bluuebunny/crossref_metadata_2025 huggingface dataset:
Neostigmine in the Treatment of Refractory Constipation in Critically Ill Children
Authors: González Rafael , López‐Herce Jesús , García Ana , Botrán Marta , Solana Maria Jose , Urbano Javier
Published: July 2011

Constipation is a common complication in critically ill children and it is occasionally resistant to the drugs typically used in treatment. Neostigmine has been used in some cases of refractory constipation in critically ill adults. There is no reference to its use in critically ill children. We describe 3 cases of refractory constipation in critically ill children treated with intravenous neostigmine by continuous infusion. Two patients responded well. There were no adverse effects. We conclude that continuous intravenous neostigmine can be effective in critically ill children with refractory constipation. Further studies are necessary to determine the dose and safety of the treatment.
Identification of Specific Foods Responsible for Inflammation in Children With Eosinophilic Esophagitis Successfully Treated With Empiric Elimination Diet
Authors: Kagalwalla Amir F. , Shah Ameesh , Li B U.K. , Sentongo Timothy A. , Ritz Sally , Manuel‐Rubio Maria , Jacques Katie , Wang Deli , Melin‐Aldana Hector , Nelson Suzanne P.
Published: July 2011

Objectives:

Eosinophilic esophagitis (EoE) is an immune‐mediated chronic inflammatory disorder triggered by food antigen(s). A 6‐food elimination diet (SFED) excluding cow's milk, soy, wheat, egg, peanuts/tree nuts, and seafood has been shown to induce remission in a majority of children with EoE. The goal of the present study was to identify specific food antigens responsible for eosinophilic esophageal inflammation in children with EoE who had achieved histological remission with the SFED.

Patients and Methods:

In this analysis, we retrospectively analyzed children with EoE who completed subsequent single‐food reintroductions that led to identification of foods causing disease recurrence. Repeat upper endoscopy with biopsies was performed after single‐food introductions. Recurrence of esophageal eosinophilia following a food reintroduction identified that food antigen as a cause of EoE.

Results:

A total of 36/46 (25 M/11F) children who were initially successfully treated with SFED completed this trial; the mean age was 7.6 ± 4.3 years. The most common foods identified were 25 to cow's milk (74%), 8 to wheat (26%), 4 to eggs (17%), 3 to soy (10%), and 1 to peanut (6%). Milk was 8 times more likely to cause EoE compared with wheat, the next most common food (95% confidence interval 2.41–26.62, P = 0.0007).

Conclusions:

Serial single‐food reintroductions following induction of histological remission with the SFED can lead to the identification of specific causal food antigen(s) in EoE. Cow's milk was the most common food identified in subjects with EoE treated with SFED. A subset of children with EoE may develop tolerance to their food sensitivities while on the SFED.
Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat
Authors: Wang Liang , Baek Sang-Hoon , Cui Yingshun , Lee Hyung-Gwan , Lee Sung-Taik
Published: July 2011

A Gram-positive, rod-shaped, xylanolytic, spore-forming bacterium, strain GTH-3T, was isolated from a tidal flat adjacent to Ganghwa Island, Republic of Korea, and was characterized to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain GTH-3Twas shown to belong to the familyPaenibacillaceae, being most closely related to the type strains ofPaenibacillus ginsengisoli(94.9 %),Paenibacillus anaericanus(94.8 %),Paenibacillus urinalis(94.4 %),Paenibacillus cookii(94.2 %),Paenibacillus alvei(94.1 %) andPaenibacillus chibensis(94.0 %). The G+C content of the genomic DNA of strain GTH-3Twas 45.9±0.2 mol% (mean±sd). The major menaquinone was MK-7. The major fatty acids were anteiso-C15 : 0and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain GTH-3Tto the genusPaenibacillus. The results of physiological and biochemical tests allowed strain GTH-3Tto be distinguished genotypically and phenotypically from recognized species of the genusPaenibacillus. Strain GTH-3Tis therefore considered to represent a novel species of the genusPaenibacillus, for which the namePaenibacillus sediminissp. nov. is proposed. The type strain is GTH-3T( = DSM 23491T = LMG 25635T).
Mycobacterium koreense sp. nov., a slowly growing non-chromogenic species closely related to

Mycobacterium triviale
Authors: Kim Byoung-Jun , Jeong Joseph , Lee Seon Ho , Kim Sung-Ryul , Yu Hee-Kyung , Park Young-Gil , Kim Ki-Jeong , Kook Yoon-Hoh , Kim Bum-Joon
Published: July 2011

A novel slow-growing, non-chromogenic mycobacterium (strain 01-305T) was isolated from a patient with pulmonary dysfunction. Growth characteristics, acid-fastness and the results of 16S rRNA gene sequencing supported the placement of this strain within the genus

Mycobacterium

. Phenotypically, strain 01-305T was generally similar to

Mycobacterium triviale

ATCC 23292T, but some unique biochemical characteristics were observed. The 16S rRNA gene sequence of strain 01-305T was similar to those of

M. triviale

ATCC 23290 (GenBank accession no. AY734996, 99.9 % similarity) and

M. triviale

ATCC 23291 (AY734995, 99.9 %); however, it differed substantially from that of

M. triviale

ATCC 23292T (X88924, 98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain 01-305T in the slow-growing

