bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of AmiBA2446, a Novel Bacteriolytic Enzyme Active against Bacillus Species
Authors: Mehta Krunal K. , Paskaleva Elena E. , Azizi-Ghannad Saba , Ley Daniel J. , Page Martin A. , Dordick Jonathan S. , Kane Ravi S. 
Published: July 2013

ABSTRACT

There continues to be a need for developing efficient and environmentally friendly treatments for
Bacillus anthracis
, the causative agent of anthrax. One emerging approach for inactivation of vegetative
B. anthracis
is the use of bacteriophage endolysins or lytic enzymes encoded by bacterial genomes (autolysins) with highly evolved specificity toward bacterium-specific peptidoglycan cell walls. In this work, we performed
in silico
analysis of the genome of
Bacillus anthracis
strain Ames, using a consensus binding domain amino acid sequence as a probe, and identified a novel lytic enzyme that we termed AmiBA2446. This enzyme exists as a homodimer, as determined by size exclusion studies. It possesses
N
-acetylmuramoyl-
l
-alanine amidase activity, as determined from liquid chromatography-mass spectrometry (LC-MS) analysis of muropeptides released due to the enzymatic digestion of peptidoglycan. Phylogenetic analysis suggested that AmiBA2446 was an autolysin of bacterial origin. We characterized the effects of enzyme concentration and phase of bacterial growth on bactericidal activity and observed close to a 5-log reduction in the viability of cells of
Bacillus cereus
4342, a surrogate for
B. anthracis
. We further tested the bactericidal activity of AmiBA2446 against various
Bacillus
species and demonstrated significant activity against
B. anthracis
and
B. cereus
strains. We also demonstrated activity against
B. anthracis
spores after pretreatment with germinants. AmiBA2446 enzyme was also stable in solution, retaining its activity after 4 months of storage at room temperature.
Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms
Authors: Jurelevicius Diogo , Alvarez Vanessa Marques , Marques Joana Montezano , de Sousa Lima Laryssa Ribeiro Fonseca , Dias Felipe de Almeida , Seldin Lucy 
Published: July 2013

ABSTRACT

Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that
Acinetobacter
and
Cloacibacterium
were the dominant genera in freshwater microcosms; the
Oceanospirillales
order and the
Marinobacter
,
Pseudomonas
, and
Cycloclasticus
genera predominated in marine microcosms; and the
Oceanospirillales
order and the
Marinobacter
genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination.
Comparative Proteomic Analysis of Streptomyces lividans Wild-Type andppkMutant Strains Reveals the Importance of Storage Lipids for Antibiotic Biosynthesis
Authors: Le Maréchal Pierre , Decottignies Paulette , Marchand Christophe H. , Degrouard Jeril , Jaillard Danièle , Dulermo Thierry , Froissard Marine , Smirnov Aleksey , Chapuis Violaine , Virolle Marie-Joelle 
Published: July 2013

ABSTRACTStreptomyces lividansTK24 is a strain that naturally produces antibiotics at low levels, but dramatic overproduction of antibiotics occurs upon interruption of theppkgene. However, the role of the Ppk enzyme in relation to the regulation of antibiotic biosynthesis remains poorly understood. In order to gain a better understanding of the phenotype of theppkmutant, the proteomes of the wild-type (wt) andppkmutant strains, grown for 96 h on R2YE medium limited in phosphate, were analyzed. Intracellular proteins were separated on two-dimensional (2D) gels, spots were quantified, and those showing a 3-fold variation or more were identified by mass spectrometry. The expression of 12 proteins increased and that of 29 decreased in theppkmutant strain. Our results suggested that storage lipid degradation rather than hexose catabolism was taking place in the mutant. In order to validate this hypothesis, the triacylglycerol contents of the wt andppkmutant strains ofS. lividansas well as that ofStreptomyces coelicolorM145, a strain that produces antibiotics at high levels and is closely related toS. lividans, were assessed using electron microscopy and thin-layer chromatography. These studies highlighted the large difference in triacylglycerol contents of the three strains and confirmed the hypothetical link between storage lipid metabolism and antibiotic biosynthesis inStreptomyces.
Physiological Role of Acyl Coenzyme A Synthetase Homologs in Lipid Metabolism in Neurospora crassa
Authors: Roche Christine M. , Blanch Harvey W. , Clark Douglas S. , Glass N. Louise 
Published: July 2013

