bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards light-mediated sensing of bacterial comfort
Authors: Zafrilla G. , Iglesias A. , Marín M. , Torralba L. , Dorado-Morales P. , Racero J.L. , Alcaina J.J. , Morales L.J. , Martínez L. , Collantes M. , Gómez L. , Vilanova C. , Porcar M. 
Published: May 2014

Abstract
Bacterial comfort is central to biotechnological applications. Here, we report the characterization of different sensoring systems, the first step within a broader synthetic biology-inspired light-mediated strategy to determine Escherichia coli perception of environmental factors critical to bacterial performance. We did so by directly ‘asking’ bacterial cultures with light-encoded questions corresponding to the excitation wavelength of fluorescent proteins placed under the control of environment-sensitive promoters. We built four genetic constructions with fluorescent proteins responding to glucose, temperature, oxygen and nitrogen; and a fifth construction allowing UV-induced expression of heterologous genes. Our engineered strains proved able to give feedback in response to key environmental factors and to express heterologous proteins upon light induction. This light-based dialoguing strategy reported here is the first effort towards developing a human–bacteria interphase with both fundamental and applied implications.

Significance and Impact of the Study
The results we present here are at the core of a larger synthetic biology research effort aiming at establishing a dialogue with bacteria. The framework is to convert the human voice into electric pulses, these into light pulses exciting bacterial fluorescent proteins, and convert light-emission back into electric pulses, which will be finally transformed into synthetic voice messages. We report here the first results of the project, in the form of light-based determination of key parameters for bacterial comfort. The ultimate goal of this strategy is to combine different engineered populations to have a combined feedback from the pool.
Diagnostics for Respondent-Driven Sampling
Authors: Gile Krista J. , Johnston Lisa G. , Salganik Matthew J. 
Published: May 2014

SummaryRespondent-driven sampling (RDS) is a widely used method for sampling from hard-to-reach human populations, especially populations at higher risk for human immunodeficiency virus or acquired immune deficiency syndrome. Data are collected through a peer referral process over social networks. RDS has proven practical for data collection in many difficult settings and has been adopted by leading public health organizations around the world. Unfortunately, inference from RDS data requires many strong assumptions because the sampling design is partially beyond the control of the researcher and not fully observable. We introduce diagnostic tools for most of these assumptions and apply them in 12 high risk populations. These diagnostics empower researchers to understand their RDS data better and encourage future statistical research on RDS sampling and inference.
Multiple Dimensions of Climate Change and Their Implications for Biodiversity
Authors: Garcia Raquel A. , Cabeza Mar , Rahbek Carsten , Araújo Miguel B. 
Published: May 2014

Background
Changes in Earth’s climate over time can be measured in many ways. The different metrics available represent alternative dimensions of climate change, each with distinct implications for biodiversity conservation and other sectors. However, this diversity is rarely recognized. At any given locality, average temperature or precipitation can increase or decrease, extreme values can become more intense or frequent, and the timing of specific climatic events can shift. At the same time, climatic conditions are redistributed at broader spatial extents. Across sets of localities, particular climatic conditions can become more or less available and can shift closer or farther in position at different velocities. Metrics quantifying these and other dimensions of change are commonly used in basic and applied sciences. In ecological contexts, individual metrics have helped to explain the role of past climate changes in driving species diversity or extinctions and to forecast the exposure of biodiversity to future climate changes. Yet, a comparison of the many alternative metrics in use is lacking to gain understanding of their properties and guide their use in biodiversity assessments.

Advances
Our review demonstrates that six commonly used metrics of climate change show contrasting patterns under 21st-century climate forecasts across the world. For example, whereas polar climates are projected to warm and shrink in area, the tropics see the emergence of novel climatic conditions and undergo local changes in average climates beyond past variability. To help interpret metrics of climate change, our review critically assesses the ecological implications of different metrics. Supported by examples of empirical links between observed changes in biological systems and different dimensions of climate change, we outline a conceptual framework for classification of climate change metrics according to the types of threat and opportunity they are likely to impose on biodiversity. Climate changes at the locality level are often associated with demographic threats and opportunities at the population level, whereas changes across localities can have positive or negative implications for the size and the position of species’ ranges.

