bluuebunny/crossref_metadata_2025_split huggingface dataset:
SC29EK, a Peptide Fusion Inhibitor with Enhanced α-Helicity, Inhibits Replication of Human Immunodeficiency Virus Type 1 Mutants Resistant to Enfuvirtide
Authors: Naito Takeshi , Izumi Kazuki , Kodama Eiichi , Sakagami Yasuko , Kajiwara Keiko , Nishikawa Hiroki , Watanabe Kentaro , Sarafianos Stefan G. , Oishi Shinya , Fujii Nobutaka , Matsuoka Masao 
Published: December 2008

ABSTRACT
Peptides derived from the α-helical domains of human immunodeficiency virus (HIV) type 1 (HIV-1) gp41 inhibit HIV-1 fusion to the cell membrane. Enfuvirtide (T-20) is a peptide-based drug that targets the step of HIV fusion, and as such, it effectively suppresses the replication of HIV-1 strains that are either wild type or resistant to multiple reverse transcriptase and/or protease inhibitors. However, HIV-1 variants with T-20 resistance have emerged; therefore, the development of new and potent inhibitors is urgently needed. We have developed a novel HIV fusion inhibitor, SC34EK, which is a gp41-derived 34-amino-acid peptide with glutamate (E) and lysine (K) substitutions on its solvent-accessible site that stabilize its α-helicity. Importantly, SC34EK effectively inhibits the replication of T-20-resistant HIV-1 strains as well as wild-type HIV-1. In this report, we introduce SC29EK, a 29-amino-acid peptide that is a shorter variant of SC34EK. SC29EK blocked the replication of T-20-resistant HIV-1 strains and maintained antiviral activity even in the presence of high serum concentrations (up to 50%). Circular dichroism analysis revealed that the α-helicity of SC29EK was well maintained, while that of the parental peptide, C29, which showed moderate and reduced inhibition of wild-type and T-20-resistant HIV-1 strains, was lower. Our results show that the α-helicity in a peptide-based fusion inhibitor is a key factor for activity and enables the design of short peptide inhibitors with improved pharmacological properties.
Antimicrobial Activity of Prulifloxacin Tested against a Worldwide Collection of Gastroenteritis-Producing Pathogens, Including Those Causing Traveler's Diarrhea
Authors: Fritsche Thomas R. , Biedenbach Douglas J. , Jones Ronald N. 
Published: December 2008

ABSTRACT

Prulifloxacin, the prodrug of ulifloxacin (active component), is a newer fluoroquinolone with broad activity against enteric and nonenteric gram-negative bacilli. Ulifloxacin and other oral comparator agents were tested for activity against 582 gastroenteritis strains from global surveillance studies. Ulifloxacin was highly active against
Escherichia coli
,
Salmonella
spp.,
Shigella
spp.,
Yersinia
spp.,
Vibrio
spp.,
Aeromonas
spp., and
Plesiomonas
spp. (MIC
50
s and MIC
90
s, ≤0.03 μg/ml and ≤0.06 μg/ml, respectively). Only rare
Aeromonas
spp.,
Campylobacter
spp., and
E. coli
displayed elevated MIC results (≥4 μg/ml). Ciprofloxacin exhibited similar activity but was two- to fourfold less potent. Presently approved for clinical use in certain European countries and Japan, ulifloxacin was the most active of the antimicrobial agents tested against these gastroenteritis-causing pathogens.
Bronchopulmonary Disposition of Micafungin in Healthy Adult Volunteers
Authors: Nicasio Anthony M. , Tessier Pamela R. , Nicolau David P. , Knauft R. Fredrick , Russomanno John , Shore Eric , Kuti Joseph L. 
Published: December 2008

ABSTRACT
By way of bronchoscopy and bronchoalveolar lavage, intrapulmonary steady-state concentrations of micafungin administered at 150 mg daily to 15 healthy volunteers were determined at 4, 12, and 24 h after the third dose. The micafungin disposition was predominantly intracellular, with approximately 106% penetration into alveolar macrophages and 5% penetration into epithelial lining fluid.
Role of
proP
and
proU
in Betaine Uptake by
Yersinia enterocolitica
under Cold and Osmotic Stress Conditions
Authors: Annamalai Thirunavukkarasu , Venkitanarayanan Kumar 
Published: December 2008

