bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA repair variants, indoor tanning, and risk of melanoma
Authors: Torres Salina M. , Luo Li , Lilyquist Jenna , Stidley Christine A. , Flores Kristina , White Kirsten A. M. , Erdei Esther , Gonzales Melissa , Paine Susan , Vogel Rachel I. , Lazovich DeAnn , Berwick Marianne 
Published: May 2013

SummaryAlthough ultraviolet radiation (UV) exposure from indoor tanning has been linked to an increased risk of melanoma, the role of DNA repair genes in this process is unknown. We evaluated the association of 92 single nucleotide polymorphisms (SNPs) in 20 DNA repair genes with the risk of melanoma and indoor tanning among 929 patients with melanoma and 817 controls from the Minnesota Skin Health Study. Significant associations with melanoma risk were identified for SNPs in ERCC4, ERCC6, RFC1, XPC, MGMT, and FBRSL1 genes; with a cutoff of P < 0.05. ERCC6 and FBRSL1 gene variants and haplotypes interacted with indoor tanning. However, none of the 92 SNPs tested met the correction criteria for multiple comparisons. This study, based on an a priori interest in investigating the role of DNA repair capacity using variants in base excision and nucleotide excision repair, identified several genes that may play a role in resolving UV‐induced DNA damage.
Interaction of small RNA–8105 and the intron of IbMYB1 RNA regulates IbMYB1 family genes through secondary siRNAs and DNA methylation after wounding
Authors: Lin Jeng‐Shane , Lin Chih‐Ching , Li Yu‐Chi , Wu Ming‐Tsung , Tsai Mong‐Hsun , Hsing Yue‐Ie C. , Jeng Shih‐Tong 
Published: May 2013

SummarySmall RNAs (sRNAs) play important roles in plants under stress conditions. However, limited research has been performed on the sRNAs involved in plant wound responses. In the present study, a novel wounding‐induced sRNA, sRNA8105, was identified in sweet potato (Ipomoea batatas cv. Tainung 57) using microarray analysis. It was found that expression of sRNA8105 increased after mechanical wounding. Furthermore, Dicer‐like 1 (DCL1) is required for the sRNA8105 precursor (pre‐sRNA8105) to generate 22 and 24 nt mature sRNA8105. sRNA8105 targeted the first intron of IbMYB1 (MYB domain protein 1) before RNA splicing, and mediated RNA cleavage and DNA methylation of IbMYB1. The interaction between sRNA8105 and IbMYB1 was confirmed by cleavage site mapping, agro‐infiltration analyses, and use of a transgenic sweet potato over‐expressing pre‐sRNA8105 gene. Induction of IbMYB1‐siRNA was observed in the wild‐type upon wounding and in transgenic sweet potato over‐expressing pre‐sRNA8105 gene without wounding, resulting in decreased expression of the whole IbMYB1 gene family, i.e. IbMYB1 and the IbMYB2 genes, and thus directing metabolic flux toward biosynthesis of lignin in the phenylpropanoid pathway. In conclusion, sRNA8105 induced by wounding binds to the first intron of IbMYB1 RNA to methylate IbMYB1, cleave IbMYB1 RNA, and trigger production of secondary siRNAs, further repressing the expression of the IbMYB1 family genes and regulating the phenylpropanoid pathway.
Performance of a clinical prediction score for thrombotic thrombocytopenic purpura in an independent cohort
Authors: Bentley M. J. , Wilson A. R. , Rodgers G. M. 
Published: May 2013