Outlook
Forecasting the long-term impacts of future climate changes on biodiversity is challenging, not least because the responses of organisms are contingent on demographic, physiological, and evolutionary mechanisms, as well as on the interaction with other human-induced stressors such as habitat fragmentation. Lack of data for the majority of species on Earth further hampers the use of available bioclimatic modeling methods. By contrast, the use of simple metrics of climate change is more easily scalable to wholesale biodiversity. When appropriately implemented, such examination can provide a first-order assessment of the challenges that species are potentially exposed to, and in many circumstances, it might be the only option available.
Diagnostic Potential of Monoclonal Antibodies Specific to the Unique O-Antigen of Multidrug-Resistant Epidemic Escherichia coli Clone ST131-O25b:H4
Authors: Szijártó Valéria , Lukasiewicz Jolanta , Gozdziewicz Tomasz K. , Magyarics Zoltán , Nagy Eszter , Nagy Gábor 
Published: May 2014

ABSTRACTTheEscherichia colilineage sequence type 131 (ST131)-O25b:H4 is a globally spread multidrug-resistant clone responsible for a great proportion of extraintestinal infections. Driven by the significant medical needs associated with this successful pathogenic lineage, we generated murine monoclonal antibodies (MAbs) against its lipopolysaccharide (LPS) O25b antigen in order to develop quick diagnostic tests. Murine monoclonal antibodies were generated by immunizing mice with whole killed nonencapsulated ST131-O25bE. colicells and screening hybridoma supernatants for binding to purified LPS molecules obtained from anE. coliST131-O25b clinical isolate. The MAbs selected for further study bound to the surface of liveE. coliO25b strains irrespective of the capsular type expressed, while they did not bind to bacteria or purified LPS from other serotypes, including the related classical O25 antigen (O25a). Using these specific MAbs, we developed a latex bead-based agglutination assay that has greater specificity and is quicker and simpler than the currently available typing methods. The high specificities of these MAbs can be explained by the novel structure of the O25b repeating unit elucidated in this article. Based on comparative analysis by nuclear magnetic resonance (NMR) and mass spectrometry, theN-acetyl-fucose in the O25a O-antigen had been replaced byO-acetyl-rhamnose in the O25b repeating unit. The genetic determinants responsible for this structural variation were identified by aligning the corresponding genetic loci and were confirmed bytrans-complementation of a rough mutant by the subserotype-specific fragments of therfboperons.
Improved Molecular Typing Assay for Rhinovirus Species A, B, and C
Authors: Bochkov Yury A. , Grindle Kristine , Vang Fue , Evans Michael D. , Gern James E. 
Published: May 2014

ABSTRACT

Human rhinoviruses (RVs), comprising three species (A, B, and C) of the genus
Enterovirus
, are responsible for the majority of upper respiratory tract infections and are associated with severe lower respiratory tract illnesses such as pneumonia and asthma exacerbations. High genetic diversity and continuous identification of new types necessitate regular updating of the diagnostic assays for the accurate and comprehensive detection of circulating RVs. Methods for molecular typing based on phylogenetic comparisons of a variable fragment in the 5′ untranslated region were improved to increase assay sensitivity and to eliminate nonspecific amplification of human sequences, which are observed occasionally in clinical samples. A modified set of primers based on new sequence information and improved buffers and enzymes for seminested PCR assays provided higher specificity and sensitivity for virus detection. In addition, new diagnostic primers were designed for unequivocal species and type assignments for RV-C isolates, based on phylogenetic analysis of partial VP4/VP2 coding sequences. The improved assay was evaluated by typing RVs in >3,800 clinical samples. RVs were successfully detected and typed in 99% of the samples that were RV positive in multiplex diagnostic assays.
Comparative Evaluation of the Diagenode Multiplex PCR Assay on the BD Max System versus a Routine In-House Assay for Detection of Bordetella pertussis
Authors: Kenicer Juliet , Hardie Alison , Hamilton Fiona , Gadsby Naomi , Templeton Kate 
Published: May 2014