Mycobacterium

group close to

M. triviale

ATCC 23290 and

M. triviale

ATCC 23291, but not

M. triviale

ATCC 23292T. Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, and the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 01-305T represents a novel mycobacterial species, for which the name Mycobacterium koreense sp. nov. is proposed. The type strain is 01-305T ( = DSM 45576T  = KCTC 19819T).
Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus

Skermanella
Authors: Luo Guosheng , Shi Zunji , Wang Hui , Wang Gejiao
Published: July 2011

A Gram-negative, aerobic, motile, rod-shaped, antimony-resistant bacterium, designated strain SB22T, was isolated from soil of Jixi coal mine, China. The major cellular fatty acids (>5 %) were C18 : 1ω7c (63.5 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I, 10.8 %) and C16 : 0 (9.9 %). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. The genomic DNA G+C content was 69.6 mol% and Q-10 was the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SB22T was most closely related to

Skermanella aerolata

5416T-32T (97.3 %),

Skermanella parooensis

ACM 2042T (95.8 %) and

Skermanella xinjiangensis

10-1-101T (92.9 %). The DNA–DNA hybridization value between strain SB22T and

S. aerolata

KACC 11604T ( = 5416T-32T) was 43.3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics of strain SB22T and related species, it is considered that the isolate represents a novel species of the genus

Skermanella

, for which the name Skermanella stibiiresistens sp. nov. is proposed. The type strain is SB22T ( = CGMCC 1.10751T = KCTC 23364T). An emended description of the genus Skermanella is provided.
Genome-scale phylogenetic function annotation of large and diverse protein families
Authors: Engelhardt Barbara E. , Jordan Michael I. , Srouji John R. , Brenner Steven E.
Published: July 2011

The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. Here we present a revised approach (SIFTER version 2.0) that enables annotations on a genomic scale. SIFTER 2.0 produces equivalently precise predictions compared to the earlier version on a carefully studied family and on a collection of 100 protein families. We have added an approximation method to SIFTER 2.0 and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER achieved 47.4% accuracy on experimental data (where BLAST achieved 34.0%). Finally, we used SIFTER to annotate all of the Schizosaccharomyces pombe proteins with experimental functional characterizations, based on annotations from proteins in 46 fungal genomes. SIFTER precisely predicted molecular function for 45.5% of the characterized proteins in this genome, as compared with four current function prediction methods that precisely predicted function for 62.6%, 30.6%, 6.0%, and 5.7% of these proteins. We use both precision-recall curves and ROC analyses to compare these genome-scale predictions across the different methods and to assess performance on different types of applications. SIFTER 2.0 is capable of predicting protein molecular function for large and functionally diverse protein families using an approximate statistical model, enabling phylogenetics-based protein function prediction for genome-wide analyses. The code for SIFTER and protein family data are available at http://sifter.berkeley.edu.
Coevolution of retroelements and tandem zinc finger genes
Authors: Thomas James H. , Schneider Sean
Published: July 2011

Vertebrate genomes encode large and highly variable numbers of tandem C2H2 zinc finger (tandem ZF) transcription factor proteins. In mammals, most tandem ZF genes also encode a KRAB domain (KZNF proteins). Very little is known about what forces have driven the number and diversity of tandem ZF genes. Recent studies suggest that one role of KZNF proteins is to bind and repress transcription of exogenous retroviruses and their endogenous counterpart LTR retroelements. We report a striking correlation across vertebrate genomes between the number of LTR retroelements and the number of host tandem ZF genes. This correlation is specific to LTR retroelements and ZF genes and was not explained by covariation in other genomic features. We further show that recently active LTR retroelements are correlated with recent tandem ZF gene duplicates across vertebrates. On branches of the primate phylogeny, we find that the appearance of new families of endogenous retroviruses is strongly predictive of the appearance of new duplicate KZNF genes. We hypothesize that retroviral and LTR retroelement burden drives evolution of host tandem ZF genes. This hypothesis is consistent with previously described molecular evolutionary patterns in duplicate ZF genes throughout vertebrates. To further explore these patterns, we investigated 34 duplicate human KZNF gene pairs, all of which underwent an early burst of divergence in the major nucleotide contact residues of their ZF domains, followed by purifying selection in both duplicates. Our results support a host-pathogen model for tandem ZF gene evolution, in which new LTR retroelement challenges drive duplication and divergence of host tandem ZF genes.
A Peroxygenase Pathway Involved in the Biosynthesis of Epoxy Fatty Acids in Oat
Authors: Meesapyodsuk Dauenpen , Qiu Xiao
Published: July 2011

