bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Second Lysine-Specific Serine Protease from
Lysobacter
sp. Strain IB-9374
Authors: Chohnan Shigeru , Shiraki Kentaro , Yokota Kiyonobu , Ohshima Makoto , Kuroiwa Natsuki , Ahmed Kashfia , Masaki Takeharu , Sakiyama Fumio 
Published: July 2004

ABSTRACT

A second lysyl endopeptidase gene (
lepB
) was found immediately upstream of the previously isolated
lepA
gene encoding a highly active lysyl endopeptidase in
Lysobacter
genomic DNA. The
lepB
gene consists of 2,034 nucleotides coding for a protein of 678 amino acids. Amino acid sequence alignment between the
lepA
and
lepB
gene products (LepA and LepB) revealed that the LepB precursor protein is composed of a prepeptide (20 amino acids [aa]), a propeptide (184 aa), a mature enzyme (274 aa), and a C-terminal extension peptide (200 aa). The mature enzyme region exhibited 72% sequence identity to its LepA counterpart and conserved all essential amino acids constituting the catalytic triad and the primary determining site for lysine specificity. The
lepB
gene encoding the propeptide and mature-enzyme portions was overexpressed in
Escherichia coli
, and the inclusion body produced generated active LepB through appropriate refolding and processing. The purified enzyme, a mature 274-aa lysine-specific endopeptidase, was less active and more sensitive to both temperature and denaturation with urea, guanidine hydrochloride, or sodium dodecyl sulfate than LepA. LepA-based modeling implies that LepB can fold into essentially the same three-dimensional structure as LepA by placing a peptide segment, composed of several inserted amino acids found only in LepB, outside the molecule and that the Tyr169 side chain occupies the site in which the indole ring of Trp169, a built-in modulator for unique peptidase functions of LepA, resides. The results suggest that LepB is an isozyme of LepA and probably has a tertiary structure quite similar to it.
Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen
Pseudomonas syringae
pv. maculicola ES4326
Authors: Stavrinides John , Guttman David S. 
Published: July 2004

ABSTRACT

Plasmids are transmissible, extrachromosomal genetic elements that are often responsible for environmental or host-specific adaptations. In order to identify the forces driving the evolution of these important molecules, we determined the complete nucleotide sequence of the five-plasmid complement of the radish and
Arabidopsis
pathogen
Pseudomonas syringae
pv. maculicola ES4326 and conducted an intraspecific comparative genomic analysis. To date, this is the most complex fully sequenced plasmid complement of any gram-negative bacterium. The plasmid complement comprises two pPT23A-like replicons, pPMA4326A (46,697 bp) and pPMA4326B (40,110 bp); a pPS10-like replicon, pPMA4326C (8,244 bp); and two atypical, replicase-deficient replicons, pPMA4326D (4,833 bp) and pPMA4326E (4,217 bp). A complete type IV secretion system is found on pPMA4326A, while the type III secreted effector
hopPmaA
is present on pPMA4326B. The region around
hopPmaA
includes a shorter
hopPmaA
homolog, insertion sequence (IS) elements, and a three-element cassette composed of a resolvase, an integrase, and an
exeA
gene that is also present in several human pathogens. We have also identified a novel genetic element (E622) that is present on all but the smallest plasmid (pPMA4326E) that has features of an IS element but lacks an identifiable transposase. This element is associated with virulence-related genes found in a wide range of
P. syringae
strains. Comparative genomic analyses of these and other
P. syringae
plasmids suggest a role for recombination and integrative elements in driving plasmid evolution.
CloningSerratia entomophilaAntifeeding Genes—a Putative Defective Prophage Active against the Grass GrubCostelytra zealandica
Authors: Hurst Mark R. H. , Glare Travis R. , Jackson Trevor A. 
Published: July 2004