Background and ObjectivesIdiopathic thrombotic thrombocytopenic purpura (TTP) is a rare, clinically diagnosed disorder characterized by widespread intravascular platelet thrombosis. The pathophysiology involves acquired deficiency of ADAMTS13 (A disintegrin and metalloprotease with thrombospondin type 1 repeats), the enzyme responsible for cleavage of high molecular weight vonWillebrand factor multimers. Disease mortality is high, although prompt treatment with plasma exchange is generally effective. A readily available and highly reliable method of identifying ADAMTS13‐deficient patients for appropriate plasma exchange is therefore of interest.Materials and MethodsOur initial study involved the assessment of multiple clinical and laboratory variables in patients with clinically suspected TTP for whom ADAMTS13 assay was performed. Five variables were found to be of significant predictive power. This enabled the development of a point‐based scoring system to efficiently determine the likelihood of TTP and response to plasma exchange in a given patient. This current study involved a separate validation cohort of patients with clinically suspected TTP who underwent ADAMTS13 testing within two large healthcare systems in Utah between 2009 and 2011. The previously derived score was applied to this cohort and its performance was analysed. Additionally, the original and validation cohorts were combined to revisit the predictive power of individual variables and the five‐variable prediction score.ResultsA total of 84 (11 paediatric cases excluded) patients comprised the validation population. The percentage of TTP diagnoses in this group (10%) was identical to that in the initial cohort. Using an ADAMTS13 activity of <10% of normal, our original score correctly predicted or excluded severe ADAMTS13 deficiency in all patients in the second cohort when data for all variables was available. Individual variables retained predictive power and the performance of a three‐variable parsimonious model, as well as the ultimate diagnoses for patients in the second cohort are described.ConclusionThis work confirms the predictive power of a simple point‐based score to exclude TTP as evidenced by severe ADAMTS13 deficiency in appropriately selected patients. It may enable clinicians to rapidly begin plasma exchange or to pursue an alternative cause of thrombotic microangiopathy.
Potential Animal and Environmental Sources of Q Fever Infection for Humans in Queensland
Authors: Tozer S. J. , Lambert S. B. , Strong C. L. , Field H. E. , Sloots T. P. , Nissen M. D. 
Published: May 2013

SummaryQ fever is a vaccine‐preventable disease; despite this, high annual notification numbers are still recorded in Australia. We have previously shown seroprevalence in Queensland metropolitan regions is approaching that of rural areas. This study investigated the presence of nucleic acid from Coxiella burnetii, the agent responsible for Q fever, in a number of animal and environmental samples collected throughout Queensland, to identify potential sources of human infection. Samples were collected from 129 geographical locations and included urine, faeces and whole blood from 22 different animal species; 45 ticks were removed from two species, canines and possums; 151 soil samples; 72 atmospheric dust samples collected from two locations and 50 dust swabs collected from domestic vacuum cleaners. PCR testing was performed targeting the IS1111 and COM1 genes for the specific detection of C. burnetii DNA. There were 85 detections from 1318 animal samples, giving a detection rate for each sample type ranging from 2.1 to 6.8%. Equine samples produced a detection rate of 11.9%, whilst feline and canine samples showed detection rates of 7.8% and 5.2%, respectively. Native animals had varying detection rates: pooled urines from flying foxes had 7.8%, whilst koalas had 5.1%, and 6.7% of ticks screened were positive. The soil and dust samples showed the presence of C. burnetii DNA ranging from 2.0 to 6.9%, respectively. These data show that specimens from a variety of animal species and the general environment provide a number of potential sources for C. burnetii infections of humans living in Queensland. These previously unrecognized sources may account for the high seroprevalence rates seen in putative low‐risk communities, including Q fever patients with no direct animal contact and those subjects living in a low‐risk urban environment.
Pulmonary vascular mechanics: important contributors to the increased right ventricular afterload of pulmonary hypertension
Authors: Wang Zhijie , Chesler Naomi C. 
Published: May 2013

New Findings
What is the topic of this review?This article reviews pulmonary vascular and right ventricular (RV) changes due to hypoxic pulmonary hypertension (HPH), which is a type of pulmonary hypertension (PH) found clinically and has been widely used to induce PH in animal models. As research into clinical PH progression broadens to include RV as well as pulmonary vascular remodelling, an improved understanding of the effects of HPH on the RV is required.
What advances does it highlight?This article highlights the moderate, adaptive and reversible nature of RV and pulmonary vascular remodelling in HPH. Moreover, we show that increased haematocrit in HPH contributes significantly to RV overload, which warrants additional attention.
Chronic hypoxia causes pulmonary vasoconstriction and vascular remodelling, which lead to hypoxic pulmonary hypertension (HPH). Hypoxic pulmonary hypertension is associated with living at high altitudes and is a complication of many lung diseases, including chronic obstructive pulmonary disease, cystic fibrosis and obstructive sleep apnoea. Pulmonary vascular changes that occur with HPH include stiffening and narrowing of the pulmonary arteries that appear to involve all vascular cell types and sublayers of the arterial wall. Right ventricular (RV) changes that occur with HPH include RV hypertrophy and RV fibrosis, often with preserved systolic and diastolic function and ventricular–vascular coupling efficiency. Both vascular stiffening and vascular narrowing are important contributors to RV afterload via increases in oscillatory and steady ventricular work, respectively. The increased blood viscosity that occurs in HPH can be dramatic and is another important contributor to RV afterload. However, the viscosity, vascular mechanics and ventricular changes that occur with HPH are all reversible. Furthermore, even with continued hypoxia the vascular remodelling does not progress to the obliterative, plexiform lesions that are seen clinically in severe pulmonary hypertension. In animal models, the RV changes appear adaptive, not maladaptive. In summary, HPH‐induced vascular mechanical changes affect ventricular function, but both are adaptive and reversible, which differentiates HPH from severe pulmonary hypertension. The mechanisms of adaptation and reversibility may provide useful insight into therapeutic targets for the clinical disease state.
An
MSH4
Homolog,
stpp1
, from Pleurotus pulmonarius Is a “Silver Bullet” for Resolving Problems Caused by Spores in Cultivated Mushrooms
Authors: Okuda Yasuhito , Murakami Shigeyuki , Honda Yoichi , Matsumoto Teruyuki 
Published: May 2013

