bluuebunny/crossref_metadata_2025 huggingface dataset:
15‐Deoxy‐Δ12,14‐prostaglandin J2Induces Upregulation of Multidrug Resistance‐Associated Protein 1 via Nrf2 Activation in Human Breast Cancer Cells
Authors: Song Na‐Young , Kim Do‐Hee , Kim Eun‐Hee , Na Hye‐Kyung , Surh Young‐Joon
Published: August 2009

15‐Deoxy‐Δ12,14‐prostaglandin J2(15d‐PGJ2), a representative J‐series cyclopentenone prostaglandin, exerts cytoprotective effects that are mainly mediated by Nrf2. Nrf2 is a major transcription factor involved in the transactivation of genes encoding many phase 2 detoxifying and antioxidant enzymes via interaction with the antioxidant response element (ARE). Recently it has been reported that expression of phase 3 efflux transporters, such as multidrug resistance‐associated proteins (MRPs), is also regulated by Nrf2. It is well known that cancer cells overexpressing MRPs are more resistant to anticancer drugs. In the present study we have found that 15d‐PGJ2induces the expression of MRP1, one of the phase 3 efflux transporters, in human breast cancer cells (MCF‐7). In addition, treatment of MCF‐7 cells with 15d‐PGJ2resulted in nuclear translocation and DNA binding of Nrf2. In contrast to 15d‐PGJ2, 9,10‐dihydro‐15d‐PGJ2, an analogue of 15d‐PGJ2that lacks an electrophilic cyclopentenone ring moiety, failed to induce not only Nrf2 activation but also MRP1 upregulation in MCF‐7 cells. 15d‐PGJ2‐induced MRP1 overexpression was abrogated by Nrf2 gene knockdown, using RNA interference. These results, taken together, suggest that 15d‐PGJ2induces MRP1 upregulation via Nrf2–ARE signaling.
Bile Acids Initiate Lineage‐Addicted Gastroesophageal Tumorigenesis by Suppressing the EGF Receptor‐AKT Axis
Authors: Gong Li , Debruyne Philip R. , Witek Matthew , Nielsen Karl , Snook Adam , Lin Jieru E. , Bombonati Alessandro , Palazzo Juan , Schulz Stephanie , Waldman Scott A.
Published: August 2009

While bile acids are a risk factor for tumorigenesis induced by reflux disease, the mechanisms by which they contribute to neoplasia remain undefined. Here, we reveal that in gastroesophageal junction (GEJ) cells bile acids activate a tissue‐specific developmental program defining the intestinal epithelial cell phenotype characterizing GEJ metaplasia. Deoxycholic acid (DCA) inhibited phosphorylation of EGF receptors (EGFRs) suppressing the proto‐oncogene AKT. Suppression of EGFRs and AKT by DCA actuated an intestine‐specific cascade in which NF‐κB transactivated the tissue‐specifi c transcription factor CDX2. In turn, CDX2 orchestrated a lineage‐specific differentiation program encompassing genes characterizing intestinal epithelial cells. Conversely, progression from metaplasia to invasive carcinoma in patients, universally associated with autonomous activation of EGFRs and/or AKT, was coupled with loss of this intestinal program. Thus, bile acids induce intestinal metaplasia at the GEJ by activating the lineage‐specifi c differentiation program involving suppression of EGFR and AKT, activating the NF‐κB‐CDX2 axis. Induction of this axis provides the context for lineage‐addicted tumorigenesis, in which autonomous activation of AKT corrupts adaptive intestinal NF‐κB signaling, amplifying tumorigenic programs.
Islet cell transplantation for Type 1 diabetes
Authors: MATSUMOTO Shinichi
Published: August 2009

Islet transplantation is an attractive concept for the treatment of Type 1 diabetes because of its potential high efficacy and minimal invasion to patients. The treatment may effectively control blood glucose for brittle Type 1 diabetes, resulting in a marked reduction in hypoglycemic episodes and improvements in HbA1c. In addition, approximately 70% of transplanted Type 1 diabetic patients have achieved insulin independence. However, there are still important issues to be addressed before this treatment is widely applicable, including difficulty in maintaining insulin independence, low islet isolation success rate, multiple donor requirements, and side effects associated with the use of immunosuppressants. Donor shortage is another dilemma. To address the issue of donor shortage, living donor islet transplantation and bioartificial islet transplantation using pig islets are being evaluated. Bioartificial islet transplantation could be the ultimate solution of the donor shortage. Currently, overcoming immunological hurdles, establishing reliable islet isolation methods, and controlling porcine endogenous retrovirus are the primary obstacles to the implementation of this treatment. If bioartificial islet transplant becomes a clinical reality, it may even be applicable in the treatment of select Type 2 diabetic patients. β‐Cell regeneration from naïve pancreas and β‐cell generation from embryonic stem cells or induced pluripotent stem cells are the next‐generation treatments for Type 1 diabetes.
Return to Sport following Arthroscopic Shoulder Stabilization
Authors: Murray Iain R , McBirnie Julie
Published: August 2009

Background

Arthroscopic shoulder stabilization for anterior instability should enable athletes to return to their full pre-injury level of sport.

Methods

We reviewed case notes and sent postal questionnaires to establish the recurrent instability rate and also the rate of return to sport in athletes after surgery.

Results

In 120 procedures, surgery achieved successful stabilization in 88%, but only 51% returned to full sporting activity. Patients aged 30 years or under were twice as likely to return to their pre-injury level of sport than those aged over 30 years. Half of those patients who did not return to sport had no subjective symptoms of instability but were inhibited by fear of further injury alone. Successful stabilization of the shoulder did not always translate into the desired outcome.

