bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering NAD+ availability for Escherichia coli whole-cell biocatalysis: a case study for dihydroxyacetone production
Authors: Zhou Yongjin J , Yang Wei , Wang Lei , Zhu Zhiwei , Zhang Sufang , Zhao Zongbao K 
Published: November 2013

Abstract

Background
Whole-cell redox biocatalysis has been intensively explored for the production of valuable compounds because excellent selectivity is routinely achieved. Although the cellular cofactor level, redox state and the corresponding enzymatic activity are expected to have major effects on the performance of the biocatalysts, our ability remains limited to predict the outcome upon variation of those factors as well as the relationship among them.

Results
In order to investigate the effects of cofactor availability on whole-cell redox biocatalysis, we devised recombinant Escherichia coli strains for the production of dihydroxyacetone (DHA) catalyzed by the NAD+-dependent glycerol dehydrogenase (GldA). In this model system, a water-forming NAD+ oxidase (NOX) and a NAD+ transporter (NTT4) were also co-expressed for cofactor regeneration and extracellular NAD+ uptake, respectively. We found that cellular cofactor level, NAD+/NADH ratio and NOX activity were not only strain-dependent, but also growth condition-dependent, leading to significant differences in specific DHA titer among different whole-cell biocatalysts. The host E. coli DH5α had the highest DHA specific titer of 0.81 g/gDCW with the highest NAD+/NADH ratio of 6.7 and NOX activity of 3900 U. The biocatalyst had a higher activity when induced with IPTG at 37°C for 8 h compared with those at 30°C for 8 h and 18 h. When cells were transformed with the ntt4 gene, feeding NAD+ during the cell culture stage increased cellular NAD(H) level by 1.44 fold and DHA specific titer by 1.58 fold to 2.13 g/gDCW. Supplementing NAD+ during the biotransformation stage was also beneficial to cellular NAD(H) level and DHA production, and the highest DHA productivity reached 0.76 g/gDCW/h. Cellular NAD(H) level, NAD+/NADH ratio, and NOX and GldA activity dropped over time during the biotransformation process.

Conclusions
High NAD+/NADH ratio driving by NOX was very important for DHA production. Once cofactor was efficiently cycled, high cellular NAD(H) level was also beneficial for whole-cell redox biocatalysis. Our results indicated that NAD+ transporter could be applied to manipulate redox cofactor level for biocatalysis. Moreover, we suggested that genetically designed redox transformation should be carefully profiled for further optimizing whole-cell biocatalysis.
Downregulation of the H-2Kd gene by siRNA affects the cytotoxicity of murine LAK cells
Authors: Liu Xin , Cui Xin , Shan Ningning , Li Ying , Fang Xiaosheng , Ding Mei , Wang Xin 
Published: November 2013

AbstractTo investigate the effect of the H-2Kdgene on the lymphocyte membrane, we constructed a small interfering RNA (siRNA) that targets the H-2Kdgene and compared the cytotoxicity of mouse lymphokine-activated killer (LAK) cells with different H-2Kdexpression states. H-2Kd-targeting siRNA was transfected into spleen lymphocytes of BALB/C mice. Flow cytometry (FCM) was then performed to examine the expression of the H-2Kdgene in the transfected and control cells. Additionally, the cytotoxicity of the transfected cells toward the H22 and K562 cell lines was evaluated in vitro using the LDH release assay. H-2Kd-targeting siRNA significantly reduced the expression levels of the target protein, whereas pure transMessenger and non-silencing siRNA did not inhibit H-2Kdexpression at the concentrations tested. The cytotoxicity of siRNA-treated LAK cells toward H22 and K562 cells was reduced significantly. The knockdown of H-2Kdgene expression by siRNA may be associated with LAK cell cytotoxicity toward neoplasm cell lines.
Evaluation of parasite subpopulations and genetic diversity of the msp1, msp2 and glurp genes during and following artesunate monotherapy treatment of Plasmodium falciparum malaria in Western Cambodia
Authors: Gosi Panita , Lanteri Charlotte A , Tyner Stuart D , Se Youry , Lon Chanthap , Spring Michele , Char Mengchuor , Sea Darapiseth , Sriwichai Sabaithip , Surasri Sittidech , Wongarunkochakorn Saowaluk , Pidtana Kingkan , Walsh Douglas S , Fukuda Mark M , Manning Jessica , Saunders David L , Bethell Delia 
Published: November 2013

