bluuebunny/crossref_metadata_2025 huggingface dataset:
Trajectories of Depressive Symptoms and Externalizing Behaviors across Adolescence: Associations with Histories of Suicide Attempt and Ideation in Early Adulthood
Authors: Kerr David C. R. , Reinke Wendy M. , Eddy J. Mark
Published: October 2012

We examined associations between adolescent problem trajectories and suicide risk outcomes in 361 community participants. Depressive symptoms (self‐report) and externalizing behaviors (parent report) were assessed six times from grades 5 to 10. Parallel process linear growth curves indicated that lifetime suicide attempt history assessed to age 25 was associated with higher intercept (grade 5) and slope (increases from grades 5 to 10) of depressive symptoms and higher slope of externalizing behaviors. Both problem intercepts predicted suicidal ideation at ages 18 to 25 years. Adolescent depressive and externalizing symptom trajectories showed independent associations with suicide risk. Preventive intervention that occurs prior to the developmental period in which suicidal thoughts and behaviors show peak prevalence is expected to prevent suicide.
Eugenosedin-A prevents high-fat diet increased adhesion molecules through inhibition of MAPK- and p65-mediated NF-κB pathway in rat model
Authors: Lin Hui-Li , Shen Kuo-Ping , Chang Wen-Tsan , Lin Jou-Chun , An Li-Mei , Chen Ing-Jun , Wu Bin-Nan
Published: October 2012

Objectives

Previous studies have shown eugenosedin-A, a 5-HT1B/2A and α1/α2/β1-adrenergic blocker, is able to decrease cholesterol levels, hyperglycaemia and inflammation in hyperlipidaemic mice induced by high-fat diet (HFD). The aim of this study is to examine the effects of eugenosedin-A on the inhibition of adhesion molecules of platelets, the aorta and acyl-coenzymeA:cholesterol acyltransferase-1 (ACAT-1) of macrophages in a hyperlipidaemic rat model.

Methods

Six-week-old Sprague–Dawley rats were randomly divided into two control and treatment groups. The control rats received either a regular diet or HFD and the treatment groups were fed HFD with either 5 mg/kg eugenosedin-A or atorvastatin for a 10-week period.

Key findings

Compared with the two control groups, the HFD group had lower levels of high-density lipoprotein, higher concentrations of triglycerides, total cholesterol, low-density lipoprotein and insulin. The expression of adhesion molecules in platelets, aorta and monocyte-macrophage were enhanced by HFD. HFD also increased upstream proteins and their phosphorylated form in the aorta. In treatment groups, eugenosedin-A and atorvastatin improved HFD-induced hyperlipidaemia and levels of insulin. Eugenosedin-A reduced the upregulation of P-selectin, ICAM-1, ICAM-2, ICAM-3, VCAM, PECAM in platelets and inhibited E-selectin, ICAM-1, ICAM-2, ICAM-3, VCAM and PECAM protein levels in the aorta. Eugenosedin-A reduced the ACAT-1 protein expression of monocyte-macrophages. The expression of PKCα, MAPKs, IKKα and p65 and their phosphorylated form were reduced in treatment groups.

Conclusions

Taken together, hyperlipidaemia enhances the expression of adhesion molecules and ACAT-1 protein, and eugenosedin-A ameliorates those increases. Through inhibition of MAPK- and p-65-mediated NF-κB pathway, eugenosedin-A decreases the quantity of adhesion molecules.
Abnormalities of autobiographical memory of patients with depressive disorders: A meta‐analysis
Authors: Liu Xianhua , Li Li , Xiao Jing , Yang Juan , Jiang Xiangqi
Published: October 2012

Background

Previous studies on the autobiographical memory (AM) of depressed patients had inconsistent findings. Various severities of depression in patients in these studies may lead to conflicting results. However, the differences in the procedure of the autobiographical memory tests (AMTs) may also influence the AM results.

Objective

In this study, we analyse the results published so far to research the AM characteristics of patients with depressive disorders and identify moderators that affect the assessment results while using AMT in this field.

Method

A systematic search was conducted using following databases: MEDLINE, PubMed, ScienceDirect, Cnki, and Google Scholar, yielding 22 studies of patients with depressive disorders and autobiographical memory published between 1986 and 2010.

Results

The results of meta‐analysis showed that, compared with the control group, the patients with depressive disorders reported less specific AMs (g = −1.051) and more overgeneralized AMs (g = 1.115). The patients with depressive disorders also recalled more slowly (g = 0.400). The effect sizes of overgeneral memory could be predicted by the self‐reported depression score of the depressed patients (B = −.329, p < .01). The mean effect sizes of AMT indices were affected by the AMT characteristics (i.e., number of cue word, max response time, prompting, presentation of cue word, taping, and so on).

Conclusions

Our results suggest that overgeneralization and response lag are the AM deficits in patients with depressive disorders. The parameters of AMT are important factors, which are related to the inconsistency in the assessment of AM in patients with depressive disorders. Some recommendations on AMT and programme research design are given for future research.

Practitioner Points

This paper provides new insight into the current understanding of the AM deficits in patients with depressive disorders.

