bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of suicide after attempted suicide in the population of Slovenia from 1970 to 1996
Authors: Ziherl Slavko , Zalar Bojan 
Published: July 2005

AbstractObjective:All suicide attempts cannot predict suicide, therefore we examined those characteristics of suicide attempt which could most accurately predict completed suicide.Subject and methods:Subjects were all individuals registered as committed suicides (N= 16,522) or attempted suicides (N= 15,057) in the register of suicides of the Republic of Slovenia between 1970 and 1996. Log linear analysis of a frequency table was used to uncover relationship between categorical variables.Results:The model we found fit between variables: mode, number of repetitions and type, then between number of repetitions, type and gender, and between mode, type and gender.Discussion:The risk of suicide in those who previously attempted suicide is approximately 773 times higher than the risk of suicide without a previous suicide attempt. Those who attempt suicide by hanging (hanging being in Slovenia the most frequent mode of completed suicide) are at even greater risk to commit suicide.Conclusion:Our data suggests that clinicians should heighten their awareness that any suicide attempt can in some 20% predict suicide. Someone who has attempted suicide by hanging is at the highest risk of suicide.
Toll‐like receptor 4 mediates mitochondrial DNA damage and biogenic responses after heat‐inactivated E. coli
Authors: Suliman Hagir B. , Welty‐Wolf Karen E. , Carraway Martha Sue , Schwartz David A. , Hollingsworth John W. , Piantadosi Claude A. 
Published: July 2005

ABSTRACTAn important site of cellular damage in bacterial sepsis is mitochondrial DNA (mtDNA), which we proposed is caused by reactive oxygen and nitrogen species generated by activation of signaling through specific toll‐like receptors (TLR). In wild‐type (Wt) mice injected with heat‐inactivated E. coli, hepatic TLR4 and TLR2 proteins were up‐regulated with TLR‐dependent increases in transcript levels for tumor necrosis factor (TNF‐α), interleukin 6, nitric oxide synthase‐II (iNOS), and NADPH oxidase 2 (Nox2). The accompanying stress significantly depleted hepatic mtDNA despite eight‐ and fourfold increases in manganese superoxide dismutase (MnSOD) and mitochondrial transcription factor A (Tfam) expression, respectively. The identical E. coli dose generated significantly less TNF‐α, NO, and Nox2 in TLR4−/− and TLR2/4−/− but not in TLR2−/− mice. TLR4−/− and TLR2/4−/− compared with Wt mice were protected from mtDNA oxidation but showed no Tfam up‐regulation and little copy number restoration. A critical role in the mtDNA damage was determined for TLR4‐mediated iNOS transcription through the MyD88 pathway. In Wt mice, mtDNA depletion was avoided by selective iNOS blockade, and residual mtDNA loss was linked to NF‐κB‐dependent TNF‐α expression. These data disclose the dual role of TLR4 in mtDNA damage and compensatory mitochondrial biogenic responses after innate immune activation.
Identification of a Gene in the Process of Being Lost from the Genus Agrostis
Authors: Li Huaijun Michael , Rotter David , Bonos Stacy A. , Meyer William A. , Belanger Faith C. 
Published: July 2005

Abstract
Lineage-specific gene loss is considered one of the processes contributing to speciation and genome diversity. Such gene loss has been inferred from interspecies comparisons of orthologous DNA segments. Examples of intraspecific gene loss are rare. Here we report identification of a gene, designated Crs-1 (creeping specific-1), that appears to be in the process of being lost from heterozygous populations of the species creeping bentgrass (Agrostis stolonifera). The Crs-1 gene encodes a protein with an N-terminal dirigent protein domain and a C-terminal lectin domain and is similar to the maize (Zea mays) β-glucosidase aggregating factor. Most individual creeping bentgrass plants examined are lacking Crs-1. Some individuals are hemizygous for the Crs-1 locus, indicating major haplotype noncolinearity at that locus. Crs-1 was not detected in several other Agrostis species, indicating it is being lost from the genus. The Crs-1 locus in creeping bentgrass provides a rare example of the evolutionary process of gene loss occurring within a plant species.
RAC GTPases in Tobacco and Arabidopsis Mediate Auxin-Induced Formation of Proteolytically Active Nuclear Protein Bodies That Contain AUX/IAA Proteins
Authors: Tao Li-zhen , Cheung Alice Y. , Nibau Candida , Wu Hen-ming 
Published: July 2005

