bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Analysis of Protein Palmitoylation in African Trypanosomes
Authors: Emmer Brian T. , Nakayasu Ernesto S. , Souther Christina , Choi Hyungwon , Sobreira Tiago J. P. , Epting Conrad L. , Nesvizhskii Alexey I. , Almeida Igor C. , Engman David M. 
Published: December 2010

ABSTRACT

Many eukaryotic proteins are posttranslationally modified by the esterification of cysteine thiols to long-chain fatty acids. This modification, protein palmitoylation, is catalyzed by a large family of palmitoyl acyltransferases that share an Asp-His-His-Cys Cys-rich domain but differ in their subcellular localizations and substrate specificities. In
Trypanosoma brucei
, the flagellated protozoan parasite that causes African sleeping sickness, protein palmitoylation has been observed for a few proteins, but the extent and consequences of this modification are largely unknown. We undertook the present study to investigate
T. brucei
protein palmitoylation at both the enzyme and substrate levels. Treatment of parasites with an inhibitor of total protein palmitoylation caused potent growth inhibition, yet there was no effect on growth by the separate, selective inhibition of each of the 12 individual
T. brucei
palmitoyl acyltransferases. This suggested either that
T. brucei
evolved functional redundancy for the palmitoylation of essential palmitoyl proteins or that palmitoylation of some proteins is catalyzed by a noncanonical transferase. To identify the palmitoylated proteins in
T. brucei
, we performed acyl biotin exchange chemistry on parasite lysates, followed by streptavidin chromatography, two-dimensional liquid chromatography-tandem mass spectrometry protein identification, and QSpec statistical analysis. A total of 124 palmitoylated proteins were identified, with an estimated false discovery rate of 1.0%. This palmitoyl proteome includes all of the known palmitoyl proteins in procyclic-stage
T. brucei
as well as several proteins whose homologues are palmitoylated in other organisms. Their sequences demonstrate the variety of substrate motifs that support palmitoylation, and their identities illustrate the range of cellular processes affected by palmitoylation in these important pathogens.
Regulation of Central Metabolism Genes of
Mycobacterium tuberculosis
by Parallel Feed-Forward Loops Controlled by Sigma Factor E (σ
E
)
Authors: Datta Pratik , Shi Lanbo , Bibi Nazia , Balázsi Gábor , Gennaro Maria Laura 
Published: December 2010

ABSTRACT

Cells respond to external stimuli through networks of regulatory interactions. The human pathogen
Mycobacterium tuberculosis
responds to stress encountered during infection by arresting multiplication and implementing critical metabolic changes that lead to or sustain the nonreplicative state. Much of this differentiation program is recapitulated when
M. tuberculosis
cultures are subjected to gradual oxygen depletion
in vitro
. Here we report that hypoxic induction of critical central metabolism genes in the glyoxylate shunt (
icl1
) and in the methylcitrate cycle (
gltA1
) involves both global and local regulators. The global regulators are accessory sigma factors σ
B
for
icl1
and σ
E
for
gltA1
. The local regulators are the products of two paralogous genes mapping at positions adjacent to the corresponding effector gene or operon. We call these genes
lrpI
and
lrpG
(for

l

ocal

r

egulatory

p

rotein of
icl1
and
gltA1
). We also found that (i) each sigma factor controls the corresponding local regulator, (ii) both global and local regulators are required for effector gene induction, and (iii) the occurrence of sigma factor control of effector gene induction is independent of its control over the corresponding local regulator. Together, these data indicate that induction of
icl1
and
gltA1
utilizes parallel feed-forward loops with an AND input function. Both feed-forward loops are affected by σ
E
, since this sigma factor is part of the
gltA1
loop and controls
sigB
in the
icl1
loop. Feed-forward loops may critically contribute to the cellular developmental program associated with
M. tuberculosis
dormancy.
Upregulation of MetC Is Essential for
d
-Alanine-Independent Growth of an
alr/dadX
-Deficient
Escherichia coli
Strain
Authors: Kang Lishan , Shaw Allan C. , Xu Daqi , Xia Wenjuan , Zhang Jingyuan , Deng Jianhui , Wöldike Helle F. , Liu Yun , Su Jing 
Published: December 2010