Conclusion

In order to increase the number of athletes returning to sport following primary arthroscopic stabilization of the shoulder, those patients with no restrictive symptoms should be encouraged to return to full activity. We plan to tailor rehabilitation to the specific needs of individual patients and now feel better able to inform athletes deciding on surgery.
The CAAT‐binding transcription factor 1/nuclear factor 1 binding site is important in β‐myosin heavy chain antisense promoter regulation in rats
Authors: Giger Julia M. , Bodell Paul W. , Baldwin Kenneth M. , Haddad Fadia
Published: August 2009

The rat heart expresses two myosin heavy chain (MHC) isoforms, β and α; these genes are arranged in tandem on the same chromosome. We have reported that an antisense (AS) β RNA starts in the intergenic (IG) region between β and α genes and extends to overlap the β gene. We propose that in adult rats, both the α sense and IG βAS RNA expression are activated by an IG bidirectional promoter and that the transcription of βAS RNA interferes with the sense β, resulting in low levels of β mRNA and high levels of α, a phenotype seen in a typical rat heart. A previous report examined the activity of the βAS promoter and showed that a 559 bp fragment of the βAS promoter (–2285 to –1726; relative to αMHC gene start site) injected into rat ventricle was activated in control heart, and decreased significantly in response to hypothyroidism (propylthiouracil induced) and diabetes (streptozotocin induced) and increased in hyperthyroid rats (T3 induced), similar in pattern to the endogenous βAS RNA. In the present paper, we demonstrate with electrophoretic mobility shift analyses that ventricular nuclear proteins are interacting with a nuclear factor 1/CAAT‐binding transcription factor 1 (NF1/CTF1) binding site, and a supershift assay indicates that the protein binding at this site is antigenetically related to the CTF1/NF1 factor. Moreover, a mutation of the CTF1/NF1 site within the 559 bp promoter region nearly abolished promoter activity in vivo in control, STZ‐ and PTU‐treated rats. Based on these findings, we conclude that the NF1 site is critical to βAS promoter regulation.
Aeromonas hydrophila
AH-3 Type III Secretion System Expression and Regulatory Network
Authors: Vilches Silvia , Jimenez Natalia , Tomás Juan M. , Merino Susana
Published: August 2009

The
Aeromonas hydrophila
type III secretion system (T3SS) has been shown to play a crucial role in this pathogen's interactions with its host. We previously described the genetic organization of the T3SS cluster and the existence of at least one effector, called AexT, in
A. hydrophila
strain AH-3. In this study, we analyzed the expression of the T3SS regulon by analyzing the activity of the
aopN-aopD
and
aexT
promoters (T3SS machinery components and effector, respectively) by means of two different techniques: promoterless
gfp
fusions and real-time PCR. The expression of the
A. hydrophila
AH-3 T3SS regulon was induced in response to several environmental factors, of which calcium depletion, a high magnesium concentration, and a high growth temperature were shown to be the major ones. Once the optimal conditions were established, we tested the expression of the T3SS regulon in the background of several virulence determinant knockouts of strain AH-3. The analysis of the data obtained from
axsA
and
aopN
mutants, both of which have been described to be T3SS regulators in other species, allowed us to corroborate their function as the major transcription regulator and valve of the T3SS, respectively, in
Aeromonas hydrophila
. We also demonstrated the existence of a complicated interconnection between the expression of the T3SS and several other different virulence factors, such as the lipopolysaccharide, the PhoPQ two-component system, the
ahyIR
quorum sensing system, and the enzymatic complex pyruvate deshydrogenase. To our knowledge, this is the first study of the
A. hydrophila
T3SS regulatory network.
Serogroup, Virulence, and Genetic Traits of
Vibrio parahaemolyticus
in the Estuarine Ecosystem of Bangladesh
Authors: Alam Munirul , Chowdhury Wasimul B. , Bhuiyan N. A. , Islam Atiqul , Hasan Nur A. , Nair G. Balakrish , Watanabe H. , Siddique A. K. , Huq Anwar , Sack R. Bradley , Akhter M. Z. , Grim Christopher J. , Kam K.-M. , Luey C. K. Y. , Endtz Hubert P. , Cravioto Alejandro , Colwell Rita R.
Published: August 2009

Forty-two strains of
Vibrio parahaemolyticus
were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes
tox
R
and
tlh
were confirmed by PCR in all but two strains, which also lacked
tox
R
. A total of 18 (41%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (
trh
) gene, but not
tdh
. Ten (23%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed
tdh
. Of the 18
tdh
-positive strains, 17 (94%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single
trh
-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., “clonal cluster,” as did pandemic strains of diverse origin. The demonstrated prevalence of
tdh
-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.
Inhibition of Nitrate Reduction by Chromium(VI) in Anaerobic Soil Microcosms
Authors: Kourtev Peter S. , Nakatsu Cindy H. , Konopka Allan
Published: August 2009

