bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Marriage Moderate Genetic Effects on Delinquency and Violence?
Authors: Li Yi , Liu Hexuan , Guo Guang 
Published: June 2015

AbstractUsing data from the National Longitudinal Study of Adolescent to Adult Health (N = 1,254), the authors investigated whether marriage can foster desistance from delinquency and violence by moderating genetic effects. In contrast to existing gene–environment research that typically focuses on one or a few genetic polymorphisms, they extended a recently developed mixed linear model to consider the collective influence of 580 single nucleotide polymorphisms in 64 genes related to aggression and risky behavior. The mixed linear model estimates the proportion of variance in the phenotype that is explained by the single nucleotide polymorphisms. The authors found that the proportion of variance in delinquency/violence explained was smaller among married individuals than unmarried individuals. Because selection, confounding, and heterogeneity may bias the estimate of the Gene × Marriage interaction, they conducted a series of analyses to address these issues. The findings suggest that the Gene × Marriage interaction results were not seriously affected by these issues.
When plant virology met Agrobacterium: the rise of the deconstructed clones
Authors: Peyret Hadrien , Lomonossoff George P. 
Published: June 2015

SummaryIn the early days of molecular farming, Agrobacterium‐mediated stable genetic transformation and the use of plant virus‐based vectors were considered separate and competing technologies with complementary strengths and weaknesses. The demonstration that ‘agroinfection’ was the most efficient way of delivering virus‐based vectors to their target plants blurred the distinction between the two technologies and permitted the development of ‘deconstructed’ vectors based on a number of plant viruses. The tobamoviruses, potexviruses, tobraviruses, geminiviruses and comoviruses have all been shown to be particularly well suited to the development of such vectors in dicotyledonous plants, while the development of equivalent vectors for use in monocotyledonous plants has lagged behind. Deconstructed viral vectors have proved extremely effective at the rapid, high‐level production of a number of pharmaceutical proteins, some of which are currently undergoing clinical evaluation.
Arterial hypertension in children with hemolytic uremic syndrome after kidney transplantation
Authors: Hoenecke Johannes , Hartmann Hans , Melk Anette 
Published: June 2015

AbstractThe development of arterial hypertension after KTX is a well‐known complication. HUS is a systemic disease associated with arterial hypertension during long‐term follow‐up. Our goal was to report on the severity of arterial hypertension after KTX in patients with typical and atypical HUS. We analyzed the course of 197 patients with HUS, of which 22 (n = 10 with typical HUS; n = 12 with atypical HUS) developed ESRF and received KTX as renal replacement therapy. We analyzed data from 1766 casual BP and 85 24‐h ABPM measurements. In addition, we evaluated the used antihypertensive strategy. Comparison between the two patient groups revealed that patients with atypical HUS had significantly higher casual SBP‐SDS and DBP‐SDS values after KTX despite similar intensity of antihypertensive treatment. These data were supported by analysis of ABPM profiles showing comparable results for the interval 1–5 yr after KTX. Patients with atypical HUS had a greater severity of arterial hypertension despite similar treatment strategies and intensity of treatment. Our observation, even though in a small cohort, supports recent genetic studies showing arterial hypertension closely associated with HUS‐causing mutations in patients with atypical HUS.
Host defences against Giardia lamblia
Authors: Lopez‐Romero G. , Quintero J. , Astiazarán‐García H. , Velazquez C. 
Published: June 2015