ABSTRACT

d
-Alanine is a central component of the cell wall in most prokaryotes.
d
-Alanine synthesis in
Escherichia coli
is carried out by two different alanine racemases encoded by the
alr
and
dadX
genes. Deletion of
alr
and
dadX
from the
E. coli
genome results in a
d
-alanine auxotrophic phenotype. However, we have observed growth of prototrophic phenotypic revertants during routine culturing of a
d
-alanine auxotrophic strain. We present a detailed comparison of the proteome and transcriptome profiles of the
d
-alanine auxotroph and a prototrophic revertant strain. Most noticeably, a general upregulation of genes involved in methionine synthesis in the revertant strain was detected. The appearance of the revertant phenotype was genetically linked to point mutations in the methionine repressor gene (
metJ
). Our results reveal an alternative metabolic pathway which can supply essential
d
-alanine for peptidoglycan synthesis of
alr
- and
dadX
-deficient
E. coli
mutants and provide evidence for significant alanine racemase coactivity of the
E. coli
cystathionine beta-lyase (MetC).
Defining the Plasmid-Borne Restriction-Modification Systems of the Lyme Disease SpirocheteBorrelia burgdorferi
Authors: Rego Ryan O. M. , Bestor Aaron , Rosa Patricia A. 
Published: December 2010

ABSTRACTThe restriction-modification (R-M) systems of many bacteria present a barrier to the stable introduction of foreign DNA. The Lyme disease spirocheteBorrelia burgdorferihas two plasmid-borne putative R-M genes,bbe02andbbq67, whose presence limits transformation by shuttle vector DNA fromEscherichia coli. We show that both thebbe02andbbq67loci in recipientB. burgdorferilimit transformation with shuttle vector DNA fromE. coli, irrespective of itsdam,dcm, orhsdmethylation status. However, plasmid DNA purified fromB. burgdorferitransformed naïveB. burgdorferimuch more efficiently than plasmid DNA fromE. coli, particularly when thebbe02andbbq67genotypes of theB. burgdorferiDNA source matched those of the recipient. We detected adenine methylation of plasmid DNA prepared fromB. burgdorferithat carriedbbe02andbbq67. These results indicate that thebbe02andbbq67loci ofB. burgdorferiencode distinct R-M enzymes that methylate endogenous DNA and cleave foreign DNA lacking the same sequence-specific modification. Our findings have basic implications for horizontal gene transfer amongB. burgdorferistrains with distinct plasmid contents. Further characterization and identification of the nucleotide sequences recognized by BBE02 and BBQ67 will facilitate efficient genetic manipulation of this pathogenic spirochete.
Specific Role of the Cyanobacterial PipX Factor in the Heterocysts of
Anabaena
sp. Strain PCC 7120
Authors: Valladares Ana , Rodríguez Virginia , Camargo Sergio , Martínez-Noël Giselle M. A. , Herrero Antonia , Luque Ignacio 
Published: December 2010

ABSTRACT

The PipX factor is a regulatory protein that seems to occur only in cyanobacteria. In the filamentous, heterocyst-forming
Anabaena
sp. strain PCC 7120, open reading frame (ORF)
asr0485
, identified as the
pipX
gene, is expressed mainly under conditions of combined-nitrogen deprivation dependent on the global N regulator NtcA and the heterocyst-specific regulator HetR. Primer extension and 5′ rapid amplification of cDNA ends (RACE) analyses detected three transcription start points corresponding to a canonical NtcA-activated promoter (to which direct binding of NtcA was observed), an NtcA- and HetR-dependent promoter, and a consensus-type promoter, the last with putative −35 and −10 determinants. Activation of
pipX
took place in cells differentiating into heterocysts at intermediate to late stages of the process. Accordingly, disruption of
pipX
led to impaired diazotrophic growth, reduced nitrogenase activity, and impaired activation of the nitrogenase structural genes. The nitrogenase activity of the mutant was low under oxic conditions, likely resulting from inefficient protection against oxygen. In line with this, the activation of the
coxB2A2C2
and
coxB3A3C3
operons, encoding heterocyst-specific terminal respiratory oxidases responsible for internal oxygen removal, was deficient in the
pipX
mutant. Therefore, the
Anabaena
PipX factor shows a spatiotemporal specificity contributing to normal heterocyst function, including full activation of the nitrogenase structural genes and genes of the nitrogenase-protective features of the heterocyst.
Phenotypic and Genotypic Evidence for
l
-Fucose Utilization by
Campylobacter jejuni
Authors: Muraoka Wayne T. , Zhang Qijing 
Published: December 2010