ABSTRACTSerratia entomophilaandSerratia proteamaculans(Enterobacteriaceae) cause amber disease in the grass grubCostelytra zealandica(Coleoptera: Scarabaeidae), an important pasture pest in New Zealand. Larval disease symptoms include cessation of feeding, clearance of the gut, amber coloration, and eventual death. A 155-kb plasmid, pADAP, carries the genessepA,sepB, andsepC, which are essential for production of amber disease symptoms. Transposon insertions in any of thesepgenes in pADAP abolish gut clearance but not cessation of feeding, indicating the presence of an antifeeding gene(s) elsewhere on pADAP. Based on deletion analysis of pADAP and subsequent sequence data, a 47-kb clone was constructed, which when placed in either anEscherichia colior aSerratiabackground exerted strong antifeeding activity and often led to rapid death of the infected grass grub larvae. Sequence data show that the antifeeding component is part of a large gene cluster that may form a defective prophage and that six potential members of this prophage are present inPhotorhabdus luminescenssubsp.laumondiiTTO1, a species which also hassepgene homologues.
The Phosphoenolpyruvate Carboxylase from
Methanothermobacter thermautotrophicus
Has a Novel Structure
Authors: Patel Hiten M. , Kraszewski Jessica L. , Mukhopadhyay Biswarup 
Published: July 2004

ABSTRACT

In
Methanothermobacter thermautotrophicus
, oxaloacetate synthesis is a major and essential CO
2
-fixation reaction. This methanogenic archaeon possesses two oxaloacetate-synthesizing enzymes, pyruvate carboxylase and phosphoenolpyruvate carboxylase. The phosphoenolpyruvate carboxylase from this organism was purified to homogeneity. The subunit size of this homotetrameric protein was 55 kDa, which is about half that of all known bacterial and eukaryotic phosphoenolpyruvate carboxylases (PPCs). The NH
2
-terminal sequence identified this enzyme as the product of MTH943, an open reading frame with no assigned function in the genome sequence. A BLAST search did not show an obvious sequence similarity between MTH943 and known PPCs, which are generally well conserved. This is the first report of a new type of phosphoenolpyruvate carboxylase that we call PpcA (“A” for “archaeal”). Homologs to PpcA were present in most archaeal genomic sequences, but only in three bacterial (
Clostridium perfringens
,
Oenococcus oeni
, and
Leuconostoc mesenteroides
) and no eukaryotic genomes. PpcA was the only recognizable oxaloacetate-producing enzyme in
Methanopyrus kandleri
, a hydrothermal vent organism. Each PpcA-containing organism lacked a PPC homolog. The activity of
M. thermautotrophicus
PpcA was not influenced by acetyl coenzyme A and was about 50 times less sensitive to aspartate than the
Escherichia coli
PPC. The catalytic core (including His
138
, Arg
587
, and Gly
883
) of the
E. coli
PPC was partly conserved in PpcA, but three of four aspartate-binding residues (Lys
773
, Arg
832
, and Asn
881
) were not. PPCs probably evolved from PpcA through a process that added allosteric sites to the enzyme. The reverse is also equally possible.
DNA Microarray Analysis of Genome Dynamics in
Yersinia pestis
: Insights into Bacterial Genome Microevolution and Niche Adaptation
Authors: Zhou Dongsheng , Han Yanping , Song Yajun , Tong Zongzhong , Wang Jin , Guo Zhaobiao , Pei Decui , Pang Xin , Zhai Junhui , Li Min , Cui Baizhong , Qi Zhizhen , Jin Lixia , Dai Ruixia , Du Zongmin , Bao Jingyue , Zhang Xiuqing , Yu Jun , Wang Jian , Huang Peitang , Yang Ruifu 
Published: July 2004

