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Activity-dependent regulation of cytochrome b gene expression in monkey visual cortex.

The recent demonstration that certain mitochondrial subunits of cytochrome oxidase (CO) are regulated by neuronal activity has stimulated interest in the molecular processes that coordinate nuclear and mitochondrial gene expression following synaptic stimulation. We have studied the constitutive expression and activity-guided regulation of cytochrome b (cyt b), a gene that is encoded by mitochondrial DNA and that was cloned by subtractive hybridization from the lateral geniculate nucleus in the monkey. We have found cyt b mRNA expression in monkey striate cortex to be similar to that of CO activity with regard to the laminar profile and the presence of blobs in the supragranular layers. Layers 2/3, 4C, and 6 contained large numbers of stained cells, many of which were judged to be excitatory neurons, because they showed a Zif268-immunopositive nucleus. We have also found that removal of functional activity reduced cyt b mRNA content in area V1. Columns of reduced cyt b staining were visible after 3 days and were especially striking after 6 days of monocular deprivation. After 3 months of deprivation, the columns lost their contrast and became blurred. Our principal finding, that neuronal activity regulates cyt b levels, suggests that expression of a mitochondrial gene can be affected in a manner similar to that of several known nuclear genes. The differences in cyt b mRNA levels and CO activity after long-term deprivation suggests that some form of differential control is exerted on cyt b. Cyt b expression, therefore, may be used as a marker of altered mitochondrial transcription that is guided by the metabolic demands of active neurons.

Animals↗

c-myc oncogene expression in colorectal cancer.

The pattern of c-myc gene organization and expression has been examined in resected colonic tumors and in the adjacent normal colon from 15 patients undergoing radical surgery. DNA hybridization showed no evidence of gene amplification or rearrangement. Transcripts of the c-myc messenger ribonucleic acid (mRNA) were elevated up to 32-fold in 12 of 15 tumors. The gene product, p62c-myc, was detected by both immunoblotting and immunohistology using a monoclonal antibody raised against a synthetic peptide immunogen. There was close correlation between c-myc mRNA copy number and p62c-myc abundance. Three well differentiated tumors contained high levels of transcript and protein, whereas four poorly differentiated tumors had the lowest levels. The assay of oncogene products may provide new biologically relevant tumor markers for determining prognosis and guiding treatment.

Aged↗

Self-splicing of a Podospora anserina group IIA intron in vitro. Effects of 3'-terminal intron alterations on cleavage at the 5' and 3' splice site.

A shortened derivative of the group IIA intron from the mitochondrial cytochrome-c-oxidase subunit I gene (COI I1) of the ascomycete Podospora anserina can undergo self-splicing in vitro. When compared to self-splicing group IIB introns from yeast mitochondria (aI5c, bI1) the autocatalytic reaction shows a lower efficiency and 5' cleavage takes place predominantly by hydrolysis. In order to test the influence on reaction efficiency and mode of 5' cleavage of the long peripheral structure of domain VI (dVI) we generated mutant Podospora introns that have different structural forms of shortened dVI. Our results show that: (1) in general the size and structure of dVI distal from the branch site is essential for 5' transesterification and influences the efficiency of the second splicing step; (2) 5' transesterification as well as the complete self-splicing reaction is more efficient when the structure of dVI is adapted to that of yeast group IIB introns. Moreover, our data indicate that the postulated gamma-gamma' tertiary interaction is also functional for group IIA introns. A weakening or disruption of this interaction in the Podospora intron leads to a greatly reduced cleavage at the 3' splice site and to a selection of cryptic sites downstream in the 3' exon that almost exclusively restore the strong wild-type gamma-gamma' pairing. The so-called "guide" interaction seems to support the selection of 3' cleavage sites but is of secondary importance in relation to the gamma-gamma' interaction.

Ascomycota↗

Sequence analysis and compositional properties of untranslated regions of human mRNAs.