SummaryGiardia spp. is a protozoan parasite that inhabits the upper small intestine of mammals and other species and is the aetiological agent of giardiasis. It has been demonstrated that nitric oxide, mast cells and dendritic cells are the first line of defence against Giardia. IL‐6 and IL‐17 play an important role during infection. Several cytokines possess overlapping functions in regulating innate and adaptive immune responses. IgA and CD4+ T cells are fundamental to the process of Giardia clearance. It has been suggested that CD4+ T cells play a double role during the anti‐Giardia immune response. First, they activate and stimulate the differentiation of B cells to generate Giardia‐specific antibodies. Second, they act through a B‐cell‐independent mechanism that is probably mediated by Th17 cells. Several Giardia proteins that stimulate humoral and cellular immune responses have been described. Variant surface proteins, α‐1 giardin, and cyst wall protein 2 can induce host protective responses to future Giardia challenges. The characterization and evaluation of the protective potential of the immunogenic proteins that are associated with Giardia will offer new insights into host–parasite interactions and may aid in the development of an effective vaccine against the parasite.
A tetratricopeptide repeat domain‐containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis
Authors: Zhang Min , Wang Cuiping , Lin Qingfang , Liu Aihua , Wang Ting , Feng Xuanjun , Liu Jie , Han Huiling , Ma Yan , Bonea Diana , Zhao Rongmin , Hua Xuejun 
Published: June 2015

SummaryAuxin polar transport mediated by a group of Pin‐formed (PIN) transporters plays important roles in plant root development. However, the mechanism underlying the PIN expression and targeting in response to different developmental and environmental stimuli is still not fully understood. Here, we report a previously uncharacterized gene SSR1, which encodes a mitochondrial protein with tetratricopeptide repeat (TPR) domains, and show its function in root development in Arabidopsis thaliana. In ssr1‐2, a SSR1 knock‐out mutant, the primary root growth was dramatically inhibited due to severely impaired cell proliferation and cell elongation. Significantly lowered level of auxin was found in ssr1‐2 roots by auxin measurement and was further supported by reduced expression of DR5‐driven reporter gene. As a result, the maintenance of the root stem cell niche is compromised in ssr1‐2. It is further revealed that the expression level of several PIN proteins, namely, PIN1, PIN2, PIN3, PIN4 and PIN7, were markedly reduced in ssr1‐2 roots. In particular, we showed that the reduced protein level of PIN2 on cell membrane in ssr1‐2 is due to impaired retrograde trafficking, possibly resulting from a defect in retromer sorting system, which destines PIN2 for degradation in vacuoles. In conclusion, our results indicated that SSR1 is functioning in root development in Arabidopsis, possibly by affecting PIN protein expression and subcellular targeting.
A host plant genome (Zizania latifolia) after a century‐long endophyte infection
Authors: Guo Longbiao , Qiu Jie , Han Zujing , Ye Zihong , Chen Chao , Liu Chuanjun , Xin Xiufang , Ye Chu‐Yu , Wang Ying‐Ying , Xie Hongqing , Wang Yu , Bao Jiandong , Tang She , Xu Jie , Gui Yijie , Fu Fei , Wang Weidi , Zhang Xingchen , Zhu Qianhua , Guang Xuanmin , Wang Chongzhi , Cui Haifeng , Cai Daguang , Ge Song , Tuskan Gerald A. , Yang Xiaohan , Qian Qian , He Sheng Yang , Wang Jun , Zhou Xue‐Ping , Fan Longjiang 
Published: June 2015

SummaryDespite the importance of host–microbe interactions in natural ecosystems, agriculture and medicine, the impact of long‐term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop ‘Jiaobai’ with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia–endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant–pathogen interaction pathway in Jiaobai. These results show that continuous long‐standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.
Quality of life in Greek family members living with leg ulcer patients
Authors: Kouris Anargyros , Christodoulou Christos , Efstathiou Vasiliki , Chatzimichail Iakovoula , Zakopoulou Nikoletta , Zouridaki Eftychia 
Published: June 2015