While oat (Avena sativa) has long been known to produce epoxy fatty acids in seeds, synthesized by a peroxygenase pathway, the gene encoding the peroxygenase remains to be determined. Here we report identification of a peroxygenase cDNA AsPXG1 from developing seeds of oat. AsPXG1 is a small protein with 249 amino acids in length and contains conserved heme-binding residues and a calcium-binding motif. When expressed in Pichia pastoris and Escherichia coli, AsPXG1 catalyzes the strictly hydroperoxide-dependent epoxidation of unsaturated fatty acids. It prefers hydroperoxy-trienoic acids over hydroperoxy-dienoic acids as oxygen donors to oxidize a wide range of unsaturated fatty acids with cis double bonds. Oleic acid is the most preferred substrate. The acyl carrier substrate specificity assay showed phospholipid and acyl-CoA were not effective substrate forms for AsPXG1 and it could only use free fatty acid or fatty acid methyl esters as substrates. A second gene, AsLOX2, cloned from oat codes for a 9-lipoxygenase catalyzing the synthesis of 9-hydroperoxy-dienoic and 9-hydroperoxy-trienoic acids, respectively, when linoleic (18:2-9c,12c) and linolenic (18:3-9c,12c,15c) acids were used as substrates. The peroxygenase pathway was reconstituted in vitro using a mixture of AsPXG1 and AsLOX2 extracts from E. coli. Incubation of methyl oleate and linoleic acid or linolenic acid with the enzyme mixture produced methyl 9,10-epoxy stearate. Incubation of linoleic acid alone with a mixture of AsPXG1 and AsLOX2 produced two major epoxy fatty acids, 9,10-epoxy-12-cis-octadecenoic acid and 12,13-epoxy-9-cis-octadecenoic acid, and a minor epoxy fatty acid, probably 12,13-epoxy-9-hydroxy-10-transoctadecenoic acid. AsPXG1 predominately catalyzes intermolecular peroxygenation.
Parallel evolution of thermophilia: daily and seasonal foraging patterns of heat‐adapted desert ants: Cataglyphis and Ocymyrmex species*
Authors: WEHNER RÜDIGER , WEHNER SIBYLLE
Published: July 2011

In the deserts of northern and southern Africa, respectively, ants of the genera Cataglyphisfoerster (Formicinae) and Ocymyrmexemery (Myrmicinae) occupy the same ecological niche, which comprises that of a strictly diurnal thermophilic scavenger. Their daily foraging activities exhibit a bimodal pattern in summer and unimodality or complete inactivity in winter. The present study investigates whether these overall patterns are a result of endogenous annual activity rhythms of the colony or are triggered directly by the prevailing ambient temperatures. By exploiting various seasonal temperature regimes and, in particular, by creating near‐nest winter conditions experimentally in summer, it is shown that the latter hypothesis is generally true. However, there are daily and annual variations in the temperature set points at which foraging activities start and finish. These temperatures are lower in the winter than in the summer months and, in summer, they are lower in the morning than in the afternoon. The level of foraging activity in the afternoon reaches maximum values at surface temperatures of 60–63 °C. This means that, in summer months, these thermophilic ants concentrate their foraging activities into a period of almost lethal temperature regimes, during which they have to devote a substantial portion of their time outside the nest to respite (i.e. cooling‐off) behaviour.
Variability of parvovirus B19 genotype 2 in plasma products with different compositions in the inactivation sensitivity by liquid‐heating
Authors: Tsujikawa M. , Nishigaki H. , Yoshikawa M. , Furuki R. , Takahashi K. , Adan‐Kubo J. , Shimamura Y. , Urayama T. , Hattori S. , Sakai K. , Yunoki M. , Ikuta K.
Published: July 2011

Background and Objectives  Our previous report showed that parvovirus B19 genotype 1 in different solutions derived from plasma preparations showed different heat‐sensitivity patterns during liquid‐heating. In this study, we similarly examined B19 genotype 2.

Materials and Methods  Two plasma samples one containing B19 genotype 1 and the other genotype 2 DNA were used. Four process samples collected immediately before the heat treatment step in the manufacture of albumin, immunoglobulin, haptoglobin and antithrombin preparations were spiked with B19 and subsequently treated at 60°C for 10 h. A low pH immunoglobulin solution was also spiked with B19 and treated at room temperature for 14 days. Infectivity was then measured.

Results  B19 genotype 2, similar to genotype 1, showed three patterns of inactivation: (i) a rapid inactivation in the albumin and immunoglobulin preparations, (ii) a slow inactivation in the haptoglobin preparation and (iii) only limited inactivation in the antithrombin preparation. Its sensitivity in the low pH immunoglobulin solutions also resembled that of genotype 1.

Conclusion  Both genotypes 1 and 2 of B19 varied in sensitivity to liquid‐heating and low pH among different plasma preparations.
ABO‐mismatched transfusions are not over‐represented in febrile non‐haemolytic transfusion reactions to platelets
Authors: Yazer M. H. , Raval J. S. , Triulzi D. J. , Blumberg N.
Published: July 2011

ABO‐mismatched plasma and platelet (PLT) transfusion have been associated with worse outcomes, including haemolysis and other reactions, compared to recipients of ABO‐identical products. The immune complexes that form in a mismatched transfusion have been demonstrated to stimulate pyrogenic cytokine release in vitro. Comparing ABO identical vs. ABO mismatched PLT transfusions, we found no significant difference in the ABO compatibilities between the PLT doses implicated in causing febrile non‐haemolytic transfusion reactions (FNHTR) in 162 recipients and both the baseline PLT donor/recipient ABO compatibility (P = 0·67) or the PLTs issued in the 30 days preceding the FNHTR (P = 0·92). ABO‐mismatched PLT transfusions do not appear to be aetiological agents of FNHTR in a population routinely receiving both ABO‐identical and ABO‐mismatched transfusions.
The Impact of Clique Membership on Children's Social Behavior and Status Nominations
Authors: Kwon Kyongboon , Lease A. Michele , Hoffman Lesa
Published: July 2011