A detailed computer analysis of the untranslated regions, 5'-UTR and 3'-UTR, of human mRNA sequences is reported. The compositional properties of these regions, compared with those of the corresponding coding regions, indicate that 5'-UTR and 3'-UTR are less affected by the isochore compartmentalization than the corresponding third codon positions of mRNAs. The presence of higher functional constraints in 5'-UTR is also reported. Dinucleotide analysis shows a depletion of CpG and TpA in both sequences. A search for significant sequence motifs using the WORDUP algorithm reveals the patterns already known to have a functional role in the mRNA UTR, and several other motifs whose functional roles remain to be demonstrated. This type of analysis may be particularly useful for guiding site-directed mutagenesis experiments. In addition, it can be used for assessing the nature of anonymous sequences now produced in large amounts in megabase sequencing projects.

Algorithms↗

Fluorescence in situ hybridisation detection of Lactobacillus plantarum group on olives to be used in natural fermentations.

At present there are very few studies on the bacterial diversity of olives and on the importance of the microbial species for the fermentation of olives aimed to table olives production. Most of the authors report on the occurrence of Lactobacillus plantarum as principal member of these communities or at least as the species responsible for the fermentation. In this study, fluorescence in situ hybridisation (FISH) with 16S rRNA probes was used to evaluate the occurrence of L. plantarum in olives. A 18-bp oligonucleotide probe was used in FISH experiments to evaluate the specificity of detection among Lactobacillus species. The probe was tested against 30 Lactobacillus species and appeared to be specific for L. plantarum, L. paraplantarum and L. pentosus. The probe was then used to investigate the occurrence of these species in 25 samples of olives (cultivar "Leccino") collected in Campania region (Southern Italy). The olives were washed in a saline solution and the suspensions were then analysed by FISH and observed by fluorescence microscopy. No hybridisation signal was detected in at least 30 fields of observation when the L. plantarum-specific probe was used, probably due to the low sensitivity of the FISH method. Olive samples were plated on Rogosa agar and about 40% of the samples did not give growth after 5 days. When colony growth was observed, bulk cells from Rogosa agar plates were collected and analysed by DNA extraction followed by 16S rDNA Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The different microbial species were identified by direct sequencing of DGGE bands. Leuconostoc pseudomesenteroides was the most frequently found species, occurring in more than 50% of the samples that had shown growth on Rogosa agar. The closest relatives of the species of the genera: Leuconostoc, Pediococcus, Pseudomonas and Raoultella were also identified suggesting that guided fermentation by using selected LAB starters is advisable for a safe and desired table olives production.

Base Sequence↗

Increase in CCR5 Delta32/Delta32 genotype in multiple sclerosis.

Chemokines and their receptors participate in the development of multiple sclerosis (MS) by guiding immune cells into the brain tissue. A CCR5 Delta32 deletion mutation abolishes functional CCR5 on the cell surface and may reduce cell entry into the lesion sites. To analyse the significance of this mutation in MS, we compared the frequencies of CCR5 genotype in peripheral blood mononuclear cells from 89 MS patients and 119 healthy controls. The CCR5 genotype was further compared with the CCR5 RNA and surface protein expression in 48 MS patients and their controls. In all MS patients, the Delta32/32 genotype was found with 6.7% frequency, whereas it was present only in 0.8% of the controls (6/89 vs 1/119, P = 0.01). Specifically, the Delta32/Delta32 genotype was increased (11.5%, P = 0.05) among primary progressive MS patients, whereas it was present only in 4.8% in other MS subtypes and only in 0.8% of the controls. The amount of CCR5 protein on CD4(+) cells analysed in 48 MS patients (nine primary progressive MS, 18 secondary progressive MS, 21 relapsing-remitting MS) and 13 controls decreased with genotype, being 8.9% in wt/wt, 7.7% in wt/Delta32 and 4.3% in Delta32/Delta32. CCR5 surface expression analysed on these 48 MS patients and 13 controls was significantly decreased in Delta32/Delta32 MS patients as compared with that in wt/wt genotype individuals (P = 0.004). The significantly increased number of Delta32/Delta32 individuals among our MS patients suggests that this genotype could contribute as a general risk factor for MS. However, neither the levels of RNA or surface protein correlated with MS subtype, neurological disability as expressed by expanded disability status scale, or disease progression index. Our results suggest that the lack of CCR5 does not protect from MS, but rather it may predispose to the chronic course of the disease. This would further imply that in view of the redundancy in the chemokine system, CCR5 ligands must be assumed to function through other closely related chemokine receptors.

