bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of a non‐invasive tool for capture–recapture studies on a seahorse Hippocampus guttulatus population
Authors: Correia M. , Palma J. , Koldewey H. , Andrade J. P. 
Published: February 2014

In this study, the spot pattern in Hippocampus guttulatus was analysed using a computer programme algorithm that allowed individual comparison. This methodology was first tested in a controlled environment using 51 adult and 55 juvenile H. guttulatus. Positive matches were obtained in 86·3 and 83·6% of the adults and juveniles, respectively. In a second experiment, monthly surveys were carried out in five selected locations in the Ria Formosa Lagoon, south Portugal, over the course of a year and a total of 980 photographs were analysed. Photographed H. guttulatus were re‐sighted one to nine times during the course of the survey period with an overall re‐sight record of over 30%. Photo‐identification was therefore shown to be a useful tool for non‐invasive mark–recapture studies that can be successfully used to survey the population abundance of H. guttulatus aged 6 months or older in consecutive years. This could be of great value when considering the assessment of H. guttulatus populations and understanding changes over time.
Melatonin alleviates Echis carinatus venom‐induced toxicities by modulating inflammatory mediators and oxidative stress
Authors: Katkar G. D. , Shanmuga Sundaram M. , Hemshekhar M. , Sharma D. Rachana , Sebastin Santhosh M. , Sunitha K. , Rangappa K. S. , Girish K. S. , Kemparaju K. 
Published: February 2014

AbstractViper bites cause high morbidity and mortality worldwide and regarded as a neglected tropical disease affecting a large healthy population. Classical antivenom therapy has appreciably reduced the snakebite mortality rate; it apparently fails to tackle viper venom‐induced local manifestations that persist even after the administration of antivenom. Recently, viper venom‐induced oxidative stress and vital organ damage is deemed as yet another reason for concern; these are considered as postmedicated complications of viper bite. Thus, treating viper bite has become a challenge demanding new treatment strategies, auxiliary to antivenin therapy. In the last decade, several studies have reported the use of plant products and clinically approved drugs to neutralize venom‐induced pharmacology. However, very few attempts were undertaken to study oxidative stress and vital organ damage. Based on this background, the present study evaluated the protective efficacy of melatonin in Echis carinatus (EC) venom‐induced tissue necrosis, oxidative stress, and organ toxicity. The results demonstrated that melatonin efficiently alleviated EC venom‐induced hemorrhage and myonecrosis. It also mitigated the altered levels of inflammatory mediators and oxidative stress markers of blood components in liver and kidney homogenates, and documented renal and hepatoprotective action of melatonin. The histopathology of skin, muscle, liver, and kidney tissues further substantiated the overall protection offered by melatonin against viper bite toxicities. Besides the inability of antivenoms to block local effects and the fact that melatonin is already a widely used drug promulgating a multitude of therapeutic functionalities, its use in viper bite management is of high interest and should be seriously considered.
Regulation of SOBIR1 accumulation and activation of defense responses in bir1–1 by specific components of ER quality control
Authors: Sun Tongjun , Zhang Qian , Gao Minghui , Zhang Yuelin 
Published: February 2014

SummaryReceptor‐like kinases play diverse roles in plant biology. Arabidopsis BAK1‐INTERACTING RECEPTOR‐LIKE KINASE 1 (BIR1) functions as a negative regulator of plant immunity. bir1‐1 mutant plants display spontaneous cell death and constitutive defense responses that are dependent on SUPPRESSOR OF BIR1,1 (SOBIR1) and PHYTOALEXIN DEFICIENT4 (PAD4). Here we report that mutations in three components of ER quality control, CALRETICULIN3 (CRT3), ER‐LOCALIZED DnaJ‐LIKE PROTEIN 3b (ERdj3b) and STROMAL‐DERIVED FACTOR‐2 (SDF2), also suppress the spontaneous cell death and constitutive defense responses in bir1‐1. Further analysis revealed that accumulation of the SOBIR1 protein is reduced in crt3‐1 and erdj3b‐1 mutant plants. These data suggest that ER quality control plays important roles in the biogenesis of SOBIR1, and is required for cell death and defense responses in bir1‐1.
Pulmonary Mycobacterium bovis BCG Vaccination Confers Dose-Dependent Superior Protection Compared to That of Subcutaneous Vaccination
Authors: Aguilo Nacho , Toledo Ana Maria , Lopez-Roman Eva Maria , Perez-Herran Esther , Gormley Eamonn , Rullas-Trincado Joaquin , Angulo-Barturen Iñigo , Martin Carlos 
Published: February 2014

