bluuebunny/crossref_metadata_2025 huggingface dataset:
Protective Effects of Human and Mouse Soluble Scavenger-Like CD6 Lymphocyte Receptor in a Lethal Model of Polymicrobial Sepsis
Authors: Martínez-Florensa Mario , Consuegra-Fernández Marta , Aranda Fernando , Armiger-Borràs Noelia , Di Scala Marianna , Carrasco Esther , Pachón Jerónimo , Vila Jordi , González-Aseguinolaza Gloria , Lozano Francisco
Published: November 2016

Sepsis still constitutes an unmet clinical need, which could benefit from novel adjunctive strategies to conventional antibiotic therapy. The soluble form of the scavenger-like human CD6 lymphocyte receptor (shCD6) binds to key pathogenic components from Gram-positive and -negative bacteria and shows time- and dose-dependent efficacy in mouse models of monobacterial sepsis. The objective of the present work was to demonstrate the effectiveness of infusing mouse and human sCD6 by different systemic routes, either alone or as adjunctive therapy to gold standard antibiotics, in a lethal model of polymicrobial sepsis. To this end, C57BL/6 mice undergoing high-grade septic shock induced by cecal ligation and puncture (CLP; ≥90% lethality) were infused via the intraperitoneal (i.p.) or intravenous (i.v.) route with shCD6 at different doses and time points, either alone or in combination with imipenem/cilastatin (I/C) at a dose of 33 mg/kg of body weight every 8 h. Significantly reduced mortality and proinflammatory cytokine levels were observed by i.p. infusion of a single shCD6 dose (1.25 mg/kg) 1 h pre- or post-CLP. When using the i.v. route, mice survival was significantly extended by starting shCD6 infusion at later time points post-CLP (up to 6 h after CLP). Significant adjunctive effects on mouse survival were observed by i.p. or i.v. infusion of shCD6 in combination with i.p. I/C post-CLP. Similar results were obtained in mice expressing high sustained levels (5 to 10 μg/ml) of mouse sCD6 in serum by means of transduction with hepatotropic adeno-associated virus (AAV). Taken together, the data support the conserved antibacterial effects of human and mouse sCD6 and their use as adjunctive therapy in experimental models of complex and severe polymicrobial sepsis.
A Naturally Occurring Single Nucleotide Polymorphism in a Multicopy Plasmid Produces a Reversible Increase in Antibiotic Resistance
Authors: Santos-Lopez Alfonso , Bernabe-Balas Cristina , Ares-Arroyo Manuel , Ortega-Huedo Rafael , Hoefer Andreas , San Millan Alvaro , Gonzalez-Zorn Bruno
Published: November 2016

ColE1 plasmids are small mobilizable replicons that play an important role in the spread of antibiotic resistance in
Pasteurellaceae
. In this study, we describe how a natural single nucleotide polymorphism (SNP) near the origin of replication of the ColE1-type plasmid pB1000 found in a
Pasteurella multocida
clinical isolate generates two independent plasmid variants able to coexist in the same cell simultaneously. Using the
Haemophilus influenzae
Rd KW20 strain as a model system, we combined antibiotic susceptibility tests, quantitative PCRs, competition assays, and experimental evolution to characterize the consequences of the coexistence of the pB1000 plasmid variants. This coexistence produced an increase of the total plasmid copy number (PCN) in the host bacteria, leading to a rise in both the antibiotic resistance level and the metabolic burden produced by pB1000. Using experimental evolution, we showed that in the presence of ampicillin, the bacteria maintained both plasmid variants for 300 generations. In the absence of antibiotics, on the other hand, the bacteria are capable of reverting to the single-plasmid genotype via the loss of one of the plasmid variants. Our results revealed how a single mutation in plasmid pB1000 provides the bacterial host with a mechanism to increase the PCN and, consequently, the ampicillin resistance level. Crucially, this mechanism can be rapidly reversed to avoid the extra cost entailed by the increased PCN in the absence of antibiotics.
Ceftazidime-Avibactam as Salvage Therapy for Infections Caused by Carbapenem-Resistant Organisms
Authors: Temkin Elizabeth , Torre-Cisneros Julian , Beovic Bojana , Benito Natividad , Giannella Maddalena , Gilarranz Raúl , Jeremiah Cameron , Loeches Belén , Machuca Isabel , Jiménez-Martín María José , Martínez José Antonio , Mora-Rillo Marta , Navas Enrique , Osthoff Michael , Pozo Juan Carlos , Ramos Ramos Juan Carlos , Rodriguez Marina , Sánchez-García Miguel , Viale Pierluigi , Wolff Michel , Carmeli Yehuda
Published: November 2016

Ceftazidime-avibactam (CAZ-AVI) is a recently approved β-lactam–β-lactamase inhibitor combination with the potential to treat serious infections caused by carbapenem-resistant organisms. Few patients with such infections were included in the CAZ-AVI clinical trials, and clinical experience is lacking. We present a case series of patients with infections caused by carbapenem-resistant
Enterobacteriaceae
(CRE) or
Pseudomonas aeruginosa
(CRPa) who were treated with CAZ-AVI salvage therapy on a compassionate-use basis. Physicians who had prescribed CAZ-AVI completed a case report form. We used descriptive statistics to summarize patient characteristics and treatment outcomes. We used the Wilcoxon rank sum test and Fisher's exact test to compare patients by treatment outcome. The sample included 36 patients infected with CRE and two with CRPa. The most common infections were intra-abdominal. Physicians categorized 60.5% of patients as having life-threatening infections. All but two patients received other antibiotics before CAZ-AVI, for a median of 13 days. The median duration of CAZ-AVI treatment was 16 days. Twenty-five patients (65.8%) concurrently received other antibiotics to which their pathogen was nonresistant
in vitro
. Twenty-eight patients (73.7%, 95% confidence interval [CI], 56.9 to 86.6%) experienced clinical and/or microbiological cure. Five patients (20.8%) with documented microbiological cure died, whereas 10 patients (71.4%) with no documented microbiological cure died (
P
= 0.01). In three-quarters of cases, CAZ-AVI (alone or combined with other antibiotics) cured infections caused by carbapenem-resistant organisms, 95% of which had failed previous therapy. Microbiological cure was associated with improved survival. CAZ-AVI shows promising clinical results for infections for which treatment options are limited.
Occurrence of Diverse AbGRI1-Type Genomic Islands in Acinetobacter baumannii Global Clone 2 Isolates from South Korea
Authors: Kim Dae Hun , Jung Sook-In , Kwon Ki Tae , Ko Kwan Soo
Published: November 2016