Abstract

Background
Despite widespread coverage of the emergence of artemisinin resistance, relatively little is known about the parasite populations responsible. The use of PCR genotyping around the highly polymorphic Plasmodium falciparum msp1, msp2 and glurp genes has become well established both to describe variability in alleles within a population of parasites, as well as classify treatment outcome in cases of recurrent disease. The primary objective was to assess the emergence of minority parasite clones during seven days of artesunate (AS) treatment in a location with established artemisinin resistance. An additional objective was to investigate whether the classification of clinical outcomes remained valid when additional genotyping was performed.

Methods
Blood for parasite genotyping was collected from 143 adult patients presenting with uncomplicated falciparum malaria during a clinical trial of AS monotherapy in Western Cambodia. Nested allelic type-specific amplification of the genes encoding the merozoite surface proteins 1 and 2 (msp1 and msp2) and the glutamate-rich protein (glurp) was performed at baseline, daily during seven days of treatment, and again at failure. Allelic variants were analysed with respect to the size of polymorphisms using Quantity One software to enable identification of polyclonal infections.

Results
Considerable variation of msp2 alleles but well-conserved msp1 and glurp were identified. At baseline, 31% of infections were polyclonal for one or more genes. Patients with recurrent malaria were significantly more likely to have polyclonal infections than patients without recurrence (seven of nine versus 36 of 127, p = 0.004). Emergence of minority alleles during treatment was detected in only one of twenty-three cases defined as being artemisinin resistant. Moreover, daily genotyping did not alter the final outcome classification in any recurrent cases.

Conclusions
The parasites responsible for artemisinin-resistant malaria in a clinical trial in Western Cambodia comprise the dominant clones of acute malaria infections rather than minority clones emerging during treatment. Additional genotyping during therapy was not beneficial. Disproportionately high rates of polyclonal infections in cases of recurrence suggest complex infections lead to poor treatment outcomes. Current research objectives should be broadened to include identification and follow-up of recurrent polyclonal infections so as to define their role as potential agents of emerging resistance.
Acetylcholinesterase (Ace-1) target site mutation 119S is strongly diagnostic of carbamate and organophosphate resistance in Anopheles gambiae s.s. and Anopheles coluzzii across southern Ghana
Authors: Essandoh John , Yawson Alexander E , Weetman David 
Published: November 2013

Abstract

Background
With high DDT resistance present throughout much of West Africa, carbamates and organophosphates are increasingly important alternatives to pyrethroids for indoor residual spraying (IRS). Though less widespread, resistance to both of these alternative insecticide classes has also been documented within the Anopheles gambiae species pair (formerly the M and S molecular forms) in West Africa. To manage insecticide efficacy, it is important to predict how and where resistance is likely to occur and spread, which could be aided by using molecular diagnostics with high predictive value.

Methods

Anopheles coluzzii and An. gambiae s.s. were collected from 18 sites throughout southern Ghana and bioassayed with bendiocarb, the most commonly applied carbamate, and an organophosphate, fenitrothion. The Ace-1 target site substitution G119S was genotyped by qPCR.

Results
Fenitrothion induced higher mortality than bendiocarb, though phenotypes correlated strongly across populations. Ace-1 119S was found at much higher frequency in An. gambiae s.s than An. coluzzii, exceeding 90% in a population from Greater Accra, the highest frequency reported to date. Ace-1 G119S was very strongly associated with resistance to both insecticides, providing high predictive power for diagnosis, though with some evidence for a differential effect between molecular forms for bendiocarb. Sequencing of the gene revealed a lack of variation in resistant alleles precluding determination of origin, but Ace-1 copy number variation was detected for the first time in Ghana.

