Quantitative PCR assay of sewage-associated Bacteroides markers to assess sewage pollution in an urban lake in Dhaka, Bangladesh

This paper aimed to assess the magnitude of sewage pollution in an urban lake in Dhaka, Bangladesh by using Quantitative PCR (qPCR) of sewage-associated Bacteroides HF183 markers. PCR was also used for the quantitative detection of ruminant wastewater-associated CF128 markers along with the enumeration of traditional fecal indicator bacteria, namely, enterococci. The number of enterococci in lake water samples ranged from 1.1 x 104 to 1.9 x 105 CFU/100 ml of water. From the 20 water samples tested, 14 (70%) and 7 (35%) were PCR positive for the HF183 and CF128 markers, respectively. The numbers of the HF183 and CF128 markers in lake water samples were 3.9 x 104 to 6.3 × 107 and 9.3 x 103 to 6.3 x 105 genomic units (GU)/100 ml of water, respectively. The high numbers of enterococci and the HF183 markers indicate sewage pollution and potential health risks to those who use the lake water for non-potable purposes such as bathing and washing clothes. This is the first study that investigated the presence of microbial source tracking (MST) markers in Dhaka, Bangladesh where diarrhoeal diseases is one of the major causes of childhood mortality. The molecular assay as used in this study can provide valuable information on the extent of sewage pollution, thus facilitating the development of robust strategies to minimise potential health risks.

Genetic analysis reveals two stocks of skipjack tuna (Katsuwonus pelamis) in the north western Indian Ocean

Skipjack (SJT) (Katsuwonus pelamis) is a medium sized, pelagic, highly dispersive tuna species that occurs widely across tropical and subtropical waters. SJT constitute the largest tuna fishery in the Indian Ocean, and are currently managed as a single stock. Patterns of genetic variation in a mtDNA gene and 6 microsatellite loci were examined to test for stock structure in the northwestern Indian Ocean. 324 individuals were sampled from five major fishing grounds around Sri Lanka, and single sites in the Maldive Islands and the Laccadive Islands. Phylogenetic reconstruction of mtDNA revealed two coexisting divergent clades in the region. AMOVA (Analysis of Molecular Variance) of mtDNA data revealed significant genetic differentiation among sites (ΦST = 0.2029, P < 0.0001), also supported by SAMOVA results. AMOVA of microsatellite data also showed significant differentiation among most sampled sites (FST = 0.0256, P<0.001) consistent with the mtDNA pattern. STRUCTURE analysis of the microsatellite data revealed two differentiated stocks. While the both two marker types examined identified two genetic groups, microsatellite analysis indicates that the sampled SJT are likely to represent individuals sourced from discrete breeding grounds that are mixed in feeding grounds in Sri Lankan waters.

Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.)

Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.

Rule-based transit signal priority control method using a real-time transit travel time prediction model

An advanced rule-based Transit Signal Priority (TSP) control method is presented in this paper. An on-line transit travel time prediction model is the key component of the proposed method, which enables the selection of the most appropriate TSP plans for the prevailing traffic and transit condition. The new method also adopts a priority plan re-development feature that enables modifying or even switching the already implemented priority plan to accommodate changes in the traffic conditions. The proposed method utilizes conventional green extension and red truncation strategies and also two new strategies including green truncation and queue clearance. The new method is evaluated against a typical active TSP strategy and also the base case scenario assuming no TSP control in microsimulation. The evaluation results indicate that the proposed method can produce significant benefits in reducing the bus delay time and improving the service regularity with negligible adverse impacts on the non-transit street traffic.

