bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome of the Opportunistic Pathogen
Streptococcus sanguinis
Authors: Xu Ping , Alves Joao M. , Kitten Todd , Brown Arunsri , Chen Zhenming , Ozaki Luiz S. , Manque Patricio , Ge Xiuchun , Serrano Myrna G. , Puiu Daniela , Hendricks Stephanie , Wang Yingping , Chaplin Michael D. , Akan Doruk , Paik Sehmi , Peterson Darrell L. , Macrina Francis L. , Buck Gregory A. 
Published: February 2007

ABSTRACT

The genome of
Streptococcus sanguinis
is a circular DNA molecule consisting of 2,388,435 bp and is 177 to 590 kb larger than the other 21 streptococcal genomes that have been sequenced. The G+C content of the
S. sanguinis
genome is 43.4%, which is considerably higher than the G+C contents of other streptococci. The genome encodes 2,274 predicted proteins, 61 tRNAs, and four rRNA operons. A 70-kb region encoding pathways for vitamin B
12
biosynthesis and degradation of ethanolamine and propanediol was apparently acquired by horizontal gene transfer. The gene complement suggests new hypotheses for the pathogenesis and virulence of
S. sanguinis
and differs from the gene complements of other pathogenic and nonpathogenic streptococci. In particular,
S. sanguinis
possesses a remarkable abundance of putative surface proteins, which may permit it to be a primary colonizer of the oral cavity and agent of streptococcal endocarditis and infection in neutropenic patients.
The Transcriptional Regulators NorG and MgrA Modulate Resistance to both Quinolones and β-Lactams inStaphylococcus aureus
Authors: Truong-Bolduc Que Chi , Hooper David C. 
Published: February 2007

ABSTRACTMgrA is a known regulator of the expression of several multidrug transporters inStaphylococcus aureus. We identified another regulator of multiple efflux pumps, NorG, by its ability, like that of MgrA, to bind specifically to the promoter of the gene encoding the NorA efflux pump. NorG is a member of the family of the GntR-like transcriptional regulators, and it binds specifically to the putative promoters of the genes encoding multidrug efflux pumps NorA, NorB, NorC, and AbcA. Overexpression ofnorGproduces a threefold increase innorBtranscripts associated with a fourfold increase in the level of resistance to quinolones. In contrast, disruption ofnorGproduces no change in the level of transcripts ofnorA,norB, andnorCbut causes an increase of at least threefold in the transcript level ofabcA, associated with a fourfold increase in resistance to methicillin, cefotaxime, penicillin G, and nafcillin. Overexpression of clonedabcAcaused an 8- to 128-fold increase in the level of resistance to all four β-lactam antibiotics. Furthermore, MgrA and NorG have opposite effects onnorBandabcAexpression. MgrA acts as an indirect repressor fornorBand a direct activator forabcA, whereas NorG acts as a direct activator fornorBand a direct repressor forabcA.
Characterization of the Signaling Domain of the NO-Responsive Regulator NorR from
Ralstonia eutropha
H16 by Site-Directed Mutagenesis
Authors: Klink Andrea , Elsner Bettina , Strube Katja , Cramm Rainer 
Published: February 2007

ABSTRACT

In
Ralstonia eutropha
H16, the nitric oxide (NO)-responsive transcriptional activator NorR controls the expression of a dicistronic operon that encodes a membrane-bound NO reductase, NorB, and a protein of unknown function, NorA. The N-terminal domain (NTD) of NorR is responsible for perception of the signal molecule, nitric oxide. Thirteen out of 29 conserved residues of the NTD were exchanged by site-directed mutagenesis. Replacement of R63, R72, D93, D96, C112, D130, or F137 strongly decreased NorR-dependent promoter activation, while the exchange of Y95 or H110 led to an increase in promoter activity compared to that of the wild type. A purified truncated NorR comprising only the NTD (NorR-NTD) contained one iron atom per molecule and was able to bind NO in the as-isolated state. Based on the iron content of NorR-NTD proteins with single amino acid replacements, residues R72, D93, D96, C112, and D130 are likely candidates for iron ligands. Residues R63, Y95, and H110 appear not to be involved in NO binding but may take part in subsequent steps of the signal transduction mechanism of NorR.
Coordinated High-Light Response of Genes Encoding Subunits of Photosystem I Is Achieved by AT-Rich Upstream Sequences in the Cyanobacterium
Synechocystis
sp. Strain PCC 6803
Authors: Muramatsu Masayuki , Hihara Yukako 
Published: February 2007