ABSTRACT

Yersinia enterocolitica
is a food-borne pathogen with the ability to grow at cold temperatures and tolerate high osmolarity. The bacterium tolerates osmotic stress by intracellular accumulation of osmolytes, such as betaine. The
proP
gene and
proU
operon of
Y. enterocolitica
were sequenced, and single (ProP
−
ProU
+
and ProP
+
ProU
−
) and double (ProP
−
ProU
−
) mutants were generated. Upon exposure to osmotic or chill stress, the single and double mutants demonstrated a reduction in betaine uptake compared to that in the wild type, suggesting that
proP
and
proU
play a role in betaine uptake during osmotic and chill stress responses of
Y. enterocolitica
.
Temporal Dynamics of South End Tidal Creek (Sapelo Island, Georgia) Bacterial Communities
Authors: Kara Emily , Shade Ashley 
Published: December 2008

ABSTRACT

Bacterial community dynamics in South End tidal creek, Sapelo Island, GA, were studied over a 74-h, five-tidal-cycle period. Observations were made hourly for the first consecutive 24 hours, every 3 hours on the second day, and every 6 hours on the third day. Tide most strongly influenced bacterial community composition (high-tide versus low-tide community analysis of similarities,
R
= 0.41,
P
< 0.03). Dissolved oxygen concentration and conductivity were important proximate drivers. However, after accounting for tide and environmental variables colinear with tide, cumulative time became more important in describing community variation. In-stream physical processes, including particulate suspension and sedimentation, may explain tide-associated trends in the bacterial community composition observed.
Diversity and Stratification of Archaea in a Hypersaline Microbial Mat
Authors: Robertson Charles E. , Spear John R. , Harris J. Kirk , Pace Norman R. 
Published: December 2008

ABSTRACT
The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.
Molecular Ecology of
Listeria monocytogenes
: Evidence for a Reservoir in Milking Equipment on a Dairy Farm
Authors: Latorre Alejandra A. , Van Kessel Jo Ann S. , Karns Jeffrey S. , Zurakowski Michael J. , Pradhan Abani K. , Zadoks Ruth N. , Boor Kathryn J. , Schukken Ynte H. 
Published: December 2008

ABSTRACT

A longitudinal study aimed to detect
Listeria monocytogenes
on a New York State dairy farm was conducted between February 2004 and July 2007. Fecal samples were collected every 6 months from all lactating cows. Approximately 20 environmental samples were obtained every 3 months. Bulk tank milk samples and in-line milk filter samples were obtained weekly. Samples from milking equipment and the milking parlor environment were obtained in May 2007. Fifty-one of 715 fecal samples (7.1%) and 22 of 303 environmental samples (7.3%) were positive for
L. monocytogenes
. A total of 73 of 108 in-line milk filter samples (67.6%) and 34 of 172 bulk tank milk samples (19.7%) were positive for
L. monocytogenes. Listeria monocytogenes
was isolated from 6 of 40 (15%) sampling sites in the milking parlor and milking equipment. In-line milk filter samples had a greater proportion of
L. monocytogenes
than did bulk tank milk samples (
P
< 0.05) and samples from other sources (
P
< 0.05). The proportion of
L. monocytogenes
-positive samples was greater among bulk tank milk samples than among fecal or environmental samples (
P
< 0.05). Analysis of 60 isolates by pulsed-field gel electrophoresis (PFGE) yielded 23 PFGE types after digestion with AscI and ApaI endonucleases. Three PFGE types of
L. monocytogenes
were repeatedly found in longitudinally collected samples from bulk tank milk and in-line milk filters.
Pichia anomalaDBVPG 3003 Secretes a Ubiquitin-Like Protein That Has Antimicrobial Activity
Authors: De Ingeniis Jessica , Raffaelli Nadia , Ciani Maurizio , Mannazzu Ilaria 
Published: December 2008

ABSTRACTThe yeast strainPichia anomalaDBVPG 3003 secretes a killer toxin (Pikt) that has antifungal activity againstBrettanomyces/Dekkerasp. yeasts. Pikt interacts with β-1,6-glucan, consistent with binding to the cell wall of sensitive targets. In contrast to that of toxin K1, secreted bySaccharomyces cerevisiae, Pikt killer activity is not mediated by an increase in membrane permeability. Purification of the toxin yielded a homogeneous protein of about 8 kDa, which showed a marked similarity to ubiquitin in terms of molecular mass and N-terminal sequences. Pikt is also specifically recognized by anti-bovine ubiquitin antibodies and, similar to ubiquitin-like peptides, is not absorbed by DEAE-cellulose. However, Pikt differs from ubiquitin in its sensitivity to proteolytic enzymes. Therefore, Pikt appears to be a novel ubiquitin-like peptide that has killer activity.
Telomere Organization in the Ligninolytic Basidiomycete
Pleurotus ostreatus
Authors: Pérez Gúmer , Pangilinan Jasmyn , Pisabarro Antonio G. , Ramírez Lucía 
Published: December 2008

