bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distance‐based multivariate analyses confound location and dispersion effects
Authors: Warton David I. , Wright Stephen T. , Wang Yi 
Published: June 2011

Summary1. A critical property of count data is its mean–variance relationship, yet this is rarely considered in multivariate analysis in ecology.2. This study considers what is being implicitly assumed about the mean–variance relationship in distance‐based analyses – multivariate analyses based on a matrix of pairwise distances – and what the effect is of any misspecification of the mean–variance relationship.3. It is shown that distance‐based analyses make implicit assumptions that are typically out‐of‐step with what is observed in real data, which has major consequences.4. Potential consequences of this mean–variance misspecification are: confounding location and dispersion effects in ordinations; misleading results when trying to identify taxa in which an effect is expressed; failure to detect a multivariate effect unless it is expressed in high‐variance taxa.5. Data transformation does not solve the problem.6. A solution is to use generalised linear models and their recent multivariate generalisations, which is shown here to have desirable properties.
Admitting evidence of a defendant's previous conviction (PCE) and its impact on juror deliberation in relation to both juror‐processing style and juror concerns over the fairness of introducing PCE
Authors: Honess T. M. , Mathews G. A. 
Published: June 2011

Purpose. To examine the impact of admitting previous conviction evidence (PCE) on juror and jury deliberation. Major questions are: (1) Is there is an association between the inclusion of PCE and confidence in a defendant's guilt using a relatively rich trial simulation? (2) Does PCE invoke jurors’ considerations of fairness to the defendant? (3) Is heuristic processing (HP) associated with a prejudicial interpretation of evidence?Methods. In experiment 1 (n= 82), individual jurors were asked to recall evidence, express opinion, and justify verdicts on the two counts of Affray and Grievous Bodily Harm (GBH). In experiment 2 (new n= 121), PCE information was emphasized and a jury deliberation condition was included.Results. There was no simple association between admitting PCE and judgements of guilt. However, both interviews and jury deliberations indicated careful consideration of evidence. In particular, juror arguments showed that some were troubled by PCE, which they saw as unwarranted and therefore unfair to the defendant. Finally, HP was associated with both a prejudicial focus on the defendant's character and a higher confidence in guilt.Conclusions. A simple link between PCE and judgements of guilt may only hold in relatively circumscribed experimental simulations. Results also indicate that the introduction of PCE is unlikely to aid evidence‐based deliberation without careful testing of different forms of judges’ explanation concerning PCE.
Genetic Control of Biosynthesis and Transport of Riboflavin and Flavin Nucleotides and Construction of Robust Biotechnological Producers
Authors: Abbas Charles A. , Sibirny Andriy A. 
Published: June 2011

SUMMARYRiboflavin [7,8-dimethyl-10-(1′-d-ribityl)isoalloxazine, vitamin B2] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded bySEF1is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains ofBacillus subtilis,Ashbya gossypii, andCandida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
cis-Antisense RNA, Another Level of Gene Regulation in Bacteria
Authors: Georg Jens , Hess Wolfgang R. 
Published: June 2011

SUMMARYA substantial amount of antisense transcription is a hallmark of gene expression in eukaryotes. However, antisense transcription was first demonstrated in bacteria almost 50 years ago. The transcriptomes of bacteria as different asHelicobacter pylori,Bacillus subtilis,Escherichia coli,Synechocystissp. strain PCC6803,Mycoplasma pneumoniae,Sinorhizobium meliloti,Geobacter sulfurreducens,Vibrio cholerae,Chlamydia trachomatis,Pseudomonas syringae, andStaphylococcus aureushave now been reported to contain antisense RNA (asRNA) transcripts for a high percentage of genes. Bacterial asRNAs share functional similarities withtrans-acting regulatory RNAs, but in addition, they use their own distinct mechanisms. Among their confirmed functional roles are transcription termination, codegradation, control of translation, transcriptional interference, and enhanced stability of their respective target transcripts. Here, we review recent publications indicating that asRNAs occur as frequently in simple unicellular bacteria as they do in higher organisms, and we provide a comprehensive overview of the experimentally confirmed characteristics of asRNA actions and intimately linked quantitative aspects. Emerging functional data suggest that asRNAs in bacteria mediate a plethora of effects and are involved in far more processes than were previously anticipated. Thus, the functional impact of asRNAs should be considered when developing new strategies against pathogenic bacteria and when optimizing bacterial strains for biotechnology.
Atomic Force Microscopy in Imaging of Viruses and Virus-Infected Cells
Authors: Kuznetsov Yurii G. , McPherson Alexander 
Published: June 2011

