C. elegans BiFC cloning vectors to enable visualization of protein interactions using either inducible heat shock promoters or native promoters; transform the constructs into worms by microinjection; and analyze and interpret the resulting data. When expression of BiFC fusion proteins is induced by heat shock, the fluorescent signals can be visualized as early as 30 min after induction and last for 24 h in transgenic animals. The entire procedure takes 2-3 weeks to complete.