ABSTRACT

Genes encoding subunits of photosystem I (PSI genes) in the cyanobacterium
Synechocystis
sp. strain PCC 6803 are actively transcribed under low-light conditions, whereas their transcription is coordinately and rapidly down-regulated upon the shift to high-light conditions. In order to identify the molecular mechanism of the coordinated high-light response, we searched for common light-responsive elements in the promoter region of PSI genes. First, the precise architecture of the
psaD
promoter was determined and compared with the previously identified structure of the
psaAB
promoter. One of two promoters of the
psaAB
genes (P1) and of the
psaD
gene (P2) possessed an AT-rich light-responsive element located just upstream of the basal promoter region. These sequences enhanced the basal promoter activity under low-light conditions, and their activity was transiently suppressed upon the shift to high-light conditions. Subsequent analysis of
psaC
,
psaE
,
psaK1
, and
psaLI
promoters revealed that their light response was also achieved by AT-rich sequences located at the −70 to −46 region. These results clearly show that AT-rich upstream elements are responsible for the coordinated high-light response of PSI genes dispersed throughout
Synechocystis
genome.
Region-Specific Insertion of Transposons in Combination with Selection for High Plasmid Transferability and Stability Accounts for the Structural Similarity of IncP-1 Plasmids
Authors: Sota Masahiro , Tsuda Masataka , Yano Hirokazu , Suzuki Haruo , Forney Larry J. , Top Eva M. 
Published: February 2007

ABSTRACTThe overall architecture of IncP-1 plasmids is very conserved in that the accessory genes are typically located in one or two specific regions: betweenoriVandtrfAand between thetraandtrboperons. Various hypotheses have been formulated to explain this, but none have been tested experimentally. We investigated whether this structural similarity is due to region-specific transposition alone or also is reliant on selection for plasmids with insertions limited to these two regions. We first examined the transposition of Tn21Km into IncP-1β plasmid pBP136 and found that most Tn21Km insertions (67%) were located aroundoriV. A similar experiment using theoriVregion of IncP-1β plasmid pUO1 confirmed these results. We then tested the transferability, stability, and fitness cost of different pBP136 derivatives to determine if impairment of these key plasmid characters explained the conserved plasmid architecture. Most of the pBP136 derivatives with insertions in transfer genes were no longer transferable. The plasmids with insertions in theoriV-trfAandtra-trbregions were more stable than other plasmid variants, and one of these also showed a significantly lower fitness cost. In addition, our detailed sequence analysis of IncP-1 plasmids showed that Tn402/5053-like transposons are situated predominantly between thetraandtrboperons and close to the putative resolution site for the ParA resolvase, a potential hot spot for those transposons. Our study presents the first empirical evidence that region-specific insertion of transposons in combination with selection for transferable and stable plasmids explains the structural similarity of IncP-1 plasmids.
In Vivo Demonstration of FNR Dimers in Response to Lower O
2
Availability
Authors: Jervis Adrian J. , Green Jeffrey 
Published: February 2007

ABSTRACT

Escherichia coli
FNR is an O
2
-sensing transcription factor. In vitro studies indicate that anaerobic iron-sulfur cluster acquisition promotes FNR dimerization. Here, two-hybrid assays show that iron-sulfur cluster-dependent FNR dimers are formed in vivo in response to lower O
2
availability, consistent with the current model of FNR activation.
His20Provides the Sole Functionally Significant Side Chain in the Essential TonB Transmembrane Domain
Authors: Larsen Ray A. , Deckert Gail E. , Kastead Kyle A. , Devanathan Surendranathan , Keller Kimberly L. , Postle Kathleen 
Published: February 2007

