bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risks of transmitting mycoplasmas by semen and embryo transfer techniques in cattle, sheep, goats and pigs.
Authors: Wrathall A. E. , Ayling R. D. , Simmons H. A. 
Published: September 2007

Abstract
This object of this review is to consider whether mycoplasmas, particularly those that are important pathogens in cattle, sheep, goats and pigs, are likely to be transmitted by semen and embryo transfer techniques, and if so, what can be done to prevent such transmission. The first part gives a brief overview of semen and embryo transfer techniques, focusing on general risks of disease transmission and on routine disease control strategies. Subsequent parts provide information about mycoplasmas, including their classification, pathogenesis, diagnosis and control. Details are then given of the specific mycoplasmas of cattle, sheep, goats and pigs, and the seriously pathogenic species are distinguished from the opportunist pathogens and harmless commensals. It is emphasized, however, that within species the virulence of different strains can vary widely. An important feature of the mycoplasmas is that they often reside in the reproductive tracts of their hosts and therefore tend to pose a higher risk of being transmitted by semen and embryos than do many other micro-organisms. They also tend to adhere to cells and tissues, including semen and embryos, and can be difficult to remove. Some mycoplasmas can also invade and reside within non-phagocytic cells. Their resistance to routine disease control procedures such as semen and embryo washing, and to the inclusion of antibiotics in semen diluents and in embryo media, adds further challenges. It remains true, nevertheless, that semen and embryo transfer techniques offer great advantages over the movement of live animals for transferring genetic material, and will minimize the risks of disease transmission between different farms or countries. The review concludes by recommending control strategies, uniquely rigorous ones in this case, to avoid the transfer of mycoplasmas via semen and embryos.
Combined genetic, genomic and transcriptomic methods in the analysis of animal traits.
Authors: Kadarmideen H. N. , Reverter A. 
Published: September 2007

Abstract
This paper reviews advances and current status in genetic, genomic and transcriptomic investigations of quantitative traits in livestock species and proposes possible strategies for integrating the vast amounts of information (outputs/datasets) arising from all three investigations into a systems genetics approach. This systems genetics approach is characterized by investigations of the genetic basis of -omic variations and gene regulatory/co-regulatory networks. This review is structured as follows. Genetics/genomics, transcriptomics, combined transcriptomics-genomics and, finally, systems genetics/biology. In the genetics or genomics part, we discuss current status and advances in quantitative trait loci (QTLs) mapping to fine-map multiple causative/candidate genes. We discuss the potential of single nucleotide polymorphism (SNP) genotyping arrays (e.g. Affymetrix GeneChip arrays) to identify SNP-trait associations and fine-map QTLs to less than 0.1 cM. We provide references and resources for SNP analytical methods and tools. In the transcriptomics part, we formulate common biological questions relevant to livestock microarray gene expression profiling (MGEP) experiments to detect differentially expressed (DE) genes. In the combined transcriptomics-genomics (known as genetical genomics), we discuss detection and mapping of expression QTL (eQTL) that harbour regulatory genes for normal trait QTLs or candidate genes detected under 'genetics' and 'genomics' approaches. Illustrations from our own recent genetical genomic investigations in mouse and pigs are provided. One of the current challenges in genetical genomics is to have a coherent approach to design an experiment with due considerations for sample size and controlling false discovery rates (FDRs), while maintaining statistical power to detect eQTLs. Here we provide some concepts for the design of genetical genomics experiments with factors affecting FDR and power. This is followed by a systems biology/genetics section where we focus on combining research outputs from four different sources, namely: genetics or genomics (e.g. SNP, QTL and eQTLs), transcriptomics (e.g. DE genes, gene networks, and heritability of gene transcripts) and phenomics (e.g. phenotypes and pedigree). As a proof of principle, we provide results from systems biology/genetics approach anchored to a gene network for myogenin (MYOG), a muscle-specific transcription factor essential for the development of skeletal muscle. Using bovine expression datasets and in silico approaches, we built a gene network for MYOG that represents 35 significant connections between genes in this network. In conclusion, this paper provides strategies and tools to integrate data from genetics and -omics experiments in animals and highlighted the value of such 'systems genetics' strategy in understanding the genetics of complex traits.
Herbicide-resistant crops as weeds in North America.
Authors: Beckie H. J. , Owen M. D. K. 
Published: September 2007

