bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the Unusual Bidirectional
ves
Promoters Driving VESA1 Expression and Associated with Antigenic Variation in Babesia bovis
Authors: Wang Xinyi , Xiao Yu-Ping , Bouchut Anne , Al-Khedery Basima , Wang Hongbin , Allred David R.
Published: January 2012

Rapid clonal antigenic variation in
Babesia bovis
involves the
v
ariant
e
rythrocyte
s
urface
a
ntigen-1 (VESA1) protein expressed on the infected-erythrocyte surface. Because of the significance of this heterodimeric protein for demonstrated mechanisms of parasite survival and virulence, there is a need to understand how expression of the
ves
multigene family encoding this protein is controlled. As an initial step toward this goal, we present here initial characterization of the
ves
promoter driving transcription of VESA1a and -1b subunits. A series of transfection constructs containing various sequence elements from the
in vivo
locus of active
ves
transcription (LAT) were used to drive expression of the firefly luciferase gene in a dual luciferase-normalized assay. The results of this approach reveal the presence of two bidirectional promoter activities within the 434-bp intergenic region (IGr), influenced by putative regulatory sequences embedded within the flanking
ves
1α and
ves
1β genes. Repressor-like effects on the apposing gene were observed for intron 1 of both
ves
1α and
ves
1β. This effect is apparently not dependent upon intronic promoter activity and acts only in
cis
. The expression of genes within the
ves
family is likely modulated by local elements embedded within
ves
coding sequences outside the intergenic promoter region in concert with chromatin modifications. These results provide a framework to help us begin to understand gene regulation during antigenic variation in
B. bovis
.
Fur-Mediated Activation of Gene Transcription in the Human Pathogen Neisseria gonorrhoeae
Authors: Yu Chunxiao , Genco Caroline Attardo
Published: January 2012

It is well established that the
f
erric
u
ptake
r
egulatory protein (Fur) functions as a transcriptional repressor in diverse microorganisms. Recent studies demonstrated that Fur also functions as a transcriptional activator. In this study we defined Fur-mediated activation of gene transcription in the sexually transmitted disease pathogen
Neisseria gonorrhoeae
. Analysis of 37 genes which were previously determined to be iron induced and which contained putative Fur boxes revealed that only 30 of these genes exhibited reduced transcription in a gonococcal
fur
mutant strain. Fur-mediated activation was established by examining binding of Fur to the putative promoter regions of 16 Fur-activated genes with variable binding affinities observed. Only ∼50% of the newly identified Fur-regulated genes bound Fur
in vitro
, suggesting that additional regulatory circuits exist which may function through a Fur-mediated indirect mechanism. The gonococcal Fur-activated genes displayed variable transcription patterns in a
fur
mutant strain, which correlated with the position of the Fur box in each (promoter) region. These results suggest that Fur-mediated direct transcriptional activation is fulfilled by multiple mechanisms involving either competing with a repressor or recruiting RNA polymerase. Collectively, our studies have established that gonococcal Fur functions as an activator of gene transcription through both direct and indirect mechanisms.
Transcriptional and Posttranscriptional Events Control Copper-Responsive Expression of a Rhodobacter capsulatus Multicopper Oxidase
Authors: Rademacher Corinna , Moser Roman , Lackmann Jan-Wilm , Klinkert Birgit , Narberhaus Franz , Masepohl Bernd
Published: January 2012

The copper-regulated
Rhodobacter capsulatus cutO
(multicopper oxidase) gene confers copper tolerance and is carried in the tricistronic
orf635
-
cutO
-
cutR
operon. Transcription of
cutO
strictly depends on the promoter upstream of
orf635
, as demonstrated by
lacZ
reporter fusions to nested promoter fragments. Remarkably,
orf635
expression was not affected by copper availability, whereas
cutO
and
cutR
were expressed only in the presence of copper. Differential regulation was abolished by site-directed mutations within the
orf635
-
cutO
intergenic region, suggesting that this region encodes a copper-responsive mRNA element. Bioinformatic predictions and RNA structure probing experiments revealed an intergenic stem-loop structure as the candidate mRNA element. This is the first posttranscriptional copper response mechanism reported in bacteria.
Inactivation of Haemophilus influenzae Lipopolysaccharide Biosynthesis Genes Interferes with Outer Membrane Localization of the Hap Autotransporter
Authors: Spahich Nicole A. , Hood Derek W. , Moxon E. Richard , St. Geme Joseph W.
Published: January 2012

Nontypeable
Haemophilus influenzae
is a major cause of localized respiratory tract disease and initiates infection by colonizing the nasopharynx. Colonization requires adherence to host epithelial cells, which is mediated by surface proteins such as the Hap adhesin. In this study, we identified a relationship between Hap levels in the outer membrane and lipopolysaccharide (LPS) biosynthesis enzymes. We found that mutation of the
rfaF
,
pgmB
,
lgtC
,
kfiC
,
orfE
,
rfbP
,
lsgB
, or
lsgD
genes, which are involved in the synthesis of the LPS oligosaccharide core in
H. influenzae
strain Rd/HapS243A, resulted in loss of Hap in the bacterial outer membrane and a decrease in
hap
transcript levels. In contrast, the same mutations had no effect on outer membrane localization of
H. influenzae
P5 or IgA1 protease or levels of
p5
or
iga1
transcripts, suggesting a Hap-specific effect. Elimination of the HtrA periplasmic protease resulted in a return of Hap to the outer membrane and restoration of
hap
transcript levels. Consistently, in
lgtC
phase-off bacteria, Hap was absent from the outer membrane, and
hap
transcript levels were reduced. Hap localization and
hap
transcript levels were not related to LPS size but to the functions of the LPS biosynthesis enzymes themselves. We speculate that the lack of certain LPS biosynthesis enzymes causes Hap to mislocalize and accumulate in the periplasm, where it is degraded by HtrA. This degradation then leads to a decrease in
hap
transcript levels. Together, these data highlight a novel interplay between Hap and LPS biosynthesis that can influence
H. influenzae
interactions with the host.
Transcriptional and Metabolomic Consequences of
luxS
Inactivation Reveal a Metabolic Rather than Quorum-Sensing Role for LuxS in Lactobacillus reuteri 100-23
Authors: Wilson Charlotte M. , Aggio Raphael B. M. , O'Toole Paul W. , Villas-Boas Silas , Tannock Gerald W.
Published: January 2012