This paper gives new recommendations on AMT and program research design for future clinical implications.
Women's experiences following severe perineal trauma: a meta‐ethnographic synthesis
Authors: Priddis Holly , Dahlen Hannah , Schmied Virginia
Published: October 2012

Aims

This article presents a meta‐ethnographic synthesis of studies on women's experiences of sustaining a third or fourth degree tear during childbirth.

Background

It has been reported that for women who sustain third or fourth degree perineal tears (severe perineal trauma) some may experience extensive physical and psychological outcomes.

Design

A meta‐ethnographic synthesis.

Data sources

The CINAHL, PubMed, Scopus, MD Consult, and SocIndex with Full Text databases were searched for the period January 1996–June 2011. Out of 478 papers retrieved four met the review aim.

Review methods

A meta‐ethnographic synthesis approach was undertaken using analytic strategies and theme synthesis techniques of reciprocal translation and refutational investigation. Quality appraisal was undertaken using the Critical Appraisal Skills Programme (CASP) tool.

Findings

Four qualitative papers were included, with three major themes identified: ‘I am broken and a failure’, ‘Dismissed, devalued and disregarded’, and ‘The practicalities of the unpredictable perineum’.

Conclusion

There is evidence to suggest that for women who experience severe perineal trauma during childbirth the physical and psychological outcomes can be complex, with some women experiencing social isolation and marginalization due to their ongoing symptomatology. Severe perineal trauma appeared to affect not only physiological and psychological well‐being but also altered the women's understanding of their identity as sexual beings. Health professionals should be mindful of the language that they use and their actions during suturing and the postpartum period to avoid causing unnecessary distress.
Selection, optimization, and compensation in nursing: exploration of job‐specific strategies, scale development, and age‐specific associations to work ability
Authors: Müller Andreas , Weigl Matthias , Heiden Barbara , Herbig Britta , Glaser Jürgen , Angerer Peter
Published: October 2012

Aims

(1) To explore ‘successful ageing’ strategies in terms of selection, optimization and compensation in nursing; (2) To develop a scale that measures these strategies in nursing; (3) To investigate the association between these strategies in nursing and work ability of nurses and the moderating effects of age on this relationship.

Background

Studies indicate impaired work ability of older nurses. Research is needed to examine if ‘successful ageing’ strategies can promote the work ability especially in older nurses.

Design

The investigation applied a mixed method design: Study (1) Semi‐structured interviews were conducted to explore selection, optimization and compensation in nursing; (Study 2) A cross‐sectional survey was used to test the association between selection, optimization and compensation in nursing and work ability.

Methods

Data were collected in 2010 and 2011. Study 1: 17 nurses ≥45 years were interviewed; Study 2: 438 nurses (21–63 years) participated. A selection, optimization and compensation‐in‐nursing‐scale was applied that was developed on the basis of study 1. Work ability was measured with the Work Ability Index (Dimension 1).

Results

Study 1, the majority of reported ageing strategies were identified as selection, optimization and compensation in nursing. Study 2, selection, optimization, and compensation in nursing was positively related with work ability. The positive relationship was stronger for older nurses.

Conclusion

Selection, optimization and compensation in nursing contributes positively to work ability, particularly in older nurses. This finding is relevant for the development of measures that promote work ability of nurses over the course of their professional careers.
Functional recovery of older people with hip fracture: does malnutrition make a difference?
Authors: Li Hsiao‐Juan , Cheng Huey‐Shinn , Liang Jersey , Wu Chi‐Chuan , Shyu Yea‐Ing Lotus
Published: October 2012

Aim

To report a study of the effects of protein‐energy malnutrition on the functional recovery of older people with hip fracture who participated in an interdisciplinary intervention.

Background

It is not clear whether protein‐energy malnutrition is associated with worse functional outcomes or it affects the interdisciplinary intervention program on the functional recovery of older people with hip fracture.

Design

A randomized experimental design.

Methods

Data were collected between 2002–2006 from older people with hip fracture (N = 162) in Taiwan. The generalized estimating equations approach was used to evaluate the effect of malnutrition on the functional recovery of older people with hip fracture.

Results

The majority of older patients with hip fracture were malnourished (48/80, 60% in the experimental group vs. 55/82, 67% in the control group) prior to hospital discharge. The results of the generalized estimating equations analysis demonstrated that subjects suffering from protein‐energy malnutrition prior to hospital discharge appeared to have significantly worse performance trajectories for their activities of daily living, instrumental activities of daily living, and recovery of walking ability compared with those without protein‐energy malnutrition. In addition, it was found that the intervention is more effective on the performance of activities of daily living and recovery of walking ability in malnourished patients than in non‐malnourished patients.

Conclusion

Healthcare providers should develop a nutritional assessment/management system in their interdisciplinary intervention program to improve the functional recovery of older people with hip fracture.
The influence of the location of the lesion on the absolute risk of the development of skin cancer in a patient with actinic keratosis
Authors: Smit P. , Plomp E. , Neumann H.A.M. , Thio H.B.
Published: October 2012

The objective of this paper is to answer the clinical question whether the location of the lesion in an individual patient with actinic keratosis (AK) influences the absolute risk of the development of skin cancer. Between 0.025% and 16% of AK lesions advance towards squamous cell carcinoma per year. It is not well known whether this risk differs between locations on the body. A systematic search of available literature resulted in seven articles of which the two highest scoring on relevance and validity were selected. These two studies indicate that the absolute risk on the development of skin cancer in patients with AK differs between locations of the lesion and that time to progression from AK to squamous cell carcinoma is not different among the locations of the lesions. However, both studies have very limited sample sizes.
Efficacy and safety of diphenylcyclopropenone among Chinese patients with steroid resistant and extensive alopecia areata
Authors: Luk N.M. , Chiu L.S. , Lee K.C. , Chau C.T.S. , Lee V.W.Y. , Chang M. , Lam Y.K. , Lee H.C.
Published: October 2012

Background  Topical immunotherapy has recently been found useful in the treatment of chronic and extensive Alopecia Areata (AA).

