Additional file 3. Effective analysis of protein coding sequences in S. dextrinosolvens strains H... more Additional file 3. Effective analysis of protein coding sequences in S. dextrinosolvens strains H5, 22B and ACV-10.
Additional file 1. KEGG genes significantly more abundant in HMY animals in the metagenome and me... more Additional file 1. KEGG genes significantly more abundant in HMY animals in the metagenome and metatranscriptome datasets by WRS and sPLS analyses.
Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control o... more Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control of pests is typically successful once a control agent has established, but this depends on the agent’s capacity to co-evolve with the host. Theoretical studies have shown that different levels of genetic variation between the host and the control agent will lead to rapid evolution of resistance in the host. Although this has been reported in one instance, the underlying genetics have not been studied. To address this, we measured the genetic variation in New Zealand populations of the pasture pest, Argentine stem weevil (Listronotus bonariensis), which is controlled with declining effectiveness by a parasitoid wasp, Microctonus hyperodae. We constructed a draft reference genome of the weevil, collected samples from a geographical survey of 10 sites around New Zealand, and genotyped them using a modified genotyping-by-sequencing approach. New Zealand populations of Argentine stem weevil ha...
Malignant melanoma in the head and neck area is rare. The incidence of oral malignant melanomas o... more Malignant melanoma in the head and neck area is rare. The incidence of oral malignant melanomas of the head and neck is approximately four per 10 million populations per year. They are derived from epidermal melanocytes and are most frequently seen on the palate and maxillary gingiva. They are asymptomatic initially but become painful with progress and enlargement. Later, they are associated with ulceration, bleeding, mobility of tooth, paresthesia and ill-fitting prosthesis. The diagnosis is often delayed due to silent growth and development of the lesion. Oral malignant melanomas are associated with poor prognosis due to their invasive and metastasizing tendencies. This case report is presented to emphasize the role of a dentist in identifying the pigmented lesions of the oral cavity.
A replicated field trial was conducted to measure the effect on liveweight gain of failing to ade... more A replicated field trial was conducted to measure the effect on liveweight gain of failing to adequately control anthelmintic resistant populations of Cooperia oncophora and to determine whether populations, and hence production losses, increased with time. Eight mobs of 10 Friesian-Hereford calves were run on independent farmlets from January to December, over each of two years. All mobs were routinely treated with a pour-on formulation of eprinomectin every six weeks, which controlled parasites other than Cooperia. Four mobs also received six weekly treatments with an oral levamisole plus albendazole combination anthelmintic to control Cooperia. Liveweights, condition scores, faecal egg counts and larval numbers on pasture were measured throughout. In the first year animals treated with eprinomectin alone were 12.9 kg lighter in November than those treated with eprinomectin plus albendazole and levamisole, however, in the second year there was no difference between the treatment g...
Twenty male Saanen goats were randomly assigned to four levels of lovastatin supplementation and ... more Twenty male Saanen goats were randomly assigned to four levels of lovastatin supplementation and used to determine the optimal dosage and sustainability of naturally produced lovastatin from fermentation of palm kernel cake (PKC) with Aspergillus terreus on enteric methane (CH4) mitigation. The effects on ruminal microbiota, rumen fermentation, feed digestibility and health of animal were determined over three measuring periods (4-, 8- and 12-weeks) and the accumulation of lovastatin in tissues was determined at the end of the experiment. The diets contained 50% rice straw, 22.8% concentrates and 27.2% of various proportions of untreated or treated PKC to achieve the target daily intake level of 0 (Control), 2, 4 or 6 mg lovastatin/kg body weight (BW). Enteric CH4 emissions per dry matter intake (DMI), decreased significantly (P<0.05) and equivalent to 11% and 20.4%, respectively, for the 2 and 4 mg/kg BW groups as compared to the Control. No further decrease in CH4 emission ther...
Ruminants are important contributors to global methane emissions via microbial fermentation in th... more Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of...
Dietary protein is considered more satiating than carbohydrate, and whey protein is more satiatin... more Dietary protein is considered more satiating than carbohydrate, and whey protein is more satiating than other protein sources. The purported satiating effect of whey protein may be due to direct effects of the unique mixture of proteins in whey, due to the effects of peptides released upon digestion and/or its amino acid composition. The objective of the present study was to compare the satiating effects of intact whey protein isolate (WPI) or a free amino acid mixture (AAM) simulating the amino acid composition of the WPI. A single-blind completely randomised block design included twenty, healthy, adult women (age 24·2 (sem 0·8) years) of normal weight (BMI 22·7 (sem 0·4) kg/m2). Following consumption of isoenergetic (approximately 1800 kJ) preload meals enriched (52 g amino acid equivalent) with WPI or AAM, consumption of an ad libitum test meal 120 min later and subjective feelings of appetite using visual analogue scales (VAS) were determined. There were no significant differenc...
Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the ... more Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts. Methane production in the rumen is strongly connected to microbial hydrogen production through fermentation processes. In this study, we investigate the contribution that rumen bacteria make to methane yield phenotypes in sheep. Using deep sequence metagenome and metatranscriptome datasets in combination with 16S rRNA gene amplicon sequencing from HMY and LMY...
Primary tasks in analysis and annotation of expressed sequence tag (EST) datasets are to identify... more Primary tasks in analysis and annotation of expressed sequence tag (EST) datasets are to identify similarity among sequences by unsupervised clustering and assign putative function based on BLAST homology searches. We investigated the usefulness of text mining as a simple approach for further higher-level clustering of EST datasets using IBM Intelligent Miner for Text v2.3 tools. Agglomerative and k-means clustering tools were used to cluster BLASTx homology search documents from two onion EST datasets and optimised by pre-processing and pruning. Subjective evaluation confirmed that these tools provided biologically useful and complementary views of the two libraries, provided new insights into their composition and revealed clusters previously identified by human experts. We compared BLASTx textual clusters for two gene families with their DNA sequence-based clusters and confirmed that these shared similar morphology.
Review of Pacific Basin Financial Markets and Policies, 2006
We use four alternative prediction models to examine the usefulness of financial ratios in predic... more We use four alternative prediction models to examine the usefulness of financial ratios in predicting business failure in China. China has unique legislation regarding business failure so it is an interesting laboratory for such a study. Earnings Before Interest and Tax to Total Assets (EBITTA), Earning Per Share (EPS), Total Debt to Total Assets (TDTA), Price to Book (PB), and the Current Ratio (CR), are shown to be significant predictors. Prediction accuracy achieves a range from 78% to 93%. Logit and Neural Network models are shown to be the optimal prediction models.
This study examines the gender pay gap in the New Zealand Public Service in 2002, using the well‐... more This study examines the gender pay gap in the New Zealand Public Service in 2002, using the well‐known Blinder‐Oaxaca method to decompose pay differentials into explained and unexplained components. The major innovation of the paper is its introduction of a ‘job size ‘ variable which proxies the seniority level of individual jobs, to supplement the standard variables such as occupation,
Additional file 3. Effective analysis of protein coding sequences in S. dextrinosolvens strains H... more Additional file 3. Effective analysis of protein coding sequences in S. dextrinosolvens strains H5, 22B and ACV-10.
Additional file 1. KEGG genes significantly more abundant in HMY animals in the metagenome and me... more Additional file 1. KEGG genes significantly more abundant in HMY animals in the metagenome and metatranscriptome datasets by WRS and sPLS analyses.
Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control o... more Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control of pests is typically successful once a control agent has established, but this depends on the agent’s capacity to co-evolve with the host. Theoretical studies have shown that different levels of genetic variation between the host and the control agent will lead to rapid evolution of resistance in the host. Although this has been reported in one instance, the underlying genetics have not been studied. To address this, we measured the genetic variation in New Zealand populations of the pasture pest, Argentine stem weevil (Listronotus bonariensis), which is controlled with declining effectiveness by a parasitoid wasp, Microctonus hyperodae. We constructed a draft reference genome of the weevil, collected samples from a geographical survey of 10 sites around New Zealand, and genotyped them using a modified genotyping-by-sequencing approach. New Zealand populations of Argentine stem weevil ha...
Malignant melanoma in the head and neck area is rare. The incidence of oral malignant melanomas o... more Malignant melanoma in the head and neck area is rare. The incidence of oral malignant melanomas of the head and neck is approximately four per 10 million populations per year. They are derived from epidermal melanocytes and are most frequently seen on the palate and maxillary gingiva. They are asymptomatic initially but become painful with progress and enlargement. Later, they are associated with ulceration, bleeding, mobility of tooth, paresthesia and ill-fitting prosthesis. The diagnosis is often delayed due to silent growth and development of the lesion. Oral malignant melanomas are associated with poor prognosis due to their invasive and metastasizing tendencies. This case report is presented to emphasize the role of a dentist in identifying the pigmented lesions of the oral cavity.
A replicated field trial was conducted to measure the effect on liveweight gain of failing to ade... more A replicated field trial was conducted to measure the effect on liveweight gain of failing to adequately control anthelmintic resistant populations of Cooperia oncophora and to determine whether populations, and hence production losses, increased with time. Eight mobs of 10 Friesian-Hereford calves were run on independent farmlets from January to December, over each of two years. All mobs were routinely treated with a pour-on formulation of eprinomectin every six weeks, which controlled parasites other than Cooperia. Four mobs also received six weekly treatments with an oral levamisole plus albendazole combination anthelmintic to control Cooperia. Liveweights, condition scores, faecal egg counts and larval numbers on pasture were measured throughout. In the first year animals treated with eprinomectin alone were 12.9 kg lighter in November than those treated with eprinomectin plus albendazole and levamisole, however, in the second year there was no difference between the treatment g...