Autoinducer-2 (AI-2)-mediated quorum sensing has been extensively studied in relation to the regulation of microbial behavior. There are, however, two potential roles for the AI-2 synthase (LuxS). The first is in the production of AI-2 and the second is as an enzyme in the activated methyl cycle, where it catalyzes the conversion of S-ribosylhomocysteine to homocysteine. The by-product of the reaction catalyzed by LuxS is (
S
)-4,5-dihydroxy-2,3-pentanedione, which spontaneously forms the furanones known collectively as AI-2. The mammalian gut contains a complex collection of bacterial species so a method of interspecies communication might influence community structure and function.
Lactobacillus reuteri
100-23 is an autochthonous inhabitant of the rodent forestomach, where it adheres to the nonsecretory epithelium, forming a biofilm. Microarray comparisons of gene expression profiles of the
L. reuteri
100-23 wild type and a
luxS
mutant under different culture conditions revealed altered transcription of genes encoding proteins associated with cysteine biosynthesis/oxidative stress response, urease activity, and sortase-dependent proteins. Metabolomic analysis showed that the
luxS
mutation affected cellular levels of fermentation products, fatty acids and amino acids. Cell density-dependent changes (log phase versus stationary phase growth) in gene transcription were not detected, indicating that AI-2 was unlikely to be involved in gene regulation mediated by quorum sensing in
L. reuteri
100-23.
Functional Analysis of the CpsA Protein of Streptococcus agalactiae
Authors: Hanson Brett R. , Runft Donna L. , Streeter Cale , Kumar Abhin , Carion Thomas W. , Neely Melody N.
Published: January 2012

Streptococcal pathogens, such as the group B streptococcus (GBS)
Streptococcus agalactiae
, are an important cause of systemic disease, which is facilitated in part by the presence of a polysaccharide capsule. The CpsA protein is a putative transcriptional regulator of the capsule locus, but its exact contribution to regulation is unknown. To address the role of CpsA in regulation, full-length GBS CpsA and two truncated forms of the protein were purified and analyzed for DNA-binding ability. Assays demonstrated that CpsA is able to bind specifically to two putative promoters within the capsule operon with similar affinity, and full-length protein is required for specificity. Functional characterization of CpsA confirmed that the Δ
cpsA
strain produced less capsule than did the wild type and demonstrated that the production of full-length CpsA or the DNA-binding region of CpsA resulted in increased capsule levels. In contrast, the production of a truncated form of CpsA lacking the extracellular LytR domain (CpsA-245) in the wild-type background resulted in a dominant-negative decrease in capsule production. GBS expressing CpsA-245, but not the Δ
cpsA
strain, was attenuated in human whole blood. However, the Δ
cpsA
strain showed significant attenuation in a zebrafish infection model. Furthermore, chain length was observed to be variable in a CpsA-dependent manner, but could be restored to wild-type levels when grown with lysozyme. Taken together, these results suggest that CpsA is a modular protein influencing multiple regulatory functions that may include not only capsule synthesis but also cell wall associated factors.
Global Transcriptional Control by NsrR in Bacillus subtilis
Authors: Kommineni Sushma , Lama Amrita , Popescu Benjamin , Nakano Michiko M.
Published: January 2012

The NO-sensitive NsrR repressor of
Bacillus subtilis
, which carries a [4Fe-4S] cluster, controls transcription of
nasD
and
hmp
(class I regulation) under anaerobic conditions. Here, we describe another class of NsrR regulation (class II regulation) that controls a more diverse collection of genes. Base substitution analysis showed that [4Fe-4S]-NsrR recognizes a partial dyad symmetry within the class I
cis
-acting sites, whereas NO-insensitive interaction of NsrR with an A+T-rich class II regulatory site showed relaxed sequence specificity. Genome-wide transcriptome studies identified genes that are under the control of the class II NsrR regulation. The class II NsrR regulon includes genes controlled by both AbrB and Rok repressors, which also recognize A+T-rich sequences, and by the Fur repressor. Transcription of class II genes was elevated in an
nsrR
mutant during anaerobic fermentative growth with pyruvate. Although NsrR binding to the class II regulatory sites was NO insensitive
in vitro
, transcription of class II genes was moderately induced by NO, which involved reversal of NsrR-dependent repression, suggesting that class II repression is also NO sensitive. In all NsrR-repressed genes tested, the loss of NsrR repressor activity was not sufficient to induce transcription as induction required the ResD response regulator. The ResD-ResE signal transduction system is essential for activation of genes involved in aerobic and anaerobic respiration. This study indicated coordinated regulation between ResD and NsrR and uncovered a new role of ResD and NsrR in transcriptional regulation during anaerobiosis of
B. subtilis
.
Asymmetric Disposal of Individual Protein Aggregates in Escherichia coli, One Aggregate at a Time
Authors: Lloyd-Price Jason , Häkkinen Antti , Kandhavelu Meenakshisundaram , Marques Ines J. , Chowdhury Sharif , Lihavainen Eero , Yli-Harja Olli , Ribeiro Andre S.
Published: January 2012