In this study, we analyzed the frequency of the AbGRI1-type genomic island (GI) and its association with genotypes. We obtained 130
Acinetobacter baumannii
isolates causing bloodstream infections from patients in South Korea. Antimicrobial susceptibility testing and multilocus sequence typing were performed. The presence of AbGRI1-type GIs and their structures were determined by sequential PCR and sequencing. Ninety-eight isolates (75.3%) representing 14 sequence types (STs) belonged to clonal complex 208 (CC208), corresponding to global clone 2 (GC2). AbGRI1-type GIs interrupted the
comM
gene in 107 isolates (82.4%). Four types of GIs were identified: Tn
6022
(50 isolates; 46.7%), AbaR4 (23 isolates; 21.5%), Tn
6166
(10 isolates; 9.3%), and Tn
6166
/Tn
2006
(24 isolates; 22.4%). In the 50 isolates with Tn
6022
, Tn
2006
or Tn
2008B
, both containing IS
Aba1-bla
OXA-23
, was present in sites other than GIs in 3 or 28 isolates, respectively. In the 10 isolates with Tn
6166
, Tn
2008B
was identified in one isolate. AbGRI1-type GIs were identified nearly exclusively in CC208 isolates, with the exception of nine non-CC208 isolates (AbaR4 in eight ST229 isolates and Tn
6022
in one ST1244 isolate). Within CC208 isolates, there was evidence of frequent recombination events, in both housekeeping genes and AbGRI1-type GIs, contributing to genotype diversification and the emergence of carbapenem resistance.
Mutations Associated with Decreased Susceptibility to Seven Antimicrobial Families in Field and Laboratory-Derived Mycoplasma bovis Strains
Authors: Sulyok Kinga M. , Kreizinger Zsuzsa , Wehmann Enikő , Lysnyansky Inna , Bányai Krisztián , Marton Szilvia , Jerzsele Ákos , Rónai Zsuzsanna , Turcsányi Ibolya , Makrai László , Jánosi Szilárd , Nagy Sára Ágnes , Gyuranecz Miklós
Published: November 2016

The molecular mechanisms of resistance to fluoroquinolones, tetracyclines, an aminocyclitol, macrolides, a lincosamide, a phenicol, and pleuromutilins were investigated in
Mycoplasma bovis
. For the identification of mutations responsible for the high MICs of certain antibiotics, whole-genome sequencing of 35
M. bovis
field isolates and 36 laboratory-derived antibiotic-resistant mutants was performed.
In vitro
resistant mutants were selected by serial passages of
M. bovis
in broth medium containing subinhibitory concentrations of the antibiotics. Mutations associated with high fluoroquinolones MICs were found at positions 244 to 260 and at positions 232 to 250 (according to
Escherichia coli
numbering) of the quinolone resistance-determining regions of the
gyrA
and
parC
genes, respectively. Alterations related to elevated tetracycline MICs were described at positions 962 to 967, 1058, 1195, 1196, and 1199 of genes encoding the 16S rRNA and forming the primary tetracycline binding site. Single transversion at position 1192 of the
rrs1
gene resulted in a spectinomycin MIC of 256 μg/ml. Mutations responsible for high macrolide, lincomycin, florfenicol, and pleuromutilin antibiotic MICs were identified in genes encoding 23S rRNA. Understanding antibiotic resistance mechanisms is an important tool for future developments of genetic-based diagnostic assays for the rapid detection of resistant
M. bovis
strains.
Multicenter Observational Study of Ceftaroline Fosamil for Methicillin-Resistant Staphylococcus aureus Bloodstream Infections
Authors: Zasowski Evan J. , Trinh Trang D. , Claeys Kimberly C. , Casapao Anthony M. , Sabagha Noor , Lagnf Abdalhamid M. , Klinker Kenneth P. , Davis Susan L. , Rybak Michael J.
Published: November 2016