Twenty male Saanen goats were randomly assigned to four levels of lovastatin supplementation and ... more Twenty male Saanen goats were randomly assigned to four levels of lovastatin supplementation and used to determine the optimal dosage and sustainability of naturally produced lovastatin from fermentation of palm kernel cake (PKC) with Aspergillus terreus on enteric methane (CH4) mitigation. The effects on ruminal microbiota, rumen fermentation, feed digestibility and health of animal were determined over three measuring periods (4-, 8- and 12-weeks) and the accumulation of lovastatin in tissues was determined at the end of the experiment. The diets contained 50% rice straw, 22.8% concentrates and 27.2% of various proportions of untreated or treated PKC to achieve the target daily intake level of 0 (Control), 2, 4 or 6 mg lovastatin/kg body weight (BW). Enteric CH4 emissions per dry matter intake (DMI), decreased significantly (P<0.05) and equivalent to 11% and 20.4%, respectively, for the 2 and 4 mg/kg BW groups as compared to the Control. No further decrease in CH4 emission ther...
Ruminants are important contributors to global methane emissions via microbial fermentation in th... more Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of...
Dietary protein is considered more satiating than carbohydrate, and whey protein is more satiatin... more Dietary protein is considered more satiating than carbohydrate, and whey protein is more satiating than other protein sources. The purported satiating effect of whey protein may be due to direct effects of the unique mixture of proteins in whey, due to the effects of peptides released upon digestion and/or its amino acid composition. The objective of the present study was to compare the satiating effects of intact whey protein isolate (WPI) or a free amino acid mixture (AAM) simulating the amino acid composition of the WPI. A single-blind completely randomised block design included twenty, healthy, adult women (age 24·2 (sem 0·8) years) of normal weight (BMI 22·7 (sem 0·4) kg/m2). Following consumption of isoenergetic (approximately 1800 kJ) preload meals enriched (52 g amino acid equivalent) with WPI or AAM, consumption of an ad libitum test meal 120 min later and subjective feelings of appetite using visual analogue scales (VAS) were determined. There were no significant differenc...
Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the ... more Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts. Methane production in the rumen is strongly connected to microbial hydrogen production through fermentation processes. In this study, we investigate the contribution that rumen bacteria make to methane yield phenotypes in sheep. Using deep sequence metagenome and metatranscriptome datasets in combination with 16S rRNA gene amplicon sequencing from HMY and LMY...
Primary tasks in analysis and annotation of expressed sequence tag (EST) datasets are to identify... more Primary tasks in analysis and annotation of expressed sequence tag (EST) datasets are to identify similarity among sequences by unsupervised clustering and assign putative function based on BLAST homology searches. We investigated the usefulness of text mining as a simple approach for further higher-level clustering of EST datasets using IBM Intelligent Miner for Text v2.3 tools. Agglomerative and k-means clustering tools were used to cluster BLASTx homology search documents from two onion EST datasets and optimised by pre-processing and pruning. Subjective evaluation confirmed that these tools provided biologically useful and complementary views of the two libraries, provided new insights into their composition and revealed clusters previously identified by human experts. We compared BLASTx textual clusters for two gene families with their DNA sequence-based clusters and confirmed that these shared similar morphology.
Review of Pacific Basin Financial Markets and Policies, 2006
We use four alternative prediction models to examine the usefulness of financial ratios in predic... more We use four alternative prediction models to examine the usefulness of financial ratios in predicting business failure in China. China has unique legislation regarding business failure so it is an interesting laboratory for such a study. Earnings Before Interest and Tax to Total Assets (EBITTA), Earning Per Share (EPS), Total Debt to Total Assets (TDTA), Price to Book (PB), and the Current Ratio (CR), are shown to be significant predictors. Prediction accuracy achieves a range from 78% to 93%. Logit and Neural Network models are shown to be the optimal prediction models.
This study examines the gender pay gap in the New Zealand Public Service in 2002, using the well‐... more This study examines the gender pay gap in the New Zealand Public Service in 2002, using the well‐known Blinder‐Oaxaca method to decompose pay differentials into explained and unexplained components. The major innovation of the paper is its introduction of a ‘job size ‘ variable which proxies the seniority level of individual jobs, to supplement the standard variables such as occupation,
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Papers by Siva Ganesh