The impact of children's clique membership on their peer nominations for social behaviors and status was examined in a sample of 455 third‐ through fifth‐grade children. Social identity theory (SIT) and children's peer group affiliation and context served as primary conceptual frameworks for this investigation. As suggested by SIT, results indicated that children displayed favorable views toward their own cliquemates, nominating cliquemates more often for positive characteristics (e.g., prosocial, cool) and high status indicators (like‐most, most‐popular) than for negative characteristics (e.g., aggression) and low status indicators (like‐least, least‐popular). At the same time, children's views toward their cliquemates were commensurate with the clique's normative reputations as determined by the broader peer group (i.e., grade). This suggests that children's perceptions toward their cliquemates, albeit favorable, are also regulated by the overall clique context. Meaningful gender and grade effects on children's cliquemate nomination patterns were found. Findings also were discussed regarding the impact of clique size on a peer‐based assessment of social reputations and status.
Family–School Connectedness and Children's Early Social Development
Authors: Serpell Zewelanji N. , Mashburn Andrew J.
Published: July 2011

This study examined the extent to which teacher ratings of the frequency of parent–teacher contacts and quality of parent–teacher relationships in prekindergarten were associated with teachers' perceptions of the quality of their relationship with children and children's social development. Participants were a diverse sample of 2966 four‐year‐olds who attended publicly funded prekindergarten programs in the USA. Results indicated that after controlling for child and family characteristics, the perceived quality of the parent–teacher relationship during prekindergarten was associated with prekindergarten teachers' ratings of children's social development during prekindergarten and kindergarten teachers' ratings at the beginning of kindergarten. Furthermore, the association between quality of the parent–teacher relationship and reductions in problem behavior was stronger among children who experienced social/economic risks.
Disentangling the Social and the Pedagogical in Infants' Learning about Tool‐Use
Authors: Sage Kara D. , Baldwin Dare
Published: July 2011

We investigated infants' response to pedagogy in the domain of tool use. In experiment 1, infants viewed a causally relevant tool‐use demonstration presented identically in either a social/pedagogical or social/non‐pedagogical context. Infants exposed to pedagogical cues displayed superior production of the tool‐use sequence. This was so despite infants displaying equivalent attention to the demonstration across conditions. In contrast, pedagogical cues had no systematic impact on infants' discrimination between causally possible vs. impossible tool‐use sequences in a looking‐time task. Interestingly, however, older infants across both conditions displayed a preference for looking toward the causally possible display. Experiment 2 documented that social cues of any sort (regardless of pedagogy) accompanying the demonstration triggered older infants to discriminate the causally possible vs. impossible events whereas a non‐social demonstration did not. Together, the two experiments implicate ‘social gating’ as well as a pedagogical stance in infants' processing and execution of causal action.
Higher Access‐Associated Bacteremia but Less Hospitalization Among Saudi Compared with US Hemodialysis Outpatients
Authors: El‐Saed Aiman , Sayyari Abdullah , Hejaili Fayez , Sallah Mahmoud , Dagunton Nimfa , Balkhy Hanan
Published: July 2011

Comparison of Saudi patients with chronic hemodialysis to an international benchmark was not performed before. We conducted a prospective surveillance study for all end‐stage kidney disease patients served by the hemodialysis unit at King Abdulaziz Medical City (KAMC) in Riyadh, SA, between May 2008 and December 2009. US National Healthcare Safety Network (NHSN) definitions were used for comparison. Among 227 patients with adverse events, 55% were women and their age was 60.2 ± 20.2 years. Events recorded included 339 all‐cause hospitalizations, 302 outpatient start of intravenous antimicrobials, and 174 access‐associated bacteremias. In comparison with NHSN, hospitalization rate per 100 patient‐months was lower (8.6 vs. 10.7, p < 0.001), rates of both antimicrobial start (7.6 vs. 3.5, p < 0.001) and access‐associated bacteremia (4.4 vs. 1.3, p < 0.001) were higher, and blood cultures were more likely to grow gram‐negative rods (47.9% vs. 21.3%, p < 0.001). Similar to NHSN, permanent catheter was associated with highest, while arterio‐venous fistula was associated with lowest event rates, irrespective of event type. KAMC had 2–4 times higher rates of access‐associated bacteremia and antimicrobial start as well as a higher catheter prevalence (42% vs. 31%). The lower hospitalization may indicate good control of comorbidities at outpatient level or underutilization of inpatient services.
Increased Plasma Chymase Concentration and Mast Cell Chymase Expression in Venous Neointimal Lesions of Patients with CKD and ESRD
Authors: Wasse Haimanot , Rivera Angel A. , Huang Rong , Martinson Deborah E. , Long Qi , McKinnon William , Naqvi Nawazish , Husain Ahsan
Published: July 2011

