bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assimilation of Nicotinamide Mononucleotide Requires Periplasmic AphA Phosphatase inSalmonella enterica
Authors: Grose Julianne H. , Bergthorsson Ulfar , Xu Yaping , Sterneckert Jared , Khodaverdian Behzad , Roth John R. 
Published: June 2005

ABSTRACTSalmonella entericacan obtain pyridine from exogenous nicotinamide mononucleotide (NMN) by three routes. In route 1, nicotinamide is removed from NMN in the periplasm and enters the cell as the free base. In route 2, described here, phosphate is removed from NMN in the periplasm by acid phosphatase (AphA), and the produced nicotinamide ribonucleoside (NmR) enters the cell via the PnuC transporter. Internal NmR is then converted back to NMN by the NmR kinase activity of NadR. Route 3 is seen only inpnuC* transporter mutants, which import NMN intact and can therefore grow on lower levels of NMN. Internal NMN produced by either route 2 or route 3 is deamidated to nicotinic acid mononucleotide and converted to NAD by the biosynthetic enzymes NadD and NadE.
Transcriptional Analysis of the Conserved
ftsZ
Gene Cluster in
Mycoplasma genitalium
and
Mycoplasma pneumoniae
Authors: Benders Gwynedd A. , Powell Bradford C. , Hutchison Clyde A. 
Published: June 2005

ABSTRACT

Several experimental approaches were used to construct a detailed transcriptional profile of the phylogenetically conserved
ftsZ
cell division gene cluster in both
Mycoplasma genitalium
and its closest relative,
Mycoplasma pneumoniae
. We determined initiation and termination points for the cluster, as well as an absolute steady-state RNA level for each gene. Transcription of this cluster in both these organisms was shown to be highly strand specific. While the four genes in this cluster are cotranscribed, their transcription unit also includes two genes of close proximity yet disparate function. A transcription initiation point immediately upstream of these two genes was detected in
M. genitalium
but not
M. pneumoniae
. In
M. pneumoniae
, transcription of the six genes terminates at a poly(U)-tailed hairpin. In
M. genitalium
, this transcription terminates at two closely spaced points by an unknown mechanism. Real-time reverse transcription-PCR analysis of this cluster in
M. pneumoniae
shows that mRNA levels for all six genes vary at most fivefold and form a gradient of decreasing quantity with increasing distance from the promoter at the beginning of the cluster. mRNA from coding regions was approximately 20- to 100-fold more abundant than that from intergenic regions. We estimated the most abundant mRNA we detected at 0.6 copy per cell. We conclude that groups of functionally related genes in
M. genitalium
and
M. pneumoniae
are often preceded by promoters but rarely followed by terminators. This causes functionally unrelated genes to be commonly cotranscribed in these organisms.
Epimerase Active Domain of
Pseudomonas aeruginosa
AlgG, a Protein That Contains a Right-Handed β-Helix
Authors: Douthit Stephanie A. , Dlakic Mensur , Ohman Dennis E. , Franklin Michael J. 
Published: June 2005

