Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions,local adaptation and geographic structure

Recent advances in sequencing allow population‐genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction‐site‐associated DNA sequence (RAD‐seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well‐characterized single nucleotide polymorphism (SNP) data set from 21 three‐spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single‐outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population‐genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population‐demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population‐genomic data set, making it especially valuable for nonmodel species.     

Removal of Arsenic(III) from Waste Water Using Lactobacillus acidophilus

Lactobacillus acidophilus was used for the removal of As(III) from 50–2000 ppb As(III)-containing water solution. Biosorption of As(III) by L. acidophilus was dependent on concentration (50 to 2000 ppb) and time (0 to 3 h).L. acidophilus(1 mg dry wt/ml) was able to remove 30, 60, 300, 420, 600 ppb As(III) from 50, 100, 500, 1000, and 2000 ppb of As(III)-containing water solution, respectively, within 3 h at pH 7. Moreover, by increasing the biomass of L. acidophilus(2 mg dry wt/ml) removal of As(III) was enhanced 1.66, 1.33, 1.16, 1.42, and 1.33 times, respectively. Fourier transform infrared (FTIR) and electron spectroscopy for chemical analysis (ESCA) spectrum of As(III)-loaded biomass was also investigated. An FTIR sample spectrum of L. acidophilus fresh biomass and As(III)-loaded biomass showed band stretching of fresh and As(III)-loaded biomass for O-H, 3423.43 to 3385.04 cm^?1, and for C-O, 1742.82 to 1731.14 cm^?1, and signified that –OH and –CO groups were also involved in the removal of As(III) from As(III)-containing water solution.     

Fine needle aspiration cytology in HIV‐related lymphadenopathy: experience at a single centre in north India

P. K. Sarma, A. K. Chowhan, V. Agrawal and V. Agarwal
Fine needle aspiration cytology in HIV‐related lymphadenopathy: experience at a single centre in north India Objective: Fine needle aspiration (FNA) is emerging as a rapid and minimally invasive tool in evaluating lymphadenopathy associated with human immunodeficiency virus (HIV). We evaluated the role of FNA in differentiating various causes of lymphadenopathy in patients with HIV and correlated the cytological diagnosis with CD4 counts. Methods: Seventy‐nine HIV‐positive patients (median age 35 years, 68 male) underwent ultrasound‐guided (n = 16) and unguided (n = 63) FNA from 1999 to 2006. Smears were stained with May–Grünwald–Giemsa, haematoxylin & eosin and Papanicolaou stains. Ziehl–Neelsen (ZN) staining for acid‐fast bacilli (AFB) was performed in all cases. Staining for fungus was performed whenever required. Results: The aspirates were adequate in 75 cases (95%). Non‐specific reactive hyperplasia was the most common FNA diagnosis (39, 52%) followed by granulomatous necrotizing lymphadenitis (15, 20%), necrotizing lymphadenitis (13, 17.3%) and granulomatous lymphadenitis (4, 5.2%). Fungal infection and non‐Hodgkin lymphoma (NHL) were seen in two patients each. ZN staining was positive for AFB in 25 (33.3%) cases. One of these was morphologically interpreted as reactive hyperplasia, 12 as necrotizing lymphadenitis and 12 as granulomatous necrotizing lymphadenitis. Both patients with NHL had CD4 counts below 100/dl. Necrotizing lymphadenitis and granulomatous lymphadenitis were significantly associated with CD4 counts below and above 200/dl, respectively (P = 0.0002). Conclusions: FNA is an important tool for assessing the cause of lymphadenopathy in HIV patients. Necrotizing inflammation is more often seen in patients with low CD4 counts. AFB are commonly found in necrotic aspirates with or without granulomas. However, a stain for AFB should be performed in all aspirates from HIV‐related lymphadenopathy including reactive hyperplasia.     

Androgen receptor status predicts response to chemotherapy, not risk of breast cancer in Indian women

Voltage gated potassium channels have been extensively studied in relation to cancer. In this review, we will focus on the role of two potassium channels, Ether à-go-go (Eag), Human ether à-go-go related gene (HERG), in cancer and their potential therapeutic utility in the treatment of cancer. Eag and HERG are expressed in cancers of various organs and have been implicated in cell cycle progression and proliferation of cancer cells. Inhibition of these channels has been shown to reduce proliferation both in vitro and vivo studies identifying potassium channel modulators as putative inhibitors of tumour progression. Eag channels in view of their restricted expression in normal tissue may emerge as novel tumour biomarkers.     

