bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineered Biosynthesis of Disaccharide-Modified Polyene Macrolides
Authors: De Poire Eimear , Stephens Niamh , Rawlings Bernard , Caffrey Patrick 
Published: August 2013

ABSTRACT

Recent work has uncovered genes for two glycosyltransferases that are thought to catalyze mannosylation of mycosaminyl sugars of polyene macrolides. These two genes are
nypY
from
Pseudonocardia
sp. strain P1 and
pegA
from
Actinoplanes caeruleus
. Here we analyze these genes by heterologous expression in various strains of
Streptomyces nodosus
, producer of amphotericins, and in
Streptomyces albidoflavus
, which produces candicidins. The NypY glycosyltransferase converted amphotericins A and B and 7-oxo-amphotericin B to disaccharide-modified forms
in vivo
. The enzyme did not act on amphotericin analogs lacking exocyclic carboxyl or mycosamine amino groups. Both NypY and PegA acted on candicidins. This work confirms the functions of these glycosyltransferases and provides insights into their acceptor substrate tolerance. Disaccharide-modified polyenes may have potential as less toxic antibiotics.
Ras Signaling Gets Fine-Tuned: Regulation of Multiple Pathogenic Traits of Candida albicans
Authors: Inglis Diane O. , Sherlock Gavin 
Published: August 2013

ABSTRACT

Candida albicans
is an opportunistic fungal pathogen that can cause disseminated infection in patients with indwelling catheters or other implanted medical devices. A common resident of the human microbiome,
C. albicans
responds to environmental signals, such as cell contact with catheter materials and exposure to serum or CO
2
, by triggering the expression of a variety of traits, some of which are known to contribute to its pathogenic lifestyle. Such traits include adhesion, biofilm formation, filamentation, white-to-opaque (W-O) switching, and two recently described phenotypes, finger and tentacle formation. Under distinct sets of environmental conditions and in specific cell types (mating type-like
a
[MTL
a
]/alpha cells, MTL homozygotes, or daughter cells),
C. albicans
utilizes (or reutilizes) a single signal transduction pathway—the Ras pathway—to affect these phenotypes. Ras1, Cyr1, Tpk2, and Pde2, the proteins of the Ras signaling pathway, are the only nontranscriptional regulatory proteins that are known to be essential for regulating all of these processes. How does
C. albicans
utilize this one pathway to regulate all of these phenotypes? The regulation of distinct and yet related processes by a single, evolutionarily conserved pathway is accomplished through the use of downstream transcription factors that are active under specific environmental conditions and in different cell types. In this minireview, we discuss the role of Ras signaling pathway components and Ras pathway-regulated transcription factors as well as the transcriptional regulatory networks that fine-tune gene expression in diverse biological contexts to generate specific phenotypes that impact the virulence of
C. albicans
.
Elucidation of the Role of Clp Protease Components in Circadian Rhythm by Genetic Deletion and Overexpression in Cyanobacteria
Authors: Imai Keiko , Kitayama Yohko , Kondo Takao 
Published: August 2013

ABSTRACT

In the cyanobacterium
Synechococcus elongatus
PCC7942, KaiA, KaiB, and KaiC are essential elements of the circadian clock, and Kai-based oscillation is thought to be the basic circadian timing mechanism. The Kai-based oscillator coupled with transcription/translation feedback and other intercellular factors maintains the stability of the 24-hour period
in vivo
. In this study, we showed that disruption of the Clp protease family genes
clpP1
,
clpP2
, and
clpX
and the overexpression of
clpP3
cause long-period phenotypes. There were no significant changes in the levels of the clock proteins in these mutants. The overexpression of
clpX
led to a decrease in
kaiBC
promoter activity, the disruption of the circadian rhythm, and eventually cell death. However, after the transient overexpression of
clpX
, the
kaiBC
gene expression rhythm recovered after a few days. The rhythm phase after recovery was almost the same as the phase before
clpX
overexpression. These results suggest that the core Kai-based oscillation was not affected by
clpX
overexpression. Moreover, we showed that the overexpression of
clpX
sequentially upregulated ribosomal protein subunit mRNA levels, followed by upregulation of other genes, including the clock genes. Additionally, we found that the disruption of
clpX
decreased the expression of the ribosomal protein subunits. Finally, we showed that the circadian period was prolonged following the addition of a translation inhibitor at a low concentration. These results suggest that translational efficiency affects the circadian period and that
clpX
participates in the control of translation efficiency by regulating the transcription of ribosomal protein genes.
ExbB Cytoplasmic Loop Deletions Cause Immediate, Proton Motive Force-Independent Growth Arrest
Authors: Bulathsinghala Charles M. , Jana Bimal , Baker Kristin R. , Postle Kathleen 
Published: August 2013