Metabolism of alpha-terpineol by Pseudomonas incognita

Details of the metabolism of alpha-terpineol by Pseudomonas incognita are presented. Degradation of alpha-terpineol by this organism resulted in the formation of a number of acidic and neutral metabolites. Among the acidic metabolites, beta-isopropyl pimelic acid, 1-hydroxy-4-isopropenyl-cyclohexane-1-carboxylic acid, 8-hydroxycumic acid, oleuropeic acid, cumic acid, and p-isopropenyl benzoic acid have been identified. Neutral metabolites identified were limonene, p-cymene-8-ol, 2-hydroxycineole, and uroterpenol. Cell-free extracts prepared from alpha-terpineol adapted cells were shown to convert alpha-terpineol, p-cymene-8-ol, and limonene to oleuropeic acid, 8-hydroxycumic acid, and perillic acid, respectively, in the presence of NADH. The same cell-free extract contained NAD+ -specific dehydrogenase(s) which converted oleuropyl alcohol, p-cymene-7,8-diol, and perillyl alcohol to their corresponding 7-carboxy acids. On the basis of various metabolites isolated from the culture medium, together with the supporting evidence obtained from enzymatic and growth studies, it appears that P. incognita degrades alpha-terpineol by at least three different routes. While one of the pathways seems to operate via oleuropeic acid, a second may be initiated through the aromatization of alpha-terpineol. The third pathway may involve the formation of limonene from alpha-terpineol and its further metabolism.

Metabolism of a monoterpene alcohol, linalool, by a soil pseudomonad

A microorganism of the genus Pseudomonas has been isolated from the soil by enrichment culture techniques with linalool(I) as the sole source of carbon and energy. The organism is also capable of utilizing limonene, citronellol, and geraniol as substrates but fails to grow on citral, critranellal, and 1,8-cineole. Fermentation of linalool by this bacterium in a mineral salt medium results in the formation of 10-hydroxylinalool(II), oleuropeic acid (IX), 2-vinyl-2-methyl-5-hydroxyisopropyl-tetraphydrofuran)linalool oxide, V), 2-vinyl-2-methyl-tetrahydrofuran-5-one(unsaturated lactone, VI), and few unidentified minor metabolities. Probable pathways for the biodegradation of linalool are presented.

Mercúrio total em Orthopristis ruber (Haemulidae) de quatro regiões costeiras do Estado do Rio de Janeiro, Brasil

O objetivo do presente estudo foi investigar as concentrações de mercúrio total (HgT) nos músculos de Orthopristis ruber de quatro ecossitemas costeiros e identificar possíveis correlações existentes entre comprimento, peso, sexo, estação do ano e índices biológicos. O HgT foi analisado nas regiões de Cabo Frio (CF, n=31), Baía de Guanabara (BG, n=61), Baía de Sepetiba (BS, n=43) e Baía da Ilha Grande (BIG, n=32), as quais apresentam diferentes níveis de degradação ambiental. A BG recebe grande quantidade de efluentes domésticos e industriais de toda região metropolitana do Rio de Janeiro e tem sido considerada como uma das áreas mais poluídas do Brasil. Já na BS, a intensa atividade metalúrgica no seu entorno faz com que esta possa ser tida com nível de degradação intermadiária, enquanto CF e BIG são duas áreas vistas como áreas bem preservadas. As concentrações de HgT foram determinadas através de CV-AAS (FIMS - 400,Perkin Elmer) - utilizando boridreto de sódio como agente redutor. Foi utilizado DORM 3 (National Research Council, Canada) como material de referência (média da recuperação DP =99,2 4,9 %). As concentrações médias de HgT DP para BIG e CF foram, respectivamente, 209,8 118,9 ng/g, e 199,9 88,2 ng/g. Estas regiões apresentaram concentrações significativamente mais elevadas, enquanto a BG mostrou concentrações intermediárias (112,9 88,0 ng/g; ANCOVA, p<0,03). Por outro lado, a BS foi a região com as menores concentrações de HgT (11,3 11,5 ng/g). Tais resultados sugerem que, mesmo sendo áreas degradadas, o HgT não está totalmente biodisponível para BG e BS. Ademais, provavelmente as correntes oceânicas são uma fonte de mercúrio para CF e BIG, carreando mercúrio biodisponível para essas áreas. Para BG análises adicionais foram feitas a fim de identificar a acumulação de HgT ao longo do desenvolvimento ontogenético de O. ruber, uma vez que as concentrações do metal foram maiores em adultos do que em juvenis (PERMANOVA, p< 0,0001). As concentrações de HgT foram positivamente relacionadas tanto com o comprimento (Spearman test; r = 0,85; p <0,001) quanto com o peso (Spearman test; r =0,85; p <0,001) dos peixes da BG, mostrando que o O.ruber acumula HgT ao longo da vida. Diferenças entre sexos foram encontradas apenas para os O. ruber da BIG, onde fêmeas (300 ng/g) apresentaram maiores concentrações de HgT que os machos (~150 ng/g). Dentre os índices biológicos analisados, o índice gonadossomático foi o de maior relevância devido sua correlação negativa entre os níveis de HgT com todos os dados em conjunto (p<0.001), tanto para fêmeas (p<0.001) quanto para machos (p<0.02), sugerindo que o mercúrio pode afetar negativamente a reprodução de O.ruber.

