bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene expression analysis of hepatic roles in cause and development of diabetes in Goto-Kakizaki rats
Authors: Almon Richard R , DuBois Debra C , Lai William , Xue Bai , Nie Jing , Jusko William J
Published: December 2008

Progression of diabetes was studied in male Goto-Kakizaki (GK) spontaneously diabetic rats between 4 and 20 weeks of age, and compared with Wistar-Kyoto (WKY) controls. Five animals from each strain were killed at 4, 8, 12, 16, and 20 weeks of age. Body weight, plasma glucose, and plasma insulin were measured. WKY rats showed a significantly larger weight gain than GK animals from 8 weeks of age onward. Plasma glucose was relatively stable in WKY. By contrast, plasma glucose was higher in GK than WKY even at 4 weeks and continued to increase up to 12 weeks and then maintained a hyperglycemic plateau throughout the remainder of the experiment. Plasma insulin was relatively stable in WKY from 8 weeks onward but was sharply elevated in GK between 4 and 8 weeks. After 8 weeks, insulin declined in GK with GK concentrations lower than WKY at 20 weeks, suggesting β-cell failure. Gene expression in liver was explored using Affymetrix 230-2 gene arrays. Data mining identified 395 probe sets out of more than 31 000 that were differentially regulated. Excluding unidentifiable probe sets and considering duplicate probe sets, there were 311 genes that were expressed differently in the liver of the two strains. A functional analysis of these genes indicated that disruption of lipid metabolism in the liver is a major consequence of the chronic hyperglycemia in the GK strain. In addition, the results suggest that chronic inflammation contributes significantly to the development of diabetes in the GK rats.
The Relationship between GATT Membership and Structural Breaks in International Trade
Authors: Abu-Bader Suleiman , Abu-Qarn Aamer S.
Published: December 2008

Using sequential structural break tests, we attempt to determine if and when a new GATT member experiences statistically significant changes in the paths of its trade with incumbent members. To test for the nature of a change, we compare the averages of the actual postbreak trade shares with the averages of the postbreak extrapolated trade shares. Should a significant structural break be detected, we compare the break year with the accession year of that country to GATT. Our results show that only a small fraction of countries experience significant positive structural breaks in their trade shares. Furthermore, any significant positive breaks generally occur far before or after the time of a country's accession to GATT.
The signaling pathways of Epstein-Barr virus-encoded latent membrane protein 2A (LMP2A) in latency and cancer
Authors: Pang Mei-Fong , Lin Kah-Wai , Peh Suat-Cheng
Published: December 2008

Epstein-Barr virus (EBV) is a ubiquitous virus with infections commonly resulting in a latency carrier state. Although the exact role of EBV in cancer pathogenesis remains not entirely clear, it is highly probable that it causes several lymphoid and epithelial malignancies, such as Hodgkin’s lymphoma, NK-T cell lymphoma, Burkitt’s lymphoma, and nasopharyngeal carcinoma. EBV-associated malignancies are associated with a latent form of infection, and several of these EBV-encoded latent proteins are known to mediate cellular transformation. These include six nuclear antigens and three latent membrane proteins. Studies have shown that EBV displays distinct patterns of viral latent gene expression in these lymphoid and epithelial tumors. The constant expression of latent membrane protein 2A (LMP2A) at the RNA level in both primary and metastatic tumors suggests that this protein might be a driving factor in the tumorigenesis of EBV-associated malignancies. LMP2A may cooperate with the aberrant host genome, and thereby contribute to malignant transformation by intervening in signaling pathways at multiple points, especially in the cell cycle and apoptotic pathway. This review summarizes the role of EBV-encoded LMP2A in EBV-associated viral latency and cancers. We will focus our discussions on the molecular interactions of each of the conserved motifs in LMP2A, and their involvement in various signaling pathways, namely the B-cell receptor blockade mechanism, the ubiquitin-mediated (Notch and Wnt) pathways, and the MAPK, PI3-K/Akt, NK-κB and STAT pathways, which can provide us with important insights into the roles of LMP2A in the EBV-associated latency state and various malignancies.
Granulation of activated sludge in a laboratory upflow sludge blanket reactor
Authors: Pagáčová Petra , Drtil Miloslav , Galbová Katarína
Published: December 2008

The creation of anoxic granulated biomass has been monitored in a laboratory USB (Upflow Sludge Blanket) reactor with the volume of 3.6 L. The objective of this research was to verify the possibilities of post-denitrification of residual NO3-N concentrations in treated wastewater (denitrification of 10-20 mg L−1 NO3-N) and to determine the maximum hydraulic and mass loading of the granulated biomass reactor. G-phase from biodiesel production and methanol were both tested as external organic denitrification substrates. The ratio of the organic substrate COD to NO3-N was 6. Only methanol was proven as a suitable organic substrate for this kind of reactor. However, the biomass adaptation to the substrate took over a week. The cultivation of anoxic granulated biomass was reached at hydraulic loading of over 0.35 m h−1. The size of granules was smaller when compared with results found and described in literary reports (granules up to 1 mm); however, settling properties were excellent and denitrification was deemed suitable for the USB reactor. Sludge volume indexes of granules ranged from 35-50 mL g−1 and settling rates reached 11 m h−1. Maximum hydraulic and mass loadings in the USB reactor were 0.95 m3 m−2 h−1 and 6.6 kg m−3 d−1. At higher loading levels, a wash-out of the biomass occurred.
A new 122 mm electromechanical drill for deep ice-sheet coring (DISC): 3. Control, electrical and electronics design
Authors: Mortensen Nicolai B. , Sendelbach Paul J. , Shturmakov Alexander J.
Published: December 2008

