Order Of Relative Abundance Research Articles

Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method

Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.

Physicochemical properties of groundwater in parts of Irun Akoko, Ondo State, Nigeria

Ten groundwater samples from hand dug wells were collected at Irun Akoko within the basement complex of part of southwestern Nigeria. The aim of the study was to determine the groundwater suitability for both drinking and irrigation purposes. The groundwater samples were analysed for some physical and chemical constituents including pH, Total Dissolved Solids (TDS), turbidity, Na, Ca, Mg, K, Cl, SO4, PO4 and NO3. The pH (7.0 – 7.9) and TDS (12.26 – 19.35 mg/l) of the groundwater indicate that the water is neutral to slightly alkaline and fresh respectively. The order of relative abundance for concentration of cations in the groundwater is K&gt;Ca&gt;Na&gt;Mg, while that of anions is Cl&gt;SO4&gt;NO3&gt;PO4. The concentrations of potassium in about 90% and chloride in about 40 % of the samples were above the World Health Organization (WHO) standard for drinking water. Other hydro-geochemical parameters Ca, Mg, Na, SO4, PO4 and NO3 falls within the WHO standards. Values of Sodium Absorption Ratio (SAR) classified the water as excellent for irrigation purposes. The Soluble Sodium Percentage (SSP) values classified eighty percent of the water to be of good quality and the remaining samples as fair for irrigation purposes. However, using the Magnesium Adsorption Ratio (55.0 – 68.9 %) the samples may have hazardous effects on the soil. Generally, groundwater in the study area is suitable for both domestic and irrigation uses.

Comparative Biochemical Evaluation of the Proximate, Mineral, and Phytochemical Constituents of Xylopia aethiopica Whole Fruit, Seed, and Pericarp.

This study evaluated the relative abundance of proximate, mineral, and phytochemical constituents of the anatomical parts of Xylopia aethiopica (XA) fruit using standard analytical procedures. The results showed that whole fruits (WF) have higher contents of crude protein, crude fiber, fat, ash, and moisture than the seeds (S) and pericarps (P). However, highest contents of crude carbohydrate and nitrogen free extracts were found in the P, followed by the S. The content of minerals (sodium, potassium, calcium, phosphorus, iron, zinc, magnesium, and copper) and phytochemicals were present in the following order of abundance: WF>S>P. Furthermore, the phytochemical constituents in each XA parts were present in the following order of relative abundance: total flavonoids>tannins>total phenolics>cardiac glycoside>alkaloids>steroids. Vitamin A was abundant in all three parts, with the abundance highest in WF [4.83±0.06 g vitamin A equivalent (vit A eq)/100 g] and lowest in P (1.64±0.02 g vit A eq/100 g). This preliminary study indicates XA fruits are rich in minerals, anti-nutrients, and phytochemicals. Therefore, these data could represent a biochemical rationale for inclusion of XA as a spice or functional ingredient in many Nigerian local soups to help prevent ailments.

Relative abundance and activity patterns of terrestrial carnivorous mammals in Península Valdés, Patagonia, Argentina

Abstract The purpose of this study was to assess the relative abundance and activity patterns of terrestrial carnivorous mammals living in San Pablo de Valdés Wildlife Reserve, which is located in Península Valdés (PV), Chubut province, Argentina. To this end, camera traps were placed in different plant communities of this reserve and they were used from January 2015 to December 2016. A total of 256 independent events, with a sampling effort of 1811 camera nights, were obtained. The following species were identified in order of relative abundance: Conepatus chinga, Lycalopex gymnocercus, Leopardus geoffroyi, Puma concolor, and Leopardus colocolo, and the activity patterns of the first three were estimated. Those of P. concolor and L. colocolo could not be estimated as insufficient independent events were obtained. Our results show a cathemeral activity pattern in C. chinga and L. geoffroyi and a more nocturnal pattern in L. gymnocercus. Our results highlight the need to expand the sampling area to obtain further details on the behavioral patterns and population parameters of the carnivores identified. Knowledge of ecological issues, such as relative abundance and activity patterns of carnivorous mammals, is imperative to formulate monitoring and conservation programs.