Tree diameter distribution modelling: introducing the logitlogistic distribution

Johnson's SB distribution is a four-parameter distribution that is transformed into a normal distribution by a logit transformation. By replacing the normal distribution of Johnson's SB with the logistic distribution, we obtain a new distributional model that approximates SB. It is analytically tractable, and we name it the "logitlogistic" (LL) distribution. A generalized four-parameter Weibull model and the Burr XII model are also introduced for comparison purposes. Using the distribution "shape plane" (with axes skew and kurtosis) we compare the "coverage" properties of the LL, the generalized Weibull, and the Burr XII with Johnson's SB, the beta, and the three-parameter Weibull, the main distributions used in forest modelling. The LL is found to have the largest range of shapes. An empirical case study of the distributional models is conducted on 107 sample plots of Chinese fir. The LL performs best among the four-parameter models.

The effects of cadence and power output upon physiological and biomechanical responses to incremental arm-crank ergometry

The aim of this study was to examine the effects of cadence and power output on physiological and biomechanical responses to incremental arm-crank ergometry (ACE). Ten male subjects (mean +/- SD age, 30.4 +/-5.4 y; height, 1.78 +/-0.07 m; mass, 86.1 +/-14.2 kg) undertook 3 incremental ACE protocols to determine peak oxygen uptake (VO2 peak; mean of 3 tests: 3.07 +/- 0.17 L.min-1) at randomly assigned cadences of 50, 70, or 90 r.min-1. Heart rate and expired air were continually monitored. Central (RPE-C) and local (RPE-L) ratings of perceived exertion were recorded at volitional exhaustion. Joint angles and trunk rotation were analysed during each exercise stage. During submaximal power outputs of 50, 70, and 90 W, oxygen consumption (VO2) was lowest for 50 r.min-1 and highest for 90 r.min-1 (p < 0.01). VO2 peak was lowest during 50 r.min-1 (2.79 +/-0.45 L.min-1; p < 0.05) when compared with both 70 r.min-1 and 90 r.min-1 (3.16 +/-0.58, 3.24 +/-0.49 L.min-1, respectively; p > 0.05). The difference between RPE-L and RPE-C at volitional exhaustion was greatest during 50 r.min-1 (2.9 +/- 1.6) when compared with 90 r.min-1 (0.9 +/- 1.9, p < 0.05). At VO2 peak, shoulder range of motion (ROM) and trunk rotation were greater for 50 and 70 r.min-1 when compared with 90 r.min-1 (p < 0.05). During submaximal power outputs, shoulder angle and trunk rotation were greatest at 50 r.min-1 when compared with 90 r.min-1 (p < 0.05). VO2 was inversely related to both trunk rotation and shoulder ROM during submaximal power outputs. The results of this study suggest that the greater forces required at lower cadences to produce a given power output resulted in greater joint angles and range of shoulder and trunk movement. Greater isometric contractions for torso stabilization and increased cost of breathing possibly from respiratory-locomotor coupling may have contributed increased oxygen consumption at higher cadences.