Vietnamese chickens: a gate towards Asian genetic diversity

BACKGROUND: Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. RESULTS: A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69).The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. CONCLUSIONS: In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation

Search for Direct CP Violation in Non-Leptonic Decays of Charged Ξ\Xi and Λ\Lambda Hyperons

A search for direct CP violation in the non-leptonic decays of hyperons has been performed. In comparing the product of the decay parameters, $\alpha_{\Xi}\alpha_{\Lambda}$, in terms of an asymmetry parameter, $A_{\Xi\Lambda}$, between hyperons and anti-hyperons in the charged $\Xi \to \Lambda \pi$ and $\Lambda \to p \pi$ decay sequence, we found no evidence of direct CP violations. The parameter $A_{\Xi\Lambda}$ was measured to be $0.012 \pm 0.014$.Comment: Submitted for publication; RevTex, 13 pages, 4 figure

Semi-discrete finite difference multiscale scheme for a concrete corrosion model: approximation estimates and convergence

We propose a semi-discrete finite difference multiscale scheme for a concrete corrosion model consisting of a system of two-scale reaction-diffusion equations coupled with an ode. We prove energy and regularity estimates and use them to get the necessary compactness of the approximation estimates. Finally, we illustrate numerically the behavior of the two-scale finite difference approximation of the weak solution.Comment: 22 pages, 1 figure, submitted to Japan Journal of Industrial and Applied Mathematic

Correlation in chicken between the marker LEI0258 alleles and Major Histocompatibility Complex sequences

<p>Abstract</p> <p>Background</p> <p>The LEI0258 marker is located within the B region of the chicken Major Histocompatibility Complex (MHC), and is surprisingly well associated with serology. Therefore, the correlation between the LEI0258 alleles and the MHC class I and the class II alleles at the level of sequences is worth investigating in chickens. Here we describe to which extent the LEI0258 alleles are associated with alleles of classical class I genes and non-classical class II genes, in reference animals as well as local breeds with unknown MHC haplotypes.</p> <p>Methods</p> <p>For the class I region, in an exploratory project, we studied 10 animals from 3 breeds: Rhode Island Red, White Leghorn and Fayoumi chickens, by cloning and sequencing <it>B-F1</it> and <it>B-F2</it> cDNA from exon 1 to 3’UTR. For the class II region, we reconstructed haplotypes of the 8.8 kb genomic region encompassing three non-classical class II genes: <it>B-DMA</it>, <it>B-DMB1</it> and <it>B-DMB2</it>, for 146 animals from more than 50 breeds including wild species of jungle fowls.</p> <p>Results</p> <p>Overall we found that the LEI0258 marker genotypes gave good indications of the MHC haplotypes, and a very good predictions (>0.95) of the heterozygosity of an animal at the MHC locus.</p> <p>Conclusions</p> <p>Our results show that the LEI0258 alleles are strongly associated with haplotypes of classical class I genes and non-classical class II genes, unravelling the reasons why this marker is becoming the reference marker for MHC genotyping in chickens.</p

Chemotherapy-Response Monitoring of Breast Cancer Patients Using Quantitative Ultrasound-Based Intra-Tumour Heterogeneities

© 2017 The Author(s). Anti-cancer therapies including chemotherapy aim to induce tumour cell death. Cell death introduces alterations in cell morphology and tissue micro-structures that cause measurable changes in tissue echogenicity. This study investigated the effectiveness of quantitative ultrasound (QUS) parametric imaging to characterize intra-tumour heterogeneity and monitor the pathological response of breast cancer to chemotherapy in a large cohort of patients (n = 100). Results demonstrated that QUS imaging can non-invasively monitor pathological response and outcome of breast cancer patients to chemotherapy early following treatment initiation. Specifically, QUS biomarkers quantifying spatial heterogeneities in size, concentration and spacing of acoustic scatterers could predict treatment responses of patients with cross-validated accuracies of 82 ± 0.7%, 86 ± 0.7% and 85 ± 0.9% and areas under the receiver operating characteristic (ROC) curve of 0.75 ± 0.1, 0.80 ± 0.1 and 0.89 ± 0.1 at 1, 4 and 8 weeks after the start of treatment, respectively. The patients classified as responders and non-responders using QUS biomarkers demonstrated significantly different survivals, in good agreement with clinical and pathological endpoints. The results form a basis for using early predictive information on survival-linked patient response to facilitate adapting standard anti-cancer treatments on an individual patient basis

Exploring variability in the diet of depredating sperm whales in the Gulf of Alaska through stable isotope analysis

