bluuebunny/crossref_metadata_2025_split huggingface dataset:
NAD-Dependent DNA-Binding Activity of the Bifunctional NadR Regulator of
Salmonella typhimurium
Authors: Penfound Thomas , Foster John W. 
Published: December 2019

ABSTRACT

NadR is a 45-kDa bifunctional regulator protein. In vivo genetic studies indicate that NadR represses three genes involved in the biosynthesis of NAD. It also participates with an integral membrane protein (PnuC) in the import of nicotinamide mononucleotide, an NAD precursor. NadR was overexpressed and purified as a His-tagged fusion in order to study its DNA-binding properties. The protein bound to DNA fragments containing NAD box consensus sequences. NAD proved to be the relevant in vivo corepressor, but full NAD dependence of repressor activity required nucleotide triphosphates. DNA footprint analysis and gel shift assays suggest that NadR binds as a multimer to adjacent NAD boxes. The DNA-repressor complex would sequester a potential RNA polymerase binding site and thereby decrease expression of the
nad
regulon.
Unraveling the Function of Glycosyltransferases in
Streptococcus thermophilus
Sfi6
Authors: Stingele Francesca , Newell John W. , Neeser Jean-Richard 
Published: December 2019

ABSTRACT

Streptococcus thermophilus
Sfi6 produces a texturizing exopolysaccharide (EPS) consisting of a →3)[α-
d
-Gal
p
-(1→6)]-β-
d
-Glc
p
-(1→3)-α-
d
-Gal
p
NAc-(1→3)-β-
d
-Gal
p
-(1→ repeating unit. We previously identified and analyzed a 14.5-kb gene cluster from
S. thermophilus
Sfi6 consisting of 13 genes responsible for its EPS production. Within this gene cluster, we found a central region of genes (
epsE
,
epsF
,
epsG
, and
epsI
) that showed similarity to glycosyltransferases. In this study, we investigated the sugar specificity of these enzymes. EpsE catalyzes the first step in the biosynthesis of the EPS repeating unit. It exhibits phosphogalactosyltransferase activity and transfers galactose onto the lipophilic carrier. The second step is fulfilled by EpsG, which transfers an α-
N
-acetylgalactosamine onto the first β-galactoside. The activity of EpsF was determined by characterizing the EPS produced by an
S. thermophilus epsF
deletion mutant. This EPS consisted of the monosaccharides Gal, Glc, and GalNAc in an approximately equimolar ratio, thus suggesting that
epsF
codes for the branching galactosyltransferase.
epsI
probably codes for the β-1,3-glucosyltransferase, since it is the only glycosyltransferase to which no gene has been assigned and it exhibits similarity to other β-glycosyltransferases. EpsE shows the conserved features of phosphoglycosyltransferases, whereas EpsF and EpsG exhibit the primary structure of α-glycosyltransferases, belonging to glycosyltransferase family 4, whose members are conserved in all major phylogenetic lineages, including the
Archaea
and
Eukaryota
.
Arg-52 in the Melibiose Carrier of
Escherichia coli
Is Important for Cation-Coupled Sugar Transport and Participates in an Intrahelical Salt Bridge
Authors: Franco Peter J. , Wilson T. Hastings 
Published: December 2019

