bluuebunny/crossref_metadata_2025 huggingface dataset:
Fossil leaves bear witness to ancient carbon dioxide levels
Authors: Hand Eric
Published: January 2017

Relics warn that climate may be more sensitive to atmospheric CO
2
than models predict.
A family analysis
Authors: Berg Jeremy
Published: January 2017

A year ago, Science's Editor-in-Chief Marcia McNutt highlighted two new journals in the Science family. Indeed, with the 2016 launches of Science Immunology and Science Robotics, the Science family now has six members including, in addition, Science, Science Signaling, Science Translational Medicine, and Science Advances. This growth has occurred through a number of distinct opportunities, involving the emergence of new multidisciplinary research areas as well as alternative ways to accelerate the communication of research. The family now embodies a range of publishing and editorial models, with the content of Science Robotics and the open-access journal Science Advances handled by academic editors. But the Science journals share a common focus on high quality and, in general, relatively broad scopes. This focus will be maintained as we consider adding to the family. We encourage enthusiasts and the curious to peruse our newest journal, Science Robotics, which is now freely available with a trial subscription through May 2017 to individuals and institutions with Science site licenses.
Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species
Authors: Szymczak Paula , Janzen Thomas , Neves Ana Rute , Kot Witold , Hansen Lars H. , Lametsch René , Neve Horst , Franz Charles M. A. P. , Vogensen Finn K.
Published: December 2016

Bacteriophages are the main cause of fermentation failures in dairy plants. The majority of
Streptococcus thermophilus
phages can be divided into either
cos
- or
pac
-type phages and are additionally characterized by examining the V2 region of their antireceptors. We screened a large number of
S. thermophilus
phages from the Chr. Hansen A/S collection, using PCR specific for the
cos
- or
pac
-type phages, as well as for the V2 antireceptor region. Three phages did not produce positive results with the assays. Analysis of phage morphologies indicated that two of these phages, CHPC577 and CHPC926, had shorter tails than the traditional
S. thermophilus
phages. The third phage, CHPC1151, had a tail size similar to those of the
cos
- or
pac
-type phages, but it displayed a different baseplate structure. Sequencing analysis revealed the genetic similarity of CHPC577 and CHPC926 with a subgroup of
Lactococcus lactis
P335 phages. Phage CHPC1151 was closely related to the atypical
S. thermophilus
phage 5093, homologous with a nondairy streptococcal prophage. By testing adsorption of the related streptococcal and lactococcal phages to the surface of
S. thermophilus
and
L. lactis
strains, we revealed the possibility of cross-interactions. Our data indicated that the use of
S. thermophilus
together with
L. lactis
, extensively applied for dairy fermentations, triggered the recombination between phages infecting different bacterial species. A notable diversity among
S. thermophilus
phage populations requires that a new classification of the group be proposed.

IMPORTANCE
Streptococcus thermophilus
is a component of thermophilic starter cultures commonly used for cheese and yogurt production. Characterizing streptococcal phages, understanding their genetic relationships, and studying their interactions with various hosts are the necessary steps for preventing and controlling phage attacks that occur during dairy fermentations.
Laboratory Surveillance of Polio and Other Enteroviruses in High-Risk Populations and Environmental Samples
Authors: Pogka Vasiliki , Labropoulou Stavroula , Emmanouil Mary , Voulgari-Kokota Androniki , Vernardaki Alexandra , Georgakopoulou Theano , Mentis Andreas F.
Published: December 2016

In the context of poliomyelitis eradication, a reinforced supplementary laboratory surveillance of enteroviruses was implemented in Greece. Between 2008 and 2014, the Hellenic Polioviruses/Enteroviruses Reference Laboratory performed detailed supplementary surveillance of circulating enteroviruses among healthy individuals in high-risk population groups, among immigrants from countries in which poliovirus is endemic, and in environmental samples. In total, 722 stool samples and 179 sewage water samples were included in the study. No wild-type polioviruses were isolated during these 7 years of surveillance, although two imported vaccine polioviruses were detected. Enterovirus presence was recorded in 25.3 and 25.1% of stool and sewage water samples, respectively. Nonpolio enteroviruses isolated from stool samples belonged to species A, B, or C; coxsackievirus A24 was the most frequently identified serotype. Only enteroviruses of species B were identified in sewage water samples, including four serotypes of echoviruses and four serotypes of coxsackie B viruses. Phylogenetic analysis revealed close genetic relationships among virus isolates from sewage water samples and stool samples, which in most cases fell into the same cluster. To the best of our knowledge, this is the first study to compare enterovirus serotypes circulating in fecal specimens of healthy individuals and environmental samples, emphasizing the burden of enterovirus circulation in asymptomatic individuals at high risk. Given that Greece continues to receive a large number of short-term arrivals, students, migrants, and refugees from countries in which poliovirus is endemic, it is important to guarantee high-quality surveillance in order to maintain its polio-free status until global eradication is achieved.