ABSTRACTThe cytoplasmic membrane protein TonB couples the protonmotive force of the cytoplasmic membrane to active transport across the outer membrane ofEscherichia coli. The uncleaved amino-terminal signal anchor transmembrane domain (TMD; residues 12 to 32) of TonB and the integral cytoplasmic membrane proteins ExbB and ExbD are essential to this process, with important interactions occurring among the several TMDs of all three proteins. Here, we show that, of all the residues in the TonB TMD, only His20is essential for TonB activity. When alanyl residues replaced all TMD residues except Ser16and His20, the resultant “all-Ala Ser16His20” TMD TonB retained 90% of wild-type iron transport activity. Ser16Ala in the context of a wild-type TonB TMD was fully active. In contrast, His20Ala in the wild-type TMD was entirely inactive. In more mechanistically informative assays, the all-Ala Ser16His20TMD TonB unexpectedly failed to support formation of disulfide-linked dimers by TonB derivatives bearing Cys substitutions for the aromatic residues in the carboxy terminus. We hypothesize that, because ExbB/D apparently cannot efficiently down-regulate conformational changes at the TonB carboxy terminus through the all-Ala Ser16His20TMD, the TonB carboxy terminus might fold so rapidly that disulfide-linked dimers cannot be efficiently trapped. In formaldehyde cross-linking experiments, the all-Ala Ser16His20TMD also supported large numbers of apparently nonspecific contacts with unknown proteins. The all-Ala Ser16His20TMD TonB retained its dependence on ExbB/D. Together, these results suggest that a role for ExbB/D might be to control rapid and nonspecific folding that the unregulated TonB carboxy terminus otherwise undergoes. Such a model helps to reconcile the crystal/nuclear magnetic resonance structures of the TonB carboxy terminus with conformational changes and mutant phenotypes observed at the TonB carboxy terminus in vivo.
Sortase-Catalyzed Assembly of Distinct Heteromeric Fimbriae in
Actinomyces naeslundii
Authors: Mishra Arunima , Das Asis , Cisar John O. , Ton-That Hung 
Published: February 2007

ABSTRACT

Two types of adhesive fimbriae are expressed by
Actinomyces
; however, the architecture and the mechanism of assembly of these structures remain poorly understood. In this study we characterized two fimbrial gene clusters present in the genome of
Actinomyces naeslundii
strain MG-1. By using immunoelectron microscopy and biochemical analysis, we showed that the
fimQ
-
fimP
-
srtC1
-
fimR
gene cluster encodes a fimbrial structure (designated type 1) that contains a major subunit, FimP, forming the shaft and a minor subunit, FimQ, located primarily at the tip. Similarly, the
fimB
-
fimA
-
srtC2
gene cluster encodes a distinct fimbrial structure (designated type 2) composed of a shaft protein, FimA, and a tip protein, FimB. By using allelic exchange, we constructed an in-frame deletion mutant that lacks the SrtC2 sortase. This mutant produces abundant type 1 fimbriae and expresses the monomeric FimA and FimB proteins, but it does not assemble type 2 fimbriae. Thus, SrtC2 is a fimbria-specific sortase that is essential for assembly of the type 2 fimbriae. Together, our experiments pave the way for several lines of molecular investigation that are necessary to elucidate the fimbrial assembly pathways in
Actinomyces
and their function in the pathogenesis of different biofilm-related oral diseases.
Molecular phylogeography of the Chinese lacertids of the genus Eremias (Lacertidae) based on 16S rRNA mitochondrial DNA sequences
Authors: Lixia Wan , Shihong Sun , Yuanting Jin , Yongfeng Yan , Naifa Liu 
Published: February 2007

Abstract
In the present study, relationships among all Chinese species of lacertids in
the genus Eremias, E. velox, E. grammica, E. vermiculata, E. przewalskii, E.
multiocellata, E. arguta, E. brenchleyi, and E. argus, were assessed using
574 aligned base positions of 16S rRNA mitochondrial DNA sequences from 103
individuals collected from 28 populations. Three kinds of phylogenetic tree
(MP, ME, and NJ) were reconstructed and were found to be concordant. All
eight species well form a monophyletic group. The resulting genetic distance
between E. przewalskii and E. multiocellata is surprisingly low, only 0.008.
The result could be due to introgression of the mtDNA molecule. All
Eastern-Asia lacertids except E. vermiculata grouped together and formed a
monophyletic clade. E. vermiculata are closely related to E. arguta, a
Central-Asia species. E. brenchleyi and E. argus formed a monophyletic clade
as the sister group of E. multiocellata. The Central-Asia species (E.
arguta, E. grammica and E. velox) originated from Central-Asia and
Eastern-Asia species (the rest) from China. The phylogenetic relationships
among E. grammica, E. velox, E. arguta-vermiculata, E. argus-brenchleyi, and
E. multiocellata-przewalskii are unclear in the study, which needs more
comprehensive taxonomic sampling from Western Asia and Europe, and
additional genetic evidence to resolve it.
Variation of hyoid morphology in geoemydid terrapins
Authors: Richter Susann , Auer Markus , Fritz Uwe 
Published: February 2007

Abstract
The hyoid apparati of 25 geoemydid species in 16 genera (including aquatic,
semiterrestrial and terrestrial taxa) are compared, and for Cuora
galbinifrons bourreti ontogenetic development of the hypoid apparatus is
described. Generally, ossification of the hyoid apparatus increases with
age. The majority of terrestrial species maintain cartilaginous or partially
cartilaginous hyoid bodies and second branchial horns throughout life
however. Also in tortoises (Testudinidae) hyoid body and second branchial
horns remain cartilaginous, suggesting a positive correlation between mode
of life and hyoid morphology (terrestrial species with partly cartilaginous
hyoid apparatus vs. aquatic species with fully ossified hyoid
apparatus).
Germinal bed condition in a polyautochronic single-clutched lizard, Bassiana duperreyi (Scincidae)
Authors: Radder Rajkumar , Shine Richard 
Published: February 2007