ABSTRACT

The
Escherichia coli
TonB system consists of the cytoplasmic membrane proteins TonB, ExbB, and ExbD and multiple outer membrane active transporters for diverse iron siderophores and vitamin B
12
. The cytoplasmic membrane proteins harvest and transmit the proton motive force (PMF) to outer membrane transporters. This system, which spans the cell envelope, has only one component with a significant cytoplasmic presence, ExbB. Characterization of sequential 10-residue deletions in the ExbB cytoplasmic loop (residues 40 to 129; referred to as Δ10 proteins) revealed that it was required for all TonB-dependent activities, including interaction between the periplasmic domains of TonB and ExbD. Expression of eight out of nine of the Δ10 proteins at chromosomal levels led to immediate, but reversible, growth arrest. Arrest was not due to collapse of the PMF and did not require the presence of ExbD or TonB. All Δ10 proteins that caused growth arrest were dominant for that phenotype. However, several were not dominant for iron transport, indicating that growth arrest was an intrinsic property of the Δ10 variants, whether or not they could associate with wild-type ExbB proteins. The lack of dominance in iron transport also ruled out trivial explanations for growth arrest, such as high-level induction. Taken together, the data suggest that growth arrest reflected a changed interaction between the ExbB cytoplasmic loop and one or more unknown growth-regulatory proteins. Consistent with that, a large proportion of the ExbB cytoplasmic loop between transmembrane domain 1 (TMD1) and TMD2 is predicted to be disordered, suggesting the need for interaction with one or more cytoplasmic proteins to induce a final structure.
New Family of Tungstate-Responsive Transcriptional Regulators in Sulfate-Reducing Bacteria
Authors: Kazakov Alexey E. , Rajeev Lara , Luning Eric G. , Zane Grant M. , Siddartha Kavya , Rodionov Dmitry A. , Dubchak Inna , Arkin Adam P. , Wall Judy D. , Mukhopadhyay Aindrila , Novichkov Pavel S. 
Published: August 2013

ABSTRACT

The trace elements molybdenum and tungsten are essential components of cofactors of many metalloenzymes. However, in sulfate-reducing bacteria, high concentrations of molybdate and tungstate oxyanions inhibit growth, thus requiring the tight regulation of their homeostasis. By a combination of bioinformatic and experimental techniques, we identified a novel regulator family, tungstate-responsive regulator (TunR), controlling the homeostasis of tungstate and molybdate in sulfate-reducing deltaproteobacteria. The effector-sensing domains of these regulators are similar to those of the known molybdate-responsive regulator ModE, while their DNA-binding domains are homologous to XerC/XerD site-specific recombinases. Using a comparative genomics approach, we identified DNA motifs and reconstructed regulons for 40 TunR family members. Positional analysis of TunR sites and putative promoters allowed us to classify most TunR proteins into two groups: (i) activators of
modABC
genes encoding a high-affinity molybdenum and tungsten transporting system and (ii) repressors of genes for toluene sulfonate uptake (TSUP) family transporters. The activation of
modA
and
modBC
genes by TunR in
Desulfovibrio vulgaris
Hildenborough was confirmed
in vivo
, and we discovered that the activation was diminished in the presence of tungstate. A predicted 30-bp TunR-binding motif was confirmed by
in vitro
binding assays. A novel TunR family of bacterial transcriptional factors controls tungstate and molybdate homeostasis in sulfate-reducing deltaproteobacteria. We proposed that TunR proteins participate in protection of the cells from the inhibition by these oxyanions. To our knowledge, this is a unique case of a family of bacterial transcriptional factors evolved from site-specific recombinases.
In Vitro
Evolution of an Archetypal Enteropathogenic Escherichia coli Strain
Authors: Nisa Shahista , Hazen Tracy H. , Assatourian Lillian , Nougayrède Jean-Philippe , Rasko David A. , Donnenberg Michael S. 
Published: August 2013