ABSTRACT

Campylobacter jejuni
remains among the leading causes of bacterial food-borne illness. The current understanding of
Campylobacter
physiology suggests that it is asaccharolytic and is unable to catabolize exogenous carbohydrates. Contrary to this paradigm, we provide evidence for
l
-fucose utilization by
C. jejuni
. The fucose phenotype, shown in chemically defined medium, is strain specific and linked to an 11-open reading frame (ORF) plasticity region of the bacterial chromosome. By constructing a mutation in
fucP
(encoding a putative fucose permease), one of the genes in the plasticity region, we found that this locus is required for fucose utilization. Consistent with their function in fucose utilization, transcription of the genes in the locus is highly inducible by fucose. PCR screening revealed a broad distribution of this genetic locus in strains derived from various host species, and the presence of this locus was consistently associated with fucose utilization. Birds inoculated with the
fucP
mutant strain alone were colonized at a level comparable to that by the wild-type strain; however, in cocolonization experiments, the mutant was significantly outcompeted by the wild-type strain when birds were inoculated with a low dose (10
5
CFU per bird). This advantage was not observed when birds were inoculated at a higher inoculum dose (10
8
CFU per bird). These results demonstrated a previously undescribed substrate that supports growth of
C. jejuni
and identified the genetic locus associated with the utilization of this substrate. These findings substantially enhance our understanding of the metabolic repertoire of
C. jejuni
and the role of metabolic diversity in
Campylobacter
pathobiology.
Characterization and Manipulation of the Pathway-Specific Late Regulator AlpW RevealsStreptomyces ambofaciensas a New Producer of Kinamycins
Authors: Bunet Robert , Song Lijiang , Mendes Marta Vaz , Corre Christophe , Hotel Laurence , Rouhier Nicolas , Framboisier Xavier , Leblond Pierre , Challis Gregory L. , Aigle Bertrand 
Published: December 2010

ABSTRACTThe genome sequence ofStreptomyces ambofaciens, a species known to produce the congocidine and spiramycin antibiotics, has revealed the presence of numerous gene clusters predicted to be involved in the biosynthesis of secondary metabolites. Among them, the type II polyketide synthase-encodingalpcluster was shown to be responsible for the biosynthesis of a compound with antibacterial activity. Here, by means of a deregulation approach, we gained access to workable amounts of the antibiotics for structure elucidation. These compounds, previously designated as alpomycin, were shown to be known members of kinamycin family of antibiotics. Indeed, a mutant lacking AlpW, a member of the TetR regulator family, was shown to constitutively produce kinamycins. Comparative transcriptional analyses showed that expression ofalpV, the essential regulator gene required for activation of the biosynthetic genes, is strongly maintained during the stationary growth phase in thealpWmutant, a stage at whichalpVtranscripts and thereby transcripts of the biosynthetic genes normally drop off. Recombinant AlpW displayed DNA binding activity toward specific motifs in the promoter region of its own gene and that ofalpVandalpZ. These recognition sequences are also targets for AlpZ, the γ-butyrolactone-like receptor involved in the regulation of thealpcluster. However, unlike that of AlpZ, the AlpW DNA-binding ability seemed to be insensitive to the signaling molecules controlling antibiotic biosynthesis. Together, the results presented in this study revealS. ambofaciensto be a new producer of kinamycins and AlpW to be a key late repressor of the cellular control of kinamycin biosynthesis.
Mental health and unintentional injurers: results from the national co-morbidity survey replication
Authors: Connorton Ellen , Miller Matthew , Perry Melissa J , Hemenway David 
Published: December 2010

ObjectiveTo examine whether unintentionally injuring others is associated with subsequent mental illness, and whether mental illness is a risk factor for unintentionally injuring others.MethodsOnset of first psychiatric diagnoses was compared with onset of first unintentional injuring. Multivariate logistic regression estimated the association between unintentional injuring and lifetime prevalence of mental illness, specifically of Diagnostic and Statistical Manual of Mental Disorders IV disorders associated with trauma exposure among respondents of part II of the National Co-morbidity Survey Replication a household survey of 5692 US adults. Analyses controlled for age, sex, race and having been injured in a serious accident.ResultsOf 5692 respondents, 110 reported unintentionally causing death or injury to another person. Unintentionally injuring others was a risk factor for subsequent mental health problems. Multivariate regression results showed an increased risk of subsequent depression (OR 3.1, CI 1.7 to 5.7), anxiety (OR 3.3, CI 1.6 to 6.6), posttraumatic stress disorder (PTSD) (OR 6.6, CI 3.1 to 14.0), alcohol use (OR 3.8, CI 1.9 to 7.3) and drug use (OR 8.0, CI 4.1 to 15.3). Conversely, mental health problems were a risk factor for unintentionally injuring another person. Multivariate regression results showed an increased risk of unintentional injuring among those with a prior diagnosis of depression, PTSD, alcohol use, and drug use.ConclusionsAfter injuring, unintentional injurers are likely to experience depression, anxiety, PTSD and drug or alcohol abuse/dependence compared with non-injurers. Those diagnosed with depression, anxiety, PTSD, alcohol or drug or alcohol abuse/dependence are more likely to cause serious injuries to others.
EGFR-Homing dsRNA Activates Cancer-Targeted Immune Response and Eliminates Disseminated EGFR-Overexpressing Tumors in Mice
Authors: Shir Alexei , Ogris Manfred , Roedl Wolfgang , Wagner Ernst , Levitzki Alexander 
Published: January 2011