IMPORTANCEThis article summarizes the results of supplementary poliovirus surveillance in Greece and the subsequent characterization of enteroviral circulation in human feces and the environment. The examination of stool samples from healthy refugees and other individuals in “high-risk” groups for poliovirus enables the identification of enterovirus cases and forms the basis for further investigation of the community-level risk of viral transmission. In addition, the examination of composite human fecal samples through environmental surveillance links poliovirus and nonpoliovirus isolates from unknown individuals to populations served by the sewage or wastewater system. Supplementary surveillance is necessary to comply with the prerequisites imposed by the World Health Organization for monitoring the emergence of vaccine-derived polioviruses, reemergence of wild polioviruses, or disappearance of all vaccine-related strains in order for countries such as Greece to maintain their polio-free status and contribute to global poliovirus eradication.
An Effective Counterselection System for Listeria monocytogenes and Its Use To Characterize the Monocin Genomic Region of Strain 10403S
Authors: Argov Tal , Rabinovich Lev , Sigal Nadejda , Herskovits Anat A.
Published: December 2016

Construction of
Listeria monocytogenes
mutants by allelic exchange has been laborious and time-consuming due to lack of proficient selection markers for the final recombination event, that is, a marker conveying substance sensitivity to the bacteria bearing it, enabling the exclusion of merodiploids and selection for plasmid loss. In order to address this issue, we engineered a counterselection marker based on a mutated phenylalanyl-tRNA synthetase gene (
pheS*
). This mutation renders the phenylalanine-binding site of the enzyme more promiscuous and allows the binding of the toxic
p
-chloro-phenylalanine analog (
p
-Cl-phe) as a substrate. When
pheS*
is introduced into
L. monocytogenes
and highly expressed under control of a constitutively active promoter, the bacteria become sensitive to
p
-Cl-phe supplemented in the medium. This enabled us to utilize
pheS*
as a negative selection marker and generate a novel, efficient suicide vector for allelic exchange in
L. monocytogenes
. We used this vector to investigate the monocin genomic region in
L. monocytogenes
strain 10403S by constructing deletion mutants of the region. We have found this region to be active and to cause bacterial lysis upon mitomycin C treatment. The future applications of such an effective counterselection system, which does not require any background genomic alterations, are vast, as it can be modularly used in various selection systems (e.g., genetic screens). We expect this counterselection marker to be a valuable genetic tool in research on
L. monocytogenes
.

IMPORTANCE
L. monocytogenes
is an opportunistic intracellular pathogen and a widely studied model organism. An efficient counterselection marker is a long-standing need in
Listeria
research for improving the ability to design and perform various genetic manipulations and screening systems for different purposes. We report the construction and utilization of an efficient suicide vector for allelic exchange which can be conjugated, leaves no marker in the bacterial chromosome, and does not require the use of sometimes leaky inducible promoters. This highly efficient genome editing tool for
L. monocytogenes
will allow for rapid sequential mutagenesis, introduction of point mutations, and design of screening systems. We anticipate that it will be extensively used by the research community and yield novel insights into the diverse fields studied using this model organism.
Cryptosporidium Attenuation across the Wastewater Treatment Train: Recycled Water Fit for Purpose
Authors: King Brendon , Fanok Stella , Phillips Renae , Lau Melody , van den Akker Ben , Monis Paul
Published: December 2016

Compliance with guideline removal targets for
Cryptosporidium
which do not provide any credit for the inactivation of oocysts through wastewater treatment processes can considerably increase the cost of providing recycled water. Here we present the application of an integrated assay to quantify both oocyst numbers and infectivity levels after various treatment stages at three Victorian and two South Australian (SA) wastewater treatment plants (WWTPs). Oocyst density in the raw sewage was commensurate with community disease burden, with early rounds of sampling capturing a widespread cryptosporidiosis outbreak in Victoria. The level of infectivity of oocysts in sewage was stable throughout the year but was significantly lower at the SA WWTPs. Removals across secondary treatment processes were seasonal, with poorer removals associated with inflow variability; however, no decrease in the oocyst infectivity was identified. For SA WWTPs, those oocysts remaining within the secondary treatment-clarified effluent were proportionally more infectious than those in raw sewage. Lagoon systems demonstrated significant inactivation or removal of oocysts, with attenuation being seasonal. Examination of a UV system emphasized its efficacy as a disinfectant barrier but conversely confirmed the importance of a multibarrier approach with the detection of infectious oocysts postdisinfection. The ability to characterize risk from infectious oocysts revealed that the risk from
Cryptosporidium
is significantly lower than previously thought and that its inclusion in quantitative risk assessments of reuse systems will more accurately direct the selection of treatment strategies and capital expenditure, influencing the sustainability of such schemes.

IMPORTANCE
Here we present the application of a recently developed integrated assay not only to quantify the removal of
Cryptosporidium
oocysts but also to quantify their infectivity across various treatment stages at five wastewater treatment plants (WWTPs), thereby better measuring the “true effect” of the treatment train on oocyst risk reduction. For a number of the WWTPs analyzed in this study the risk, is significantly lower than previously thought. Therefore, the inclusion of oocyst infectivity in guideline values and in quantitative microbial risk assessment (QMRA) has the potential to affect future treatment directions and capital expenditure.
Loop 3 of Fungal Endoglucanases of Glycoside Hydrolase Family 12 Modulates Catalytic Efficiency
Authors: Yang Hong , Shi Pengjun , Liu Yun , Xia Wei , Wang Xiaoyu , Cao Huifang , Ma Rui , Luo Huiying , Bai Yingguo , Yao Bin
Published: December 2016

