bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic association of OPRgenes with resistance to Hessian fly in hexaploid wheat
Authors: Tan Chor Tee , Carver Brett F , Chen Ming-Shun , Gu Yong-Qiang , Yan Liuling 
Published: June 2013

AbstractBackgroundHessian fly (Mayetiola destructor) is one of the most destructive pests of wheat. The genes encoding 12-oxo-phytodienoic acid reductase (OPR) and lipoxygenase (LOX) play critical roles in insect resistance pathways in higher plants, but little is known about genes controlling resistance to Hessian fly in wheat.ResultsIn this study, 154 F6:8recombinant inbred lines (RILs) generated from a cross between two cultivars, ‘Jagger’ and ‘2174’ of hexaploid wheat (2n = 6 × =42; AABBDD), were used to map genes associated with resistance to Hessian fly. Two QTLs were identified. The first one was a major QTL on chromosome 1A (QHf.osu-1A), which explained 70% of the total phenotypic variation. The resistant allele at this locus in cultivar 2174 could be orthologous to one or more of the previously mapped resistance genes (H9,H10,H11,H16, andH17) in tetraploid wheat. The second QTL was a minor QTL on chromosome 2A (QHf.osu-2A), which accounted for 18% of the total phenotypic variation. The resistant allele at this locus in 2174 is collinear to anYr17-containing-fragment translocated from chromosome 2N ofTriticum ventricosum(2n = 4 × =28; DDNN) in Jagger. Genetic mapping results showed that twoOPRgenes,TaOPR1-AandTaOPR2-A, were tightly associated withQHf.osu-1AandQHf.osu-2A,respectively. AnotherOPRgene and threeLOXgenes were mapped but not associated with Hessian fly resistance in the segregating population.ConclusionsThis study has located two major QTLs/genes in bread wheat that can be directly used in wheat breeding programs and has also provided insights for the genetic association and disassociation of Hessian fly resistance withOPRandLOXgenes in wheat.
A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries
Authors: Zylicz-Stachula Agnieszka , Zolnierkiewicz Olga , Jasiecki Jacek , Skowron Piotr M 
Published: June 2013

Abstract

Background
Genomics and metagenomics are currently leading research areas, with DNA sequences accumulating at an exponential rate. Although enormous advances in DNA sequencing technologies are taking place, progress is frequently limited by factors such as genomic contig assembly and generation of representative libraries. A number of DNA fragmentation methods, such as hydrodynamic sharing, sonication or DNase I fragmentation, have various drawbacks, including DNA damage, poor fragmentation control, irreproducibility and non-overlapping DNA segment representation. Improvements in these limited DNA scission methods are consequently needed. An alternative method for obtaining higher quality DNA fragments involves partial digestion with restriction endonucleases (REases).
We have shown previously that class-IIS/IIC/IIG TspGWI REase, the prototype member of the Thermus sp. enzyme family, can be chemically relaxed by a cofactor analogue, allowing it to recognize very short DNA sequences of 3-bp combined frequency. Such frequently cleaving REases are extremely rare, with CviJI/CviJI*, SetI and FaiI the only other ones found in nature. Their unusual features make them very useful molecular tools for the development of representative DNA libraries.

Results
We constructed a horse genomic library and a deletion derivative library of the butyrylcholinesterase cDNA coding region using a novel method, based on TaqII, Thermus sp. family bifunctional enzyme exhibiting cofactor analogue specificity relaxation. We used sinefungin (SIN) – an S-adenosylmethionine (SAM) analogue with reversed charge pattern, and dimethylsulfoxide (DMSO), to convert the 6-bp recognition site TaqII (5′-GACCGA-3′ [11/9]) into a theoretical 2.9-bp REase, with 70 shortened variants of the canonical recognition sequence detected. Because partial DNA cleavage is an inherent feature of the Thermus sp. enzyme family, this modified TaqII is uniquely suited to quasi-random library generation.

Conclusions
In the presence of SIN/DMSO, TaqII REase is transformed from cleaving every 4096 bp on average to cleaving every 58 bp. TaqII SIN/DMSO thus extends the palette of available REase prototype specificities. This phenomenon, employed under partial digestion conditions, was applied to quasi-random DNA fragmentation. Further applications include high sensitivity probe generation and metagenomic DNA amplification.
Metabolic evolution of Corynebacterium glutamicum for increased production of L-ornithine
Authors: Jiang Ling-Yan , Chen Shang-Guang , Zhang Yuan-Yuan , Liu Jian-Zhong 
Published: June 2013

Abstract

Background
L-ornithine is effective in the treatment of liver diseases and helps strengthen the heart. The commercial applications mean that efficient biotechnological production of L-ornithine has become increasingly necessary. Adaptive evolution strategies have been proven a feasible and efficient technique to achieve improved cellular properties without requiring metabolic or regulatory details of the strain. The evolved strains can be further optimised by metabolic engineering. Thus, metabolic evolution strategy was used for engineering Corynebacterium glutamicum to enhance L-ornithine production.