AbstractAuxin signaling relies on ubiquitin ligase SCFTIR1-mediated 26S proteasome-dependent proteolysis of a large family of short-lived transcription regulators, auxin/indole acetic acid (Aux/IAA), resulting in the derepression of auxin-responsive genes. We have shown previously that a subset of Rac GTPases is activated by auxin, and they in turn stimulate auxin-responsive gene expression. We show here that increasing Rac signaling activity promotes Aux/IAA degradation, whereas downregulating that activity results in the reduction of auxin-accelerated Aux/IAA proteolysis. Observations reported here reveal a novel function for these Rac GTPases as regulators for ubiquitin/26S proteasome-mediated proteolysis and further consolidate their role in auxin signaling. Moreover, our study reveals a cellular process whereby auxin induces and Rac GTPases mediate the recruitment of nucleoplasmic Aux/IAAs into proteolytically active nuclear protein bodies, into which components of the SCFTIR1, COP9 signalosome, and 26S proteasome are also recruited.
Pyruvate Decarboxylase Provides Growing Pollen Tubes with a Competitive Advantage in Petunia
Authors: Gass Nathalie , Glagotskaia Tatiana , Mellema Stefan , Stuurman Jeroen , Barone Mario , Mandel Therese , Roessner-Tunali Ute , Kuhlemeier Cris 
Published: July 2005

AbstractRapid pollen tube growth places unique demands on energy production and biosynthetic capacity. The aim of this work is to understand how primary metabolism meets the demands of such rapid growth. Aerobically grown pollen produce ethanol in large quantities. The ethanolic fermentation pathway consists of two committed enzymes: pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH). Because adh mutations do not affect male gametophyte function, the obvious question is why pollen synthesize an abundant enzyme if they could do just as well without. Using transposon tagging in Petunia hybrida, we isolated a null mutant in pollen-specific Pdc2. Growth of the mutant pollen tubes through the style is reduced, and the mutant allele shows reduced transmission through the male, when in competition with wild-type pollen. We propose that not ADH but rather PDC is the critical enzyme in a novel, pollen-specific pathway. This pathway serves to bypass pyruvate dehydrogenase enzymes and thereby maintain biosynthetic capacity and energy production under the unique conditions prevailing during pollen–pistil interaction.
Escherichia coli
HypA Is a Zinc Metalloprotein with a Weak Affinity for Nickel
Authors: Atanassova Anelia , Zamble Deborah B. 
Published: July 2005

ABSTRACT

The
hyp
operon encodes accessory proteins that are required for the maturation of the [NiFe] hydrogenase enzymes and, in some organisms, for the production of urease enzymes as well. HypA or a homologous protein is required for nickel insertion into the hydrogenase precursor proteins. In this study, recombinant HypA from
Escherichia coli
was purified and characterized in vitro. Metal analysis was used to demonstrate that HypA simultaneously binds stoichiometric Zn
2+
and stoichiometric Ni
2+
. Competition experiments with a metallochromic indicator reveal that HypA binds zinc with nanomolar affinity. Spectroscopic analysis of cobalt-containing HypA provides evidence for a tetrathiolate coordination sphere, suggesting that the zinc site has a structural role. In addition, HypA can exist as several oligomeric complexes and the zinc content modulates the quaternary structure of the protein. Fluorescence titration experiments demonstrate that HypA binds nickel with micromolar affinity and that the presence of zinc does not dramatically affect the nickel-binding activity. Finally, complex formation between HypA and HypB, another accessory protein required for nickel insertion, was observed. These experiments suggest that HypA is an architectural component of the hydrogenase metallocenter assembly pathway and that it may also have a direct role in the delivery of nickel to the hydrogenase large subunit.
The
Burkholderia pseudomallei
BpeAB-OprB Efflux Pump: Expression and Impact on Quorum Sensing and Virulence
Authors: Chan Ying Ying , Chua Kim Lee 
Published: July 2005