ABSTRACT

Arg-52 of the
Escherichia coli
melibiose carrier was replaced by Ser (R52S), Gln (R52Q), or Val (R52V). While the level of carrier in the membrane for each mutant remained similar to that for the wild type, analysis of melibiose transport showed an uncoupling of proton cotransport and a drastic reduction in Na
+
-coupled transport. Second-site revertants were selected on MacConkey plates containing melibiose, and substitutions were found at nine distinct locations in the carrier. Eight revertant substitutions were isolated from the R52S strain: Asp-19→Gly, Asp-55→Asn, Pro-60→Gln, Trp-116→Arg, Asn-244→Ser, Ser-247→Arg, Asn-248→Lys, and Ile-352→Val. Two revertants were also isolated from the R52V strain: Trp-116→Arg and Thr-338→Arg revertants. The R52Q strain yielded an Asp-55→Asn substitution and a first-site revertant, Lys-52 (R52K). The R52K strain had transport properties similar to those of the wild type. Analysis of melibiose accumulation showed that proton-driven accumulation was still defective in the second-site revertant strains, and only the Trp-116→Arg, Ser-247→Arg, and Asn-248→Lys revertants regained significant Na
+
-coupled accumulation. In general, downhill melibiose transport in the presence of Na
+
was better in the revertant strains than in the parental mutants. Three revertant strains, Asp-19→Gly, Asp-55→Asn, and Thr-338→Arg strains, required a high Na
+
concentration (100 mM) for maximal activity. Kinetic measurements showed that the N248K and W116R revertants lowered the

K
m

for melibiose, while other revertants restored transport velocity. We suggest that the insertion of positive charges on membrane helices is compensating for the loss of Arg-52 and that helix II is close to helix IV and VII. We also suggest that Arg-52 is salt bridged to Asp-55 (helix II) and Asp-19 (helix I).
The
Archaeoglobus fulgidus
d
-Lactate Dehydrogenase Is a Zn
2+
Flavoprotein
Authors: Reed David W. , Hartzell Patricia L. 
Published: December 2019

ABSTRACT

Archaeoglobus fulgidus
, a hyperthermophilic, archaeal sulfate reducer, is one of the few organisms that can utilize
d
-lactate as a sole source for both carbon and electrons. The
A. fulgidus
open reading frame, AF0394, which is predicted to encode a
d
-(−)-lactate dehydrogenase (Dld), was cloned, and its product was expressed in
Escherichia coli
as a fusion with the maltose binding protein (MBP). The 90-kDa MBP-Dld fusion protein was more efficiently expressed in
E. coli
when coexpressed with the
E. coli dnaY
gene, encoding the arginyl tRNA for the codons AGA and AGG. When cleaved from the fusion protein by treatment with factor Xa, the recombinant Dld (rDld) has an apparent molecular mass of 50 kDa, similar to that of the native
A. fulgidus
Dld enzyme. Both the purified MBP-Dld fusion protein and its rDld cleavage fragment have lactate dehydrogenase activities specific for
d
-lactate, are stable at 80°C, and retain activity after exposure to oxygen. The flavin cofactor FAD, which binds rDld apoprotein with a 1:1 stoichiometry, is essential for activity.
sn
-Glycerol-1-Phosphate-Forming Activities in
Archaea
: Separation of Archaeal Phospholipid Biosynthesis and Glycerol Catabolism by Glycerophosphate Enantiomers
Authors: Nishihara Masateru , Yamazaki Tomoko , Oshima Tairo , Koga Yosuke 
Published: December 2019

ABSTRACT

In
Methanobacterium thermoautotrophicum
,
sn
-glycerol-1-phosphate (G-1-P) dehydrogenase is responsible for the formation of the
Archaea
-specific backbone of phospholipids, G-1-P, from dihydroxyacetonephosphate (DHAP). The possible G-1-P-forming activities were surveyed in cell-free extracts of six species of
Archaea
. All the archaeal cell-free homogenates tested revealed the ability to form G-1-P from DHAP. In addition, activities of G-3-P-forming glycerol kinase and G-3-P dehydrogenase were also detected in four heterotrophic archaea, while glycerol kinase activity was not detected in two autotrophic methanogens. These results show that G-1-P is produced from DHAP by G-1-P dehydrogenase in a wide variety of archaea while exogenous glycerol is catabolized via G-3-P.
Conserved Organization in the
cps
Gene Clusters for Expression of
Escherichia coli
Group 1 K Antigens: Relationship to the Colanic Acid Biosynthesis Locus and the
cps
Genes from
Klebsiella pneumoniae
Authors: Rahn Andrea , Drummelsmith Jolyne , Whitfield Chris 
Published: December 2019