ABSTRACTLeg ulcers have been shown to have a significant impact on a patient's quality of life (QoL). Little is known, however, about the secondary impact of the disease on the QoL of the relatives and partners of patients with leg ulcers. The aim of this study was to explore the impact of chronic leg ulcers on the lives of both patients and their family members. Two hundred sixteen patients with leg ulcers and their family members were recruited. All patients entered were evaluated for QoL using the Dermatology Life Quality Index (DLQI) scale, and family members were similarly evaluated using the Family Dermatology Life Quality Index (FDLQI).The study included 56 female and 52 male patients, and 50 female and 58 male family members. The FDLQI score for the latter group was 14.37 ± 2.46 with over 96% of family members reporting a large effect on their QoL due to their relative's disease. The DLQI score in patients with leg ulcers was 13.18 ± 2.88. A significant positive and high correlation between DLQI and FDLQI scores (r = 0.71, p < 0.001) was documented, while DLQI contributed significantly to the prediction of FDLQI (standardized β = 0.71, p < 0.001). Our study results indicate that the QoL of the family was also affected by the patient's condition of chronic leg ulcers and clearly associated with that of the patients.
Diversity of O Antigens within the Genus Cronobacter: from Disorder to Order
Authors: Blažková Martina , Javůrková Barbora , Vlach Jiří , Göselová Sandra , Karamonová Ludmila , Ogrodzki Pauline , Forsythe Stephen , Fukal Ladislav 
Published: June 2015

ABSTRACT

Cronobacter
species are Gram-negative opportunistic pathogens that can cause serious infections in neonates. The lipopolysaccharides (LPSs) that form part of the outer membrane of such bacteria are possibly related to the virulence of particular bacterial strains. However, currently there is no clear overview of O-antigen diversity within the various
Cronobacter
strains and links with virulence. In this study, we tested a total of 82 strains, covering each of the
Cronobacter
species. The nucleotide variability of the O-antigen gene cluster was determined by restriction fragment length polymorphism (RFLP) analysis. As a result, the 82 strains were distributed into 11 previously published serotypes and 6 new serotypes, each defined by its characteristic restriction profile. These new serotypes were confirmed using genomic analysis of strains available in public databases: GenBank and PubMLST
Cronobacter
. Laboratory strains were then tested using the current serotype-specific PCR probes. The results show that the current PCR probes did not always correspond to genomic O-antigen gene cluster variation. In addition, we analyzed the LPS phenotype of the reference strains of all distinguishable serotypes. The identified serotypes were compared with data from the literature and the MLST database (
www.pubmlst.org/cronobacter/
). Based on the findings, we systematically classified a total of 24 serotypes for the
Cronobacter
genus. Moreover, we evaluated the clinical history of these strains and show that
Cronobacter sakazakii
O2, O1, and O4,
C. turicensis
O1, and
C. malonaticus
O2 serotypes are particularly predominant in clinical cases.
Community-Level and Species-Specific Associations between Phytoplankton and Particle-Associated Vibrio Species in Delaware's Inland Bays
Authors: Main Christopher R. , Salvitti Lauren R. , Whereat Edward B. , Coyne Kathryn J. 
Published: June 2015

ABSTRACT

Vibrio
species are an abundant and diverse group of bacteria that form associations with phytoplankton. Correlations between
Vibrio
and phytoplankton abundance have been noted, suggesting that growth is enhanced during algal blooms or that association with phytoplankton provides a refuge from predation. Here, we investigated relationships between particle-associated
Vibrio
spp. and phytoplankton in Delaware's inland bays (DIB). The relative abundances of particle-associated
Vibrio
spp. and algal classes that form blooms in DIB (dinoflagellates, diatoms, and raphidophytes) were determined using quantitative PCR. The results demonstrated a significant correlation between particle-associated
Vibrio
abundance and phytoplankton, with higher correlations to diatoms and raphidophytes than to dinoflagellates. Species-specific associations were examined during a mixed bloom of
Heterosigma akashiwo
and
Fibrocapsa japonica
(Raphidophyceae) and indicated a significant positive correlation for particle-associated
Vibrio
abundance with
H. akashiwo
but a negative correlation with
F. japonica
. Changes in
Vibrio
assemblages during the bloom were evaluated using automated ribosomal intergenic spacer analysis (ARISA), which revealed significant differences between each size fraction but no significant change in
Vibrio
assemblages over the course of the bloom. Microzooplankton grazing experiments showed that losses of particle-associated
Vibrio
spp. may be offset by increased growth in the
Vibrio
population. Moreover, analysis of
Vibrio
assemblages by ARISA also indicated an increase in the relative abundance for specific members of the
Vibrio
community despite higher grazing pressure on the particle-associated population as a whole. The results of this investigation demonstrate links between phytoplankton and
Vibrio
that may lead to predictions of potential health risks and inform future management practices in this region.
Mesaconase Activity of Class I Fumarase Contributes to Mesaconate Utilization by Burkholderia xenovorans
Authors: Kronen Miriam , Sasikaran Jahminy , Berg Ivan A. 
Published: June 2015