The underlying inflammatory component of chronic kidney disease may predispose blood vessels to intimal hyperplasia (IH), which is the primary cause of dialysis access failure. We hypothesize that vascular pathology and markers of IH formation are antecedent to arteriovenous (AV) fistula creation. Blood, cephalic, and basilic vein segments were collected from predialysis chronic kidney disease (CKD) patients with no previous AV access and patients with end‐stage renal disease (ESRD). Immunohistochemistry was performed with antibodies against mast cell chymase, transforming growth factor‐beta (TGF‐β) and interleukin‐6 (IL‐6), which cause IH. Plasma chymase was measured by ELISA. IH was present in 91% of CKD and 75% of ESRD vein segments. Chymase was abundant in vessels with IH, with the greatest expression in intima and medial layers, and virtually absent in the controls. Chymase colocalized with TGF‐β1 and IL‐6. Plasma chymase concentration was elevated up to 33‐fold in patients with CKD versus controls and was associated with increased chymase in vessels with IH. We show that chymase expression in vessels with IH corresponds with plasma chymase concentrations. As chymase inhibition attenuates IH in animal models, and we find chymase is highly expressed in IH lesions of patients with CKD and ESRD, we speculate that chymase inhibition could have therapeutic value in humans.
New insights into family learning for refugees: bonding, bridging and building transcultural capital
Authors: Hope Julia
Published: July 2011

For over 20 years, researchers and evaluators worldwide have criticised the traditional formula of family learning courses for their narrow vision, and have emphasised their potential to provide a bridge between home and school experiences, building on resources that parents already have, but which are unknown or unacknowledged. This article argues that research into family learning can usefully be linked to Bourdieu's theory of ‘symbolic capitals’ to acknowledge the stores of wealth that refugee families may possess, which can be activated in the new environment to create ‘transcultural capital’– a relatively new concept in the area of migration studies. Putnam's notions of bonding and bridging capital are also helpful in the design of family learning programmes to consider how best to stimulate social cohesion at the present time. An ethnographic study of a family learning course for refugee parents in two South London schools highlights the need for an understanding of the specific strengths and needs of refugee parents. However, this can only be achieved by taking time to find out about their existing networks, the experience that they bring with them, involving them in course design and delivery, and engaging in discussion about their plans for the future.
Questioning as thinking: a metacognitive framework to improve comprehension of expository text
Authors: Wilson Nance Speizman , Smetana Linda
Published: July 2011

Despite a push to develop high levels of active engagement in learning by helping students reflect, refine and extend their ideas through effective questioning strategies, evidence suggests that teacher‐dominated interaction patterns permeate classroom instruction. This Initiate, Respond and Evaluate process leads students to maintain a passive stance towards learning and non‐engagement with text. As a result students fail to develop the strategies to solve comprehension problems and monitor their own learning with text. In contrast, effective, active instructional patterns provide students with opportunities to negotiate textual meaning. Through the use of the Question as Thinking framework we provide teachers with tools to enable pupils to reflect on their reading and understanding of expository texts. This article describes a framework for questioning designed to assist in the development of an active instructional pattern promoting the joint negotiation of meaning.
Temporal Variation and Host Association in the Campylobacter Population in a Longitudinal Ruminant Farm Study
Authors: Sproston Emma L. , Ogden Iain D. , MacRae Marion , Dallas John F. , Sheppard Samuel K. , Cody Alison J. , Colles Frances M. , Wilson Michael J. , Forbes Ken J. , Strachan Norval J. C.
Published: July 2011

Campylobacter jejuniandC. coliwere quantified and typed, using multilocus sequence typing (MLST), from fecal samples collected from a mixed cattle and sheep farm during summer. Cattle had a significantly higher prevalence than sheep (21.9% [74/338] and 14.0% [30/214], respectively), but both decreased over time. There were no differences in the averageCampylobacterconcentrations shed by cattle (600 CFU g−1) and sheep (820 CFU g−1), although sheep did show a significant temporal reduction in the number ofCampylobacterorganisms shed in their feces. A total of 21 different sequence types (STs) (97.7%C. jejuni, 2.3%C. coli) were isolated from cattle, and 9 different STs were isolated from sheep (40.6%C. jejuni, 59.4%C. coli). TheCampylobacterpopulation in cattle was relatively stable, and the frequencies of genotypes isolated showed little temporal variation. However, the composition of subtypes isolated from sheep did show significant temporal differences. The cattle and sheep consistently showed significant differences in their carriage ofCampylobacterspecies, STs, and CCs despite the fact that both were exposed to the same farming environment. This work has highlighted the patterns of aCampylobacterpopulation on a ruminant farm by identifying the existence of both temporal and between-host variations.
Biodiversity and Biogeography of Rhizobia Associated with Soybean Plants Grown in the North China Plain
Authors: Zhang Yan Ming , Li Ying , Chen Wen Feng , Wang En Tao , Tian Chang Fu , Li Qin Qin , Zhang Yun Zeng , Sui Xin Hua , Chen Wen Xin
Published: July 2011

As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera
Sinorhizobium
and
Bradyrhizobium
, including four novel groups, with
S. fredii
(68.28%) as the dominant group. The phylogeny of symbiotic genes
nodC
and
nifH
defined four lineages among the isolates associated with
Sinorhizobium fredii
,
Bradyrhizobium
elkanii
,
B. japonicum
, and
B. yuanmingense
, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns:
Sinorhizobium
spp. were superdominant in sampling sites with alkaline-saline soils, while
Bradyrhizobium
spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.
Role of Alcohols in Growth, Lipid Composition, and Membrane Fluidity of Yeasts, Bacteria, and Archaea
Authors: Huffer Sarah , Clark Melinda E. , Ning Jonathan C. , Blanch Harvey W. , Clark Douglas S.
Published: July 2011