Novel therapies for methicillin-resistant
Staphylococcus aureus
(MRSA) bloodstream infection (BSI) are needed in the setting of reduced antibiotic susceptibilities and therapeutic failure. Ceftaroline is a cephalosporin antibiotic with MRSA activity. Although not FDA approved for MRSA BSI, ceftaroline has generated much interest as a potential treatment option. However, detailed descriptions of its use in this setting remain limited. To address this, we conducted a retrospective, multicenter, observational study of adult patients with MRSA BSI treated with at least 72 h of ceftaroline from 2011 to 2015. Safety outcomes were examined in the overall cohort, while efficacy outcomes were examined among patients who had not cleared their BSI prior to ceftaroline initiation. Data were also stratified by ceftaroline monotherapy or combination therapy. Predictors of clinical failure on ceftaroline treatment were also sought. Overall, 211 patients were included in the safety population;
Clostridium difficile
infection, rash, and neutropenia occurred in 6 patients (2.8%), 7 patients (3.3%), and 3 patients (1.4%), respectively. Clinical success was observed in 86 (68.3%) of the 126 patients included in the efficacy population. The monotherapy and combination therapy subgroups had similar proportions of patients experiencing success (69.7 and 64.9%, respectively). The median BSI durations post-ceftaroline treatment were 2 days (interquartile range, 1 to 4 days) for monotherapy and 3 days (interquartile range, 1.5 to 5 days) for combination therapy. Higher acute physiology and chronic health evaluation II scores and comorbid malignancy independently predicted treatment failure. Ceftaroline appears effective for MRSA BSI as both monotherapy and combination therapy. However, comparative studies are needed to further delineate the role of ceftaroline in MRSA BSI treatment.
Characterization of the Pathogenicity of Streptococcus intermedius TYG1620 Isolated from a Human Brain Abscess Based on the Complete Genome Sequence with Transcriptome Analysis and Transposon Mutagenesis in a Murine Subcutaneous Abscess Model
Authors: Hasegawa Noriko , Sekizuka Tsuyoshi , Sugi Yutaka , Kawakami Nobuhiro , Ogasawara Yumiko , Kato Kengo , Yamashita Akifumi , Takeuchi Fumihiko , Kuroda Makoto
Published: November 2016

Streptococcus intermedius
is known to cause periodontitis and pyogenic infections in the brain and liver. Here we report the complete genome sequence of strain TYG1620 (genome size, 2,006,877 bp; GC content, 37.6%; 2,020 predicted open reading frames [ORFs]) isolated from a brain abscess in an infant. Comparative analysis of
S. intermedius
genome sequences suggested that TYG1620 carries a notable type VII secretion system (T7SS), two long repeat regions, and 19 ORFs for cell wall-anchored proteins (CWAPs). To elucidate the genes responsible for the pathogenicity of TYG1620, transcriptome analysis was performed in a murine subcutaneous abscess model. The results suggest that the levels of expression of small hypothetical proteins similar to phenol-soluble modulin β1 (PSMβ1), a staphylococcal virulence factor, significantly increased in the abscess model. In addition, an experiment in a murine subcutaneous abscess model with random transposon (Tn) mutant attenuation suggested that Tn mutants with mutations in 212 ORFs in the Tn mutant library were attenuated in the murine abscess model (629 ORFs were disrupted in total); the 212 ORFs are putatively essential for abscess formation. Transcriptome analysis identified 37 ORFs, including paralogs of the T7SS and a putative glucan-binding CWAP in long repeat regions, to be upregulated and attenuated
in vivo
. This study provides a comprehensive characterization of
S. intermedius
pathogenicity based on the complete genome sequence and a murine subcutaneous abscess model with transcriptome and Tn mutagenesis, leading to the identification of pivotal targets for vaccines or antimicrobial agents for the control of
S. intermedius
infections.
Characterization of Runella slithyformis HD-Pnk, a Bifunctional DNA/RNA End-Healing Enzyme Composed of an N-Terminal 2′,3′-Phosphoesterase HD Domain and a C-Terminal 5′-OH Polynucleotide Kinase Domain
Authors: Munir Annum , Shuman Stewart
Published: November 2016

5′- and 3′-end-healing reactions are key steps in nucleic acid break repair in which 5′-OH ends are phosphorylated by a polynucleotide kinase (Pnk) and 3′-PO
4
or 2′,3′-cyclic-PO
4
ends are hydrolyzed by a phosphoesterase to generate the 5′-PO
4
and 3′-OH termini required for sealing by classic polynucleotide ligases. End-healing and sealing enzymes are present in diverse bacterial taxa, often organized as modular units within a single multifunctional polypeptide or as subunits of a repair complex. Here we identify and characterize
Runella slithyformis
HD-Pnk as a novel bifunctional end-healing enzyme composed of an N-terminal 2′,3′-phosphoesterase HD domain and a C-terminal 5′-OH polynucleotide kinase P-loop domain. HD-Pnk phosphorylates 5′-OH polynucleotides (9-mers or longer) in the presence of magnesium and any nucleoside triphosphate donor. HD-Pnk dephosphorylates RNA 2′,3′-cyclic phosphate, RNA 3′-phosphate, RNA 2′-phosphate, and DNA 3′-phosphate ends in the presence of a transition metal cofactor, which can be nickel, copper, or cobalt. HD-Pnk homologs are present in genera from 11 bacterial phyla and are often encoded in an operon with a putative ATP-dependent polynucleotide ligase.

IMPORTANCE
The present study provides insights regarding the diversity of nucleic acid repair strategies via the characterization of
Runella slithyformis
HD-Pnk as the exemplar of a novel clade of dual 5′- and 3′-end-healing enzymes that phosphorylate 5′-OH termini and dephosphorylate 2′,3′-cyclic-PO
4
, 3′-PO
4
, and 2′-PO
4
ends. The distinctive feature of HD-Pnk is its domain composition, i.e., a fusion of an N-terminal HD phosphohydrolase module and a C-terminal P-loop polynucleotide kinase module. Homologs of
Runella
HD-Pnk with the same domain composition, same domain order, and similar polypeptide sizes are distributed widely among genera from 11 bacterial phyla.
Isolation and characterization of a novel oxygenase that catalyzes the first step of n-alkane oxidation in Acinetobacter sp. strain M-1
Authors: Maeng J H , Sakai Y , Tani Y , Kato N
Published: November 2016