ABSTRACT

BpeAB-OprB is a multidrug efflux pump of the bacterial pathogen
Burkholderia pseudomallei
and is responsible for conferring antimicrobial resistance to aminoglycosides and macrolides. Expression of
bpeAB-oprB
is inducible by its substrate erythromycin and upon entry into stationary phase. BpeR, a member of the TetR family, functions as a repressor of the
bpeAB-oprB
operon.
bpeR
expression was similarly induced at stationary phase but lagged behind the induction of
bpeAB-oprB
expression. The induction of
bpeAB-oprB
expression could be advanced to the early exponential phase by exogenous addition of the
B. pseudomallei
autoinducers
N
-octanoyl-homoserine lactone (C8HSL) and
N
-decanoyl-homoserine lactone (C10HSL), suggesting that the
bpeAB-oprB
operon may be quorum regulated. On the other hand, acyl-homoserine lactone (acyl-HSL) production was undetectable in the
bpeAB
-null mutant and strains which overexpress
bpeR
. The failure of these strains to produce acyl-HSLs seemed to be at the level of synthesis of acyl-HSLs, as growth-phase-dependent expression of the autoinducer synthase BpsI was abolished in the
bpeAB
-null mutant.
bpsI
expression remained growth phase dependent in the
bpeR
mutant which had functional BpeAB-OprB. BpeAB-OprB function is likewise necessary for optimal production of quorum-sensing-controlled virulence factors such as siderophore and phospholipase C and for biofilm formation. Cell invasion and cytotoxicity towards human lung epithelial (A549) and human macrophage (THP-1) cells were also significantly attenuated in both the
bpeAB
mutant and
bpeR-
overexpressing strains, thus suggesting the possibility of attenuating
B. pseudomallei
virulence using inhibitors of the BpeAB-OprB efflux pump.
The Genome of
Salmonella enterica
Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements
Authors: Wu Kai-Yu , Liu Gui-Rong , Liu Wei-Qiao , Wang Austin Q. , Zhan Sen , Sanderson Kenneth E. , Johnston Randal N. , Liu Shu-Lin 
Published: July 2005

ABSTRACT

Salmonella enterica
serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in chickens. It has the same antigenic formula (1,9,12:—:—) as
S. enterica
serovar Pullorum, which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness but distinct pathogeneses make this pair of fowl pathogens good models for studies of bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and characterize the genomic differences between serovar Gallinarum and other salmonellae, we constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two insertions and six deletions relative to the genome of
S. enterica
serovar Typhimurium LT2, which we used as a reference
Salmonella
genome. Four of the genomic regions with reduced lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the others contained several smaller deletions relative to serovar Typhimurium LT2, including regions containing
srfJ
,
std
, and
stj
and gene clusters encoding a type I restriction system in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two inversions and several translocations. Further characterization of these insertions, deletions, and rearrangements will provide new insights into the molecular basis for the specific host-pathogen interactions and mechanisms of genomic evolution to create a new pathogen.
Analysis of theEscherichia coliAlp Phenotype: Heat Shock Induction inssrAMutants
Authors: Munavar Hussain , Zhou YanNing , Gottesman Susan 
Published: July 2005

ABSTRACTThe major phenotypes oflonmutations, UV sensitivity and overproduction of capsule, are due to the stabilization of two substrates, SulA and RcsA. Inactivation of transfer mRNA (tmRNA) (encoded byssrA), coupled with a multicopy kanamycin resistance determinant, suppressed bothlonphenotypes and restored the rapid degradation of SulA. This novel protease activity was named Alp but was never identified further. We report here the identification, mapping, and characterization of a chromosomal mutation,faa(forfunctionaffectingAlp), that leads to full suppression of a Δlon ssrA::cathost and thus bypasses the requirement for multicopy Kanr;faaandssrAmutants are additive in their ability to suppresslonmutants. Thefaamutation was mapped to the C terminus ofdnaJ(G232);dnaJnull mutants have similar effects. The identification of alonsuppressor indnaJsuggested the possible involvement of heat shock. We find thatssrAmutants alone significantly induce the heat shock response. The suppression of UV sensitivity, both in the original Alp strain and infaamutants, is reversed by mutations inclpY, encoding a subunit of the heat shock-induced ClpYQ protease that is known to degrade SulA. However, capsule synthesis is not restored byclpYmutants, probably because less RcsA accumulates in the Alp strain and because the RcsA that does accumulate is inactive. BothssrAeffects are partially relieved byssrAderivatives encoding protease-resistant tags, implicating ribosome stalling as the primary defect. Thus,ssrAandfaaeach suppress twolonmutant phenotypes but by somewhat different mechanisms, with heat shock induction playing a major role.
Identification of Phthiodiolone Ketoreductase, an Enzyme Required for Production of Mycobacterial Diacyl Phthiocerol Virulence Factors
Authors: Onwueme Kenolisa C. , Vos Cheryl J. , Zurita Juan , Soll Clifford E. , Quadri Luis E. N. 
Published: July 2005