Glycoside hydrolase (GH) family 12 comprises enzymes with a wide range of activities critical for the degradation of lignocellulose. However, the important roles of the loop regions of GH12 enzymes in substrate specificity and catalytic efficiency remain poorly understood. This study examined how the loop 3 region affects the enzymatic properties of GH12 glucanases usingNfEG12A fromNeosartorya fischeriP1 and EG (PDB1KS4) fromAspergillus niger. Acidophilic and thermophilicNfEG12A had the highest catalytic efficiency (kcat/Km, 3,001 and 263 ml/mg/s toward lichenin and carboxymethyl cellulose sodium [CMC-Na], respectively) known so far. Based on the multiple-sequence alignment and homology modeling, two specific sequences (FN and STTQA) were identified in the loop 3 region of GH12 endoglucanases from fungi. To determine their functions, these sequences were introduced intoNfEG12A, or the counterpart sequence STTQA was removed from EG. These modifications had no effects on the optimal pH and temperature or substrate specificity but changed the catalytic efficiency (kcat/Km) of these enzymes (in descending order,NfEG12A [100%],NfEG12A-FN [140%], andNfEG12A-STTQA [190%]; EG [100%] and EGΔSTTQA [41%]). Molecular docking and dynamic simulation analyses revealed that the longer loop 3 in GH12 may strengthen the hydrogen-bond interactions between the substrate and protein, thereby increasing the turnover rate (kcat). This study provides a new insight to understand the vital roles of loop 3 for GH12 endoglucanases in catalysis.

IMPORTANCELoop structures play critical roles in the substrate specificity and catalytic hydrolysis of GH12 enzymes. Three typical loops exist in these enzymes. Loops 1 and 2 are recognized as the catalytic loops and are closely related to the substrate specificity and catalytic efficiency. Loop 3 locates in the −1 or +1 subsite and varies a lot in amino acid composition, which may play a role in catalysis. In this study, two GH12 glucanases,NfEG12A and EG, which were mutated by introducing or deleting partial loop 3 sequences FN and/or STTQA, were selected to identify the function of loop 3. It revealed that the longer loop 3 of GH12 glucanases may strengthen the hydrogen network interactions between the substrate and protein, consequently increasing the turnover rate (kcat). This study proposes a strategy to increase the catalytic efficiency of GH12 glucanases by improving the hydrogen network between substrates and catalytic loops.
N-Glycosylation Is Important for Proper Haloferax volcanii S-Layer Stability and Function
Authors: Tamir Adi , Eichler Jerry
Published: December 2016

N-Glycosylation, the covalent linkage of glycans to select Asn residues of target proteins, is an almost universal posttranslational modification in archaea. However, whereas roles for N-glycosylation have been defined in eukarya and bacteria, the function of archaeal N-glycosylation remains unclear. Here, the impact of perturbed N-glycosylation on the structure and physiology of the haloarchaeon
Haloferax volcanii
was considered. Cryo-electron microscopy was used to examine right-side-out membrane vesicles prepared from cells of a parent strain and from strains lacking genes encoding glycosyltransferases involved in assembling the N-linked pentasaccharide decorating the surface layer (S-layer) glycoprotein, the sole component of the S-layer surrounding
H. volcanii
cells. Whereas a regularly repeating S-layer covered the entire surface of vesicles prepared from parent strain cells, vesicles from the mutant cells were only partially covered. To determine whether such N-glycosylation-related effects on S-layer assembly also affected cell function, the secretion of a reporter protein was addressed in the parent and N-glycosylation mutant strains. Compromised S-layer glycoprotein N-glycosylation resulted in impaired transfer of the reporter past the S-layer and into the growth medium. Finally, an assessment of S-layer glycoprotein susceptibility to added proteases in the mutants revealed that in cells lacking AglD, which is involved in adding the final pentasaccharide sugar, a distinct S-layer glycoprotein conformation was assumed in which the N-terminal region was readily degraded. Perturbed N-glycosylation thus affects S-layer glycoprotein folding. These findings suggest that
H. volcanii
could adapt to changes in its surroundings by modulating N-glycosylation so as to affect S-layer architecture and function.

IMPORTANCE
Long held to be a process unique to eukaryotes, it is now accepted that bacteria and archaea also perform N-glycosylation, namely, the covalent attachment of sugars to select asparagine residues of target proteins. Yet, while information on the importance of N-glycosylation in eukaryotes and bacteria is available, the role of this posttranslational modification in archaea remains unclear. Here, insight into the purpose of archaeal N-glycosylation was gained by addressing the surface layer (S-layer) surrounding cells of the halophilic species
Haloferax volcanii
. Relying on mutant strains defective in N-glycosylation, such efforts revealed that compromised N-glycosylation affected S-layer integrity and the transfer of a secreted reporter protein across the S-layer into the growth medium, as well as the conformation of the S-layer glycoprotein, the sole component of the S-layer. Thus, by modifying N-glycosylation,
H. volcanii
cells can change how they interact with their surroundings.
Dynamics of Salmonella Shedding and Welfare of Hens in Free-Range Egg Production Systems
Authors: Gole Vaibhav C. , Woodhouse Rebecca , Caraguel Charles , Moyle Talia , Rault Jean-Loup , Sexton Margaret , Chousalkar Kapil
Published: December 2016