Objective  To evaluate the efficacy and safety of diphenylcyclopropenone (DPCP) use among Chinese patients with steroid resistant and extensive AA in our institute.

Methods  The medical records of 31 Chinese patients treated with DPCP were analysed retrospectively. The efficacy, adverse effects, and relapse rate of DPCP treatment were reviewed.

Results  Thirty‐one (16 male, 15 female) Chinese patients with extensive, steroid resistant Alopecia Areata and a mean age of 28.9 years (SE 10.4) were treated. The mean age of onset was 17.8 years (SE 8.8) with an average disease duration of 11.2 years (SE 7.7). Ten patients had a history of atopy and 4 had a history of thyroid disease. Nail changes were found in 14 patients and a family history of AA was found in 2 patients. Thirteen patients (41.9%) had experienced total hair loss. Two patients abandoned the treatment due to severe side effects. Of the remaining 29 patients, 4 (13.8%), 7 (24.1%), 5 (17.2%), and 13 (44.8%) achieved >90% complete response, >50–90% partial response, >10–50% minimal response, and <10% no response hair regrowth, respectively. Adverse effects included pruritus, erythema, vesiculation, scaling, cervical lymphadenopathy, dyspigmentation and urticarial reactions. Relapse occurred (>25% hair loss) in 69.23% of patients after 18 months of follow up.

Conclusions  DPCP is an effective and tolerable treatment for Chinese patients with extensive, steroid resistant AA.
Sensory and Physicochemical Properties of Sweet Potato Chips Made by Vacuum‐Belt Drying
Authors: Xu Suxuan , Pegg Ronald B. , Kerr William L.
Published: October 2012

Sweet potato chips were produced by vacuum‐belt drying and compared to deep‐fat fried (DFF) chips. Two thicknesses (0.8 and 1.5 mm) and four drying temperatures (100, 120, 140C and mixed temperature [T‐mix] = 100/120/140C) were investigated. Vacuum‐belt dried (VBD) chips exhibited a similar texture to those DFF while maintaining their natural color and β‐carotene content. T‐mix chips were found to have the greatest likability. VBD products prepared at the lower temperatures maintained L* C* h values closest to unprocessed sweet potatoes. Environmental scanning electron microscopy micrographs demonstrated that T‐mix chips possessed the most uniform cell structure. VBD chips prepared at the T‐mix conditions, along with DFF chips, had the lowest degree of hardness but exhibited high fracturability. The former gave a hardness of 504.7 g force with 7.75 fracture peaks, while the latter had a hardness of 500.6 g force and 9.25 fracture peaks. VBD chips manufactured at the lower temperatures retained 55.5 to 65.9% of the sweet potato's β‐carotene content, while those prepared at 140C or by frying retained only 33.1 to 34.2%.

Practical Applications

Sweet potatoes are a major world food crop, and a valuable source of carotenoids, vitamin C and dietary fiber. Drying and other thermal processes have been employed to preserve sweet potatoes and to convert them into an ingredient form that is convenient for use in food products. Furthermore, there has been a rising demand for low‐fat, healthy fruit‐ and vegetable‐based snack items. This study examines the applicability of relatively low‐temperature vacuum drying as a process to remove water without substantially altering the vegetable's phytonutrients, yet, can create a structure that produces crispness. Vacuum‐belt drying at 100–120C, or at a specific temperature combination, can yield sweet potato chips that are crisp, have good color, retain a marked quantity of β‐carotene and are well‐liked by consumers.
APP independent and dependent effects on neurite outgrowth are modulated by the receptor associated protein (RAP)
Authors: Billnitzer Andrew J. , Barskaya Irina , Yin Cailing , Perez Ruth G.
Published: October 2012

Amyloid precursor protein (APP) and its secreted form, sAPP, contribute to the development of neurons in hippocampus, a brain region critical for learning and memory. Full‐length APP binds the low‐density lipoprotein receptor‐related protein (LRP), which stimulates APP endocytosis. LRP also contributes to neurite growth. Furthermore, the receptor associated protein (RAP) binds LRP in a manner that blocks APP–LRP interactions. To elucidate APP contributions to neurite growth for full‐length APP and sAPP, we cultured wild type (WT) and APP knockout (KO) neurons in sAPPα and/or RAP and measured neurite outgrowth at 1 day in vitro. Our data reveal that WT neurons had less axonal outgrowth including less axon branching. RAP treatment potentiated the inhibitory effects of APP. KO neurons had significantly more outgrowth and branching, especially in response to RAP, effects which were also associated with ERK2 activation. Our results affirm a major inhibitory role by full‐length APP on all aspects of axonal and dendritic outgrowth, and show that RAP–LRP binding stimulated axon growth independently of APP. These findings support a major role for APP as an inhibitor of neurite growth and reveal novel signaling functions for LRP that may be disrupted by Alzheimer's pathology or therapies aimed at APP processing.
Improvement in patients with a TMD‐pain report. A 6‐month follow‐up study
Authors: Rollman A. , Visscher C. M. , Gorter R. C. , Naeije M.
Published: October 2012

