bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of genetic diversity in outcrossing and selfing populations ofArabidopsis lyrata
Authors: MABLE BARBARA K. , ADAM A. 
Published: July 2007

AbstractArabidopsis lyratais normally considered an obligately outcrossing species with a strong self‐incompatibility system, but a shift in mating system towards inbreeding has been found in some North American populations (subspeciesA. lyrata ssp. lyrata). This study provides a survey of the Great Lakes region of Canada to determine the extent of this mating system variation and how outcrossing rates are related to current population density, geographical distribution, and genetic diversity. Based on variation at microsatellite markers (progeny arrays to estimate multilocus outcrossing rates and population samples to estimate diversity measures) and controlled greenhouse pollinations, populations can be divided into two groups: (i) group A, consisting of individuals capable of setting selfed seed (including autogamous fruit set in the absence of pollinators), showing depressed outcrossing rates (Tm = 0.2–0.6), heterozygosity (HO = 0.02–0.06) and genetic diversity (HE = 0.08–0.10); and (ii) group B, consisting of individuals that are predominantly self‐incompatible (Tm > 0.8), require pollinators for seeds set, and showing higher levels of heterozygosity (HO = 0.13–0.31) and diversity (HE = 0.19–0.410). Current population density is not related to the shift in mating system but does vary with latitude. Restricted gene flow among populations was evident among all but two populations (FST = 0.11–0.8). Group A populations were more differentiated from one another (FST = 0.78) than they were from group B populations (FST = 0.59), with 41% of the variation partitioned within populations, 47% between populations, and 12% between groups. No significant relationship was found between genetic and geographical distance. Results are discussed in the context of possible postglacial expansion scenarios in relation to loss of self‐incompatibility.
Identifying the early genetic consequences of habitat degradation in a highly threatened tropical conifer, Araucaria nemorosa Laubenfels
Authors: KETTLE C. J. , HOLLINGSWORTH P. M. , JAFFRÉ T. , MORAN B. , ENNOS R. A. 
Published: July 2007

AbstractThe early genetic effects of habitat degradation were investigated in the critically endangered conifer Araucaria nemorosa. This species occurs in New Caledonia, a global biodiversity hotspot where the world's greatest concentration of endemic conifer species coincides with an extremely high level of habitat destruction due to fire and mining. Using seven microsatellite loci, estimates were made of genetic marker variation, inbreeding coefficients and population differentiation of adult and seedling cohorts of A. nemorosa. These were contrasted with equivalent estimates, made over similar spatial scales and with the same marker loci, in the locally common and more widespread sister species Araucaria columnaris. There were no significant differences in population genetic parameters between adult populations of the two species, despite their different abundances. However, in A. nemorosa, the juvenile cohort showed a loss of rare alleles and elevated levels of inbreeding when compared to the adult cohort. These genetic differences between the cohorts were not observed in the locally common A. columnaris. This suggests that recent environmental degradation is influencing the genetic structure of A. nemorosa populations. Although this is not detectable among predisturbance adult populations, an early warning of these impacts is evident in more recently established seedling cohorts. The conservation implications of these results are discussed.
Explicit experimental evidence for the effectiveness of proximity as mate‐guarding behaviour in reducing extra‐pair fertilization in the Seychelles warbler
Authors: KOMDEUR J. , BURKE T. , RICHARDSON D. S. 
Published: July 2007

AbstractExtra‐pair copulations (EPCs; copulations outside the pair bond) are widespread in birds and may result in extra‐pair fertilizations (EPFs). To increase reproductive success, males should not only seek to gain EPFs, but also prevent their own females from gaining EPFs. Although males could reduce the number of EPCs by their mates, this does not necessarily mean that they reduce the number of EPFs; indeed several studies have found no association between EPCs and EPFs. Male Seychelles warblers (Acrocephalus sechellensis) follow their partner closely during the period when the pair female is most receptive (fertile period). We show that males that guarded their mates more closely were less likely to have extra‐pair young in their nest. This study on the Seychelles warbler is the first to provide explicit experimental evidence that mate guarding is effective in reducing EPFs. First, in territories where free‐living males were induced to stop mate guarding during the pair female's fertile period, extra‐pair parentage was higher than in the control group. Second, in the experimental group, the probability of having an extra‐pair nestling in the nest was positively associated with the number of days during the fertile period for which mate guarding was artificially stopped. Thus, male mate guarding was effective in reducing the risk of cuckoldry.
Ancient differentiation in the single‐island avian radiation of endemic Hispaniolan chat‐tanagers (Aves: Calyptophilus)
Authors: TOWNSEND ANDREA K. , RIMMER CHRISTOPHER C. , LATTA STEVEN C. , LOVETTE IRBY J. 
Published: July 2007