ABSTRACT

Genomics research provides an unprecedented opportunity for us to probe into the pathogenicity and evolution of the world's most deadly pathogenic bacterium,
Yersinia pestis
, in minute detail. In our present work, extensive microarray analysis in conjunction with PCR validation revealed that there are considerable genome dynamics, due to gene acquisition and loss, in natural populations of
Y. pestis
. We established a genomotyping system to group homologous isolates of
Y. pestis
, based on profiling or gene acquisition and loss in their genomes, and then drew an outline of parallel microevolution of the
Y. pestis
genome. The acquisition of a number of genomic islands and plasmids most likely induced
Y. pestis
to evolve rapidly from
Yersinia pseudotuberculosis
to a new, deadly pathogen. Horizontal gene acquisition also plays a key role in the dramatic evolutionary segregation of
Y. pestis
lineages (biovars and genomovars). In contrast to selective genome expansion by gene acquisition, genome reduction occurs in
Y. pestis
through the loss of DNA regions. We also theorized about the links between niche adaptation and genome microevolution. The transmission, colonization, and expansion of
Y. pestis
in the natural foci of endemic plague are parallel and directional and involve gradual adaptation to the complex of interactions between the environment, the hosts, and the pathogen itself. These adaptations are based on the natural selections against the accumulation of genetic changes within genome. Our data strongly support that the modern plague originated from Yunnan Province in China, due to the arising of biovar orientalis from biovar antiqua rather than mediaevalis.
Genetics of Metabolic Variations between
Yersinia pestis
Biovars and the Proposal of a New Biovar, microtus
Authors: Zhou Dongsheng , Tong Zongzhong , Song Yajun , Han Yanping , Pei Decui , Pang Xin , Zhai Junhui , Li Min , Cui Baizhong , Qi Zhizhen , Jin Lixia , Dai Ruixia , Du Zongmin , Wang Jin , Guo Zhaobiao , Wang Jian , Huang Peitang , Yang Ruifu 
Published: July 2004

ABSTRACT

Yersinia pestis
has been historically divided into three biovars: antiqua, mediaevalis, and orientalis. On the basis of this study, strains from
Microtus
-related plague foci are proposed to constitute a new biovar, microtus. Based on the ability to ferment glycerol and arabinose and to reduce nitrate,
Y. pestis
strains can be assigned to one of four biovars: antiqua (glycerol positive, arabinose positive, and nitrate positive), mediaevalis (glycerol positive, arabinose positive, and nitrate negative), orientalis (glycerol negative, arabinose positive, and nitrate positive), and microtus (glycerol positive, arabinose negative, and nitrate negative). A 93-bp in-frame deletion in
glpD
gene results in the glycerol-negative characteristic of biovar orientalis strains. Two kinds of point mutations in the
napA
gene may cause the nitrate reduction-negative characteristic in biovars mediaevalis and microtus, respectively. A 122-bp frameshift deletion in the
araC
gene may lead to the arabinose-negative phenotype of biovar microtus strains. Biovar microtus strains have a unique genomic profile of gene loss and pseudogene distribution, which most likely accounts for the human attenuation of this new biovar. Focused, hypothesis-based investigations on these specific genes will help delineate the determinants that enable this deadly pathogen to be virulent to humans and give insight into the evolution of
Y. pestis
and plague pathogenesis. Moreover, there may be the implications for development of biovar microtus strains as a potential vaccine.
PBP1 Is a Component of theBacillus subtilisCell Division Machinery
Authors: Scheffers Dirk-Jan , Errington Jeffery 
Published: July 2004

ABSTRACTBacillus subtilispenicillin-binding protein PBP1 has been implicated in cell division. We show here that a PBP1 knockout strain is affected in the formation of the asymmetric sporulation septum and that green fluorescent protein-PBP1 localizes to the sporulation septum. Localization of PBP1 to the vegetative septum is dependent on various cell division proteins. This study proves that PBP1 forms part of theB. subtiliscell division machinery.
Cellular Levels of
trp
RNA-Binding Attenuation Protein in
Bacillus subtilis
Authors: McCabe Barbara C. , Gollnick Paul 
Published: July 2004