Combined effects of sediment and lead (PbCl<Subscript>2</Subscript>) on the demography of <Emphasis Type="Italic">Brachionus patulus</Emphasis> (Rotifera: Brachionidae)

We studied the response of Brachionus patulus to different concentrations of the heavy metal Pb in the presence and absence of sediments. We conducted acute (LC₅₀) and chronic (life table demography and population growth) toxicity tests using sediment levels of 0, 30 and 280 mg l⁻¹ (=0, 17 and 170 NTU) and Pb at 0, 0.06 and 0.6 mg l⁻¹. Experiments were conducted at 20 ± 1°C on a horizontal shaker and algal food (Chlorella vulgaris) was added at a density of 1.0 × 10⁶ cells ml⁻¹. The median lethal concentration (LC₅₀ ± 95% Confidence intervals) of PbCl₂ for B. patulus was 6.15 ± 1.08 mg l⁻¹. Age-specific survivorship and fecundity curves showed increase in turbidity level resulted in decreased survival and offspring production of the rotifers. Increase in Pb concentration too had a negative effect on the survival and reproductive output of B. patulus. Statistically, average lifespan, life expectancy at birth, gross and net reproductive rates and the rate of population increase were all significantly influenced by the concentration of Pb, turbidity level as well as the interaction of Pb concentration × turbidity level. Rotifers exposed to 170 NTU did not grow regardless of the heavy metal concentration in the medium. Similarly, B. patulus exposed to 0.6 mg l⁻¹ Pb did not survive beyond 10 days regardless of the turbidity level in the medium. The rate of population increase of B. patulus derived from the growth experiments was negative in all treatments containing Pb as low as 0.06 mg l⁻¹ or turbidity level as low as 17 NTU. In treatments containing Pb or sediments, there existed no relation between the egg ratio and the population density. Guest editors: S. S. S. Sarma, R. D. Gulati, R. L. Wallace, S. Nandini, H. J. Dumont and R. Rico-Martínez Advances in Rotifer Research     

Effect of pulsed exposure to heavy metals (copper and cadmium) on some population variables of <Emphasis Type="Italic">Brachionus calyciflorus</Emphasis> Pallas (Rotifera: Brachionidae: Monogononta)

Heavy metals are widely recognized as potential toxic agents to zooplankton, yet experiments are usually performed with a continuous exposure to the metal being analyzed. Here we describe experiments that examined the influence of pulsed exposure of the heavy metals copper and cadmium to a parthenogenetic population of the planktonic rotifer Brachionus calyciflorus. Our protocol called for exposure durations of 3, 6, 12, and 24 h to either copper (as CuSO₄) at concentrations of 0.0375, 0.075, 0.15 mg l⁻¹ or cadmium (as CdCl₂) at concentration of 0.025, 0.05, 0.1 mg l⁻¹. Control animals were treated in similar ways but did not receive exposure to heavy metals. Four end points were used to evaluate the outcome of exposure: population growth (r), body size, egg ratio, and egg hatching percent. Increase in heavy metal concentration and exposure time had an adverse influence on the population growth of B. calyciflorus. However, while the response of B. calyciflorus was similar for both heavy metals, the magnitude of the impact of cadmium was more severe. Population growth varied depending on which heavy metal was tested, as well as its concentration and the duration of exposure (r = 0.11–0.28 day⁻¹). There was a significant reduction in lorica size of B. calyciflorus subjected to different exposure times and concentrations of both Cd and Cu. Egg ratios were inversely related to population density in controls and in treatments involving Cu, but not for Cd. While nearly 100% of eggs hatched in the control treatments, egg hatching in experimental treatments containing Cu, were reduced (range = 16–41%) depending on the exposure time and the concentration. Guest editors: S. S. S. Sarma, R. D. Gulati, R. L. Wallace, S. Nandini, H. J. Dumont & R. Rico-Martínez Advances in Rotifer Research     