The current study investigated the effect of environmental stressors (i.e., weather changes) on
Salmonella
shedding in free-range production systems and the correlations with behavioral and physiological measures (i.e., fecal glucocorticoid metabolites). This involved longitudinal and point-in-time surveys of
Salmonella
shedding and environmental contamination on four commercial free-range layer farms. The shedding of
Salmonella
was variable across free-range farms and in different seasons. There was no significant effect of season on the
Salmonella
prevalence during this investigation. In this study, the combined
Salmonella
most probable number (MPN) counts in environmental (including feces, egg belt, dust, nest box, and ramp) samples were highest in samples collected during the summer season (4th sampling, performed in February). The predominant serovars isolated during this study were
Salmonella enterica
serovar Mbandaka and
Salmonella enterica
serovar Typhimurium phage types 135 and 135a. These two phage types were involved in several egg product-related
Salmonella
outbreaks in humans. Multilocus variable-number tandem-repeat analysis (MLVA) results indicated that MLVA types detected from human food poisoning cases exhibited MLVA patterns similar to the strains isolated during this study. All
Salmonella
isolates (
n =
209) were tested for 15 different genes involved in adhesion, invasion, and survival of
Salmonella
spp. We also observed variations for
sopA
,
ironA
, and
misL
. There were no positive correlations between fecal corticosterone metabolite (FCM) and
Salmonella
prevalence and/or shedding in feces. Also, there were no positive correlations between
Salmonella
prevalence and
Salmonella
count (log MPN) and any of the other welfare parameters.

IMPORTANCE
In this study, the welfare of laying hens and
Salmonella
shedding were compared over a prolonged period of time in field conditions. This study investigated the long-term shedding of
Salmonella
serovars in a free-range egg production system. Given that there is increasing demand for free-range eggs, it is essential to understand the risks associated with such a production system.
Cell-associated oligosaccharides of Bradyrhizobium spp
Authors: Miller K J , Gore R S , Johnson R , Benesi A J , Reinhold V N
Published: January 2017

We report the initial characterization of the cell-associated oligosaccharides produced by four Bradyrhizobium strains: Bradyrhizobium japonicum USDA 110, USDA 94, and ATCC 10324 and Bradyrhizobium sp. strain 32H1. The cell-associated oligosaccharides of these strains were found to be composed solely of glucose and were predominantly smaller than the cyclic beta-1,2-glucans produced by Agrobacterium and Rhizobium species. Linkage studies and nuclear magnetic resonance analyses demonstrated that the bradyrhizobial glucans are linked primarily by beta-1,6 and beta-1,3 glycosidic bonds. Thus, the bradyrhizobia appear to synthesize cell-associated oligosaccharides of structural character substantially different from that of the cyclic beta-1,2-glucans produced by Agrobacterium and Rhizobium species.
Increased expression of the bifunctional protein PrlF suppresses overproduction lethality associated with exported beta-galactosidase hybrid proteins in Escherichia coli
Authors: Kiino D R , Phillips G J , Silhavy T J
Published: January 2017

We have cloned and determined the nucleotide sequence of the prlF gene. An open reading frame predicting a 111-amino-acid protein (Mr 12,351) with an acidic carboxy terminus was identified. The DNA sequence preceding this open reading frame revealed a putative promoter and a ribosome-binding site. The nucleotide sequence of the prlF1 mutation revealed a 7-base-pair duplication resulting in a slightly smaller predicted gene product of Mr 12,009 that lacked the acidic carboxy terminus. Maxicell analysis of prlF and prlF1 subclones identified peptides of sizes similar to those predicted by the nucleotide sequences. The prlF sequence was shown to be expressed in vivo by both maxicell analysis and construction of a prlF-lacZ fusion. Two kanamycin resistance insertions within the prlF open reading frame were introduced into the chromosome, replacing the wild-type gene. In contrast to the prlF1 mutation, these insertions had no detectable effect on cell growth or on the beta-galactosidase activity or maltose sensitivity (two sensitive indicators of hybrid protein export) conferred by the lamB-lacZ42-1 gene fusion. Overproduction of the wild-type prlF gene product from a plasmid carrying an active hybrid promoter, however, conferred a prlF1 phenotype. In addition, both the prlF1 mutation and both kanamycin resistance insertions increased the beta-galactosidase activity of a prlF-lacZ fusion. These results suggest that prlF is autoregulated and that overproduction of the prlF gene product increases the export efficiency of beta-galactosidase hybrid proteins from the cytoplasm.
Identification, distribution, and sequence analysis of new insertion elements in Caulobacter crescentus
Authors: Ohta N , Mullin D A , Tarleton J , Ely B , Newton A
Published: January 2017

We describe two insertion elements isolated from Caulobacter crescentus that are designated IS298 and IS511. These insertion elements were cloned from spontaneous flagellar (fla) gene mutants SC298 and SC511 derived from the wild-type strain CB15 (ATCC 19089), in which they were originally identified as insertions in the flbG operon of the hook gene cluster (N. Ohta, E. Swanson, B. Ely, and A. Newton, J. Bacteriol. 158:897-904, 1984). IS298 and IS511 were each present in C. crescentus CB2 and CB15 in at least four different positions, but neither was present in strain CB13 or in several Caulobacter species examined, including C. vibrioides, C. leidyia, and C. henricii. Nucleotide sequence analysis across the chromosome-insertion element junctions showed that IS298 is located 152 base pairs (bp) upstream from the ATG translation start of the hook protein gene flaK, where it is bounded by a 4-bp direct repeat derived from the site of insertion, and that IS511 is inserted at codon 186 of the flaK coding sequence, where it is also bounded by a 4-bp direct repeat duplicated from the site of insertion. The ilvB102 mutation in strain SC125 was also shown to result from insertion sequence IS511, but no duplication of the genomic sequence was present at the insertion element junctions. IS298 contains an imperfect terminal inverted repeat 16 bp long, and IS511 contains a 32-bp inverted repeat at the termini. IS298 and IS511 are the first insertion elements described in C. crescentus.
The rpoN gene product of Pseudomonas aeruginosa is required for expression of diverse genes, including the flagellin gene
Authors: Totten P A , Lara J C , Lory S
Published: January 2017

