bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuromelanin selectively induces apoptosis in dopaminergic SH‐SY5Y cells by deglutathionylation in mitochondria: involvement of the protein and melanin component
Authors: Naoi Makoto , Maruyama Wakako , Yi Hong , Yamaoka Yuriko , Shamoto‐Nagai Masayo , Akao Yukihiro , Gerlach Manfred , Tanaka Masashi , Riederer Peter 
Published: March 2008

AbstractParkinson’s disease (PD) is characterized by selective depletion of nigral dopamine (DA) neurons containing neuromelanin (NM), suggesting the involvement of NM in the pathogenesis. This study reports induction of apoptosis by NM in SH‐SY5Y cells, whereas protease‐K‐treated NM, synthesized DA‐ and cysteinyl dopamine melanin showed much less cytotoxicity. Cell death was mediated by mitochondria‐mediated apoptotic pathway, namely collapse of mitochondrial membrane potential, release of cytochrome c, and activation of caspase 3, but Bcl‐2 over‐expression did not suppress apoptosis. NM increased sulfhydryl content in mitochondria, and a major part of it was identified as GSH, whereas dopamine melanin significantly reduced sulfhydryl levels. Western blot analysis for protein‐bound GSH demonstrated that only NM reduced S‐glutathionylated proteins in mitochondria and dissociated macromolecular structure of complex I. Reactive oxygen and nitrogen species were required for the deglutathionylation by NM, which antioxidants reduced significantly with prevention of apoptosis. These results suggest that NM may be related to cell death of DA neurons in PD and aging through regulation of mitochondrial redox state and S‐glutathionylation, for which NM‐associated protein is absolutely required. The novel function of NM is discussed in relation to the pathogenesis of PD.
Comparison of neuroprotective and neurorestorative capabilities of rasagiline and selegiline against lactacystin‐induced nigrostriatal dopaminergic degeneration
Authors: Zhu Wen , Xie Wenjie , Pan Tianhong , Jankovic Joseph , Li Jun , Youdim Moussa B. H. , Le Weidong 
Published: March 2008

AbstractNigrostriatal neurodegeneration in Parkinson’s disease (PD) has been postulated to be caused by various pathological conditions, such as mitochondrial defects, oxidative stress, and ubiquitin‐proteasome system (UPS) dysfunction. Pharmacological strategies designed to interfere with these pathological pathways may effectively counteract the degeneration. Rasagiline and selegiline are selective and irreversible monoamine oxidase‐B inhibitors that possess significant protective properties on dopamine neurons in various pre‐clinical models of PD. In the present study, the neuroprotective and neurorestorative effects of rasagiline and selegiline were compared in an animal model of PD produced by inhibition of the UPS. C57BL/6 male mice were microinjected bilaterally with UPS inhibitor lactacystin (1.25 μg/side), into the medial forebrain bundle. Administration of rasagiline (0.2 mg/kg, i.p. once per day) or selegiline (1 mg/kg, i.p. once per day), started 7 days before or after (up to 28 days) after lactacystin microinjection. We found that both rasagiline and selegiline exerted a significant neuroprotective effect against lactacystin‐induced neurodegeneration; but only rasagiline managed to restore the nigrostriatal degeneration. Furthermore, rasagiline showed a modest protection against lactacystin‐induced inhibition of proteasomal activity. Our study indicates that compared with selegiline, rasagiline is more potent in protecting neurodegeneration induced by UPS impairment and may, therefore, exert disease‐modifying effects in PD.
Band 4.1 proteins are expressed in the retina and interact with both isoforms of the metabotropic glutamate receptor type 8
Authors: Rose Melanie , Dütting Eva , Enz Ralf 
Published: March 2008

