bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sept8 controls the binding of vesicle‐associated membrane protein 2 to synaptophysin
Authors: Ito Hidenori , Atsuzawa Kimie , Morishita Rika , Usuda Nobuteru , Sudo Kaori , Iwamoto Ikuko , Mizutani Kosuke , Katoh‐Semba Ritsuko , Nozawa Yoshinori , Asano Tomiko , Nagata Koh‐ichi 
Published: December 2008

AbstractSeptins, a conserved family of GTP/GDP‐binding proteins, are present in organisms as diverse as yeast and mammals. We analyzed the distribution of five septins, Sept6, Sept7, Sept8, Sept9 and Sept11, in various rat tissues by western blot analyses and found all septins to be expressed in brain. We also examined the developmental changes of expression of these septins in the rat brain and found that the level of Sept8 increased during post‐natal development. Morphological analyses revealed that Sept8 is enriched at pre‐synapses. Using yeast two‐hybrid screening, we identified vesicle‐associated membrane protein 2 (VAMP2), a soluble N‐ethylmaleimide‐sensitive factor attachment protein receptor (SNARE), as an interacting protein for Sept8. Synaptophysin is reported to associate with and recruit VAMP2 to synaptic vesicles and dissociate prior to forming the SNARE complex consisting of VAMP2, syntaxin and synaptosome‐associated protein of 25 kDa. We showed that Sept8 suppresses the interaction between VAMP2 and synaptophysin through binding to VAMP2. In addition, we found that Sept8 forms a complex with syntaxin1A, and the Sept8‐VAMP2 interaction is disrupted by synaptosome‐associated protein of 25 kDa. These results suggest that Sept8 may participate in the process of the SNARE complex formation and subsequent neurotransmitter release.
Development of Chemically Defined Media Supporting High-Cell-Density Growth of Lactococci, Enterococci, and Streptococci
Authors: Zhang Guiying , Mills David A. , Block David E. 
Published: December 2008

ABSTRACT

Lactococcus lactis
IL1403 was used as an experimental strain to develop a chemically defined medium for study of the physiology and metabolic pathways of lactococci. An experimental leave-one-out technique was employed to determine the necessity of each of the 57 chemical components used in medium development. A statistical experimental design approach including three fractional factorial designs and a central composite design was used to optimize the fermentation process with 21 variables composed of 19 nutritional factors grouped from the 57 components and two environmental factors (initial pH and temperature). For
L. lactis
IL1403, the maximum biomass concentrations obtained with the two optimal chemically defined media developed in this study (ZMB1 and ZMB2) were generally 3.5- to 4-fold higher than the maximum biomass concentrations obtained with the previously described best synthetic media (SA) and 50% to 68% higher than the maximum biomass concentrations obtained with M17, a complex medium commonly used for lactococci. The new chemically defined media support high-cell-density growth of numerous strains of
L. lactis
,
Enterococcus faecalis
, and
Streptococcus thermophilus
.
Incorporation of Ceramides intoSaccharomyces cerevisiaeGlycosylphosphatidylinositol-Anchored Proteins Can Be Monitored In Vitro
Authors: Bosson Régine , Guillas Isabelle , Vionnet Christine , Roubaty Carole , Conzelmann Andreas 
Published: December 2008

ABSTRACTAfter glycosylphosphatidylinositols (GPIs) are added to GPI proteins ofSaccharomyces cerevisiae, a fatty acid of the diacylglycerol moiety is exchanged for a C26:0fatty acid through the subsequent actions of Per1 and Gup1. In most GPI anchors this modified diacylglycerol-based anchor is subsequently transformed into a ceramide-containing anchor, a reaction which requires Cwh43. Here we show that the last step of this GPI anchor lipid remodeling can be monitored in microsomes. The assay uses microsomes from cells that have been grown in the presence of myriocin, a compound that blocks the biosynthesis of dihydrosphingosine (DHS) and thus inhibits the biosynthesis of ceramide-based anchors. Such microsomes, when incubated with [3H]DHS, generate radiolabeled, ceramide-containing anchor lipids of the same structure as made by intact cells. Microsomes fromcwh43Δ ormcd4Δ mutants, which are unable to make ceramide-based anchors in vivo, do not incorporate [3H]DHS into anchors in vitro. Moreover,gup1Δ microsomes incorporate [3H]DHS into the same abnormal anchor lipids asgup1Δ cells synthesize in vivo. Thus, the in vitro assay of ceramide incorporation into GPI anchors faithfully reproduces the events that occur in mutant cells. Incorporation of [3H]DHS into GPI proteins is observed with microsomes alone, but the reaction is stimulated by cytosol or bovine serum albumin, ATP plus coenzyme A (CoA), or C26:0-CoA, particularly if microsomes are depleted of acyl-CoA. Thus, [3H]DHS cannot be incorporated into proteins in the absence of acyl-CoA.
Regulation and Activity of a Zinc Uptake Regulator, Zur, in
Corynebacterium diphtheriae
Authors: Smith Kelsy F. , Bibb Lori A. , Schmitt Michael P. , Oram Diana M. 
Published: December 2008