Chromium is often found as a cocontaminant at sites polluted with organic compounds. For nitrate-respiring microbes, Cr(VI) may be not only directly toxic but may also specifically interfere with N reduction. In soil microcosms amended with organic electron donors, Cr(VI), and nitrate, bacteria oxidized added carbon, but relatively low doses of Cr(VI) caused a lag and then lower rates of CO
2
accumulation. Cr(VI) strongly inhibited nitrate reduction; it occurred only after soluble Cr(VI) could not be detected. However, Cr(VI) additions did not eliminate Cr-sensitive populations; after a second dose of Cr(VI), bacterial activity was strongly inhibited. Differences in microbial community composition (assayed by PCR-denaturing gradient gel electrophoresis) driven by different organic substrates (glucose and protein) were smaller than when other electron acceptors had been used. However, the selection of bacterial phylotypes was modified by Cr(VI). Nine isolated clades of facultatively anaerobic Cr(VI)-resistant bacteria were closely related to cultivated members of the phylum
Actinobacteria
or
Firmicutes
. In
Bacillus cereus
GNCR-4, the nature of the electron donor (fermentable or nonfermentable) affected Cr(VI) resistance level and anaerobic nitrate metabolism. Our results indicate that carbon utilization and nitrate reduction in these soils were contingent upon the reduction of added Cr(VI). The amount of Cr(VI) required to inhibit nitrate reduction was 10-fold less than for aerobic catabolism of the same organic substrate. We speculate that the resistance level of a microbial process is directly related to the diversity of microbes capable of conducting it.
Molecular Analysis of Virulence Profiles and Shiga Toxin Genes in Food-Borne Shiga Toxin-Producing
Escherichia coli
Authors: Slanec T. , Fruth A. , Creuzburg K. , Schmidt H.
Published: August 2009

In this study, 75 Shiga toxin (Stx)-producing
Escherichia coli
(STEC) strains originating from foods (
n
= 73) and drinking water (
n
= 2) were analyzed for their
stx
genotype, as well as for further chromosome-, phage-, and plasmid-encoded virulence factors. A broad spectrum of
stx
genes was detected. Fifty-three strains (70.7%) contained
stx
2
or
stx
2
variants, including
stx
2d
, mucus-activatable
stx
2d
,
stx
2e
, and
stx
2g
. Seven strains (9.3%) harbored
stx
1
or
stx
1c
, and 15 strains (20.0%) carried both
stx
2
and/or
stx
2
variants and
stx
1
or
stx
1c
. Beside
stx
, the most abundant accessory virulence markers in STEC food isolates were
iha
(57.3%),
ehxA
(40.0%),
espP
(28.0%), and
subAB
(25.3%). Only four strains were
eae
positive; three of these belonged to the serogroups O26, O103, and O157 and contained a typical enterohemorrhagic
E. coli
virulence spectrum. The results of this study show that a number of STEC strains that occur in foods appear to be pathogenic for humans, based on their virulence profiles. Analysis of
stx
subtypes and detection of additional virulence factors in
eae
-negative strains may help to better assess the risk of such strains for causing human infection.
Neurotoxin Gene Clusters in
Clostridium botulinum
Type Ab Strains
Authors: Lúquez Carolina , Raphael Brian H. , Maslanka Susan E.
Published: August 2009

There is limited knowledge of the neurotoxin gene diversity among
Clostridium botulinum
type Ab strains. Only the sequences of the
bont/A
and
bont/B
genes in
C. botulinum
type Ab strain CDC1436 and the sequence of the
bont/B
gene in
C. botulinum
type Ab strain CDC588 have been reported. In this study, we sequenced the entire
bont/A
- and
bont/B
-associated neurotoxin gene clusters of
C. botulinum
type Ab strain CDC41370 and the
bont/A
gene of strain CDC588. In addition, we analyzed the organization of the neurotoxin gene clusters in strains CDC588 and CDC1436. The
bont/A
nucleotide sequence of strain CDC41370 differed from those of the known
bont/A
subtypes A1 to A4 by 2 to 7%, and the predicted amino acid sequence differed by 4% to 14%. The
bont/B
nucleotide sequence in strain CDC41370 showed 99.7% identity to the sequence of subtype B1. The
bont/A
nucleotide sequence of strain CDC588 was 99.9% identical to that of subtype A1. Although all of the
C. botulinum
type Ab strains analyzed contained the two sets of neurotoxin clusters, similar to what has been found in other bivalent strains, the intergenic spacing of
p21
-
orfX1
and
orfX2
-
orfX3
varied among these strains. The type Ab strains examined in this study had differences in their toxin gene cluster compositions and
bont/A
and
bont
/B
nucleotide sequences, suggesting that they may have arisen from separate recombination events.
Survival of
Lactobacillus reuteri
DSM 17938 and
Lactobacillus rhamnosus
GG in the Human Gastrointestinal Tract with Daily Consumption of a Low-Fat Probiotic Spread
Authors: Dommels Yvonne E. M. , Kemperman Robèr A. , Zebregs Yvonne E. M. P. , Draaisma René B. , Jol Arne , Wolvers Danielle A. W. , Vaughan Elaine E. , Albers Ruud
Published: August 2009