In the Finnerty pathway for n-alkane, oxidation in Acinetobacter sp., n-alkanes are postulated to be attacked by a dioxygenase and the product, n-alkyl hydroperoxide, is further metabolized to the corresponding aldehyde via the peroxy acid [W. R. Finnerty, P. 184-188, in A. H. Applewhite (ed.), Proceedings of the World Conference on Biotechnology for the Fats and Oil Industry, 1988]. However, no biochemical evidence regarding the first-step reaction is available. In this study, we found a novel n-alkane-oxidizing enzyme that requires only molecular oxygen, i.e., not NAD(P)H, in our isolate, Acinetobacter sp. strain M-1, and purified it to apparent homogeneity by gel electrophoresis. The purified enzyme is a homodimeric protein with a molecular mass of 134 kDa, contains 1 mol of flavin adenine dinucleotide per mol of subunit, and requires CU2+ for its activity. The enzyme uses n-alkanes ranging in length from 10 to 30 carbon atoms and is also active toward n-alkenes (C12 to C20) and some aromatic compounds with substituted alkyl groups but not toward a branched alkane, alcohol, or aldehyde. Transient accumulation of n-alkyl hydroperoxide was detected in the course of the reaction, and no oxygen radical scavengers affected the enzyme activity. From these properties, the enzyme is most probably a dioxygenase that catalyzes the introduction of two atoms of oxygen to the substrate, leading to the formation of the corresponding n-alkyl hydroperoxide. The enzymatic evidence strongly supports the existence of an n-alkane oxidation pathway, which is initiated by a dioxygenase reaction, in Acinetobacter spp.
Detection and characterization of the flagellar master operon in the four Shigella subgroups
Authors: Al Mamun A A , Tominaga A , Enomoto M
Published: November 2016

Strains in the genus Shigella are nonmotile, but they retain some cryptic flagellar operons whether functional or defective (A.Tominaga, M. A.-H. Mahmoud, T. Mukaihara, and M. Enomoto, Mol. Microbiol. 12:277-285, 1994). To disclose the cause of motility loss in shigellae, the presence or defectiveness of the flhD and flhC genes, composing the master operon whose mutation causes inactivation of the entire flagellar regulon, was examined in the four Shigella subgroups. The flhD operon cloned from Shigella boydii and Shigella sonnei can activate, though insufficiently, the regulon in the Escherichia coli flhD or flhC mutant background. The clone from Shigella dysenteriae has a functional flhD gene and nonfunctional flhC gene, and its inactivation has been caused by the IS1 element inserted in its 5' end. The operon of Shigella flexneri is nonfunctional and has suffered an IS1-insertion mutation at the 5' end of the flhD gene. Comparison of restriction maps indicates that only the central 1.8-kb region, including part of the flhC gene and its adjacent mot operon, is conserved among the four Shigella subgroups as well as in E. coli, but in Salmonella typhimurium the whole map is quite different from the others. Motility loss in shigellae is not attributable to genetic damage in the master operon of a common ancestor, but it occurs separately in respective ancestors of the four subgroups, and in both S. dysenteriae and S.flexneri IS1 insertion in the master operon might be the primary cause of motility loss.
Role of the propilin leader peptide in the maturation of F pilin
Authors: Majdalani N , Moore D , Maneewannakul S , Ippen-Ihler K
Published: November 2016

F-pilin maturation and translocation result in the cleavage of a 51-amino-acid leader sequence from propilin and require LepB and TraQ but not the SecA-SecY secretion pathway. The unusual propilin leader peptide and the dependence of its cleavage on TraQ suggested that TraQ recognition may be specific for the leader peptide. An in vitro propilin cleavage assay yielded propilin (13 kDa), the pilin polypeptide (7 kDa), and a 5.5-kDa protein as the traA products. The 5.5-kDa protein comigrates with the full-length 51-amino-acid leader peptide, and [14C]proline labeling confirmed its identity since the only proline residues of propilin are found within the leader peptide. The in vitro and in vivo propilin-processing reactions proceed similarly in a single polypeptide cleavage step. Furthermore, TraQ dependence is a property of F-pilin maturation specifically rather than a property of the leader peptide. A propilin derivative with an amino-terminal signal sequence generated by deleting codons 2 to 28 required TraQ for processing in vivo. On the other hand, a chimeric protein with the propilin wild-type leader peptide fused to the mature portion of beta-lactamase was processed in a TraQ-independent manner. Thus, despite its unusual length, the propilin leader peptide seems to perform a function similar to that of the typical amino-terminal signal sequence. This work suggests that TraQ is not necessary for the proteolysis of propilin and therefore is likely to act as a chaperone-like protein that promotes the translocation of propilin.
Loss of overproduction of polypeptide release factor 3 influences expression of the tryptophanase operon of Escherichia coli
Authors: Yanofsky C , Horn V , Nakamura Y
Published: November 2016

Expression of the tryptophanase (tna) operon of Escherichia coli is regulated by catabolite repression and by tryptophan-induced inhibition of Rho-mediated transcription termination. Previous studies indicated that tryptophan induction might involve leader peptide inhibition of ribosome release at the stop codon of tnaC, the coding region for the operon-specified leader peptide. In this study we examined tna operon expression in strains in which the structural gene for protein release factor 3, prfC, is either disrupted or overexpressed. We find that prfC inactivation leads to a two- to threefold increase in basal expression of the tna operon and a slight increase in induced expression. Overexpression of prfC has the opposite effect and reduces both basal and induced expression. These effects occur in the presence of glucose and cyclic AMP, and thus Rho-dependent termination rather than catabolite repression appears to be the event influenced by the prfC alterations. prfC inactivation also leads to an increase in basal tna operon expression in various rho and rpoB mutants but not in a particular rho mutant in which the basal level of expression is very high. The effect of prfC inactivation was examined in a variety of mutants with alterations in the tna leader region. Our results suggest that translation of tnaC is essential for the prfC effect. The tryptophan residue specified by tnaC codon 12, which is essential for induction, when replaced by another amino) acid, allows the prfC effect. Introducing UAG or UAA stop codons rather than the normal tnaC UGA stop codon, in a strain with an inactive prfC gene, also leads to an increase in the basal level of expression. Addition of the drug bicyclomycin increases basal operon expression of all mutant strains except a strain with a tnaC'-'lacZ fusion. Expression in the latter strain is unaffected by prfC alterations. Our findings are consistent with the interpretation that ribosome release at the tnaC stop codon can influence tna operon expression.
Efficient translation of the RpoS sigma factor in Salmonella typhimurium requires host factor I, an RNA-binding protein encoded by the hfq gene
Authors: Brown L , Elliott T
Published: November 2016