ABSTRACT

Expression of the
Bacillus subtilis trp
genes is negatively regulated by an 11-subunit
trp
RNA-binding attenuation protein (TRAP), which is activated to bind RNA by binding
l
-tryptophan. We used Western blotting to estimate that there are 200 to 400 TRAP 11-mer molecules per cell in cells grown in either minimal or rich medium.
Expression of a Functional Secreted YopN-TyeA Hybrid Protein inYersinia pestisIs the Result of a +1 Translational Frameshift Event
Authors: Ferracci Franco , Day James B. , Ezelle Heather J. , Plano Gregory V. 
Published: July 2004

ABSTRACTYopN is a secreted protein that prior to secretion directly interacts with the cytosolic SycN/YscB chaperone complex and TyeA. This study identifies a secreted YopN-TyeA hybrid protein that is expressed byYersinia pestis, but not byYersinia enterocolitica. DNA sequence analysis and site-directed mutagenesis studies demonstrate that the hybrid protein is the result of a +1 translational frameshift event.
The
ompU
Paralogue
vca1008
Is Required for Virulence of
Vibrio cholerae
Authors: Osorio Carlos G. , Martinez-Wilson Hector , Camilli Andrew 
Published: July 2004

ABSTRACT

We made single and combined mutations in
ompU
,
ompT
, and the two putative porin genes
vca1008
and
vc0972
. The fitness of the strains was tested in vitro and in the infant mouse model of intestinal infection. We also studied the transcriptional induction of
vca1008
in vitro and during mouse infection. We show that
vca1008
is induced during infection and is necessary and sufficient (in the absence of
ompU
,
ompT
, and
vc0972
) for infection.
Biochemical Study of Multiple CheY Response Regulators of the Chemotactic Pathway of
Rhodobacter sphaeroides
Authors: Ferré Axelle , de la Mora Javier , Ballado Teresa , Camarena Laura , Dreyfus Georges 
Published: July 2004

ABSTRACT

The six copies of the response regulator CheY from
Rhodobacter sphaeroides
bind to the switch protein FliM. Phosphorylation by acetyl phosphate (AcP) was detected by tryptophan fluorescence quenching in three of the four CheYs that contain this residue. Autophosphorylation with Ac
32
P was observed in five CheY proteins. We also show that all of the
cheY
genes are expressed simultaneously; therefore, in vivo all of the CheY proteins could bind to FliM to control the chemotactic response. Consequently, we hypothesize that in this complex chemotactic system, the binding of some CheY proteins to FliM, does not necessarily imply switching of the flagellar motor.
Polyphosphate Synthetic Activity of Polyphosphate:AMP Phosphotransferase in
Acinetobacter johnsonii
210A
Authors: Itoh Hiromichi , Shiba Toshikazu 
Published: July 2004

ABSTRACT

Polyphosphate:AMP phosphotransferase (PAP) has been identified as an enzyme that catalyzes the phosphorylation of AMP with inorganic polyphosphates [poly(P)] as phosphate donors. We found that the purified PAP of
Acinetobacter johnsonii
210A has poly(P) synthetic activity. The PAP catalyzes the dephosphorylation of ADP and processively synthesizes poly(P) of 200 to 700 residues. Comparatively lower concentrations of MgCl
2
(20 mM) were required to obtain optimum poly(P) synthetic activity, whereas higher concentrations of MgCl
2
(100 mM) were necessary for optimum PAP activity. ADP is preferred over GDP as a phosphate donor for poly(P) synthesis. The

K
m

and
V
max
values for ADP in the poly(P) synthetic activity of PAP were 8.3 mM and 55 μmol min
−1
mg
−1
, respectively. We concluded that the PAP of
A. johnsonii
210A is a novel type of poly(P) kinase that uses ADP and GDP as substrates.
Evolution of the
Helicobacter pylori
Vacuolating Cytotoxin in a Human Stomach
Authors: Aviles-Jimenez Francisco , Letley Darren P. , Gonzalez-Valencia Gerardo , Salama Nina , Torres Javier , Atherton John C. 
Published: July 2004