SUMMARY

Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (
T
). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer),
in situ
on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM.
Regulatory Circuitry Governing Fungal Development, Drug Resistance, and Disease
Authors: Shapiro Rebecca S. , Robbins Nicole , Cowen Leah E. 
Published: June 2011

SUMMARY

Pathogenic fungi have become a leading cause of human mortality due to the increasing frequency of fungal infections in immunocompromised populations and the limited armamentarium of clinically useful antifungal drugs.
Candida albicans
,
Cryptococcus neoformans
, and
Aspergillus fumigatus
are the leading causes of opportunistic fungal infections. In these diverse pathogenic fungi, complex signal transduction cascades are critical for sensing environmental changes and mediating appropriate cellular responses. For
C. albicans
, several environmental cues regulate a morphogenetic switch from yeast to filamentous growth, a reversible transition important for virulence. Many of the signaling cascades regulating morphogenesis are also required for cells to adapt and survive the cellular stresses imposed by antifungal drugs. Many of these signaling networks are conserved in
C. neoformans
and
A. fumigatus
, which undergo distinct morphogenetic programs during specific phases of their life cycles. Furthermore, the key mechanisms of fungal drug resistance, including alterations of the drug target, overexpression of drug efflux transporters, and alteration of cellular stress responses, are conserved between these species. This review focuses on the circuitry regulating fungal morphogenesis and drug resistance and the impact of these pathways on virulence. Although the three human-pathogenic fungi highlighted in this review are those most frequently encountered in the clinic, they represent a minute fraction of fungal diversity. Exploration of the conservation and divergence of core signal transduction pathways across
C. albicans
,
C. neoformans
, and
A. fumigatus
provides a foundation for the study of a broader diversity of pathogenic fungi and a platform for the development of new therapeutic strategies for fungal disease.
Nucleosome Positioning in Saccharomyces cerevisiae
Authors: Jansen An , Verstrepen Kevin J. 
Published: June 2011

SUMMARY

The DNA of eukaryotic cells is spooled around large histone protein complexes, forming nucleosomes that make up the basis for a high-order packaging structure called chromatin. Compared to naked DNA, nucleosomal DNA is less accessible to regulatory proteins and regulatory processes. The exact positions of nucleosomes therefore influence several cellular processes, including gene expression, chromosome segregation, recombination, replication, and DNA repair. Here, we review recent technological advances enabling the genome-wide mapping of nucleosome positions in the model eukaryote
Saccharomyces cerevisiae
. We discuss the various parameters that determine nucleosome positioning
in vivo
, including
cis
factors like AT content, variable tandem repeats, and poly(dA:dT) tracts that function as chromatin barriers and
trans
factors such as chromatin remodeling complexes, transcription factors, histone-modifying enzymes, and RNA polymerases. In the last section, we review the biological role of chromatin in gene transcription, the evolution of gene regulation, and epigenetic phenomena.
Characterization of a plant-transformation-ready large-insert BIBAC library ofArabidopsisand bombardment transformation of a large-insert BIBAC of the library into tobacco
Authors: Chang Yueh-Long , Chuang Huey-Wen , Meksem Khalid , Wu Fang-Chun , Chang Chang-Yee , Zhang Meiping , Zhang Hong-Bin 
Published: June 2011

Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2× equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding.
Transcript profiling and gene characterization of three fatty acid desaturase genes in high, moderate, and low linolenic acid genotypes of flax (Linum usitatissimumL.) and their role in linolenic acid accumulation
Authors: Banik Mitali , Duguid Scott , Cloutier Sylvie 
Published: June 2011