ABSTRACT

Telomeres are structural and functional chromosome regions that are essential for the cell cycle to proceed normally. They are, however, difficult to map genetically and to identify in genome-wide sequence programs because of their structure and repetitive nature. We studied the telomeric and subtelomeric organization in the basidiomycete
Pleurotus ostreatus
using a combination of molecular and bioinformatics tools that permitted us to determine 19 out of the 22 telomeres expected in this fungus. The telomeric repeating unit in
P. ostreatus
is TTAGGG, and the numbers of repetitions of this unit range between 25 and 150. The mapping of the telomere restriction fragments to linkage groups 6 and 7 revealed polymorphisms compatible with those observed by pulsed field gel electrophoresis separation of the corresponding chromosomes. The subtelomeric regions in
Pleurotus
contain genes similar to those described in other eukaryotic systems. The presence of a cluster of laccase genes in chromosome 6 and a bipartite structure containing a Het-related protein and an alcohol dehydrogenase are especially relevant; this bipartite structure is characteristic of the Pezizomycotina fungi
Neurospora crassa
and
Aspergillus terreus
. As far as we know, this is the first report describing the presence of such structures in basidiomycetes and the location of a laccase gene cluster in the subtelomeric region, where, among others, species-specific genes allowing the organism to adapt rapidly to the environment usually map.
Role of the Hya Hydrogenase in Recycling of Anaerobically Produced H
2
in
Salmonella enterica
Serovar Typhimurium
Authors: Zbell Andrea L. , Maier Robert J. 
Published: December 2008

ABSTRACT

Double and triple uptake-type hydrogenase mutants were used to determine which hydrogenase recycles fermentatively produced hydrogen. The Δ
hyb
Δ
hya
and Δ
hyd
Δ
hya
double mutants evolved H
2
at rates similar to that of the triple mutant strain, so Hya alone oxidizes the bulk of H
2
produced during fermentation. When only Hya was present, no hydrogen production was observed in nutrient-limited medium. H
2
uptake assays showed that Hya can oxidize both exogenously added H
2
and formate hydrogen lyase-evolved H
2
anaerobically. Even after anaerobic growth, all three uptake-type hydrogenases could function in the presence of oxygen, including using O
2
as a terminal acceptor.
Targeted Engineering of the Antibacterial Peptide Apidaecin, Based on an In Vivo Monitoring Assay System
Authors: Taguchi Seiichi , Mita Kensuke , Ichinohe Kenta , Hashimoto Shigeki 
Published: December 2008

ABSTRACT
Seven mutant forms of the antibacterial peptide apidaecin with increased activity were created by combinatorial mutagenesis targeted to the three N-terminal amino acid residues that had previously been identified as a nonessential region. An in vitro MIC assay revealed that the amino acid substitutions in the functionally variable region were effective in improving differential activity toward the four gram-negative bacteria tested, while a gram-positive bacterium was unaffected.
Poultry-Associated
Salmonella enterica
subsp.
enterica
Serovar 4,12:d:− Reveals High Clonality and a Distinct Pathogenicity Gene Repertoire
Authors: Huehn Stephan , Bunge Cornelia , Junker Ernst , Helmuth Reiner , Malorny Burkhard 
Published: December 2008

ABSTRACT

A European baseline survey during the years 2005 and 2006 has revealed that the monophasic
Salmonella enterica
subsp.
enterica
serovar 4,12:d:− was, with a prevalence of 23.6%, the most frequently isolated serovar in German broiler flocks. In Denmark and the United Kingdom, its serovar prevalences were 15.15% and 2.8%, respectively. Although poultry is a major source of human salmonellosis, serovar 4,12:d:− is rarely isolated in humans (approximately 0.09% per year). Molecular typing studies using pulsed-field gel electrophoresis and DNA microarray analysis show that the serovar is highly clonal and lacks genes with known contributions to pathogenicity. In contrast to other poultry-associated serovars, all strains were susceptible to 17 antimicrobial agents tested and did not encode any resistance determinant. Furthermore, serovar 4,12:d:− lacked the genes involved in galactonate metabolism and in the glycolysis and glyconeogenesis important for energy production in the cells. The conclusion of the study is that serovar 4,12:d:− seems to be primarily adapted to broilers and therefore causes only rare infections in humans.
Iron Requirement for Mn(II) Oxidation by
Leptothrix discophora
SS-1
Authors: El Gheriany Iman A. , Bocioaga Daniela , Hay Anthony G. , Ghiorse William C. , Shuler Michael L. , Lion Leonard W. 
Published: December 2008