ABSTRACT

The enormous number of spores produced by fruiting bodies during cultivation of mushrooms can lead to allergic reactions of workers, reduction of commercial value, spread of mushroom disease, pollution of facilities, and depletion of genetic diversity in natural populations. A cultivar harboring a sporulation-deficient (sporeless) mutation would be very useful for preventing these problems, but sporeless commercial cultivars are very limited in usefulness because sporeless traits are often linked with traits that are unfavorable for commercial cultivation. Thus, identifying a causal gene of a sporeless phenotype not linked to the adverse traits in breeding and cultivation is crucial for the establishment of sporeless breeding using a strategy employing targeting induced local lesions in genomes (TILLING) in cultivated mushrooms. We used a
Pleurotus pulmonarius
(Fr.) Quél. sporeless strain to identify and characterize the single recessive gene controlling the mutation. The 3,853-bp
stpp1
gene encodes a protein of 854 amino acids and belongs to the MutS homolog (MSH) family associated with mismatch repair in DNA synthesis or recombination in meiosis. Gene expression analysis of the fruiting body showed that this gene is strongly expressed in the gills. Phenotypic analysis of disruptants formed by gene targeting suggested a reproducible sporeless phenotype. Mutants deficient in a functional copy of this gene have no unfavorable traits for sporeless cultivar breeding, so this gene will be an extremely useful target for efficient and versatile sporeless breeding in
P. pulmonarius
and various other cultivated mushrooms.
The Unfolded Protein Response in the Protozoan Parasite Toxoplasma gondii Features Translational and Transcriptional Control
Authors: Joyce Bradley R. , Tampaki Zoi , Kim Kami , Wek Ronald C. , Sullivan William J. 
Published: May 2013

ABSTRACT

The unfolded protein response (UPR) is an important regulatory network that responds to perturbations in protein homeostasis in the endoplasmic reticulum (ER). In mammalian cells, the UPR features translational and transcriptional mechanisms of gene expression aimed at restoring proteostatic control. A central feature of the UPR is phosphorylation of the α subunit of eukaryotic initiation factor-2 (eIF2) by PERK (EIF2AK3/PEK), which reduces the influx of nascent proteins into the ER by lowering global protein synthesis, coincident with preferential translation of key transcription activators of genes that function to expand the processing capacity of this secretory organelle. Upon ER stress, the apicomplexan parasite
Toxoplasma gondii
is known to induce phosphorylation of
Toxoplasma
eIF2α and lower translation initiation. To characterize the nature of the ensuing UPR in this parasite, we carried out microarray analyses to measure the changes in the transcriptome and in translational control during ER stress. We determined that a collection of transcripts linked with the secretory process are induced in response to ER stress, supporting the idea that a transcriptional induction phase of the UPR occurs in
Toxoplasma.
Furthermore, we determined that about 500 gene transcripts showed enhanced association with translating ribosomes during ER stress. Many of these target genes are suggested to be involved in gene expression, including JmjC5, which continues to be actively translated during ER stress. This study indicates that
Toxoplasma
triggers a UPR during ER stress that features both translational and transcriptional regulatory mechanisms, which is likely to be important for parasite invasion and development.
Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance
Authors: Cao Yi , Tian Baoyu , Liu Yanxia , Cai Liuti , Wang Hancheng , Lu Ning , Wang Maosheng , Shang Shenghua , Luo Zhengyou , Shi Junxiong 
Published: May 2013