AbstractThe function of the CNS depends on the correct regulation of neurotransmitter receptors by interacting proteins. Here, we screened a retinal cDNA library for proteins interacting with the intracellular C‐terminus of the metabotropic glutamate receptor isoform 8a (mGluR8a). The band 4.1B protein binds to the C‐termini of mGluR8a and mGluR8b, co‐localizes with these glutamate receptors in transfected mammalian cells, facilitates their cell surface expression and inhibits the mGluR8 mediated reduction of intracellular cAMP concentrations. In contrast, no interaction with 4.1B was observed for other mGluRs tested. Amino acids encoded by exons 19 and 20 of 4.1B and a stretch of four basic amino acids present in the mGluR8 C‐termini mediate the protein interaction. Besides binding to 4.1B, mGluR8 isoforms interact with 4.1G, 4.1N, and 4.1R. Because band 4.1 transcripts undergo extensive alternative splicing, we analyzed the splicing pattern of interacting regions and detected a 4.1B isoform expressed specifically in the retina. Within this tissue, mGluR8 and 4.1B, 4.1G, 4.1N, and 4.1R show a comparable distribution, being expressed in both synaptic layers and in somata of the ganglion cell layer. In summary, our studies identified band 4.1 proteins as new players for the mGluR8 mediated signal transduction.
Effect of sport‐tinted contact lenses for contrast enhancement on retinal straylight measurements
Authors: Cerviño Alejandro , Gonzalez‐Meijome Jose M. , Linhares João M. M. , Hosking Sarah L. , Montes‐Mico Robert 
Published: March 2008

AbstractPurpose:  To investigate the effect of two tinted contact lenses (CL) designed for outdoor sports activity on the psychometric determination of retinal straylight using the compensation comparison method.Methods:  Thirteen emmetropic subjects were randomly fitted with two different tinted Nike Maxsight® (Bausch & Lomb, Rochester, NY, USA) CL in one eye, while the contralateral eye was fitted with a clear lens made of the same material (Optima 38, Bausch & Lomb). Three valid straylight measurements were taken on each eye before and a few minutes after lens insertion, when lens stabilization had occurred.Results:  The subjects’ mean straylight values were 0.90 ± 0.09 at baseline and 0.95 ± 0.10 with the clear Optima 38 CL. Straylight values were 0.97 ± 0.10 and 1.0 ± 0.10 log units with the amber and grey–green tinted CL, respectively. Differences in straylight between baseline (without CL) and with the clear CL in place were neither statistically significant (p = 0.066) nor was there a significant difference between baseline and the amber CL (p = 0.052). However, the grey–green CL showed a statistically significant difference from baseline (p = 0.006). Differences in straylight with the clear CL compared with the grey–green CL were also statistically different from zero (p = 0.002) showing an increased straylight value for the tinted CL. These differences were variable, but consistent for each subject, thus those showing higher or lower changes with one tinted lens tended to show the same trend with the second lens (r2 = 0.736).Conclusions:  Despite increases having been found in straylight values with tinted contact lenses, those changes are not likely to induce clinically significant changes in visual function under photopic conditions, even for the grey–green CL, which seems to increase straylight values more significantly than the amber CL. This difference between the tinted CL could suggest a wavelength dependence of straylight values, although this should be investigated further by controlling for pupil size and subjects’ pigmentation, as well as by using neutral density filters.
Ca2+‐dependent Regulation of Phototransduction†
Authors: Stephen Ricardo , Filipek Sławomir , Palczewski Krzysztof , Sousa Marcelo Carlos 
Published: March 2008

AbstractPhoton absorption by rhodopsin triggers the phototransduction signaling pathway that culminates in degradation of cGMP, closure of cGMP‐gated ion channels and hyperpolarization of the photoreceptor membrane. This process is accompanied by a decrease in free Ca2+ concentration in the photoreceptor cytosol sensed by Ca2+‐binding proteins that modulate phototransduction and activate the recovery phase to reestablish the photoreceptor dark potential. Guanylate cyclase‐activating proteins (GCAPs) belong to the neuronal calcium sensor (NCS) family and are responsible for activating retinal guanylate cyclases (retGCs) at low Ca2+ concentrations triggering synthesis of cGMP and recovery of the dark potential. Here we review recent structural insight into the role of the N‐terminal myristoylation in GCAPs and compare it to other NCS family members. We discuss previous studies identifying regions of GCAPs important for retGC1 regulation in the context of the new structural data available for myristoylated GCAP1. In addition, we present a hypothetical model for the Ca2+‐triggered conformational change in GCAPs and retGC1 regulation. Finally, we briefly discuss the involvement of mutant GCAP1 proteins in the etiology of retinal degeneration as well as the importance of other Ca2+ sensors in the modulation of phototransduction.
Functional
nodFE
Genes Are Present in
Sinorhizobium
sp. Strain MUS10, a Symbiont of the Tropical Legume
Sesbania rostrata
Authors: Krishnan Hari B. , Chronis Demosthenis 
Published: March 2008