Even though chronic TMD pain tends to persist in most patients, some chronic patients show improvement. It is largely unknown which factors contribute to the improvement of chronic pain. The aim of this study is to investigate which factors, from a biopsychosocial perspective, help to predict improvement in patients with a report of TMD pain. Methods: Subjects with a report of TMD pain were recruited in seven TMD clinics. They received a baseline questionnaire which included a wide range of possible predictors for improvement. After 6 months they received a follow‐up questionnaire which included a measure to determine which participants were ‘improved’ or ‘not improved’. To study which predictive variables were associated with improvement, multiple regression models were built. Results: From the 129 patients who responded to the baseline questionnaire, 100 patients also filled in the follow‐up questionnaire (85% women, mean age (years) ± s.d. = 46·0 ± 13·8). Fifty percentage of these subjects had improved at the 6‐month follow‐up. Pain duration was the strongest (negative) predictor for 6‐month improvement (P = 0·009). Also the number of care providers (P = 0·017) and the degree of hindrance on function (P = 0·045) helped to predict improvement. Conclusions: The duration of the TMD‐pain complaint, the number of care practitioners attended and the degree of hindrance on function (negatively) helped to predict 6‐month improvement. No evidence is found to support the role of psychological or social factors on the improvement in patients with a report of TMD pain.
Identification and Molecular Characterization of Nocardia sp. as a New Causal Agent of Tobacco False Broomrape
Authors: Morán Yunior , Chacón Osmani , Córdoba‐Sellés Maria del Carmen , Domínguez‐Larrinaga Rosario , Herrera Lidcay , Borrás‐Hidalgo Orlando
Published: October 2012

Tobacco false broomrape disease is a serious problem in tropical countries. To identify its cause, experiments were conducted in tobacco fields. Six actinomycete strains were isolated from white succulent outgrowths of tobacco roots and their pathogenicity was confirmed by biological testing. Based on phenotypic and 16S rRNA gene sequence BLAST analysis, the strains were identified as members of the genus Nocardia. This association was also confirmed by secA1 gene phylogenetic analysis. This is the first report of Nocardia sp. as the cause of tobacco false broomrape.
One‐step Multiplex RT‐PCR for Simultaneous Detection of Four Viruses in Tobacco
Authors: Zhang Junqi , Wang Ran , Song Jizhen , Luo Zhaopeng , Yang Jun , Lin Fucheng
Published: October 2012

A one‐step multiplex RT‐PCR method has been developed for the simultaneous detection of four viruses frequently occurring in tobacco (Cucumber mosaic virus, Tobacco mosaic virus, Tobacco etch virus and Potato virus Y). Four sets of specific primers were designed to work with the same reaction reagents and cycling conditions, resulting in four distinguishable amplicons representative of the four viruses independently. This one‐step multiplex RT‐PCR is consistently specific using different combinations of virus RNA as templates, and no non‐specific band was observed. It has high sensitivity compared to single RT‐PCR. Moreover, field samples in China can be tested by this method for virus detection. Our results show that one‐step multiplex RT‐PCR is a high‐throughput, specific, sensitive method for tobacco virus detection.
Effect of concentration and addition method of glycerol on the quality of cryopreserved mithun (Bos frontalis) spermatozoa
Authors: Baruah K. K. , Dhali A. , Mech A. , Bora B. , Das J. , Bora R. , Mondal M. , Sarmah B. C. , Deka B. C. , Rajkhowa C.
Published: October 2012

The effect of concentration and addition method of glycerol on the quality of cryopreserved mithun (Bos frontalis) spermatozoa was investigated. Semen samples were collected from five healthy mithun bulls through rectal massage method and cryopreserved in liquid nitrogen. The samples were diluted in Tris–egg yolk–glycerol extender, equilibrated for 4 h at 4 °C and loaded into 0.50‐ml straws. The straws were then frozen in liquid nitrogen vapour for 10 min and finally plunged into liquid nitrogen for storage. The required amount of glycerol was added into the diluted samples either in a single dose (3%, 4%, 5%, 6% or 7%; added at 37 °C immediately before equilibration) or in split doses (5%, 6% or 7%; the total amount was divided into four equal parts, and a part was added at 37 °C immediately before equilibration, and the remaining parts were added subsequently at 1, 2 and 3 h of equilibration at 4 °C). In the single‐dose addition method, following freeze‐thawing, greater (p < 0.05) motility (%) and proportion of live spermatozoa with intact acrosome (LSIA, %) in 5% glycerol (40.6 ± 1.7 and 43.4 ± 1.8 respectively) and lesser (p < 0.05) total morphological abnormalities (%) in 5% (14.1 ± 0.8) and 6% (13.7 ± 1.0) glycerol were observed compared to the other glycerol concentrations. In the split‐dose addition method, following freeze‐thawing, greater (p < 0.05) motility (%) and LSIA proportion (%) were found in 5% (50.2 ± 1.9 and 53.3 ± 1.8 respectively) compared to 6% or 7% glycerol, but the total morphological abnormalities were not different among the glycerol concentrations. In addition, in all the glycerol concentrations, better (p < 0.05) post‐freeze‐thaw motility and LSIA proportions were observed when glycerol was added in split doses compared to a single dose. In conclusion, Tris–egg yolk extender with 5% glycerol added in split doses was found most suitable for cryopreserving mithun sperm.
Impact of matrix metalloproteinases on inhibition of mineralization by fetuin
Authors: Schure R. , Costa K. D. , Rezaei R. , Lee W. , Laschinger C. , Tenenbaum H. C. , McCulloch C. A.
Published: October 2012