Increased membrane fluidity, which causes cofactor leakage and loss of membrane potential, has long been documented as a cause for decreased cell growth during exposure to ethanol, butanol, and other alcohols. Reinforcement of the membrane with more complex lipid components is thus thought to be beneficial for the generation of more tolerant organisms. In this study, organisms with more complex membranes, namely, archaea, did not maintain high growth rates upon exposure to alcohols, indicating that more complex lipids do not necessarily fortify the membrane against the fluidizing effects of alcohols. In the presence of alcohols, shifts in lipid composition to more saturated and unbranched lipids were observed in most of the organisms tested, including archaea, yeasts, and bacteria. However, these shifts did not always result in a decrease in membrane fluidity or in greater tolerance of the organism to alcohol exposure. In general, organisms tolerating the highest concentrations of alcohols maintained membrane fluidity after alcohol exposure, whereas organisms that increased membrane rigidity were less tolerant. Altered lipid composition was a common response to alcohol exposure, with the most tolerant organisms maintaining a modestly fluid membrane. Our results demonstrate that increased membrane fluidity is not the sole cause of growth inhibition and that alcohols may also denature proteins within the membrane and cytosol, adversely affecting metabolism and decreasing cell growth.
Defining Components of the Chromosomal Origin of Replication of the Hyperthermophilic Archaeon Pyrococcus furiosus Needed for Construction of a Stable Replicating Shuttle Vector
Authors: Farkas Joel , Chung Daehwan , DeBarry Megan , Adams Michael W. W. , Westpheling Janet
Published: July 2011

We report the construction of a series of replicating shuttle vectors that consist of a low-copy-number cloning vector for
Escherichia coli
and functional components of the origin of replication (
oriC
) of the chromosome of the hyperthermophilic archaeon
Pyrococcus furiosus
. In the process of identifying the minimum replication origin sequence required for autonomous plasmid replication in
P. furiosus
, we discovered that several features of the origin predicted by bioinformatic analysis and
in vitro
binding studies were not essential for stable autonomous plasmid replication. A minimum region required to promote plasmid DNA replication was identified, and plasmids based on this sequence readily transformed
P. furiosus
. The plasmids replicated autonomously and existed in a single copy. In contrast to shuttle vectors based on a plasmid from the closely related hyperthermophile
Pyrococcus abyssi
for use in
P. furiosus
, plasmids based on the
P. furiosus
chromosomal origin were structurally unchanged after transformation and were stable without selection for more than 100 generations.
Effective Antibiotic Resistance Mitigation during Cheese Fermentation
Authors: Li Xinhui , Li Yingli , Alvarez Valente , Harper Willis James , Wang Hua H.
Published: July 2011

Controlling antibiotic-resistant (ART) bacteria in cheese fermentation is important for food safety and public health. A plant-maintained culture was found to be a potential source for ART bacterial contamination in cheese fermentation. Antibiotics had a detectable effect on the ART population from contamination in the finished product. The decrease in the prevalence of antibiotic resistance (AR) in retail cheese samples from 2010 compared to data from 2006 suggested the effectiveness of targeted AR mitigation in related products.
Detection of Coxiella burnetii in Complex Matrices by Using Multiplex Quantitative PCR during a Major Q Fever Outbreak in The Netherlands
Authors: de Bruin A. , de Groot A. , de Heer L. , Bok J. , Wielinga P. R. , Hamans M. , van Rotterdam B. J. , Janse I.
Published: July 2011

Q fever, caused by
Coxiella burnetii
, is a zoonosis with a worldwide distribution. A large rural area in the southeast of the Netherlands was heavily affected by Q fever between 2007 and 2009. This initiated the development of a robust and internally controlled multiplex quantitative PCR (qPCR) assay for the detection of
C. burnetii
DNA in veterinary and environmental matrices on suspected Q fever-affected farms. The qPCR detects three
C. burnetii
targets (
icd
,
com1
, and IS
1111
) and one
Bacillus thuringiensis
internal control target (
cry1b
).
Bacillus thuringiensis
spores were added to samples to control both DNA extraction and PCR amplification. The performance of the qPCR assay was investigated and showed a high efficiency; a limit of detection of 13.0, 10.6, and 10.4 copies per reaction for the targets
icd
,
com1
, and IS
1111
, respectively; and no cross-reactivity with the nontarget organisms tested. Screening for
C. burnetii
DNA on 29 suspected Q fever-affected farms during the Q fever epidemic in 2008 showed that swabs from dust-accumulating surfaces contained higher levels of
C. burnetii
DNA than vaginal swabs from goats or sheep. PCR inhibition by coextracted substances was observed in some environmental samples, and 10- or 100-fold dilutions of samples were sufficient to obtain interpretable signals for both the
C. burnetii
targets and the internal control. The inclusion of an internal control target and three
C. burnetii
targets in one multiplex qPCR assay showed that complex veterinary and environmental matrices can be screened reliably for the presence of
C. burnetii
DNA during an outbreak.
Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont “Candidatus Liberibacter asiaticus” as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats
Authors: Zhou Lijuan , Powell Charles A. , Hoffman Michele T. , Li Wenbin , Fan Guocheng , Liu Bo , Lin Hong , Duan Yongping
Published: July 2011