Probiotics are live microorganisms which, when administered in adequate amounts, confer a health benefit on the host. Therefore, probiotic strains should be able to survive passage through the human gastrointestinal tract. Human gastrointestinal tract survival of probiotics in a low-fat spread matrix has, however, never been tested. The objective of this randomized, double-blind, placebo-controlled human intervention study was to test the human gastrointestinal tract survival of
Lactobacillus reuteri
DSM 17938 and
Lactobacillus rhamnosus
GG after daily consumption of a low-fat probiotic spread by using traditional culturing, as well as molecular methods. Forty-two healthy human volunteers were randomly assigned to one of three treatment groups provided with 20 g of placebo spread (
n
= 13), 20 g of spread with a target dose of 1 × 10
9
CFU of
L. reuteri
DSM 17938 (
n
= 13), or 20 g of spread with a target dose of 5 × 10
9
CFU of
L. rhamnosus
GG (
n
= 16) daily for 3 weeks. Fecal samples were obtained before and after the intervention period. A significant increase, compared to the baseline, in the recovery of viable probiotic lactobacilli in fecal samples was demonstrated after 3 weeks of daily consumption of the spread containing either
L. reuteri
DSM 17938 or
L. rhamnosus
GG by selective enumeration. In the placebo group, no increase was detected. The results of selective enumeration were supported by quantitative PCR, detecting a significant increase in DNA resulting from the probiotics after intervention. Overall, our results indicate for the first time that low-fat spread is a suitable carrier for these probiotic strains.
Cytoplasmic Bulk Flow Propels Nuclei in Mature Hyphae of
Neurospora crassa
Authors: Ramos-García Silvia L. , Roberson Robert W. , Freitag Michael , Bartnicki-García Salomón , Mouriño-Pérez Rosa R.
Published: August 2009

We used confocal microscopy to evaluate nuclear dynamics in mature, growing hyphae of
Neurospora crassa
whose nuclei expressed histone H1-tagged green fluorescent protein (GFP). In addition to the H1-GFP wild-type (WT) strain, we examined nuclear displacement (passive transport) in four mutants deficient in microtubule-related motor proteins (
ro-1
,
ro-3
,
kin-1
, and a
ro-1 kin-1
double mutant). We also treated the WT strain with benomyl and cytochalasin A to disrupt microtubules and actin microfilaments, respectively. We found that the degree of nuclear displacement in the subapical regions of all strains correlated with hyphal elongation rate. The WT strain and that the
ro-1 kin-1
double mutant showed the highest correlation between nuclear movement and hyphal elongation. Although most nuclei seemed to move forward passively, presumably carried by the cytoplasmic bulk flow, a small proportion of the movement detected was either retrograde or accelerated anterograde. The absence of a specific microtubule motor in the mutants
ro-1
,
ro-3
, or
kin-1
did not prevent the anterograde and retrograde migration of nuclei; however, in the
ro-1 kin-1
double mutant retrograde migration was absent. In the WT strain, almost all nuclei were elongated, whereas in all other strains a majority of nuclei were nearly spherical. With only one exception, a sizable exclusion zone was maintained between the apex and the leading nucleus. The
ro-1
mutant showed the largest nucleus exclusion zone; only the treatment with cytochalasin A abolished the exclusion zone. In conclusion, the movement and distribution of nuclei in mature hyphae appear to be determined by a combination of forces, with cytoplasmic bulk flow being a major determinant. Motor proteins probably play an active role in powering the retrograde or accelerated anterograde migrations of nuclei and may also contribute to passive anterograde displacement by binding nuclei to microtubules.
Dual Acylation Accounts for the Localization of α19-Giardin in the Ventral Flagellum Pair of
Giardia lamblia
Authors: Šarić Mirela , Vahrmann Anke , Niebur Daniela , Kluempers Verena , Hehl Adrian B. , Scholze Henning
Published: August 2009

A
Giardia
-specific protein family denominated as α-giardins, represents the major protein component, besides tubulin, of the cytoskeleton of the human pathogenic parasite
Giardia lamblia
. One of its members, α19-giardin, carries an N-terminal sequence extension of MGCXXS, which in many proteins serves as a target for dual lipid conjugation: myristoylation at the glycine residue after removal of the methionine and palmitoylation at the cysteine residue. As the first experimental evidence of a lipid modification, we found α19-giardin to be associated with the membrane fraction of disrupted trophozoites. After heterologous coexpression of α19-giardin with giardial
N
-myristoyltransferase (NMT) in
E
scherichia coli
, we found the protein in a myristoylated form. Additionally, after heterologous expression together with the palmitoyl transferase Pfa3 in
Saccharomyces cerevisiae
, α19-giardin associates with the membrane of the main vacuole. Immunocytochemical colocalization studies on wild-type
Giardia
trophozoites with tubulin provide evidence that α19-giardin exclusively localizes to the ventral pair of the giardial flagella. A mutant in which the putatively myristoylated N-terminal glycine residue was replaced by alanine lost this specific localization. Our findings suggest that the dual lipidation of α19-giardin is responsible for its specific flagellar localization.
Capsular Polysaccharide Production in
Enterococcus faecalis
and Contribution of CpsF to Capsule Serospecificity
Authors: Thurlow Lance R. , Thomas Vinai Chittezham , Hancock Lynn E.
Published: August 2009

Many bacterial species produce capsular polysaccharides that contribute to pathogenesis through evasion of the host innate immune system. The gram-positive pathogen
Enterococcus faecalis
was previously reported to produce one of four capsule serotypes (A, B, C, or D). Previous studies describing the four capsule serotypes of
E. faecalis
were based on immunodetection methods; however, the underlying genetics of capsule production did not fully support these findings. Previously, it was shown that capsule production for serotype C (Maekawa type 2) was dependent on the presence of nine open reading frames (
cpsC
to
cpsK
). Using a novel genetic system, we demonstrated that seven of the nine genes in the
cps
operon are essential for capsule production, indicating that serotypes A and B do not make a capsular polysaccharide. In support of this observation, we showed that serotype C and D capsule polysaccharides mask lipoteichoic acid from detection by agglutinating antibodies. Furthermore, we determined that the genetic basis for the difference in antigenicity between serotypes C and D is the presence of
cpsF
in serotype C strains. High-pH anion-exchange chromatography with pulsed amperometric detection analysis of serotype C and D capsules indicated that
cpsF
is responsible for glucosylation of serotype C capsular polysaccharide in
E. faecalis
.
The Uracil DNA Glycosylase UdgB ofMycobacterium smegmatisProtects the Organism from the Mutagenic Effects of Cytosine and Adenine Deamination
Authors: Wanner Roger M. , Castor Dennis , Güthlein Carolin , Böttger Erik C. , Springer Burkhard , Jiricny Josef
Published: August 2009