The deep ice-sheet coring (DISC) drill developed by Ice Coring and Drilling Services under contract to the US National Science Foundation is an electromechanical drill designed to take 122 mm ice cores to depths of 4000 m. Electronic, electrical and control systems are major aspects of the DISC drill. The drill sonde, the down-hole portion of the drill system, requires approximately 5 kW of d.c. power for the cutter and drill motors and instrumentation. Power is transmitted via a drill cable from a modified, commercially available surface d.c. power supply operating at 1000V to power modules in the sonde instrumentation section. These modules regulate the power to the motors to 300 V d.c. and to lower voltages for the instrumentation and control electronics. Cutter and pump motors are controlled by electronics that include motor controllers. There are 20 distinct sensors in the drill sonde which measure conditions such as hole fluid temperature, motor fluid temperature, drill orientation, etc. On-board electronics facilitate communication of control commands and data between the surface and the drill sonde. Electronics also play an integral part in the operation of surface equipment such as the winch in raising and lowering the sonde in the borehole. Overall control of the DISC drill system is provided by a PC-based supervisory control system that allows the drill operators to monitor and control all aspects of the drilling operation.
Koci drill for drilling in ice, sand and rock: drill requirements, design, performance, difficulties
Authors: Green J. , Koci B. , Kyne J.
Published: December 2008

A new man-portable drill designed to perform in ice with entrained sand and rock has been built. Designated the ‘Koci drill’, it was first used on rock-covered glaciers in the McMurdo Dry Valleys, Antarctica, during the 2006/07 field season. This drill is designed to be disassembled into component parts no heavier than 30 kg (not including the generator). For stability, the drill platform weight can be augmented with available rock. The field performance of the drill was generally good and both ice and rock were successfully penetrated and acceptable-quality ice cores up to 1 m long were collected during the 2007/08 season. The maximum depth achieved was 10.25 m. Given a concentrated effort at one or two sites per season, a depth of 40 m is achievable. Problems encountered in the field will be addressed in the next-generation design.
A new 122 mm electromechanical drill for deep ice-sheet coring (DISC): 4. Drill cable
Authors: Shturmakov Alexander J. , Sendelbach Paul J.
Published: December 2008

The deep ice-sheet coring (DISC) drill developed by Ice Coring and Drilling Services (ICDS) under contract with the US National Science Foundation requires a drill cable capable of transmitting high amounts of electrical power as well as high rates of data. The DISC cable was designed and manufactured by the Rochester Corporation to core ice to depths of 4000 m. In addition to the steel strength members to support the drill, the cable has copper wires for conducting electrical power for the drill sonde cutter, pump motors and the sonde electronics and an optical fiber core for data transmission. The outer steel layers are filled with a special compound to minimize fluid penetration of the cable.
Pollination biology of basal angiosperms (ANITA grade)
Authors: Thien Leonard B. , Bernhardt Peter , Devall Margaret S. , Chen Zhi‐duan , Luo Yi‐bo , Fan Jian‐Hua , Yuan Liang‐Chen , Williams Joseph H.
Published: December 2008

The first three branches of the angiosperm phylogenetic tree consist of eight families with ∼201 species of plants (the ANITA grade). The oldest flower fossil for the group is dated to the Early Cretaceous (115–125 Mya) and identified to the Nymphaeales. The flowers of extant plants in the ANITA grade are small, and pollen is the edible reward (rarely nectar or starch bodies). Unlike many gymnosperms that secrete “pollination drops,” ANITA‐grade members examined thus far have a dry‐type stigma. Copious secretions of stigmatic fluid are restricted to the Nymphaeales, but this is not nectar. Floral odors, floral thermogenesis (a resource), and colored tepals attract insects in deceit‐based pollination syndromes throughout the first three branches of the phylogenetic tree. Self‐incompatibility and an extragynoecial compitum occur in some species in the Austrobaileyales. Flies are primary pollinators in six families (10 genera). Beetles are pollinators in five families varying in importance as primary (exclusive) to secondary vectors of pollen. Bees are major pollinators only in the Nymphaeaceae. It is hypothesized that large flowers in Nymphaeaceae are the result of the interaction of heat, floral odors, and colored tepals to trap insects to increase fitness.
Angiosperm diversification through time
Authors: Magallón Susana , Castillo Amanda
Published: December 2008

The extraordinary diversity of angiosperms is the ultimate outcome of the interplay of speciation and extinction, which determine the net diversification of different lineages. We document the temporal trends of angiosperm diversification rates during their early history. Absolute diversification rates were estimated for order‐level clades using ages derived from relaxed molecular clock analyses that included or excluded a maximal constraint to angiosperm age. Diversification rates for angiosperms as a whole ranged from 0.0781 to 0.0909 net speciation events per million years, with dates from the constrained analysis. Diversification through time plots show an inverse relationship between clade age and rate, where the younger clades tend to have the highest rates. Angiosperm diversity is found to have mixed origins: slightly less than half of the living species belong to lineages with low to moderate diversification rates, which appeared between 130 and 102 Mya (Barremian‐uppermost Albian; Lower Cretaceous). Slightly over half of the living species belong to lineages with moderate to high diversification rates, which appeared between 102 and 77 Mya (Cenomanian‐mid Campanian; Upper Cretaceous). Terminal lineages leading to living angiosperm species, however, may have originated soon or long after the phylogenetic differentiation of the clade to which they belong.
More is better: the uses of developmental genetic data to reconstruct perianth evolution
Authors: Hileman Lena C. , Irish Vivian F.
Published: December 2008