Abstract
Purpose: The cause of most cancer deaths is incurable dissemination of cancer cells into vital organs. Current systemic therapies for disseminated cancers provide limited efficacy and are often accompanied by toxic side effects. We have recently shown that local application of epidermal growth factor receptor (EGFR)–targeted polyinosine-cytosine (polyIC) eradicates preestablished EGFR-overexpressing tumors. Here we show for the first time the high efficiency of systemic application of polyIC/melittin-polyethyleneimine-polyethyleneglycol-EGF (polyIC/MPPE) in combination with human immune cells.
Experimental design: Cancer-targeted activation of immune cells was examined in vitro and in vivo following transfection with polyIC/MPPE. The therapeutic efficiency of the strategy was then examined on disseminated EGFR-overexpressing tumors grown in severe combined immunodeficient (SCID) mice.
Results: Intravenous delivery of polyIC/MPPE followed by intraperitoneal injection of peripheral blood mononuclear cells induced the complete cure of SCID mice with preestablished disseminated EGFR-overexpressing tumors, with no adverse toxic effects. The immune cells and the cytokines they produce are localized to the tumor site of the treated animal and contribute decisively to the demise of the tumor cells. The immune system homes to the tumors, due to the chemokines produced by the internalized polyIC.
Conclusion: The EGFR-homing vector loaded with polyIC can be used to treat and possibly cure patients with disseminated EGFR-overexpressing tumors. The possibility of adopting this strategy to treat other tumors that express a protein capable of ligand induced internalization is discussed. Clin Cancer Res; 17(5); 1033–43. ©2010 AACR.
Influence of Diabetes Mellitus on Prognostic Utility of Imaging of Myocardial Sympathetic Innervation in Heart Failure Patients
Authors: Gerson Myron C. , Caldwell James H. , Ananthasubramaniam Karthik , Clements Ian P. , Henzlova Milena J. , Amanullah Aman , Jacobson Arnold F. 
Published: December 2010

Background—
Patients with diabetes mellitus have accelerated progression of heart failure and often have impaired cardiac sympathetic innervation. The present study examines the implications for heart failure progression of cardiac sympathetic denervation, assessed by I-123 metaiodobenzylguanidine imaging, in diabetic compared with nondiabetic subjects.

Methods and Results—
We evaluated 343 diabetic and 618 nondiabetic subjects with New York Heart Association class II or III heart failure and a left ventricular ejection fraction ≤35% over a median follow-up of 17 months. A multivariable Cox proportional hazards model was used to examine the influence of clinical variables, b-type natriuretic peptide, plasma norepinephrine, left ventricular ejection fraction, and I-123 metaiodobenzylguanidine imaging parameters on time to a heart failure event. The late heart-to-mediastinum (H/M) ratio and the interaction term of diabetes mellitus with the prospectively selected late H/M ratio <1.6 were independent predictors of heart failure progression, providing incremental prognostic information beyond that available from all other variables. In diabetic subjects, late H/M ratio <1.6 was associated with a 2.99-fold greater 2-year rate of heart failure progression (33.5%) than late H/M ratio ≥1.6 (11.2% event rate).

Conclusions—
The combination of diabetes mellitus and I-123 metaiodobenzylguanidine H/M ratio is an independent predictor of heart failure progression, confirming the high risk of diabetic subjects with impaired cardiac sympathetic nerve function.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00126438 and NCT00126425.
Characteristics of Childhood Arterial Ischemic Stroke With Normal MR Angiography
Authors: Munot Pinki , Saunders Dawn , Ganesan Vijeya 
Published: December 2010

Background and Purpose—
The purposes of this study were to describe clinical and radiological characteristics of children with arterial ischemic stroke and normal MRA to compare them with children with arterial ischemic stroke and abnormal MRA.

Methods—
We conducted a retrospective review of clinical records and imaging.