ABSTRACT

Regulation of metal ion homeostasis is essential to bacterial cell survival, and in most species it is controlled by metal-dependent transcriptional regulators. In this study, we describe a
Corynebacterium diphtheriae
ferric uptake regulator-family protein, Zur, that controls expression of genes involved in zinc uptake. By measuring promoter activities and mRNA levels, we demonstrate that Zur represses transcription of three genes (
zrg
,
cmrA
, and
troA
) in zinc-replete conditions. All three of these genes have similarity to genes involved in zinc uptake. Transcription of
zrg
and
cmrA
was also shown to be regulated in response to iron and manganese, respectively, by mechanisms that are independent of Zur. We demonstrate that the activity of the
zur
promoter is slightly decreased under low zinc conditions in a process that is dependent on Zur itself. This regulation of
zur
transcription is distinctive and has not yet been described for any other
zur
. An adjacent gene, predicted to encode a metal-dependent transcriptional regulator in the ArsR/SmtB family, is transcribed from a separate promoter whose activity is unaffected by Zur. A
C. diphtheriae zur
mutant was more sensitive to peroxide stress, which suggests that
zur
has a role in protecting the bacterium from oxidative damage. Our studies provide the first evidence of a zinc specific transcriptional regulator in
C. diphtheriae
and give new insights into the intricate regulatory network responsible for regulating metal ion concentrations in this toxigenic human pathogen.
Characterization of YvcJ, a Conserved P-Loop-Containing Protein, and Its Implication in Competence in
Bacillus subtilis
Authors: Luciano Jennifer , Foulquier Elodie , Fantino Jean-Raphael , Galinier Anne , Pompeo Frédérique 
Published: December 2008

ABSTRACT

The uncharacterized protein family UPF0042 of the Swiss-Prot database is predicted to be a member of the conserved group of bacterium-specific P-loop-containing proteins. Here we show that two of its members, YvcJ from
Bacillus subtilis
and YhbJ, its homologue from
Escherichia coli
, indeed bind and hydrolyze nucleotides. The cellular function of
yvcJ
was then addressed. In contrast to results recently obtained for
E. coli
, which indicated that
yhbJ
mutants strongly overproduced glucosamine-6-phosphate synthase (GlmS), comparison of the wild type with the
yvcJ
mutant of
B. subtilis
showed that GlmS expression was quite similar in the two strains. However, in mutants defective in
yvcJ
, the transformation efficiency and the fraction of cells that expressed competence were reduced. Furthermore, our data show that YvcJ positively controls the expression of late competence genes. The overexpression of
comK
or
comS
compensates for the decrease in competence of the
yvcJ
mutant. Our results show that even if YvcJ and YhbJ belong to the same family of P-loop-containing proteins, the deletion of corresponding genes has different consequences in
B. subtilis
and in
E. coli
.
Chromatin Organization and Radio Resistance in the Bacterium
Gemmata obscuriglobus
Authors: Lieber Arnon , Leis Andrew , Kushmaro Ariel , Minsky Abraham , Medalia Ohad 
Published: December 2008

ABSTRACT

The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures.
Gemmata obscuriglobus
, a member of the phylum
Planctomycetes
, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase
G. obscuriglobus
cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.
Expression and distribution of Toll-like receptors 11–13 in the brain during murine neurocysticercosis
Authors: Mishra Bibhuti B , Gundra Uma Mahesh , Teale Judy M 
Published: December 2008