Abstract
In lizards, the eggs are produced within small regions of the ovary known as
germinal beds (GBs); previous literature suggests that the number of GBs per
ovary may be linked to life-history traits such as clutch size and breeding
frequency. In the oviparous montane Australian skink Bassiana duperreyi,
females produce a single clutch of 3 to 11 eggs each year. Our histological
examination of ovaries of this species revealed a single GB per ovary. In
combination with previous studies, our results suggest that scincid lizards
may offer ideal model systems to explore the functional link between ovarian
morphology and life-history traits in lizards.
Thermal ecology of a population of the lizard, Liolaemus pseudoanomalus in western Argentina
Authors: Villavicencio Héctor , Acosta Juan , Marinero José , Cánovas María 
Published: February 2007

Abstract
The thermal ecology of the lizard Liolaemus pseudoanomalus was studied at La
Laja, Albardón Department, San Juan Province, Argentina. Data were collected
every 10 days from August 2000 to August 2001 by randomly revisiting bushes
and low flagstones across the study site. Each individual was captured by
hand, and the cloacal (Tb), substrate (Ts) and air (Ts) temperatures were
measured (to nearest 0.1°C) with a rapid reading Miller-Weber thermometer.
Tb was not influenced by season, sex or age group. There was a significant
positive linear association between Tb/Ta and Tb/Ts. Tb and SVL were not
correlated. The average field temperature of the study species was similar
to other Liolaemus in the same geographic province. It is concluded that the
thermal strategy of the species was heliothermy and thigmothermy.
Spatial distribution and seasonal pattern in road mortality of the common toad Bufo bufo in an agricultural landscape of south-western Poland
Authors: Orłowski Grzegorz 
Published: February 2007

AbstractAmphibians are the group of animals suffering particularly from the presence of roads and vehicle traffic. The seasonal migration to breeding places undertaken by amphibians in the temperate climate zone is the main reason for their appearance on roads. Between June 2001 and August 2003, 957 common toads Bufo bufo were recorded killed on 48.8 km road network with various traffic volumes (350-10500 cars per 24 h), situated in the agricultural landscape of south-western Poland. The highest mortality was recorded in April (57% of all road-kills). The places with highest recorded mortality varied markedly throughout the year. In spring, many more animals died within the built-up areas, while in summer and autumn their number increased in the open countryside. During the whole study period, 73% of all road-kills were recorded on roads (55% of all controlled) with the lowest traffic volume (350-470 cars per 24 h). The average number of road-kills on roads with the high traffic volume (5700-10500 cars per 24 h) was over 15 times lower than on the roads with low traffic (0-0.17 road-kills per 100 m on roads with high traffic vs 2.59 road-kills per 100 m on roads with low traffic). The number of road-kills on 15 road sections was most closely related to the abundance of local populations of Bufo bufo and to the size of water bodies situated in the road vicinity. The yearly level of local mortality in breeding populations of Bufo bufo due to the vehicle traffic ranged from 2 to 18%.
An accumulation of bone remains of two Liolaemus species (Iguanidae) in an Holocene archaeological site of the Argentine Puna
Authors: Albino Adriana , Kligmann Débora 
Published: February 2007

AbstractAn accumulation of iguanian bone remains was found inside a rodent burrow in an Holocene archaeological site of the Argentine southern Puna. Characters of the preserved bones suggest that a minimum of two species of the Liolaemus genus is represented. One of them is undoubtedly attributed to the montanus group, probably L. poecilochromus or L. andinus. The finding of Liolaemus bone remains in the Argentine Puna Region represents the first record of this genus in an archaeological site of South America and suggests that specimens of at least two Liolaemus species exploited the same refuge simultaneously, including both adult and juvenile individuals.
Molecular phylogeny of Acrobeloides and Cephalobus (Nematoda: Cephalobidae) reveals paraphyletic taxa and recurrent evolution of simple labial morphology
Authors: Nadler Steven , Smythe Ashleigh 
Published: February 2007