The RpoS transcription factor (also called sigma Sor sigma 38) is required for the expression of a number of stationary-phase and osmotically inducible genes in Escherichia coli. RpoS is also a virulence factor for several pathogenic bacteria, including Salmonella typhimurium. The activity of RpoS is regulated in response to several different signals, at the transcriptional and translational levels as well as by proteolysis. Here we report that host factor I (HF-I), the product of the hfq gene, is required for efficient expression of rpoS in S. typhimurium. HF-I is a small, heat-stable, site-specific RNA-binding protein originally characterized for its role in replication of the RNA bacteriophage Q beta of E. coli. Its role in the uninfected bacterial cell has previously been unknown. Assays of Beta-galactosidase in strains with rpoS-lac fusions, Western blot (immunoblot) analysis, and pulse-labeling and immunoprecipitation of both fusion proteins and native RpoS show that an S. typhimurium hfq mutant has a four- to sevenfold reduction in expression of rpoS that is attributable primarily to a defect in translation. These results add a new level of complexity to the regulation of RpoS activity.
Two-step secretion of the Serratia marcescens extracellular nuclease
Authors: Suh Y , Jin S , Ball T K , Benedik M J
Published: November 2016

The extracellular nuclease of Serratia marcescens is one of a wide variety of enzymes secreted into the growth medium. Its appearance occurs late in the growth of a culture, and its gene, nucA, is transcriptionally regulated in a complex fashion by growth phase and other factors. Pulse-labeling studies reveal that extracellular secretion of nuclease occurs as a two-step process. In the first step, nuclease is rapidly translocated across the cytoplasmic membrane into the periplasm, where it accumulates as a mature active nuclease. A precursor protein, nuclease still carrying its signal sequence, was detected in the presence of carbonyl cyanide m-chlorophenylhydrazone or sodium azide, suggesting that this initial translocation and signal processing step involves an energy-dependent and Sec-dependent pathway in S. marcescens. The second step of secretion across the outer membrane is a slow process requiring between 30 to 120 min, depending on growth conditions.
Oxygen-controlled regulation of the flavohemoglobin gene in Bacillus subtilis
Authors: LaCelle M , Kumano M , Kurita K , Yamane K , Zuber P , Nakano M M
Published: November 2016

A gene, hmp, which encodes a ubiquitous protein homologous to hemoglobin was isolated among genes from Bacillus subtilis that are induced under anaerobic conditions. The hmp protein belongs to the family of two-domain flavohemoproteins, homologs of which have been isolated from various organisms such as Escherichia coli, Alcaligenes eutrophus, and Saccharomyces cerevisiae. These proteins consist of an amino-terminal hemoglobin domain and a carboxy-terminal redox active site domain with potential binding sites for NAD(P)H and flavin adenine dinucleotide. The expression of hmp is strongly induced upon oxygen limitation, and the induction is dependent on a two-component regulatory pair, ResD and ResE, an anaerobic regulator, FNR, and respiratory nitrate reductase, NarGHJI. The requirement of FNR and NarGHJI for hmp expression is completely bypassed by the addition of nitrite in the culture medium, indicating that fnr is required for transcriptional activation of narGHJI, which produces nitrite, leading to induction of hmp expression. In contrast, induction of hmp was still dependent on resDE in the presence of nitrite. A defect in hmp in B. subtilis has no significant effect on anaerobic growth.
Mutation in the structural gene for release factor 1 (RF-1) of Salmonella typhimurium inhibits cell division
Authors: Olafsson O , Ericson J U , VanBogelen R , Björk G R
Published: November 2016

A temperature-sensitive mutant of Salmonella typhimurium LT2 was isolated. At the nonpermissive temperature cell division stopped and multinucleated filaments were formed. DNA, RNA, or protein synthesis was not affected until after about two generations. Different physiological conditions, such as anaerobiosis and different growth media, suppress the division deficiency at high temperatures. Certain mutations causing a reduced polypeptide chain elongation rate also suppress the division deficiency. The mutation is recessive and shown to be in the structural gene for release factor I (prfA). DNA sequencing of both the wild-type (prfA+) and mutant (prfA101) allele revealed a GC-to-AT transition in codon 168. Like other known prfA mutants, prfA101 can suppress amber mutations. The division defect in the prfA101 mutant strain could not be suppressed by overexpression of the ftsQAZ operon. Moreover, at the nonpermissive temperature the mutant shows a normal heat shock and SOS response and has a normal ppGpp level. We conclude that the prfA101-mediated defect in cell division is not directed through any of these metabolic pathways, which are all known to affect cell division. We speculate that the altered release factor I induces aberrant synthesis of an unidentified protein(s) involved in the elaborate process of septation.
Plasmid recombination by the RecBCD pathway of Escherichia coli
Authors: Zaman M M , Boles T C
Published: November 2016