Results
A C. glutamicum strain was engineered by using a combination of gene deletions and adaptive evolution with 70 passages of growth-based selection. The metabolically evolved C. glutamicum strain, named ΔAPE6937R42, produced 24.1 g/L of L-ornithine in a 5-L bioreactor. The mechanism used by C. glutamicum ΔAPE6937R42 to produce L-ornithine was investigated by analysing transcriptional levels of select genes and NADPH contents. The upregulation of the transcription levels of genes involved in the upstream pathway of glutamate biosynthesis and the elevated NADPH concentration caused by the upregulation of the transcriptional level of the ppnK gene promoted L-ornithine production in C. glutamicum ΔAPE6937R42.

Conclusions
The availability of NADPH plays an important role in L-ornithine production in C. glutamicum. Our results demonstrated that the combination of growth-coupled evolution with analysis of transcript abundances provides a strategy to engineer microbial strains for improving production of target compounds.
A cross sectional study examining social desirability bias in caregiver reporting of children’s oral health behaviors
Authors: Sanzone Lauren A , Lee Jessica Y , Divaris Kimon , DeWalt Darren A , Baker A Diane , Vann Jr William F 
Published: June 2013

AbstractBackgroundOur previous research (Pediatrics2010:126) found a strong association between caregiver oral health literacy (OHL) and children’s oral health status; however, we found a weak association with oral health behaviors (OHBs). We hypothesize that this may be due to social desirability bias (SDB). Our objectives were to compare caregivers’ responses to traditional OHB items and newer SDB-modulating items, and to examine the association of caregiver literacy with OHBs.MethodsWe performed a cross-sectional study of 102 caregiver-child dyads, collecting data for OHBs using both traditional and new SDB-modulating items. We measured OHL using REALD-30, a validated word recognition test. We relied upon percent agreement and Cohen’skappa(k) to quantify the concordance in caregivers’ responses and multivariate log-binomial regression to estimate the impact of OHL on OHBs.ResultsCaregivers’ mean REALD-30 score was 20.7 (SD = 6.0), range 1-30. We found an association between OHL and 4 of 8 OHBs examined. A subset of behavior questions compared traditionalversusSDB-modulating items: history of bottle-feeding: agreement = 95%, k = 0.83 (95% CL:0.68,0.99); daily tooth brushing: agreement = 78%, k = 0.25 (95% CL:0.04,0.46); fluoridated toothpaste use: agreement = 88%, k = 0.67 (95% CL:0.49,0.85). After controlling for caregivers’ race, marital status and study site, higher literacy scores remained associated with a decreased prevalence of parental report of “decided not brush the child’s teeth because it would be frustrating”.ConclusionsAgreement between responses was high for 2 of 3 behavior items. Item 3 (tooth brushing frequency) revealed discordance, likely due to SDB. Use of the SDB-modulating items appears to yield a better estimate of OHB.
BAD overexpression inhibits cell growth and induces apoptosis via mitochondrial-dependent pathway in non-small cell lung cancer
Authors: Jiang Li , Luo Man , Liu Dan , Chen Bojiang , Zhang Wen , Mai Lin , Zeng Jing , Huang Na , Huang Yi , Mo Xianming , Li Weimin 
Published: June 2013

Abstract

Background
The pro-apoptotic Bcl-2 protein BAD initiated apoptosis in human cells and has been identified as a prognostic marker in non-small cell lung cancer (NSCLC). In this study, we aimed to explore the functions of BAD in NSCLC.

Methods
Overexpression of BAD was performed by transfecting different NSCLC cell lines with wild-type BAD. Cell proliferation, cell cycle, apoptosis, and invasion were characterized in vitro. Tumorigenicity was analyzed in vivo. Western blot was performed to determine the effects of BAD overexpression on the Bcl-2 family proteins and apoptosis-related proteins.