Background and Objective

Human subjects affected by inflammatory diseases, such as periodontitis, may be at increased risk for the development of cardiovascular diseases and calcification of atheromas; however, the potential mechanisms have not been defined. Alpha‐2‐Heremans Schmid glycoprotein (fetuin A) is an abundant serum glycoprotein of ~49 kDa that inhibits ectopic arterial calcification. We examined whether matrix metalloproteinases (MMPs), which are increased in inflammatory diseases, including periodontitis, bind and degrade fetuin and alter its ability to inhibit calcification in vitro.

Material and Methods

Binding and cleavage of fetuin by MMPs were assessed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis, in‐silico analyses and mass spectrometry. The effects of intact and MMP‐degraded human fetuin on mineralization were measured in a cell‐free assay.

Results

From in‐silico analyses and literature review, we found that only MMP‐3 (stromelysin) and MMP‐7 (matrilysin) were predicted to cleave human fetuin at levels that were physiologically relevant. In‐vitro assays showed that MMP‐7, and, to a lesser extent, MMP‐3, degraded human fetuin in a time‐ and dose‐dependent manner. Fetuin peptides generated by MMP‐7 cleavage were identified and sequenced by mass spectrometry; novel cleavage sites were found. Hydroxyapatite mineralization in vitro was strongly inhibited by fetuin (> 1 μm), as was MMP‐3‐cleaved fetuin, while MMP‐7‐cleaved fetuin was threefold less effective in blocking mineralization.

Conclusion

MMP‐7 and, to a lesser extent, MMP‐3, affect the ability of fetuin to inhibit the formation of hydroxyapatite in vitro. These data suggest that the MMPs increased in inflammatory diseases, such as periodontitis, could affect regulation of mineralization and potentially enhance the risk of calcified atheroma formation.
Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick‐lippedMidas cichlid fishes fromNicaragua
Authors: Manousaki Tereza , Hull Pincelli M. , Kusche Henrik , Machado‐Schiaffino Gonzalo , Franchini Paolo , Harrod Chris , Elmer Kathryn R. , Meyer Axel
Published: October 2012

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips inMidas cichlid fishes (theAmphilophus citrinellusspecies complex)—from two Great Lakes and two crater lakes inNicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next‐generation sequencing technology, we characterize transcriptome‐wide differential gene expression in the lips of wild‐caught sympatric thick‐ and thin‐lipped cichlids from all four instances of repeated thick‐lip evolution. Six genes (apolipoproteinD, myelin‐associated glycoprotein precursor, four‐and‐a‐halfLIMdomain protein 2, calpain‐9, GTPaseIMAPfamily member 8‐like and one hypothetical protein) are significantly underexpressed in the thick‐lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake‐specific pattern, including the magnitude of differentially expressed genes (97‐510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the olderGreatLakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in theGreatLakeNicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick‐ and thin‐lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism
Authors: Sato Hirotoshi , Tsujino Riyou , Kurita Kazuki , Yokoyama Kazumasa , Agata Kiyokazu
Published: October 2012

Microbes are usually believed to have cosmopolitan distributions. However, for estimating the global distributions of microorganisms, discriminating among cryptic species and eliminating undersampling biases are important challenges. We used a novel approach to address these problems and infer the global distribution of a given fungal ecological guild. We collected mushroom‐forming fungi from Yakushima, Japan. We sequenced the internal transcribed spacer 2 (ITS2) from these samples and queried their sequences against GenBank. After identifying similar sequences, we tracked down the geographical origins of samples that yielded those sequences. We used Bayesian zero‐inflated models to allow for species whose DNA sequences have not yet been deposited in GenBank. Results indicated that the geographical distribution of ectomycorrhizal (ECM) fungi was strongly constrained by host specificity, resulting in the occurrence of these fungi intensively in the neighbouring regions. On the other hand, saprotrophic (SAP) fungi were less constrained by climatic conditions, resulting in a much broader distribution range. We inferred that differences in constraints during colonization between ECM and SAP fungi were responsible for the different geographical distribution ranges. We hypothesize that the degree of host/habitat specificity and the degree of isolation of potentially suitable habitats determine microbial biogeographic patterns.
Natural selection maintains a single‐locus leaf shape cline in Ivyleaf morning glory, Ipomoea hederacea
Authors: Campitelli Brandon E. , Stinchcombe John R.
Published: October 2012