ABSTRACT

A common form of biocatalysis of Mn(II) oxidation results in the formation of biogenic Mn(III, IV) oxides and is a key reaction in the geochemical cycling of Mn. In this study, we grew the model Mn(II)-oxidizing bacterium
Leptothrix discophora
SS-1 in media with limited iron (0.1 μM iron/5.8 mM pyruvate) and sufficient iron (0.2 μM iron/5.8 mM pyruvate). The influence of iron on the rate of extracellular Mn(II) oxidation was evaluated. Cultures in which cell growth was limited by iron exhibited reduced abilities to oxidize Mn(II) compared to cultures in medium with sufficient iron. While the extracellular Mn(II)-oxidizing factor (MOF) is thought to be a putative multicopper oxidase, Mn(II) oxidation in the presence of zero added Cu(II) was detected and the decrease in the observed Mn(II) oxidation rate in iron-limited cultures was not relieved when the medium was supplemented with Cu(II). The decline of Mn(II) oxidation under iron-limited conditions was not accompanied by siderophore production and is unlikely to be an artifact of siderophore complex formation with Mn(III). The temporal variations in
mofA
gene transcript levels under conditions of limited and abundant iron were similar, indicating that iron limitation did not interfere with the transcription of the
mofA
gene. Our quantitative PCR results provide a step forward in understanding the regulation of Mn(II) oxidation. The mechanistic role of iron in Mn(II) oxidation is uncertain; the data are consistent with a direct requirement for iron as a component of the MOF or an indirect effect of iron resulting from the limitation of one of many cellular functions requiring iron.
Physicochemical Basis for the Inhibitory Effects of Organic and Inorganic Salts on the Growth of
Pectobacterium carotovorum
subsp.
carotovorum
and
Pectobacterium atrosepticum
Authors: Yaganza Elian-Simplice , Tweddell Russell J. , Arul Joseph 
Published: December 2008

ABSTRACT

Twenty-one salts were tested for their effects on the growth of
Pectobacterium carotovorum
subsp.
carotovorum
and
Pectobacterium atrosepticum
. In liquid medium, 11 salts (0.2 M) exhibited strong inhibition of bacterial growth. The inhibitory action of salts relates to the water-ionizing capacity and the lipophilicity of their constituent ions.
DNA Sequencing and Homologous Expression of a Small Peptide Conferring Immunity to Gassericin A, a Circular Bacteriocin Produced by
Lactobacillus gasseri
LA39
Authors: Kawai Yasushi , Kusnadi Joni , Kemperman Rober , Kok Jan , Ito Yoshiyuki , Endo Mikiko , Arakawa Kensuke , Uchida Hideaki , Nishimura Junko , Kitazawa Haruki , Saito Tadao 
Published: December 2008

ABSTRACT

Gassericin A, produced by
Lactobacillus gasseri
LA39, is a hydrophobic circular bacteriocin. The DNA region surrounding the gassericin A structural gene,
gaaA
, was sequenced, and seven open reading frames (ORFs) of 3.5 kbp (
gaaBCADITE
) were found with possible functions in gassericin A production, secretion, and immunity. The deduced products of the five consecutive ORFs
gaaADITE
have homology to those of genes involved in butyrivibriocin AR10 production, although the genetic arrangements are different in the two circular bacteriocin genes. GaaI is a small, positively charged hydrophobic peptide of 53 amino acids containing a putative transmembrane segment. Heterologous expression and homologous expression of GaaI in
Lactococcus lactis
subsp.
cremoris
MG1363 and
L. gasseri
JCM1131
T
, respectively, were studied. GaaI-expressing strains exhibited at least sevenfold-higher resistance to gassericin A than corresponding control strains, indicating that
gaaI
encodes an immunity peptide for gassericin A. Comparison of GaaI to peptides with similar characteristics found in the circular bacteriocin gene loci is discussed.
Anaerobic Biodegradation of
n
-Hexadecane by a Nitrate-Reducing Consortium
Authors: Callaghan Amy V. , Tierney Meghan , Phelps Craig D. , Young L. Y. 
Published: December 2008