ABSTRACT

This study looked at 128 nasopharyngeal aspirates (NPA) and 162 throat swabs (TS) tested with the Diagenode multiplex assay on the BD Max system versus our in-house
Bordetella pertussis
PCR. Sensitivity and specificity were 97.3% and 100% for NPA and 88.3% and 98% for TS, respectively. Of positive NPA, 42.1% were coinfected with respiratory viruses.
First Human Case of Fastidiosipila sanguinis Infection
Authors: Beauruelle Clémence , Le Bars Hervé , Pougnet Laurence , Lesecq Ludovic , Buisson Philippe , Héry-Arnaud Geneviève 
Published: May 2014

ABSTRACT

Fastidiosipila sanguinis
is a Gram-positive anaerobic coccus. We report the first case of osteitis implicating this species. The strain was accurately identified by 16S rRNA sequence analysis, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identification having failed. The reservoir remained unclear; an endogenous origin is suspected.
Emergence of New CMRSA7/USA400 Methicillin-Resistant Staphylococcus aureus
spa
Types in Alberta, Canada, from 2005 to 2012
Authors: Li Vincent , Chui Linda , Simmonds Kimberley , Nguyen Thuha , Golding George R. , Yacoub Wadieh , Ferrato Christina , Louie Marie 
Published: May 2014

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) has become one of the most significant pathogens affecting global public health and health care systems. In Canada and the United States, the spread of MRSA is primarily attributed to a single dominant epidemic clone: CMRSA10/USA300. Despite this, the CMRSA7/USA400 epidemic clone has been reported to be the predominate epidemic clone in several Canadian provinces and some parts of the United States. This study examined the epidemiology of CMRSA7/USA400 MRSA in Alberta, Canada, from June 2005 to December 2012. Molecular characterization of CMRSA7/USA400 isolates was done using
spa
, SCC
mec
, PVL, and PFGE typing and identified two predominant
spa
types in Alberta: t128 and t1787. Although closely related, these
spa
types have distinct geographic distributions. From 2010 to 2012, the number of t128 infections has remained stable while there has been a nearly 3-fold increase in the number of provincial t1787 infections, accompanied by 10-fold increases in t1787 infection rates in some communities. Most t128 and t1787 patients were First Nations or Inuit people, and isolates were usually from skin and soft tissue infections in outpatients. t128 patients were significantly older than t1787 patients. Antimicrobial susceptibility testing showed higher mupirocin resistance in t1787 than in t128 MRSA. Improved strategies to reduce or stabilize t1787 infections in Alberta are needed.
Viral Load Detection Using Dried Blood Spots in a Cohort of HIV-1-Infected Children in Uganda: Correlations with Clinical and Immunological Criteria for Treatment Failure
Authors: Costenaro Paola , Lundin Rebecca , Petrara Maria Raffaella , Penazzato Martina , Massavon William , Kizito Susan , Nabachwa Sandra Monica , Nannyonga Musoke Maria , Namisi Charles , Morelli Erika , Bilardi Davide , Mazza Antonio , Zanchetta Marisa , Giaquinto Carlo , De Rossi Anita 
Published: May 2014

ABSTRACT
Correlations between clinical/immunological treatment failure and viral load (VL) detected by dried blood spot (DBS) sampling were explored in HIV-1-infected children in Uganda. Of 104 children on combined antiretroviral treatment (cART), 12.5% experienced clinical and/or immunological failure, while 28.8%, 44.2%, and 26.9% had VLs of <1,000, 1,000 to 5,000, and >5,000 copies/ml, respectively. Clinical/immunological failure poorly predicted virological failure.
Comparison of Rates of Positivity for Bordetella pertussis by Real-Time PCR between Specimens Collected with Rayon Swabs on Aluminum Wire Shaft in Amies Gel with Charcoal and Specimens Collected with Flocked Swabs in Universal Viral Transport Medium during an Epidemic
Authors: Arbefeville Sophie , Ferrieri Patricia 
Published: May 2014