Conclusions
The results validate G119S as a useful diagnostic of organophosphate and carbamate resistance within and among populations, whilst highlighting the potential for an aggregate nature of Ace-1 genotypes, which may comprise both single-copy and duplicated genes. Further work is now required to determine the distribution and resistance-association of Ace-1 duplication.
Dynamics of vitamin D in patients with mild or inactive inflammatory bowel disease and their families
Authors: Grunbaum Avigyle , Holcroft Christina , Heilpern Debra , Gladman Stephanie , Burstein Barry , Menard Maryse , Al-Abbad Jasim , Cassoff Jamie , MacNamara Elizabeth , Gordon Philip H , Szilagyi Andrew 
Published: November 2013

Abstract

Background
25(OH) vitamin D levels may be low in patients with moderately or severely active inflammatory bowel diseases (IBD: Crohn’s disease and Idiopathic Ulcerative Colitis) but this is less clear in patients with mild or inactive IBD. Furthermore there is limited information of any family influence on 25(OH) vitamin D levels in IBD. As a possible risk factor we hypothesize that vitamin D levels may also be low in families of IBD patients.

Objectives
To evaluate 25[OH] vitamin D levels in patients with IBD in remission or with mild activity. A second objective is to evaluate whether there are relationships within IBD family units of 25[OH] vitamin D and what are the influences associated with these levels.

Methods
Participants underwent medical history, physical examination and a 114 item diet questionnaire. Serum 25[OH] vitamin D was measured, using a radioimmunoassay kit, (replete ≥ 75, insufficient 50–74, deficient < 25–50, or severely deficient < 25 nmol/L). Associations between 25[OH] vitamin D and twenty variables were evaluated using univariate regression. Multivariable analysis was also applied and intrafamilial dynamics were assessed.

Results
55 patients and 48 controls with their respective families participated (N206). 25[OH] vitamin D levels between patients and controls were similar (71.2 ± 32.8 vs. 68.3 ±26.2 nmol/L). Vitamin D supplements significantly increased intake but correlation with serum 25[OH] vitamin D was significant only during non sunny months among patients. Within family units, patients’ families had mean replete levels (82.3 ± 34.2 nmol/L) and a modest correlation emerged during sunny months between patients and family (r2 =0.209 p = 0.032). These relationships were less robust and non significant in controls and their families.

Conclusions
In patients with mild or inactive IBD 25[OH] vitamin D levels are less than ideal but are similar to controls. Taken together collectively, the results of this study suggest that patient family dynamics may be different in IBD units from that in control family units. However contrary to the hypothesis, intra familial vitamin D dynamics do not pose additional risks for development of IBD.
First-line treatment patterns and lipid target levels attainment in very high cardiovascular risk outpatients
Authors: Xanthopoulou Ioanna , Davlouros Periklis , Siahos Simos , Perperis Angelos , Zaharioglou Evangelia , Alexopoulos Dimitrios 
Published: November 2013

Abstract

Objectives
Previous studies have demonstrated gaps in achievement of low-density lipoprotein-cholesterol (LDL-C) goals among patients at very high cardiovascular risk. We aimed to investigate lipid treatment patterns, rates and predictors of lipid targets attainment, in such outpatients in an urban area of Greece.

Methods
This was a prospective observational study, conducted in 19 outpatient clinics of Western Greece. We recruited patients with established cardiovascular disease (CVD) and/or diabetes mellitus (DM), previously (at least 3 months before baseline assessment) untreated with any lipid lowering medication. Lipid profile assessment was performed at baseline (prior to lipid-lowering treatment initiation) and at follow-up. Lipid lowering treatment choice was at physicians’ discretion and was kept constant until follow-up.

Results
We recruited 712 patients with a mean age 61.4 ± 10.4 years, 68.0% males, 43.0% with DM, 64.7% with prior coronary artery disease-CAD. In total, 237/712 (33.3%) of prescribed regimens were of high or very high LDL-C lowering efficacy and out of them 113/237 (47.7%) comprised a combination of statin and ezetimibe. At follow-up the primary target of LDL-C < 70 mg/dL (1.8 mmol/L) was achieved in 71(10.0%) patients. The secondary target of non-HDL-C < 100 mg/dL (2.6 mmol/L) in the subgroup of patients with DM or increased triglycerides levels (>150 mg/dl or 1.7 mmol/L) was achieved in 45(11.6%) of patients. In multivariate logistic regression analysis (AUC = 0.71, 95% CIs 0.65-0.77, p < 0.001) male gender, smoking, baseline LDL-C and very high potency LDL-C lowering regimen emerged as independent predictors of LDL-C goal attainment (OR = 1.88, 95% CIs 1.03-3.44, p = 0.04, OR = 0.57, 95% CIs 0.33-0.96, p = 0.04, OR = 0.98, 95% CIs 0.98-0.99, p < 0.001 and OR = 2.21, 95% CIs 1.15-4.24, p = 0.02 respectively).