Clines in phenotypic traits with an underlying genetic basis potentially implicate natural selection. However, neutral evolutionary processes such as random colonization, spatially restricted gene flow, and genetic drift could also result in similar spatial patterns, especially for single‐locus traits because of their susceptibility to stochastic events. One way to distinguish between adaptive and neutral mechanisms is to compare the focal trait to neutral genetic loci to determine whether neutral loci demonstrate clinal variation (consistent with a neutral cline), or not. Ivyleaf morning glory, Ipomoea hederacea, exhibits a latitudinal cline for a Mendelian leaf shape polymorphism in eastern North America, such that lobed genotypes dominate northern populations and heart‐shaped genotypes are restricted to southern populations. Here, we evaluate potential evolutionary mechanisms for this cline by first determining the allele frequencies at the leaf shape locus for 77 populations distributed throughout I. hederacea's range and then comparing the geographical pattern at this locus to neutral amplified fragment length polymorphism (AFLP) loci. We detected both significant clinal variation and high genetic differentiation at the leaf shape locus across all populations. In contrast, 99% of the putatively neutral loci do not display clinal variation, and I. hederacea populations show very little overall genetic differentiation, suggesting that there is a moderate level of gene flow. In addition, the leaf shape locus was identified as a major FST outlier experiencing divergent selection, relative to all the AFLP loci. Together, these data strongly suggest that the cline in leaf shape is being maintained by spatially varying natural selection.
Role of ATP binding and hydrolysis in assembly of MacAB–TolC macrolide transporter
Authors: Lu Shuo , Zgurskaya Helen I.
Published: October 2012

MacB is a founding member of the Macrolide Exporter family of transporters belonging to the ATP‐Binding Cassette superfamily. These proteins are broadly represented in genomes of both Gram‐positive and Gram‐negative bacteria and are implicated in virulence and protection against antibiotics and peptide toxins. MacB transporter functions together with MacA, a periplasmic membrane fusion protein, which stimulates MacB ATPase. In Gram‐negative bacteria, MacA is believed to couple ATP hydrolysis to transport of substrates across the outer membrane through a TolC‐like channel. In this study, we report a real‐time analysis of concurrent ATP hydrolysis and assembly of MacAB–TolC complex. MacB binds nucleotides with a low millimolar affinity and fast on‐ and off‐rates. In contrast, MacA–MacB complex is formed with a nanomolar affinity, which further increases in the presence of ATP. Our results strongly suggest that association between MacA and MacB is stimulated by ATP binding to MacB but remains unchanged during ATP hydrolysis cycle. We also found that the large periplasmic loop of MacB plays the major role in coupling reactions separated in two different membranes. This loop is required for MacA‐dependent stimulation of MacB ATPase and at the same time, contributes to recruitment of TolC into a trans‐envelope complex.
Comparative genotyping of Streptococcus mutans by repetitive extragenic palindromic polymerase chain reaction and multilocus sequence typing
Authors: Momeni S.S. , Whiddon J. , Moser S.A. , Cheon K. , Ruby J.D. , Childers N.K.
Published: October 2012

The genetic diversity of Streptococcus mutans has been extensively studied using a variety of genotyping methods. Repetitive extragenic palindromic‐polymerase chain reaction (rep‐PCR) is a genotyping approach used for screening large numbers of bacterial isolates. This two‐part study used multilocus sequence typing (MLST) analysis to evaluate genotypes previously identified as unique using rep‐PCR. In part one, an isolate was selected from each of the 22 S. mutans rep‐PCR genotype groups representing 8000 clinical isolates. For part two, four additional isolates were selected from the six most commonly occurring genotype groups (GG) for further analysis. Real‐time PCR was performed using eight housekeeping S. mutans gene loci and the amplicons were sequenced. Sequence data analysis was performed using CLC DNA Workbench and alleles were compared with the PubMLST database for Oral Streptococcus using the Nakano scheme. Concatenated sequences were evaluated with MEGA using a minimum evolution method with bootstrap. All 22 rep‐PCR genotypes were unique by MLST analysis. Within rep‐PCR GGs, MLST matched rep‐PCR in three groups demonstrating clonality; three groups exhibited more diversity with MLST. The discovery of three clonal groups is unique to this study and suggests that S. mutans genotypes are shared between unrelated subjects. Furthermore, MLST defined 19 new alleles and 26 new sequence types that have been confirmed and registered with PubMLST. Methods for processing were streamlined and a process for using MLST with rep‐PCR is suggested. In conclusion, MLST verified that rep‐PCR is a reliable and cost‐effective method for screening large numbers of S. mutans strains for epidemiological study.
Electrochemical detection of extracellular hydrogen peroxide in Arabidopsis thaliana: a real‐time marker of oxidative stress
Authors: GONZÁLEZ‐SÁNCHEZ M. I. , GONZÁLEZ‐MACIA L. , PÉREZ‐PRIOR M. T. , VALERO E. , HANCOCK J. , KILLARD A. J.
Published: October 2012