Results
Overexpression of BAD significantly inhibited cell proliferation in H1299, H292, and SPC-A1 but not in SK-MES-1 and H460 cell lines in vitro. BAD overexpression also reduced the tumorigenicity of H1299/SPC-A1 cell in vivo. However, no appreciable effects on cell cycle distribution and invasion were observed in all these cell lines. BAD overexpression also induced apoptosis in all cell types, in which process expression of mitochondrial cytochrom c (cyto-c) and caspase 3 were increased, whereas Bcl-xl, Bcl-2, Bax and caspase 8 expressions did not changed. These findings indicated that a mitochondrial pathway, in which process cyto-c was released from mitochondrial to activate caspase 3, was involved in BAD overexpression-mediated apoptosis.

Conclusions
Our data suggested that increased expression of BAD enhance apoptosis and has negative influence on cell proliferation and tumor growth in NSCLC. Bad is a new potential target for tumor interventions.
Hyperendemic malaria transmission in areas of occupation-related travel in the Peruvian Amazon
Authors: Parker Benjamin S , Paredes Olortegui Maribel , Peñataro Yori Pablo , Escobedo Karin , Florin David , Rengifo Pinedo Silvia , Cardenas Greffa Roldan , Capcha Vega Luis , Rodriguez Ferrucci Hugo , Pan William K , Banda Chavez Cesar , Vinetz Joseph M , Kosek Margaret 
Published: June 2013

Abstract

Background

Plasmodium vivax and Plasmodium falciparum cause a significant illness burden in Peru. Anopheline indices for populated communities in the peri-Iquitos region of Loreto have been reported to be remarkably low, with entomological inoculation rates (EIR) estimated at one to 30 infective bites per year based on a few studies in close proximity to the urban centre of Iquitos and surrounding deforested areas. Local reports suggest that a large number of the reported cases are contracted outside of populated communities in undeveloped riverine areas frequented by loggers and fishermen.

Methods
To better understand vectorial capacity in suspected high malaria transmission zones in a rural district near Iquitos, Peru, mosquito collections were conducted at different points in the seasonality of malaria transmission in 21 sites frequented by occupational labourers. Prevalence of Plasmodium spp in vectors was determined by circumsporozoite protein ELISA on individual mosquitoes. Slide surveillance was performed for humans encountered in the zone.

Results
In total, of 8,365 adult female mosquitoes examined, 98.5% were identified as Anopheles darlingi and 117 (1.4%) tested positive for sporozoites (P. falciparum, P. vivax VK210 or P. vivax VK247). Measured human biting rates at these sites ranged from 0.102 to 41.13 bites per person per hour, with EIR values as high as 5.3 infective bites per person per night. Six percent of the 284 blood films were positive for P. vivax or P. falciparum; however, 88% of the individuals found to be positive were asymptomatic at the time of sampling.

Conclusions
The results of this study provide key missing indices of prominent spatial and temporal heterogeneity of vectorial capacity in the Amazon Basin of Peru. The identification of a target human subpopulation as a principal reservoir and dispersion source of Plasmodium species has important implications for vaccine development and the delivery of effective targeted malaria control strategies.
Signal transducer and activator of transcription (STAT)-3 regulates microRNA gene expression in chronic lymphocytic leukemia cells
Authors: Rozovski Uri , Calin George A , Setoyama Tetsuro , D’Abundo Lucilla , Harris David M , Li Ping , Liu Zhiming , Grgurevic Srdana , Ferrajoli Alessandra , Faderl Stefan , Burger Jan A , O’Brien Susan , Wierda William G , Keating Michael J , Estrov Zeev 
Published: June 2013

Abstract

Backgrounds
Approximately 1,000 microRNAs (miRs) are present in the human genome; however, little is known about the regulation of miR transcription. Because miR levels are deregulated in chronic lymphocytic leukemia (CLL) and signal transducer and activator of transcription (STAT)-3 is constitutively activated in CLL, we sought to determine whether STAT3 affects the transcription of miR genes in CLL cells.

Methods
We used publically available data from the ENCODE project to identify putative STAT3 binding sites in the promoters of miR genes. Then we transfected CLL cells with STAT3-shRNA or with an empty vector, and to determine which miRs are differentially expressed, we used a miR microarray approach followed by validation of the microarray results for 6 miRs using quantitative real-time polymerase chain reaction (qRT-PCR).

Results
We identified putative STAT3 binding sites in 160 promoter regions of 200 miRs, including miR-21, miR-29, and miR-155, whose levels have been reported to be upregulated in CLL. Levels of 72 miRs were downregulated (n = 63) or upregulated (n = 9). qRT-PCR confirmed the array data in 5 of 6 miRs.