Abstract

Growers have rapidly adopted transgenic herbicide-resistant (HR) crops, such as canola (
Brassica napus
L.), soyabean [
Glycine max
(L.) Merr.], maize (
Zea mays
L.) and cotton (
Gossypium hirsutum
L.), across North America (USA and Canada) since their commercial introduction in the 1990s. With their widespread cultivation, increasing attention is focused on management of HR volunteers in crops that follow in rotation. In this review, we describe the impact and management of HR crop volunteers in different agroecosystems in North America. The relative risks of planting HR crops and subsequent potential for volunteerism of these crops are assessed. HR volunteers are common weeds and the relative weediness depends on species, genotype, seed shatter prior to harvest and disbursement of seed at harvest, management practices, and environment. Chemical control options may be more limited if the crop volunteers are HR. There are generally no marked changes in volunteer weed problems associated with these crops, except in no-tillage systems when glyphosate (GLY) is used alone to control volunteers. The increasing use of GLY in North American cropping systems, spurred by increasing area and frequency in rotation of GLY - HR crops, may require increased alternative herbicide use or other novel tactics to control GLY-HR crop volunteers.
Role of immunostimulants in disease resistance of fish.
Authors: Sahoo P. K. 
Published: September 2007

Abstract
There is an increasing demand to prevent and control a broad spectrum of fish diseases occurring in aquaculture systems without recourse to antibiotics and chemotherapeutics. Application of immunostimulants alone or together with vaccination has emerged as one of the more promising approaches to prevent or control fish diseases. Many such substances viz. glucans, levamisole, lactoferrin, chitosan, chitin, vitamins C and E, prolactin, growth hormone, triiodothyronine, Freund's complete adjuvant, lipopolysaccharides, animal or plant extracts, double-stranded RNA, CpG motifs and other biological substances have been reported to produce increased protection against major bacterial, few viral and parasitic pathogens. These immunostimulants mainly promote the function of phagocytes and increase their microbicidal power. They also enhance production of acute phase proteins that trigger the innate defence mechanism of the host. However, a controversy exists over the use of these substances, as in a few cases they have failed to render enhanced protection or increase in immunity. Long-term exposure, over- and under-dosing problems, timing and method of application of these substances are discussed here. This review article mainly considers the recent developments in this area to control fish diseases describing the newer molecular approaches going on to evaluate these substances, discusses the practicaldifficulties on their applications and emphasizes further research needs in this important area.
Mechanisms of S-RNase-based self-incompatibility.
Authors: Sims T. L. 
Published: September 2007

Abstract
Gametophytic self-incompatibility (GSI), a genetic mechanism that acts to prevent self-fertilization in many angiosperms, is based on the ability of the pistil to selectively inhibit growth of self pollen while allowing the growth of non-self pollen. In the most widespread variant of GSI (studied most thoroughly in the Solanaceae, Rosaceae and Plantaginaceae), a style-expressed ribonuclease (the S-RNase) is imported into both self and non-self pollen tubes. In pollen tubes recognized as self, the S-RNase degrades RNA, slowing protein synthesis and growth of the pollen tube, whereas in non-self pollen tubes the action of the S-RNase is inhibited and growth continues normally. Recognition of self versus non-self in pollen appears to be mediated through the action of the recently identified SLF/SFB protein. Protein interaction studies suggest that SLF/SFB acts via a modified SCFSLF E3 ubiquitin ligase complex. Several questions remain, however, about the precise mechanism by which the S-RNase remains inactive in non-self pollen tubes. Experiments tracking the fate of protein components of self-incompatibility in pollinated styles suggest that in compatible pollinations, the S-RNase remains sequestered in a membrane-bounded vacuolar compartment, while it is released in incompatible pollen tubes. Other experiments suggest that ubiquitination, and possibly degradation, of S-RNases occurs preferentially in incompatible pollen compared with compatible pollen. Finally, the analysis of SFB mutants in the Rosaceae, along with investigations into the breakdown of GSI in tetraploid plants, suggest that details of the GSI response may differ in the Rosaceae compared with the Solanaceae and Plantaginaceae.
Context-dependent clustering for dynamic cellular state modeling of microarray gene expression
Authors: Yuan Shinsheng , Li Ker-Chau 
Published: September 2007