ABSTRACT

Acyl coenzyme A (CoA) synthetase (ACS) enzymes catalyze the activation of free fatty acids (FAs) to CoA esters by a two-step thioesterification reaction. Activated FAs participate in a variety of anabolic and catabolic lipid metabolic pathways, including
de novo
complex lipid biosynthesis, FA β-oxidation, and lipid membrane remodeling. Analysis of the genome sequence of the filamentous fungus
Neurospora crassa
identified seven putative fatty ACSs (ACS-1 through ACS-7). ACS-3 was found to be the major activator for exogenous FAs for anabolic lipid metabolic pathways, and consistent with this finding, ACS-3 localized to the endoplasmic reticulum, plasma membrane, and septa. Double-mutant analyses confirmed partial functional redundancy of ACS-2 and ACS-3. ACS-5 was determined to function in siderophore biosynthesis, indicating alternative functions for ACS enzymes in addition to fatty acid metabolism. The
N. crassa
ACSs involved in activation of FAs for catabolism were not specifically defined, presumably due to functional redundancy of several of ACSs for catabolism of exogenous FAs.
Novel Thioredoxin-Like Proteins Are Components of a Protein Complex Coating the Cortical Microtubules of Toxoplasma gondii
Authors: Liu Jun , Wetzel Laura , Zhang Ying , Nagayasu Eiji , Ems-McClung Stephanie , Florens Laurence , Hu Ke 
Published: July 2013

ABSTRACTMicrotubules are versatile biopolymers that support numerous vital cellular functions in eukaryotes. The specific properties of microtubules are dependent on distinct microtubule-associated proteins, as the tubulin subunits and microtubule structure are exceptionally conserved. Highly specialized microtubule-containing assemblies are often found in protists, which are rich sources for novel microtubule-associated proteins. A protozoan parasite,Toxoplasma gondii, possesses several distinct tubulin-containing structures, including 22 microtubules closely associated with the cortical membrane. Early ultrastructural studies have shown that the cortical microtubules are heavily decorated with associating proteins. However, little is known about the identities of these proteins. Here, we report the discovery of a novel protein, TrxL1 (forThioredoxin-Like protein 1), and an associating complex that coats the cortical microtubules. TrxL1 contains a thioredoxin-like fold. To visualize its localization in live parasites by fluorescence, we replaced the endogenous TrxL1 gene with an mEmeraldFP-TrxL1 fusion gene. Structured illumination-based superresolution imaging of this parasite line produced a detailed view of the microtubule cytoskeleton. Despite its stable association with the cortical microtubules in the parasite, TrxL1 does not seem to bind to microtubules directly. Coimmunoprecipitation experiments showed that TrxL1 associates with a protein complex containing SPM1, a previously reported microtubule-associated protein inT. gondii. We also found that SPM1 recruits TrxL1 to the cortical microtubules. Besides SPM1, several other novel proteins are found in the TrxL1-containing complex, including TrxL2, a close homolog of TrxL1. Thus, our results reveal for the first time a microtubule-associated complex inT. gondii.
Synchronous Activation of Cell Division by Light or Temperature Stimuli in the Dimorphic Yeast Schizosaccharomyces japonicus
Authors: Okamoto Sho , Furuya Kanji , Nozaki Shingo , Aoki Keita , Niki Hironori 
Published: July 2013

ABSTRACT

Many fungi respond to light and regulate fungal development and behavior. A blue light-activated complex has been identified in
Neurospora crassa
as the product of the
wc-1
and
wc-2
genes. Orthologs of WC-1 and WC-2 have hitherto been found only in filamentous fungi and not in yeast, with the exception of the basidiomycete pathogenic yeast
Cryptococcus
. Here, we report that the fission yeast
Schizosaccharomyces japonicus
responds to blue light depending on Wcs1 and Wcs2, orthologs of components of the WC complex. Surprisingly, those of ascomycete
S. japonicus
are more closely related to those of the basidiomycete.
S. japonicus
reversibly changes from yeast to hyphae in response to environmental stresses. After incubation at 30°C, a colony of yeast was formed, and then hyphal cells extended from the periphery of the colony. When light cycles were applied, distinct dark- and bright-colored hyphal cell stripes were formed because the growing hyphal cells had synchronously activated cytokinesis. In addition, temperature cycles of 30°C for 12 h and 35°C for 12 h or of 25°C for 12 h and 30°C for 12 h during incubation in the dark induced a response in the hyphal cells similar to that of light. The stripe formation of the temperature cycles was independent of the
wcs
genes. Both light and temperature, which are daily external cues, have the same effect on growing hyphal cells. A dual sensing mechanism of external cues allows organisms to adapt to daily changes of environmental alteration.
Independent Localization of Plasma Membrane and Chloroplast Components during Eyespot Assembly
Authors: Mittelmeier Telsa M. , Thompson Mark D. , Öztürk Esra , Dieckmann Carol L. 
Published: July 2013