Escherichia colicells employ an asymmetric strategy at division, segregating unwanted substances to older poles, which has been associated with aging in these organisms. The kinetics of this process is still poorly understood. Using the MS2 coat protein fused to green fluorescent protein (GFP) and a reporter construct with multiple MS2 binding sites, we tracked individual RNA-MS2-GFP complexes inE. colicells from the time when they were produced. Analyses of the kinetics and brightness of the spots showed that these spots appear in the midcell region, are composed of a single RNA-MS2-GFP complex, and reach a pole before another target RNA is formed, typically remaining there thereafter. The choice of pole is probabilistic and heavily biased toward one pole, similar to what was observed by previous studies regarding protein aggregates. Additionally, this mechanism was found to act independently on each disposed molecule. Finally, while the RNA-MS2-GFP complexes were disposed of, the MS2-GFP tagging molecules alone were not. We conclude that this asymmetric mechanism to segregate damage at the expense of aging individuals acts probabilistically on individual molecules and is capable of the accurate classification of molecules for disposal.
Reduced Aeration Affects the Expression of the NorB Efflux Pump of Staphylococcus aureus by Posttranslational Modification of MgrA
Authors: Truong-Bolduc Que Chi , Hsing Liao Chun , Villet Regis , Bolduc Gilles R. , Estabrooks Zoe , Taguezem G Florent , Hooper David C.
Published: January 2012

We previously showed that at acid pH, the transcription of
norB
, encoding the NorB efflux pump, increases due to a reduction in the phosphorylation level of MgrA, which in turn leads to a reduction in bacterial killing by moxifloxacin, a substrate of the NorB efflux pump. In this study, we demonstrated that reduced oxygen levels did not affect the transcript levels of
mgrA
but modified the dimerization of the MgrA protein, which remained mostly in its monomeric form. Under reduced aeration, we also observed a 21.7-fold increase in the
norB
transcript levels after 60 min of growth that contributed to a 4-fold increase in the MICs of moxifloxacin and sparfloxacin for
Staphylococcus aureus
RN6390. The relative proportions of MgrA in monomeric and dimeric forms were altered by treatment with H
2
O
2
, but incubation of purified MgrA with extracts of cells grown under reduced but not normal aeration prevented MgrA from being converted to its dimeric DNA-binding form. This modification was associated with cleavage of a fragment of the dimerization domain of MgrA without change in MgrA phosphorylation and an increase in transcript levels of genes encoding serine proteases in cells incubated at reduced aeration. Taken together, these data suggest that modification of MgrA by proteases underlies the reversal of its repression of
norB
and increased resistance to NorB substrates in response to reduced-aeration conditions, illustrating a third mechanism of posttranslational modification, in addition to oxidation and phosphorylation, that modulates the regulatory activities of MgrA.
Phosphatidylglycerol::Prolipoprotein Diacylglyceryl Transferase (Lgt) of Escherichia coli Has Seven Transmembrane Segments, and Its Essential Residues Are Embedded in the Membrane
Authors: Pailler Jérémy , Aucher Willy , Pires Magali , Buddelmeijer Nienke
Published: January 2012

Lgt ofEscherichia colicatalyzes the transfer of ansn-1,2-diacylglyceryl group from phosphatidylglycerol to prolipoproteins. The enzyme is essential for growth, as demonstrated here by the analysis of anlgtdepletion strain. Cell fractionation demonstrated that Lgt is an inner membrane protein. Its membrane topology was determined by fusing Lgt to β-galactosidase and alkaline phosphatase and bysubstitutedcysteineaccessibilitymethod (SCAM) studies. The data show that Lgt is embedded in the membrane by seven transmembrane segments, that its N terminus faces the periplasm, and that its C terminus faces the cytoplasm. Highly conserved amino acids in Lgt of both Gram-negative and Gram-positive bacteria were identified. Lgt enzymes are characterized by a so-called Lgt signature motif in which four residues are invariant. Ten conserved residues were replaced with alanine, and the activity of these Lgt variants was analyzed by their ability to complement thelgtdepletion strain. Residues Y26, N146, and G154 are absolutely required for Lgt function, and R143, E151, R239, and E243 are important. The results demonstrate that the majority of the essential residues of Lgt are located in the membrane and that the Lgt signature motif faces the periplasm.
Differentiation of Function among the RsbR Paralogs in the General Stress Response of Bacillus subtilis with Regard to Light Perception
Authors: van der Steen Jeroen B. , Ávila-Pérez Marcela , Knippert Doreen , Vreugdenhil Angie , van Alphen Pascal , Hellingwerf Klaas J.
Published: January 2012