Relative Abundance of Thiolated Species of As, Mo, W, and Sb in Hot Springs of Yellowstone National Park and Iceland.

Geothermal waters often are enriched in trace metal(loid)s, such as arsenic, antimony, molybdenum, and tungsten. The presence of sulfide can lead to the formation of thiolated anions; however, their contributions to total element concentrations typically remain unknown because nonsuitable sample stabilization and chromatographic separation methods convert them to oxyanions. Here, the concurrent widespread occurrence of thioarsenates, thiomolybdates, thiotungstates, and thioantimonates, in sulfide-rich hot springs from Yellowstone National Park and Iceland is shown. More thiolation was generally observed at higher molar sulfide to metal(loid) excess (Iceland > Yellowstone). Thioarsenates were the most prominent and ubiquitous thiolated species, with trithioarsenate typically dominating arsenic speciation. In some Icelandic hot springs, arsenic was nearly quantitatively thiolated. Also, for molybdenum, thioanions dominated over oxyanions in many Icelandic hot springs. For tungsten and antimony, oxyanions typically dominated and thioanions were observed less frequently, but still contributed up to a few tens of percent in some springs. This order of relative abundance (thioarsenates > thiomolybdates > thiotungstates ≈ thioantimonates) was also observed when looking at processes triggering transformation of thioanions such as mixing with non-geothermal waters or H2S degassing and oxidation with increasing distance from a discharge. Even though to different extents, thiolation contributed substantially to speciation of all four elements studied, indicating that their analysis is required when studying geothermal systems.

Protein signatures of molecular pathways in non-small cell lung carcinoma (NSCLC): comparison of glycoproteomics and global proteomics

BackgroundNon-small cell lung carcinoma (NSCLC) remains the leading cause of cancer deaths in the United States. More than half of NSCLC patients have clinical presentations with locally advanced or metastatic disease at the time of diagnosis. The large-scale genomic analysis of NSCLC has demonstrated that molecular alterations are substantially different between adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). However, a comprehensive analysis of proteins and glycoproteins in different subtypes of NSCLC using advanced proteomic approaches has not yet been conducted.MethodsWe applied mass spectrometry (MS) technology featuring proteomics and glycoproteomics to analyze six primary lung SqCCs and eleven ADCs, and we compared the expression level of proteins and glycoproteins in tumors using quantitative proteomics. Glycoproteins were analyzed by enrichment using a chemoenzymatic method, solid-phase extraction of glycopeptides, and quantified by iTRAQ-LC–MS/MS. Protein quantitation was further annotated via Ingenuity Pathway Analysis.ResultsOver 6000 global proteins and 480 glycoproteins were quantitatively identified in both SqCC and ADC. ADC proteins (8337) consisted of enzymes (22.11%), kinases (5.11%), transcription factors (6.85%), transporters (6.79%), and peptidases (3.30%). SqCC proteins (6967) had a very similar distribution. The identified glycoproteins, in order of relative abundance, included membrane (42%) and extracellular matrix (>33%) glycoproteins. Oncogene-coded proteins (82) increased 1.5-fold among 1047 oncogenes identified in ADC, while 124 proteins from SqCC were up-regulated in tumor tissues among a total of 827 proteins. We identified 680 and 563 tumor suppressor genes from ADC and SqCC, respectively.ConclusionOur systematic analysis of proteins and glycoproteins demonstrates changes of protein and glycoprotein relative abundance in SqCC (TP53, U2AF1, and RXR) and in ADC (SMARCA4, NOTCH1, PTEN, and MST1). Among them, eleven glycoproteins were upregulated in both ADC and SqCC. Two glycoproteins (ELANE and IGFBP3) were only increased in SqCC, and six glycoproteins (ACAN, LAMC2, THBS1, LTBP1, PSAP and COL1A2) were increased in ADC. Ingenuity Pathway Analysis (IPA) showed that several crucial pathways were activated in SqCC and ADC tumor tissues.