“
Candidatus
Liberibacter asiaticus” is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of “
Ca
. Liberibacter” associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (
hyv
I
and
hyv
II
) were identified in the prophage regions of the Psy62 “
Ca.
Liberibacter asiaticus” genome. Sequence analyses of the
hyv
I
and
hyv
II
genes in 35 “
Ca.
Liberibacter asiaticus” DNA isolates collected globally revealed that the
hyv
I
gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while
hyv
II
contains up to 2 NITRs and 4 partial repeats and shares homology with
hyv
I
. Frequent deletions or insertions of these repeats within the
hyv
I
and
hyv
II
genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of “
Ca.
Liberibacter asiaticus” bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single “
Ca.
Liberibacter asiaticus”-infected sample. This is the first evidence of different “
Ca.
Liberibacter asiaticus” populations coexisting in a single HLB-affected sample. The Florida “
Ca.
Liberibacter asiaticus” isolates contain both
hyv
I
and
hyv
II
, while all other global “
Ca.
Liberibacter asiaticus” isolates contain either one or the other. Interclade assignments of the putative Hyv
I
and Hyv
II
proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple “
Ca.
Liberibacter asiaticus” populations in the world and a multisource introduction of the “
Ca.
Liberibacter asiaticus” bacterium into Florida.
Low Relative Abundances of the Mucolytic Bacterium Akkermansia muciniphila and Bifidobacterium spp. in Feces of Children with Autism
Authors: Wang Lv , Christophersen Claus T. , Sorich Michael J. , Gerber Jacobus P. , Angley Manya T. , Conlon Michael A.
Published: July 2011

Gastrointestinal disturbance is frequently reported for individuals with autism. We used quantitative real-time PCR analysis to quantify fecal bacteria that could influence gastrointestinal health in children with and without autism. Lower relative abundances of
Bifidobacteria
species and the mucolytic bacterium
Akkermansia muciniphila
were found in children with autism, the latter suggesting mucus barrier changes.
Isolation of Generalized Transducing Bacteriophages for Uropathogenic Strains of Escherichia coli
Authors: Battaglioli E. J. , Baisa G. A. , Weeks A. E. , Schroll R. A. , Hryckowian A. J. , Welch R. A.
Published: July 2011

The traditional genetic procedure for random or site-specific mutagenesis in
Escherichia coli
K-12 involves mutagenesis, isolation of mutants, and transduction of the mutation into a clean genetic background. The transduction step reduces the likelihood of complications due to secondary mutations. Though well established, this protocol is not tenable for many pathogenic
E. coli
strains, such as uropathogenic strain CFT073, because it is resistant to known K-12 transducing bacteriophages, such as P1. CFT073 mutants generated via a technique such as lambda Red mutagenesis may contain unknown secondary mutations. Here we describe the isolation and characterization of transducing bacteriophages for CFT073. Seventy-seven phage isolates were acquired from effluent water samples collected from a wastewater treatment plant in Madison, WI. The phages were differentiated by a host sensitivity-typing scheme with a panel of
E. coli
strains from the ECOR collection and clinical uropathogenic isolates. We found 49 unique phage isolates. These were then examined for their ability to transduce antibiotic resistance gene insertions at multiple loci between different mutant strains of CFT073. We identified 4 different phages capable of CFT073 generalized transduction. These phages also plaque on the model uropathogenic
E. coli
strains 536, UTI89, and NU14. The highest-efficiency transducing phage, ΦEB49, was further characterized by DNA sequence analysis, revealing a double-stranded genome 47,180 bp in length and showing similarity to other sequenced phages. When combined with a technique like lambda Red mutagenesis, the newly characterized transducing phages provide a significant development in the genetic tools available for the study of uropathogenic
E. coli
.
Novel [NiFe]- and [FeFe]-Hydrogenase Gene Transcripts Indicative of Active Facultative Aerobes and Obligate Anaerobes in Earthworm Gut Contents
Authors: Schmidt Oliver , Wüst Pia K. , Hellmuth Susanne , Borst Katharina , Horn Marcus A. , Drake Harold L.
Published: July 2011

The concomitant occurrence of molecular hydrogen (H2) and organic acids along the alimentary canal of the earthworm is indicative of ongoing fermentation during gut passage. Fermentative H2production is catalyzed by [FeFe]-hydrogenases and group 4 [NiFe]-hydrogenases in obligate anaerobes (e.g.,Clostridiales) and facultative aerobes (e.g.,Enterobacteriaceae), respectively, functional groups that might respond differently to contrasting redox conditions. Thus, the objectives of this study were to assess the redox potentials of the alimentary canal ofLumbricus terrestrisand analyze the hydrogenase transcript diversities of H2producers in glucose-supplemented gut content microcosms. Although redox potentials in the core of the alimentary canal were variable on an individual worm basis, average redox potentials were similar. The lowest redox potentials occurred in the foregut and midgut regions, averaging 40 and 110 mV, respectively. Correlation plots between hydrogenase amino acid sequences and 16S rRNA gene sequences indicated that closely related hydrogenases belonged to closely related taxa, whereas distantly related hydrogenases did not necessarily belong to distantly related taxa. Of 178 [FeFe]-hydrogenase gene transcripts, 177 clustered in 12Clostridiales-affiliated operational taxonomic units, the majority of which were indicative of heretofore unknown hydrogenases. Of 86 group 4 [NiFe]-hydrogenase gene transcripts, 79% and 21% were affiliated with organisms in theEnterobacteriaceaeandAeromonadaceae, respectively. The collective results (i) suggest that fermenters must cope with variable and moderately oxidative redox conditions along the alimentary canal, (ii) demonstrate that heretofore undetected hydrogenases are present in the earthworm gut, and (iii) corroborate previous findings implicatingClostridiaceaeandEnterobacteriaceaeas active fermentative taxa in earthworm gut content.
Unexpected Stress-Reducing Effect of PhaP, a Poly(3-Hydroxybutyrate) Granule-Associated Protein, in Escherichia coli
Authors: de Almeida Alejandra , Catone Mariela V. , Rhodius Virgil A. , Gross Carol A. , Pettinari M. Julia
Published: July 2011