The product of the rpoN gene is an alternative sigma factor of RNA polymerase which is required for transcription of a number of genes in members of the family Enterobacteriaceae, including those that specify enzymes of nitrogen assimilation, amino acid uptake, and degradation of a variety of organic molecules. We have previously shown that transcription of the pilin gene of Pseudomonas aeruginosa also requires RpoN (K. S. Ishimoto and S. Lory, Proc. Natl. Acad. Sci. USA 86:1954-1957, 1989) and have undertaken a more extensive survey of genes under RpoN control. Strains of P. aeruginosa that carry an insertionally inactivated rpoN gene were constructed and shown to be nonmotile because of the inability of these mutants to synthesize flagellin. The mutation in rpoN had no effect on expression of extracellular polypeptides, outer membrane proteins, and the alginate capsule. However, the rpoN mutants were glutamine auxotrophs and were defective in glutamine synthetase, indicating defects in nitrogen assimilation. In addition, the P. aeruginosa rpoN mutants were defective in urease activity. These findings indicate that the sigma factor encoded by the rpoN gene is used by P. aeruginosa for transcription of a diverse set of genes that specify biosynthetic enzymes, degradative enzymes, and surface components. These rpoN-controlled genes include pili and flagella which are required for full virulence of the organism.
Nucleotide sequence and cloning in Bacillus subtilis of the Bacillus stearothermophilus pleiotropic regulatory gene degT
Authors: Takagi M , Takada H , Imanaka T
Published: January 2017

The regulatory gene (degT) from Bacillus stearothermophilus NCA1503 which enhanced production of extracellular alkaline protease (Apr) was cloned in Bacillus subtilis with pTB53 as a vector. When B. subtilis MT-2 (Npr- [deficiency of neutral protease] Apr+) was transformed with the recombinant plasmid, pDT145, the plasmid carrier produced about three times more alkaline protease than did the wild-type strain. In contrast, when B. subtilis DB104 (Npr- Apr-) was used as a host, the transformant with pDT145 could not exhibit any protease activity. After construction of the deletion plasmids, DNA sequencing was done. A large open reading frame was found, and nucleotide sequence analysis showed that the degT gene was composed of 1,116 bases (372 amino acid residues, molecular weight of 41,244). A Shine-Dalgarno sequence was found nine bases upstream from the open reading frame. A B. subtilis strain carrying degT showed the following pleiotropic phenomena: (i) enhancement of production of extracellular enzymes such as alkaline protease and levansucrase, (ii) repression of autolysin activity, (iii) decrease of transformation efficiency for B. subtilis (competent cell procedure), (iv) altered control of sporulation, (v) loss of flagella, and (vi) abnormal cell division. When B. stearothermophilus SIC1 was transformed with the recombinant plasmid carrying degT, the transformants exhibited abnormal cell division. These phenomena are similar to those of the phenotypes of degSU(Hy) (hyperproduction), degQ(Hy), and degR mutants of B. subtilis. However, the amino acid sequence of the degT product (DegT) is different from those of the reported gene products. Furthermore, DegT includes a hydrophobic core region in the N-terminal portion (amino acid numbers 50 to 160), a consensus sequence for a DNA binding region (amino acid numbers 160 to 179), and a region homologous to transcription activator proteins (amino acid numbers 351 to 366). We discuss the possibility that the membrane protein DegT functions as a sensor protein and transfers the signal of environmental stimuli to the regulatory region of target genes to activate or repress transcription of the genes.
The spoIIJ gene, which regulates early developmental steps in Bacillus subtilis, belongs to a class of environmentally responsive genes
Authors: Antoniewski C , Savelli B , Stragier P
Published: January 2017

The Bacillus subtilis spoIIJ locus is defined by a Tn917 insertion which leads to an oligosporogenous phenotype. Here we show that this mutation severely decreases transcription of spoIIA, spoIIE, and spoIIG, three operons involved in asymmetric septation, the earliest morphological event of sporulation. A 14.3-kilobase region overlapping the site of the spoIIJ::Tn917 insertion was cloned and the exact location of the spoIIJ gene was defined with various integrative plasmids carrying subfragments of that region. DNA sequencing established that spoIIJ is a monocistronic locus encoding a 606-amino-acid polypeptide which contains a canonical "transmitter" domain, indicating that spoIIJ is a new member of the "sensor" class of signal-transducing systems in bacteria. Thus, spoIIj, which is transcribed during vegetative growth, presumably under the control of sigma H, encodes a protein that could interact with major regulators of early sporulation stages, such as SpoOA and/or SpoOF.
Mechanisms of ACL injury in professional rugby union: a systematic video analysis of 36 cases
Authors: Montgomery Connor , Blackburn Jeff , Withers Daniel , Tierney Gregory , Moran Cathal , Simms Ciaran
Published: December 2016

Background

The mechanisms of ACL injury in rugby are not well defined.