The origin and evolution of the perianth remains enigmatic. While it seems likely that an undifferentiated perianth consisting of tepals arose early in angiosperm evolution, it is unclear when and how differentiated perianths consisting of distinct organs, such as petals and sepals, arose. Phylogenetic reconstructions of ancestral perianth states across angiosperms have traditionally relied on morphological data from extant species, but these analyses often produce equivocal results. Here we describe the use of developmental genetic data as an additional strategy to infer the ancestral perianth character state for different angiosperm clades. By assessing functional data in combination with expression data in a maximum likelihood framework, we provide a novel approach for investigating the evolutionary history of the perianth. Results of this analysis provide new insights into perianth evolution and provide a proof of concept for using this strategy to explore the incorporation of developmental genetic data in character state reconstructions. As the assumptions outlined here are tested and more genetic data are generated, we hope that ancestral state reconstructions based on multiple lines of evidence will converge.
CYCLOPS, a mediator of symbiotic intracellular accommodation
Authors: Yano Koji , Yoshida Satoko , Müller Judith , Singh Sylvia , Banba Mari , Vickers Kate , Markmann Katharina , White Catharine , Schuller Bettina , Sato Shusei , Asamizu Erika , Tabata Satoshi , Murooka Yoshikatsu , Perry Jillian , Wang Trevor L. , Kawaguchi Masayoshi , Imaizumi-Anraku Haruko , Hayashi Makoto , Parniske Martin
Published: December 2008

The initiation of intracellular infection of legume roots by symbiotic rhizobia bacteria and arbuscular mycorrhiza (AM) fungi is preceded by the induction of calcium signatures in and around the nucleus of root epidermal cells. Although a calcium and calmodulin-dependent kinase (CCaMK) is a key mediator of symbiotic root responses, the decoding of the calcium signal and the molecular events downstream are only poorly understood. Here, we characterize
Lotus japonicus cyclops
mutants on which microbial infection was severely inhibited. In contrast, nodule organogenesis was initiated in response to rhizobia, but arrested prematurely. This arrest was overcome when a deregulated
CCaMK
mutant version was introduced into
cyclops
mutants, conferring the development of full-sized, spontaneous nodules. Because
cyclops
mutants block symbiotic infection but are competent for nodule development, they reveal a bifurcation of signal transduction downstream of CCaMK. We identified
CYCLOPS
by positional cloning. CYCLOPS carries a functional nuclear localization signal and a predicted coiled-coil domain. We observed colocalization and physical interaction between CCaMK and CYCLOPS in plant and yeast cell nuclei in the absence of symbiotic stimulation. Importantly, CYCLOPS is a phosphorylation substrate of CCaMK in vitro.
Cyclops
mutants of rice were impaired in AM, and rice
CYCLOPS
could restore symbiosis in
Lotus cyclops
mutants, indicating a functional conservation across angiosperms. Our results suggest that
CYCLOPS
forms an ancient, preassembled signal transduction complex with CCaMK that is specifically required for infection, whereas organogenesis likely requires additional yet-to-be identified CCaMK interactors or substrates.
Discontinuous movement of mRNP particles in nucleoplasmic regions devoid of chromatin
Authors: Siebrasse Jan Peter , Veith Roman , Dobay Akos , Leonhardt Heinrich , Daneholt Bertil , Kubitscheck Ulrich
Published: December 2008

Messenger ribonucleoprotein particles (mRNPs) move randomly within nucleoplasm before they exit from the nucleus. To further understand mRNP trafficking, we have studied the intranuclear movement of a specific mRNP, the BR2 mRNP, in salivary gland cells in
Chironomus tentans
. Their polytene nuclei harbor giant chromosomes separated by vast regions of nucleoplasm, which allows us to study mRNP mobility without interference of chromatin. The particles were fluorescently labeled with microinjected oligonucleotides (DNA or RNA) complementary to BR2 mRNA or with the RNA-binding protein hrp36, the
C. tentans
homologue of hnRNP A1. Using high-speed laser microscopy, we followed the intranuclear trajectories of single mRNPs and characterized their motion within the nucleoplasm. The Balbiani ring (BR) mRNPs moved randomly, but unexpectedly, in a discontinuous manner. When mobile, they diffused with a diffusion coefficient corresponding to their size. Between mobile phases, the mRNPs were slowed down 10-to 250-fold but were never completely immobile. Earlier electron microscopy work has indicated that BR particles can attach to thin nonchromatin fibers, which are sometimes connected to discrete fibrogranular clusters. We propose that the observed discontinuous movement reflects transient interactions between freely diffusing BR particles and these submicroscopic structures.
Linking adverbials
Authors: Liu Dilin
Published: December 2008

Liking adverbials (LAs) play a very important role in discourse cohesion. This study examines the frequency and usage patterns of English LAs (110 in total) across five registers (Spoken English, Academic Writing, Fiction, News Writing, and Other writings) in the BNC. While the data analyses offer support for some previous research results, they also yield new findings regarding, among other things, variations in the adverbials’ frequency distribution and usage patterns across the five registers. For example, while fiction’s overall use of LAs is much lower than that of speaking and academic writing, its use of the sequential type of LAs is actually higher than the latter registers’. Also although news has the lowest overall LA frequency among the five registers, it boasts the highest use of LAs that express simultaneity (e.g. meanwhile). Besides discussing new findings, the paper also addresses their implications for language description, learning, and teaching.
Independence and interdependence in collective decision making: an agent-based model of nest-site choice by honeybee swarms
Authors: List Christian , Elsholtz Christian , Seeley Thomas D
Published: December 2008