ABSTRACT

Enteropathogenic
Escherichia coli
(EPEC) is a leading cause of infantile diarrhea in developing countries. EPEC strain E2348/69 is used worldwide as a prototype to study EPEC genetics and disease. However, isolates of E2348/69 differ phenotypically, reflecting a history of
in vitro
selection. To identify the genomic and phenotypic changes in the prototype strain, we sequenced the genome of the nalidixic acid-resistant (Nal
r
) E2348/69 clone. We also sequenced a recent
nleF
mutant derived by one-step PCR mutagenesis from the Nal
r
strain. The sequencing results revealed no unintended changes between the mutant and the parent strain. However, loss of the pE2348-2 plasmid and 3 nonsynonymous mutations were found in comparison to the published streptomycin-resistant (Str
r
) E2348/69 reference genome. One mutation is a conservative amino acid substitution in
ftsK
. Another, in
gyrA
, is a mutation known to result in resistance to nalidixic acid. The third mutation converts a stop codon to a tryptophan, predicted to result in the fusion of
hflD
, the lysogenization regulator, to
purB
. The
purB
gene encodes an adenylosuccinate lyase involved in purine biosynthesis. The Nal
r
clone has a lower growth rate than the Str
r
isolate when cultured in minimal media, a difference which is corrected upon addition of adenine or by genetic complementation with
purB
. Addition of adenine or genetic complementation also restored the invasion efficiency of the Nal
r
clone. This report reconciles longstanding inconsistencies in phenotypic properties of an archetypal strain and provides both reassurance and cautions regarding intentional and unintentional evolution
in vitro
.
Bacterial Floras and Biofilms of Malignant Wounds Associated with Breast Cancers
Authors: Fromantin Isabelle , Seyer Damien , Watson Sarah , Rollot Florence , Elard Jacqueline , Escande Marie Christine , De Rycke Yann , Kriegel Irène , Larreta Garde Véronique 
Published: August 2013

ABSTRACT

The risk of infections and the appearance of symptoms (e.g., odors) represent the main troubles resulting from malignant wounds. The aim of this study was to characterize the balance of bacterial floras and the relationships between biofilms and bacteria and the emergence of symptoms. Experimental research was carried out for 42 days on malignant wounds associated with breast cancer. Investigations of bacterial floras (aerobes, aero-anaerobes, and anaerobes), detection of the presence of biofilms by microscopic epifluorescence, and clinical assessment were performed. We characterized biofilms in 32 malignant wounds associated with breast cancer and bacterial floras in 25 such wounds. A mixed group of floras, composed of 54 different bacterial types, was identified, with an average number per patient of 3.6 aerobic species and 1.7 anaerobic species; the presence of strict anaerobic bacterial strains was evidenced in 70% of the wounds; biofilm was observed in 35% of the cases. Odor was a reliable indicator of colonization by anaerobes, even when this symptom was not directly linked to any of the identified anaerobic bacteria. Bacteria are more likely to be present during myelosuppression and significantly increase the emergence of odors and pain when present at amounts of >10
5
· g
−1
. The presence of biofilms was not associated with clinical signs or with precise types of bacteria. No infections occurred during the 42-day evaluation period. This study provides a dynamic description of the bacterial floras of tumoral wounds. The study results highlight the absolute need for new therapeutic options that are effective for use on circulating bacteria as well as on bacteria organized in biofilm.
Directed Evolution of a Virus Exclusively Utilizing Human Epidermal Growth Factor Receptor as the Entry Receptor
Authors: Dai Hong-Sheng , Liu Zheng , Jiang Wen , Kuhn Richard J. 
Published: August 2013

ABSTRACT
Rational design and directed evolution are powerful tools to generate and improve protein function; however, their uses are mostly limited to enzyme and antibody engineering. Here we describe a directed-evolution strategy, named the tandem selection and enrichment system (TSES), and its use in generating virus with exclusive specificity for a particular cellular receptor. In TSES, evolving viruses are sequentially and iteratively transferred between two different host cells, one for selection of receptor specificity and the other for enrichment of the fittest virus. By combining rational design and TSES, we generated human epidermal growth factor receptor (EGFR)-specific virus 1 (ESV1). ESV1 has the backbone of Sindbis virus (SINV) and displays an EGF domain engrafted onto structural protein E2 after residue Pro192, together with eight amino acid changes stabilizing the E2-EGF chimera. ESV1 uses EGFR to initiate infection and has lost the capacity to interact with all known SINV receptors. A 12.2-Å cryoelectron microscopic (cryoEM) reconstruction of ESV1 reveals that the E2-EGF fusion adopts a fixed conformation, with EGF sitting at the top of the E2 spike; The EGFR binding interface faces outward, and the EGF domain completely masks SINV receptor binding. The cryoEM structure of ESV1 explains the desirable properties of ESV1 and provides insights for its further modification. TSES expands the scope of directed evolution and can be easily extended to other targeting molecules and viral systems.
Transient Compartmentalization of Simian Immunodeficiency Virus Variants in the Breast Milk of African Green Monkeys
Authors: Ho Carrie , Wu Steven , Amos Joshua D. , Colvin Lisa , Smith Shannon D. , Wilks Andrew B. , DeMarco C. Todd , Brinkley Christie , Denny Thomas N. , Schmitz Joern E. , Rodrigo Allen G. , Permar Sallie R. 
Published: August 2013