Spontaneous hydrolytic deamination of DNA bases represents a considerable mutagenic threat to all organisms, particularly those living in extreme habitats. Cytosine is readily deaminated to uracil, which base pairs with adenine during replication, and most organisms encode at least one uracil DNA glycosylase (UDG) that removes this aberrant base from DNA with high efficiency. Adenine deaminates to hypoxanthine approximately 10-fold less efficiently, and its removal from DNA in vivo has to date been reported to be mediated solely by alkyladenine DNA glycosylase. We previously showed that UdgB fromPyrobaculum aerophilum, a hyperthermophilic crenarchaeon, can excise hypoxanthine from oligonucleotide substrates, but as this organism is not amenable to genetic manipulation, we were unable to ascertain that the enzyme also has this role in vivo. In the present study, we show that UdgB fromMycobacterium smegmatisprotects this organism against mutagenesis associated with deamination of both cytosine and adenine. Together with Ung-type uracil glycosylase,M. smegmatisUdgB also helps attenuate the cytotoxicity of the antimicrobial agent 5-fluorouracil.
tIS
Cpe8
, an IS
1595
-Family Lincomycin Resistance Element Located on a Conjugative Plasmid in
Clostridium perfringens
Authors: Lyras Dena , Adams Vicki , Ballard Susan A. , Teng Wee L. , Howarth Pauline M. , Crellin Paul K. , Bannam Trudi L. , Songer J. Glenn , Rood Julian I.
Published: August 2009

Clostridium perfringens
is a normal gastrointestinal organism that is a reservoir for antibiotic resistance genes and can potentially act as a source from which mobile elements and their associated resistance determinants can be transferred to other bacterial pathogens. Lincomycin resistance in
C. perfringens
is common and is usually encoded by
erm
genes that confer macrolide-lincosamide-streptogramin B resistance. In this study we identified strains that are lincomycin resistant but erythromycin sensitive and showed that the lincomycin resistance determinant was plasmid borne and could be transferred to other
C. perfringens
isolates by conjugation. The plasmid, pJIR2774, is the first conjugative
C. perfringens
R-plasmid to be identified that does not confer tetracycline resistance. Further analysis showed that resistance was encoded by the
lnuP
gene, which encoded a putative lincosamide nucleotidyltransferase and was located on tIS
Cpe8
, a functional transposable genetic element that was a member of the IS
1595
family of transposon-like insertion sequences. This element had significant similarity to the mobilizable lincomycin resistance element tIS
Sag10
from
Streptococcus agalactiae
. Like tIS
Sag10
, tIS
Cpe8
carries a functional origin of transfer within the resistance gene, allowing the element to be mobilized by the conjugative transposon Tn
916
. The similarity of these elements and the finding that they both contain an
oriT
-like region support the hypothesis that conjugation may result in the movement of DNA modules that are not obviously mobile since they are not linked to conjugation or mobilization functions. This process likely plays a significant role in bacterial adaptation and evolution.
Characterization of aMycobacterium tuberculosisESX-3 Conditional Mutant: Essentiality and Rescue by Iron and Zinc
Authors: Serafini Agnese , Boldrin Francesca , Palù Giorgio , Manganelli Riccardo
Published: August 2009

Recently, a novel type of secretory pathway, type VII secretion systems (T7SSs), has been characterized in mycobacteria. The chromosomes ofMycobacterium tuberculosisandMycobacterium bovisencode five T7SSs (ESX-1 to ESX-5). The best characterized of them, ESX-1, is involved in host-pathogen interactions, and its deletion is one of the main causes ofM. bovisBCG attenuation. Another T7SS, ESX-3, has been previously shown to be transcriptionally controlled by the zinc uptake repressor (Zur) and by the iron-dependent transcriptional repressor (IdeR), suggesting that it might be involved in zinc and iron homeostasis. In this study, we characterized anM. tuberculosisconditional mutant in which transcription of the ESX-3 gene cluster can be downregulated by anhydrotetracycline. We showed that this T7SS is essential for growth and that this phenotype can be complemented by zinc, iron, or supernatant from a wild-type parental strain culture, demonstrating that the ESX-3 secretion system is responsible for the secretion of some soluble factor(s) required for growth that is probably involved in optimal iron and zinc uptake.
Scavenging of Cytosolic Octanoic Acid by Mutant LplA Lipoate Ligases Allows Growth of
Escherichia coli
Strains Lacking the LipB Octanoyltransferase of Lipoic Acid Synthesis
Authors: Hermes Fatemah A. M. , Cronan John E.
Published: August 2009

The LipB octanoyltransferase catalyzes the first step of lipoic acid synthesis in
Escherichia coli
, transfer of the octanoyl moiety from octanoyl-acyl carrier protein to the lipoyl domains of the E2 subunits of the 2-oxoacid dehydrogenases of aerobic metabolism. Strains containing null mutations in
lipB
are auxotrophic for either lipoic acid or octanoic acid. We report the isolation of two spontaneously arising mutant strains that allow growth of
lipB
strains on glucose minimal medium; we determined that suppression was caused by single missense mutations within the coding sequence of the gene (
lplA
) that encodes lipoate-protein ligase. The LplA proteins encoded by the mutant genes have reduced