ABSTRACT

Nitrate-reducing enrichments, amended with
n
-hexadecane, were established with petroleum-contaminated sediment from Onondaga Lake. Cultures were serially diluted to yield a sediment-free consortium. Clone libraries and denaturing gradient gel electrophoresis analysis of 16S rRNA gene community PCR products indicated the presence of uncultured alpha- and betaproteobacteria similar to those detected in contaminated, denitrifying environments. Cultures were incubated with H
34
-hexadecane, fully deuterated hexadecane (
d
34
-hexadecane), or H
34
-hexadecane and NaH
13
CO
3
. Gas chromatography-mass spectrometry analysis of silylated metabolites resulted in the identification of [H
29
]pentadecanoic acid, [H
25
]tridecanoic acid, [1-
13
C]pentadecanoic acid, [3-
13
C]heptadecanoic acid, [3-
13
C]10-methylheptadecanoic acid, and
d
27
-pentadecanoic,
d
25
-, and
d
2
4
-tridecanoic acids. The identification of these metabolites suggests a carbon addition at the C-3 position of hexadecane, with subsequent β-oxidation and transformation reactions (chain elongation and C-10 methylation) that predominantly produce fatty acids with odd numbers of carbons. Mineralization of [1-
14
C]hexadecane was demonstrated based on the recovery of
14
CO
2
in active cultures.
Capsule Polysaccharide Conjugate Vaccine against Diarrheal Disease Caused by
Campylobacter jejuni
Authors: Monteiro Mario A. , Baqar Shahida , Hall Eric R. , Chen Yu-Han , Porter Chad K. , Bentzel David E. , Applebee Lisa , Guerry Patricia 
Published: December 2008

ABSTRACT

The capsule polysaccharide (CPS) of
Campylobacter jejuni
is one of the few identified virulence determinants of this important human pathogen. Since CPS conjugate vaccines have been so effective against other mucosal pathogens, we evaluated this approach using CPSs from two strains of
C. jejuni
, 81-176 (HS23 and HS36 serotype complex) and CG8486 (HS4 serotype complex). The CPSs of 81-176 and CG8486 were independently linked to the carrier protein CRM
197
by reductive amination between an aldehyde(s), strategically created at the nonreducing end of each CPS, and accessible amines of CRM
197
. In both cases, the CPS:CRM
197
ratio used was 2:1 by weight. Mass spectrometry and gel electrophoresis showed that on average, each glycoconjugate preparation contained, at least in part, two to five CPSs attached to one CRM
197
. When administered subcutaneously to mice, these vaccines elicited robust immune responses and significantly reduced the disease following intranasal challenge with the homologous strains of
C. jejuni
. The CPS
81-176
-CRM
197
vaccine also provided 100% protection against diarrhea in the New World monkey
Aotus nancymaae
following orogastric challenge with
C. jejuni
81-176.
Essential Role of the SycP Chaperone in Type III Secretion of the YspP Effector
Authors: Matsumoto Hiroyuki , Young Glenn M. 
Published: December 2008

ABSTRACTThe Ysa type III secretion (T3S) system enhances gastrointestinal infection byYersinia enterocoliticabv. 1B. One effector protein targeted into host cells is YspP, a protein tyrosine phosphatase. It was determined in this study that the secretion of YspP requires a chaperone, SycP. Genetic analysis showed that deletion ofsycPcompletely abolished the secretion of YspP without affecting the secretion of other Ysps by the Ysa T3S system. Analysis of the secretion and translocation signals of YspP defined the first 73 amino acids to form the minimal region of YspP necessary to promote secretion and translocation by the Ysa T3S system. Function of the YspP secretion/translocation signals was dependent on SycP. Curiously, when YspP was constitutively expressed inY. enterocoliticabv. 1B, it was recognized and secreted by the Ysc T3S system and the flagellar T3S system. In these cases, the first 21 amino acids were sufficient to promote secretion, and while SycP did enhance secretion, it was not essential. However, neither the Ysc T3S system nor the flagellar T3S system translocated YspP into mammalian cells. This supports a model where SycP confers secretion/translocation specificities for YspP by the Ysa T3S system. A series of biochemical approaches further established that SycP specifically interacts with YspP and protected YspP degradation in the cell prior to secretion. Collectively, the evidence suggests that YspP secretion by the Ysa T3S system is a posttranslational event.