Condorcet's jury theorem shows that when the members of a group have noisy but independent information about what is best for the group as a whole, majority decisions tend to outperform dictatorial ones. When voting is supplemented by communication, however, the resulting interdependencies between decision makers can strengthen or undermine this effect: they can facilitate information pooling, but also amplify errors. We consider an intriguing non-human case of independent information pooling combined with communication: the case of nest-site choice by honeybee (
Apis mellifera
) swarms. It is empirically well documented that when there are different nest sites that vary in quality, the bees usually choose the best one. We develop a new agent-based model of the bees' decision process and show that its remarkable reliability stems from a particular interplay of independence and interdependence between the bees.
Phytochelatin Synthesis Is Essential for the Detoxification of Excess Zinc and Contributes Significantly to the Accumulation of Zinc
Authors: Tennstedt Pierre , Peisker Daniel , Böttcher Christoph , Trampczynska Aleksandra , Clemens Stephan
Published: December 2008

The synthesis of phytochelatins (PCs) is essential for the detoxification of nonessential metals and metalloids such as cadmium and arsenic in plants and a variety of other organisms. To our knowledge, no direct evidence for a role of PCs in essential metal homeostasis has been reported to date. Prompted by observations in Schizosaccharomyces pombe and Saccharomyces cerevisiae indicating a contribution of PC synthase expression to Zn2+ sequestration, we investigated a known PC-deficient Arabidopsis (Arabidopsis thaliana) mutant, cad1-3, and a newly isolated second strong allele, cad1-6, with respect to zinc (Zn) homeostasis. We found that in a medium with low cation content PC-deficient mutants show pronounced Zn2+ hypersensitivity. This phenotype is of comparable strength to the well-documented Cd2+ hypersensitivity of cad1 mutants. PC deficiency also results in significant reduction in root Zn accumulation. To be able to sensitively measure PC accumulation, we established an assay using capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry of derivatized extracts. Plants grown under control conditions consistently showed PC2 accumulation. Analysis of plants treated with same-effect concentrations revealed that Zn2+-elicited PC2 accumulation in roots reached about 30% of the level of Cd2+-elicited PC2 accumulation. We conclude from these data that PC formation is essential for Zn2+ tolerance and provides driving force for the accumulation of Zn. This function might also help explain the mysterious occurrence of PC synthase genes throughout the plant kingdom and in a wide range of other organisms.
Crucial roles of MZF‐1 in the transcriptional regulation of apomorphine‐induced modulation of FGF‐2 expression in astrocytic cultures
Authors: Luo Xiaoying , Zhang Xinhua , Shao Wei , Yin Yanqin , Zhou Jiawei
Published: December 2008

Apomorphine (APO), a potent D1/D2 dopamine receptor agonist, is used as an anti‐parkinsonian drug. It stimulates the synthesis and release of multiple trophic factors in mesencephalic and striatal neurons, preventing the loss of dopaminergic neurons in vitro. Furthermore, APO enhances the biosynthesis and release of FGF‐2 by activating dopamine receptors in striatal astrocytes, where cAMP/PKA and PKC/MAPK signalling cascades mediate this process. We investigate the effects of APO on the fibroblast growth factor‐2 (FGF‐2) promoter and its regulation in astrocytes and identify the transcription factor and cis element underlying these effects. In screening for cis‐acting elements over the entire region of the FGF‐2 promoter stimulated by APO in the astrocytes, a sequence located in the –785/–745 region was found to serve as the cis element. This element was recognized by the human myeloid zinc finger protein 1 (MZF‐1) transcription factor. Introducing human MZF‐1 plasmid and human MZF‐1‐specific siRNA has different effects on the FGF‐2 promoter. Furthermore, it increases FGF‐2 protein expression in HeLa cells and primary astrocytes, indicating that APO stimulates the FGF‐2 promoter via the MZF‐1 transcription factor. These data suggest that APO can enhance the biosynthesis and release of FGF‐2 through the activation of the MZF‐1 transcription factor in striatal astrocytes.
Helix 3 is necessary and sufficient for prion protein’s anti‐Bax function
Authors: Laroche‐Pierre Stéphanie , Jodoin Julie , LeBlanc Andréa C.
Published: December 2008

To identify the structural elements of the prion protein (PrP) necessary for its protective function against Bcl‐2 associated protein X (Bax), we performed structure–function analyses of the anti‐Bax function of cytosolic PrP (CyPrP) in MCF‐7 cells. Deletions of 1, 2, or 3 N‐terminal Bcl‐2 homology domain 2‐like octapeptide repeats (BORs), but not deletion of all four BORs, abolish CyPrPs anti‐Bax function. Deletion of α‐helix 3 (PrP23–199) or further C‐terminal deletions of α‐helix 1 and 2, and β‐strand 1 and 2 (PrP23–172, PrP23–160, PrP23–143, and PrP23–127) eliminates CyPrPs protection against Bax‐mediated cell death. The substitution of helix 3 amino acid residues K204, V210, and E219 by proline inhibits the anti‐Bax function of CyPrP. The substitution of K204, but not V210 and E219, by alanine residues also prevents CyPrPs anti‐Bax function. Expression of PrPs helix 3 displays anti‐Bax activity in MCF‐7 cells and in human neurons. Together, these results indicate that although the BOR domain has an influence on PrPs anti‐Bax function, the helix 3 is necessary and sufficient for the anti‐Bax function of CyPrP. Identification of helix 3 as the structural element for the anti‐Bax function thus provides a molecular target to modulate PrPs anti‐Bax function in cancer and neurodegeneration.
A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase
Authors: Mihola Ondrej , Trachtulec Zdenek , Vlcek Cestmir , Schimenti John C. , Forejt Jiri
Published: December 2008