ABSTRACT

A comparison of real-time PCR positivity rates for
Bordetella pertussis
between specimens collected with rayon swabs on an aluminum wire shaft in Amies gel with charcoal and those collected with flocked swabs in universal viral transport medium during an epidemic revealed that their performances were comparable.
Rearrangement of a Large Novel Pseudomonas aeruginosa Gene Island in Strains Isolated from a Patient Developing Ventilator-Associated Pneumonia
Authors: Singh G. , Srinivasan R. , Cheng J. , Peng Z. , Fujimura K. , Baek M. S. , Panzer A. R. , Tringe S. G. , Chen F. , Sorek R. , Weng L. , Bristow J. , Wiener-Kronish J. P. , Lynch S. V. 
Published: May 2014

ABSTRACT

Bacterial gene islands add to the genetic repertoire of opportunistic pathogens. Here, we perform comparative analyses of three
Pseudomonas aeruginosa
strains isolated sequentially over a 3-week period from a patient with ventilator-associated pneumonia (VAP) who received clindamycin and piperacillin-tazobactam as part of their treatment regime. While all three strains appeared to be clonal by standard pulsed-field gel electrophoresis, whole-genome sequencing revealed subtle alterations in the chromosomal organization of the last two strains; specifically, an inversion event within a novel 124-kb gene island (PAGI 12) composed of 137 open reading frames [ORFs]. Predicted ORFs in the island included metabolism and virulence genes. Overexpression of a gene island-borne putative β-lactamase gene was observed following piperacillin-tazobactam exposure and only in those strains that had undergone the inversion event, indicating altered gene regulation following genomic remodeling. Examination of a separate cohort of 76 patients with VAP for integration at this tRNA
lys
recombination site demonstrated that patients exhibiting evidence of integration at this site had significantly higher 28-day mortality. These findings provide evidence that
P. aeruginosa
can integrate, rapidly remodel, and express exogenous genes, which likely contributes to its fitness in a clinical setting.
Development and Application of a Multilocus Sequence Typing Scheme for Streptococcus gallolyticus subsp. gallolyticus
Authors: Dumke J. , Hinse D. , Vollmer T. , Knabbe C. , Dreier J. 
Published: May 2014

ABSTRACT

Streptococcus gallolyticus
subsp.
gallolyticus
(formerly known as
S. bovis
biotype I) is a commensal of the gastrointestinal tract in animals and in up to 15% of healthy humans. Furthermore, it is a facultative pathogen that can cause infectious endocarditis, mastitis, and septicemia. The number of infections is increasing, but the transmission routes and zoonotic potential remain unknown. To assess the zoonotic potential and characterize the epidemiological structure of
S. gallolyticus
subsp.
gallolyticus
, we established a multilocus sequence typing (MLST) scheme. We amplified and sequenced internal fragments of seven housekeeping genes. The resulting sequences were analyzed with BioNumerics software 6.6 by using the unweighted-pair group method using average linkages algorithm. A total of 101
S. gallolyticus
subsp.
gallolyticus
strains isolated from animals, humans, and environmental samples were analyzed and divided into 50 sequence types. Our first results highlight the importance of this MLST scheme for investigating the epidemiology, transmission patterns, and infection chains of
S. gallolyticus
subsp.
gallolyticus
.
Breakthrough Invasive Candida glabrata in Patients on Micafungin: a Novel
FKS
Gene Conversion Correlated with Sequential Elevation of MIC
Authors: Saraya Takeshi , Tanabe Koichi , Araki Koji , Yonetani Shota , Makino Hiroshi , Watanabe Takayasu , Tsujimoto Naoki , Takata Saori , Kurai Daisuke , Ishii Haruyuki , Miyazaki Yoshitsugu , Takizawa Hajime , Goto Hajime 
Published: May 2014

ABSTRACT

Candida glabrata
strains sequentially isolated from blood developed resistance to micafungin (MICs from <0.015 to 4 μg/ml). A novel mutation identified in micafungin-resistant strains at bp 262 of
FKS2
(containing a deletion of F659 [F659del]) was inserted into the homologous region in
FKS1
.
Ineffectual Targeting of HIV-1 Nef by Cytotoxic T Lymphocytes in Acute Infection Results in No Functional Impairment or Viremia Reduction
Authors: De La Cruz Justin , Vollbrecht Thomas , Frohnen Patricia , Ng Hwee L. , Daar Eric S. , Yang Otto O. , Lewis Martha J. 
Published: May 2014