Conclusions
First-line management of dyslipidemia among very-high cardiovascular risk outpatients in Western Greece is unsatisfactory, with the majority of treated individuals failing to attain the LDL-C and non-HDL-C targets. This finding points out the need for intensification of statin treatment in such patients.
Interface coupling-induced enhancement of magnetoimpedance effect in heterogeneous nanobrush by adjusting textures of Co nanowires
Authors: Zhang Yi , Dong Juan , Sun Xiaojun , Liu Qingfang , Wang Jianbo 
Published: November 2013

Abstract
Interface coupling-induced and interface coupling-enhanced magnetoimpedance (MI) effect in heterogeneous nanobrush has been investigated. The nanobrush is composed of Fe25Ni75 nanofilm and textured hexagonal close-packed cobalt nanowire array, respectively fabricated by RF magnetron sputtering and electrochemical deposition. The design of this structure is based on the vortex distribution of magnetic moments in thin film, which can be induced by the exchange coupling effect at the interfaces of the nanobrush. The texture of nanowires plays an important role in the MI effect of the nanobrush, which is regulated by controlling the pH values and temperatures of the deposition process. The ‘parallel’ and ‘perpendicular’ coupling models were used to explain the different MI results of the nanobrush with cobalt nanowires, which have (100) and (002) textures, respectively. The optimized MI effect of the nanobrush brought by (100) nanowires can be magnified by 300% with more than 80%/Oe magnetic sensitivity at a low frequency, which has great application potentials in low-frequency MI sensors.
A new general iterative algorithm with Meir-Keeler contractions for variational inequality problems in q-uniformly smooth Banach spaces
Authors: Guan Jinlin , Hu Changsong , Wang Xin 
Published: November 2013

Abstract
In this paper, we generalize the iterative scheme and extend the space studied in (Fixed Point Theory and Applications 2012:46, 2012). Further, we prove some strong convergence theorems of the new iterative scheme for variational inequality problems in q-uniformly smooth Banach spaces under very mild conditions. Our results improve and extend corresponding ones announced by many others.

MSC:47H09, 47H10.
Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats
Authors: Harun Mohammad Syamsul Reza , Kuan Choong Oi , Selvarajah Gayathri Thevi , Wei Tan Sheau , Arshad Siti Suri , Bejo Mohd Hair , Omar Abdul Rahman 
Published: November 2013

Abstract

Background
Feline Infectious Peritonitis (FIP) is a lethal systemic disease, caused by the FIP Virus (FIPV); a virulent mutant of Feline Enteric Coronavirus (FECV). Currently, the viruses virulence determinants and host gene expressions during FIPV infection are not fully understood.

Methods
RNA sequencing of Crandell Rees Feline Kidney (CRFK) cells, infected with FIPV strain 79–1146 at 3 hours post infection (h.p.i), were sequenced using the Illumina next generation sequencing approach. Bioinformatic’s analysis, based on Felis catus 2X annotated shotgun reference genome, using CLC bio Genome Workbench mapped both control and infected cell reads to 18899 genes out of 19046 annotated genes. Kal’s Z test statistical analysis was used to analyse the differentially expressed genes from the infected CRFK cells. Real time RT-qPCR was developed for further transcriptional profiling of three genes (PD-1, PD-L1 and A3H) in infected CRFK cells and Peripheral Blood Mononuclear Cells (PBMCs) from healthy and FIP-diseased cats.

Results
Based on Kal’s Z-test, with False Discovery Rate (FDR) <0.05 and >1.99 fold change on gene expressions, a total of 61 genes were differentially expressed by both samples, where 44 genes were up-regulated and the remainder were down-regulated. Most genes were closely clustered together, suggesting a homogeneous expression. The majority of the genes that were significantly regulated, were those associated with monocytes-macrophage and Th1 cell functions, and the regulation of apoptosis. Real time RT-qPCR developed focusing on 2 up-regulated genes (PD-L1 and A3H) together with an apoptosis associated gene PD-1 expressions in FIPV infected CRFK cells and in PBMCs from healthy and FIP diagnosed cats produced concordant results with transcriptome data.