AbstractThe functions of Toll-like receptors (TLRs) 11–13 in central nervous system (CNS) infections are currently unknown. Using a murine model of neurocysticercosis, we investigated the expression and distribution of TLRs 11–13 by using both gene specific real-time PCR analysis andin situimmunofluoresence microscopy in both control and neurocysticercosis brains. In the mock infected brain, mRNAs of TLRs 11–13 were constitutively expressed. Parasite infection caused an increase of both mRNAs and protein levels of all three TLRs by several fold. All three TLR proteins were present in both CNS and immune cell types. Among them TLR13 was expressed the most in terms of number of positive cells and brain areas expressing it, followed by TLR11 and TLR12 respectively. Among the nervous tissue cells, TLRs 11–13 protein levels appeared highest in neurons. However, TLR13 expression was also present in ependymal cells, endothelial cells of pial blood vessels, and astrocytes. In contrast, infiltrating CD11b and CD11c positive myeloid cells predominantly produced TLR11 protein, particularly early during infection at 1 wk post infection (~50% cells). TLRs 12 and 13 proteins were present on approximately 5% of infiltrating immune cells. The infiltrating cells positive for TLRs 11–13 were mostly of myeloid origin, CD11b+ cells. This report provides a comprehensive analysis of the expression of TLRs 11–13 in normal and parasite infected mouse brains and suggests a role for them in CNS infections.
CCR7-deficient mice develop atypically persistent germinal centers in response to thymus-independent type 2 antigens
Authors: Achtman Ariel H , Höpken Uta E , Bernert Carola , Lipp Martin 
Published: December 2008

AbstractThymus-independent type 2 (TI-2) antigens are repetitive antigens capable of eliciting antibody responses without T cell help. They are important in the immune response against encapsulated bacteria and as a rapid first line of defense against pathogens. TI-2 antigens induce strong proliferation in extrafollicular foci. However, any germinal centers forming in response to TI-2 antigens involute synchronously 5 days after immunization. This is thought to be caused by the lack of T cell help. Surprisingly, immunization of mice deficient for the homeostatic chemokine receptor CCR7 with TI-2 antigens resulted not only in the expected, vigorous extrafollicular plasma cell response but also in persisting splenic germinal centers. This was observed for two different TI-2 antigens, heat-killed Streptococcus pneumoniae and (4-hydroxy-3-nitrophenyl)acetyl-Ficoll (NP-Ficoll). Germinal centers induced by TI-2 and thymus-dependent (TD) antigens were located in the periarteriolar area of the white pulp in CCR7 knockout mice, corresponding to the T zone of wild-type (WT) mice. The TI-2-induced germinal centers contained peripheral rings of follicular dendritic cells and unusually for TI-2-induced germinal centers, T cells. The licensing responsible for their atypical persistence did not endow TI-2-induced germinal centers with the full range of characteristics of classic germinal centers induced by TD antigens. Thus, class-switching, affinity maturation, and memory B cell generation were not increased in CCR7-deficient mice. It seems unlikely that a defect in regulatory T cell (Treg) location was responsible for the atypical persistence of TI-2-induced germinal centers, as Tregs were comparably distributed in germinal centers of CCR7-deficient and WT mice.
Towards a Dual‐Tip STM Application in Mesoscopic Electron Transport
Authors: Dana Rami , Kiruschev Irina , Tran Phong Dinh , Doppelt Pascal , Manassen Yishay 
Published: December 2008

AbstractA new design for a dual‐tip scanning tunneling microscope (STM) is presented. The design is a variation on the mechanically controllable break‐junction with two electron beam‐induced deposition nano‐tips. The new design enables one to scan surfaces simultaneously with two probes having a nano‐gap separation. By collecting the lateral current flowing between the tips, the transconductance map can then be compared with the STM images for local characterizations of the electron transport. Since the lateral beam carries the property of the density of states of the surface at momentum space, the dispersion of the electronic structure should give an orientation and position dependence of the local transconductance current. In addition, the reduced terminal separation, on the order of the characteristic mesoscopic length scales, is likely to be sensitive to a variety of typically observed interactions and interference effects.
Corneal Limbal Microenvironment Can Induce Transdifferentiation of Hair Follicle Stem Cells into Corneal Epithelial-like Cells
Authors: Blazejewska Ewa Anna , Schlötzer-Schrehardt Ursula , Zenkel Matthias , Bachmann Björn , Chankiewitz Erik , Jacobi Christina , Kruse Friedrich E. 
Published: December 2008