AbstractThe simple geographic structure of island systems often makes them tractable for studies of the patterns and processes of biological diversification. The Calyptophilus chat‐tanagers of Hispaniola are of general evolutionary interest because their multiple lineages might have arisen on a single island, of conservation concern because several isolated populations are nearly extinct, and taxonomically ambiguous because they have been variously lumped or split into one to four species. To explore the context of diversification of the seven extant Calyptophilus populations, we conducted a multilocus coalescent analysis based on sequences of mitochondrial ND2 and three nuclear intron loci. We then compared patterns of phylogeographic genetic variation with the morphological differences that distinguish these populations. Mitochondrial haplotypes formed two reciprocally monophyletic groups separated by a large magnitude of nucleotide divergence. Intron structure largely paralleled the geographic grouping pattern of the mitochondrial DNA (mtDNA), but these groups were only reciprocally monophyletic at one of the three introns. Also, the magnitude of between‐group divergence was much lower in the introns than mtDNA genealogies. Multilocus coalescent analyses inferred a nonzero divergence time between these two major geographic groups, but suggested that they have experienced a low level of gene flow. All four markers showed substantial allele sharing within each of the two groups, demonstrating that many now separated montane populations do not have long histories of isolation. Considered in concert, our multilocus phylogeographic reconstructions support the recognition of two species within the Calyptophilus complex, and raise the possibility that these taxa differentiated prior to the fusion of the two palaeo‐islands that form present‐day Hispaniola.
CLASSIFICATION OF PANCREATIC CYSTIC LESIONS USING SELDI‐TOF MASS SPECTROMETRY
Authors: Scarlett Christopher J. , Samra Jaswinder S. , Xue AiQun , Baxter Robert C. , Smith Ross C. 
Published: July 2007

Background:  The diagnosis of pancreatic cystic lesions is problematical with difficulties arising in the differentiation between malignant, premalignant or benign lesions. This preliminary study aimed to analyse pancreatic cyst fluid, using a proteomic approach, to generate reproducible protein profiles to assist in the classification of malignant and non‐carcinoma samples.Methods:  Pancreatic cyst fluid samples from patients with pancreatic adenocarcinoma and non‐carcinoma cystic lesions were analysed on hydrophobic protein chip arrays by surface‐enhanced laser desorption/ionization time‐of‐flight mass spectrometry (SELDI‐TOF MS).Results:  Differential protein expression profiles were observed between pancreatic adenocarcinoma and non‐carcinoma cyst fluid samples using SELDI‐TOF MS, with 12 protein peaks differentially expressed between pancreatic adenocarcinoma and non‐carcinoma. Additionally, unique patterns were observed between the different subtypes of non‐carcinoma samples as well as malignant adenocarcinoma.Conclusions:  In this preliminary study we used SELDI‐TOF MS to identify protein expression profiles of pancreatic cyst fluid, showing a potential to aid in the differential diagnosis of pancreatic cystic lesions.
RISK FACTORS ASSOCIATED WITH PERFORATED APPENDICITIS IN ELDERLY PATIENTS PRESENTING WITH SIGNS AND SYMPTOMS OF ACUTE APPENDICITIS
Authors: Sheu Bor‐Fuh , Chiu Te‐Fa , Chen Jih‐Chang , Tung Meng‐Sheng , Chang Meng‐Wei , Young Yui‐Rwei 
Published: July 2007