The general stress response of
Bacillus subtilis
can be activated by a wide range of signals, including low intensities of visible light. It is regulated by a dedicated σ factor via a complex signal transduction pathway that makes use of stressosomes: hetero-oligomeric complexes that include one or more of the RsbR proteins (RsbRA, RsbRB, RsbRC, and RsbRD). The response to blue light is mediated by the photoreceptor YtvA. We show here which of the four RsbR proteins are necessary for the activation of the σ
B
response by blue light. Experiments performed with single-, double-, and triple-deletion strains in the
rsbR
genes show that RsbRB and RsbRA function antagonistically, with the former being a negative regulator and the latter a positive regulator of the YtvA-dependent light activation of the stress response. A strain with RsbRB as the only RsbR protein is unable to respond to light-activation of σ
B
. Furthermore, RsbRC and RsbRD can replace RsbRA's function only in the absence of RsbRB. This differentiation of function is confined to light stress, since strains with RsbRA or RsbRB as the only RsbR protein behave similarly in our experimental conditions in response to physicochemical stresses. Interestingly, RsbRB's absence is sufficient to result in light activation of the general stress response at wild-type expression levels of
ytvA
, while it was previously reported that YtvA could only activate σ
B
when overproduced, or when cells are supplemented with an additional environmental stress.
Mutational Analyses Reveal Overall Topology and Functional Regions of NilB, a Bacterial Outer Membrane Protein Required for Host Association in a Model of Animal-Microbe Mutualism
Authors: Bhasin Archna , Chaston John M. , Goodrich-Blair Heidi
Published: January 2012

The gammaproteobacterium
Xenorhabdus nematophila
is a mutualistic symbiont that colonizes the intestine of the nematode
Steinernema carpocapsae
.
nilB
(
n
ematode
i
ntestine
l
ocalization) is essential for
X. nematophila
colonization of nematodes and is predicted to encode an integral outer membrane beta-barrel protein, but evidence supporting this prediction has not been reported. The function of NilB is not known, but when expressed with two other factors encoded by
nilA
and
nilC
, it confers upon noncognate
Xenorhabdus
spp. the ability to colonize
S. carpocapsae
nematodes. We present evidence that NilB is a surface-exposed outer membrane protein whose expression is repressed by NilR and growth in nutrient-rich medium. Bioinformatic analyses reveal that NilB is the only characterized member of a family of proteins distinguished by N-terminal region tetratricopeptide repeats (TPR) and a conserved C-terminal domain of unknown function (DUF560). Members of this family occur in diverse bacteria and are prevalent in the genomes of mucosal pathogens. Insertion and deletion mutational analyses support a beta-barrel structure model with an N-terminal globular domain, 14 transmembrane strands, and seven extracellular surface loops and reveal critical roles for the globular domain and surface loop 6 in nematode colonization. Epifluorescence microscopy of these mutants demonstrates that NilB is necessary at early stages of colonization. These findings are an important step in understanding the function of NilB and, by extension, its homologs in mucosal pathogens.
Adaptor Protein MecA Is a Negative Regulator of the Expression of Late Competence Genes in Streptococcus thermophilus
Authors: Boutry Céline , Wahl Astrid , Delplace Brigitte , Clippe André , Fontaine Laetitia , Hols Pascal
Published: January 2012

In
Streptococcus thermophilus
, the ComRS regulatory system governs the transcriptional level of
comX
expression and, hence, controls the early stage of competence development. The present work focuses on the posttranslational control of the activity of the sigma factor ComX and, therefore, on the late stage of competence regulation.
In silico
analysis performed on the
S. thermophilus
genome revealed the presence of a homolog of
mecA
(
mecA
St
), which codes for the adaptor protein that is involved in ComK degradation by ClpCP in
Bacillus subtilis
. Using reporter strains and microarray experiments, we showed that MecA
St
represses late competence genes without affecting the early competence stage under conditions that are not permissive for competence development. In addition, this repression mechanism was found not only to act downstream of
comX
expression but also to be fully dependent on the presence of a functional
comX
gene. This negative control was similarly released in strains deleted for
clpC
,
mecA
, and
clpC-mecA
. Under artificial conditions of
comX
expression, we next showed that the abundance of ComX is higher in the absence of MecA or ClpC. Finally, results of bacterial two-hybrid assays strongly suggested that MecA interacts with both ComX and ClpC. Based on these results, we proposed that ClpC and MecA act together in the same regulatory circuit to control the abundance of ComX in
S. thermophilus
.
The ChrA Response Regulator in Corynebacterium diphtheriae Controls Hemin-Regulated Gene Expression through Binding to the
hmuO
and
hrtAB
Promoter Regions
Authors: Burgos Jonathan M. , Schmitt Michael P.
Published: January 2012