Abstract
The aim of this study was to investigate the transdifferentiation potential of murine vibrissa hair follicle (HF) stem cells into corneal epithelial-like cells through modulation by corneal- or limbus-specific microenvironmental factors. Adult epithelial stem cells were isolated from the HF bulge region by mechanical dissection or fluorescence-activated cell sorting using antibodies to α6 integrin, enriched by clonal expansion, and subcultivated on various extracellular matrices (type IV collagen, laminin-1, laminin-5, fibronectin) and in different conditioned media derived from central and peripheral corneal fibroblasts, limbal stromal fibroblasts, and 3T3 fibroblasts. Cellular phenotype and differentiation were evaluated by light and electron microscopy, real-time reverse transcription-polymerase chain reaction, immunocytochemistry, and Western blotting, using antibodies against putative stem cell markers (K15, α6 integrin) and differentiation markers characteristic for corneal epithelium (K12, Pax6) or epidermis (K10). Using laminin-5, a major component of the corneo-limbal basement membrane zone, and conditioned medium from limbal stromal fibroblasts, clonally enriched HF stem and progenitor cells adhered rapidly and formed regularly arranged stratified cell sheets. Conditioned medium derived from limbal fibroblasts markedly upregulated expression of cornea-specific K12 and Pax6 on the mRNA and protein level, whereas expression of the epidermal keratinocyte marker K10 was strongly downregulated. These findings suggest that adult HF epithelial stem cells are capable of differentiating into corneal epithelial-like cells in vitro when exposed to a limbus-specific microenvironment. Therefore, the HF may be an easily accessible alternative therapeutic source of autologous adult stem cells for replacement of the corneal epithelium and restoration of visual function in patients with ocular surface disorders.
Evidence for Transcriptional Regulation of the Glucose-6-Phosphate Transporter by HIF-1α: Targeting G6PT with Mumbaistatin Analogs in Hypoxic Mesenchymal Stromal Cells
Authors: Lord-Dufour Simon , Copland Ian B. , Levros Louis-Charles , Post Martin , Das Abhirup , Khosla Chaitan , Galipeau Jacques , Rassart Eric , Annabi Borhane 
Published: December 2008

Abstract
Mesenchymal stromal cell (MSC) markers are expressed on brain tumor-initiating cells involved in the development of hypoxic glioblastoma. Given that MSCs can survive hypoxia and that the glucose-6-phosphate transporter (G6PT) provides metabolic control that contributes to MSC mobilization and survival, we investigated the effects of low oxygen (1.2% O2) exposure on G6PT gene expression. We found that MSCs significantly expressed G6PT and the glucose-6-phosphatase catalytic subunit β, whereas expression of the glucose-6-phosphatase catalytic subunit α and the islet-specific glucose-6-phosphatase catalytic subunit-related protein was low to undetectable. Analysis of the G6PT promoter sequence revealed potential binding sites for hypoxia inducible factor (HIF)-1α and for the aryl hydrocarbon receptor (AhR) and its dimerization partner, the AhR nuclear translocator (ARNT), AhR:ARNT. In agreement with this, hypoxia and the hypoxia mimetic cobalt chloride induced the expression of G6PT, vascular endothelial growth factor (VEGF), and HIF-1α. Gene silencing of HIF-1α prevented G6PT and VEGF induction in hypoxic MSCs whereas generation of cells stably expressing HIF-1α resulted in increased endogenous G6PT gene expression. A semisynthetic analog of the polyketide mumbaistatin, a potent G6PT inhibitor, specifically reduced MSC-HIF-1α cell survival. Collectively, our data suggest that G6PT may account for the metabolic flexibility that enables MSCs to survive under conditions characterized by hypoxia and could be specifically targeted within developing tumors.
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

AbstractEpstein-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

AbstractThe 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

AbstractThe 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.