Previously, we demonstrated that exonuclease I-deficient strains of Escherichia coli accumulate high-molecular-weight linear plasmid concatemers when transformed with plasmids carrying the chi sequence (5'- GCTGGTGG-3') (M. M. Zaman and T. C. Boles, J. Bacteriol. 176:5093-5100, 1994). Since high-molecular weight linear DNA is believed to be the natural substrate for RecBCD-mediated recombination during conjugation (A. J. Clark and K. B. Low, p. 155-215, in K. B. Low, ed., The Recombination of Genetic Material, 1988), we analyzed the recombination frequencies of chi+ and chi0 plasmids in sbcB strains. Here, we report that chi sites stimulate plasmid recombination frequency by 16-fold in sbcB strains. Chi-stimulated plasmid recombination is dependent on RecBCD but is independent of RecF pathway genes. The distribution of recombination products suggests that high-molecular-weight linear plasmid DNA is a substrate for RecBCD-mediated recombination. Surprisingly, our data also suggest that chi+ plasmids also recombine by the RecBCD pathway in rec+ sbcB+ cells.
Homologous pairs of regulatory proteins control activity of Bacillus subtilis transcription factor sigma(b) in response to environmental stress
Authors: Kang C M , Brody M S , Akbar S , Yang X , Price C W
Published: November 2016

In Bacillus subtilis, activity of the general stress transcription factor sigma B is controlled posttranslationally by a regulatory network that transmits signals of environmental and metabolic stress. These signals include heat, ethanol, or osmotic challenge, or a sharp decrease in cellular energy levels, and all ultimately control sigma B activity by influencing the binding decision of the RsbW anti-sigma factor. In the absence of stress, RsbW binds to sigma B and prevents its association with RNA polymerase core enzyme. However, following stress, RsbW binds instead to the RsbV anti-anti-sigma factor, thereby releasing sigma B to direct transcription of its target genes. These two principal regulators of sigmaB activity are encoded in the eight-gene sigB operon, which has the gene order rsbR-rsbS-rsbT-rsbU-rsbV-rsbW-sig B-rsbX (where rsb stands for regulator of sigma B). Notably, the predicted rsbS product has significant amino acid identity to the RsbV anti-anti-sigma factor and the predicted rsbT product resembles the RsbW anti-sigma factor. To determine the roles of rsbS and rsbT, null or missense mutations were constructed in the chromosomal copies or each and tested for their effects on expression of a sigma B-dependent reporter fusion. On the basis of this genetic analysis, our principal conclusions are that (i) the rsbS product is a negative regulator of or" activity, (ii) the rsbT product is a positive regulator, (iii) RsbS requires RsbT for function, and (iv) the RsbS-RsbT and RsbV-RsbW pairs act hierarchically by a common mechanism in which key protein-protein interactions are controlled by phosphorylation events.
Multicopy suppressors of the cold-sensitive phenotype of the pcsA68 (dinD68) mutation in Escherichia coli
Authors: Yasuda T , Nagata T , Ohmori H
Published: November 2016

The Escherichia coli strain cs2-68 is a cold-sensitive (c) mutant that forms a long filamentous cell at 20 degrees C with a large nucleoid mass in its central region. We have recently shown that the pcsA68 mutation causing the cs phenotype is a single-base substitution within the dinD gene, a DNA damage-inducible gene which maps at 82 min. Since null mutants of the pcsA (dinD) gene are viable, with no discernible defect in cell growth, the cs phenotype is attributed to a toxic effect by the mutant protein. In an attempt to identify a target(s) for the toxic pcsA68 mutant protein, we screened for chromosomal fragments on multicopy plasmids that could suppress the cs phenotype. Three different BamHI fragments were found to suppress cold sensitivity, and the lexA, dinG, and dinI genes were identified to be responsible for the suppression in each fragment. DinG shares multiple motifs with many DNA helicases. The complete sequence of dinI revealed that DinI is a small protein of 81 amino acids. It is similar in size and sequence to ImpC of the Salmonella typhimurium plasmid TP110 and to a protein (ORFfs) of the retronphage phi R67, both of which are also under the control of LexA.
FtsZ ring formation in fts mutants
Authors: Addinall S G , Bi E , Lutkenhaus J
Published: November 2016

The formation of FtsZ rings (Z rings) in various fts mutants was examined by immunoelectron microscopy and immunofluorescence. In two temperature-sensitive ftsZ mutants which form filaments with smooth morphology, the Z ring was unable to form. In ftsA, ftsI, and ftsQ mutants, which form filaments with an indented morphology, Z rings formed but their contraction was blocked. These results indicate that fully functional ftsA, ftsQ, and ftsI genes are not required for Z-ring formation and are unlikely to have a role in localization of the Z ring. The results also suggest that one function of the Z ring is to localize the activity of other fts gene products.
RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli
Authors: Kido M , Yamanaka K , Mitani T , Niki H , Ogura T , Hiraga S
Published: November 2016

We have isolated suppressor mutants that suppress temperature-sensitive colony formation and anucleate cell production of a mukB mutation. A linkage group (smbB) of the suppressor mutations is located in the rne/ams/hmp gene encoding the processing endoribonuclease RNase E. All of the rne (smbB) mutants code for truncated RNase E polypeptides lacking a carboxyl-terminal half. The amount of MukB protein was higher in these rne mutants than that in the rne+ strain. These rne mutants grew nearly normally in the mukB+ genetic background. The copy number of plasmid pBR322 in these rne mutants was lower than that in the rne+ isogenic strain. The results suggest that these rne mutations increase the half-lives of mukB mRNA and RNAI of pBR322, the antisense RNA regulating ColE1-type plasmid replication. We have demonstrated that the wild-type RNase E protein bound to polynucleotide phosphorylase (PNPase) but a truncated RNase E polypeptide lacking the C-terminal half did not. We conclude that the C-terminal half of RNase E is not essential for viability but plays an important role for binding with PNPase. RNase E and PNPase of the multiprotein complex presumably cooperate for effective processing and turnover of specific substrates, such as mRNAs and other RNAs in vivo.
Structure modification induced in the narG promoter by binding of integration host factor and NARL-P
Authors: Zhang X , DeMoss J A
Published: November 2016