Aim

To describe the mechanisms of ACL injury in male professional rugby players using systematic video analysis.

Methods

36 cases from games played in top professional leagues and international matches were analysed. 5 analysts independently assessed all videos to record the estimated frame/time of initial ground contact, frame/time of ACL tear and a range of play specific variables. This included contact versus non-contact ACL injuries, injury timing, joint flexion angles and foot contact with the ground. 37 side-stepping manoeuvres from a control game were analysed to allow comparison of non-injury versus injury situations.

Results

57% of ACL injuries occurred in a contact manner. 2 main scenarios were identified: (1) offensive running and (2) being tackled, indicating that the ball carrier might be at higher risk of ACL injury. The majority of non-contact ACL injuries resulted from a side-stepping manoeuvre. In most non-contact cases, initial ground contact was through heel strike. Statistical assessment of heel strike at initial ground contact versus non-heel strike cases showed a significant difference in injury versus non-injury outcomes, with heel strike associated with higher injury risk. Non-contact ACL injuries had lower median knee flexion angles and a more dorsiflexed ankle when compared with a control group (10° vs 20°, p≤0.001 and 10° vs 0°, p=0.033 respectively).

Conclusions

Over half of ACL injuries in rugby in our analysis resulted from a contact mechanism. For non-contact injuries, lower knee flexion angles and heel-first ground contact in a side-stepping manoeuvre were associated with ACL injury.
Are Olympic athletes free from cardiovascular diseases? Systematic investigation in 2352 participants from Athens 2004 to Sochi 2014
Authors: Pelliccia Antonio , Adami Paolo Emilio , Quattrini Filippo , Squeo Maria Rosaria , Caselli Stefano , Verdile Luisa , Maestrini Viviana , Di Paolo Fernando , Pisicchio Cataldo , Ciardo Roberto , Spataro Antonio
Published: December 2016

Context

Olympic athletes represent model of success in our society, by enduring strenuous conditioning programmes and achieving astonishing performances. They also raise scientific and clinical interest, with regard to medical care and prevalence of cardiovascular (CV) abnormalities.

Objective

Our aim was to assess the prevalence and type of CV abnormalities in this selected athlete's cohort.

Design, setting and participants

2352 Olympic athletes, mean age 25±6, 64% men, competing in 31 summer or 15 winter sports, were examined with history, physical examination, 12-lead and exercise ECG and echocardiography. Additional testing (cardiac MRI, CT scan) or electrophysiological assessments were selectively performed when indicated.

Main outcome measures

Prevalence and type of CV findings, abnormalities and diseases found in Olympic athletes over 10 years.

Results

A subset of 92 athletes (3.9%) showed abnormal CV findings. Structural abnormalities included inherited cardiomyopathies (n=4), coronary artery disease (n=1), perimyocarditis (n=4), myocardial bridges (n=2), valvular and congenital diseases (n=45) and systemic hypertension (n=10). Primary electrical diseases included atrial fibrillation (n=2), supraventricular reciprocating tachycardia (n=14), complex ventricular tachyarrhythmias (non-sustained ventricular tachycardia, n=7; bidirectional ventricular tachycardia, n=1) or major conduction disorders (Wolff-Parkinson-White (WPW), n=1; Long QT syndrome (LQTS), n=2).

Conclusions

Our study revealed an unexpected prevalence of CV abnormalities among Olympic athletes, including a small, but not negligible proportion of pathological conditions at risk. This observation suggests that Olympic athletes, despite the absence of symptoms or astonishing performances, are not immune from CV disorders and might be exposed to unforeseen high-risk during sport activity.
Determinants of adherence to antiretroviral therapy among HIV-positive adults in sub-Saharan Africa: a systematic review
Authors: Heestermans Tessa , Browne Joyce L , Aitken Susan C , Vervoort Sigrid C , Klipstein-Grobusch Kerstin
Published: December 2016

Objective

The rapid scale up of antiretroviral treatment (ART) in sub-Saharan Africa (SSA) has resulted in an increased focus on patient adherence. Non-adherence can lead to drug-resistant HIV caused by failure to achieve maximal viral suppression. Optimal treatment requires the identification of patients at high risk of suboptimal adherence and targeted interventions. The aim of this review was to identify and summarise determinants of adherence to ART among HIV-positive adults.

Design

Systematic review of adherence to ART in SSA from January 2002 to October 2014.

Methods

A systematic search was performed in 6 databases (PubMed, Cochrane Library, EMBASE, Web of Science, Popline, Global Health Library) for qualitative and quantitative articles. Risk of bias was assessed. A meta-analysis was conducted for pooled estimates of effect size on adherence determinants.

Results

Of the 4052 articles screened, 146 were included for final analysis, reporting on determinants of 161 922 HIV patients with an average adherence score of 72.9%. Main determinants of non-adherence were use of alcohol, male gender, use of traditional/herbal medicine, dissatisfaction with healthcare facility and healthcare workers, depression, discrimination and stigmatisation, and poor social support. Promoters of adherence included counselling and education interventions, memory aids, and active disclosure among people living with HIV. Determinants of health status had conflicting influence on adherence.

Conclusions

The sociodemographic, psychosocial, health status, treatment-related and intervention-related determinants are interlinked and contribute to optimal adherence. Clinics providing ART in SSA should therefore design targeted interventions addressing these determinants to optimise health outcomes.
How long do patients with chronic disease expect to live? A systematic review of the literature
Authors: Hole Barnaby , Salem Joseph
Published: December 2016

Objective

To systematically identify and summarise the literature on perceived life expectancy among individuals with non-cancer chronic disease.