ABSTRACT

We have cloned the
nodFE
operon from
Sinorhizobium
sp. strain MUS10. MUS10 NodF shows sequence homology to acyl carrier protein and enables an
S. meliloti nodF
mutant to effectively nodulate alfalfa. Our results demonstrate the occurrence of
nodFE
in a symbiont that nodulates a legume host not belonging to the galegoid group.
Cysteine Scanning Mutagenesis of α4, a Putative Pore-Lining Helix of the
Bacillus thuringiensis
Insecticidal Toxin Cry1Aa
Authors: Girard Frédéric , Vachon Vincent , Préfontaine Gabrielle , Marceau Lucie , Su Yanhui , Larouche Geneviève , Vincent Charles , Schwartz Jean-Louis , Masson Luke , Laprade Raynald 
Published: March 2008

ABSTRACT

Helix α4 of
Bacillus thuringiensis
Cry toxins is thought to line the lumen of the pores they form in the midgut epithelial cells of susceptible insect larvae. To define its functional role in pore formation, most of the α4 amino acid residues were replaced individually by a cysteine in the Cry1Aa toxin. The toxicities and pore-forming abilities of the mutated toxins were examined, respectively, by bioassays using neonate
Manduca sexta
larvae and by a light-scattering assay using midgut brush border membrane vesicles isolated from
M
.
sexta
. A majority of these mutants had considerably reduced toxicities and pore-forming abilities. Most mutations causing substantial or complete loss of activity map on the hydrophilic face of the helix, while most of those having little or only relatively minor effects map on its hydrophobic face. The properties of the pores formed by mutants that retain significant activity appear similar to those of the pores formed by the wild-type toxin, suggesting that mutations resulting in a loss of activity interfere mainly with pore formation.
Comparison of BGM and PLC/PRC/5 Cell Lines for Total Culturable Viral Assay of Treated Sewage
Authors: Rodríguez Roberto A. , Gundy Patricia M. , Gerba Charles P. 
Published: March 2008

ABSTRACT
The objective of this study was to compare PLC/PRF/5 and BGM cell lines for use in a total culturable viral assay (TCVA) of treated sewage effluents. Samples were collected before and after chlorination from an activated sludge wastewater treatment plant and from the effluent of a high-rate enhanced flocculation system, followed by UV light disinfection. Cell monolayers were observed for cytopathic effect (CPE) after two passages of 14 days each. Monolayers exhibiting viral CPE were tested for the presence of adenoviruses and enteroviruses by PCR or reverse transcription-PCR. Eight percent of the samples exhibited CPE on BGM cells, and 57% showed CPE on PLC/PRF/5 cells. Only enteroviruses were detected on the BGM cells, while 30% and 52% of the samples were positive for enteroviruses and adenoviruses, respectively, on the PLC/PRF/5 cells. Thirty percent of the samples were positive for both adenoviruses and enteroviruses in chlorinated activated sludge effluent. Thirty percent of the samples were positive for adenoviruses in the UV treatment effluent, but no enteroviruses were detected. In conclusion, the PLC/PRF/5 cells were more susceptible than BGM cells to viruses found in treated sewage. The use of BGM cells for TCVA may underestimate viral concentration in sewage effluent samples. The PLC/PRF/5 cells were more susceptible to adenoviruses, which is important in the evaluation of UV disinfection systems because adenoviruses are highly resistant to UV inactivation.
Feasibility of Transferring Fluorescent In Situ Hybridization Probes to an 18S rRNA Gene Phylochip and Mapping of Signal Intensities
Authors: Metfies Katja , Medlin Linda K. 
Published: March 2008