Interaction of integration host factor (IHF) with linear DNA fragments containing the narG promoter region induced an apparent sharp bend in the DNA centered at the IHF-binding site. Binding of NARL-P to two sites adjacent to the IHF site did not induce bending or modify the apparent bending induced by IHF.
Thyroid abscess in case of Pre B acute lymphoblastic leukaemia: a rare presentation
Authors: Kalantri Siddhesh Arun , Datta Saikat , Maitra Dhritiman , Bhattacharyya Maitreyee
Published: November 2016

Thyroid abscess is a very rare clinical condition. It usually occurs in immunocompromised individuals or those with underlying malignancy. We report a case of multiple thyroid abscesses in the patient with Pre B acute lymphoblastic leukaemia which developed secondary to hematogenous spread from pyomyositis of right calf muscle. The patient developed sepsis-associated disseminated intravascular coagulation, which got resolved after thyroidectomy. He became afebrile after surgical intervention. Unfortunately, all the cultures were negative. Since there are few case series and reports, there are no clear guidelines for management of thyroid abscess. We conclude that though rare, thyroid abscess may be the cause of persistent fever in immunocompromised patients.
Social determinants and maternal exposure to intimate partner violence of obstetric patients with severe maternal morbidity in the intensive care unit: a systematic review protocol
Authors: Ayala Quintanilla Beatriz Paulina , Taft Angela , McDonald Susan , Pollock Wendy , Roque Henriquez Joel Christian
Published: November 2016

Introduction

Maternal mortality is a potentially preventable public health issue. Maternal morbidity is increasingly of interest to aid the reduction of maternal mortality. Obstetric patients admitted to the intensive care unit (ICU) are an important part of the global burden of maternal morbidity. Social determinants influence health outcomes of pregnant women. Additionally, intimate partner violence has a great negative impact on women's health and pregnancy outcome. However, little is known about the contextual and social aspects of obstetric patients treated in the ICU. This study aimed to conduct a systematic review of the social determinants and exposure to intimate partner violence of obstetric patients admitted to an ICU.

Methods and analysis

A systematic search will be conducted in MEDLINE, CINAHL, ProQuest, LILACS and SciELO from 2000 to 2016. Studies published in English and Spanish will be identified in relation to data reporting on social determinants of health and/or exposure to intimate partner violence of obstetric women, treated in the ICU during pregnancy, childbirth or within 42 days of the end of pregnancy. Two reviewers will independently screen for study eligibility and data extraction. Risk of bias and assessment of the quality of the included studies will be performed by using the Critical Appraisal Skills Programme (CASP) checklist. Data will be analysed and summarised using a narrative description of the available evidence across studies. This systematic review protocol will be reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) guidelines.

Ethics and dissemination

Since this systematic review will be based on published studies, ethical approval is not required. Findings will be presented at La Trobe University, in Conferences and Congresses, and published in a peer-reviewed journal.

Trial registration number

CRD42016037492.
Changes in objectively measured smoking in pregnancy by time and legislative changes in Finland: a retrospective cohort study
Authors: Männistö T , Bloigu A , Heino A , Gissler M , Surcel H M
Published: November 2016

Objectives

To study the changes in prevalence, characteristics and outcomes of pregnant smokers over time and legislative changes.

Design and setting

Retrospective nationwide cohort.

Participants

Our study consisted of 9627 randomly selected pregnancies from the Finnish Maternity Cohort (1987–2011), with demographic characteristics and pregnancy and perinatal data obtained from the Medical Birth Registry and early pregnancy serum samples analysed for cotinine levels. Women were categorised based on their self-reported smoking status and measured cotinine levels (with ≥4.73 ng/mL deemed high). Data were stratified to three time periods based on legislative changes in the Tobacco Act.

Primary and secondary outcome measures

Prevalence of pregnant smokers and demographics, and perinatal and pregnancy outcomes of pregnant smokers over time.

Results

Overall, 71.6% of women were non-smokers, 16.2% were active cigarette smokers, 7.7% undisclosed smoking but had high cotinine levels and 4.5% were inactive cigarette smokers. The prevalence of active cigarette smokers decreased from mid-1990s onwards among women aged ≥30 years, probably due to the ban of cigarette smoking in most workplaces. We observed no changes in the prevalence of inactive smokers or women who undisclosed smoking by time or legislative changes.

Women who undisclosed smoking had similar characteristics and perinatal outcomes as inactive and active smokers. Compared with non-smokers, women who undisclosed smoking were more likely to be young, unmarried, have a socioeconomic status lower than white-collar worker and have a preterm birth.

Conclusions

Women who undisclosed smoking were very similar to pregnant cigarette smokers. We observed a reduction in the prevalence of active pregnant cigarette smokers after the ban of indoor smoking in workplaces and restaurants, mostly among women aged ≥30 years.
Serum levels of immunoglobulins and severity of community-acquired pneumonia
Authors: de la Torre Mari C , Torán Pere , Serra-Prat Mateu , Palomera Elisabet , Güell Estel , Vendrell Ester , Yébenes Joan Carles , Torres Antoni , Almirall Jordi
Published: November 2016

Instruction

There is evidence of a relationship between severity of infection and inflammatory response of the immune system. The objective is to assess serum levels of immunoglobulins and to establish its relationship with severity of community-acquired pneumonia (CAP) and clinical outcome.