ABSTRACT

Natural hosts of simian immunodeficiency virus (SIV), African green monkeys (AGMs), rarely transmit SIV via breast-feeding. In order to examine the genetic diversity of breast milk SIV variants in this limited-transmission setting, we performed phylogenetic analysis on
envelope
sequences of milk and plasma SIV variants of AGMs. Low-diversity milk virus populations were compartmentalized from that in plasma. However, this compartmentalization was transient, as the milk virus lineages did not persist longitudinally.
Lung sounds: how doctors draw crackles and wheeze
Authors: Scott Gregory , Presswood Edward J , Makubate Boikanyo , Cross Frank 
Published: August 2013

Abstract

Background
The content of medical records is a potential source of miscommunication between clinicians. Doctors' written entries have been criticised for their illegibility and ambiguity, but no studies have examined doctors' drawings that are commonly used for recording auscultation findings.

Objective
To compare doctors' drawings of auscultation findings, based on identical clinical information.

Methods
Doctors at the Royal London Hospital and a group of London based general practitioners (GPs) documented a respiratory examination with a drawing of the auscultation findings of bilateral mid and lower zone wheeze and right lower zone crackles. The graphical properties of each drawing were examined and the use of written captions and labels recorded. Drawings were classified into styles according to the use of symbols (defined as discrete characters or icons) and shading (cross-hatching, speckling or darkening) to depict the auscultation findings. The study was conducted between September and November 2011.

Results
Sixty-nine hospital doctors and 13 GPs participated. Ten drawing styles were identified from 78 completed drawings. Ten distinct symbols and a range of shading techniques were used. The most frequent style (21% of drawings) combined ‘X’ symbols representing crackles with musical notes for wheeze. There was inconsistency of representation across the drawings. Forty-seven (60%) drawings used an ‘X’ symbol exclusively to represent crackles, but six (8%) used ‘X’ only to represent wheeze, and 10 (13%) used ‘X’ to represent both findings. 91% of participants included captions or labels with their drawing.

Conclusions
There was wide variation in doctors' drawings of identical auscultation findings, and inconsistency in the meaning of symbols both between and within drawings. Doctors risk incorrectly interpreting each other's drawings when they are not effectively labelled. We recommend doctors consider using a written description instead, or draw different findings with distinct symbols or shading, labelling all findings clearly.
Where to deploy pre-exposure prophylaxis (PrEP) in sub-Saharan Africa?
Authors: Verguet Stéphane , Stalcup Meg , Walsh Julia A 
Published: August 2013

ObjectiveTwo randomised controlled trials showed that pre-exposure prophylaxis (PrEP) reduces HIV transmission between heterosexual men and women. We model the potential impact on transmission and cost-effectiveness of providing PrEP in sub-Saharan Africa.MethodsWe use a deterministic, compartmental model of HIV transmission to evaluate the potential of a 5-year PrEP intervention targeting the adult population of 42 sub-Saharan African countries. We examine the incremental impact of adding PrEP at pre-existing levels of male circumcision and antiretroviral therapy (ART). The base case assumes efficacy of 68%; adherence at 80%; country coverage at 10% of the HIV-uninfected adult population; and annual costs of PrEP and ART at US$200 and US$880 per person, respectively.ResultsAfter 5 years, 390 000 HIV infections (95% UR 190 000 to 630 000) would be prevented, 24% of these in South Africa. HIV infections averted per 100 000 people (adult) would range from 500 in Lesotho to 10 in Somalia. Incremental cost-effectiveness would be US$5800/disability-adjusted life year (DALY) (95% UR 3100 to 13500). Cost-effectiveness would range from US$500/DALY in Lesotho to US$44 600/DALY in Eritrea.ConclusionsIn a general adult population, PrEP is a high-cost intervention which will have maximum impact and be cost-effective only in countries that have high levels of HIV burden and low levels of male circumcision in the population. Hence, PrEP will likely be most effective in Southern Africa as a targeted intervention added to existing strategies to control the HIV pandemic.
Solid and drift geology in forensic investigations
Authors: Ruffell Alastair 
Published: August 2013