ABSTRACT

Pseudomonas aeruginosa
,
Yersinia pestis
, and many other bacteria are able to utilize the C
5
-dicarboxylic acid itaconate (methylenesuccinate). Itaconate degradation starts with its activation to itaconyl coenzyme A (itaconyl-CoA), which is further hydrated to (
S
)-citramalyl-CoA, and citramalyl-CoA is finally cleaved into acetyl-CoA and pyruvate. The xenobiotic-degrading betaproteobacterium
Burkholderia xenovorans
possesses a
P. aeruginosa
-like itaconate degradation gene cluster and is able to grow on itaconate and its isomer mesaconate (methylfumarate). Although itaconate degradation proceeds in
B. xenovorans
in the same way as in
P. aeruginosa
, the pathway of mesaconate utilization is not known. Here, we show that mesaconate is metabolized through its hydration to (
S
)-citramalate. The latter compound is then metabolized to acetyl-CoA and pyruvate with the participation of two enzymes of the itaconate degradation pathway, a promiscuous itaconate-CoA transferase able to activate (
S
)-citramalate in addition to itaconate and (
S
)-citramalyl-CoA lyase. The first reaction of the pathway, the mesaconate hydratase (mesaconase) reaction, is catalyzed by a class I fumarase. As this enzyme (Bxe_A3136) has similar efficiencies (
k
cat
/

K
m

) for both fumarate and mesaconate hydration, we conclude that
B. xenovorans
class I fumarase is in fact a promiscuous fumarase/mesaconase. This promiscuity is physiologically relevant, as it allows the growth of this bacterium on mesaconate as a sole carbon and energy source.
Within-Farm Changes in Dairy Farm-Associated Salmonella Subtypes and Comparison to Human Clinical Isolates in Michigan, 2000-2001 and 2009
Authors: Habing Greg G. , Manning Shannon , Bolin Carole , Cui Yuehua , Rudrik James , Dietrich Stephen , Kaneene John B. 
Published: June 2015

ABSTRACT

Temporal changes in the distribution of
Salmonella
subtypes in livestock populations may have important impacts on human health. The first objective of this research was to determine the within-farm changes in the population of subtypes of
Salmonella
on Michigan dairy farms that were sampled longitudinally in 2000-2001 and again in 2009. The second objective was to determine the yearly frequency (2001 through 2012) of reported human illnesses in Michigan associated with the same subtypes. Comparable sampling techniques were used to collect fecal and environmental samples from the same 18 Michigan dairy farms in 2000-2001 and 2009. Serotypes, multilocus sequence types (STs), and pulsed-field gel electrophoresis (PFGE) banding patterns were identified for isolates from 6 farms where >1
Salmonella
isolate was recovered in both 2000-2001 and 2009. The distribution of STs was significantly different between time frames (
P
< 0.05); only two of 31 PFGE patterns were identified in both time frames, and each was recovered from the same farm in each time frame. Previously reported within-farm decreases in the frequency of multidrug-resistant (MDR)
Salmonella
were due to recovery of MDR subtypes of
S. enterica
serotypes Senftenberg and Typhimurium in 2000-2001 and genetically distinct, pansusceptible subtypes of the same serotypes in 2009. The annual frequency of human illnesses between 2001 and 2012 with a PFGE pattern matching a bovine strain decreased for patterns recovered from dairy farms in 2000-2001 and increased for patterns recovered in 2009. These data suggest important changes in the population of
Salmonella
on dairy farms and in the frequency of human illnesses associated with cattle-derived subtypes.
Identification of a Specific Maleate Hydratase in the Direct Hydrolysis Route of the Gentisate Pathway
Authors: Liu Kun , Xu Ying , Zhou Ning-Yi 
Published: June 2015