Background:  The aim of this study was to identify factors associated with rupture in elderly patients with acute appendicitis.Methods:  The medical records of 601 consecutive patients >60 years of age with acute appendicitis between 1995 and 2005 were retrospectively reviewed. Historical, clinical and laboratory factors in patients with both intact and ruptured appendices were examined with univariate and multivariate analyses by logistic regressions.Results:  Nine factors predicted appendiceal rupture age (odds ratio (OR) 1.05, confidence interval (CI) 1.02–1.07), male sex (OR 1.96, CI 1.35–2.06), preadmission duration of pain (OR 1.23, CI 1.11–1.36), interval of time from admission to surgery (OR 1.02, CI 1.01–1.04), fever >38°C (OR 2.59, CI 1.78–3.77), left shift in leucocyte count >76% (OR 2.34, CI 1.27–4.32), anorexia (OR 2.03, CI 1.38–2.99) and a retrocaecally positioned appendix (OR 1.93, CI 1.15–3.24).Conclusion:  The incidence of appendiceal rupture, or complications secondary to appendiceal rupture, in elderly patients may be decreased if surgery is expedited when the temperature is >38°C or there is a left shift in leucocyte count >76%, especially in men with anorexia.
PARATHYROID HORMONE ASSAY PREDICTS HYPOCALCAEMIA AFTER TOTAL THYROIDECTOMY
Authors: Sywak Mark S. , Palazzo Fausto F. , Yeh Michael , Wilkinson Margaret , Snook Kylie , Sidhu Stan B. , Delbridge Leigh W. 
Published: July 2007

Background:  Postoperative parathyroid gland function after total thyroidectomy (TT) has traditionally been monitored by the measurement of serum calcium concentrations. The purpose of this study is to determine whether measurement of parathyroid hormone (PTH) concentrations in the early postoperative period accurately predicts patients at risk of developing hypocalcaemia.Methods:  A prospective cohort study of patients undergoing TT was carried out. PTH concentrations were measured preoperatively and at 4 and 23 h postoperatively. Serum calcium concentration was measured preoperatively and twice daily for 48 h after surgery.Results:  One hundred patients undergoing TT were recruited into the study in the period June 2004 to July 2005. Benign multinodular goitre was the most common indication for surgery (77%). The incidence of temporary hypocalcaemia (Ca < 2.0 mmol/L) was 18%. The mean PTH concentration at 4 h after surgery was 22.3 ng/L and was not significantly different from the 23‐h concentration of 23.2 ng/L (P = 0.18). A PTH concentration of ≤3 ng/L measured at 4 h after surgery had a sensitivity, specificity and likelihood ratio of 0.71, 0.94 and 11.3, respectively, for predicting postoperative hypocalcaemia. The accuracy of a single PTH concentration at 4 h was good for predicting hypocalcaemia (area under receiver–operator characteristic curve 0.90; confidence interval 0.81–0.96). There was no significant difference in accuracy between the 4‐ and 24‐h PTH concentrations (P = 0.14).Conclusions:  A single measurement of PTH concentration in the early postoperative period after TT reliably predicts patients who are likely to develop hypocalcaemia. This approach facilitates early discharge and may decrease the need for multiple postoperative blood tests.
Diversity of the human gastrointestinal tract microbiota revisited
Authors: Rajilić‐Stojanović Mirjana , Smidt Hauke , De Vos Willem M. 
Published: July 2007

SummarySince the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation‐based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species‐level phylogenetic types (phylotypes). Such knowledge is essential for the design of high‐throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.
Bacterial diversity in soil enrichment cultures amended with 2 (2‐methyl‐4‐chlorophenoxy) propionic acid (mecoprop)
Authors: Zakaria Dalia , Lappin‐Scott Hilary , Burton Sara , Whitby Corinne 
Published: July 2007