Sperm whales interact with commercially important groundfish fisheries offshore in the Gulf of Alaska (GOA). This study aims to use stable isotope analysis to better understand the trophic variability of sperm whales and their potential prey, and to use dietary mixing models to estimate the importance of prey species to sperm whale diets. We analysed tissue samples from sperm whales and seven potential prey (five groundfish and two squid species). Samples were analysed for stable carbon and nitrogen isotope ratios, and diet composition was estimated using Bayesian isotopic mixing models. Mixing model results suggest that an isotopically combined sablefish/ dogfish group, skates and rockfish make up the largest proportion of sperm whale diets (35%, 28% and 12%) in the GOA. The top prey items of whales that interact more frequently with fishing vessels consisted of skates (49%) and the sablefish/dogfish group (24%). This is the first known study to provide an isotopic baseline of adult male sperm whales and these adult groundfish and offshore squid species, and to assign contributions of prey to whale diets in the GOA. This study provides information to commercial fishermen and fisheries managers to better understand trophic connections of important commercial species.Data were collected in collaboration with Cascadia Research Collective, Scripps Institution of Oceanography, Alaska Sea Life Center, Alaska Longline Fishermen’s Association and the Sitka Sound Science Center. SEASWAP co-PIs were all integral in making this project happen: Linda Behnken, Dan Falvey, Victoria O’Connell, Aaron Thode and Russ Andrews. John Calambokidis and Greg Schorr collected biopsy samples used in this project. Kelly Robertson and Gabriela Serra-Valente archived samples at Southwest Fisheries Science Center. Special thanks to the commercial longline fishermen who donated fish and squid that they caught: Frank Balovich and Cale Laduke (F/V Carole D), Paul Ipok (F/V Myra), Walt Cunningham and Jeff Farvour (F/V Christi-Rob), Ryan Nichols (F/V Nekton), Stephen Rhoads and Nick Nekeferof (F/V Magia), Phil Wyman and Kevin Johnson (F/V Archangel), Lucas Skordahl (F/V Tyee), Tyrus Moffitt and Alek Dyakanoff. NMFS GOA longline survey, bottom trawl survey and ecosystem assessment cruise personnel collected specimens: Chris Lunsford, Cindy Tribuzio, Pete Hulson, Dana Hanselman, Cheryl Barnes, Nancy Roberson, Jamal Moss and Wes Strasburger. Laboratory and analysis assistance provided by Illiana Ruiz-Cooley, Todd Miller, Casey Clark, John Logan, Andrew Parnell, Ellen Chenoweth, Madison Kosma, Mike Sigler, Corey Fugate, Matt Rogers, Kate Hauch, Michelle Parke, Kristina Long, Nevé Baker, Emily Whitney and Annie Masterman. Jen Cedarleaf archived historical samples and managed the database. The Inter-Library-Loan folks with the UAF Rasmussen library found all kinds of crazy whaling documents. Finally, special thanks to the Alaska Stable Isotope Facility team of MatWooller, Tim Howe and Norma Haubenstock for their work running bulk isotopes for all of these samples.Ye

Measurement of Decay Parameters for Ξ−→Λπ−\Xi^{-} \to \Lambda \pi^{-} Decay

Based on 1.35 million polarized $\Xi^{-}$ events, we measure the parameter $\phi_{\Xi}$ to be $-1.61^{\circ} \pm 2.66^{\circ} \pm 0.37^{\circ}$ for $\Xi^{-} \to \Lambda \pi^{-}$ decay. New results for the parameters $\beta_{\Xi}$ and $\gamma_{\Xi}$ are also presented. Assuming that the CP-violating phase-shift difference is negligible, we deduce the strong phase-shift difference between the P-wave and S-wave amplitudes of the $\Lambda\pi$ final state to be $3.17^{\circ} \pm 5.28^{\circ} \pm 0.73^{\circ}$. This strong phase-shift difference reduces the theoretical uncertainty in estimating the level of CP violation in $\Xi$-hyperon decay.Comment: To be published in Physical Review Letter

Identification of Shell Colour Pigments in Marine Snails Clanculus pharaonius and C. margaritarius (Trochoidea; Gastropoda)

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. https://creativecommons.org/publicdomain/zero/1.0/ The attached file is the published version of the article

The effectiveness of sewage treatment processes to remove faecal pathogens and antibiotic residues

Pathogens and antibiotics enter the aquatic environment via sewage effluents and may pose a health risk to wild life and humans. The aim of this study was to determine the levels of faecal bacteria, and selected antibiotic residues in raw wastewater and treated sewage effluents from three different sewage treatment plants in the Western Cape, South Africa. Sewage treatment plant 1 and 2 use older technologies, while sewage treatment plant 3 has been upgraded and membrane technologies were incorporated in the treatment processes. Coliforms and Escherichia coli (E. coli) were used as bioindicators for faecal bacteria. A chromogenic test was used to screen for coliforms and E. coli. Fluoroquinolones and sulfamethoxazole are commonly used antibiotics and were selected to monitor the efficiency of sewage treatment processes for antibiotic removal. Enzyme Linked Immunosorbent Assays (ELISAs) were used to quantitate antibiotic residues in raw and treated sewage. Raw intake water at all treatment plants contained total coliforms and E. coli. High removal of E. coli by treatment processes was evident for treatment plant 2 and 3 only. Fluoroquinolones and sulfamethoxazole were detected in raw wastewater from all sewage treatment plants. Treatment processes at plant 1 did not reduce the fluoroquinolone concentration in treated sewage effluents. Treatment processes at plant 2 and 3 reduced the fluoroquinolone concentration by 21% and 31%, respectively. Treatment processes at plant 1 did not reduce the sulfamethoxazole concentration in treated sewage effluents. Treatment processes at plant 2 and 3 reduced sulfamethoxazole by 34% and 56%, respectively. This study showed that bacteria and antibiotic residues are still discharged into the environment. Further research needs to be undertaken to improve sewage treatment technologies, thereby producing a better quality treated sewage effluent