Three genes encoding fatty acid desaturase 3 (fad3a, fad3b, and a novel fad3c) were cloned from four flax genotypes varying in linolenic acid content. Real-time PCR was used to quantify expression levels of the three fad3 genes during seed development. High amounts of both fad3a and fad3b transcripts were observed and reached their peak levels at 20 days after anthesis, except for fad3a from SP2047 where only low level expression was observed throughout seed development. Transcript accumulation of the novel fad3c gene was at similar background levels. The fatty acid composition was analysed for all genotypes and stages of development and compared with the fad3 gene expression patterns. α-Linolenic acid gradually accumulated during seed development, while linoleic acid was transient and decreased in M5791, UGG5-5, and AC McDuff. In contrast, the linolenic acid present in the early stages of development nearly completely disappeared in SP2047, while linoleic acid steadily accumulated. fad3a of the low linolenic acid line SP2047 encoded a truncated protein caused by a premature stop codon resulting from a single point mutation, and the low level of transcript accumulation in this genotype is likely due to nonsense-mediated mRNA decay caused by the premature termination of translation as a result of this early stop codon. Although substantial amounts of transcript accumulation occurred with fad3b of SP2047 genotype, cloning of the gene revealed a mutation in the first histidine box causing an amino acid change. Heterologous expression in yeast of the SP2047 and UGG5-5 fad3b genes showed that the mutation in the histidine box in SP2047 caused the enzyme inactivity. Taken together, these results showed that fad3a and fad3b are responsible for linolenic acid accumulation in flax seeds but did not support a major role for the novel fad3c. These observations were further supported by phenotypic and genotypic assessment of a doubled haploid population. Expression patterns of fad3a and fad3b were highly correlated with linolenic acid accumulation during seed development, with the exception of fad3b in SP2047 whose lack of activity was caused by the histidine box mutation despite its transcript accumulation being similar to that of the fad3b of the other genotypes.
Genetic analysis of Eucalyptus globulus diameter, straightness, branch size, and forking in Western Australia
Authors: Callister A.N. , England N. , Collins S. 
Published: June 2011

Eucalyptus globulus Labill. is increasingly considered for supply of solid-wood products such as sawlogs, yet genetic studies of solid-wood traits have been lacking. We estimated genetic parameters of growth and form traits that affect log value in full-sib families from two advanced-generation breeding populations on eight sites in Western Australia. Mean single-site heritability was 0.11 ± 0.01 for diameter at breast height (DBH), 0.28 ± 0.05 for stem straightness, 0.09 ± 0.02 for branch thickness, and 0.05 ± 0.02 for forking incidence. Dominance effects were significant (p < 0.05) at four sites for DBH and branch thickness and at three sites (one population) for straightness. Mean intersite additive genetic correlations were 0.76 ± 0.06 for DBH (n = 7), 0.75 ± 0.11 for stem straightness (n = 7), and 0.58 ± 0.07 for branch thickness (n = 4). Mean intersite dominance genetic correlations were 0.90 ± 0.04 for DBH (n = 7), 0.26 ± 0.27 (n = 4) for straightness, and 0.68 ± 0.11 for branch thickness (n = 3). Additive genetic correlations between DBH and straightness ranged from –0.71 ± 0.23 to 0.33 ± 0.19 with an average of –0.18 ± 0.12 (n = 8). Genetic correlations between DBH and branch thickness were mostly weak although straightness was generally associated with thinner branches (mean additive correlation 0.44 ± 0.15, n = 6). We conclude that prospects appear favourable for improving the solid-wood value of E. globulus by selection and breeding.
Stiffness of Douglas-fir lumber: effects of wood properties and genetics
Authors: Vikram Vikas , Cherry Marilyn L. , Briggs David , Cress Daniel W. , Evans Robert , Howe Glenn T. 
Published: June 2011