Speciation genes restrict gene flow between the incipient species and related taxa. Three decades ago, we mapped a mammalian speciation gene, hybrid sterility 1 (
Hst1
), in the intersubspecific hybrids of house mouse. Here, we identify this gene as
Prdm9
, encoding a histone H3 lysine 4 trimethyltransferase. We rescued infertility in male hybrids with bacterial artificial chromosomes carrying
Prdm9
from a strain with the “fertility”

Hst1
f

allele. Sterile hybrids display down-regulated microrchidia 2B (
Morc2b
) and fail to compartmentalize γH2AX into the pachynema sex (XY) body. These defects, seen also in
Prdm9
-null mutants, are rescued by the
Prdm9
transgene. Identification of a vertebrate hybrid sterility gene reveals a role for epigenetics in speciation and opens a window to a hybrid sterility gene network.
Type II Thioesterase ScoT, Associated with
Streptomyces coelicolor
A3(2) Modular Polyketide Synthase Cpk, Hydrolyzes Acyl Residues and Has a Preference for Propionate
Authors: Kotowska Magdalena , Pawlik Krzysztof , Smulczyk-Krawczyszyn Aleksandra , Bartosz-Bechowski Hubert , Kuczek Katarzyna
Published: December 2008

Type II thioesterases (TE IIs) were shown to maintain the efficiency of polyketide synthases (PKSs) by removing acyl residues blocking extension modules. However, the substrate specificity and kinetic parameters of these enzymes differ, which may have significant consequences when they are included in engineered hybrid systems for the production of novel compounds. Here we show that thioesterase ScoT associated with polyketide synthase Cpk from
Streptomyces coelicolor
A3(2) is able to hydrolyze acetyl, propionyl, and butyryl residues, which is consistent with its editing function. This enzyme clearly prefers propionate, in contrast to the TE IIs tested previously, and this indicates that it may have a role in control of the starter unit. We also determined activities of ScoT mutants and concluded that this enzyme is an α/β hydrolase with Ser90 and His224 in its active site.
Identification and Characterization of Class 1 Integron Resistance Gene Cassettes among
Salmonella
Strains Isolated from Imported Seafood
Authors: Khan Ashraf A. , Ponce Elizabeth , Nawaz M. S. , Cheng Chorng-Ming , Khan Junaid A. , West Christine S.
Published: December 2008

A total of 210
Salmonella
isolates, representing 64 different serovars, were isolated from imported seafood samples, and 55/210 isolates were found to be resistant to at least one antibiotic. Class 1 integrons from three multidrug-resistant
Salmonella enterica
strains (
Salmonella enterica
serovars Newport [strain 62], Typhimurium var. Copenhagen [strain 629], and Lansing [strain 803], originating from Hong Kong, the Philippines, and Taiwan, respectively) were characterized. Southern hybridization of plasmids isolated from these strains, using a class 1 integron probe, showed that trimethoprim-sulfamethoxazole and streptomycin resistance genes were located on a megaplasmid in strain 629. Our study indicates that imported seafood could be a reservoir for
Salmonella
isolates resistant to multiple antibiotics.
The Spore-Specific Alanine Racemase of
Bacillus anthracis
and Its Role in Suppressing Germination during Spore Development
Authors: Chesnokova Olga N. , McPherson Sylvia A. , Steichen Christopher T. , Turnbough Charles L.
Published: December 2008

Spores of
Bacillus anthracis
are enclosed by an exosporium composed of a basal layer and an external hair-like nap. The nap is apparently formed by a single glycoprotein, while the basal layer contains many different structural proteins and several enzymes. One of the enzymes is Alr, an alanine racemase capable of converting the spore germinant
l
-alanine to the germination inhibitor
d
-alanine. Unlike other characterized exosporium proteins, Alr is nonuniformly distributed in the exosporium and might have a second spore location. In this study, we demonstrated that expression of the
alr
gene, which encodes Alr, is restricted to sporulating cells and that the bulk of
alr
transcription and Alr synthesis occurs during the late stages of sporulation. We also mapped two
alr
promoters that are differentially active during sporulation and might be involved in the atypical localization of Alr. Finally, we constructed a Δ
alr
mutant of
B. anthracis
that lacks Alr and examined the properties of the spores produced by this strain. Mature Δ
alr
spores germinate more efficiently in the presence of
l
-alanine, presumably because of their inability to convert exogenous
l
-alanine to
d
-alanine, but they respond normally to other germinants. Surprisingly, the production of mature spores by the Δ
alr
mutant is defective because approximately one-half of the nascent spores germinate and lose their resistance properties before they are released from the mother cell. This phenotype suggests that an important function of Alr is to produce
d
-alanine during the late stages of sporulation to suppress premature germination of the developing spore.
Synthesis of CDP-Activated Ribitol for Teichoic Acid Precursors in
Streptococcus pneumoniae
Authors: Baur Stefanie , Marles-Wright Jon , Buckenmaier Stephan , Lewis Richard J. , Vollmer Waldemar
Published: December 2008