AbstractMembers of the family Cephalobidae (Nematoda) are among the most common and morphologically striking soil nematodes. Many members of Cephalobidae have extensive lip elaborations called probolae, but two taxonomically problematic genera, Acrobeloides and Cephalobus, have simple, low probolae. We sequenced a portion of the nuclear large subunit ribosomal DNA for 33 cultures of Acrobeloides and Cephalobus. A phylogenetic analysis of these data, plus sequences representing other members of Cephalobina, revealed a core clade of 22 closely related taxa, but did not represent Acrobeloides and Cephalobus as monophyletic. The dominant feature used in morphological taxonomy of Cephalobidae, the lip region, was homoplastic according to the molecular phylogenetic hypothesis. Contrary to previous suggestions, taxa with simple probolae have arisen multiple times from taxa with complex probolae. Cultures were also examined for mode of reproduction (presumed parthenogenetic vs sexual) and three morphological characters commonly used in generic diagnoses: the shape of the corpus in profile; the number of lateral incisures; and the terminal extent of the lateral field. Most cultures, including all 22 members of the core clade, lacked males and were presumed to be parthenogenetic, but several independent origins of sexually reproducing taxa were found. Of the morphological characters, only the corpus shape was consistent with the molecular phylogeny, however, the utility of this character is also questioned. Many genera with complex probolae were also paraphyletic, including Nothacrobeles, Zeldia and Cervidellus, indicating the need for more comprehensive phylogenies and a broad taxonomic revision of the family.
The influence of root diffusate and host age on hatching of the root-knot nematodes, Meloidogyne chitwoodi and M. fallax
Authors: Wesemael Wim , Perry Roland , Moens Maurice 
Published: February 2007

AbstractThe root-knot nematodes, Meloidogyne chitwoodi and M. fallax, cause severe damage to economically important crops and, in 1998, both species were listed as quarantine pests in Europe. Comparative studies were made on the effects of root diffusates and host age on the in vitro hatching of M. chitwoodi and M. fallax. There is a marked contrast in the hatching response of the two species. Hatching of second-stage juveniles (J2) of M. chitwoodi produced on young plants did not require host root diffusate stimulus, whereas at the end of the plant growing season, egg masses contained a percentage of unhatched J2 that require host root diffusate to cause hatch. This form of obligate quiescence at the end of the host growing season was not found in M. fallax. This species hatched well in water and did not require hatch stimulation from root diffusate, irrespective of the age of the plant on which the egg masses were produced. The number of eggs per egg mass for M. fallax collected on senescing plants was significantly greater than the number of eggs per egg mass for M. chitwoodi. The number of eggs per egg mass of M. chitwoodi decreased with plant age. The results are discussed in the context of the differing survival strategies of the two species.
Iotonchus aequatorialis sp. n. (Nematoda: Mononchida) from Ecuador with a key to the species of Iotonchus Cobb, 1916 and remarks on the identity of the genus
Authors: Orselli Lara , Vinciguerra Maria 
Published: February 2007

AbstractA new species of nematode, Iotonchus aequatorialis sp. n., found in a soil sample from Ecuador, is described and illustrated. Iotonchus aequatorialis sp. n. is a species of medium length (2.24–2.36 mm) with a large, barrel-shaped mouth cavity 57.5–65 μ m long and 32.5–38.5 μ m diam., basal dorsal tooth, didelphic female reproductive apparatus with short, symmetrical, reflexed ovaries, relatively short vagina provided with sclerotised pieces, large uterus, no sphincter between uterus and oviducts, paravulval papillae absent, a long, slender tail 8–10 times as long as the anal body diam., and a terminal spinneret. The identities of the genera Iotonchus Cobb, 1916 and Iotonchulus Andrássy, 1994 are discussed, new diagnoses of the two genera given and their species listed. A key to the species of Iotonchus is provided. Iotonchulus darreni n. comb. (= Iotonchus darreni n. syn.) is proposed.
The banana burrowing nematode, Radopholus similis (Cobb) Thorne, in the Lake Victoria region of East Africa: its introduction, spread and impact
Authors: Price Nigel 
Published: February 2007

AbstractIn the Lake Victoria region of East Africa bananas are a starchy staple of major importance. Whilst concerns over banana cultivation in the region have been expressed for well over 50 years, over the last 30 years these have grown more serious, with data suggesting that banana yields have halved in some areas since the 1970s. Historical and survey evidence demonstrate that the banana burrowing nematode, Radopholus similis, and the associated 'black-head toppling disease' were absent from the region prior to the 1960s. It is suggested that the introduction of R. similis to Uganda and its subsequent rapid spread in many of the banana growing areas of the Lake Victoria region is a major component of the severe production difficulties the crop is presently facing. Evidence for the continuing spread of R. similis in East and Central Africa and the implications of this are discussed.