ABSTRACT

Group 1 capsules of
Escherichia coli
are similar to the capsules produced by strains of
Klebsiella
spp. in terms of structure, genetics, and patterns of expression. The striking similarities between the capsules of these organisms prompted a more detailed investigation of the
cps
loci encoding group 1 capsule synthesis. Six strains of
K. pneumoniae
and 12 strains of
E. coli
were examined. PCR analysis showed that the clusters in these strains are conserved in their chromosomal locations. A highly conserved block of four genes,
orfX-wza-wzb-wzc
, was identified in all of the strains. The
wza
and
wzc
genes are required for translocation and surface assembly of
E. coli
K30 antigen. The conservation of these genes points to a common pathway for capsule translocation. A characteristic JUMPstart sequence was identified upstream of each cluster which may function in conjunction with RfaH to inhibit transcriptional termination at a stem-loop structure found immediately downstream of the “translocation-surface assembly” region of the cluster. Interestingly, the sequence upstream of the
cps
clusters in five
E. coli
strains and one
Klebsiella
strain indicated the presence of IS elements. We propose that the IS elements were responsible for the transfer of the
cps
locus between organisms and that they may continue to mediate recombination between strains.
ANTIBODIES AGAINSTSTAPHYLOCOCCUS AUREUSIN NONIMMUNIZED RABBITS
Authors: Cohen Jay O. , Cowart Glenda S. , Cherry William B. 
Published: January 2020

Cohen, JayO. (Communicable Disease Center, Atlanta, Ga.),Glenda S. Cowart, and William B. Cherry. Antibodies againstStaphylococcus aureusin nonimmunized rabbits. J. Bacteriol.82:110–114. 1961.—Antibody against staphylococci was demonstrated in the serum of each of 36 nonimmunized specific-pathogen-free rabbits that were tested. Evidence obtained is in agreement with the proposition that two distinct staphylococcal antibodies are present in the sera from these nonimmunized rabbits. One is responsible for agglutination ofStaphylococcus aureusCowan serotype I, and the other for the formation of a reaction line observed in Ouchterlony plates with soluble antigens of both Cowan serotype I and Cowan serotype III.Fluorescent antibody reagent prepared from preimmune rabbit serum stained some strains of coagulase positive staphylococci, including Cowan's types I and III, and failed to stain any of 14 coagulase negative strains.The sera of rabbits obtained from a commercial source were shown to contain other antibodies for staphylococci in addition to the two found in the sera of specific-pathogen-free rabbits. The data suggested that rabbits from commercial sources have had contact with a great variety of antigens capable of stimulating staphylococcal antibody.Evidence demonstrated that normal rabbit serum from specific-pathogen-free animals of our colony could be used for differentiation of certain staphylococcal strains.
EFFECT OF VACCINES PREPARED FROMHISTOPLASMA CAPSULATUMAND OTHER YEASTS ON EXPERIMENTAL TUBERCULOSIS
Authors: Hedgecock Loyd W. 
Published: January 2020

Hedgecock, LoydW. (Veterans Administration Hospital, Kansas City, Mo.). Effect of vaccines prepared fromHistoplasma capsulatumand other yeasts on experimental tuberculosis. J. Bacteriol.82:115–123. 1961.—Resistance to experimental tuberculosis was enhanced by the injection of a nonviable vaccine prepared fromHistoplasma capsulatumin the mycelial phase but not by the organism in the yeast phase. Acquired resistance was established within 7 days or less and usually maintained for at least 29 days. When both mycelium vaccine ofH. capsulatumand a vaccine prepared from tubercle bacilli were utilized in vaccination, the results were additive (in terms of acquired resistance) provided that an interval of 3 weeks was maintained between injection of each of the vaccines.Resistance to tuberculosis was also demonstrable 14 days after the injection of nonviable preparations ofBrucella abortusandCryptococcus neoformans, as well as by yeast and mycelial vaccines ofBlastomyces dermatitidisandSporotrichum schenckii. Resistance decreased significantly when the animals were challenged 29 days after vaccination, with the exception of those injected with the yeast phase ofB. dermatitidis.
THIAMINE AND NICOTINIC ACID: ANAEROBIC GROWTH FACTORS FOR
MUCOR ROUXII
Authors: Bartnicki-Garcia S. , Nickerson Walter J. 
Published: January 2020