ABSTRACT

DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be <150 bp in length to minimize the formation of a secondary structure in the molecule so that the probe could bind to the target site. We found different results with the 18S rRNA molecule. Four out of 12 FISH probes exhibited false-negative signals on the microarray; eight exhibited strong but variable signals using full-length 18S RNA molecules. A systematic investigation of the probe's accessibility to the 18S rRNA gene was made using
Prymenisum parvum
as the target. Fourteen additional probes identical to this target covered the regions not tested with existing FISH probes. Probes with a binding site in the first 900 bp of the gene generated positive signals. Six out of nine probes binding in the last 900 bp of the gene produced no signal. Our results suggest that although secondary structure affected probe binding, the effect is not the same for the 18S rRNA gene and the 16S rRNA gene. For the 16S rRNA gene, the secondary structure is stronger in the first half of the molecule, whereas in the 18S rRNA gene, the last half of the molecule is critical. Probe-binding sites within 18S rRNA gene molecules are important for the probe design for DNA phylochips because signal intensity appears to be correlated with the secondary structure at the binding site in this molecule. If probes are designed from the first half of the 18S rRNA molecule, then full-length 18S rRNA molecules can be used in the hybridization on the chip, avoiding the fragmentation and the necessity for the short PCR amplicons that are associated with using the 16S rRNA molecule. Thus, the 18S rRNA molecule is a more attractive molecule for use in environmental studies where some level of quantification is desired. Target size was a minor problem, whereas for 16S rRNA molecules target size rather than probe site was important.
Cultivation and Ecosystem Role of a Marine
Roseobacter
Clade-Affiliated Cluster Bacterium
Authors: Mayali Xavier , Franks Peter J. S. , Azam Farooq 
Published: March 2008

ABSTRACT

Isolation and cultivation are a crucial step in elucidating the physiology, biogeochemistry, and ecosystem role of microorganisms. Many abundant marine bacteria, including the widespread
Roseobacter
clade-affiliated (RCA) cluster group, have not been cultured with traditional methods. Using novel techniques of cocultivation with algal cultures, we have accomplished successful isolation and propagation of a strain of the RCA cluster. Our experiments revealed that, in addition to growing on alga-excreted organic matter, additions of washed bacterial cells led to significant biomass decrease of dinoflagellate cultures as measured by in vivo fluorescence. Bacterial filtrate did not adversely affect the algal cultures, suggesting attachment-mediated activity. Using an RCA cluster-specific rRNA probe, we documented increasing attachment of these algicidal bacteria during a dinoflagellate bloom, with a maximum of 70% of the algal cells colonized just prior to bloom termination. Cross-correlation analyses between algal abundances and RCA bacterial colonization were statistically significant, in agreement with predator-prey models suggesting that RCA cluster bacteria caused algal bloom decline. Further investigation of molecular databases revealed that RCA cluster bacteria were numerically abundant during algal blooms sampled worldwide. Our findings suggest that the widespread RCA cluster bacteria may exert significant control over phytoplankton biomass and community structure in the oceans. We also suggest that coculture with phytoplankton may be a useful strategy to isolate and successfully grow previously uncultured but ecologically abundant marine heterotrophs.
Quantifying Genes and Transcripts To Assess the In Situ Physiology of “
Dehalococcoides
” spp. in a Trichloroethene-Contaminated Groundwater Site
Authors: Lee Patrick K. H. , Macbeth Tamzen W. , Sorenson Kent S. , Deeb Rula A. , Alvarez-Cohen Lisa 
Published: March 2008

ABSTRACT

Quantitative PCR (qPCR) was coupled with reverse transcription (RT) to analyze both gene copy numbers and transcripts of the 16S rRNA gene and three reductive dehalogenase (RDase) genes (
tceA
,
vcrA
, and
bvcA
) as biomarkers of “
Dehalococcoides
” spp. in the groundwater of a trichloroethene-dense nonaqueous-phase liquid site at Fort Lewis, WA, that was sequentially subjected to biostimulation and bioaugmentation.
Dehalococcoides
cells carrying the
tceA
,
vcrA
, and
bvcA
genes were indigenous to the site. The sum of the three identified RDase gene copy numbers closely correlated to 16S rRNA gene copy numbers throughout the biostimulation and bioaugmentation activity, suggesting that these RDase genes represented the major
Dehalococcoides
metabolic functions at this site. Biomarker quantification revealed an overall increase of more than 3 orders of magnitude in the total
Dehalococcoides
population through the 1-year monitoring period (spanning biostimulation and bioaugmentation), and measurement of the respective RDase gene concentrations indicated different growth dynamics among
Dehalococcoides
cells. The
Dehalococcoides
cells containing the
tceA
gene consistently lagged behind other
Dehalococcoides
cells in population numbers and made up less than 5% of the total
Dehalococcoides
population, whereas the
vcrA
- and
bvcA
-containing cells represented the dominant fractions. Quantification of transcripts in groundwater samples verified that the 16S rRNA gene and the
bvcA
and
vcrA
genes were consistently highly expressed in all samples examined, while the
tceA
transcripts were detected inconsistently, suggesting a less active physiological state of the cells with this gene. The production of vinyl chloride and ethene toward the end of treatment supported the physiological activity of the
bvcA
- and
vcrA
-carrying cells. A clone library of the expressed RDase genes in field samples produced with degenerate primers revealed the expression of two putative RDase genes that were not previously monitored with RT-qPCR. The level of abundance of one of the putative RDase genes (
FtL-RDase-1638
) identified in the cDNA clone library tracked closely in field samples with abundance of the
bvcA
gene, suggesting that the
FtL-RDase-1638
gene was likely colocated in genomes containing the
bvcA
gene. Overall, results from this study demonstrate that quantification of biomarker dynamics at field sites can provide useful information about the in situ physiology of
Dehalococcoides
strains and their associated activity.
Complete Genome Sequence of
Nitrobacter hamburgensis
X14 and Comparative Genomic Analysis of Species within the Genus
Nitrobacter
Authors: Starkenburg Shawn R. , Larimer Frank W. , Stein Lisa Y. , Klotz Martin G. , Chain Patrick S. G. , Sayavedra-Soto Luis A. , Poret-Peterson Amisha T. , Gentry Mira E. , Arp Daniel J. , Ward Bess , Bottomley Peter J. 
Published: March 2008