Because stiffness (modulus of elasticity (MOE)) is important for structural wood products, breeders and silviculturists seek to efficiently measure and improve this trait. We studied MOE in a 25-year-old progeny test of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) using field-based tools (ST300 and HM200) to measure stress wave MOE of standing trees and logs. We measured density, static bending MOE, and transverse vibration MOE on 2 × 4s, and density, SilviScan MOE, and SilviScan microfibril angle on small clearwood samples. Bending MOE had moderate to strong phenotypic and genetic correlations with stress wave MOE of trees and logs, transverse vibration MOE of 2 × 4s, and the densities of 2 × 4s and basal wood discs but was weakly correlated with the numbers and sizes of knots. The best lumber grade had the highest bending stiffness and smallest edge knots. Bending stiffness had a strong positive correlation with the density of small clearwood samples and a moderate negative correlation with microfibril angle. Compared with microfibril angle and edge knots, path analyses indicated that density had the strongest direct effect on bending MOE. We recommend that breeders measure and select for stress wave velocity to improve bending stiffness in Douglas-fir. Genetic gains can be increased by including wood density, but genetic selection for fewer or smaller knots will be ineffective.
Efficacy of tree defense physiology varies with bark beetle population density: a basis for positive feedback in eruptive species
Authors: Boone Celia K. , Aukema Brian H. , Bohlmann Jörg , Carroll Allan L. , Raffa Kenneth F. 
Published: June 2011

We evaluated the ability of constitutive and inducible defenses to protect trees and restrict herbivore reproduction across the endemic, incipient (i.e., transitory), and eruptive phases of a native bark beetle species. Host defenses were major constraints when mountain pine beetle (Dendroctonus ponderosae Hopkins) populations were low, but inconsequential after stand-level densities surpassed a critical threshold. We annually examined all lodgepole pines (Pinus contorta Douglas var. latifolia) in six 12–18 ha stands for 3–6 years for beetle attack and establishment as beetle densities progressed through various population phases. We also assayed a suite of tree physiological and chemical attributes and related them to subsequent attacks during that year. Rapidly inducible defenses appeared more important than constitutive defenses, and total monoterpenes were more important than particular constituents. Trees that exude more resin and accumulate higher monoterpene concentrations in response to simulated attack largely escaped natural attacks when populations were low. In stands where beetles had reached incipient densities, these defenses were ineffective. Larger diameter trees had more pronounced defenses than smaller diameter trees. As populations increased, beetles selected increasingly larger, more resource-rich trees, despite their better defenses. When populations were too low for cooperative attack, beetles exploited trees weakened by lower-stem insects. Behavioral plasticity allows beetles to persist at endemic levels until conditions shift, after which positive feedbacks predominate.
Ethanol synthesis by anoxic root segments from five cedar species relates to their habitat attributes but not their known differences in vulnerability to Phytophthora lateralis root disease
Authors: Kelsey Rick G. , Joseph Gladwin , McWilliams Michael G. 
Published: June 2011

Ethanol synthesis by anoxic root segments from Port Orford cedar (Chamaecyparis lawsoniana (A. Murray bis) Parl.); yellow cedar (Chamaecyparis nootkatensis (D. Don) Spach); Atlantic white cedar (Chamaecyparis thyoides (L.) Britton, Sterns & Poggenb.); western redcedar (Thuja plicata Donn ex D. Don), and incense cedar (Calocedrus decurrens (Torr.) Florin ) was compared to determine whether the amounts that they produced during flooding could contribute the known greater vulnerability of Port Orford cedar to infection by Phytophthora lateralis Tucker & Milbrat. Roots were incubated in water at 5, 15, 25, and 35 °C for 14 days with periodic sampling. After 12 h of anoxic stress, Atlantic white cedar and yellow cedar roots produced equal quantities of ethanol that were about two times more than produced by the other three species, which did not differ from one another. The roots remained anoxic for 14 days, with ethanol concentrations increasing 6 to 11 times depending on the species. After 14 days, Atlantic white cedar remained the highest ethanol producer at two to three times more than the other species, whereas incense cedar yields were the lowest. Yellow cedar, western redcedar, and Port Orford cedar had intermediate levels of ethanol. The similarity in responses of Port Orford cedar to the other species is strong evidence that ethanol is not an important contributor to its known greater vulnerability to P. lateralis infection. In general, root incubation temperature affected ethanol synthesis similarly for all species. Increases in temperature from 5 to 15 °C or 15 to 25 °C doubled the ethanol yields at 12 h. Literature ratings of anaerobic tolerance for these cedars were compared with ratings based on their ethanol yields after 12 h or 14 days of anoxia. The latter rating appears to more closely correspond with the cedars associations to wet, mesic environments and their likelihood of experiencing anoxia via flooding.