ABSTRACT

Worldwide, the
Mycobacterium bovis
BCG vaccine is one of the most widely used vaccines. However, it appears to be ineffective in preventing pulmonary tuberculosis. Here, we show that pulmonary BCG vaccination of mice with a broad dose range provides superior protection against
Mycobacterium tuberculosis
challenge compared to that of subcutaneous vaccination.
Immune Responses of Iranian Patients with Visceral Leishmaniasis and Recovered Individuals to LCR1 of Leishmania infantum
Authors: M. Niknam Hamid , Abrishami Firoozeh , Doroudian Mohammad , Rostamian Mosayeb , Moradi Maryam , Khaze Vahid , Iravani Davood 
Published: February 2014

ABSTRACT

Visceral leishmaniasis is a serious public health problem.
Leishmania infantum
is one of its causative agents. LCR1 is an immunogen from
L. infantum
. Antibodies against this protein have been detected in visceral leishmaniasis patients. The aim of this study was to define the antibody and cellular immune responses against LCR1 in Iranian visceral leishmaniasis patients and recovered individuals. The LCR1 protein was produced in recombinant form. Antibody responses against this protein were studied in Iranian individuals with a recent history of visceral leishmaniasis. Responses of peripheral blood mononuclear cells to this protein were studied in Iranian individuals who had recovered from visceral leishmaniasis. Our data show that (i) there was an antibody response to LCR1 in each individual with a recent history of visceral leishmaniasis studied, (ii) there was neither a proliferative response nor production of gamma interferon (IFN-γ) or interleukin 10 in response to LCR1 by mononuclear cells from individuals who had recovered from visceral leishmaniasis, and (iii) individuals who have recovered from visceral leishmaniasis show ongoing immune responses long after recovery from the disease. These data show that there are no detectable cellular memory responses to LCR1 in Iranian individuals who have recovered from visceral leishmaniasis, while there are detectable antibody responses in patients with this disease. Our data suggest that LCR1 has potential applications for the diagnosis of leishmaniasis through antibody detection, while the application of LCR1 alone for induction of IFN-γ in individuals who recovered from this disease is not supported. The presence of long-lasting immune reactivities in individuals who recovered from the disease may show the necessity of extended medical surveillance for these individuals.
Distribution of Nontuberculous Mycobacteria by Multigene Sequence-Based Typing and Clinical Significance of Isolated Strains
Authors: Jang Mi-Ae , Koh Won-Jung , Huh Hee Jae , Kim Su-Young , Jeon Kyeongman , Ki Chang-Seok , Lee Nam Yong 
Published: February 2014

ABSTRACT

Species identification of nontuberculous mycobacteria (NTM) is challenging due to the increasing number of identified NTM species and the lack of standardized testing strategies. The objectives of this study were to investigate the distribution of NTM species recovered from respiratory specimens by multigene sequence-based typing and to evaluate the clinical significance of identified species. Two hundred thirty-two consecutive clinical NTM isolates were subjected to sequencing of multiple genes, including
hsp65
,
rpoB
, and 16S-23S rRNA internal transcribed spacer (ITS) sequence. In addition, clinical data from all patients whose specimens had NTM isolates were analyzed to examine clinical virulence and treatment history. Eighteen strains from 227 isolates from 169 patients were successfully identified at the species level by multigene sequence-based typing.
Mycobacterium avium
complex and
M. abscessus
complex made up the majority of isolated NTM (88%; 199/227), followed by
M. fortuitum
complex (4%; 10/227). The pathogenic potential of NTM differs enormously by species, and
M. avium
complex and
M. abscessus
complex revealed especially high levels of virulence compared with findings for other NTM species. The results from our work support
M. avium
complex and
M. abscessus
complex being the most common NTM species with highly pathogenic potential isolated from clinical respiratory specimens and could be a good resource for molecular epidemiology of NTM species in South Korea.
Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing
Authors: Gordon N. C. , Price J. R. , Cole K. , Everitt R. , Morgan M. , Finney J. , Kearns A. M. , Pichon B. , Young B. , Wilson D. J. , Llewelyn M. J. , Paul J. , Peto T. E. A. , Crook D. W. , Walker A. S. , Golubchik T. 
Published: February 2014