Adult↗

Expression studies on clustered trypanosomatid box C/D small nucleolar RNAs.

We analyzed three chromosomal loci of the trypanosomatid Leptomonas collosoma encoding box C/D small nucleolar RNAs (snoRNAs). All the snoRNAs that were analyzed here carry two sequences complementary to rRNA target sites and obey the +5 rule for guide methylation. Studies on transgenic parasites carrying the snoRNA-2 gene in the episomal expression vector (pX-neo) indicated that no promoter activity was found immediately adjacent to this gene. Deleting the flanking sequences of snoRNA-2 affected the expression; in the absence of the 3'-flanking (but not 5'-flanking) sequence, the expression was almost completely abolished. The snoRNA genes are transcribed as polycistronic RNA. All snoRNAs can be folded into a common stem-loop structure, which may play a role in processing the polycistronic transcript. snoRNA B2, a member of a snoRNA cluster, was expressed when cloned into the episomal vector, suggesting that each gene within a cluster is individually processed. Studies with permeable cells indicated that snoRNA gene transcription was relatively sensitive to alpha-amanitin, thus supporting transcription by RNA polymerase II. We propose that snoRNA gene expression, similar to protein-coding genes in this family, is regulated at the processing level.

Amanitins↗

Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics.

Elongation factor (EF-) Tu.GTP is the carrier of aminoacyl-tRNA to the programmed ribosome. Enacyloxin IIa inhibits bacterial protein synthesis by hindering the release of EF-Tu.GDP from the ribosome. The crystal structure of the Escherichia coli EF-Tu.guanylyl iminodiphosphate (GDPNP).enacyloxin IIa complex at 2.3 A resolution presented here reveals the location of the antibiotic at the interface of domains 1 and 3. The binding site overlaps that of kirromycin, an antibiotic with a structure that is unrelated to enacyloxin IIa but that also inhibits EF-Tu.GDP release. As one of the major differences, the enacyloxin IIa tail borders a hydrophobic pocket that is occupied by the longer tail of kirromycin, explaining the higher binding affinity of the latter. EF-Tu.GDPNP.enacyloxin IIa shows a disordered effector region that in the Phe-tRNAPhe.EF-Tu (Thermus aquaticus).GDPNP.enacyloxin IIa complex, solved at 3.1 A resolution, is stabilized by the interaction with tRNA. This work clarifies the structural background of the action of enacyloxin IIa and compares its properties with those of kirromycin, opening new perspectives for structure-guided design of novel antibiotics.

Anti-Bacterial Agents↗

Analysis of transcription control signals using artificial neural networks.

The role of the upstream region in controlling the transcription efficiency of a gene is well established. However, the question of predicting the extent of gene expressed given the upstream region has so far remained unresolved. Using an artificial neural network (ANN) to capture the internal representation associated with the transcription control signal, the present work predicts the rate of mRNA synthesis based on the pattern contained in the upstream region. Further, the model has been used to predict the transcription efficiency for all possible single base mutations associated with the beta-globin promoter. The simulation results reveal that apart from the experimental observation that alpha-79G-A and -78G-A mutation increases the efficiency of transcription, mutation in these regions by C or T also causes an increase in transcription. Furthermore the simulation results verify that mutations in the conserved region, in general, decrease the transcriptional efficiency. However, the results also show that certain sequence elements, when mutated, either cause a marginal increase in the level of transcription or have no effect on transcription levels. The simulation results can be used as a guide in designing mutation experiments since an a priori estimate of the possible outcome of a mutation can be obtained.

Animals↗

Nerve-dependent and -independent tenascin expression in the developing chick limb bud.