Provenance of Holocene calcareous beach-dune sediments, Western Eyre Peninsula, Great Australian Bight, Australia

Much of western Eyre Peninsula adjacent to the Great Australian Bight is veneered with siliceous and calcareous Quaternary aeolian dunes. The lengthy coastline adjacent to this cool-water carbonate factory is a series of Precambrian crystalline bedrock-Pleistocene aeolianite headlands that separate many long, sweeping, Holocene carbonate sand beaches and their backbeach dunes. Incessant SW waves, rolling swells, and onshore winds have resulted in >350km of semi-continuous calcareous strandline aeolian sands. The sediment is composed of quartz grains, Cenozoic limestone clasts, and relict particles (extraclasts) but the deposits are overwhelmingly dominated by contemporaneous biofragments from offshore. These skeletal grains are, in order of relative abundance, molluscs>benthic foraminifers>coralline algae>bryozoans, and echinoids. Benthic foraminifers are mostly small (especially rotaliids and miliolids) but the large relict symbiont-bearing protistMarginopora vertebralis, which grew in the latter stages of MIS 2, is present locally. There are no significant onshore-offshore trends within individual beach-dune complexes. There is, however, a prominent spatial partitioning, with extraclast-rich sediments in the north and biofragment-rich deposits in the south. This areal trend is interpreted to result from more active seafloor carbonate production in the south, an area of conspicuous seasonal nutrient upwelling and profound nektic and benthic biological productivity. The overall system is strikingly similar to Holocene and Pleistocene aeolianites along the inboard margin of the Lacepede Shelf and Bonney Coast some 500km to the southeast, implying a potential universality to the nature of cool-water carbonate aeolianite deposition. The composition of these cool-water aeolianites is more multifaceted than those formed on warm-water, shallow flat-topped platforms, largely because of the comparatively deep, temperate shelf, the high-energy wave and swell climate impacting the shoreline, and thus the different geohistory during sea level change.

The Environmental Deposition of Some Elements Enrichment Using Ditch Cuttings Samples From X – Well in Oliogo, Onshore Niger Delta

Ditch cuttings were collected at various intervals from X well in onshore Niger Delta. The study area which is Oliogo community Delta State Nigeria is located in North – North East (NNE) of Umutu. The purpose of the study is to evaluate the elemental concentration and determine the environment as well as the prevailing conditions under which the elements were deposited. The elemental concentration was determined with Atomic Absorption Spectrometer (AAS) model 969 unicam series. From the lithos tratigraphic study of the selected interval, two lithologic types were determined which are sandy shale and shale. Studies on the geochemical concentration of some elements and their variations with depth show various levels of elemental enrichment in the following order of relative abundance>Na>Ca>Fe>Mg>Mn> Ni>Co>Pb. The degrees of enrichment suggest a significant difference in depositional environment during accumulation. Further studies on the paleo redox proxies of the samples suggest a high oxygen (oxic) environment. http://dx.doi.org/10.4314/njt.v34i3.28

Oligocene pancheloniid sea turtles from the vicinity of Charleston, South Carolina, U.S.A.

ABSTRACT In the Oligocene Ashley and Chandler Bridge formations near Charleston, South Carolina, remains of three species of pancheloniid sea turtle are common. In their relative order of abundance, they are Carolinochelys wilsoni, Ashleychelys palmeri, gen. et sp. nov., and Procolpochelys charlestonensis, sp. nov. Unlike the other two Oligocene South Carolina genera, Procolpochelys persisted into the middle Miocene. An isolated skull, referable to the Miocene species Procolpochelys grandaeva, is described here to supplement description of the poorly known skull of the Oligocene species P. charlestonensis. These turtles, all referable to Pancheloniidae, represent an endemic, moderately advanced sea turtle assemblage that occupied the Oligocene coastal waters of the southeastern United States. This tendency toward endemism also is seen in some parts of the co-occurring cetacean assemblage, which included at least two endemic families. Regionally restricted endemic assemblages appear to have been the norm among pre-Miocene pancheloniid sea turtles. It is not until the Miocene that crown cheloniids appear and begin to achieve very widespread to global distributions. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP

Terpinen-4-ol is the Most Active Ingredient of Tea Tree Oil to KillDemodexMites

To determine the active ingredient in tea tree oil (TTO) responsible for its reported killing effect on Demodex mites, the most common ectoparasite found in the human skin extending to the eye. Using a reported in vitro killing assay to measure the survival time of adult Demodex folliculorum up to 150 minutes, we have screened serial concentrations of 13 of the 15 known ingredients of TTO (ISO4730:2004) that were soluble in mineral oil and examined their synergistic relationships in killing mites. The most potent ingredient was then tested for its efficacy in killing Demodex in vivo. All ingredients exhibited a dose-dependent killing effect. Besides Terpinen-4-ol, the order of relative potency did not correlate with the order of relative abundance in TTO for the remaining 12 ingredients. Terpinen-4-ol was the most potent ingredient followed by α-Terpineol, 1,8-Cineole and Sabinene. Terpinen-4-ol, the most abundant ingredient in TTO, was more potent than TTO at equivalent concentrations and its killing effect was even observable at a mere concentration of 1%. Terpinen-4-ol exhibited a significant synergistic effect with Terpinolene, but an antagonistic effect with α-Terpineol in killing mites (both P < 0.05). In vivo, Terpinen-4-ol was shown to eradicate mites. The above finding suggests that deployment of Terpinen-4-ol alone should enhance its potency in killing Demodex mites by reducing the adverse and antagonistic effects from other ingredients in TTO. Terpinen-4-ol can be adopted in future formulations of acaricides to treat a number of ocular and cutaneous diseases caused by demodicosis.

Manipulation of fruit dry matter accumulation and fruit size in ‘Scifresh’ apple through alteration of the carbon supply, and its relationship with apoplastic sugar composition

SummaryThe supply of carbon to fruit on whole apple trees of ‘Scifresh’ grafted onto M.9 rootstock was altered by adjustment of the crop load [43% removal at 60 d or 90 d after full bloom (DAFB)], by three periods of 75% shading (from 60 – 90, 90 – 120, or 60 – 120 DAFB), or by a combined treatment of fruit removal at 60 DAFB and shading from 60 – 120 DAFB. Altering the timing and duration of shading, and crop load adjustment, resulted in changes in fruit dry matter concentration (DMC), with a range at harvest from 14.0 – 17.5%. Thinning to reduce the crop load enhanced fruit DMC, with greater effects on both fruit DMC and mean fruit fresh weight the earlier it was done. Shading reduced fruit DMC, with greater reductions the longer the shade was left over the trees. All treatments had greater effects on fruit DMC and fruit quality (flesh firmness and soluble solids concentration) at harvest than on mean fruit fresh weight. This trial also provided fruit samples for measurements of both the carbohydrate content and apoplastic composition of cortical tissues. Starch contents and total apoplastic sugar concentrations were increased by reductions in crop load and were decreased by shading, with starch content being the most responsive. Apoplastic sugar concentrations increased during fruit development. The relative order of abundance of sugars in the apoplast and in the symplast plus vacuole was similar, although differences in the ratios of sugars were evident, with sorbitol accounting for ≤ 10% of the total sugar content in the apoplast and ≤ 3% in the symplast plus vacuole. This work has revealed the possibility of using apoplastic sugar concentration as an indicator of the carbohydrate supply to apple fruit.

Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis

To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.

Analysis and optimization of a synthetic milkweed floral attractant for mosquitoes.