Conclusions
The presence of activated STAT3 has a profound effect on miR expression in CLL cells.
Protein expression profiling of nuclear membrane protein reveals potential biomarker of human hepatocellular carcinoma
Authors: Khan Rizma , Zahid Saadia , Wan Yu-Jui Yvonne , Forster Jameson , Karim A-Bashar Abdul , Nawabi Atta M , Azhar Abid , Rahman M Ataur , Ahmed Nikhat 
Published: June 2013

Abstract

Background
Complex molecular events lead to development and progression of liver cirrhosis to HCC. Differentially expressed nuclear membrane associated proteins are responsible for the functional and structural alteration during the progression from cirrhosis to carcinoma. Although alterations/ post translational modifications in protein expression have been extensively quantified, complementary analysis of nuclear membrane proteome changes have been limited. Deciphering the molecular mechanism that differentiate between normal and disease state may lead to identification of biomarkers for carcinoma.

Results
Many proteins displayed differential expression when nuclear membrane proteome of hepatocellular carcinoma (HCC), fibrotic liver, and HepG2 cell line were assessed using 2-DE and ESI-Q-TOF MS/MS. From the down regulated set in HCC, we have identified for the first time a 15 KDa cytochrome b5A (CYB5A), ATP synthase subunit delta (ATPD) and Hemoglobin subunit beta (HBB) with 11, 5 and 22 peptide matches respectively. Furthermore, nitrosylation studies with S-nitrosocysteine followed by immunoblotting with anti SNO-cysteine demonstrated a novel and biologically relevant post translational modification of thiols of CYB5A in HCC specimens only. Immunofluorescence images demonstrated increased protein S-nitrosylation signals in the tumor cells and fibrotic region of HCC tissues. The two other nuclear membrane proteins which were only found to be nitrosylated in case of HCC were up regulated ATP synthase subunit beta (ATPB) and down regulated HBB. The decrease in expression of CYB5A in HCC suggests their possible role in disease progression. Further insight of the functional association of the identified proteins was obtained through KEGG/ REACTOME pathway analysis databases. String 8.3 interaction network shows strong interactions with proteins at high confidence score, which is helpful in characterization of functional abnormalities that may be a causative factor of liver pathology.

Conclusion
These findings may have broader implications for understanding the mechanism of development of carcinoma. However, large scale studies will be required for further verification of their critical role in development and progression of HCC.
A one step real-time RT-PCR assay for the quantitation of Wheat yellow mosaic virus(WYMV)
Authors: Liu Wenwen , Zhao Xiaojuan , Zhang Peng , Mar Thi Thi , Liu Yan , Zhang Zongying , Han Chenggui , Wang Xifeng 
Published: June 2013

Abstract

Background

Wheat yellow mosaic virus (WYMV) is an important pathogen in China and other countries. It is the member of the genus Bymovirus and transmitted primarily by Polymyxa graminis. The incidence of wheat infections in endemic areas has risen in recent years. Prompt and dependable identification of WYMV is a critical component of response to suspect cases.

Methods
In this study, a one step real-time RT-PCR, followed by standard curve analysis for the detection and identification of WYMV, was developed. Two reference genes, 18s RNA and β-actin were selected in order to adjust the veracity of the real-time RT-PCR assay.

Results
We developed a one-step Taqman-based real-time quantitative RT-PCR (RT-qPCR) assay targeting the conserved region of the 879 bp long full-length WYMV coat protein gene. The accuracy of normalized data was analyzed along with appropriate internal control genes: β-actin and 18s rRNA which were included in detecting of WYMV-infected wheat leaf tissues. The detectable end point sensitivity in RT-qPCR assay was reaching the minimum limit of the quantitative assay and the measurable copy numbers were about 30 at106-fold dilution of total RNA. This value was close to 104-fold more sensitive than that of indirect enzyme-linked immunosorbent assay. More positive samples were detected by RT-qPCR assay than gel-based RT-PCR when detecting the suspected samples collected from 8 regions of China. Based on presented results, RT-qPCR will provide a valuable method for the quantitative detection of WYMV.