The extracellular matrix protein, tenascin, appears in a restricted pattern during organ morphogenesis. Tenascin accumulates along developing peripheral nerves as they leave the spinal cord and enter the limb mesenchyme (Wehrle and Chiquet, Development 110, 401-415, 1990). Here we found that most but not all tenascin deposited along growing nerves is of glial origin. By in situ hybridization with a tenascin cDNA probe, we determined the site of tenascin mRNA accumulation both in normal and nerve-free limbs. In normal wing buds, tenascin mRNA was first detected within the developing limb nerves. Vinculin-positive glial precursor cells, which comigrate with the axons, are the likely source of this tenascin message. In nerveless wing grafts, tenascin was first expressed in tendon primordia in the absence, and thus independently, from innervation. In contrast to normal limbs, grafted wing buds neither contained vinculin-positive glial precursor cells, nor expressed tenascin in regions proximal to tendon primordia. In normal wing buds, tenascin deposited by tendon primordia transiently parallels and surrounds certain developing nerves. After the major nerve pattern is established, tenascin mRNA disappears from nerves in the upper limb, but is expressed in perichondrium and tendons. We propose that glial tenascin facilitates the penetration of axons into the limb bud and is important for nerve fasciculation. In some places, early tendon primordia might help to guide the migration of axons and glial precursor cells towards their target.

Animals↗

Genome-scale analysis of lung cancer progression.

Among cancers, lung cancer is the single biggest killer in the US. It is estimated that lung cancer was responsible for 171900 newly diagnosed cases of cancer in the US in 2003, and for 157200 deaths. Over many years, however, there has been little improvement in the clinical outcome of lung cancer, and any improvement in the incidence or mortality from lung cancer can largely be attributed to smoking cessation and not to the success of therapy. The histopathology of lung cancer reveals that it is a disease with many faces. Lung cancer is often nonresponsive to traditional therapy, leaving few, if any, alternatives in the management of the advanced stages of the disease. The molecular pathogenesis of lung cancer, only recently illuminated, involves numerous molecular and cell biological changes revealing a very complex disease progression. Large-scale mRNA expression analysis has been recently used to classify lung cancers molecularly. These techniques have been used successfully to differentiate lung cancer histotypes based on patterns of genes expressed. The use of protein analysis to this end has also been attempted, with limited correlation with RNA experiments. This likely reflects the limited sensitivity of the technologies and complex, poorly understood post-synthesis protein modifications. In any event, there have been great strides made in understanding the nature of lung cancer from a molecular perspective; these effects represent a great advancement in the diagnosis and prognosis of lung cancer. Moreover, these advances may lead to the improvement of patient survival by guiding the choice of more efficacious therapy.

Antineoplastic Agents↗

Stromelysin-3 mRNA expression and malignancy: comparison with clinicopathological features and type IV collagenase mRNA expression in breast tumors.

mRNA expression of stromelysin-3 (ST3) and 72K type IV collagenase (cIVase) in 4 human breast cancer cell lines and 55 resected breast tumors were examined using Northern blot analysis. In 4 cell lines ST3 was not expressed at all, while cIVase gene expression was detected in 3 of them. The ST3 expression was found more specifically in malignant tumors (39/40, 97.5%) than in benign ones (4/15, 26.7%), although cIVase was expressed in all tumor specimens. The quantitative analysis showed that ST3 expression in malignancies was significantly greater than that in benign tumors (P = 0.0007), while cIVase expression was not (P = 0.1381). ST3 gene expression was also closely related to the presence of lymph node metastasis (P = 0.047), while cIVase was not (P = 0.1091). These results suggest, therefore, that ST3 is expressed more specifically by stromal cells surrounding cancer cells than cIVase. Since ST3 mRNA expression was independent of the EGFR, ER and erbB2 protein expression, ST3 may be a new potent prognostic guide for breast carcinomas, which can detect highly malignant subpopulations.

Breast Neoplasms↗

Distribution of BDNF and trkB mRNA in the otic region of 3.5 and 4.5 day chick embryos as revealed with a combination of in situ hybridization and tract tracing.