An electrochemical approach to directly measure the dynamic process of H2O2 release from cultures of Arabidopsis thaliana cells is reported. This approach is based on H2O2 oxidation on a Pt electrode in conjunction with continuous measurement of sample pH. For [H2O2] <1 mm, calibration plots were linear and the amperometric response of the electrode was maximum at pH 6. At higher concentrations ([H2O2] >1 mm), the amperometric response can be described by Michaelian‐type kinetics and a mathematical expression relating current intensity and pH was obtained to quantitatively determine H2O2 concentration. At pH 5.5, the detection limit of the sensor was 3.1 µm (S/N = 3), with a response sensitivity of 0.16 Am−1 cm−2 and reproducibility was within 6.1% in the range 1–5 × 10−3 m (n = 5). Cell suspensions under normal physiological conditions had a pH between 5.5–5.7 and H2O2 concentrations in the range 7.0–20.5 µm (n = 5). The addition of exogenous H2O2, as well as other potential stress stimuli, was made to the cells and the change in H2O2 concentration was monitored. This real‐time quantitative H2O2 analysis is a potential marker for the evaluation of oxidative stress in plant cell cultures.
Plant hydraulics and photosynthesis of 34 woody species from different successional stages of subtropical forests
Authors: ZHU SHI‐DAN , SONG JUAN‐JUAN , LI RONG‐HUA , YE QING
Published: October 2012

It is important to understand the ecophysiological characters of plants when exploring mechanisms underlying species substitution in the process of plant succession. In the present study, we selected 34 woody species from different stages of secondary succession in subtropical forests of southern China, and measured their hydraulic conductivity, gas exchange rates, leaf nutrients and drought‐tolerance traits such as xylem resistance to cavitation, turgor loss point and carbon isotope ratio. Principal component analysis revealed that early‐, mid‐ and late‐successional species were significantly separated along axis 1, which was strongly associated with hydraulic‐photosynthetic coordination. In contrast to species distributed in late‐successional forest, early‐successional species had the highest hydraulic conductivity, net photosynthetic rates, photosynthetic nitrogen and phosphorus use efficiencies, but had the lowest photosynthetic water‐use efficiency. However, changes of the measured drought‐tolerance traits of the 34 species along the succession did not demonstrate a clear trend – no significant correlations between these traits and plant successional stages were found. Moreover, the trade‐off between hydraulic efficiency and safety was not identified. Taken together, our results suggested that hydraulic efficiency and photosynthetic function, rather than drought tolerance, play an important role in species distributions along plant succession in subtropical forests.
Comparison of Different Glycerol and Egg Yolk Concentrations Added toTris‐based Extender for the Collared Peccaries (Tayassu tajacu) Semen Freezing
Authors: Alves HM , Oliveira IRS , Castelo TS , Lima GL , Souza ALP , Moreira MAP , de Paula VV , Silva AR
Published: October 2012

Contents

This study aimed to evaluate various concentrations of egg yolk (5, 10, or 20%) in combination with different concentrations of glycerol (3% or 6%) added to aTris‐based extender on the post‐thaw characteristics of sperm obtained fromTayassu tajacu. For this purpose, semen from 10 sexually male mature collared peccaries was collected by electroejaculation and evaluated for sperm motility, vigour, viability, morphology and functional membrane integrity. The ejaculates were initially extended inTris‐fructose plus egg yolk (5%, 10% or 20%). After cooling, the semen was added toTris‐egg yolk plus glycerol (6% or 12%), resulting in a final concentration of 3% or 6% glycerol of the extender. Straws were frozen using liquid nitrogen and thawed in a water bath at 37°C for 30 s. The frozen–thawed semen was evaluated as reported for fresh semen. After thawing, a significant decrease was verified for sperm motility and vigour, for all the samples in comparison with fresh semen. However, no differences were evidenced among treatments for any sperm characteristics evaluated (p > 0.05), except for the combination between 10% egg yolk and 6% glycerol, which provided the worst preservation of functional membrane integrity (p < 0.05). The interactions between higher concentrations of egg yolk (20%) and glycerol (6%) and also between lower concentrations of the same substances (5% egg yolk and 3% glycerol) added to the Tris‐based extender negatively affected the preservation of the normal sperm morphology after thawing (p < 0.05). In conclusion, the use of Tris‐based extender added to 10% or 20% egg yolk plus 3% glycerol is recommended for effective sperm cryopreservation in collared peccaries.
Dolomite formation in the shallow seas of the Alpine Triassic
Authors: Meister Patrick , Mckenzie Judith A. , Bernasconi Stefano M. , Brack Peter
Published: October 2012