ABSTRACT

In contrast to the well-characterized and more common maleylpyruvate isomerization route of the gentisate pathway, the direct hydrolysis route occurs rarely and remains unsolved. In
Pseudomonas alcaligenes
NCIMB 9867, two gene clusters,
xln
and
hbz
, were previously proposed to be involved in gentisate catabolism, and HbzF was characterized as a maleylpyruvate hydrolase converting maleylpyruvate to maleate and pyruvate. However, the complete degradation pathway of gentisate through direct hydrolysis has not been characterized. In this study, we obtained from the NCIMB culture collection a
Pseudomonas alcaligenes
spontaneous mutant strain that lacked the
xln
cluster and designated the mutant strain SponMu. The
hbz
cluster in strain SponMu was resequenced, revealing the correct location of the stop codon for
hbzI
and identifying a new gene,
hbzG
. HbzIJ was demonstrated to be a maleate hydratase consisting of large and small subunits, stoichiometrically converting maleate to enantiomerically pure
d
-malate. HbzG is a glutathione-dependent maleylpyruvate isomerase, indicating the possible presence of two alternative pathways of maleylpyruvate catabolism. However, the
hbzF
-disrupted mutant could still grow on gentisate, while disruption of
hbzG
prevented this ability, indicating that the direct hydrolysis route was not a complete pathway in strain SponMu. Subsequently, a
d
-malate dehydrogenase gene was introduced into the
hbzG
-disrupted mutant, and the engineered strain was able to grow on gentisate via the direct hydrolysis route. This fills a gap in our understanding of the direct hydrolysis route of the gentisate pathway and provides an explanation for the high yield of
d
-malate from maleate by this
d
-malate dehydrogenase-deficient natural mutant.
Directed Evolution and Structural Analysis of Alkaline Pectate Lyase from the Alkaliphilic Bacterium Bacillus sp. Strain N16-5 To Improve Its Thermostability for Efficient Ramie Degumming
Authors: Zhou Cheng , Ye Jintong , Xue Yanfen , Ma Yanhe 
Published: June 2015

ABSTRACT

Thermostable alkaline pectate lyases have potential applications in the textile industry as an alternative to chemical-based ramie degumming processes. In particular, the alkaline pectate lyase from
Bacillus
sp. strain N16-5 (BspPelA) has potential for enzymatic ramie degumming because of its high specific activity under extremely alkaline conditions without the requirement for additional Ca
2+
. However, BspPelA displays poor thermostability and is inactive after incubation at 50°C for only 30 min. Here, directed evolution was used to improve the thermostability of BspPelA for efficient and stable degumming. After two rounds of error-prone PCR and screening of >12,000 mutants, 10 mutants with improved thermostability were obtained. Sequence analysis and site-directed mutagenesis revealed that single E124I, T178A, and S271G substitutions were responsible for improving thermostability. Structural and molecular dynamic simulation analysis indicated that the formation of a hydrophobic cluster and new H-bond networks was the key factor contributing to the improvement in thermostability with these three substitutions. The most thermostable combined mutant, EAET, exhibited a 140-fold increase in the
t
50
(time at which the enzyme loses 50% of its initial activity) value at 50°C, accompanied by an 84.3% decrease in activity compared with that of wild-type BspPelA, while the most advantageous combined mutant, EA, exhibited a 24-fold increase in the
t
50
value at 50°C, with a 23.3% increase in activity. Ramie degumming with the EA mutant was more efficient than that with wild-type BspPelA. Collectively, our results suggest that the EA mutant, exhibiting remarkable improvements in thermostability and activity, has the potential for applications in ramie degumming in the textile industry.
Phenolic Amides Are Potent Inhibitors ofDe NovoNucleotide Biosynthesis
Authors: Pisithkul Tippapha , Jacobson Tyler B. , O'Brien Thomas J. , Stevenson David M. , Amador-Noguez Daniel 
Published: June 2015

ABSTRACTAn outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, usingEscherichia colias a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step inde novopurine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.