We have used a recently developed technique which combines fluorescent tract tracing and in situ hybridization to study co-localization of neurotrophin mRNA and neurotrophin receptor mRNA expression simultaneously with the pattern of innervation in the developing chick ear. Efferent and afferent fibersfrom the VII/VIIIth cranial nerves were retrogradely and anterogradely filled with Dextran amines conjugated to Texas red and the brain stem was incubated for 2 hours in tissue culture medium. The tissue was subsequently fixed, sectioned frozen, mounted and subjected to in situ hybridization analysis using probes for brain-derived neurotrophic factor (BDNF) and its tyrosine kinase receptor, trkB. The results show that afferent and efferent fibers to the ear innervate areas of the developing otocyst which express BDNF mRNA. We also found that neurons in the stato-acoustic ganglion express high levels of trkB mRNA whereas the subset of facial motor neurons that is efferent to the ear only had no or very low levels of trkB mRNA. From our results we conclude that chicken otic efferent fibers preferentially project to areas with BDNF mRNA expression. The very low levels of trkB mRNA in these motor neurons compared to afferent neurons innervating the same region suggest that other factors, perhaps co-expressed with BDNF, may support efferents. A possible involvement of afferents in guiding efferents to specific areas of the ear is suggested.

Animals↗

Gamma-tubulin is essential for acentrosomal microtubule nucleation and coordination of late mitotic events in Arabidopsis.

Gamma-tubulin is required for microtubule (MT) nucleation at MT organizing centers such as centrosomes or spindle pole bodies, but little is known about its noncentrosomal functions. We conditionally downregulated gamma-tubulin by inducible expression of RNA interference (RNAi) constructs in Arabidopsis thaliana. Almost complete RNAi depletion of gamma-tubulin led to the absence of MTs and was lethal at the cotyledon stage. After induction of RNAi expression, gamma-tubulin was gradually depleted from both cytoplasmic and microsomal fractions. In RNAi plants with partial loss of gamma-tubulin, MT recovery after drug-induced depolymerization was impaired. Similarly, immunodepletion of gamma-tubulin from Arabidopsis extracts severely compromised in vitro polymerization of MTs. Reduction of gamma-tubulin protein levels led to randomization and bundling of cortical MTs. This finding indicates that MT-bound gamma-tubulin is part of a cortical template guiding the microtubular network and is essential for MT nucleation. Furthermore, we found that cells with decreased levels of gamma-tubulin could progress through mitosis, but cytokinesis was strongly affected. Stepwise diminution of gamma-tubulin allowed us to reveal roles for MT nucleation in plant development, such as organization of cell files, anisotropic and polar tip growth, and stomatal patterning. Some of these functions of gamma-tubulin might be independent of MT nucleation.

Arabidopsis↗

Mutations conferring resistance to a potent hepatitis C virus serine protease inhibitor in vitro.

BILN 2061 is a novel, specific hepatitis C virus (HCV) NS3 serine protease inhibitor discovered by Boehringer Ingelheim that has shown potent activity against HCV replicons in tissue culture and is currently under clinical investigation for the treatment of HCV infection. The poor fidelity of the HCV RNA-dependent RNA polymerase will likely lead to the development of drug-resistant viruses in treated patients. The development of resistance to BILN 2061 was studied by the in vitro passage of HCV genotype 1b replicon cells in the presence of a fixed concentration of the drug. Three weeks posttreatment, four colonies were expanded for genotypic and phenotypic characterization. The 50% inhibitory concentrations of BILN 2061 for these colonies were 72- to 1,228-fold higher than that for the wild-type replicon. Sequencing of the individual colonies identified several mutations in the NS3 serine protease gene. Molecular clones containing the single amino acid substitution A156T, R155Q, or D168V resulted in 357-fold, 24-fold, and 144-fold reductions in susceptibility to BILN 2061, respectively, compared to the level of susceptibility shown by the wild-type replicon. Modeling studies indicate that all three of these residues are located in close proximity to the inhibitor binding site. These findings, in addition to the three-dimensional structure analysis of the NS3/NS4A serine protease inhibitor complex, provide a strategic guide for the development of next-generation inhibitors of HCV NS3/NS4A serine protease.