ABSTRACT

The alphaproteobacterium
Nitrobacter hamburgensis
X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the
Nitrobacter hamburgensis
X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp). Over 20% of the genome is composed of pseudogenes and paralogs. Whole-genome comparisons were conducted between
N. hamburgensis
and the finished and draft genome sequences of
Nitrobacter winogradskyi
and
Nitrobacter
sp. strain Nb-311A, respectively. Most of the plasmid-borne genes were unique to
N. hamburgensis
and encode a variety of functions (central metabolism, energy conservation, conjugation, and heavy metal resistance), yet ∼21 kb of a ∼28-kb “autotrophic” island on the largest plasmid was conserved in the chromosomes of
Nitrobacter winogradskyi
Nb-255 and
Nitrobacter
sp. strain Nb-311A. The
N. hamburgensis
chromosome also harbors many unique genes, including those for heme-copper oxidases, cytochrome
b
561
, and putative pathways for the catabolism of aromatic, organic, and one-carbon compounds, which help verify and extend its mixotrophic potential. A
Nitrobacter
“subcore” genome was also constructed by removing homologs found in strains of the closest evolutionary relatives,
Bradyrhizobium japonicum
and
Rhodopseudomonas palustris
. Among the
Nitrobacter
subcore inventory (116 genes), copies of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes associated with a dissimilatory nitrite reductase (NirK), PII-like regulators, and polysaccharide formation were identified. Many of the subcore genes have diverged significantly from, or have origins outside, the alphaproteobacterial lineage and may indicate some of the unique genetic requirements for nitrite oxidation in
Nitrobacter
.
Biochemical and Molecular Characterization of a Novel Type of Mutanase from
Paenibacillus
sp. Strain RM1: Identification of Its Mutan-Binding Domain, Essential for Degradation of
Streptococcus mutans
Biofilms
Authors: Shimotsuura Isao , Kigawa Hiromitsu , Ohdera Motoyasu , Kuramitsu Howard K. , Nakashima Syozi 
Published: March 2008

ABSTRACT

A novel type of mutanase (termed mutanase RM1) was isolated from
Paenibacillus
sp. strain RM1. The purified enzyme specifically hydrolyzed α-1,3-glucan (mutan) and effectively degraded biofilms formed by
Streptococcus mutans
, a major etiologic agent in the progression of dental caries, even following brief incubation. The nucleotide sequence of the gene for this protein contains a 3,873-bp open reading frame encoding 1,291 amino acids with a calculated molecular mass of 135 kDa. The protein contains two major domains, the N-terminal domain (277 residues) and the C-terminal domain (937 residues), separated by a characteristic sequence composed of proline and threonine repeats. The characterization of the recombinant proteins for each domain which were expressed in
Escherichia coli
demonstrated that the N-terminal domain had strong mutan-binding activity but no mutanase activity whereas the C-terminal domain was responsible for mutanase activity but had mutan-binding activity significantly lower than that of the intact protein. Importantly, the biofilm-degrading activity observed with the intact protein was not exhibited by either domain alone or in combination with the other. Therefore, these results indicate that the structural integrity of mutanase RM1 containing the N-terminal mutan-binding domain is required for the biofilm-degrading activity.