ABSTRACT

We describe two subclones of
Helicobacter pylori
, isolated contemporaneously from a human stomach, which differ markedly in the vacuolating cytotoxin gene,
vacA
, but whose near identity in sequences outside this locus implies a very recent common origin. The differences are consistent with homologous recombination with DNA from another strain and result in a changed
vacA
midregion and, importantly, in changed toxicity.
APPROXIMATIONS OF HOLOMORPHIC FUNCTIONS IN CERTAIN BANACH SPACES
Authors: JOSEFSON BENGT 
Published: July 2004

Let E be a Banach space and let B(R)⊂E denote the open ball with centre at 0 and radius R. The following problem is studied: given 0<r<R, ∊>0 and a function f holomorphic on B(R), does there always exist an entire function g on E such that |f-g|<∊ on B(r)? L. Lempert has proved that the answer is positive for Banach spaces having an unconditional basis with unconditional constant 1. In this paper a somewhat shorter proof of Lemperts result is given. In general it is not possible to approximate f by polynomials since f does not need to be bounded on B(r).
Adrenergic Modulation of Survival and Cellular Immune Functions during Polymicrobial Sepsis
Authors: Oberbeck Reiner , Schmitz Daniel , Wilsenack Klaus , Schüler Marc , Pehle Birthe , Schedlowski Manfred , Exton Michael S. 
Published: July 2004

<i>Objective: </i>An immunomodulatory effect of epinephrine has been reported that is supposed to be mediated via β-adrenergic receptors. The effect of epinephrine and/or β-adrenergic blockade on cellular immune functions during systemic inflammation has not yet been investigated. <i>Methods:</i> Male NMRI mice were treated with either an infusion of epinephrine (0.05 mg/kg/h i.p.), administration of the nonselective β-adrenoceptor antagonist propranolol (0.5 mg/kg s.c.), or a combination of epinephrine and propranolol after induction of a polymicrobial sepsis by cecal ligation and puncture. Forty-eight hours thereafter survival and cellular immune functions (splenocyte proliferation, splenocyte apoptosis and cytokine release, distribution of leukocyte subsets) were determined. <i>Results:</i> Infusion of epinephrine did not affect lethality of septic mice but induced alterations of splenocyte apoptosis, splenocyte proliferation and IL-2 release and was associated with profound changes of circulating immune cell subpopulations. Treatment with propranolol augmented the epinephrine-induced increase of splenocyte apoptosis, did not affect the decrease of splenocyte proliferation and IL-2 release, augmented the release of IL-6 and antagonized the mobilization of natural killer cells observed in epinephrine-treated animals. Furthermore, these immunologic alterations were accompanied by a significant increase of sepsis-induced mortality. Coadministration of propranolol and epinephrine augmented the propranolol-induced changes of splenocyte apoptosis and IL-6 release and was associated with the highest mortality of septic mice. <i>Conclusion:</i> Epinephrine infusion modulated cellular immune functions during systemic inflammation without an impact on survival. A pharmacologic β-adrenergic blockade partly augmented the epinephrine-induced immune alterations and was associated with a pronounced increase of mortality. This effect was further augmented by a combination of epinephrine infusion and β-adrenergic blockade. These data indicate that adrenergic mechanisms modulate cellular immune functions and survival during sepsis, with these effects being mediated via α- and β-adrenergic pathways.
Influence of Indocyanine Green Staining on the Biomechanical Strength of Porcine Internal Limiting Membrane
Authors: Wollensak Gregor , Spoerl Eberhard , Wirbelauer Christopher , Pham Duy-Thoai 
Published: July 2004