Bartnicki-Garcia
, S. (Rutgers, the State University, New Brunswick, N. J.),
and Walter J. Nickerson
. Thiamine and nicotinic acid: Anaerobic growth factors for
Mucor rouxii
. J. Bacteriol. 82:142–148. 1961.—
Mucor rouxii
requires preformed thiamine and nicotinic acid for anaerobic growth. Such requirements are not manifested during aerobic incubation. Aerobically, the fungus was shown to be able to synthesize both vitamins.

The yeastlike form and the filamentous form of anaerobically grown
M. rouxii
exhibit the same vitamin requirements.

Thiamine can be substituted by its thiazole moiety. Under certain conditions, nicotinic acid was partly substituted by tryptophan, kynurenine, 3-hydroxykynurenine, and 3-hydroxyanthranilic acid.
Anaerobically. the fungus (thiamine requiring) was about ten times more susceptible to pyrithiamine antagonism than the same organism grown aerobically (thiamine independent).
SEROLOGICAL GROUPING OF ACTINOMYCES BY MEANS OF FLUORESCENT ANTIBODIES
Authors: Slack John M. , Winger Ann , Moore Dane W. 
Published: January 2020

Slack, JohnM. (West Virginia University, Morgantown),Ann Winger, and Dane W. Moore, Jr.Serological grouping of actinomyces by means of fluorescent antibodies. J. Bacteriol.82:54–65. 1961.—Serological groups A, B, C and D of actinomyces were established using fluorescent antibody techniques. One hundred and thirty-eight cultures were included in the study. Eighty-nine were classed in group A, 15 in B, 13 in C, and 21 in D.The isolates were from patients and animals with actinomycosis and from healthy human beings. There was no correlation between source of the isolate and serological group. Furthermore, no one species could be placed exclusively in one group although the majority of those designated asActinomyces boviswere in group A.Seventeen anaerobic diphtheroids and sevenCorynebacterium acnesisolates were placed in group A. One diphtheroid was in each of groups B and D. On this basis it is suggested that these organisms be included in the genusActinomyces.Additional species ofCorynebacteriumas well asLactobacillus Propionibacterium, Streptomyces, andNocardiadid not fluoresce with any of the group antisera.
Typing of
Nocardia farcinica
by Pulsed-Field Gel Electrophoresis Reveals an Endemic Strain as Source of Hospital Infections
Authors: Blümel J. , Blümel E. , Yassin A. F. , Schmidt-Rotte H. , Schaal K. P. 
Published: December 2019

ABSTRACT

Severe postoperative wound infections caused by
Nocardia farcinica
were repeatedly observed in a German hospital surgical ward. A pulsed-field gel electrophoresis (PFGE) protocol was established to characterize the genetic relatedness of the bacterial isolates from these infections. All 18 isolates from postoperative infections that have occurred since 1985 belong to a common endemic genotype; organisms of this genotype were also detected in the air of two rooms of the department where these postoperative infections occurred. In contrast, two environmental isolates from another building on the same campus showed a distinct genotype. Three cases of pulmonary infections, at a department which is located in proximity to the surgical department, were also caused by the endemic type, which suggests aerogenic spread of the endemic strain to these patients. Controls consisting of epidemiologically unrelated isolates from sporadic infections in other towns belonged in each case to a different genotype. PFGE was well suited to differentiate various types of
N. farcinica
and revealed an endemic strain causing postoperative wound infections possibly after aerogenic transmission.
Determination of Penicillin MICs for
Streptococcus pneumoniae
by Using a Two- or Three-Disk Diffusion Procedure
Authors: Jacobs Michael R. , Bajaksouzian Saralee , Palavecino-Fasola Elizabeth L. , Holoszyc Henry M. , Appelbaum Peter C. 
Published: December 2019