ABSTRACT

Diacyl phthiocerol esters and their congeners are mycobacterial virulence factors. The biosynthesis of these complex lipids remains poorly understood. Insight into their biosynthesis will aid the development of rationally designed drugs that inhibit their production. In this study, we investigate a biosynthetic step required for diacyl (phenol)phthiocerol ester production, i.e., the reduction of the keto group of (phenol)phthiodiolones. We utilized comparative genomics to identify phthiodiolone ketoreductase gene candidates and provide a genetic analysis demonstrating gene function for two of these candidates. Moreover, we present data confirming the existence of a diacyl phthiotriol intermediate in diacyl phthiocerol biosynthesis. We also elucidate the mechanism underlying diacyl phthiocerol deficiency in some mycobacteria, such as
Mycobacterium ulcerans
and
Mycobacterium kansasii
. Overall, our findings shed additional light on the biosynthesis of an important group of mycobacterial lipids involved in virulence.
The Ubiquitous Protein Domain EAL Is a Cyclic Diguanylate-Specific Phosphodiesterase: Enzymatically Active and Inactive EAL Domains
Authors: Schmidt Andrew J. , Ryjenkov Dmitri A. , Gomelsky Mark 
Published: July 2005

ABSTRACT

The EAL domain (also known as domain of unknown function 2 or DUF2) is a ubiquitous signal transduction protein domain in the
Bacteria
. Its involvement in hydrolysis of the novel second messenger cyclic dimeric GMP (c-di-GMP) was demonstrated in vivo but not in vitro. The EAL domain-containing protein Dos from
Escherichia coli
was reported to hydrolyze cyclic AMP (cAMP), implying that EAL domains have different substrate specificities. To investigate the biochemical activity of EAL, the
E. coli
EAL domain-containing protein YahA and its individual EAL domain were overexpressed, purified, and characterized in vitro. Both full-length YahA and the EAL domain hydrolyzed c-di-GMP into linear dimeric GMP, providing the first biochemical evidence that the EAL domain is sufficient for phosphodiesterase activity. This activity was c-di-GMP specific, optimal at alkaline pH, dependent on Mg
2+
or Mn
2+
, strongly inhibited by Ca
2+
, and independent of protein oligomerization. Linear dimeric GMP was shown to be 5′pGpG. The EAL domain from Dos was overexpressed, purified, and found to function as a c-di-GMP-specific phosphodiesterase, not as a cAMP-specific phosphodiesterase, in contrast to previous reports. The EAL domains can hydrolyze 5′pGpG into GMP, however, very slowly, thus implying that this activity is irrelevant in vivo. Therefore, c-di-GMP is the exclusive substrate of EAL. Multiple-sequence alignment revealed two groups of EAL domains hypothesized to correspond to enzymatically active and inactive domains. The domains in the latter group have mutations in residues conserved in the active domains. The enzymatic inactivity of EAL domains may explain their coexistence with GGDEF domains in proteins possessing c-di-GMP synthase (diguanulate cyclase) activity.
ExpR, a LuxR Homolog ofErwinia carotovorasubsp.carotovora, Activates Transcription ofrsmA, Which Specifies a Global Regulatory RNA-Binding Protein
Authors: Cui Yaya , Chatterjee Asita , Hasegawa Hiroaki , Dixit Vaishali , Leigh Nathan , Chatterjee Arun K. 
Published: July 2005