K
m

values for free octanoic acid and thus are able to scavenge cytosolic octanoic acid for octanoylation of lipoyl domains.
Synthetic Microcin C Analogs Targeting Different Aminoacyl-tRNA Synthetases
Authors: Van de Vijver Pieter , Vondenhoff Gaston H. M. , Kazakov Teymur S. , Semenova Ekaterina , Kuznedelov Konstantin , Metlitskaya Anastasia , Van Aerschot Arthur , Severinov Konstantin
Published: August 2009

Microcin C (McC) is a potent antibacterial agent produced by some strains of
E
scherichia coli
. McC consists of a ribosomally synthesized heptapeptide with a modified AMP attached through a phosphoramidate linkage to the α-carboxyl group of the terminal aspartate. McC is a Trojan horse inhibitor: it is actively taken inside sensitive cells and processed there, and the product of processing, a nonhydrolyzable aspartyl-adenylate, inhibits translation by preventing aminoacylation of tRNA
Asp
by aspartyl-tRNA synthetase (AspRS). Changing the last residue of the McC peptide should result in antibacterial compounds with targets other than AspRS. However, mutations that introduce amino acid substitutions in the last position of the McC peptide abolish McC production. Here, we report total chemical synthesis of three McC-like compounds containing a terminal aspartate, glutamate, or leucine attached to adenosine through a nonhydrolyzable sulfamoyl bond. We show that all three compounds function in a manner similar to that of McC, but the first compound inhibits bacterial growth by targeting AspRS while the latter two inhibit, respectively, GluRS and LeuRS. Our approach opens a way for creation of new antibacterial Trojan horse agents that target any 1 of the 20 tRNA synthetases in the cell.
Comparative Biology of Two Natural Variants of the IncQ-2 Family Plasmids, pRAS3.1 and pRAS3.2
Authors: Loftie-Eaton Wesley , Rawlings Douglas E.
Published: August 2009

Plasmids pRAS3.1 and pRAS3.2 are two closely related, natural variants of the IncQ-2 plasmid family that have identical plasmid backbones except for two differences. Plasmid pRAS3.1 has five 6-bp repeat sequences in the promoter region of themobBgene and four 22-bp iterons in itsoriVregion, whereas pRAS3.2 has only four 6-bp repeats and three 22-bp iterons. Plasmid pRAS3.1 was found to have a higher copy number than pRAS3.2, and we show that the extra 6-bp repeat results in an increase inmobBand downstreammobA/repBexpression. Placement ofrepB(primase) behind an arabinose-inducible promoter intransresulted in an increase inrepBexpression and an approximately twofold increase in the copy number of plasmids with identical numbers of 22-bp iterons. The pRAS3 plasmids were shown to have a previously unrecognized toxin-antitoxin plasmid stability module within their replicons. The ability of the pRAS3 plasmids to mobilize theoriTregions of two other plasmids of the IncQ-2 family, pTF-FC2 and pTC-F14, suggested that the mobilization proteins pRAS3 are relaxed and can mobilizeoriTregions with substantially different sequences. Plasmids pRAS3.1 and pRAS3.2 were highly incompatible with plasmids pTF-FC2 and pTC-F14, and this incompatibility was removed on inactivation of an open reading frame situated downstream of themobCDEmobilization genes rather than being due to the 22-bporiV-associated iterons. We propose that the pRAS3 plasmids represent a third, γ incompatibility group within the IncQ-2 family plasmids.
Characterization of Hydrogen Peroxide-Induced DNA Release by
Streptococcus sanguinis
and
Streptococcus gordonii
Authors: Kreth Jens , Vu Hung , Zhang Yongshu , Herzberg Mark C.
Published: August 2009

Extracellular DNA (eDNA) is produced by several bacterial species and appears to contribute to biofilm development and cell-cell adhesion. We present data showing that the oral commensals
Streptococcus sanguinis
and
Streptococcus gordonii
release DNA in a process induced by pyruvate oxidase-dependent production of hydrogen peroxide (H
2
O
2
). Surprisingly,
S. sanguinis
and
S. gordonii
cell integrity appears unaffected by conditions that cause autolysis in other eDNA-producing bacteria. Exogenous H
2
O
2
causes release of DNA from
S. sanguinis
and
S. gordonii
but does not result in obvious lysis of cells. Under DNA-releasing conditions, cell walls appear functionally intact and ribosomes are retained over time. During DNA release, intracellular RNA and ATP are not coreleased. Hence, the release mechanism appears to be highly specific for DNA. Release of DNA without detectable autolysis is suggested to be an adaptation to the competitive oral biofilm environment, where autolysis could create open spaces for competitors to invade. Since eDNA promotes cell-to-cell adhesion, release appears to support oral biofilm formation and facilitates exchange of genetic material among competent strains.
Rbf Promotes Biofilm Formation byStaphylococcus aureusvia Repression oficaR, a Negative Regulator oficaADBC
Authors: Cue David , Lei Mei G. , Luong Thanh T. , Kuechenmeister Lisa , Dunman Paul M. , O'Donnell Sinead , Rowe Sarah , O'Gara James P. , Lee Chia Y.
Published: August 2009