Conclusions
The Taqman-based RT-qPCR assay is a faster, simpler, more sensitive and less expensive procedure for detection and quantification of WYMV than other currently used methods.
Surgical treatment of innominate artery and aortic aneurysm: a case report and review of the literature
Authors: Soylu Erdinc , Harling Leanne , Ashrafian Hutan , Anagnostakou Vania , Tassopoulos Dimitris , Charitos Christos , Kokotsakis John , Athanasiou Thanos 
Published: June 2013

Abstract
Innominate artery (IA) aneurysms represent 3% of all arterial aneurysms. Due to the risk of thromboembolic complications and spontaneous rupture, surgical repair is usually recommended on an early elective basis. We present the case of 81-year-old Caucasian male presenting with atypical anterior chest pain secondary to a large innominate artery aneurysm who underwent successful open surgical repair at our institution. In our experience, open correction via median sternotomy with extension into the right neck provides excellent exposure and facilitates rapid reconstruction with good short and long-term outcomes. Minimally invasive and endovascular approaches provide emerging alternatives to open IA aneurysm repair, however further research is required to better define optimal patient selection criteria and determine the long-term outcomes of these novel therapies.
Expression of Lewis y antigen and integrin αv, β3 in ovarian cancer and their relationship with chemotherapeutic drug resistance
Authors: Gao Jian , Hu Zhenhua , Liu Dawo , Liu Juanjuan , Liu Chuan , Hou Rui , Gao Song , Zhang Danye , Zhang Shulan , Lin Bei 
Published: June 2013

Abstract

Objective
This study investigates the expression of Lewis y antigen, integrin αv, β3 in epithelial ovarian cancer tissues. We further evaluate the relationship between their expression and chemotherapy resistance of ovarian cancer and its possible clinical significance.

Methods
Tissues of 92 patients with ovarian cancer meeting the inclusion criteria with complete follow-up data were enrolled and divided into chemotherapy resistant group and sensitive group. The expression and relationship of Lewis y antigen and integrin αv, β3 are assessed in paraffin sections using immunohistochemistry and double-labeling immunofluorescence method. Multivariate logistic regression analysis was used to investigate the relationship between age, clinical stage, differentiation, histologic subtype, Lewis y antigen and integrin αv, β3 expression in ovarian cancer patients.

Results
The expression rates of Lewis y antigen and integrin αv in the resistant group, significantly higher than the rates found in the sensitive group (p <0.05). Multivariate analysis showed that the expression of Lewis y antigen, integrin αv and ovarian cancer’s clinical stage were independent, drug resistance-related risk factors. The expression levels of Lewis y antigen and integrin αv, β3 were positively correlated with each other.

Conclusions
A close correlation between Lewis y antigen, integrin αv, β3 and ovarian cancer was observed. Lewis y antigen can influence the biological behavior of a tumor cell as an important composition of integrin αv, β3 by some signal pathway. And the expression of Lewis y antigen, integrin αv and ovarian cancer’s clinical stage are both independent, drug resistance-related risk factors.
Hamartomatous polyposis syndromes
Authors: Stojcev Zoran , Borun Pawel , Hermann Jacek , Krokowicz Piotr , Cichy Wojciech , Kubaszewski Lukasz , Banasiewicz Tomasz , Plawski Andrzej 
Published: June 2013

Abstract
Hamartomas are tumour-like malformations, consisting of disorganized normal tissues, typical of the site of tumour manifestation. Familial manifestation of hamartomatous polyps can be noted in juvenile polyposis syndrome (JPS), Peutz-Jeghers’ syndrome (PJS), hereditary mixed polyposis syndrome (HMPS) and PTEN hamartoma tumour syndrome (PHTS). All the aforementioned syndromes are inherited in an autosomal dominant manner and form a rather heterogenous group both in respect to the number and localization of polyps and the risk of cancer development in the alimentary tract and other organs. Individual syndromes of hamartomatous polyposis frequently manifest similar symptoms, particularly during the early stage of the diseases when in several cases their clinical pictures do not allow for differential diagnosis. The correct diagnosis of the disease using molecular methods allows treatment to be implemented earlier and therefore more effectively since it is followed by a strict monitoring of organs that manifest a predisposition for neoplastic transformation.
Synthesis, characterization, and experimental investigation of surface activity of SERS substrates using neodymium oxide (Nd2O3)
Authors: Sadeghi Fatemeh , Khani Farzad , Azandaryani Abbas Hemati , Mansouri Yadollah , Mehrabadi Zahra Shaykhi , Nikjou Amir 
Published: June 2013

Abstract
The activity of two surface-enhanced Raman scattering (SERS) substrates was investigated using neodymium oxide (Nd2O3) molecules. Colloidal silver solution, containing nano-sized silver particles and silver-coated filter papers were used as the SERS substrates. In order to characterize the substrates, ultraviolet–visible spectroscopy, dynamic light scattering, and scanning electron microscopy were used. Subsequently, gain enhancement factors were calculated from the measured spectra to monitor the change in effectiveness of the SERS substrates under prolonged storage time. Experimental results show that for enhancing the Raman signal, the activity of two fabricated substrates is very effective.