A pentane extract of flowers of common milkweed, Asclepias syriaca (Asclepiadaceae), elicited significant orientation from both male and female Culex pipiens in a dual-port flight olfactometer. Analysis of the extract by gas chromatography–mass spectrometry revealed six major constituents in order of relative abundance: benzaldehyde, (E)-β-ocimene, phenylacetaldehyde, benzyl alcohol, nonanal, and (E)-2-nonenal. Although not all were collected from the headspace profile of live flowers, a synthetic blend of these six compounds, when presented to mosquitoes in the same levels and proportions that occur in the extract, elicited a response comparable to the extract. Subtractive behavioral bioassays demonstrated that a three-component blend consisting of benzaldehyde, phenylacetaldehyde, and (E)-2-nonenal was as attractive as the full blend. These findings suggest the potential use of synthetic floral-odor blends for monitoring or control of both male and female disease-vectoring mosquitoes.

Influence of wet distillers grains diets on beef cattle fecal bacterial community structure

BackgroundThe high demand for ethanol in the U.S. has generated large stocks of wet distillers grains (DG), a byproduct from the manufacture of ethanol from corn and sorghum grains. Little is known, however, about the potential influence of dietary DG on fecal microbial community structure. A better understanding of the microbial population in beef cattle feces could be an important monitoring tool to facilitate goals of improving nutrient management, increasing animal growth performance and decreasing odors and/or shedding of pathogens. Five diets consisting of a traditional diet fed to finishing beef cattle in the Southern High Plains of Texas-CON (steam-flaked corn control with 0% DG), and four concentrations of DG in the dietary dry matter; 10 C (10% corn-based DG), 5S (5% sorghum-based DG), 10S (10% sorghum DG), and 15S (15% sorghum DG) were fed to steers at the Texas Tech University Burnett Animal Center. Diets were essentially isonitrogenous with a formulated crude protein value of 13.5%.ResultsFecal grab samples were obtained from 20 steers (n = 4 per diet) and the barcoded DNA pyrosequencing method was used to generate 127,530 16S operational taxonomic units (OTUs). A total of 24 phyla were observed, distributed amongst all beef cattle on all diets, revealing considerable animal to animal variation, however only six phyla (core set) were observed in all animals regardless of dietary treatment. The average abundance and range of abundance, respectively of the core phyla were as follows: Firmicutes (61%, 19 to 83%), Bacteroidetes (28%, 11 to 63%), Proteobacteria (3%, 0.34 to 17.5%), Tenericutes (0.15%, 0.0 to 0.35%), Nitrospirae (0.11%, 0.03 to 0.22%), and Fusobacteria (0.086%, 0.017 to 0.38%). Feeding DG-based diets resulted in significant shifts in the fecal microbial community structure compared with the traditional CON. Four low abundance phyla significantly responded to dietary treatments: Synergistetes (p = 0.01), WS3 (p = 0.054), Actinobacteria (p = 0.06), and Spirochaetes (p = 0.06).ConclusionsThis is, to our knowledge, the first study using this method to survey the fecal microbiome of beef cattle fed various concentrations of wet DG. Comparison of our results with other cattle DNA sequencing studies of beef and dairy cattle feces from a variety of geographical locations and different management practices identifies a core set of three phyla shared across all cattle. These three phyla, in order of relative abundance are; Firmicutes, Bacteroidetes, and Proteobacteria. The presence of large animal-to-animal variation in cattle microbiome was noted in our study as well as by others.

A Reconnaissance of Small Mammal Communities in Garland and Government Prairies, Arizona