Influence of recirculation on the performance of anaerobic sequencing batch biofilm reactor (AnSBBR) treating hypersaline composite chemical wastewater

Influence of recirculation on the performance of anaerobic sequencing batch biofilm reactor (AnSBBR) was studied in the process of treating hypersaline (total dissolved inorganic solids (TDIS) approximately 26 g/l) and low biodegradable (BOD/COD approximately 0.3) composite chemical wastewater. Significant enhancement in the substrate removal efficiency and biogas yield was observed after introducing the recirculation to the system. Maximum efficiency (COD removal efficiency - 51%; SDR - 3.14 kg COD/cum-day) was observed at recirculation to feed (R/F) ratio of 2 (OLR - 6.15 kg C OD/cum-day; HLR - 2.30 cum (liquid)/cum day; UFV(A) - 0.023 m/h). Subsequent increase of R/F to 3 (OLR - 6.15 kg COD/cum-day; HLR - 3.07cum (liquid)/cum-day; UFV(A) - 0.035 m/h) resulted in reduction in COD removal efficiency (32%; SDR - 1.97 kg COD/cum-day). The enhanced performance of the system due to the introduction of recirculation was attributed to the improvement in the mass transfer between the substrate present in the bulk liquid and the attached biofilm. The hydrodynamic behavior due to recirculation mode of operation reduced the concentration gradient (substrate inhibition) of substrate and reaction by-products (VFA) resulting in mixed flow conditions.     

Prevalence of duodenal ulcer-promoting gene (dupA) of Helicobacter pylori in patients with duodenal ulcer in North Indian population

BACKGROUND: The duodenal ulcer (DU)-promoting gene (dupA) of Helicobacter pylori has been identified as a novel virulent marker associated with an increased risk for DU. The presence or absence of dupA gene of H. pylori present in patients with DU and functional dyspepsia in North Indian population was studied by polymerase chain reaction (PCR) and hybridization analysis. MATERIALS AND METHODS: One hundred and sixty-six patients (96 DU and 70 functional dyspepsia) were included in this study. In addition, sequence diversity of dupA gene of H. pylori found in these patients was analyzed by sequencing the PCR products jhp0917 and jhp0918 on both strands with appropriate primers. RESULTS: PCR and hybridization analyses indicated that dupA gene was present in 37.5% (36/96) of H. pylori strains isolated from DU patients and 22.86% (16/70) of functional dyspepsia patients (p < or = .05). Of these, 35 patients with DU (97.2%) and 14 patients with functional dyspepsia (81.25%) were infected by H. pylori positive for cagA genotype. Furthermore, the presence of dupA was significantly associated with the cagA-positive genotype (p < or = .02). CONCLUSION: Results of our study have shown that significant association of dupA gene with DU in this population. The dupA gene can be considered as a novel virulent marker for DU in this population.     

Activation of Microtubule Dynamics Increases Neuronal Growth via the Nerve Growth Factor (NGF)- and Gαs-mediated Signaling Pathways

Signals that activate the G protein Gα_s and promote neuronal differentiation evoke Gα_s internalization in rat pheochromocytoma (PC12) cells. These agents also significantly increase Gα_s association with microtubules, resulting in an increase in microtubule dynamics because of the activation of tubulin GTPase by Gα_s. To determine the function of Gα_s/microtubule association in neuronal development, we used real-time trafficking of a GFP-Gα_s fusion protein. GFP-Gα_s concentrates at the distal end of the neurites in differentiated living PC12 cells as well as in cultured hippocampal neurons. Gα_s translocates to specialized membrane compartments at tips of growing neurites. A dominant-negative Gα chimera that interferes with Gα_s binding to tubulin and activation of tubulin GTPase attenuates neurite elongation and neurite number both in PC12 cells and primary hippocampal neurons. This effect is greatest on differentiation induced by activated Gα_s. Together, these data suggest that activated Gα_s translocates from the plasma membrane and, through interaction with tubulin/microtubules in the cytosol, is important for neurite formation, development, and outgrowth. Characterization of neuronal G protein dynamics and their contribution to microtubule dynamics is important for understanding the molecular mechanisms by which G protein-coupled receptor signaling orchestrates neuronal growth and differentiation.