ABSTRACT

The polysaccharide alginate forms a protective capsule for
Pseudomonas aeruginosa
during chronic pulmonary infections. The structure of alginate, a linear polymer of β1-4-linked O-acetylated
d
-mannuronate (M) and
l
-guluronate (G), is important for its activity as a virulence factor. Alginate structure is mediated by AlgG, a periplasmic C-5 mannuronan epimerase. AlgG also plays a role in protecting alginate from degradation by the periplasmic alginate lyase AlgL. Here, we show that the C-terminal region of AlgG contains a right-handed β-helix (RHβH) fold, characteristic of proteins with the
c
arbohydrate-binding
a
nd
s
ugar
h
ydrolase (CASH) domain. When modeled based on pectate lyase C of
Erwinia chrysanthemi
, the RHβH of AlgG has a long shallow groove that may accommodate alginate, similar to protein/polysaccharide interactions of other CASH domain proteins. The shallow groove contains a 324-DPHD motif that is conserved among AlgG and the extracellular mannuronan epimerases of
Azotobacter vinelandii
. Point mutations in this motif disrupt mannuronan epimerase activity but have no effect on alginate secretion. The D324A mutation has a dominant negative phenotype, suggesting that the shallow groove in AlgG contains the catalytic face for epimerization. Other conserved motifs of the epimerases, 361-NNRSYEN and 381-NLVAYN, are predicted to lie on the opposite side of the RHβH from the catalytic center. Point mutations N362A, N367A, and V383A result in proteins that do not protect alginate from AlgL, suggesting that these mutant proteins are not properly folded or not inserted into the alginate biosynthetic scaffold. These motifs are likely involved in asparagine and hydrophobic stacking, required for structural integrity of RHβH proteins, rather than for mannuronan catalysis. The results suggest that the AlgG RHβH protects alginate from degradation by AlgL by channeling the alginate polymer through the proposed alginate biosynthetic scaffold while epimerizing approximately every second
d
-mannuronate residue to
l
-guluronate along the epimerase catalytic face.
Identification of a Second Collagen-Like Glycoprotein Produced by
Bacillus anthracis
and Demonstration of Associated Spore-Specific Sugars
Authors: Waller Lashanda N. , Stump Michael J. , Fox Karen F. , Harley William M. , Fox Alvin , Stewart George C. , Shahgholi Mona 
Published: June 2005

ABSTRACT

Certain carbohydrates (rhamnose, 3-
O
-methyl rhamnose, and galactosamine) have been demonstrated to be present in
Bacillus anthracis
spores but absent in vegetative cells. Others have demonstrated that these spore-specific sugars are constituents of the glycoprotein BclA. In the current work, spore extracts were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A second collagen-like glycoprotein, BclB, was identified in
B. anthracis
. The protein moiety of this glycoprotein was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS) and the carbohydrate components by gas chromatography-mass spectrometry and tandem mass spectrometry. Spore-specific sugars were also demonstrated to be components of BclB.
Genomic Sequence of an Otitis Media Isolate of Nontypeable
Haemophilus influenzae
: Comparative Study with
H. influenzae
Serotype d, Strain KW20
Authors: Harrison Alistair , Dyer David W. , Gillaspy Allison , Ray William C. , Mungur Rachna , Carson Matthew B. , Zhong Huachun , Gipson Jenny , Gipson Mandy , Johnson Linda S. , Lewis Lisa , Bakaletz Lauren O. , Munson Robert S. 
Published: June 2005

ABSTRACT

In 1995, the Institute for Genomic Research completed the genome sequence of a rough derivative of
Haemophilus influenzae
serotype d, strain KW20. Although extremely useful in understanding the basic biology of
H. influenzae
, these data have not provided significant insight into disease caused by nontypeable
H. influenzae
, as serotype d strains are not pathogens. In contrast, strains of nontypeable
H. influenzae
are the primary pathogens of chronic and recurrent otitis media in children. In addition, these organisms have an important role in acute otitis media in children as well as other respiratory diseases. Such strains must therefore contain a gene repertoire that differs from that of strain Rd. Elucidation of the differences between these genomes will thus provide insight into the pathogenic mechanisms of nontypeable
H. influenzae
. The genome of a representative nontypeable
H. influenzae
strain, 86-028NP, isolated from a patient with chronic otitis media was therefore sequenced and annotated. Despite large regions of synteny with the strain Rd genome, there are large rearrangements in strain 86-028NP's genome architecture relative to the strain Rd genome. A genomic island similar to an island originally identified in
H. influenzae
type b is present in the strain 86-028NP genome, while the mu-like phage present in the strain Rd genome is absent from the strain 86-028NP genome. Two hundred eighty open reading frames were identified in the strain 86-028NP genome that were absent from the strain Rd genome. These data provide new insight that complements and extends the ongoing analysis of nontypeable
H. influenzae
virulence determinants.
Architecture and Adhesive Activity of the
Haemophilus influenzae
Hsf Adhesin
Authors: Cotter Shane E. , Yeo Hye-Jeong , Juehne Twyla , St. Geme Joseph W. 
Published: June 2005