Setting

Published and grey literature up to and including September 2016 where adults with non-cancer chronic disease were asked to estimate their own life expectancy.

Participants

From 6837 screened titles, 9 articles were identified that met prespecified criteria for inclusion. Studies came from the UK, Netherlands and USA. A total of 729 participants were included (heart failure (HF) 573; chronic obstructive pulmonary disease (COPD) 89; end-stage renal failure 62; chronic kidney disease (CKD) 5). No papers reporting on other lung diseases, neurodegenerative disease or cirrhosis were found.

Primary and secondary outcome measures

All measures of self-estimated life expectancy were accepted. Self-estimated life expectancy was compared, where available, with observed survival, physician-estimated life expectancy and model-estimated life expectancy. Meta-analysis was not conducted due to the heterogeneity of the patient groups and study methodologies.

Results

Among patients with HF, median self-estimated life expectancy was 40% longer than predicted by a validated model. Outpatients receiving haemodialysis were more optimistic about prognosis than their nephrologists and overestimated their chances of surviving 5 years. Patients with HF and COPD were approximately three times more likely to die in the next year than they predicted. Data available for patients with CKD were of insufficient quality to draw conclusions.

Conclusions

Individuals with chronic disease may have unrealistically optimistic expectations of their prognosis. More research is needed to understand how perceived life expectancy affects behaviour. Meanwhile, clinicians should attempt to identify each patient's prognostic preferences and provide information in a way that they can understand and use to inform their decisions.

Trial registration number

CRD42015020732.
Can recombinant human thrombomodulin increase survival among patients with severe septic-induced disseminated intravascular coagulation: a single-centre, open-label, randomised controlled trial
Authors: Hagiwara Akiyoshi , Tanaka Noriko , Uemura Tatsuki , Matsuda Wataru , Kimura Akio
Published: December 2016

Objective

To determine whether treatment with recombinant human thrombomodulin (rhTM) increases survival among patients with severe septic-induced disseminated intravascular coagulation (DIC).

Design

Single-centre, open-label, randomised controlled trial.

Setting

Single tertiary hospital.

Participant

92 patients with severe septic-induced DIC.

Interventions

Patients with DIC scores ≥4, as defined by the Japanese Association of Acute Medicine, were diagnosed with DIC. The envelope method was used for randomisation. The treatment group (rhTM group, n=47) was intravenously treated with rhTM within 24 hours of admission (day 0), and the control group (n=45) did not receive any anticoagulants, except in cases of deep venous thrombosis and pulmonary embolism.

Primary and secondary measurements

Data were collected on days 0 (admission), 1, 2, 3, 5, 7 and 10. The primary outcome was survival at 28 and 90 days. The secondary end points comprised changes in DIC scores, platelet counts,d-dimer, antithrombin III and C reactive protein levels, and Sequential Organ Failure Assessment (SOFA) scores. All analyses were conducted on an intent-to-treat basis.

Main results

The 28-day survival rates were 84% and 83% in the control and rhTM groups, respectively (p=0.745, log-rank test). The 90-day survival rates were 73% and 72% in the control and rhTM groups, respectively (p=0.94, log-rank test). Meanwhile, the rates of recovery from DIC (<4) were significantly higher in the rhTM group than in the control group (p=0.001, log-rank test). Relative change from baseline ofd-dimer levels was significantly lower in the rhTM group than in the control group, on days 3 and 5.

Conclusions

rhTM treatment decreasedd-dimer levels and facilitated DIC recovery in patients with severe septic-induced DIC. However, the treatment did not improve survival in this cohort.

Trial registration number

UMIN000008339.
To condition or not condition? Analysing ‘change’ in longitudinal randomised controlled trials
Authors: Coffman Cynthia J , Edelman David , Woolson Robert F
Published: December 2016

Objective

The statistical analysis for a 2-arm randomised controlled trial (RCT) with a baseline outcome followed by a few assessments at fixed follow-up times typically invokes traditional analytic methods (eg, analysis of covariance (ANCOVA), longitudinal data analysis (LDA)). ‘Constrained’ longitudinal data analysis (cLDA) is a well-established unconditional technique that constrains means of baseline to be equal between arms. We use an analysis of fasting lipid profiles from the Group Medical Clinics (GMC) longitudinal RCT on patients with diabetes to illustrate applications of ANCOVA, LDA and cLDA to demonstrate theoretical concepts of these methods including the impact of missing data.

Methods

For the analysis of the illustrated example, all models were fit using linear mixed models to participants with only complete data and to participants using all available data.

Results

With complete data (n=195), 95% CI coverage are equivalent for ANCOVA and cLDA with an estimated 11.2 mg/dL (95% CI −19.2 to −3.3; p=0.006) lower mean low-density lipoprotein (LDL) cholesterol in GMC compared with usual care. With all available data (n=233), applying the cLDA model yielded an LDL improvement of 8.9 mg/dL (95% CI −16.7 to −1.0; p=0.03) for GMC compared with usual care. The less efficient, LDA analysis yielded an LDL improvement of 7.2 mg/dL (95% CI −17.2 to 2.8; p=0.15) for GMC compared with usual care.