Amino Acid Sequence↗

Maturation of dendritic cells and T-cell responses in sentinel lymph nodes from patients with breast carcinoma.

BACKGROUND: Methods for identifying sentinel lymph nodes (SNs) and their clinical significance have been established. Recent advances in molecular immunology have enabled the analysis of precise immune responses. The objective of the current study was to clarify the dendritic cell (DC) maturation, T-helper type 1 (Th-1) and Th-2 responses, and regulatory T-cell responses of SNs in patients with breast carcinoma. METHODS: SNs and non-SNs were identified by radioguided and blue dye-guided methods in 70 consecutive patients with clinically lymph node negative (N0) breast carcinoma. Lymphocytes were collected from SNs and non-SNs and were subjected to flow cytometric analysis (FCM) using antibodies of CD83-fluorescein isothiocyanate (FITC), CD80-phycoerythrin (PE), CD86-PE, CD40-PE, human leukemic D-related antigen (HLA-DR)-FITC, CD4-FITC, and CD25-PE. Total RNA was extracted from SNs and non-SNs, and the expression of CD83, interleukin 12p40 (IL-12p40), interferon gamma (IFN-gamma), IL-4, IL-10, and Foxp3 was evaluated by using quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. The immunologic status of SNs was analyzed further with regard to micrometastases, which were identified as negative microscopically but positive according to an RT-PCR analysis that was specific for mammaglobin. RESULTS: SNs were detectable in 70 of 71 consecutive patients (98.6%) with clinically N0 breast carcinoma. Fourteen of 70 patients (20.0%) had positive metastasis in SNs. When SNs were compared with non-SNs in 56 metastasis-negative patients, FCM revealed that HLA-DR-positive, CD80-positive, CD86-positive, and CD40-positive cell populations were decreased significantly in SNs. RT-PCR analysis demonstrated that, among 44 patients with metastasis-negative SNs, the expression levels of CD83 and IFN-gamma mRNA were significantly lower in SNs compared with non-SNs. Immunologic parameters also were compared between 44 metastasis-negative SNs and 14 metastasis-positive SNs. The metastasis-positive SNs demonstrated significantly higher expression of CD83, IL-12p40, IFN-gamma, IL-10, and Foxp3 mRNA than the metastasis-negative SNs. Correction of micrometastasis detected by mammaglobin enhanced these differences consistently. CONCLUSIONS: In patients with breast carcinoma, cellular immune responses, from DC maturation to Th-1 responses, appeared to be less active in SNs compared with non-SNs before metastasis developed. Once metastasis was established in SNs, DC maturation was triggered and was followed by the up-regulation of Th-1 responses, which may reflect antigen-specific immune responses in SNs. Unlike DC maturation and Th-1 responses after metastasis in SNs, up-regulation of Th-2 and regulatory T-cell responses developed in parallel.

Adult↗

Structure-guided discovery of novel aminoglycoside mimetics as antibacterial translation inhibitors.

We report the structure-guided discovery, synthesis, and initial characterization of 3,5-diamino-piperidinyl triazines (DAPT), a novel translation inhibitor class that targets bacterial rRNA and exhibits broad-spectrum antibacterial activity. DAPT compounds were designed as structural mimetics of aminoglycoside antibiotics which bind to the bacterial ribosomal decoding site and thereby interfere with translational fidelity. We found that DAPT compounds bind to oligonucleotide models of decoding-site RNA, inhibit translation in vitro, and induce translation misincorporation in vivo, in agreement with a mechanism of action at the ribosomal decoding site. The novel DAPT antibacterials inhibit growth of gram-positive and gram-negative bacteria, including the respiratory pathogen Pseudomonas aeruginosa, and display low toxicity to human cell lines. In a mouse protection model, an advanced DAPT compound demonstrated efficacy against an Escherichia coli infection at a 50% protective dose of 2.4 mg/kg of body weight by single-dose intravenous administration.

Aminoglycosides↗