ABSTRACT

The potential for the use of the disk diffusion method to accurately predict penicillin MICs for
Streptococcus pneumoniae
was investigated with penicillin (6 μg), methicillin (5 μg), and oxacillin (1 μg) disks. A total of 183
S. pneumoniae
isolates were tested by three MIC procedures (agar dilution, microdilution, and E-test). Regression analyses of the geometric mean of the three MIC results against (i) the sum of the zone diameters for methicillin, penicillin, and oxacillin disks; (ii) the sum of the zone diameters for methicillin and penicillin disks; and (iii) each of the three individual zone diameters were performed. Calculated MICs were determined from each of these regression analyses and compared to the mean reference MICs. A high level of correlation was obtained with both the two- and the three-disk procedures (
r
= 0.97), with essential agreement rates (±1 doubling dilution) between MICs calculated by the three-disk procedure and the two-disk procedure and the mean reference MICs of 98.4 and 98.9%, respectively. No major or very major errors were obtained with the two- or three-disk procedures. The accuracy of the disks used individually was lower (
r
= 0.84 to 0.93). However, oxacillin and methicillin disk testing remain excellent for screening strains, with all penicillin-susceptible strains having zones of >21 and >22 mm, respectively. The combination disk procedure, which involves the use of three disks (methicillin, oxacillin, and penicillin) or two disks (methicillin and penicillin) for testing
S. pneumoniae
, can provide accurate penicillin MICs and qualitative category results that are comparable to results obtained by the E-test, agar, and microdilution MIC methods.
Enterobacter cloacae
Endophthalmitis: Report of Four Cases
Authors: Okhravi N. , Ficker L. , Matheson M. M. , Lightman S. 
Published: December 2019

ABSTRACT

Members of the genus
Enterobacter
are commensal organisms of the gastrointestinal tract and are considered pathogenic only for patients with lowered resistance to infection (e.g., chronic infection, cancer, or diabetes mellitus) or those with impaired immunity (congenital, acquired, or impaired immunity secondary to therapy). We report on four cases of endophthalmitis caused by
Enterobacter cloacae
: two in patients with acute postoperative endophthalmitis, one in a patient with delayed bleb-related endophthalmitis, and one in a patient presenting with presumed posttraumatic endophthalmitis. Each patient presented with severe disease many days after the onset of ocular symptoms, and two patients had systemic risk factors accounting for a reduced resistance to infection. Endophthalmitis caused by gram-negative bacilli is characterized by acute onset, rapid progression, and poor final visual outcome. Each of these patients was treated by a standard protocol with intravitreal, systemic, and topical antibiotics and systemic steroids. Despite treatment, the final visual outcomes for three of these patients was no perception of light, and that for one patient remained perception of hand movements only. In common with endophthalmitis caused by other gram-negative organisms, intraocular infection secondary to
Enterobacter cloacae
infection is a devastating disease which, despite treatment, results in extensive ocular damage and severe visual loss. Since 1966, only four cases of endophthalmitis secondary to infection with members of this genus have been reported. This report presents four cases which occurred over a period of 14 months and, to the best of our knowledge, the first case of bleb-related endophthalmitis secondary to
E. cloacae
infection.
Clinical Evaluation of the Automated COBAS AMPLICOR MTB Assay for Testing Respiratory and Nonrespiratory Specimens
Authors: Reischl Udo , Lehn Norbert , Wolf Hans , Naumann Ludmila 
Published: December 2019