ABSTRACTLike many algae,Chlamydomonas reinhardtiiis phototactic, using two anterior flagella to swim toward light optimal for photosynthesis. The flagella are responsive to signals initiated at the photosensory eyespot, which comprises photoreceptors in the plasma membrane and layers of pigment granules in the chloroplast. Phototaxis depends on placement of the eyespot at a specific asymmetric location relative to the flagella, basal bodies, and bundles of two or four highly acetylated microtubules, termed rootlets, which extend from the basal bodies toward the posterior of the cell. Previous work has shown that the eyespot is disassembled prior to cell division, and new eyespots are assembled in daughter cells adjacent to the nascent four-membered rootlet associated with the daughter basal body (D4), but the chronology of these assembly events has not been determined. Here we use immunofluorescence microscopy to follow assembly and acetylation of the D4 rootlet, localization of individual eyespot components in the plasma membrane or chloroplast envelope, and flagellar emergence during and immediately following cell division. We find that the D4 rootlet is assembled before the initiation of eyespot assembly, which occurs within the same time frame as rootlet acetylation and flagellar outgrowth. Photoreceptors in the plasma membrane are correctly localized in eyespot mutant cells lacking pigment granule layers, and chloroplast components of the eyespot assemble in mutant cells in which photoreceptor localization is retarded. The data suggest that plasma membrane and chloroplast components of the eyespot are independently responsive to a cytoskeletal positioning cue.
Protein Kinase CK2 Holoenzyme Promotes Start-Specific Transcription in Saccharomyces cerevisiae
Authors: Tripodi Farida , Nicastro Raffaele , Busnelli Sara , Cirulli Claudia , Maffioli Elisa , Tedeschi Gabriella , Alberghina Lilia , Coccetti Paola 
Published: July 2013

ABSTRACT

In
Saccharomyces cerevisiae
, the entrance into S phase requires the activation of a specific burst of transcription, which depends on SBF (SCB binding factor, Swi4/Swi6) and MBF (MCB binding factor, Mbp1/Swi6) complexes. CK2 is a pleiotropic kinase involved in several cellular processes, including the regulation of the cell cycle. CK2 is composed of two catalytic subunits (α and α′) and two regulatory subunits (β and β′), both of which are required to form the active holoenzyme. Here we investigate the function of the CK2 holoenzyme in Start-specific transcription. The
ckb1
Δ
ckb2
Δ mutant strain, bearing deletions of both genes encoding CK2 regulatory subunits, shows a delay of S-phase entrance due to a severe reduction of the expression of SBF- and MBF-dependent genes. This transcriptional defect is caused by an impaired recruitment of Swi6 and Swi4 to G
1
gene promoters. Moreover, CK2 α and β′ subunits interact with RNA polymerase II, whose binding to G
1
promoters is positively regulated by the CK2 holoenzyme. Collectively, these findings suggest a novel role for the CK2 holoenzyme in the activation of G
1
transcription.
Candida albicans Czf1 and Efg1 Coordinate the Response to Farnesol during Quorum Sensing, White-Opaque Thermal Dimorphism, and Cell Death
Authors: Langford Melanie L. , Hargarten Jessica C. , Patefield Krista D. , Marta Elizabeth , Blankenship Jill R. , Fanning Saranna , Nickerson Kenneth W. , Atkin Audrey L. 
Published: July 2013

ABSTRACT

Quorum sensing by farnesol in
Candida albicans
inhibits filamentation and may be directly related to its ability to cause both mucosal and systemic diseases. The Ras1-cyclic AMP signaling pathway is a target for farnesol inhibition. However, a clear understanding of the downstream effectors of the morphological farnesol response has yet to be unraveled. To address this issue, we screened a library for mutants that fail to respond to farnesol. Six mutants were identified, and the
czf1
Δ/
czf1
Δ mutant was selected for further characterization. Czf1 is a transcription factor that regulates filamentation in embedded agar and also white-to-opaque switching. We found that Czf1 is required for filament inhibition by farnesol under at least three distinct environmental conditions: on agar surfaces, in liquid medium, and when embedded in a semisolid agar matrix. Since Efg1 is a transcription factor of the Ras1-cyclic AMP signaling pathway that interacts with and regulates Czf1, an
efg1
Δ/
efg1
Δ
czf1
Δ/
czf1
Δ mutant was tested for filament inhibition by farnesol. It exhibited an opaque-cell-like temperature-dependent morphology, and it was killed by low farnesol levels that are sublethal to wild-type cells and both
efg1
Δ/
efg1
Δ and
czf1
Δ/
czf1
Δ single mutants. These results highlight a new role for Czf1 as a downstream effector of the morphological response to farnesol, and along with Efg1, Czf1 is involved in the control of farnesol-mediated cell death in
C. albicans
.
Physiological Consequences of Multiple-Target Regulation by the Small RNA SgrS in Escherichia coli
Authors: Sun Yan , Vanderpool Carin K. 
Published: July 2013