ABSTRACT

Ralstonia solanacearum
strain FQY_4 was isolated from a bacterial wilt nursery, which is used for breeding crops for
Ralstonia
resistance in China. Here, we report the complete genome sequence of FQY_4 and its comparison with other published
R. solanacearum
genomes, especially with the strains GMI1000 and Y45 in the same group.
Complete Genome Sequence of a European Genotype Porcine Reproductive and Respiratory Syndrome Virus in China
Authors: Zhou Zhi , Liu Qi , Hu Dongmei , Yue Xiaojuan , Yu Xiuling , Zhang Qian , Gu Xiaoxue , Ni Jianqiang , Li Xiangdong , Zhai Xinyan , Tian Kegong 
Published: May 2013

ABSTRACT
Here, we report a novel European genotype porcine reproductive and respiratory syndrome virus (PRRSV) strain with 15 nucleotide deletions in the nonstructural protein 2 region and 3 nucleotide deletions in the overlapping regions of the open reading frame 3 (ORF3) and ORF4 regions. This study will aid in further exploration of the genetic and antigenic diversity of the European genotype of the PRRSV in China.
Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi
Authors: Passos da Silva Daniel , Devescovi Giulia , Paszkiewicz Konrad , Moretti Chiaraluce , Buonaurio Roberto , Studholme David J. , Venturi Vittorio 
Published: May 2013

ABSTRACT

Erwinia toletana
was first reported in 2004 as a bacterial species isolated from olive knots caused by the plant bacterium
Pseudomonas savastanoi
pv. savastanoi. Recent studies have shown that the presence of this bacterium in the olive knot environment increases the virulence of the disease, indicating possible interspecies interactions with
P. savastanoi
pv. savastanoi. Here, we report the first draft genome sequence of an
E. toletana
strain.
Genome Sequence of a Gamma- and UV-Ray-Resistant Strain, Deinococcus wulumuqiensis R12
Authors: Xu Xian , Jiang Ling , Zhang Zhidong , Shi Yuhu , Huang He 
Published: May 2013

ABSTRACT

Deinococcus wulumuqiensis
R12, isolated from radiation-polluted soil, is a red-pigmented strain of the extremely radioresistant genus
Deinococcus
. It contains a major carotenoid, namely, deinoxanthin. Here, we present a 3.39-Mb assembly of its genome sequence, which might provide various kinds of useful information related to
Deinococcus
, such as about the key enzymes of its radioresistance mechanism and carotenoid biosynthetic pathways.
Draft Genome Sequence of Strain JLT2015
T
, Belonging to the Family
Sphingomonadaceae
of the
Alphaproteobacteria
Authors: Tang Kai , Liu Kesao , Li Shuhui , Jiao Nianzhi 
Published: May 2013

ABSTRACT

Strain JLT2015
T
was isolated from the southeastern Pacific, as a representative of a new genus of the family
Sphingomonadaceae
of the
Alphaproteobacteria
. Here, we present the draft genome sequence of strain JLT2015
T
, which provides insight into the oligotrophic strategy of this organism.
GENE EXPRESSION OF MATRIX-DEGRADING ENZYMES IN PATELLAR TENDINOPATHY
Authors: Samiric T , Handley C J , Cook J , Parkinson J 
Published: May 2013