Streptococcus pneumoniae
has unusually complex cell wall teichoic acid and lipoteichoic acid, both of which contain a ribitol phosphate moiety. The
lic
region of the pneumococcal genome contains genes for the uptake and activation of choline, the attachment of phosphorylcholine to teichoic acid precursors, and the transport of these precursors across the cytoplasmic membrane. The role of two other, so far uncharacterized, genes, spr1148 and spr1149, in the
lic
region was determined.
TarJ
(spr1148) encodes an NADPH-dependent alcohol dehydrogenase for the synthesis of ribitol 5-phosphate from ribulose 5-phosphate.
TarI
(spr1149) encodes a cytidylyl transferase for the synthesis of cytidine 5′-diphosphate (CDP)-ribitol from ribitol 5-phosphate and cytidine 5′-triphosphate. We also present the crystal structure of TarI with and without bound CDP, and the structures present a rationale for the substrate specificity of this key enzyme. No transformants were obtained with insertion plasmids designed to interrupt the
tarIJ
genes, indicating that their function could be essential for cell growth. CDP-activated ribitol is a precursor for the synthesis of pneumococcal teichoic acids and some of the capsular polysaccharides. Thus, all eight genes in the
lic
region have a role in teichoic acid synthesis.
A Fatty Acid Messenger Is Responsible for Inducing Dispersion in Microbial Biofilms
Authors: Davies David G. , Marques Cláudia N. H.
Published: December 2008

It is well established that in nature, bacteria are found primarily as residents of surface-associated communities called biofilms. These structures form in a sequential process initiated by attachment of cells to a surface, followed by the formation of matrix-enmeshed microcolonies, and culminating in dispersion of the bacteria from the mature biofilm. In the present study, we have demonstrated that, during growth,Pseudomonas aeruginosaproduces an organic compound we have identified ascis-2-decenoic acid, which is capable of inducing the dispersion of established biofilms and of inhibiting biofilm development. When added exogenously toP. aeruginosaPAO1 biofilms at a native concentration of 2.5 nM,cis-2-decenoic acid was shown to induce the dispersion of biofilm microcolonies. This molecule was also shown to induce dispersion of biofilms, formed byEscherichia coli,Klebsiella pneumoniae,Proteus mirabilis,Streptococcus pyogenes,Bacillus subtilis,Staphylococcus aureus, and the yeastCandida albicans. Active at nanomolar concentrations,cis-2-decenoic acid appears to be functionally and structurally related to the class of short-chain fatty acid signaling molecules such as diffusible signal factor, which act as cell-to-cell communication molecules in bacteria and fungi.
UvrD303, a Hyperhelicase Mutant That Antagonizes RecA-Dependent SOS Expression by a Mechanism That Depends on Its C Terminus
Authors: Centore Richard C. , Leeson Michael C. , Sandler Steven J.
Published: December 2008

Genomic integrity is critical for an organism's survival and ability to reproduce. In
Escherichia coli
, the UvrD helicase has roles in nucleotide excision repair and methyl-directed mismatch repair and can limit reactions by RecA under certain circumstances. UvrD303 (D403A D404A) is a hyperhelicase mutant, and when expressed from a multicopy plasmid, it results in UV sensitivity (UV
s
), recombination deficiency, and antimutability. In order to understand the molecular mechanism underlying the UV
s
phenotype of
uvrD303
cells, this mutation was transferred to the
E. coli
chromosome and studied in single copy. It is shown here that
uvrD303
mutants are UV sensitive, recombination deficient, and antimutable and additionally have a moderate defect in inducing the SOS response after UV treatment. The UV-sensitive phenotype is epistatic with
recA
and additive with
uvrA
and is partially suppressed by removing the LexA repressor. Furthermore,
uvrD303
is able to inhibit constitutive SOS expression caused by the
recA730
mutation. The ability of UvrD303 to antagonize SOS expression was dependent on its 40 C-terminal amino acids. It is proposed that UvrD303, via its C terminus, can decrease the levels of RecA activity in the cell.
Mutations in
ampG
and Lytic Transglycosylase Genes Affect the Net Release of Peptidoglycan Monomers from
Vibrio fischeri
Authors: Adin Dawn M. , Engle Jacquelyn T. , Goldman William E. , McFall-Ngai Margaret J. , Stabb Eric V.
Published: December 2008

The light-organ symbiont
Vibrio fischeri
releases
N
-acetylglucosaminyl-1,6-anhydro-
N
-acetylmuramylalanyl-γ-glutamyldiaminopimelylalanine, a disaccharide-tetrapeptide component of peptidoglycan that is referred to here as “PG monomer.” In contrast, most gram-negative bacteria recycle PG monomer efficiently, and it does not accumulate extracellularly. PG monomer can stimulate normal light-organ morphogenesis in the host squid
Euprymna scolopes
, resulting in regression of ciliated appendages similar to that triggered by infection with
V. fischeri
. We examined whether the net release of PG monomers by
V. fischeri
resulted from lytic transglycosylase activity or from defects in AmpG, the permease through which PG monomers enter the cytoplasm for recycling. An
ampG
mutant displayed a 100-fold increase in net PG monomer release, indicating that AmpG is functional. The
ampG
mutation also conferred the uncharacteristic ability to induce light-organ morphogenesis even when placed in a nonmotile
flaJ
mutant that cannot infect the light-organ crypts. We targeted five potential lytic transglycosylase genes singly and in specific combinations to assess their role in PG monomer release. Combinations of mutations in
ltgA
,
ltgD
, and
ltgY
decreased net PG monomer release, and a triple mutant lacking all three of these genes had little to no accumulation of PG monomers in culture supernatants. This mutant colonized the host as well as the wild type did; however, the mutant-infected squid were more prone to later superinfection by a second
V. fischeri
strain. We propose that the lack of PG monomer release by this mutant results in less regression of the infection-promoting ciliated appendages, leading to this propensity for superinfection.
Effect of curcumin on acidic pH-induced expression of IL-6 and IL-8 in human esophageal epithelial cells (HET-1A): role of PKC, MAPKs, and NF-κB
Authors: Rafiee Parvaneh , Nelson Victoria M. , Manley Sharon , Wellner Michael , Floer Martin , Binion David G. , Shaker Reza
Published: December 2008