ABSTRACT

Cells use complex mechanisms to regulate glucose transport and metabolism to achieve optimal energy and biomass production while avoiding accumulation of toxic metabolites. Glucose transport and glycolytic metabolism carry the risk of the buildup of phosphosugars, which can inhibit growth at high concentrations. Many enteric bacteria cope with phosphosugar accumulation and associated stress (i.e., sugar-phosphate stress) by producing a small RNA (sRNA) regulator, SgrS, which decreases phosphosugar accumulation in part by repressing translation of sugar transporter mRNAs (
ptsG
and
manXYZ
) and enhancing translation of a sugar phosphatase mRNA (
yigL
). Despite a molecular understanding of individual target regulation by SgrS, previously little was known about how coordinated regulation of these multiple targets contributes to the rescue of cell growth during sugar-phosphate stress. This study examines how SgrS regulation of different targets impacts growth under different nutritional conditions when sugar-phosphate stress is induced. The severity of stress-associated growth inhibition depended on nutrient availability. Stress in nutrient-rich media necessitated SgrS regulation of only sugar transporter mRNAs (
ptsG
or
manXYZ
). However, repression of transporter mRNAs was insufficient for growth rescue during stress in nutrient-poor media; here SgrS regulation of the phosphatase (
yigL
) and as-yet-undefined targets also contributed to growth rescue. The results of this study imply that regulation of only a subset of an sRNA's targets may be important in a given environment. Further, the results suggest that SgrS and perhaps other sRNAs are flexible regulators that modulate expression of multigene regulons to allow cells to adapt to an array of stress conditions.
Association of work-related stress with mental health problems in a special police force unit
Authors: Garbarino Sergio , Cuomo Giovanni , Chiorri Carlo , Magnavita Nicola 
Published: July 2013

ObjectivesLaw and order enforcement tasks may expose special force police officers to significant psychosocial risk factors. The aim of this work is to investigate the relationship between job stress and the presence of mental health symptoms while controlling sociodemographical, occupational and personality variables in special force police officers.MethodAt different time points, 292 of 294 members of the ‘VI Reparto Mobile’, a special police force engaged exclusively in the enforcement of law and order, responded to our invitation to complete questionnaires for the assessment of personality traits, work-related stress (using the Demand–Control–Support (DCS) and the Effort–Reward–Imbalance (ERI) models) and mental health problems such as depression, anxiety and burnout.ResultsRegression analyses showed that lower levels of support and reward and higher levels of effort and overcommitment were associated with higher levels of mental health symptoms. Psychological screening revealed 21 (7.3%) likely cases of mild depression (Beck Depression Inventory, BDI≥10). Officers who had experienced a discrepancy between work effort and rewards showed a marked increase in the risk of depression (OR 7.89, 95% CI 2.32 to 26.82) when compared with their counterparts who did not perceive themselves to be in a condition of distress.ConclusionsThe findings of this study suggest that work-related stress may play a role in the development of mental health problems in police officers. The prevalence of mental health symptoms in the cohort investigated here was low, but not negligible in the case of depression. Since special forces police officers have to perform sensitive tasks for which a healthy psychological functioning is needed, the results of this study suggest that steps should be taken to prevent distress and improve the mental well-being of these workers.
Belimumab: a technological advance for systemic lupus erythematosus patients? Report of a systematic review and meta-analysis
Authors: Kandala Ngianga-Bakwin , Connock Martin , Grove Amy , Sutcliffe Paul , Mohiuddin Syed , Hartley Louise , Court Rachel , Cummins Ewen , Gordon Caroline , Clarke Aileen 
Published: July 2013

ObjectivesTo undertake a systematic review and meta-analysis to investigate clinical effectiveness of belimumab for patients with systemic lupus erythematosus (SLE) and antinuclear and/or anti-double-stranded DNA (dsDNA) autoantibodies.MethodsWe searched eight electronic databases and reference lists for randomised controlled trials (RCTs) of belimumab against placebo or best supportive care. Quality assessment and random effects meta-analysis were undertaken.DesignA meta-analysis of RCTs.Participants2133 SLE patients.Primary and secondary outcome measuresSLE Responder Index (SRI) at week 52.ResultsThree double-blind placebo-controlled RCTs (L02, BLISS-52 BLISS-76) investigated 2133 SLE patients. BLISS-52 and BLISS-76 trials recruited patients with antinuclear and/or anti-dsDNA autoantibodies and demonstrated belimumab effectiveness for the SRI at week 52. Ethnicity and geographical location of participants varied considerably between BLISS trials. Although tests for statistical heterogeneity were negative, BLISS-52 results were systematically more favourable for all measured outcomes. Meta-analysis of pooled 52-week SRI BLISS results showed benefit for belimumab (OR 1.63, 95% CI 1.27 to 2.09). By week 76, the primary SRI outcome in BLISS-76 was not statistically significant (OR 1.31, 95% CI 0.919 to 1.855).