SummaryThe tfdA gene encodes for an α‐ketoglutarate‐dependent dioxygenase enzyme which catalyses the first step of the degradation of phenoxyalkanoic acid herbicides such as 2 (2‐methyl‐4‐chlorophenoxy) propionic acid (mecoprop). The bacterial diversity of soil enrichment cultures containing mecoprop was examined by Denaturing Gradient Gel Electrophoresis (DGGE) and clone libraries of both 16S rRNA genes and tfdA genes. The 16S rRNA gene sequences were diverse and clustered with either the Beta‐ or Gammaproteobacteria. The 16S rRNA gene sequence from a bacterial strain isolated from an enrichment culture, grown on R‐mecoprop, which represented a dominant band in the DGGE profiles, had a high 16S rRNA sequence identity (100%) to Burkholderia glathei. This is the first report that B. glathei is implicated in mecoprop degradation. PCR amplification of the tfdA genes detected class III tfdA genes only, and no class I or class II tfdA sequences were detected. To understand the genes involved the degradation of specific mecoprop (R‐) and (S‐) enantiomers, oligonucleotide probes targeting the tfdA, rdpA, sdpA and cadA genes were hybridized to DNA extracted from enrichment cultures grown on either R‐mecoprop or (R/S) racemic mecoprop. Strong hybridization signals were obtained with sdpA and tfdA probes using DNA extracted from cultures grown on racemic mecoprop. A strong hybridization signal was also obtained with the rdpA probe with DNA extracted from the cultures grown on R‐mecoprop. This suggests the rdpA gene is involved in R‐mecoprop degradation while tfdA, sdpA and cadA genes are involved in the degradation of both R‐ and S‐mecoprop.
Resource dynamics during infection of Micromonas pusilla by virus MpV‐Sp1
Authors: Brown Christopher M. , Campbell Douglas A. , Lawrence Janice E. 
Published: July 2007

SummaryViruses infecting marine phytoplankton drive phytoplankton diversity, terminate blooms and shuttle genetic material. Assessments of the scale of viral impacts on trophic networks are, however, speculative. We investigated fluxes of DNA between host and virus during infection of the prasinophyte alga Micromonas pusilla by phycodnavirus MpV SP1. Under a light–dark regimen, viral genomes accumulated to a transient peak within 24 h, at the expense of both host DNA synthesis and nuclear DNA. Viral genome abundance then declined soon after host lysis. This release of a phosphate‐rich nucleotide pool during viral infection of phytoplankton should be considered in trophic models. Lysis required light and was stalled in darkness, meanwhile viral genome replication proceeded slowly in the dark. Viral exploitation of this host is therefore only partially light‐dependent and infected phytoplankton are poised to lyse at dawn or if mixed to the photic zone. The chloroplast genome remained intact until lysis, indicating that either this DNA pool is inaccessible or the virus spares the chloroplast for its energy and reductant generation. The photochemical turnover of residual Photosystem II complexes accelerated during lysis, indicating that events in late infection heighten demands on the remaining host photosynthetic systems, consistent with the light dependency of lysis.
Comparative aspects of cortical neurogenesis in vertebrates
Authors: Cheung Amanda F. P. , Pollen Alexander A. , Tavare Aniket , DeProto Jamin , Molnár Zoltán 
Published: July 2007

AbstractThe mammalian neocortex consists of six layers. By contrast, the reptilian and avian cortices have only three, which are believed to be equivalent to layers I, V and VI of mammals. In mammals, the majority of cortical cell proliferation occurs in the ventricular and subventricular zones, but there are a small number of scattered individual divisions throughout the cortex. Neurogenesis in the cortical subventricular zone is believed to contribute to the supragranular layers. To estimate the proportions of different forms of divisions in reptiles and birds, we examined the site of proliferation in embryonic turtle (stages 18–25) and chick (embryonic days 8–15) brains using phospho‐histone H3 (a G2 and M phase marker) immunohistochemistry. In turtle, only few scattered abventricular H3‐immunoreactive cells were found outside the ventricular zone; the majority of the H3‐immunoreactive cells were located in the ventricular zone throughout the entire turtle brain. Ventricular zone cell proliferation peaks at stages 18 and 20, before an increase of abventricular proliferation at stages 23 and 25. In turtle cortex, however, abventricular proliferation at any given stage never exceeded 17.5 ± 2.47% of the total division and the mitotic profiles did not align parallel to the ventricular zone. Phospho‐histone H3 immunoreactivity in embryonic chick brains suggests the lack of subventricular zone in the dorsal cortex, but the presence of subventricular zone in the ventral telencephalon. We were able to demonstrate that the avian subventricular zone is present in both pallial and subpallial regions of the ventral telencephalon during embryonic development, and we characterize the spatial and temporal organization of the subventricular zone. Comparative studies suggest that the subventricular zone was involved in the laminar expansion of the cortex to six layers in mammals from the three‐layered cortex found in reptiles and birds. Within mammals, the number of neurons in a cortical column appears to be largely constant; nevertheless, there are considerable differences between the germinal zones in mammalian species. It is yet to be determined whether these elaborations of the subventricular zone may have contributed to cell diversity, tangential expansion or gyrus formation of the neocortex and whether it might have been the major driving force behind the evolution of the six‐layered neocortex in mammals.
Cocaine exposurein vitroinduces apoptosis in fetal locus coeruleus neurons through TNF‐α‐mediated induction of Bax and phosphorylated c‐Jun NH2‐terminal kinase
Authors: Dey Swatee , Snow Diane M. 
Published: July 2007