Methods

This was an observational and cross-sectional study in which 3 groups of patients diagnosed with CAP were compared: patients treated in the outpatient setting (n=54), patients requiring in-patient care (hospital ward) (n=173), and patients requiring admission to the intensive care unit (ICU) (n=191).

Results

Serum total IgG (and IgG subclasses IgG1, IgG2, IgG3, IgG4), IgA and IgM were measured at the first clinical visit. Normal cutpoints were defined as the lowest value obtained in controls (≤680, ≤323, ≤154, ≤10, ≤5, ≤30 and ≤50 mg/dL for total IgG, IgG1, IgG2, IgG3, IgG4, IgM and IgA, respectively). Serum immunoglobulin levels decreased in relation to severity of CAP. Low serum levels of total IgG, IgG1 and IgG2 showed a relationship with ICU admission. Low serum level of total IgG was independently associated with ICU admission (OR=2.45, 95% CI 1.4 to 4.2, p=0.002), adjusted by the CURB-65 severity score and comorbidities (chronic respiratory and heart diseases). Low levels of total IgG, IgG1 and IgG2 were significantly associated with 30-day mortality.

Conclusions

Patients with severe CAP admitted to the ICU showed lower levels of immunoglobulins than non-ICU patients and this increased mortality.
Management, prevention and treatment of canine leishmaniosis in north‐eastern Spain: an online questionnaire‐based survey in the province of Girona with special emphasis on new preventive methods (CaniLeish vaccine and domperidone)
Authors: Lladró S. , Picado A. , Ballart C. , Portús M. , Gállego M.
Published: November 2016

Knowledge of how canine leishmaniosis (CanL) is being managed clinically and its epidemiology is very important, since dogs are the main reservoir of human leishmaniosis. This study reports the results obtained through a questionnaire‐based survey of veterinary practitioners in Girona province, a recognised, but non‐documented endemic area in north‐eastern Spain. The primary objective was to obtain data on the clinical management of CanL, focusing particularly on new preventive methods and therapeutic tools. The results show an extensive routine management of CanL cases and a widespread use of the CaniLeish (Virbac) vaccine and domperidone (Leisguard, Esteve). Adverse reactions were detected by a vast majority of the vaccine users (82 per cent), the most frequent being local reactions, apathy, fever and gastroenteritis. All the respondents had treated confirmed cases, and the therapeutic protocol most used was the combination of meglumine antimoniate (Glucantime, Merial) and allopurinol (Zyloric, GlaxoSmithKline).
A differentiable optimization model for the management of single-species, even-aged stands
Authors: Arias-Rodil Manuel , Diéguez-Aranda Ulises , Vázquez-Méndez Miguel Ernesto
Published: November 2016

This paper presents a model for optimizing the management of single-species, even-aged stands. The model comprises a number of state variables, given by functions initially differentiable with respect to time, which cease to be due to the discontinuities that cause instant silvicultural treatments. Nevertheless, the proposed model maintains its differentiability with respect to the decision variables (timing, type, and intensity of each thinning, and rotation age). This allows for formulation of the problem of optimal management of this type of stands as a linearly constrained smooth optimization problem, which can be efficiently solved by any derivative-based optimization method. The effectiveness of this formulation is shown by using a sequential quadratic programming (SQP) algorithm to design the optimal management of Pinus pinaster Ait. in Asturias (northwestern Spain) from an economic perspective. These results are compared with those obtained using two methods that do not require derivatives. The SQP, as representative of gradient-type methods, proved robust and much more efficient than the derivative-free methods.
Analysis of entropy generation and natural convection in an inclined partially porous layered cavity filled with a nanofluid
Authors: Armaghani T. , Ismael Muneer A. , Chamkha Ali J.
Published: November 2016

The present numerical study investigates the analysis of thermodynamic irreversibility generation and the natural convection in inclined partially porous layered cavity filled with a Cu–water nanofluid. The finite difference method with up-wind scheme is used to solve the governing equations. The study is achieved by examining the effects of nanoparticle volume fraction, inclination angle, and the porous layer thickness. Besides, the computations are achieved within the laminar range of the Rayleigh number. The results show that at Ra = 104, a reduction of total entropy generation is recorded with increasing nanoparticle volume fraction when the porous layer thickness is greater than 0.2. Moreover, when Ra is less than 105, the nanoparticle volume fraction increases the heat transfer irreversibility, and improves the overall thermal performance. It is found also that for a low Rayleigh number, the largest porous layer thickness and the highest cavity orientation improve the thermal performance. On the contrary, at high Rayleigh numbers, these parameter ranges give the worst thermal performance.
Data Envelopment Analysis with Output-Bounded Data
Authors: Du Juan , Huo Jiazhen , Zhu Joe
Published: November 2016

In conventional data envelopment analysis (DEA), data are usually assumed to be non-negative with no specific bounds. However, many practical applications require some data, and thus their projections, to fall within certain limits. For example, percentage data such as the satisfactory rate cannot exceed 100% to make sense. This data characteristic is very likely to be violated under the assumption of constant returns to scale (CRS), due to its ray expansion property. In order to tackle this issue under CRS, a series of radial models are developed to constrain DEA projections within imposed bounds from the output side. Then efficient decision making units (DMUs) can be further discriminated simply by eliminating it from the reference set, avoiding the infeasibility problem existing in the VRS super-efficiency measures. The methodology is demonstrated with data consisting of 119 general acute care hospitals located in Pennsylvania, USA.