Small mammals play key ecological roles in grassland ecosystems, yet little is known regarding small mammal communities in large (>50 km2), high-elevation prairies embedded in ponderosa pine (Pinus ponderosa) forests in north central Arizona. To provide information on community composition and habitat relationships, we live-trapped small mammals on 6 transects in 2 prairies in 2008. We captured 78 individuals in 5501 trap occasions. Capture rates were low and varied widely among transects. Community composition was simple, with only 3 species of small mammals captured. In order of relative abundance, these species were deer mouse (Peromyscus maniculatus, n = 44 individuals), Mogollon vole (Microtus mogollonensis, n = 22), and spotted ground squirrel (Spermophilus spilosoma, n = 12). Deer mice were captured on all transects and voles on all but one transect. In contrast, spotted ground squirrels were captured on only 2 transects and were relatively common on only one transect. There were no previous records of spotted ground squirrels in these prairies. Deer mice were positively associated with rock cover and vegetation height. Voles were positively associated with shrub cover and combined cover of live and dead vegetation and were negatively associated with bare ground. Spotted ground squirrels were positively associated with forb cover. This study provides baseline data on small mammal communities in these prairies and documents the presence of a previously unknown species. Further studies would be desirable to better understand spatial and temporal variation in these communities, habitat relationships, and effects of land-use practices on small mammals and their habitats.

Gas-Phase Fragmentation of Long-Lived Cysteine Radical Cations Formed Via NO Loss from Protonated S-Nitrosocysteine

In this work, we describe two different methods for generating protonated S-nitrosocysteine in the gas phase. The first method involves a gas-phase reaction of protonated cysteine with t-butylnitrite, while the second method uses a solution-based transnitrosylation reaction of cysteine with S-nitrosoglutathione followed by transfer of the resulting S-nitrosocysteine into the gas phase by electrospray ionization mass spectrometry (ESI-MS). Independent of the way it was formed, protonated S-nitrosocysteine readily fragments via bond homolysis to form a long-lived radical cation of cysteine (Cys(*+)), which fragments under collision-induced dissociation (CID) conditions via losses in the following relative abundance order: *COOH CH(2)S >> *CH(2)SH approximately = H(2)S. Deuterium labeling experiments were performed to study the mechanisms leading to these pathways. DFT calculations were also used to probe aspects of the fragmentation of protonated S-nitrosocysteine and the radical cation of cysteine. NO loss is found to be the lowest energy channel for the former ion, while the initially formed distonic Cys(*+) with a sulfur radical site undergoes proton and/or H atom transfer reactions that precede the losses of CH(2)S, *COOH, *CH(2)SH, and H(2)S.

Characterization and appraisal of facets influencing geochemistry of groundwater in the Kulpawn sub-basin of the White Volta Basin, Ghana

Groundwater composition in the Kulpawn basin is largely controlled by aluminosilicates dissolution and cation exchange resulting in mainly Ca-Mg-HCO3 and NaHCO3 water types. Principal component analysis, Piper graphical classification, and stable isotope (18O and 2H) of groundwater and surface-water samples were used to delineate geochemical processes and groundwater facies. The groundwater is mildly acid to neutral and low in conductivity. Chemical constituents except HCO3− and SiO2 have low concentration. No cation shows clear majority, however, the order of relative abundance is Na+ > Ca2+ > Mg2+ > K+. HCO3− is the predominant anion and the order of abundance is HCO3− > NO3− > SO42− > Cl−. SiO2 concentration is high compared with the major cations. Dissolution of plagioclase, pyroxene and biotite and cation exchange are responsible for groundwater composition. Isotopic data suggest integrative, smooth and rapid recharge from meteoric origin. The groundwater quality is generally good for domestic usage; however, 18 and 47% of boreholes respectively have NO3− and F− levels outside WHO recommended limits suggesting potential physiological problems in some localities. The groundwater has low sodium absorption ratio and low to moderate salinity hazard but significant magnesium hazard partially limiting its use for irrigation.