ABSTRACT

Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism's phenotype. However, its ability to provide accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities. The whole genomes of 501 unrelated
Staphylococcus aureus
isolates were sequenced, and the assembled genomes were interrogated using BLASTn for a panel of known resistance determinants (chromosomal mutations and genes carried on plasmids). Results were compared with phenotypic susceptibility testing for 12 commonly used antimicrobial agents (penicillin, methicillin, erythromycin, clindamycin, tetracycline, ciprofloxacin, vancomycin, trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin) performed by the routine clinical laboratory. We investigated discrepancies by repeat susceptibility testing and manual inspection of the sequences and used this information to optimize the resistance determinant panel and BLASTn algorithm. We then tested performance of the optimized tool in an independent validation set of 491 unrelated isolates, with phenotypic results obtained in duplicate by automated broth dilution (BD Phoenix) and disc diffusion. In the validation set, the overall sensitivity and specificity of the genomic prediction method were 0.97 (95% confidence interval [95% CI], 0.95 to 0.98) and 0.99 (95% CI, 0.99 to 1), respectively, compared to standard susceptibility testing methods. The very major error rate was 0.5%, and the major error rate was 0.7%. WGS was as sensitive and specific as routine antimicrobial susceptibility testing methods. WGS is a promising alternative to culture methods for resistance prediction in
S. aureus
and ultimately other major bacterial pathogens.
Multiple-Strain Colonization in Nasal Carriers of Staphylococcus aureus
Authors: Votintseva A. A. , Miller R. R. , Fung R. , Knox K. , Godwin H. , Peto T. E. A. , Crook D. W. , Bowden R. , Walker A. S. 
Published: February 2014

ABSTRACT

Staphylococcus aureus
is a commensal that can also cause invasive infection. Reports suggest that nasal cocolonization occurs rarely, but the resources required to sequence multiple colonies have precluded its large-scale investigation. A staged protocol was developed to maximize detection of mixed-
spa
-type colonization while minimizing laboratory resources using 3,197
S. aureus
-positive samples from a longitudinal study of healthy individuals in Oxfordshire, United Kingdom. Initial typing of pooled material from each sample identified a single unambiguous strain in 89.6% of samples. Twelve single-colony isolates were typed from samples producing ambiguous initial results. All samples could be resolved into one or more
spa
types using the protocol. Cocolonization point prevalence was 3.4 to 5.8% over 24 months of follow-up in 360 recruitment-positives. However, 18% were cocolonized at least once, most only transiently. Cocolonizing
spa
types were completely unrelated in 56% of samples. Of 272 recruitment-positives returning ≥12 swabs, 166 (61%) carried
S. aureus
continuously but only 106 (39%) carried the same single
spa
type without any cocolonization; 31 (11%) switched
spa
type and 29 (11%) had transient cocarriage.
S. aureus
colonization is dynamic even in long-term carriers. New unrelated cocolonizing strains could increase invasive disease risk, and ongoing within-host evolution could increase invasive potential, possibilities that future studies should explore.
Cutaneous Blastomycosis Masquerading as Pyoderma Gangrenosum
Authors: Azar Marwan M. , Relich Ryan F. , Schmitt Bryan H. , Spech Robert W. , Hage Chadi A. 
Published: February 2014