Conclusion
The possible roles of these genes, and their importance in feline coronaviruses infection, are discussed.
Molecular epidemiology of Newcastle disease virus isolates from vaccinated commercial poultry farms in non-epidemic areas of Japan
Authors: Umali Dennis Villaseñor , Ito Hiroshi , Suzuki Terumasa , Shirota Kazutoshi , Katoh Hiromitsu , Ito Toshihiro 
Published: November 2013

Abstract

Background
Newcastle Disease (ND) is a highly contagious and economically devastating disease of poultry. At present, limited molecular epidemiological data are available regarding the causes of ND outbreaks in vaccinated commercial poultry farms. Knowing the genomic characteristics of Newcastle disease virus (NDV) infecting commercial poultry operations in spite of vaccination might give important insights on the infection dynamics of these viruses. In addition, molecular analyses at the subgenotype level and studies on the relationship of Japanese NDVs with other isolates from around the world are lacking. Therefore, in the present study, a molecular epidemiological investigation was conducted to characterize nine NDVs isolated from vaccinated commercial poultry flocks in five different Prefectures in non-epidemic areas of Japan between 1969 and 2002.

Methods
Nucleotide sequencing and phylogenetic studies were performed to characterize the complete fusion (F)-protein gene, 3-prime end of the nucleoprotein (NP)-gene and 5-prime end of the RNA dependent RNA polymerase (L)-gene. Sequence data were compared with 180 NDV strains from GenBank representing different NDV genotypes and subgenotypes from different regions of the world at different time periods. Deduced amino acids were analyzed for homologies, recombination and mutation. Recombination events were estimated using Recombination Detection Program (RDP) version 3.44. Phylogenetic trees were constructed to determine evolutionary relationships among strains.

Results
Mean death time (MDT: 48-56 hr), Intracerebral Pathogenicity Index (ICPI: 1.7-1.9) and deduced amino acid sequences of the F0 proteolytic cleavage site (112RRQKR116) revealed that all nine field isolates were velogenic. Phylogenetic analysis showed that these isolates could be classified into two genetic lineages and three sublineages namely genotypes VIa (lineage 4a), VId (lineage 4d) and VIId (lineage 5d). No recombination events were observed but a point mutation in one of the neutralizing epitope of the F-protein was identified in the field isolates from Japan.

Conclusions
All field isolates from vaccinated commercial poultry in non-epidemic areas of Japan were part of much bigger outbreaks in provinces and regions and, in some cases, continents. In general, four ND panzootics occurred in Japan and that these outbreaks were mostly characterized by co-circulation of genetically distinct virus lineages due to involvements of infected wild birds. The point mutation identified in the field isolates from Japan may be due to escape from vaccine pressure. The identification of such mutation may be useful for future site-directed mutagenesis to understand the dynamics of NDV infection in vaccinated chickens.
Recombinant lentogenic Newcastle disease virus expressing Ebola virus GP infects cells independently of exogenous trypsin and uses macropinocytosis as the major pathway for cell entry
Authors: Wen Zhiyuan , Zhao Bolin , Song Kun , Hu Xule , Chen Weiye , Kong Dongni , Ge Jinying , Bu Zhigao 
Published: November 2013

Abstract

Background
Using reverse genetics, we generated a recombinant low-pathogenic LaSota strain Newcastle disease virus (NDV) expressing the glycoprotein (GP) of Ebola virus (EBOV), designated rLa-EBOVGP, and evaluated its biological characteristic in vivo and in vitro.

Results
The introduction and expression of the EBOV GP gene did not increase the virulence of the NDV vector in poultry or mice. EBOV GP was incorporated into the particle of the vector virus and the recombinant virus rLa-EBOVGP infected cells and spread within them independently of exogenous trypsin. rLa-EBOVGP is more resistant to NDV antiserum than the vector NDV and is moderately sensitive to EBOV GP antiserum. More importantly, infection with rLa-EBOVGP was markedly inhibited by IPA3, indicating that rLa-EBOVGP uses macropinocytosis as the major internalization pathway for cell entry.

Conclusions
The results demonstrate that EBOV GP in recombinant NDV particles functions independently to mediate the viral infection of the host cells and alters the cell-entry pathway.