Involvement of P2Y Receptors in TGFβ‐Induced EMT of MDCK Cells

Epithelial‐to‐mesenchymal transition (EMT) contributes to renal tubulointerstitial fibrosis, a common pathway leading to end‐stage renal disease. EMT can be induced in certain renal cells by transforming growth factor beta (TGFβ) and results in the phenotypic conversion of tubular epithelia to fibroblasts, reduction of E‐Cadherin expression and induction of α‐smooth muscle actin (αSMA). Since nucleotides can be released during renal injury, we hypothesized that P2Y (nucleotide) receptors contribute to EMT of renal epithelial cells. To test this hypothesis, we used a well‐characterized renal epithelial cell line, Madin Darby Kidney Cells (MDCK), and examined the role of P2Y receptors in TGFβ‐induced EMT. Quantative PCR experiments (used to identify P2Y receptor expression) revealed P2Y2 &gt; P2Y11 &gt; P2Y1 = P2Y14 &gt; P2Y6 = P2Y13 &gt; P2Y12 = P2Y4 as the relative order of abundance. TGFβ treatment reduced the expression of P2Y13 mRNA, elevated P2Y11 and P2Y14 mRNA levels without substantial changes in mRNA expression of P2Y1 and P2Y2. The P2Y agonist ATPγS inhibited protein expression of the EMT marker αSMA in response to TGFβ without influencing the E‐Cadherin decrease or morphological changes. These results indicate that TGFβ‐promoted EMT differentially regulates expression of P2Y receptor subtypes of MDCK cells and that P2Y receptor activation potentially blunts features of the EMT phenotype. Supported by grants from NIH.

Complex Graph Matrix Representations and Characterizations of Proteomic Maps and Chemically Induced Changes to Proteomes

We have presented a complex graph matrix representation to characterize proteomics maps obtained from 2D-gel electrophoresis. In this method, each bubble in a 2D-gel proteomics map is represented by a complex number with components which are charge and mass. Then, a graph with complex weights is constructed by connecting the vertices in the relative order of abundance. This yields adjacency matrices and distance matrices of the proteomics graph with complex weights. We have computed the spectra, eigenvectors, and other properties of complex graphs and the Euclidian/graph distance obtained from the complex graphs. The leading eigenvalues and eigenvectors and, likewise, the smallest eigenvalues and eigenvectors, and the entire graph spectral patterns of the complex matrices derived from them yield novel weighted biodescriptors that characterize proteomics maps with information of charge and masses of proteins. We have also applied these eigenvector and eigenvalue maps to contrast the normal cells and cells exposed to four peroxisome proliferators, namely, clofibrate, diethylhexyl phthalate (DEHP), perfluorodecanoic acid (PFDA), and perfluoroctanoic acid (PFOA). Our complex eigenspectra show that the proteomic response induced by DEHP differs from the corresponding responses of other three chemicals consistent with their chemical structures and properties.

Surfaceome of Leptospira spp

The identification of the subset of outer membrane proteins exposed on the surface of a bacterial cell (the surfaceome) is critical to understanding the interactions of bacteria with their environments and greatly narrows the search for protective antigens of extracellular pathogens. The surfaceome of Leptospira was investigated by biotin labeling of viable leptospires, affinity capture of the biotinylated proteins, two-dimensional gel electrophoresis, and mass spectrometry (MS). The leptospiral surfaceome was found to be predominantly made up of a small number of already characterized proteins, being in order of relative abundance on the cell surface: LipL32 > LipL21 > LipL41. Of these proteins, only LipL32 had not been previously identified as surface exposed. LipL32 surface exposure was subsequently verified by three independent approaches: surface immunofluorescence, whole-cell enzyme-linked immunosorbent assay (ELISA), and immunoelectron microscopy. Three other proteins, Q8F8Q0 (a putative transmembrane outer membrane protein) and two proteins of 20 kDa and 55 kDa that could not be identified by MS, one of which demonstrated a high degree of labeling potentially representing an additional, as-yet-uncharacterized, surface-exposed protein. Minor labeling of p31(LipL45), GroEL, and FlaB1 was also observed. Expression of the surfaceome constituents remained unchanged under a range of conditions investigated, including temperature and the presence of serum or urine. Immunization of mice with affinity-captured surface components stimulated the production of antibodies that bound surface proteins from heterologous leptospiral strains. The surfaceomics approach is particularly amenable to protein expression profiling using small amounts of sample (<10(7) cells) offering the potential to analyze bacterial surface expression during infection.