ABSTRACT
Cutaneous blastomycosis (CB) is associated with a variety of skin manifestations. Among other entities, CB may be mistaken for pyoderma gangrenosum due to overlap of findings on histopathologic examination. We report a case of CB, initially diagnosed as pyoderma gangrenosum and treated with steroids, leading to disseminated blastomycosis and acute respiratory distress syndrome (ARDS).
Rapid and Specific Detection, Molecular Epidemiology, and Experimental Virulence of the O16 Subgroup within Escherichia coli Sequence Type 131
Authors: Johnson James R. , Clermont Olivier , Johnston Brian , Clabots Connie , Tchesnokova Veronika , Sokurenko Evgeni , Junka Adam F. , Maczynska Beata , Denamur Erick 
Published: February 2014

ABSTRACT

Escherichia coli
sequence type 131 (ST131), a widely disseminated multidrug-resistant extraintestinal pathogen, typically exhibits serotype O25b:H4. However, certain ST131 isolates exhibit serotype O16:H5 and derive from a phylogenetic clade that is distinct from the classic O25b:H4 ST131 clade. Both clades are assigned to ST131 by the Achtman multilocus sequence typing (MLST) system and a screening PCR assay that targets ST131-specific sequence polymorphisms in the
mdh
and
gyrB
genes. However, they are classified as separate STs by the Pasteur Institute MLST system, and an ST131 PCR method that targets the O25b
rfb
region and an ST131-specific polymorphism in
pabB
detects only the O25b-associated clade. Here, we describe a novel PCR-based method that allows for rapid and specific detection of the O16-associated ST131 clade. The clade members uniformly contained allele 41 of
fimH
(type 1 fimbrial adhesin) and a narrow range of alleles of
gyrA
and
parC
(fluoroquinolone target genes). The virulence genotypes of the clade members resembled those of classic O25b:H4 ST131 isolates; representative isolates were variably lethal in a mouse subcutaneous sepsis model. Several pulsotypes spanned multiple sources (adults, children, pets, and human fecal samples) and locales. An analysis of recent clinical
E. coli
collections showed that the O16 ST131 clade is globally distributed, accounts for 1 to 5% of
E. coli
isolates overall, and, when compared with other ST131 isolates, it is associated with resistance to ampicillin, gentamicin, and trimethoprim-sulfamethoxazole and with susceptibility to fluoroquinolones and extended-spectrum cephalosporins. Attention to this O16-associated ST131 clade, which is facilitated by our novel PCR-based assay, is warranted in future epidemiological studies of ST131 and, conceivably, in clinical applications.
Vaccinia Virus Requires Glutamine but Not Glucose for Efficient Replication
Authors: Fontaine Krystal A. , Camarda Roman , Lagunoff Michael 
Published: February 2014

ABSTRACT

Viruses require host cell metabolism to provide the necessary energy and biosynthetic precursors for successful viral replication. Vaccinia virus (VACV) is a member of the
Poxviridae
family, and its use as a vaccine enabled the eradication of variola virus, the etiologic agent of smallpox. A global metabolic screen of VACV-infected primary human foreskin fibroblasts suggested that glutamine metabolism is altered during infection. Glutamine and glucose represent the two main carbon sources for mammalian cells. Depriving VACV-infected cells of exogenous glutamine led to a substantial decrease in infectious virus production, whereas starving infected cells of exogenous glucose had no significant impact on replication. Viral yield in glutamine-deprived cells or in cells treated with an inhibitor of glutaminolysis, the pathway of glutamine catabolism, could be rescued by the addition of multiple tricarboxylic acid (TCA) cycle intermediates. Thus, VACV infection induces a metabolic alteration to fully rely on glutamine to anaplerotically maintain the TCA cycle. VACV protein synthesis, but not viral transcription, was decreased in glutamine-deprived cells, which corresponded with a dramatic reduction in all VACV morphogenetic intermediates. This study reveals the unique carbon utilization program implemented during poxvirus infection and provides a potential metabolic pathway to target viral replication.