AbstractMotivation: High-throughput expression profiling allows researchers to study gene activities globally. Genes with similar expression profiles are likely to encode proteins that may participate in a common structural complex, metabolic pathway or biological process. Many clustering, classification and dimension reduction approaches, powerful in elucidating the expression data, are based on this rationale. However, the converse of this common perception can be misleading. In fact, many biologically related genes turn out uncorrelated in expression.Results: In this article, we present a novel method for investigating gene co-expression patterns. We assume the correlation between functionally related genes can be strengthened or weakened according to changes in some relevant, yet unknown, cellular states. We develop a context-dependent clustering (CDC) method to model the cellular state variable. We apply it to the transcription regulatory study for Saccharomyces cerevisiae, using the Stanford cell-cycle gene expression data. We investigate the co-expression patterns between transcription factors (TFs) and their target genes (TGs) predicted by the genome-wide location analysis of Harbison et al. Since TF regulates the expression of its TGs, correlation between TFs and TGs expression profiles can be expected. But as many authors have observed, the expression of transcription factors do not correlate well with the expression of their target genes. Instead of attributing the main reason to the lack of correlation between the transcript abundance and TF activity, we search for cellular conditions that would facilitate the TF-TG correlation. The results for sulfur amino acid pathway regulation by MET4, respiratory genes regulation by HAP4, and mitotic cell cycle regulation by ACE2/SWI5 are discussed in detail. Our method suggests a new way to understand the complex biological system from microarray data.Availability: The program is written in ANSI C. The source code could be downloaded from http://kiefer.stat.sinica.edu.tw/CDC/index.phpContact: kcli@stat.ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online.
The impact of later trading hours for hotels (public houses) on breath alcohol levels of apprehended impaired drivers
Authors: Chikritzhs Tanya , Stockwell Tim 
Published: September 2007

ABSTRACTAim To examine the impact of extended trading permits (ETPs) for licensed hotels in Perth, Western Australia on impaired driver breath alcohol levels (BALs) between July 1993 and June 1997.Design Forty‐three hotels obtained ETPs allowing later closing hours and 130 maintained standard closing time (controls). Impaired driver BALs were linked to ‘last place of drinking’ hotels. Before and after period BALs of drivers who last drank at ETP or non‐ETP hotels were compared by time of day of apprehension and sex, controlling for age.Findings Impaired female drivers apprehended between 10.01 p.m. and 12 midnight (before closing time) had significantly lower BALs after drinking at ETP hotels. Male drivers aged 18–25 years and apprehended between 12.01 and 2.00 a.m. after drinking at ETP hotels had significantly higher BALs than drivers who drank at non‐ETP hotels.Conclusions At peak times for alcohol‐related offences, late trading is associated with higher BALs among those drinkers most at risk of alcohol‐related harm.
PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci in the North Island brown kiwi, Apteryx mantelli
Authors: JENSEN THOMAS , NUTT KAREN J. , SEAL BRUCE S. , FERNANDES LUIZA B. , DURRANT BARBARA 
Published: September 2007

AbstractWe report the isolation and characterization of eight polymorphic and five monomorphic microsatellites in North Island brown kiwi (NIBK, Apteryx mantelli), using two polymerase chain reaction (PCR) techniques employing either short‐tandem repeat primers (STR method) or random PCR‐based isolation of microsatellite arrays (PIMA method). Microsatellite polymorphism was subsequently determined using 65 individuals. There were two to seven alleles for each polymorphic locus with heterozygozity ranging between 0.04 and 0.86. These primers will be used in future studies to determine the level of extra‐pair copulation, dispersal patterns, and genetic diversity within and between wild populations of NIBK.
PERMANENT GENETIC RESOURCES: Microsatellite markers for the threatened Bliss Rapids snail (Taylorconcha serpenticola) and cross‐amplification in its congener, T. insperata
Authors: LIU H. ‐P. , HERSHLER R. 
Published: September 2007