We previously reported the identification of a gene,rbf, involved in the regulation of biofilm formation byStaphylococcus aureus8325-4. In an effort to study the mechanism of regulation, microarrays were used to compare the transcription profiles of the wild-type strain with anrbfmutant and anrbfoverexpression strain of the clinical isolate UAMS-1. Among the genes affected byrbfoverexpression are those of the intercellular adhesion (ica) locus; however, expression of these genes was not affected by anrbfdeletion in the chromosome. TheicaADBCgenes are responsible for production of poly-N-acetylglucosamine (PNAG), a major constituent of biofilm. TheicaRgene encodes a negative regulator oficaADBC. In UAMS-1 carrying an Rbf-encoding plasmid, Rbf was found to repressicaRtranscription with a concomitant increase inicaADBCexpression and increased PNAG and biofilm production relative to isogenic strains lacking the plasmid. Sequencing of therbfgene from UAMS-1 showed that there was a 2-bp insertion affecting the 50th codon of therbfopen reading frame, suggesting thatrbfis a pseudogene in UAMS-1. This finding explains why deletion ofrbfhad no effect on biofilm formation in UAMS-1. To further characterize the Rbf regulation on biofilm we compared biofilm formation,icaAandicaRtranscription, and PNAG production in 8325-4 and its isogenicrbfandicaRsingle mutants and anrbf icaRdouble mutant. Our results are consistent with a model whereinrbfrepresses synthesis oficaR, which in turn results in derepression oficaADBCand increased PNAG production. Furthermore, purifiedrbfdid not bind to theicaRoricaApromoter region, suggesting thatrbfcontrols expression of an unknown factor(s) that repressesicaR. The role ofrbfin controlling theS. aureusbiofilm phenotype was further demonstrated in a clinical strain, MW2.
An age-independent individual tree height prediction model for boreal spruce–aspen stands in Alberta
Authors: Huang Shongming , Titus Stephen J.
Published: August 2009

This study presents an individual tree height prediction model for white spruce (Piceaglauca (Moench) Voss) and trembling aspen (Populustremuloides Michx.) grown in boreal mixed-species stands in Alberta. The model is based on a three-parameter Chapman–Richards function fitted to data from 164 permanent sample plots using the parameter prediction method. It is age independent and expresses tree height as a function of tree diameter, tree basal area, stand density, species composition, site productivity, and stand average diameter. This height-prediction model was fitted by weighted nonlinear regression for spruce and unweighted nonlinear regression for aspen. Almost all estimates of parameters were significant at α = 0.05 and model R2-values were high (0.9192 for white spruce and 0.9087 for aspen). No consistent underestimate or overestimate of tree heights was evident in plots of studentized residuals against predicted heights. The model was also tested on an independent data set representing the population on which the model was to be used. Results showed that the average prediction biases were not significant at α = 0.05 for either species, indicating that the model appropriately described the data and performed well when predictions were made.
Relative stocking index: a proposed index of site quality
Authors: Berguson William E. , Grigal David F. , Bates Peter C.
Published: August 2009

Site index is difficult to implement and interpret in multispecies, multiple-aged stands, and its relationship to site factors is obscure. Using data from the USDA forest inventory and analysis (FIA) for the Lake States, we developed log-log relationships between mean tree size and stand density for five cover types. Fits were good, with r2 from 0.96 to 0.98 and slopes from −0.948 to −0.995. We define an alternative index of site quality, the relative stocking index (RSI), as the ratio of a stand's measured density to that predicted using the log–log relationship for its cover type (the norm). We divided the range of RSI into three classes for each type (<0.9 of norm, >0.91 but <1.1 of norm, and >1.1 of norm). Based on analyses of the 1977 and 1990 FIA data from Minnesota, class assignments for individual stands remained constant over that 13-year period. Relationships between site factors and either RSI classes or analogous classes based on site index were examined in a subset of 169 stands. Temperature, precipitation, silt content of surface soil, and calculated annual water deficit all differed significantly among RSI classes, but not among site-index classes. The RSI is easy to apply, robust (resistant to change), and related to site factors. It merits additional examination as an index of site quality, especially in heterogenous stands.
Geostatistically modeling stem size and increment in an old-growth forest
Authors: Biondi Franco , Myers Donald E. , Avery Charles C.
Published: August 2009

Geostatistics provides tools to model, estimate, map, and eventually predict spatial patterns of tree size and growth. Variogram models and kriged maps were used to study spatial dependence of stem diameter (DBH), basal area (BA), and 10-year periodic basal area increment (BAI) in an old-growth forest stand. Temporal variation of spatial patterns was evaluated by fitting spatial stochastic models at 10-year intervals, from 1920 to 1990. The study area was a naturally seeded stand of southwestern ponderosa pine (Pinusponderosa Dougl. ex Laws. var. scopulorum) where total BA and tree density have steadily increased over the last decades. Our objective was to determine if increased stand density simply reduced individual growth rates or if it also altered spatial interactions among trees. Despite increased crowding, stem size maintained the same type of spatial dependence from 1920 to 1990. An isotropic Gaussian variogram was the model of choice to represent spatial dependence at all times. Stem size was spatially autocorrelated over distances no greater than 30 m, a measure of average patch diameter in this forest ecosystem. Because patch diameter remained constant through time, tree density increased by increasing the number of pine groups, not their horizontal dimension. Spatial dependence of stem size (DBH and BA) was always much greater and decreased less through time than that of stem increment (BAI). Spatial dependence of BAI was close to zero in the most recent decade, indicating that growth rates in 1980–1990 varied regardless of mutual tree position. Increased tree crowding corresponded not only to lower average and variance of individual growth rates, but also to reduced spatial dependence of BAI. Because growth variation was less affected by intertree distance with greater local crowding, prediction of individual growth rates benefits from information on horizontal stand structure only if tree density does not exceed threshold values. Simulation models and area estimates of tree performance in old-growth forests may be improved by including geostatistical components to summarize ecological spatial dependence.
Effects of prolonged cold storage on carbohydrate and protein content and field performance of white spruce bareroot seedlings
Authors: Jiang Yong , Zwiazek Janusz J. , Macdonald S. Ellen
Published: August 2009