ABSTRACT

Haemophilus influenzae
type b is an important cause of meningitis and other serious invasive diseases and initiates infection by colonizing the upper respiratory tract. Among the major adhesins in
H. influenzae
type b is a nonpilus protein called Hsf, a large protein that forms fiber-like structures on the bacterial surface and shares significant sequence similarity with the nontypeable
H. influenzae
Hia autotransporter. In the present study, we characterized the structure and adhesive activity of Hsf. Analysis of the predicted amino acid sequence of Hsf revealed three regions with high-level homology to the HiaBD1 and HiaBD2 binding domains in Hia. Based on examination of glutathione
S
-transferase fusion proteins corresponding to these regions, two of the three had adhesive activity and one was nonadhesive in assays with cultured epithelial cells. Structural modeling demonstrated that only the two regions with adhesive activity harbored an acidic binding pocket like the binding pocket identified in the crystal structure of HiaBD1. Consistent with these results, disruption of the acidic binding pockets in the adhesive regions eliminated adhesive activity. These studies advance our understanding of the architecture of Hsf and the family of trimeric autotransporters and provide insight into the structural determinants of
H. influenzae
type b adherence.
Phylogenetic analysis of the subfamily Hylodinae (Anura, Leptodactylidae) based on morphological characters
Authors: Nuin Paulo A.S. , do Val Francisca C. 
Published: June 2005

Abstract
The systematics and phylogenetic relationships of the family Leptodactylidae
are controversial as is the intrafamilial phylogeny of the leptodactylids.
Here we analyze the relationships of the leptodactylid subfamily Hylodinae.
This subfamily has been considered to be monophyletic and composed of three
genera, Hylodes, Crossodactylus and Megaelosia. In the present study 49
characters were used, based on different studies on Leptodactylidae
phylogeny. Maximum parsimony methods with unweighted and successively
weighted characters were used to estimate the phylogeny of the Hylodinae.
Upon analysis, the data provided further evidence of the monophyletic status
of the three genera, with Megaelosia being the basal genus and the other two
genera being sister taxa. The analysis with successive weighting results in
a more resolved topology of the species subgroups of the genus Hylodes and
separates this genus from Crossodactylus and confirms that the hylodines are
monophyletic.
A multivariate analysis of geographic variation in the Trapelus agilis complex (Sauria: Agamidae)
Authors: Rastegar-Pouyani Nasrullah 
Published: June 2005

AbstractThe "Trapelus agilis complex" encompasses three conventional taxa: T. a. agilis (Olivier), T. a. isolepis (Boulenger), and T. a. sanguinolentus (= T. sanguinolentus) (Pallas). In previous studies the author revised this complex, synonymized T. a. isolepis with T. a. agilis, and recognized four distinct subspecies within the complex: T. a. agilis from central Iranian Plateau, southern Afghanistan, and southwestern Pakistan; T. a. sanguinolentus from northeastern Iran, northern Afghanistan, and the Central Asian Republics of the former USSR as well as Daghestan; T. a. khuzistanensis from the lowland southwestern Iran; and T. a. pakistanensis from southeastern Pakistan as well as adjoining northwestern India. In order to re-evaluate this judgment and to resolve the patterns of geographic variation within and among the mentioned four taxa, cluster analysis, principal components analysis, and canonical variate analysis were employed using 18 most informative morphological characters recorded for 522 undamaged and fully-grown specimens belonging to 19 operational taxonomic units (OTUs) throughout the range. The principal components as well as canonical variate analyses identified four primary groups of individuals corresponding to the four taxa recognized by the previous studies.
A new species of the genus Physalaemus Fitzinger, 1826 (Anura, Leptodactylidae) from the Atlantic Rain Forest of southern Bahia, Brazil
Authors: Pimenta Bruno V.S. , Cruz Carlos Alberto Gonçalves , Silvano Débora L. 
Published: June 2005