Human esophageal epithelial cells play a key role in esophageal inflammation in response to acidic pH during gastroesophageal reflux disease (GERD), increasing secretion of IL-6 and IL-8. The mechanisms underlying IL-6 and IL-8 expression and secretion in esophageal epithelial cells after acid stimulation are not well characterized. We investigated the role of PKC, MAPK, and NF-κB signaling pathways and transcriptional regulation of IL-6 and IL-8 expression in HET-1A cells exposed to acid. Exposure of HET-1A cells to pH 4.5 induced NF-κB activity and enhanced IL-6 and IL-8 secretion and mRNA and protein expression. Acid stimulation of HET-1A cells also resulted in activation of MAPKs and PKC (α and ε). Curcumin, as well as inhibitors of NF-κB (SN-50), PKC (chelerythrine), and p44/42 MAPK (PD-098059) abolished the acid-induced expression of IL-6 and IL-8. The JNK inhibitor SP-600125 blocked expression/secretion of IL-6 but only partially attenuated IL-8 expression. The p38 MAPK inhibitor SB-203580 did not inhibit IL-6 expression but exerted a stronger inhibitory effect on IL-8 expression. Together, these data demonstrate that 1) acid is a potent inducer of IL-6 and IL-8 production in HET-1A cells; 2) MAPK and PKC signaling play a key regulatory role in acid-mediated IL-6 and IL-8 expression via NF-κB activation; and 3) the anti-inflammatory plant compound curcumin inhibits esophageal activation in response to acid. Thus IL-6 and IL-8 expression by acid may contribute to the pathobiology of mucosal injury in GERD, and inhibition of the NF-κB/proinflammatory cytokine pathways may emerge as important therapeutic targets for treatment of esophageal inflammation.
Adiponectin deficiency does not affect development and progression of spontaneous colitis in IL-10 knockout mice
Authors: Pini Maria , Gove Melissa E. , Fayad Raja , Cabay Robert J. , Fantuzzi Giamila
Published: December 2008

The goal of this study was to investigate the role of the adipokine adiponectin (APN) in development of spontaneous colitis in IL-10 knockout (KO) mice. To this aim, we generated double IL-10 APN KO mice and compared their disease development to that of single IL-10 KO mice. Both IL-10 KO and double IL-10 APN KO mice spontaneously developed colitis of comparable severity. No significant differences in inflammatory infiltrate or crypt elongation were observed in colonic tissue obtained from IL-10 KO and double IL-10 APN KO mice at either 12 or 20 wk of age. A comparable increase in circulating levels of serum amyloid A and IFN-γ was observed in IL-10 KO and double IL-10 APN KO mice as disease progressed. In vitro stimulation of lymphocytes from mesenteric lymph nodes with anti-CD3 and anti-CD28 induced a significantly higher production of IL-17 and TNF-α in IL-10 KO and double IL-10 APN KO mice compared with their healthy littermates. No significant differences in cytokine production from lymphocytes or colonic mRNA expression of cytokines were observed between IL-10 KO and double IL-10 APN KO mice. Both IL-10 KO and double IL-10 APN KO mice had a similar decrease in body weight and bone mass compared with their respective healthy littermates. Finally, APN deficiency did not lead to development of insulin resistance, either in APN KO or double IL-10 APN KO mice. In conclusion, lack of APN does not play a significant role in the pathogenesis of spontaneous colonic inflammation in the IL-10 KO model.
Blocking eukaryotic initiation factor 4F complex formation does not inhibit the mTORC1-dependent activation of protein synthesis in cardiomyocytes
Authors: Huang Brandon P. H. , Wang Yanni , Wang Xuemin , Wang Zhuren , Proud Christopher G.
Published: December 2008

Activation of the mammalian target of rapamycin complex 1 (mTORC1) causes the dissociation of eukaryotic initiation factor 4E complex (eIF4E)-binding protein 1 (4E-BP1) from eIF4E, leading to increased eIF4F complex formation. mTORC1 positively regulates protein synthesis and is implicated in several diseases including cardiac hypertrophy, a potentially fatal disorder involving increased cardiomyocyte size. The importance of 4E-BP1 in mTORC1-regulated protein synthesis was investigated by overexpressing 4E-BP1, which blocks eIF4F formation in isolated primary cardiomyocytes without affecting other targets for mTORC1 signaling. Interestingly, blocking eIF4F formation did not impair the degree of activation of overall protein synthesis by the hypertrophic agent phenylephrine (PE), which, furthermore, remained dependent on mTORC1. Overexpressing 4E-BP1 also only had a small effect on PE-induced cardiomyocyte growth. Overexpressing 4E-BP1 did diminish the PE-stimulated synthesis of luciferase encoded by structured mRNAs, confirming that such mRNAs do require eIF4F for their translation in cardiomyocytes. These data imply that the substantial inhibition of cardiomyocyte protein synthesis and growth caused by inhibiting mTORC1 cannot be attributed to the activation of 4E-BP1 or loss of eIF4F complexes. Our data indicate that increased eIF4F formation plays, at most, only a minor role in the mTORC1-dependent activation of overall protein synthesis in these primary cells but is required for the translation of structured mRNAs. Therefore, other mTORC1 targets are more important in the inhibition by rapamycin of the rapid activation of protein synthesis and of cell growth.
Caveolin-1–dependent apoptosis induced by fibrin degradation products
Authors: Guo Yi-He , Hernandez Irene , Isermann Berend , Kang Tae-bong , Medved Leonid , Sood Rashmi , Kerschen Edward J. , Holyst Trudy , Mosesson Michael W. , Weiler Hartmut
Published: December 2008