AbstractWe developed and tested microsatellite markers to investigate population structure of a threatened North American freshwater gastropod, Taylorconcha serpenticola. Of the 21 primer pairs that were evaluated, 11 were readily optimized and scored, providing amplification of 12 loci that were screened for 820 specimens from 29 populations. The number of alleles across 11 of these polymorphic loci ranged from three to 20 and the observed heterozygosity varied from 0.0061 to 0.7561. All loci yielded suitable amplification products in the second species of Taylorconcha (T. insperata) and three proved to be diagnostic for these congeners, demonstrating that these markers are also useful for species identification studies.
Negation – An Overview of Typological Research
Authors: Miestamo Matti 
Published: September 2007

AbstractThis article is an overview of the current state of typological research on negation. Structures expressing standard negation – the negation of declarative verbal main clauses – can be classified on the basis of the status of the negative marker, or on the basis of the structure of the negative clause as a whole. Structural similarities and differences (symmetry and asymmetry) between negatives and affirmatives can be observed and classified into different types which can then be offered functional explanations. Negative strategies used in imperatives, existentials and nonverbal clauses often differ from standard negation; these differences are exemplified and discussed. The interaction between negative indefinite pronouns and standard negation shows interesting cross‐linguistic variation in terms of whether the latter co‐occurs with the indefinite and whether the indefinite is inherently negative. Some cross‐linguistic observations on diachronic developments and on the interaction between negation and modality and negation and focus are also briefly discussed.
Video‐Based Studies of Work Practice
Authors: Hindmarsh Jon , Heath Christian 
Published: September 2007

AbstractThe use of the visual, let alone video, is surprisingly rare within social scientific studies of work and organisations. Nevertheless there is an emerging corpus of research that use video recordings, augmented by field work, as their principal data; recordings that provide access to the fine details of work as it is accomplished within everyday organisational settings. They include studies of work in a broad range of domains, including call centres, mobile offices, operating theatres, construction sites and control centres. This paper outlines the nature of these video‐based studies of work and organisation and highlights some of their major contributions to our understanding of issues such as the nature of skill and expertise, the use of technology and the organisation of teamwork. It also reflects on the impact that these studies, and this approach, are having within the practical fields of industrial and market research.
Evaluation of Tigecycline Penetration into Colon Wall Tissue and Epithelial Lining Fluid Using a Population Pharmacokinetic Model and Monte Carlo Simulation
Authors: Rubino Christopher M. , Ma Lei , Bhavnani Sujata M. , Korth-Bradley Joan , Speth John , Ellis-Grosse Evelyn , Rodvold Keith R. , Ambrose Paul G. , Drusano George L. 
Published: September 2007

ABSTRACT

The objective of these analyses was to assess the penetration of tigecycline into colon wall tissue and epithelial lining fluid (ELF). The analyses included data from subjects without infection (phase 1) and patients with intra-abdominal infections (phase 2/3). Steady-state serum samples were collected from all subjects/patients (
n
= 577), while colon wall specimens (
n
= 23) and ELF specimens (
n
= 30) were obtained from subjects without infection. Tissue and serum data were simultaneously comodeled by using the BigNPAG program, and a four-compartment, open model with zero-order intravenous input and first-order elimination was employed. To examine the full range of tissue penetration and the associated probabilities of occurrence, a 9,999-subject Monte Carlo simulation was performed with two outputs, one for ELF penetration and one for colon wall tissue penetration. Data were well fit using models described above, with all
r
2
values above 0.95. For subjects without infection, the median (5th and 95th percentiles) colon wall and ELF penetration ratios were 1.73 (0.160 and 199) and 1.15 (0.561 and 5.23), respectively. Simulation results predict that tissue penetration varies considerably and likely explain unexpected clinical outcomes for those patients infected with strains at margins of the MIC distribution.
Effect of Oral Treatment with Hexadecyloxypropyl-[(
S
)-9-(3-Hydroxy-2- Phosphonylmethoxypropyl)Adenine] [(
S
)-HPMPA] or Octadecyloxyethyl-(
S
)-HPMPA on Cowpox or Vaccinia Virus Infections in Mice
Authors: Quenelle Debra C. , Collins Deborah J. , Herrod Bridgett P. , Keith Kathy A. , Trahan Julissa , Beadle James R. , Hostetler Karl Y. , Kern Earl R. 
Published: September 2007