ABSTRACTN-acyl homoserine lactone (AHL) is required byErwinia carotovorasubspecies for the expression of various traits, including extracellular enzyme and protein production and pathogenicity. Previous studies withE. carotovorasubsp.carotovorahave shown that AHL deficiency causes the production of high levels of RsmA, an RNA binding protein that functions as a global negative regulator of extracellular enzymes and proteins and secondary metabolites (Rsm, regulator of secondary metabolites). We document here that ExpR, a putative AHL receptor belonging to the LuxR family of regulators, activates RsmA production. In the absence of AHL, an ExpR+E. carotovorasubsp.carotovorastrain compared to its ExpR−mutant, produces higher levels ofrsmARNA and better expresses anrsmA-lacZtranscriptional fusion. Moreover, the expression of thersmA-lacZfusion inEscherichia coliis much higher in the presence ofexpR71(theexpRgene ofE. carotovorasubsp.carotovorastrain Ecc71) than in its absence. We also show that purified preparation of MBP-ExpR71binds (MBP, maltose binding protein)rsmADNA. By contrast, MBP-ExpR71does not bindahlI(gene for AHL synthase),pel-1(gene for pectate lyase), orrsmB(gene for regulatory RNA that binds RsmA), nor does ExpR71activate expression of these genes. These observations strongly suggest transcriptional activation ofrsmAresulting from a direct and specific interaction between ExpR71and thersmApromoter. Several lines of evidence establish thatN-3-oxohexanoyl-l-homoserine lactone (3-oxo-C6-HL), the major AHL analog produced byE. carotovorasubsp.carotovorastrain Ecc71, inhibits ExpR71-mediated activation ofrsmAexpression. These findings for the first time establish that theexpReffect inE. carotovorasubsp.carotovorais channeled via RsmA, a posttranscriptional regulator ofE. carotovorasubspecies, and AHL neutralizes this ExpR effect.
Mutational Analysis of 16S and 23S rRNA Genes of
Thermus thermophilus
Authors: Gregory Steven T. , Carr Jennifer F. , Rodriguez-Correa Daniel , Dahlberg Albert E. 
Published: July 2005

ABSTRACT

Structural studies of the ribosome have benefited greatly from the use of organisms adapted to extreme environments. However, little is known about the mechanisms by which ribosomes or other ribonucleoprotein complexes have adapted to functioning under extreme conditions, and it is unclear to what degree mutant phenotypes of extremophiles will resemble those of their counterparts adapted to more moderate environments. It is conceivable that phenotypes of mutations affecting thermophilic ribosomes, for instance, will be influenced by structural adaptations specific to a thermophilic existence. This consideration is particularly important when using crystal structures of thermophilic ribosomes to interpret genetic results from nonextremophilic species. To address this issue, we have conducted a survey of spontaneously arising antibiotic-resistant mutants of the extremely thermophilic bacterium
Thermus thermophilus
, a species which has featured prominently in ribosome structural studies. We have accumulated over 20 single-base substitutions in
T. thermophilus
16S and 23S rRNA, in the decoding site and in the peptidyltransferase active site of the ribosome. These mutations produce phenotypes that are largely identical to those of corresponding mutants of mesophilic organisms encompassing a broad phylogenetic range, suggesting that
T. thermophilus
may be an ideal model system for the study of ribosome structure and function.
Analysis of theospCRegulatory Element Controlled by the RpoN-RpoS Regulatory Pathway inBorrelia burgdorferi
Authors: Yang Xiaofeng F. , Lybecker Meghan C. , Pal Utpal , Alani Sophie M. , Blevins Jon , Revel Andrew T. , Samuels D. Scott , Norgard Michael V. 
Published: July 2005

ABSTRACTOuter surface lipoprotein C (OspC) is a key virulence factor ofBorrelia burgdorferi. ospCis differentially regulated during borrelial transmission from ticks to rodents, and such regulation is essential for maintaining the spirochete in its natural enzootic cycle. Recently, we showed that the expression ofospCinB. burgdorferiis governed by a novel alternative sigma factor regulatory network, the RpoN-RpoS pathway. However, the precise mechanism by which the RpoN-RpoS pathway controlsospCexpression has been unclear. In particular, there has been uncertainty regarding whetherospCis controlled directly by RpoS (σs) or indirectly through a transactivator (induced by RpoS). Using deletion analyses and genetic complementation in an OspC-deficient mutant ofB. burgdorferi, we analyzed theciselement(s) required for the expression ofospCin its native borrelial background. Two highly conserved upstream inverted repeat elements, previously implicated inospCregulation, were not required forospCexpression inB. burgdorferi. Using similar approaches, a minimal promoter that contained a canonical −35/−10 sequence necessary and sufficient for σs-dependent regulation ofospCwas identified. Further, targeted mutagenesis of a C at position −15 within the extended −10 region ofospC, which is postulated to function like the strategic C residue important for Eσsbinding inEscherichia coli, abolishedospCexpression. The minimalospCpromoter also was responsive to coumermycin A1, further supporting its σscharacter. The combined data constitute a body of evidence that the RpoN-RpoS regulatory network controlsospCexpression by direct binding of σsto a σs-dependent promoter ofospC. The implication of our findings to understanding howB. burgdorferidifferentially regulatesospCand otherospC-like genes via the RpoN-RpoS regulatory pathway is discussed.