Abstract
Forensic geology, forensic geoscience and geoforensics (see the text for definitions) are largely concerned with searches for buried objects or the use of sediment and soil analysis as evidence. Geophysics, remote sensing, geostatistics, geochemistry and geomorphology are considered part of these disciplines. Traditional outcrop geology is not often considered, with very few publications considering the role of mapped and logged geology. This work comprises a review of the few published works, followed by a range of case studies that demonstrate how traditional, outcrop-scale drift and solid geology can be used in forensic geology. These include: using geology in the search for buried explosives and human remains; the logging of solid and drift geology for analysis of disputed rock quality; and modelling groundwater flow from an illegal landfill site. Geological mapping may assist in limiting a search area or in understanding what failed in a search or forensic investigation. The scale of forensic geology discussed bridges the gap between the two traditions of forensic geology outlined above: that of searching large areas of ground and trace evidence analysis.
A Novel Algorithm for Simplification of Complex Gene Classifiers in Cancer
Authors: Wilson Raphael A. , Teng Ling , Bachmeyer Karen M. , Bissonnette Mei Lin Z. , Husain Aliya N. , Parham David M. , Triche Timothy J. , Wing Michele R. , Gastier-Foster Julie M. , Barr Frederic G. , Hawkins Douglas S. , Anderson James R. , Skapek Stephen X. , Volchenboum Samuel L. 
Published: August 2013

AbstractThe clinical application of complex molecular classifiers as diagnostic or prognostic tools has been limited by the time and cost needed to apply them to patients. Using an existing 50-gene expression signature known to separate two molecular subtypes of the pediatric cancer rhabdomyosarcoma, we show that an exhaustive iterative search algorithm can distill this complex classifier down to two or three features with equal discrimination. We validated the two-gene signatures using three separate and distinct datasets, including one that uses degraded RNA extracted from formalin-fixed, paraffin-embedded material. Finally, to show the generalizability of our algorithm, we applied it to a lung cancer dataset to find minimal gene signatures that can distinguish survival. Our approach can easily be generalized and coupled to existing technical platforms to facilitate the discovery of simplified signatures that are ready for routine clinical use. Cancer Res; 73(18); 5625–32. ©2013 AACR.
Targeting the Tumor Microenvironment: From Understanding Pathways to Effective Clinical Trials
Authors: Fang Hua , DeClerck Yves A. 
Published: August 2013

Abstract
It is clear that tumor cells do not act alone but in close interaction with the extracellular matrix and with stromal cells in the tumor microenvironment (TME). As our understanding of tumor cell–stroma interactions increased over the last two decades, significant efforts have been made to develop agents that interfere with these interactions. Here, we discuss four different therapeutic strategies that target the TME, focusing on agents that are at the most advanced stage of preclinical or clinical development. We end this review by outlining some of the lessons we have learned so far from the development of TME-targeting agents. Cancer Res; 73(16); 4965–77. ©2013 AACR.
p63, Sharp1, and HIFs: Master Regulators of Metastasis in Triple-Negative Breast Cancer
Authors: Piccolo Stefano , Enzo Elena , Montagner Marco 
Published: August 2013

Abstract
Metastasis is the most significant cause of cancer-associated morbidity and mortality but remains poorly understood. Recent work revealed that metastasis of aggressive triple-negative breast cancers is suppressed by Sharp1, a factor that promotes degradation of hypoxia-inducible factors (HIF) and blunts HIF-induced malignant cell behavior. Cancer Res; 73(16); 4978–81. ©2013 AACR.
What's in a Label? Radioimmunotherapy for Metastatic Prostate Cancer
Authors: Simone Charles B. , Hahn Stephen M. 
Published: August 2013

Abstract
Prostate cancer has a highly tumor-restricted prostate-specific membrane antigen (PSMA) and may be the ideal solid-organ malignancy for treatment with radioimmunotherapy. Encouraging results using lutetium-177–labeled anti-PSMA monoclonal antibody J591 from a phase II study by Tawaga and colleagues support the continued clinical and preclinical development of radioimmunotherapy for solid tumors. Clin Cancer Res; 19(18); 4908–10. ©2013 AACR.