Conclusions

Under reasonable missing data assumptions, cLDA will yield efficient treatment effect estimates and robust inferential statistics. It may be regarded as the method of choice over ANCOVA and LDA.
Cohort study of early literacy and childbearing over the reproductive lifecourse
Authors: Seymour Jane W , Frasso Rosemary , Shofer Frances S , Bennett Ian M
Published: December 2016

Introduction

Literacy is linked to a range of health outcomes, but its association with reproductive health in high-income countries is not well understood. We assessed the relationship between early-life literacy and childbearing across the reproductive lifecourse in the USA.

Study design

A prospective cohort design was employed to assess early-life literacy and subsequent childbearing, using data from the National Longitudinal Survey of Youth 1979. The US youth aged 14–22 years in 1979, including 6283 women, were surveyed annually through 1994 and biannually thereafter. Literacy was assessed in 1980 using the Armed Services Vocational Aptitude Battery Reading Grade Level (RGL). Cumulative childbearing and grand multiparity (≥5 births) were assessed in 2010. Summary statistics, χ2, Kruskal-Wallis, test for trend and logistic regression, were used.

Results

Of 6283 women enrolled, 4025 (64%) had complete data and were included in the analyses. In 1980, these women were on average 18 years old and in 2010 they were 45. Median cumulative parity decreased for each RGL and ranged from 3.0 (<5th grade) to 2.0 (>12th grade) (p=0.001). Adjusting for race/ethnicity, poverty status, whether a woman had had a child in 1980, and age in 1980, odds of grand multiparity were 1.9 (95% CI 1.1 to 3.5) and 1.8 (95% CI 1.0 to 3.3), greater among women with <5th or 5–6th grade literacy compared with those ≥12th literacy.

Discussion

In the USA, early-life literacy is associated with total parity over a woman's lifecourse. Literacy is a powerful social determinant of reproductive health in this high-income nation just as it has been shown to be in low-income nations.
Effectiveness of Senior Dance on risk factors for falls in older adults (DanSE): a study protocol for a randomised controlled trial
Authors: Franco Marcia R , Sherrington Catherine , Tiedemann Anne , Pereira Leani S , Perracini Monica R , Faria Claudia R S , Pinto Rafael Z , Pastre Carlos M
Published: December 2016

Introduction

Strong evidence shows that exercise is effective to improve fall risk factors among older people. However, older people's participation and adherence to exercise programmes is suboptimal. Type of exercise and apathy are reported to be barriers to exercise participation, suggesting that new effective interventions are needed. The primary aim of this randomised controlled trial is to investigate the effect of Senior Dance plus brief education for falls prevention on balance among people aged 60 years or over, compared with a control group receiving only brief education.

Methods and analysis

This single-blind randomised controlled trial will involve 82 community-dwelling older people aged 60 years or over who are cognitively intact. Participants allocated to the intervention group will attend a single educational class on strategies to prevent falls, and will participate in a 12-week, twice-weekly group-based programme of Senior Dance. The Senior Dance consists of different choreographies, which include rhythmic and simple movements with rhythmic folk songs. Participants allocated to the control group will attend the same educational class that intervention group participants will receive, and will be instructed not to take part in any regular exercise programme. The primary outcome will be single-leg stance with eyes closed. Secondary outcomes include: Short Physical Performance Battery, Falls Efficacy Scale, Trail Making Test and the Montreal Cognitive Assessment. Continuous outcomes will be reported using mean (SD) or median (IQR), depending on the distribution of the data. The linear regression approach to analysis of covariance will be used to compare the mean effect between groups. All patients will be included in the analyses following an intention-to-treat approach.

Ethics and dissemination

Ethics approval has been granted by the Human Ethics Committee of the São Paulo State University (CAAE 48665215.9.0000.5402). Outcomes will be disseminated through publication in peer-reviewed journals and presentations at conferences.

Trial registration number

NCT02603523, Pre-results.
Realistic evaluation of Situation Awareness for Everyone (SAFE) on paediatric wards: study protocol
Authors: Deighton J , Edbrooke-Childs J , Stapley E , Sevdalis N , Hayes J , Gondek D , Sharples E , Lachman P
Published: December 2016

Introduction

Evidence suggests that health outcomes for hospitalised children in the UK are worse than other countries in Europe, with an estimated 1500 preventable deaths in hospital each year. It is presumed that some of these deaths are due to unanticipated deterioration, which could have been prevented by earlier intervention, for example, sepsis. The Situation Awareness For Everyone (SAFE) intervention aims to redirect the ‘clinical gaze’ to encompass a range of prospective indicators of risk or deterioration, including clinical indicators and staff concerns, so that professionals can review relevant information for any given situation. Implementing the routine use of huddles is central to increasing situation awareness in SAFE.

Methods and analysis

In this article, we describe the realistic evaluation framework within which we are evaluating the SAFE programme. Multiple methods and data sources are used to help provide a comprehensive understanding of what mechanisms for change are triggered by an intervention and how they have an impact on the existing social processes sustaining the behaviour or circumstances that are being targeted for change.

Ethics and dissemination

Ethics approval was obtained from London—Dulwich Research Ethics Committee (14/LO/0875). It is anticipated that the findings will enable us to understand what the important elements of SAFE and the huddle are, the processes by which they might be effective and—given the short timeframes of the project—initial effects of the intervention on outcomes. The present research will add to the extant literature by providing the first evidence of implementation of SAFE and huddles in paediatric wards in the UK.