Corynebacterium diphtheriae
, the etiologic agent of diphtheria, utilizes heme and hemoglobin (Hb) as iron sources for growth. Heme-iron utilization involves HmuO, a heme oxygenase that degrades cytosolic heme, resulting in the release of heme-associated iron. Expression of the
hmuO
promoter is under dual regulation, in which transcription is repressed by DtxR and iron and activated by a heme source, such as hemin or Hb. Hemin-dependent activation is mediated primarily by the ChrAS two-component system, in which ChrS is a putative heme-responsive sensor kinase while ChrA is proposed to serve as a response regulator that activates transcription. It was recently shown that the ChrAS system similarly regulates the
hrtAB
genes, which encode an ABC transporter involved in the protection of
C. diphtheriae
from hemin toxicity. In this study, we characterized the phosphorelay mechanism in the ChrAS system and provide evidence for the direct regulation of the
hmuO
and
hrtAB
promoters by ChrA. A fluorescence staining method was used to show that ChrS undergoes autophosphorylation and that the phosphate moiety is subsequently transferred to ChrA. Promoter fusion studies identified regions upstream of the
hmuO
and
hrtAB
promoters that are critical for the heme-dependent regulation by ChrA. Electrophoretic mobility shift assays revealed that ChrA specifically binds at the
hmuO
and
hrtAB
promoter regions and that binding is phosphorylation dependent. A phosphorylation-defective mutant of ChrA [ChrA(D50A)] exhibited significantly diminished binding to the
hmuO
promoter region relative to that of wild-type ChrA. DNase I footprint analysis further defined the sequences in the
hmuO
and
hrtAB
promoters that are involved in ChrA binding, and this analysis revealed that the DtxR binding site at the
hmuO
promoter partially overlaps the binding site for ChrA. DNase I protection studies as well as promoter fusion analysis suggest that ChrA and DtxR compete for binding at the
hmuO
promoter. Collectively, these data demonstrate that the ChrA response regulator directly controls the expression of
hmuO
and the
hrtAB
genes and the binding activity of ChrA is dependent on phosphorylation by its cognate sensor kinase ChrS.
Autoregulation of the Synthesis of the MobM Relaxase Encoded by the Promiscuous Plasmid pMV158
Authors: Lorenzo-Díaz Fabián , Solano-Collado Virtu , Lurz Rudi , Bravo Alicia , Espinosa Manuel
Published: January 2012

The streptococcal promiscuous plasmid pMV158 (5,540 bp) replicates by the rolling-circle mechanism and can be mobilized among a wide number of Gram-positive and -negative bacteria. The plasmid region involved in its conjugative transfer includes the
mobM
gene, which encodes the MobM relaxase, and the
cis
-acting origin of transfer (
oriT
). MobM initiates transfer by cleavage of supercoiled pMV158 DNA at a specific dinucleotide within
oriT
. In the present work, we have performed a detailed transcriptional analysis to assess the role of MobM in the control of its own gene expression. By
in vivo
and
in vitro
approaches, we demonstrated that
mobM
transcription in
Escherichia coli
was mostly initiated from a promoter (
Pmob2
) different from the one (
Pmob1
) used in
Lactococcus lactis
. Whereas promoter
Pmob1
was embedded within the
oriT
sequence, promoter
Pmob2
was placed apart from but adjacent to
oriT
. Further, MobM was able to repress the expression of its own gene from both promoters. Given the promiscuity of pMV158, the organization of the
mobM
promoter region suggests a strategy of the plasmid to cope with different transcription machineries of the hosts it colonizes.
Mammalian-Transmissible H5N1 Influenza: the Dilemma of Dual-Use Research
Authors: Webster Robert G.
Published: February 2012

The National Science Advisory Board for Biosecurity (NSABB)’s recommendation to restrict publication of the details of the generation of mammalian-transmissible H5N1 influenza virus is unprecedented. Dual-use considerations indicated that the potential biosecurity risks of a transmissible H5N1 virus with a possible mortality of 50% in humans outweigh the substantial benefits of open and complete scientific exchange in this case, although the benefits include potential early detection strategies for H5N1 viruses with specific genetic markers and control strategies, including development of antivirals and vaccines. It is argued that both the funding agency (the National Institute of Allergy and Infectious Diseases) and the scientists were responding to societal needs and acted entirely responsibly. These studies usher in a new era for life sciences, compelling the research community to confront important decisions: under what conditions should such research be done? How can the principle of full release of information be balanced with the moral imperative to protect the public health?
Natural Competence Is a Major Mechanism for Horizontal DNA Transfer in the Oral Pathogen Porphyromonas gingivalis
Authors: Tribble Gena D. , Rigney Todd W. , Dao Doan-Hieu V. , Wong Cindy T. , Kerr Jennifer E. , Taylor Brendan E. , Pacha Sara , Kaplan Heidi B.
Published: February 2012

Porphyromonas gingivalis
is a Gram-negative anaerobe that resides exclusively in the human oral cavity. Long-term colonization by
P. gingivalis
requires the bacteria to evade host immune responses while adapting to the changing host physiology and alterations in the composition of the oral microflora. The genetic diversity of
P. gingivalis
appears to reflect the variability of its habitat; however, little is known about the molecular mechanisms generating this diversity. Previously, our research group established that chromosomal DNA transfer occurs between
P. gingivalis
strains. In this study, we examine the role of putative DNA transfer genes in conjugation and transformation and demonstrate that natural competence mediated by
comF
is the dominant form of chromosomal DNA transfer, with transfer by a conjugation-like mechanism playing a minor role. Our results reveal that natural competence mechanisms are present in multiple strains of
P. gingivalis
, and DNA uptake is not sensitive to DNA source or modification status. Furthermore, extracellular DNA was observed for the first time in
P. gingivalis
biofilms and is predicted to be the major DNA source for horizontal transfer and allelic exchange between strains. We propose that exchange of DNA in plaque biofilms by a transformation-like process is of major ecological importance in the survival and persistence of
P. gingivalis
in the challenging oral environment.