In mice lacking the blood coagulation regulator thrombomodulin, fibrinolytic degradation products (FDP) of fibrin induce apoptotic cell death of a specialized cell type in the placenta, polyploid trophoblast giant cells. Here, we document that this bioactivity of FDP is conserved in human FDP, is not limited to trophoblast cells, and is associated with an Aα-chain segment of fibrin fragment E (FnE). The majority of proapoptotic activity is arginine-glycine-aspartic acid (RGD)-independent and requires caveolin-1–dependent cellular internalization of FnE. Internalization through caveoli is mediated by an epitope contained within Aα52-81 that is necessary and sufficient for cellular uptake of FnE. Aα52-81 does not cause apoptosis itself, and competitively inhibits FnE internalization and apoptosis induction. Apoptotic activity per se resides within Aα17-37 and requires the N-terminal neoepitope generated by release of fibrinopeptide A. Cellular internalization of FnE elicits depression of mitochondrial function and consequent apoptosis that is strictly dependent on the activity of caspases 9 and 3. These findings describe the molecular details of a novel mechanism linking fibrin degradation to cell death in the placenta, which may also contribute to pathologic alterations in nonplacental vascular beds that are associated with fibrinolysis.
Swallowed dental bridge causing ileal perforation: a case report
Authors: Rashid Farhan , Simpson John , Ananthakrishnan G , Tierney Gillian M
Published: December 2008

We report the case of a 53 year old gentleman who had accidentally swallowed his dental bridge. One week following this he experienced a sudden onset of generalised abdominal pain and underwent laparotomy. At operation he was found to have a distal ileal perforation and an ileocaecal resection was performed. Although most swallowed foreign bodies pass through the gastrointestinal tract without problem, serious complications including intestinal perforation can occur.
Evidence that Intestinal Glucagon-Like Peptide-1 Plays a Physiological Role in Satiety
Authors: Williams Diana L. , Baskin Denis G. , Schwartz Michael W.
Published: December 2008

A physiological role in satiety is proposed for glucagon-like peptide-1 (GLP-1), secreted by the distal intestine in response to ingested nutrients. Here we report that in rats, ip injection of the GLP-1 receptor (GLP-1-R) antagonist exendin 9-39 (Ex9) elicited hyperphagia, but only at times of day when intake is otherwise low. Furthermore, ip administration of Ex9 attenuated satiety induced by either a voluntarily consumed sucrose meal (by 100%) or an intragastric glucose load (by 40%). To determine whether these effects involve blockade of GLP-1-R in brain or at a peripheral site, we injected Ex9 either centrally (into the third ventricle) or peripherally (ip) prior to GLP-1 injected either centrally or peripherally. Anorexia induced by peripheral GLP-1 was fully blocked by peripheral, but not central, pretreatment with Ex9, whereas the opposite was true for anorexic effect of central GLP-1. Thus, ip Ex9 appears to attenuate satiety via peripheral GLP-1-R blockade. Finally, anorexia induced by ip injection of exendin-4 (a GLP-1-R agonist) was due to both reduced meal size and increased duration between meals. We conclude that GLP-1 released from the intestine in response to ingested nutrients is a physiologically active satiety signal.
Apoptotic spermatogenic cells can be energy sources for Sertoli cells
Authors: Xiong Weipeng , Wang Haikun , Wu Hui , Chen Yongmei , Han Daishu
Published: December 2008

Apoptotic spermatogenic cells and residual bodies are phagocytosed and degraded by Sertoli cells during mammalian spermatogenesis. The meaning of this event remains to be clarified. In this report, we demonstrate that apoptotic spermatogenic cells and residual bodies can be used to produce ATP by Sertoli cells after phagocytosis of them. Sertoli cells produced the highest level of ATP compared with other testicular cells. Phagocytosis assayin vitroshowed that engulfment of apoptotic spermatogenic cells increases ATP production by Sertoli cells. The increased ATP production was detected in seminiferous tubules at the stages where phagocytosis occurs. Induced apoptosis of spermatogenic cellsin vivoincreased ATP production in seminiferous tubules. The augmentation of ATP production bothin vitroandin vivoassociated with the lipid formation in Sertoli cells after phagocytosis of apoptotic spermatogenic cells. The lipid β-oxidation was a predominant pathway to produce ATP in Sertoli cells. We conclude that after phagocytosis by Sertoli cells, apoptotic spermatogenic cells are degraded to form lipids that are then used to produce ATP. The results suggest that apoptotic spermatogenic cells can be energy sources for Sertoli cells that may define a novel meaning of spermatogenic cell death.
Structural Understanding of Self‐Assembled Rare Earth Disilicide Nanostructures Via Scanning Probe Microscopy and First Principles Studies
Authors: Shinde Aniketa , Cao Juexian , Wu Ruqian , Ragan Regina
Published: December 2008

We performed systematic experimental and computational studies to investigate the adsorption geometries of Y atoms on the Si(001) surface. This paves a way for understanding and eventually controlling the growth of rare earth disilicide wires on the Si(001) substrate that are promising for various applications. For a single Y atom, the interrowdn site was found to be at least 400 meV lower in energy than other possible binding sites. The emulated STM images are in good agreement with experimental results of Er on Si(001). The strong bias and coverage dependence indicates the need for theoretical guidance for the correct interpretation of experimental data. We elucidate the Y‐Si binding mechanism and provide insights toward the onset of formation of hexagonal rare earth disilicide wires.