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) accessory protein Nef is heavily targeted by CD8
+
T lymphocytes (CTLs) during acute infection and therefore is included in many candidate vaccines. We investigated whether CTL targeting of Nef during acute infection contributes to immune control by disrupting the function of Nef. The sequence and function of Nef in parallel with CTL responses were assessed longitudinally from peak viremia until the viremia set point in a cohort of six subjects with acute infection. All but one individual had a single founder strain. Nef-specific CTL responses were detected in all subjects and declined in magnitude over time. These responses were associated with mutations, but none of the mutations were detected in important functional motifs. Nef-mediated downregulation of CD4 and major histocompatibility complex (MHC) class I molecules was better preserved in acute infection than in chronic infection. Finally, Nef-specific CTL responses were not associated with a reduction in viremia from its acute-phase peak. Our results indicate that CTLs targeting Nef epitopes outside critical functional domains have little effect on the pathogenic functions of Nef, rendering these responses ineffective in acute infection.

IMPORTANCE
These data indicate that using the whole Nef protein as a vaccine immunogen likely allows immunodominance that leads to targeting of CTL responses that are rapidly escaped with little effect on Nef-mediated pathogenic functions. Pursuing vaccination approaches that can more precisely direct responses to vulnerable areas would maximize efficacy. Until vaccine-induced targeting can be optimized, other approaches, such as the use of Nef function inhibitors or the pursuit of immunotherapies such as T cell receptor gene therapy or adoptive transfer, may be more likely to result in successful control of viremia.
Transcriptional Suppression of miR-181c by Hepatitis C Virus Enhances Homeobox A1 Expression
Authors: Mukherjee Anupam , Shrivastava Shubham , Bhanja Chowdhury Joydip , Ray Ranjit , Ray Ratna B. 
Published: May 2014

ABSTRACT

Hepatitis C virus (HCV)-induced chronic liver disease is one of the leading causes of hepatocellular carcinoma (HCC). The molecular events leading to HCC following chronic HCV infection remain poorly defined. MicroRNAs (miRNAs) have been implicated in the control of many biological processes, and their deregulation is associated with different viral infections. In this study, we observed that HCV infection of hepatocytes transcriptionally downregulates miR-181c expression by modulating CCAAT/enhancer binding protein β (C/EBP-β). Reduced expression of the pri-miR-181c transcript was noted following HCV infection.
In silico
prediction suggests that homeobox A1 (HOXA1) is a direct target of miR-181c. HOXA1 is a member of the homeodomain-containing transcription factor family and possesses pivotal roles in normal growth, development, and differentiation of mammalian tissues. Our results demonstrated that HOXA1 expression is enhanced in HCV-infected hepatocytes. Exogenous expression of the miR-181c mimic inhibits HOXA1 and its downstream molecules STAT3 and STAT5, which are involved in cell growth regulation. Interestingly, overexpression of miR-181c inhibited HCV replication by direct binding with E1 and NS5A sequences. Furthermore, accumulation of HCV genotype 2a RNA with miR-181c was observed in an RNA-induced silencing complex in Huh7.5 cells. Our results provide new mechanistic insights into the role of miR-181c in HCV-hepatocyte interactions, and miR-181c may act as a target for therapeutic intervention.

IMPORTANCE
Chronic HCV infection is one of the major causes of end-stage liver disease, including hepatocellular carcinoma. An understanding of the molecular mechanisms of HCV-mediated hepatocyte growth promotion is necessary for therapeutic intervention against HCC. In this study, we have provided evidence of HCV-mediated transcriptional downregulation of miR-181c. HCV-infected liver biopsy specimens also displayed lower expression levels of miR-181c. We have further demonstrated that inhibition of miR-181c upregulates homeobox A1 (HOXA1), which is important for hepatocyte growth promotion. Exogenous expression of miR-181c inhibited HCV replication by directly binding with HCV E1 and NS5A sequences. Taken together, our results provided new mechanistic insights for an understanding of the role of miR-181c in HCV-hepatocyte interactions and revealed miR-181c as a potential target for therapeutic intervention.