ABSTRACT

We evaluated the COBAS AMPLICOR PCR system (Roche Diagnostics) for the routine detection of
Mycobacterium tuberculosis
complex (MTBC) in clinical specimens. Diagnostic culture, considered as the reference method, was performed with BACTEC, Löwenstein-Jensen, Stonebrink, and Kirchner media. Occasionally MB-Redox, ESP, or MGIT medium was also used. A total of 643 respiratory and 506 nonrespiratory specimens collected from 807 patients were investigated. Of the 95 culture-positive specimens, 80 were COBAS AMPLICOR MTB positive, and of the 1,054 culture-negative specimens, 1,044 were COBAS AMPLICOR MTB negative. After resolving discrepancies by review of the medical history, the overall sensitivity, specificity, and positive and negative predictive values for the COBAS AMPLICOR MTB assay, respectively, were 83.5, 98.8, 86.7, and 98.6% compared to those of diagnostic culture. In smear-positive specimens, the sensitivity of the COBAS AMPLICOR MTB assay was 96%, versus 48% for smear-negative specimens. No significant differences in the test performance between respiratory and nonrespiratory specimens were observed. The overall inhibition rate was less than 2%, excluding stool specimens. The clear advantages of the COBAS AMPLICOR PCR system are standardized procedures and reagents for specimen processing as well as an internal control for reliable monitoring of PCR inhibitors. By simplifying the work flow through a completely automated amplification and amplicon detection procedure, the COBAS AMPLICOR PCR system proved itself as a very useful component for routine diagnostic procedures.
Comparison of Systems for Identification and Differentiation of Species within the Genus
Yersinia
Authors: Neubauer Heinrich , Sauer Thomas , Becker Heinz , Aleksic Stojanca , Meyer Hermann 
Published: December 2019

ABSTRACT

Of four tested identification systems (API 20E, API Rapid 32 IDE, Micronaut E, and the PCR-based
Yersinia enterocolitica
Amplification Set), API 20E is still the system of choice for identifying pathogenic
Yersinia
isolates. It provides the highest sensitivity both at the genus and at the species level and has the best cost-effectiveness correlation.
Automated RIBA Hepatitis C Virus (HCV) Strip Immunoblot Assay for Reproducible HCV Diagnosis
Authors: Martin P. , Fabrizi F. , Dixit V. , Quan S. , Brezina M. , Kaufman E. , Sra , K. , DiNello R. , Polito A. , Gitnick G. 
Published: December 2019

ABSTRACT
A comparison between the CHIRON RIBA hepatitis C virus (HCV) processor and manual systems was performed by using 88 specimens repeatedly reactive by the second-generation HCV enzyme-linked immunosorbent assay (ELISA) (HCV 2.0 ELISA) and 111 random specimens from volunteer donors. For the second-generation RIBA HCV strip immunoblot assay (SIA) (RIBA HCV 2.0 SIA), test results correlated strongly between the manual and the automated runs (kappa value, 0.937). For the RIBA HCV 3.0 SIA, the correlation of the test results was also high (kappa value, 0.899). Among the specimens with positive results by RIBA HCV 2.0 and 3.0 SIAs, there was a very strong concordance of the test results between the manual and the automated runs with regard to the reactive bands. Nine samples had discordant results between the manual and the automated runs; this was probably attributable to increased variability in antigen scores close to the cutoff values for both tests. Run-to-run and within-run testing by the CHIRON RIBA HCV Processor System showed a very low rate of conflicting values. In conclusion, the CHIRON RIBA HCV Processor System is capable of performing RIBA HCV 2.0 and 3.0 SIAs accurately with minimal operator involvement. In addition, the CHIRON RIBA HCV Processor System shows excellent reproducibility, with the potential for operator-to-operator and site-to-site variability being greatly reduced. Our data indicate that this novel methodology may be very useful for supplemental anti-HCV testing of specimens repeatedly reactive by ELISA in routine clinical assessments and epidemiologic evaluations.