IntroductionA predominant feature of tendinopathy is a change in the appearance and organisation of the extracellular matrix including greater amounts of the large aggregating proteoglycans, aggrecan and versican. We have shown that in patellar tendinopathy these large proteoglycans are also rapidly degraded so that mainly fragments remain in the tissue.1 This catabolism of large proteoglycans is likely to be mediated by a number of matrix-degrading proteinases such as the matrix metalloproteinases (MMPs) and the aggrecanases (ADAMTSs).The aim of this work was to investigate whether in patellar tendinopathy there is a change in the gene expression of the matrix proteinases involved in proteoglycan catabolism including the MMPs and ADAMTSs, as well as their inhibitors, the tissue inhibitor of metalloproteinases (TIMPs).MethodsTotal mRNA isolated from ∼100mg tissue samples of normal (n=9) and pathologic (n=12) tendon was assayed by relative quantitative RT-PCR for MMP (-1, -2, -3, -9, and -13), ADAMTS (-1, -4, -5), and TIMP (-1, -2, -3, and -4), and normalised to GAPDH.ResultsExpression of mRNA for MMP-9 and TIMP-1 was significantly up-regulated in pathologic tendons (p=0.019 and p=0.013, respectively). A trend toward a down-regulation of expression of MMP-3 was observed in pathologic tendons (p=0.06). There were no significant changes in ADAMTS-1, -4, or -5 gene expressions.DiscussionThese results suggest that the elevated expression of MMP-9 and TIMP-1 genes is likely to reflect the changes in collagen metabolism in pathologic tendons. However, these results also suggest that the proteolysis of proteoglycans in the pathologic tendons is not likely to be affected at the gene expression level of proteinases and their inhibitors. These observations are consistent with others, who showed no difference in the expression of ADAMTS-1, -4, and -5 genes between human Achilles tendons with chronic pain and normal tendons.2 3 Therefore, it is likely that proteoglycan catabolism is elevated by the activation of ADAMTSs and possibly MMPs and not by increased gene expression. This activation may be driven by growth factors and cytokines such as IL-1α, TGF-β and TNF-α, which are shown to be increased in overuse tendinopathy. However, the details of the mechanisms of these regulatory processes warrant further investigation.
FULL-THICKNESS SUPRASPINATUS TEARS DEMONSTRATE SIGNIFICANT DETERIORATION OF MUSCLE REGENERATIVE POTENTIAL
Authors: Lundgreen K , Lian Ø , Scott A , Engebretsen L 
Published: May 2013

IntroductionRotator cuff tendinopathy is a significant source of musculoskeletal disability. Accompanying muscle changes may be important determinants of the prognosis. The aim of this study was to compare histological muscle changes in partial-thickness to full-thickness tears of the supraspinatus tendon.MethodsMuscle biopsies of nine partially torn and 15 fully torn supraspinatus tendons were compared histologically. H&E staining was performed to assess degenerative changes. Immunohistochemistry was used to assess slow and fast myosin heavy chains (type I and II fibres; Anti-slow skeletal myosin heavy chain antibody and Anti-fast skeletal myosin heavy chain antibody), satellite cells (CD56), proliferation (Ki67) and apoptotic cells (activated caspase-3; Asp175).ResultsFull-thickness tears demonstrated significant atrophy of both slow (type I) and fast (type II) myosin heavy chains compared to partial tears. The area ratio of type II to type I was doubled in full-thickness tears. Partial thickness tears revealed significantly more satellite cells and proliferative activity than full-thickness tears. There was no detectable apoptosis using an antibody recognising active caspase-3.DiscussionProgression of rotator cuff tendinopathy is accompanied by a change in muscle fibre phenotype from endurance type I fibres to type II fibres more prone to fatigue, illustrating an aspect of muscle disuse. The rotator cuff muscle's ability to regenerate appears to be reduced when a full-thickness tear is established. Apoptosis does not appear to be of importance in muscle changes accompanying rotator cuff tendinopathy.
ULTRASOUND-GUIDED PERCUTANEOUS ASPIRATION IN CALCIFYING TENDINITIS OF THE SHOULDER
Authors: López J S S , Pazos F B , Valero A R , Silván D M , Jaén T F F 
Published: May 2013

IntroductionTendinopathy is a common pathology; calcifying tendinitis of the shoulder is less frequent and there are controversies regarding its treatment. The aim was to study the short-term efficiency of ultrasound-guided percutaneous aspiration in patients with calcifying tendinitis of the shoulder, and compare the results with other treatment techniques. The second aim was to study the shape of the acromion in calcifying tendinitis and correlate this with the shape of the acromion in the general population.Method13 patients diagnosed with calcifying tendinitis of the shoulder were treated using an ultrasound and radiology study. They underwent the Constant and Oxford questionnaire to assess shoulder pain and function. The technique employed was ultrasound-guided percutaneous aspiration. Two groups were formed: group 1 with the aspirated patients; group 2 with patients in which calcification was fragmented. The patients were monitored after 1 month and 3 months from commencement of treatment.ResultsThe treated patients consisted of seven men and six women, aged between 40 and 57. In the functional assessment of the shoulder prior to treatment and 3 months following treatment, the difference in the Constant score was 58.69 points and 17.38 points in the Oxford score. The differences were statistically significant (p=0.001) for both scores. In the clinical assessment and in the decrease of calcification, better results are obtained in the group that had the calcium deposits aspirated, compared to the other group where calcification was fragmented.DiscussionPatients that had calcification removed had better clinical results than patients that did not. Ultrasound-guided percutaneous aspiration is a good treatment.