IMPORTANCE
Viruses are dependent on the metabolic machinery of the host cell to supply the energy and molecular building blocks needed for critical processes including genome replication, viral protein synthesis, and membrane production. This study investigates how vaccinia virus (VACV) infection alters global cellular metabolism, providing the first metabolomic analysis for a member of the poxvirus family. Unlike most viruses examined to date, VACV does not activate glycolysis, and exogenous glucose is not required for maximal virus production. Instead, VACV requires exogenous glutamine for efficient replication, and inhibition of glutamine metabolism effectively blocks VACV protein synthesis. This study defines a major metabolic perturbation essential for the replication of a poxvirus and may lead to the discovery of novel antiviral therapies based on metabolic inhibitors.
BAFF Receptor Deficiency Limits Gammaherpesvirus Infection
Authors: Frederico Bruno , May Janet S. , Efstathiou Stacey , Stevenson Philip G. 
Published: February 2014

ABSTRACTLymphocyte colonization by gammaherpesviruses (γHVs) is an important target for cancer prevention. However, how it works is not clear. Epstein-Barr virus drives autonomous B cell proliferationin vitrobutin vivomay more subtly exploit the proliferative pathways provided by lymphoid germinal centers (GCs). Murid herpesvirus 4 (MuHV-4), which realistically infects inbred mice, provides a useful tool with which to understand further how a γHV colonizes B cellsin vivo. Not all γHVs necessarily behave the same, but common events can with MuHV-4 be assigned an importance for host colonization and so a potential as therapeutic targets. MuHV-4-driven B cell proliferation depends quantitatively on CD4+T cell help. Here we show that it also depends on T cell-independent survival signals provided by the B cell-activating factor (BAFF) receptor (BAFF-R). B cells could be infected in BAFF-R−/−mice, but virus loads remained low. This corresponded to a BAFF-R-dependent defect in GC colonization. The close parallels between normal, antigen-driven B cell responses and virus-infected B cell proliferation argue thatin vivo, γHVs mostly induce infected B cells into normal GC reactions rather than generating large numbers of autonomously proliferating blasts.IMPORTANCEγHVs cause cancers by driving the proliferation of infected cells. B cells are a particular target. Thus, we need to know how virus-driven B cell proliferation works. Controversy exists as to whether viral genes drive it directly or less directly orchestrate the engagement of normal, host-driven pathways. Here we show that the B cell proliferation driven by a murid γHV requires BAFF-R. This supports the idea that γHVs exploit host proliferation pathways and suggests that interfering with BAFF-R could more generally reduce γHV-associated B cell proliferation.
Roles of Serine and Threonine Residues of Mumps Virus P Protein in Viral Transcription and Replication
Authors: Pickar Adrian , Xu Pei , Elson Andrew , Li Zhuo , Zengel James , He Biao 
Published: February 2014

ABSTRACT
Mumps virus (MuV), a paramyxovirus containing a negative-sense nonsegmented RNA genome, is a human pathogen that causes an acute infection with symptoms ranging from parotitis to mild meningitis and severe encephalitis. Vaccination against mumps virus has been effective in reducing mumps cases. However, recently large outbreaks have occurred in vaccinated populations. There is no anti-MuV drug. Understanding replication of MuV may lead to novel antiviral strategies. MuV RNA-dependent RNA polymerase minimally consists of the phosphoprotein (P) and the large protein (L). The P protein is heavily phosphorylated. To investigate the roles of serine (S) and threonine (T) residues of P in viral RNA transcription and replication, P was subjected to mass spectrometry and mutational analysis. P, a 392-amino acid residue protein, has 64 S and T residues. We have found that mutating nine S/T residues significantly reduced and mutating residue T at 101 to A (T101A) significantly enhanced activity in a minigenome system. A recombinant virus containing the P-T101A mutation (rMuV-P-T101A) was recovered and analyzed. rMuV-P-T101A grew to higher titers and had increased protein expression at early time points. Together, these results suggest that phosphorylation of MuV-P-T101 plays a negative role in viral RNA synthesis. This is the first time that the P protein of a paramyxovirus has been systematically analyzed for S/T residues that are critical for viral RNA synthesis.

IMPORTANCE
Mumps virus (MuV) is a reemerging paramyxovirus that caused large outbreaks in the United States, where vaccination coverage is very high. There is no anti-MuV drug. In this work, we have systematically analyzed roles of Ser/Thr residues of MuV P in viral RNA synthesis. We have identified S/T residues of P critical for MuV RNA synthesis and phosphorylation sites that are important for viral RNA synthesis. This work leads to a better understanding of viral RNA synthesis as well as to potential novel strategies to control mumps.