Results—

Forty children with arterial ischemic stroke and normal MRA were identified (24 male; median age, 55 months). MRA had been acquired <24 hours of symptom onset in 4, at 24 to 48 hours in 10, 48 to 96 hours in 10, 4 to 7 days in 10, and >1 week in 6 children (median, 4 days). Ten of 40 had prior diagnoses (5 cardiac, 5 malignancies). Other risk factors were identified in 30 (1 in 17 and >1 in 13; prothrombotic abnormalities in 14, prior
Varicella
in 7, anemia in 7, minor trauma in 4). Infarction was confined to the lenticulostriate branches of the middle cerebral artery in 21 of 40. Two patients had further clinical events, both with new infarcts; 28 patients were reimaged and MRA remained normal in all. Although similar in terms of age and gender to those with abnormal MRA, children with normal MRA were significantly more likely to have at least 1 RF (
P
=0.012). Those with abnormal MRA were significantly more likely to have multiple territory infarcts (
P
<0.001), but lesion topography was otherwise not predictive of abnormal MRA (
P
=0.45). Abnormal MRA was significantly associated with clinical recurrence (
P
<0.001).

Conclusions—
Children with arterial ischemic stroke and normal MRA are not a distinct demographic group but are more likely to have single-territory lesions and have nonvascular risk factors. The stroke mechanism in children with normal MRA remains unclear.
Wide Variation in Definition, Detection, and Description of Lacunar Lesions on Imaging
Authors: Potter Gillian M. , Marlborough Fergal J. , Wardlaw Joanna M. 
Published: December 2010

Background and Purpose—
Variation in the definition of lacunar lesions on imaging and difficulties in their detection may be hampering lacunar stroke research. We assessed literature definitions of imaging lacunar lesions and the definitions and detection of lacunar lesions among small-vessel disease researchers.

Methods—
We assessed definitions of imaging lacunar lesion in 50 randomly selected articles from 3 stroke-related journals and an online survey of small-vessel disease researchers. In the literature review, we assessed clinical/imaging definitions of lacunar stroke. In the survey, we assessed lacunar lesion detection, effects of lesion appearance, background white matter lesions, and provision of relevant data.

Results—
Among 50 articles, imaging definitions were varied and often limited; size was stated in 21 of 43 (49%) studies of acute and in 9 of 20 (45%) studies of old lesions and site in 18 (42%) and 4 (20%), respectively. Clinical definitions also varied, and images were read mostly by nonradiologists. Among 56 survey respondents, multiple descriptions were used for recent and old, symptomatic and asymptomatic, lesions on imaging. Most agreed on definitions for site (98%) and “old lacunar infarct” (61%) size. Cavitated (vs noncavitated) lesions were usually identified as lacunar lesions; with increasing white matter lesions, however, noncavitated lesions were very unlikely to be identified, even with prior imaging available (7.8%).

Conclusions—
Imaging definitions of lacunar lesions vary widely, in part due to variation in lesion detection and classification. A consensus for imaging definitions of small-vessel disease features would be helpful.
Diffusion Tensor Imaging and Gait in Elderly Persons With Cerebral Small Vessel Disease
Authors: de Laat Karlijn F. , van Norden Anouk G.W. , Gons Rob A.R. , van Oudheusden Lucas J.B. , van Uden Inge W.M. , Norris David G. , Zwiers Marcel P. , de Leeuw Frank-Erik 
Published: December 2010

Background and Purpose—
Although cerebral small vessel disease, including white matter lesions (WML) and lacunar infarcts, is associated with gait disturbances, not all individuals with small vessel disease have these disturbances. Identical-appearing WML on MRI could reflect different degrees of microstructural integrity. Moreover, conventional MRI does not assess the integrity of normal-appearing white matter (NAWM). We therefore investigated the relation between white matter integrity assessed by diffusion tensor imaging in WML, NAWM, several regions of interest, and gait.

Methods—
A total of 484 nondemented elderly persons between 50 and 85 years old with cerebral small vessel disease were included in this analysis and underwent MRI and diffusion tensor imaging scanning. Mean diffusivity and fractional anisotropy within WML, NAWM, and regions of interest were related to quantitative and semiquantitative gait parameters.

Results—

Mean diffusivity in the WML was inversely related with gait (velocity β=−0.15;
P
=0.002). For the fractional anisotropy, this relation was less evident. The same was found in the NAWM (velocity β=−0.21;
P
<0.001) and for some parameters also after additional adjustment for WML and lacunar infarcts.

Conclusion—
This study indicates that integrity of both WML and NAWM, beyond the detection limit of conventional MRI, is associated with gait disturbances.