The Alpine Triassic units of Switzerland, Northern Italy and Western Austria offer an extensive geological archive, in which the enigmatic process of dolomite formation can be studied in a palaeoenvironmental context. Recent studies clearly demonstrate that large amounts of the Alpine Triassic dolomites are late diagenetic or hydrothermal. Nevertheless, as part of multiple generations of diagenetic overprint, some generations of fine‐crystalline, Ca‐rich dolomite appear strictly confined to their depositional facies and show signs of very early formation at surface temperatures in specific ancient depositional environments. In this review, three cases of Alpine Triassic dolomites are discussed, where dolomite rocks may have formed during or soon after sedimentation. The sedimentary facies indicate contrasting palaeoenvironmental conditions and, hence, document three different possible processes of dolomite formation: (i) In the Dolomite Mountains (Northern Italy), dolomite beds of the partly isolated Middle Triassic (Anisian/Ladinian) Latemar Platform are confined to the very top of shallowing‐upward lagoonal facies cycles. (ii) Dolomite beds of the San Giorgio Basin (Southern Switzerland), an intra‐platform basin that opened during the Anisian/Ladinian transition, are associated with organic carbon‐rich shales, which were deposited in a deeper water environment under anoxic conditions. (iii) In the entirely dolomitized platform facies of the Dolomia Principale (Hauptdolomit Formation), a very early generation of fine‐crystalline dolomite occurs in the shallowest part of evaporative peritidal cycles. This platform extended over thousands of square kilometres along the Tethys margin during the Late Triassic (Carnian and Norian) and large amounts of carbonate were deposited under hypersaline sabkha‐like conditions. Representing three distinct depositional environments, these three different Triassic systems show features in common with several dolomitization models developed from the study of modern dolomite‐forming environments; for example, the sabkha model, the evaporative lagoon/lake model, the organogenic model and the microbial model. Although these actualistic models may be applicable to reconstruct the palaeoenvironmental conditions during dolomite formation, dolomite‐forming processes during the Triassic were apparently quite different from the modern world in terms of distribution and scale. Recent developments in stable‐isotope geochemistry and high‐resolution geochemical probing offer the possibility to make better reconstructions of Triassic palaeoceanographic conditions and suggest a non‐actualistic approach to better understand dolomite formation during the Triassic.
Beyond Welfare Regimes: From Empirical Typology to Conceptual Ideal types
Authors: Rice Deborah
Published: October 2012

The welfare regime concept introduced byGøstaEsping‐Andersen in 1990 is still widely used in comparative political research, although it has been challenged extensively both on empirical and analytical grounds. Besides the fact that many empirical welfare states seem to be hybrid cases of the established welfare regime categories, the argument that welfare regimes exist not only at the country level but also at the local level and at the level of particular welfare programmes has recently gained momentum in the academic literature. In this article, it is argued that the welfare regime concept should be stripped of its historical‐geographical connotations and turned into an ideal‐typical approach. To this end, a three‐dimensional model is proposed here that allows for analyzing the attributes of welfare states, welfare regions and welfare programmes on three analytical dimensions: welfare culture, welfare institutions and socio‐structural effects.
Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates, and cooperates with polynucleotide phosphorylase in 3′ end maturation
Authors: Germain Arnaud , Kim Sang Hu , Gutierrez Ryan , Stern David B.
Published: October 2012

Ribonuclease R (RNR1) and polynucleotide phosphorylase (cpPNPase) are the two known 3′→5′ exoribonucleases in Arabidopsis chloroplasts, and are involved in several aspects of rRNA and mRNA metabolism. In this work, we show that mutants lacking both RNR1 and cpPNPase exhibit embryo lethality, akin to the non‐viability of the analogous double mutant in Escherichia coli. We were successful, however, in combining an rnr1 null mutation with weak pnp mutant alleles, and show that the resulting chlorotic plants display a global reduction in RNA abundance. Such a counterintuitive outcome following the loss of RNA degradation activity suggests a major importance of RNA maturation as a determinant of RNA stability. Detailed analysis of the double mutant demonstrates that the enzymes catalyze a two‐step maturation of mRNA 3′ ends, with RNR1 polishing 3′ termini created by cpPNPase. The bulky quaternary structure of cpPNPase compared with RNR1 could explain this activity split between the two enzymes. In contrast to the double mutants, the rnr1 single mutant overaccumulates most mRNA species when compared with the wild type. The excess mRNAs in rnr1 are often present in non‐polysomal fractions, and half‐life measurements demonstrate a substantial increase in the stability of most mRNA species tested. Together, our data reveal the cooperative activity of two 3′→5′ exoribonucleases in chloroplast mRNA 3′ end maturation, and support the hypothesis that RNR1 plays a significant role in the destabilization of mRNAs unprotected by ribosomes.
Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana
Authors: Degenkolbe Thomas , Giavalisco Patrick , Zuther Ellen , Seiwert Bettina , Hincha Dirk K. , Willmitzer Lothar
Published: October 2012

Freezing injury is a major factor limiting the geographical distribution of plant species and the growth and yield of crop plants. Plants from temperate climates are able to increase their freezing tolerance during exposure to low but non‐freezing temperatures in a process termed cold acclimation. Damage to cellular membranes is the major cause of freezing injury in plants, and membrane lipid composition is strongly modified during cold acclimation. Forward and reverse genetic approaches have been used to probe the role of specific lipid‐modifying enzymes in the freezing tolerance of plants. In the present paper we describe an alternative ecological genomics approach that relies on the natural genetic variation within a species. Arabidopsis thaliana has a wide geographical range throughout the Northern Hemisphere with significant natural variation in freezing tolerance that was used for a comparative analysis of the lipidomes of 15 Arabidopsis accessions using ultra‐performance liquid chromatography coupled to Fourier‐transform mass spectrometry, allowing the detection of 180 lipid species. After 14 days of cold acclimation at 4°C the plants from most accessions had accumulated massive amounts of storage lipids, with most of the changes in long‐chain unsaturated triacylglycerides, while the total amount of membrane lipids was only slightly changed. Nevertheless, major changes in the relative amounts of different membrane lipids were also evident. The relative abundance of several lipid species was highly correlated with the freezing tolerance of the accessions, allowing the identification of possible marker lipids for plant freezing tolerance.