AbstractA new species of the Physalaemus signifer group from the Atlantic Rain Forest of the state of Bahia is described and illustrated. It is characterized by a well-developed vocal sac, second finger with the same size or longer than fourth, finely rugose dorsal skin, and distinct structure of advertisement call, composed of densely aggregated pulses. Information on tadpole external morphology and advertisement call structure are presented. Uma nova espécie do grupo de Physalaemus signifer da Mata Atlântica do Estado da Bahia é descrita e ilustrada. É caracterizada pelo saco vocal bem desenvolvido, o segundo dedo com comprimento igual ou maior que o quarto, pele do dorso finamente rugosa e estrutura distinta do canto de anúncio, composto por pulsos densamente agregados. Informações sobre a morfologia externa do girino e a estrutura do canto de anúncio são apresentadas.
Fluctuating asymmetry in Podarcis muralis populations from Southern Montenegro: detection of environmental stress in insular populations
Authors: Crnobrnja-Isailovic Jelka , Aleksic Ivan , Bejakovic Davor 
Published: June 2005

Abstract
We examined degree of between-sides difference in number of femoral pores
(fluctuating asymmetry, FA) in Podarcis muralis populations, distributed on
islands and in coastal area of Lake Skadar (Southern Montenegro). The aim of
this study was to test sensitivity of fluctuating asymmetry of chosen trait
to isolation effect in the absence of anthropogenic impacts. The results
indicate that FA in the number of femoral pores do not vary significantly
between insular populations of P. muralis. Generally, there is negative but
non-significant correlation between island size and FA level. Also,
overdominance hypothesis of enhanced developmental homeostasis at higher
levels of heterozygosity was not confirmed in this study. The results
support earlier conclusions obtained from electrophoretic studies, that
analyzed insular populations from Lake Skadar archipelago still do not
suffer deleterious effects as a result of isolation.
Annual variation of breeding patterns of the toad, Melanophryniscus rubriventris (Vellard, 1947)
Authors: Vaira Marcos 
Published: June 2005

AbstractClimate may play a direct role in determining patterns of reproductive activity in anurans. Investigating the responses of males and females attending a breeding site to environmental variation are of particular interest regardless the possible effect of climate change on the decline of populations. I studied annual variation over two years in the breeding population size and breeding phenology of the diurnal toad, Melanophryniscus rubriventris, in a seasonal environment characterized by temporal and spatial uncertainty due to climatic conditions. Breeding activity of this toad was opportunistic throughout a prolonged spring-summer breeding season. Direct influence of rainfall on the onset and extent of breeding activity was detected in both years. Spawning activity showed a clear pattern of two three-day peaks mostly related to heavy rainfall events. Males always significantly outnumbered females at breeding sites. The disparity of rainy season extent between the two breeding seasons studied resulted in different annual patterns of arrival and length of residence of adults. Males and females remained several days longer during the second year than during the first year. Because adults showed highly variable annual patterns of breeding activity studies involving only a few years may yield misleading results concerning the nature and extent of the decline of the species or populations. Future studies on the ecology and conservation of the species should include long-term monitoring.
Mixing and Entrainment in the Red Sea Outflow Plume. Part II: Turbulence Characteristics
Authors: Peters Hartmut , Johns William E. 
Published: June 2005

AbstractSouth of the Strait of Bab el Mandeb, saline Red Sea Water flows downslope into the Gulf of Aden mainly along the narrow 130-km-long “Northern Channel” (NC) and the shorter and wider “Southern Channel” (SC). In the NC, the Red Sea plume simultaneously exhibited weak entrainment into a 35–120-m-thick, weakly stratified bottom layer while a 35–285-m-thick interfacial layer above showed signs of vigorous mixing, overturns up to 30 m thick, and extensive zones of gradient Richardson numbers below 1/4. Turbulent overturning scales, or Thorpe scales, are extracted from regular CTD profiles and equated to Ozmidov scales. On this basis, interfacial mixing is quantified in terms of estimated turbulent dissipation rates, vertical turbulent salt flux, and interfacial stress. Even though these estimates are subject to significant uncertainty, they demonstrate the intensity of mixing during strong winter outflow in terms of eddy diffusivities Kρ on the order of 10−2 m2 s−1. The large Kρ occur in strong stratification such that vertical turbulent salt fluxes are also large. Along the NC, relative maxima of Kρ correspond to maxima in the bulk Froude number. Direct short-term measurements of the Reynolds stress just above the seafloor at two locations, one in the NC and one in the SC, allow comparisons of the bottom stress τb with the interfacial turbulent stress τi. The ratio τi/τb shows large scatter in a small sample, with maximum values on the order of 1. An appendix outlines procedures of making and reducing lowered acoustic Doppler current profiler measurements optimized for observing descending plumes.
On Deep-Water Renewals in Indian Arm, British Columbia: Sensitivity to the Production of Turbulent Kinetic Energy Caused by Horizontal Variations in the Flow Field
Authors: Stacey Michael W. , Pond S. 
Published: June 2005