IMPORTANCE
P. gingivalis
colonizes the oral cavities of humans worldwide. The long-term persistence of these bacteria can lead to the development of chronic periodontitis and host morbidity associated with tooth loss.
P. gingivalis
is a genetically diverse species, and this variability is believed to contribute to its successful colonization and survival in diverse human hosts, as well as evasion of host immune defenses and immunization strategies. We establish here that natural competence is the major driving force behind
P. gingivalis
DNA exchange and that conjugative DNA transfer plays a minor role. Furthermore, we reveal for the first time the presence of extracellular DNA in
P. gingivalis
biofilms, which is most likely the source of DNA exchanged between strains within dental plaque. These studies expand our understanding of the mechanisms used by this important member of the human oral flora to transition its relationship with the host from a commensal to a pathogenic relationship.
Novel Transporter Required for Biogenesis of
cbb
3
-Type Cytochrome
c
Oxidase in Rhodobacter capsulatus
Authors: Ekici Seda , Yang Honghui , Koch Hans-Georg , Daldal Fevzi
Published: February 2012

The acquisition, delivery, and incorporation of metals into their respective metalloproteins are important cellular processes. These processes are tightly controlled in order to prevent exposure of cells to free-metal concentrations that could yield oxidative damage. Copper (Cu) is one such metal that is required as a cofactor in a variety of proteins. However, when present in excessive amounts, Cu is toxic due to its oxidative capability. Cytochrome
c
oxidases (Coxs) are among the metalloproteins whose assembly and activity require the presence of Cu in their catalytic subunits. In this study, we focused on the acquisition of Cu for incorporation into the heme-Cu binuclear center of the
cbb
3
-type Cox (
cbb
3
-Cox) in the facultative phototroph
Rhodobacter capsulatus
. Genetic screens identified a
cbb
3
-Cox defective mutant that requires Cu
2+
supplementation to produce an active
cbb
3
-Cox. Complementation of this mutant using wild-type genomic libraries unveiled a novel gene (
ccoA
) required for
cbb
3
-Cox biogenesis. In the absence of CcoA, the cellular Cu content decreases and
cbb
3
-Cox assembly and activity become defective. CcoA shows homology to major facilitator superfamily (MFS)-type transporter proteins. Members of this family are known to transport small solutes or drugs, but so far, no MFS protein has been implicated in
cbb
3
-Cox biogenesis. These findings provide novel insights into the maturation and assembly of membrane-integral metalloproteins and on a hitherto-unknown function(s) of MFS-type transporters in bacterial Cu acquisition.

IMPORTANCE
Biogenesis of energy-transducing membrane-integral enzymes, like the heme copper-containing cytochrome
c
oxidases, and the acquisition of transition metals, like copper, as their catalytic cofactors are vital processes for all cells. These widespread and well-controlled processes are poorly understood in all organisms, including bacteria. Defects in these processes lead to severe mitochondrial diseases in humans and poor crop yields in plants. In this study, using the facultative phototroph
Rhodobacter capsulatus
as a model organism, we report on the discovery of a novel major facilitator superfamily (MFS)-type transporter (CcoA) that affects cellular copper content and
cbb
3
-type cytochrome
c
oxidase production in bacteria.
Approach to the cardiac autopsy
Authors: Sheppard Mary N
Published: January 2012

This article deals with a detailed analysis of the dissection of the heart at autopsy. Since most of causes of death are cardiac it is essential that all pathologists are familiar with the approach to dissection of the heart, taking of blocks for histology and possible analysis of the conduction tissue.
The relationship between serum TSH and free T4 in older people: Figure 1
Authors: Clark Penny M , Holder Roger L , Haque Sayeed M , Hobbs F D Richard , Roberts Lesley M , Franklyn Jayne A
Published: January 2012

The frequency distribution of serum thyroid stimulating hormone (TSH) shows a skewed pattern that may change with age. The set point of the hypothalamic-pituitary-thyroid axis for an individual is thought to be genetically determined and has been described as a log-linear relationship of serum TSH to free thyroxine (T4); however, the validity of this hypothesis has yet to be established in older people. The aim of the study was to describe the relationship between serum TSH and free T4 in older people and define factors influencing this relationship. We conducted a cross-sectional, observational study of thyroid function in a community population of older subjects over 65 years of age. The relationship between serum TSH and free T4 was not linear as previously described, but is best described as a fourth-order polynomial. Both gender and smoking status affected the relationship. This suggests that more complex modelling is required when investigating the hypothalamic-pituitary-thyroid axis.
Accuracy of the revised 2010 TNM classification in predicting the prognosis of patients treated for renal cell cancer in the north east of England
Authors: Veeratterapillay R , Simren R , El-Sherif A , Johnson M I , Soomro N , Heer R
Published: January 2012

Background

The TNM classification for renal cell cancer (RCC) should accurately predict and assign prognostic information for patients. In this study the recent 2010 revision to the TNM classification was compared with the previous 2002 classification with regard to survival outcomes.

Methods

All patients having radical nephrectomy for RCC in the 5-year period 2004–8 at a tertiary referral centre were included. Pathological and radiological records were reviewed to identify TNM stage (2002 and 2010 classification) and survival data were captured.

Results

345 patients with RCC were identified. Based on the 2002 TNM staging system and using outcomes in T1 staged tumours as a baseline, statistically significant differences in disease-specific survival were noted between patients with T1 and T3b tumours (log rank p<0.001) but not between those with T1 and T3a tumours (p=0.33). However, when tumour stage was reassigned according to the 2010 classification, patients with T3a tumours were also found to do statistically worse than T1 staged disease (p<0.001).