Phasins (PhaP) are proteins normally associated with granules of poly(3-hydroxybutyrate) (PHB), a biodegradable polymer accumulated by many bacteria as a reserve molecule. These proteins enhance growth and polymer production in natural and recombinant PHB producers. It has been shown that the production of PHB causes stress in recombinant
Escherichia coli
, revealed by an increase in the concentrations of several heat stress proteins. In this work, quantitative reverse transcription (qRT)-PCR analysis was used to study the effect of PHB accumulation, and that of PhaP from
Azotobacter
sp. strain FA8, on the expression of stress-related genes in PHB-producing
E. coli
. While PHB accumulation was found to increase the transcription of
dnaK
and
ibpA
, the expression of these genes and of
groES
,
groEL
,
rpoH
,
dps
, and
yfiD
was reduced, when PhaP was coexpressed, to levels even lower than those detected in the non-PHB-accumulating control. These results demonstrated the protective role of PhaP in PHB-synthesizing
E. coli
and linked the effects of the protein to the expression of stress-related genes, especially
ibpA
. The effect of PhaP was also analyzed in non-PHB-synthesizing strains, showing that expression of this heterologous protein has an unexpected protective effect in
E. coli
, under both normal and stress conditions, resulting in increased growth and higher resistance to both heat shock and superoxide stress by paraquat. In addition, PhaP expression was shown to reduce RpoH protein levels during heat shock, probably by reducing or titrating the levels of misfolded proteins.
Cell Wall Chitosan Is Necessary for Virulence in the Opportunistic Pathogen Cryptococcus neoformans
Authors: Baker Lorina G. , Specht Charles A. , Lodge Jennifer K.
Published: July 2011

Cryptococcus neoformans
is an opportunistic fungal pathogen that causes meningoencephalitis. Its cell wall is composed of glucans, proteins, chitin, and chitosan. Multiple genetic approaches have defined a chitosan-deficient syndrome that includes slow growth and decreased cell integrity. Here we demonstrate chitosan is necessary for virulence and persistence in the mammalian host.
Pseudomonas aeruginosa tssC1
Links Type VI Secretion and Biofilm-Specific Antibiotic Resistance
Authors: Zhang Li , Hinz Aaron J. , Nadeau Jean-Paul , Mah Thien-Fah
Published: July 2011

Biofilm-specific antibiotic resistance is influenced by multiple factors. We demonstrated that
Pseudomonas aeruginosa tssC1
, a gene implicated in type VI secretion (T6S), is important for resistance of biofilms to a subset of antibiotics. We showed that
tssC1
expression is induced in biofilms and confirmed that
tssC1
is required for T6S.
Proteolytic Cleavage Inactivates the Staphylococcus aureus Lipoteichoic Acid Synthase
Authors: Wörmann Mirka E. , Reichmann Nathalie T. , Malone Cheryl L. , Horswill Alexander R. , Gründling Angelika
Published: July 2011

Lipoteichoic acid (LTA) is a crucial cell envelope component in Gram-positive bacteria. In
Staphylococcus aureus
, the polyglycerolphosphate LTA molecule is synthesized by LtaS, a membrane-embedded enzyme with five N-terminal transmembrane helices (5TM domain) that are connected via a linker region to the C-terminal extracellular enzymatic domain (eLtaS). The LtaS enzyme is processed during bacterial growth, and the eLtaS domain is released from the bacterial membrane. Here we provide experimental evidence that the proteolytic cleavage following residues
215
Ala-Leu-Ala
217
is performed by the essential
S. aureus
signal peptidase SpsB, as depletion of
spsB
results in reduced LtaS processing. In addition, the introduction of a proline residue at the +1 position with respect to the cleavage site, a substitution known to inhibit signal peptidase-dependent cleavage, abolished LtaS processing at this site. It was further shown that the 5TM domain is crucial for enzyme function. The observation that the construction of hybrid proteins between two functional LtaS-type enzymes resulted in the production of proteins unable to synthesize LTA suggests that specific interactions between the 5TM and eLtaS domains are required for function. No enzyme activity was detected upon expression of the 5TM and eLtaS domains as separate fragments, indicating that the two domains cannot assemble postsynthesis to form a functional enzyme. Taken together, our data suggest that only the full-length LtaS enzyme is active in the LTA synthesis pathway and that the proteolytic cleavage step is used as a mechanism to irreversibly inactivate the enzyme.