Abstract
A two-dimensional (i.e., laterally averaged) numerical model of the circulation in Burrard Inlet and Indian Arm near British Columbia, Canada, is used to examine the sensitivity of deep-water renewal events in Indian Arm to the turbulent mixing in the lee of the narrow sills in Burrard Inlet. Horizontal variations in the flow field can have an important influence on the production of turbulent kinetic energy near the sills and therefore also on the renewal events in Indian Arm. An ad hoc modification to the expression for the production of turbulent kinetic energy, required to obtain an acceptable simulation downstream of Second Narrows in Burrard Inlet, also results in a reasonable simulation of the observed circulation in Indian Arm. The modified laterally averaged model can reproduce the main features of the circulation away from the narrow sills. However, it seems that a three-dimensional model will be required if the circulation is to be simulated with greater accuracy and without the ad hoc modification, which has a free parameter.
The North Atlantic Subpolar Gyre in Four High-Resolution Models
Authors: Treguier A. M. , Theetten S. , Chassignet E. P. , Penduff T. , Smith R. , Talley L. , Beismann J. O. , Böning C. 
Published: June 2005

Abstract
The authors present the first quantitative comparison between new velocity datasets and high-resolution models in the North Atlantic subpolar gyre [1/10° Parallel Ocean Program model (POPNA10), Miami Isopycnic Coordinate Ocean Model (MICOM), ⅙° Atlantic model (ATL6), and Family of Linked Atlantic Ocean Model Experiments (FLAME)]. At the surface, the model velocities agree generally well with World Ocean Circulation Experiment (WOCE) drifter data. Two noticeable exceptions are the weakness of the East Greenland coastal current in models and the presence in the surface layers of a strong southwestward East Reykjanes Ridge Current. At depths, the most prominent feature of the circulation is the boundary current following the continental slope. In this narrow flow, it is found that gridded float datasets cannot be used for a quantitative comparison with models. The models have very different patterns of deep convection, and it is suggested that this could be related to the differences in their barotropic transport at Cape Farewell. Models show a large drift in watermass properties with a salinization of the Labrador Sea Water. The authors believe that the main cause is related to horizontal transports of salt because models with different forcing and vertical mixing share the same salinization problem. A remarkable feature of the model solutions is the large westward transport over Reykjanes Ridge [10 Sv (Sv ≡ 106 m3 s−1) or more].
On the Effect of Topographically Enhanced Mixing on the Global Ocean Circulation
Authors: Saenko O. A. , Merryfield W. J. 
Published: June 2005

Abstract
The strong influence of enhanced diapycnal mixing over rough topography on bottom-water circulation is illustrated using results from two global ocean model experiments. In the first, diapycnal diffusivity is set to the observed background level of 10−5 m2 s−1 in regions not subject to shear instability, convection, or surface-driven mixing. In the second experiment, mixing is enhanced above rough bottom topography to represent the dissipation of internal tides. Three important results are obtained. First, without the enhanced mixing in the abyssal ocean, the deep North Pacific Ocean becomes essentially a stagnant basin, with little bottom-water circulation and very weak deep stratification. Allowing for the enhanced diapycnal mixing above rough bottom topography leads to increased bottom-water circulation and deep stratification and a potential vorticity distribution in the North Pacific that is much more realistic. Second, the enhanced diapycnal mixing above rough topography results in a significant intensification and deepening of the Antarctic Circumpolar Current, as well as in stronger bottom-water formation around Antarctica. Last, our experiments suggest that dissipation of internal tides and the associated enhanced diapycnal mixing in the abyssal ocean play no part in the circulation of deep water forming in the North Atlantic Ocean and in the associated transport of heat in the ocean.