Conclusion

In our cohort, the new 2010 TNM reclassification of T3 tumours showed better correlation with predicting worsening outcomes compared with localised disease.
Hereditary colorectal cancer diagnostics: morphological features of familial colorectal cancer type X versus Lynch syndrome
Authors: Klarskov Louise , Holck Susanne , Bernstein Inge , Nilbert Mef
Published: January 2012

Background

The hereditary non-polyposis colorectal cancer (HNPCC) subset of tumours can broadly be divided into tumours caused by an underlying mismatch-repair gene mutation, referred to as Lynch syndrome, and those that develop in families with similar patterns of heredity but without disease-predisposing germline mismatch repair mutations, referred to as familial colorectal cancer type X (FCCTX). Recognition of HNPCC-associated colorectal cancers is central since surveillance programmes effectively reduce morbidity and mortality. The characteristic morphological features linked to Lynch syndrome can aid in the identification of this subset, whereas the possibility to use morphological features as an indicator of FCCTX is uncertain.

Objective and methods

To perform a detailed morphological evaluation of HNPCC-associated colorectal cancers and demonstrate significant differences between tumours associated with FCCTX and Lynch syndrome.

Results

The morphological features associated with Lynch syndrome, that is, right-sided tumour location, poor differentiation, expansive growth pattern, tumour-infiltrating lymphocytes, peritumorous lymphocytes, Crohn-like reactions, and lack of dirty necrosis, were significantly less often observed in FCCTX tumours.

Discussion

The less typical morphology in FCCTX implies that family history of cancer needs to be taken into account since these tumours cannot readily be recognised based on histopathological features.
Current and future delivery of diagnostic electron microscopy in the UK: results of a national survey
Authors: de Haro Tracey , Furness Peter
Published: January 2012

Aims

Electron microscopy (EM) remains essential to delivering several specialist areas of diagnosis, especially the interpretation of native renal biopsies. However, there is anecdotal evidence of EM units struggling to survive, for a variety of reasons. The authors sought to obtain objective evidence of the extent and the causes of this problem.

Methods

An online survey was undertaken of Fellows of the Royal College of Pathologists who use EM in diagnosis.

Results

A significant number of EM units anticipate having to close and hence outsource their EM work in the coming years. Yet most existing units are working to full capacity and would be unable to take on the substantial amounts of extra work implied by other units outsourcing their needs. Equipment and staffing are identified by most EM units as the major barriers to growth and are also the main reasons cited for units facing potential closure.

Conclusions

In the current financial climate it seems unlikely that units will be willing to make the large investment in equipment and staff needed to take on extra work, unless they can be reasonably confident of an acceptable financial return as a result of increased external referral rates. The case is thus made for a degree of national coordination of the future provision of this specialist service, possibly through the National Commissioning Group or the new National Commissioning Board. Without this, the future of diagnostic EM services in the UK is uncertain. Its failure would pose a threat to good patient care.
EFFICIENTLY MATCHING FREQUENT PATTERNS BASED ON BITMAP INVERTED FILES BUILT FROM CLOSED ITEMSETS
Authors: QIAO MEI , ZHANG DEGAN
Published: February 2012

Online pattern matching has become an increasingly important method for utilizing the discovered frequent patterns to build various intelligent systems, and obviously it demands high pattern matching efficiency. Memory-based online pattern matching is a solution, but it requires a frequent pattern base with small storage size. The closed itemsets are a lossless and condensed representation of all frequent itemsets, however, their itemset format does not facilitate implementing efficient pattern matching. This paper proposes a novel method that builds the bitmap inverted file from the closed itemsets and uses it to substitute for the closed itemsets to perform pattern matching. The bitmap inverted files use bitmaps instead of the referential lists to keep the maps of frequent items in the closed itemsets, so as to reduce the storage size and promote the intersecting operation efficiency. In order to completely substitute for the closed itemsets in pattern matching, the bitmap inverted files also keep other information relevant to the closed itemsets, such as their supports and lengths. Experiments show that on dense datasets, the storage size of the bitmap inverted files is much smaller than that of the set of closed itemsets, and the pattern matching based on the bitmap inverted files resident in memory is orders of magnitude more efficient than that based on the closed itemsets.
COOPERATIVE KNOWLEDGE BASED PERCEPTUAL ANCHORING
Authors: DAOUTIS MARIOS , CORADESCHI SILVIA , LOUTFI AMY
Published: February 2012

In settings where heterogenous robotic systems interact with humans, information from the environment must be systematically captured, organized and maintained in time. In this work, we propose a model for connecting perceptual information to semantic information in a multi-agent setting. In particular, we present semantic cooperative perceptual anchoring, that captures collectively acquired perceptual information and connects it to semantically expressed commonsense knowledge. We describe how we implemented the proposed model in a smart environment, using different modern perceptual and knowledge representation techniques. We present the results of the system and investigate different scenarios in which we use the commonsense together with perceptual knowledge, for communication, reasoning and exchange of information.
OPTICALLY ADDRESSED SPATIAL LIGHT MODULATORS FOR 3D DISPLAY
Authors: COLLINGS N.
Published: February 2012

An optically addressed spatial light modulator (OASLM) records the image on a write beam and transfers it to a read beam. Some example application areas are: image transduction; optical correlation; adaptive optics; and optical neural networks. Current interest in OASLMs has been generated by the work of Qinetiq on 3D display. This work is based on Active tiling, where an image can be recorded in one part of the device and is memorised, whilst the remainder of the device is updated with images. This paper will explain this system and survey the technological alternatives for this application.
LINEAR AND NONLINEAR OPTICAL PROPERTIES OF GOLD NANOPARTICLES STABILIZED WITH POLYVINYL ALCOHOL
Authors: HARI MISHA , JOSEPH SANTHI ANI , BALAN NITHYAJA , MATHEW S  , KUMAR RAVI , MISHRA GIRIDHAR , YADHAV R. R. , RADHAKRISHNAN P. , NAMPOORI V. P. N.
Published: February 2012