ABSTRACT

We have previously reported that (
S
)-9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine, or (
S
)-HPMPA, is active in vitro against cowpox virus (CV) and vaccinia virus (VV) but is not active orally in animals. However, the ether lipid esters of (
S
)-HPMPA, hexadecyloxypropyl-[(
S
)-HPMPA] [HDP-(
S
)-HPMPA] and octadecyloxyethyl-[(
S
)-HPMPA] [ODE-(
S
)-HPMPA], had significantly enhanced activity in vitro and are orally bioavailable in mice. In the current study, HDP-(
S
)-HPMPA and ODE-(
S
)-HPMPA were prepared in water and administered once daily by oral gavage to mice at doses of 30, 10, and 3 mg/kg of body weight for 5 days beginning 24, 48, or 72 h after inoculation with CV or VV. Oral HDP-(
S
)-HPMPA and ODE-(
S
)-HPMPA were both highly effective (
P
< 0.001) at preventing mortality due to CV at 30 mg/kg, even when treatments were delayed until up to 72 h postinfection. ODE-(
S
)-HPMPA or HDP-(
S
)-HPMPA were also highly effective (
P
< 0.001) at preventing mortality in mice infected with VV at 30 mg/kg when treatments were delayed until to 48 or 72 h postinfection, respectively. Protection against both viruses was associated with a significant reduction of virus replication in the liver, spleen, and kidney but not in the lung. These data indicate that HDP-(
S
)-HPMPA and ODE-(
S
)-HPMPA are active when given orally against lethal CV and VV infections in mice, and further evaluation is warranted to provide additional information on the potential of these orally active compounds for treatment of human orthopoxvirus infection.
Small-Molecule Scaffolds for CYP51 Inhibitors Identified by High-Throughput Screening and Defined by X-Ray Crystallography
Authors: Podust Larissa M. , von Kries Jens P. , Eddine Ali Nasser , Kim Youngchang , Yermalitskaya Liudmila V. , Kuehne Ronald , Ouellet Hugues , Warrier Thulasi , Alteköster Markus , Lee Jong-Seok , Rademann Jörg , Oschkinat Hartmut , Kaufmann Stefan H. E. , Waterman Michael R. 
Published: September 2007

ABSTRACT

Sterol 14α-demethylase (CYP51), a major checkpoint in membrane sterol biosynthesis, is a key target for fungal antibiotic therapy. We sought small organic molecules for lead candidate CYP51 inhibitors. The changes in CYP51 spectral properties following ligand binding make CYP51 a convenient target for high-throughput screening technologies. These changes are characteristic of either substrate binding (type I) or inhibitor binding (type II) in the active site. We screened a library of 20,000 organic molecules against
Mycobacterium tuberculosis
CYP51 (CYP51
Mt
), examined the top type I and type II binding hits for their inhibitory effects on
M. tuberculosis
in broth culture, and analyzed them spectrally for their ability to discriminate between CYP51
Mt
and two reference
M. tuberculosis
CYP proteins, CYP130 and CYP125. We determined the binding mode for one of the top type II hits, α-ethyl-
N
-4-pyridinyl-benzeneacetamide (EPBA), by solving the X-ray structure of the CYP51
Mt
-EPBA complex to a resolution of 1.53 Å. EPBA binds coordinately to the heme iron in the CYP51
Mt
active site through a lone pair of nitrogen electrons and also through hydrogen bonds with residues H259 and Y76, which are invariable in the CYP51 family, and hydrophobic interactions in a phylum- and/or substrate-specific cavity of CYP51. We also identified a second compound with structural and binding properties similar to those of EPBA, 2-(benzo[d]-2,1,3-thiadiazole-4-sulfonyl)-2-amino-2-phenyl-
N
-(pyridinyl-4)-acetamide (BSPPA). The congruence between the geometries of EPBA and BSPPA and the CYP51 binding site singles out EPBA and BSPPA as lead candidate CYP51 inhibitors with optimization potential for efficient discrimination between host and pathogen enzymes.