Three-year-old bareroot white spruce (Piceaglauca (Moench) Voss) seedlings from three seedlots were either lifted in the fall of 1990 and stored over winter at −2 °C, or lifted in the spring of 1991. The soluble sugar, starch, and protein contents of needles, stems, and roots were measured in fall-lifted seedlings before, during, and at the end of cold storage and compared with those in spring-lifted seedlings 10 days before outplanting. The soluble sugar content of the seedlings decreased significantly in all tissues during cold storage. At the time of spring planting, sugar and protein levels were similar in fall- and spring-lifted seedlings, but starch content was about two times higher in spring-lifted seedlings. After outplanting, spring-lifted seedlings flushed and resumed root growth sooner than the fall-lifted, cold-stored seedlings. Spring-lifted seedlings also had initially higher photosynthetic rates and water potentials compared with the fall-lifted seedlings. However, both types of seedlings had similar survival rates and 1st year shoot growth in the field. The responses of seedlings to cold storage were similar among seed lots.
Interior spruce seedlings compared with emblings produced from somatic embryogenesis. II. Stock quality assessment prior to field planting
Authors: Grossnickle S.C. , Major J.E.
Published: August 2009

Interior spruce (Piceaglauca (Moench) Voss × Piceaengelmannii Parry) seedlings and emblings produced through somatic embryogenesis tissue culture were removed from frozen storage and tested with a stock quality assessment procedure prior to spring planting. Seedlings, compared with emblings, had greater height as well as shoot and root dry weights. Seedlings and emblings had similar root-collar diameter, buds per total shoot length, and needle primordia in their terminal buds. Seedlings and emblings had similar shoot form (i.e., branch quotient) and balance between their shoot and root system (i.e., plant water balance ratio). Emblings, compared with seedlings, had a lower osmotic potential at turgor loss point and symplastic fraction, plus a higher dry weight fraction and total turgor. Seedlings and emblings had similar osmotic potential at saturation and relative water content at turgor loss point. Seedlings and emblings had similar resistance to water movement through the plant–atmosphere continuum (Rpac) at 22 °C root temperature, though emblings had greater Rpac at 7.5 °C root temperature. Seedlings had greater net photosynthesis (Pn) than emblings over a 14-day period at both 7.5 and 22 °C root temperatures. Seedlings, compared with emblings, had greater root development over a 14-day period at 22 °C root temperature, though they had low and similar root development at 7.5 °C root temperature. Both Pn and needle conductance (gwv) decreased as predawn shoot water potential (Ψpd) declined in seedlings and emblings. Nearly complete stomatal closure occurred at Ψpd less than −1.5 MPa, while similarly low Pn readings (seedlings: −0.01 ± 0.04 μmol•m−2•s−1; emblings: 0.02 + 0.04 μmol•m−2•s−1) occurred between a Ψpd of −1.0 and −2.0 MPa. A performance potential index (PPI), which combines material and performance attributes in a comprehensive characterization of field performance potential, indicated that seedlings had a better PPI under optimum environmental conditions. However, seedlings and emblings had similar PPI under low temperature and drought conditions.
Application of the Kalman filter model in site index equation construction
Authors: Wang Yonghe , Payandeh Bijan
Published: August 2009

Extension of the Richards biological growth function has been applied extensively to describe height growth patterns or to develop site index equations. We introduce a linear filter model to achieve the same goals. Although derivation of the filter model involves more computation, it compares well with the Richards growth model in accuracy when applied to a black spruce (Piceamariana (Mill.) B.S.P) stem analysis data set from northern Ontario. The main advantage of the filter model, however, is that it can be used as a base-age invariant site index model.
Copper deficiency a probable cause of stem deformity in fertilised Eucalyptusnitens
Authors: Turnbull C.R.A. , Beadle C.L. , West P.W. , Cromer R.N.
Published: August 2009

Serious malformation of tree stems and branches was first observed 17 months after planting Eucalyptusnitens (Deane & Maiden) Maiden trees on an improved pasture site in southern Tasmania. The trees were planted in a 52 factorial fertiliser trial with application of nitrogen at 0, 60, 120, 240, and 480 kg/ha and phosphorus at 0, 30, 60, 120, and 240 kg/ha. The phosphorus was semibroadcast as a single dose just after planting in September 1990 and the nitrogen was applied over a 2-year period from planting. At 21 months of age, the degree of malformation increased significantly with increasing levels of nitrogen or phosphorus fertilisers and was most severe at the highest levels of application. There was a significant linear trend of decreasing diameter growth with increasing levels of phosphorus fertiliser. The concentration of Cu in the foliage was significantly lower in malformed than unaffected trees whilst other macro- and micro-nutrient foliar levels were within the normal range for healthy individuals. Whilst the symptoms appear similar to those of "Toorour syndrome" previously reported for Pinusradiata D. Don on improved pasture sites in Australia, we believe the present symptoms may result from Cu deficiency induced at high fertiliser levels. The deformations substantially reduce the merchantability of trees from the plantation.