AbstractCocaine exposure results in aberrant outgrowth and decreased survival for locus coeruleus (LC), a noradrenergic population of neurons that putatively regulates attentional function; however, the underlying mechanisms for these events are not known. We previously showed that cocaine exposurein vitroactivates pro‐apoptotic Bax, caspase‐9, and caspase‐3 in LC neurons dissected from embryonic day 14 rats, implicating that apoptosis may be orchestrated via signal transduction events. In the current studyin vitro, we examined upstream events to determine the role of the pro‐inflammatory cytokine, tumor necrosis factor alpha (TNF‐α), on LC signal transduction, because cocaine exposure to LC neurons triggered TNF‐α expression at 30 min as measured by ELISA. Exposure of LC neurons torecombinant‐TNF‐α resulted in decreased metabolic activity, an indicator of reduced neuron viability [3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay], and increased apoptosis (terminal deoxynucleotidyl transferase‐mediated DNA nick end labeling assay). Pro‐apoptotic caspase‐3 was induced by cocaine starting at 30 min.Recombinant‐TNF‐α induced caspase‐3 activity earlier than cocaine (15 and 20 min). The caspase‐3 levels were significantly reduced when cocaine and TNF‐α were combined with neutralizing‐TNF‐α (nTNF‐α), respectively. Further, cocaine alone elevated phospho‐p38‐mitogen‐activated protein kinases that persisted when combined with nTNF‐α. However, both cocaine and TNF‐α independently increased phospho‐c‐Jun NH2‐terminal kinase and Bax levels at concurrent time periods (30 min and 1 h), and this elevation was attenuated in the presence of nTNF‐α. These simultaneous molecular events triggered by cocaine and TNF‐α implicate a potential apoptotic signal transduction pathway via induction of phospho‐c‐Jun NH2‐terminal kinase and Bax that may lead to caspase‐3 activation and apoptosis in cocaine‐exposed fetal LC neurons.
Alpha‐synuclein protects cerebellar granule neurons against 6‐hydroxydopamine‐induced death
Authors: Monti Barbara , Polazzi Elisabetta , Batti Laura , Crochemore Christophe , Virgili Marco , Contestabile Antonio 
Published: July 2007

AbstractThe physiological role of alpha‐synuclein, a protein found enriched in intraneuronal deposits characterizing Parkinson’s disease, is debated. While its aggregation is usually considered linked to neuropathology, its normal function may be related to fundamental processes of synaptic transmission and plasticity. By using antisense oligonucleotide strategy, we report in this study that alpha‐synuclein silencing in cultured cerebellar granule cells results in widespread death of these neurons, thus demonstrating an essential pro‐survival role of the protein towards primary neurons. To study alpha‐synuclein expression and processing in a Parkinson’s disease model of neurotoxicity, we exposed differentiated cultures of cerebellar granule neurons to toxic concentrations of 6‐hydroxydopamine (6‐OHDA). This resulted in neuronal death accompanied by a decrease of the monomeric form of alpha‐synuclein, which was due to both decreased synthesis of the protein and its increased mono‐ubiquitination accompanied by nuclear translocation. The essential neuroprotective role of alpha‐synuclein was confirmed by the fact that subchronic valproate treatment, which increases alpha‐synuclein expression and prevents its nuclear translocation in cerebellar granule cells exposed to 6‐OHDA, significantly protected these neurons from 6‐OHDA insult. In agreement with the pro‐survival role of alpha‐synuclein in this model, subtoxic concentrations of alpha‐synuclein antisense oligonucleotides, aggravated 6‐OHDA toxicity towards granule neurons. Our results demonstrate that normal alpha‐synuclein expression is essential for the viability of primary neurons and that its pro‐survival role is abolished in 6‐OHDA neurotoxic challenge. These results are relevant to more precisely define the role of alpha‐synuclein in neuronal cells and to better understand its putative involvement in neurodegeneration.