<i>Purpose:</i> Indocyanine green (ICG) has recently been introduced to stain selectively the internal limiting membrane (ILM) of the retina for ILM peeling. The aim of the present in vitro study was to examine the effect of ICG staining on the biomechanical properties of porcine ILM. <i>Methods:</i> Two parallel 10 × 7 mm strips of central retina were prepared from each of the 40 porcine eyes. 0.005% ICG staining combined with white light illumination for 3 min was performed. Unstained, nonilluminated and 0.1% glutaraldehyde-treated specimens were used as controls. Biomechanical-force elongation measurements were performed using an automated material tester. The absorption spectrum of the ICG solution and the emission spectrum of the light source was measured. <i>Results:</i> After ICG staining of the retina combined with 3 min of illumination, a significant increase in ultimate force by 45% and a decrease in ultimate elongation by 24% was found. Without light exposure, there was no such effect, suggesting a light-dependent process. After 30 min of 0.1% glutaraldehyde treatment, there was an increase in ultimate force by 107% and a decrease in ultimate elongation by 66.6%. The absorption spectrum of the light source was continuous in the range from 400 to 800 nm including the absorption peak of ICG at 700 nm. <i>Conclusions:</i> ICG staining of the retina including the ILM causes a significant increase in the biomechanical stiffness thereby facilitating ILM peeling. The effect is due to a photosensitizing effect of ICG leading to collagen cross-linking.
Stop Place Coding: An Acoustic Study of CV, VC#, and C#V Sequences
Authors: Modarresi Golnaz , Modarresi Golnaz , Sussman Harvey , Sussman Harvey , Lindblom Bjorn , Lindblom Bjorn , Burlingame Elizabeth , Burlingame Elizabeth 
Published: July 2004

Abstract
This study investigated stop + vowel coarticulation as a coding mechanism for differentiation of stop place categories in an F2-defined stimulus space. Locus equations (LEs) were used to index the extent of coarticulation in three contexts: (1) onset stop + vowel utterances [.CV]; (2) within-syllable vowel + coda stop utterances [VC#], and (3) across-syllable/word coda stop + vowel utterances [C#V]. Five speakers of American English and 2 speakers of Persian produced [CV<sub>1</sub>.CV<sub>2</sub>] (English and Persian), [tV<sub>1</sub>C#V<sub>2</sub>t] (English) and [dV<sub>1</sub>C#V<sub>2</sub>t] (Persian) tokens with voiced labial, alveolar/dental, and velar stops surrounded by a variety of vowels. In the across-syllable/word boundary condition [C#V<sub>2</sub>] the extent of anticipatory coarticulation was much reduced relative to traditionally measured onset [CV<sub>2</sub>] syllables. LE slopes derived across the syllable/word boundary, however, still differed between stop places in the same order as onset CVs. LE slopes derived from within-syllable [V<sub>1</sub>C#] sequences, however, did not differ between stop places.
On the Back of the Tongue: Dorsal Sounds in Australian Languages
Authors: Butcher Andrew , Butcher Andrew , Tabain Marija , Tabain Marija 
Published: July 2004

AbstractIn this paper we provide an overview of dorsovelar articulations and acoustics in several Australian Aboriginal languages, and we compare these results with data from English. We examine languages that have a single dorsal, as well as languages that have two dorsal places of articulation. Using direct palatography and F<sub>2</sub> transition measures, we show that Australian languages appear to have a distinct velar target for each of the three major vowel contexts, with a high degree of coarticulation between each velar allophone and its following vowel target, whilst English has only two velar targets – back and non-back, with a lower degree of coarticulation between velar allophones and their corresponding vowel targets. Thus, whilst the range of allophonic variation for velars extends further back in the Australian Aboriginal languages than in English, there appears to be no difference in the articulation of velars in the front vowel context. Drawing on results from the biomechanics, language acquisition, speech perception and acoustics literatures, we suggest that this result may be due to conflict between systemic constraints imposed by the place-rich consonant systems of Aboriginal languages and universal acoustic constraints on the identity of front-velar sounds, which may contribute to the instability of such articulations and the relative infrequency of velar + high vowel combinations in the world’s languages.