The nonlinear optical absorption of gold nanoparticles dispersed in polyvinyl alcohol (Au:PVA) is investigated using open aperture Z-scan technique. Au :PVA nanocomposite material is synthesized by chemical method. The characterization of the material is done by UV/Vis absorption spectroscopy, transmission electron microscopy and X-ray diffractometry (XRD). It is observed that the nature of the nonlinear absorption depends on the excitation wavelength. The optical limiting capability of the sample is also demonstrated at a wavelength of 532 nm.
ALLEVIATING THE SPARSITY PROBLEM OF COLLABORATIVE FILTERING USING AN EFFICIENT ITERATIVE CLUSTERED PREDICTION TECHNIQUE
Authors: ABDELWAHAB AMIRA , SEKIYA HIROO , MATSUBA IKUO , HORIUCHI YASUO , KUROIWA SHINGO
Published: February 2012

Collaborative filtering (CF) is one of the most prevalent recommendation techniques, providing personalized recommendations to users based on their previously expressed preferences and those of other similar users. Although CF has been widely applied in various applications, its applicability is restricted due to the data sparsity, the data inadequateness of new users and new items (cold start problem), and the growth of both the number of users and items in the database (scalability problem). In this paper, we propose an efficient iterative clustered prediction technique to transform user-item sparse matrix to a dense one and overcome the scalability problem. In this technique, spectral clustering algorithm is utilized to optimize the neighborhood selection and group the data into users' and items' clusters. Then, both clustered user-based and clustered item-based approaches are aggregated to efficiently predict the unknown ratings. Our experiments on MovieLens and book-crossing data sets indicate substantial and consistent improvements in recommendations accuracy compared to the hybrid user-based and item-based approach without clustering, hybrid approach with k-means and singular value decomposition (SVD)-based CF. Furthermore, we demonstrated the effectiveness of the proposed iterative technique and proved its performance through a varying number of iterations.
AN INTEGRATED STRATEGIC APPROACH TO SUPPLIER EVALUATION AND SELECTION
Authors: KHORRAMSHAHGOL REZA
Published: February 2012

This paper, using goal programming (GP) and the analytic hierarchy process (AHP), proposes an integrated methodology to aid decision makers in (1) evaluating, screening and selecting best suppliers from among an exhaustive list of available suppliers and (2) determining the amount to be purchased from the selected suppliers. Along the supply chain, the suppliers, by being situated at the upstream of the chain, play a crucial role in successful management of the entire (subsequent) members of the chain and can have a significant impact on the efficiency and effectiveness of the activities of the rest of the chain, and ultimately, on the delivery of the desired products/services. Thus supplier selection can certainly contribute greatly to a firm's competitive advantage and its organizational success. This study suggests a screening and evaluation method, named supplier priority index matrix, to eliminate the least qualified suppliers and to choose the most promising ones. The remaining potential suppliers are evaluated and the best are selected from among them. Finally the AHP and GP are used to allocate the firm's total supplies among the chosen/selected suppliers.
Adiponectin promoter activator NP-1 reduces body weight and hepatic steatosis in high-fat diet-fed animals
Authors: Serrano Antonia , Pavón Francisco J. , Suarez Juan , Rivera Patricia , Vida Margarita , Bermúdez-Silva Francisco J. , Alonso Mónica , Martínez Ana , López-Ogalla Javier , Alonso-Gascón Mercedes , Santamaría Gema , Romero-Cuevas Miguel , Pérez-Valero Vidal , Baixeras Elena , Rodríguez de Fonseca Fernando
Published: February 2012

Enhancement of adiponectin level has been shown to have beneficial effects, including antiobesity, antidiabetic, and hepatoprotective effects. This evidence supports the therapeutic utility of adiponectin in complicated obesity. The present study characterized the in vivo effects of sustained adiponectin release by NP-1, a new class of thiazol derivative that increases adiponectin levels. Acute administration of NP-1 reduced feeding, increased plasma adiponectin, and improved insulin sensitivity without inducing malaise, as revealed by conditioned taste aversion studies. Short-term (7 days) treatment with NP-1 also reduced feeding and body weight gain and increased phosphorylation of AMPK in muscle, a main intracellular effector of adiponectin. NP-1 was also evaluated in diet-induced obesity, and adult male Wistar rats were fed two different types of diet: a standard high-carbohydrate/low-fat diet (SD) and a high-fat diet (HFD). Once obesity was established, animals were treated daily with NP-1 (5 mg/kg) for 14 consecutive days. Chronic NP-1 induced body weight loss and reduction of food intake and resulted in both a marked decrease in liver steatosis and an improvement of biochemical indexes of liver damage in HFD-fed rats. However, a marked induction of tolerance in adiponectin gene transcription and release was observed after chronic NP-1 with respect to the acute actions of this drug. The present results support the role of adiponectin signaling in diet-induced obesity and set in place a potential use of compounds able to induce adiponectin release for the treatment of obesity and nonalcoholic fatty liver, with the limits imposed by the induction of pharmacological tolerance.