bluuebunny/crossref_metadata_2025_split huggingface dataset:
Koci drill for drilling in ice, sand and rock: drill requirements, design, performance, difficulties
Authors: Green J. , Koci B. , Kyne J. 
Published: December 2008

AbstractA 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

AbstractThe 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.
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

AbstractThe 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

AbstractApomorphine (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

AbstractTo 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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTIt 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

ABSTRACT

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

ABSTRACT

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.
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

AbstractIn 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

Abstract
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.
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

AbstractWe 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.
Scanning Tunneling Spectroscopy Study of Temperature‐Dependent Magnetization Switching Dynamics in Magnetic Nanoparticle Arrays
Authors: Tirosh Einat , Taub Nurit , Majetich Sara A. , Markovich Gil 
Published: December 2008

AbstractScanning tunneling microscopy measurements were performed on close‐packed arrays of surfactant‐capped magnetite (Fe3O4) nanocrystals. Current noise measurements over individual nanoparticles (NPs) at 2–3‐particle‐thick positions displayed enhanced low‐frequency noise power around the magnetization blocking temperature of the array. This noise originated in a time‐varying spin filter effect due to slow magnetization switching of individual particles in the arrays, changing their magnetization orientation with respect to their neighbors. The magnetite nanocrystals, being half‐metallic, highly spin‐polarized conductors, enabled this new observation. Consequently, this type of experiment may provide new insight into the microscopic details of magnetization dynamics in strongly interacting arrays of dipoles, which resemble spin‐glasses.
After-School Supervision and Children's Cognitive Achievement
Authors: Welsch David M. , Zimmer David M. 
Published: December 2008

Abstract
This paper estimates the relationship between after-school supervision and cognitive achievement using a nationally-representative sample of children. The topic has important public policy implications due to the large role assumed by the government in providing childcare. The effects of family and nonfamily supervision are considered separately. Estimates suggest that adult supervision, regardless of whether it is provided by a family or nonfamily member, is not directly related to a child's cognitive performance. Instead, children who are likely to receive after-school adult supervision from a family member possess unmeasured personal- or family-specific traits that induce improved cognitive performance. In contrast, children who are likely to receive supervision from nonfamily members possess unmeasured traits that lead to lower cognitive outcomes.
The SideWinder for powering a hand-coring auger in drilling and lifting
Authors: Kyne Jay , McConnell Joe 
Published: December 2008

AbstractThe SideWinder is a power delivery system for a hand-coring ice auger. It not only greatly increases the rate of drilling, it also makes it possible for a single operator to drill to depths difficult and cumbersome for hand-coring systems. The SideWinder power is delivered by an electric drill that is used for both the drilling and the lifting of the drill string. A high-strength low-stretch synthetic-fiber rope lifts and lowers the drill string as it winds around a tube attached to the electric drill. During winding, the synthetic-fiber rope is guided onto the winding tube by rope cleats that also serve as a quick way to secure the rope for drilling. The end of the winding tube connects directly to the protruding extension of the drill string for drilling. The rope always remains attached to the drill string by a rope-pin that replaces the bottommost connecting pin; the winding tube holds the rope and always stays attached to the electric drill. For lifting and lowering the drill string, cradle arms on a frame that hinges on a plywood platform hold the winding tube.