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PubMed2000

Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae.

Bacterial communities in the large intestines of pigs were compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S ribosomal DNA. The pigs were fed different experimental diets based on either modified standard feed or cooked rice supplemented with dietary fibers. After feeding of the animals with the experimental diets for 2 weeks, differences in the bacterial community structure in the spiral colon were detected in the form of different profiles of terminal restriction fragments (T-RFs). Some of the T-RFs were universally distributed, i.e., they were found in all samples, while others varied in distribution and were related to specific diets. The reproducibility of the T-RFLP profiles between individual animals within the diet groups was high. In the control group, the profiles remained unchanged throughout the experiment and were similar between two independent but identical experiments. When the animals were experimentally infected with Brachyspira hyodysenteriae, causing swine dysentery, many of the T-RFs fluctuated, suggesting a destabilization of the microbial community.

Animals↗
PubMed2005

Microbial community structure and density under different tree species in an acid forest soil (Morvan, France).

Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of "Breuil-Chenue" in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0-5, 5-10, and 10-15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation-extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.

Bacteria↗
PubMed2005

Weekly 24 h infusion of aviscumine (rViscumin): a phase I study in patients with solid tumours.

Aviscumine is a ribosome-inactivating protein with potent antitumour activity in vitro and in vivo and is an Escherichia coli-derived recombinant counterpart of natural mistletoe lectin-I. The current study was performed to determine the safety profile, dose-limiting toxicity (DLT) and maximum tolerated dose (MTD) of a prolonged infusion of aviscumine in cancer patients. Aviscumine was given once weekly as a 24 h central intravenous infusion in patients with advanced, refractory progressive solid malignant tumours. Fourteen fully eligible patients (11 male, 3 female) with a median age 58 yrs (range 41-77) were enrolled. They had histologically verified disease, were 18 yrs old, had an ECOG PS 2 and adequate bone marrow, liver and renal function. DLT was defined as any non-haematological grade 3-4 toxicity (Common Toxicity Criteria [CTC] version 2.0), neutrophil count <500/ microl for 7 days, febrile neutropenia or thrombocytopenia grade 4. The MTD was defined as the dose level below the dose at which 2 patients per dose level experienced a DLT during the first treatment cycle. Colorectal cancer, soft tissue sarcoma and pancreatic cancer were the most common tumour types. Dose levels of aviscumine ranged from 4 to 6 microg/kg. The median number of cycles was 2.8 (range, 2-8). Common side effects in cycle 1 were fatigue, fever, nocturia, urticaria, erythema and pruritus. DLTs occurred in 2/3 patients on the 6 microg/kg dose level and consisted of increases in ASAT grade 3, ALAT grade 3, gammaGT grade 3/4, hypokalemia grade 3 and fatigue grade 3. No DLTs were observed on dose levels 4 and 5 microg/kg. The best response (RECIST) was stable disease in 4 pts, lasting for 4-8 cycles. Pharmacokinetics indicated that potentially active plasma levels of the compound were maintained during the entire infusion. We conclude that the recommended dose for weekly 24 h infusions of Aviscumine should be 5 microg/kg.

Adult↗
PubMed1998

Functional quantitative analysis of the genome in cultured human mesangial cells. Technical note.

For normal physiological function, each cell tightly regulates gene expression in a specific fashion so that critical proteins are synthesized in a well-coordinated manner. Therefore, it is very important to uncover which genes are expressed in specific cells. Recent technological advances combined with rapid large-scale DNA sequencing and computerized data processing have allowed us to investigate the expression levels of a variety of transcripts in the mesangial cells, a target of injury in many forms of glomerulonephritis. Utilizing a large scale sequencing of a 3'-directed cDNA library, which allows us to avoid variable cloning efficiencies reflecting the size of cDNA, we investigated expression profiles of various molecules in cultured human mesangial cells. Among the 1,193 sequenced clones, 688 (57.7%) appeared more than once (redundant sequence group), representing 203 different species. Thirty-nine of these appeared more than three times. The most abundant mRNA was that of fibronectin, which consisted of 3.9% of the total mRNA population. Except for mitochondrial or ribosomal genes, calcyclin came next (2.5%), followed by two cytoskeletal genes, gamma-actin gene and calpactin 1 light chain gene, in addition to an amyloid precursor protein homolog (0.7%). In conclusion, we performed a molecular biological quantification of transcripts in mesangial cells. Fibronectin was the most abundantly expressed, followed by calcyclin, gamma-actin, calpactin 1 light chain, and an amyloid precursor protein homolog. We also discovered some candidate genes specific for human mesangial cells. The expression profile of the transcripts serves as an important tool in understanding the biological properties of mesangial cells.

Actins↗
PubMed2004

Acidic proteome of growing and resting Lactococcus lactis metabolizing maltose.

The acidic proteome of Lactococcus lactis grown anaerobically was compared for three different growth conditions: cells growing on maltose, resting cells metabolizing maltose, and cells growing on glucose. In maltose metabolizing cells several proteins were up-regulated compared with glucose metabolizing cells, however only some of the up-regulated proteins had apparent relation to maltose metabolism. Cells growing on maltose produced formate, acetate and ethanol in addition to lactate, whereas resting cells metabolizing maltose and cells growing on glucose produced only lactate. Increased levels of alcohol-acetaldehyde dehydrogenase (ADH) and phosphate acetyltransferase (PTA) in maltose-growing cells compared with glucose-growing cells coincided with formation of mixed acids in maltose-growing cells. The resting cells did not grow due to lack of an amino acid source and fermented maltose with lactate as the sole product, although ADH and PTA were present at high levels. The maltose consumption rate was approximately three times lower in resting cells than in exponentially growing cells. However, the enzyme levels in resting and growing cells metabolizing maltose were similar, which indicates that the difference in product formation in this case is due to regulation at the enzyme level. The levels of 30S ribosomal proteins S1 and S2 increased with increasing growth rate for resting cells metabolizing maltose, maltose-growing cells and glucose-growing cells. A modified form of HPr was synthesized under amino acid starvation. This is suggested to be due to alanine misincorporation for valine, which L. lactis is auxotrophic for. L. lactis conserves the protein profile to a high extent, even after prolonged amino acid starvation, so that the protein expression profile of the bacterium remains almost invariant.

Acetates↗
PubMed2004

Downregulation of ATP synthase subunit-6, cytochrome c oxidase-III, and NADH dehydrogenase-3 by bright cyclic light in the rat retina.

PURPOSE: Retinas of albino rats born and raised in bright cyclic light (300-800 lux) are less susceptible to light-induced apoptosis than retinas of animals born and raised in dim cyclic light (5 lux). In this study, the objective was to study the mechanisms of neuroprotection in the bright cyclic light-reared retina by identification of differentially expressed genes with differential display (DD)-PCR. METHODS: Albino rats were born and raised in 5- or 400-lux cyclic light (12 hours on/off). At 6 to 8 weeks of age, animals were either killed to harvest retinas or exposed to 1700 lux illumination for 12 or 24 hours. The neuroprotection of 400-lux cyclic light rearing was evaluated by DNA fragmentation and quantitative histology. The differentially expressed candidate genes were identified by DD-PCR. Northern blot analysis was used to quantitate differential expression of selected genes. Differential expression of protein was determined by Western blot and enzyme activity analysis. Cellular localization of transcripts was determined by in situ hybridization. RESULTS: DNA fragmentation and quantitative histology results indicated that 400-lux cyclic light rearing protected the retina from light-induced apoptosis compared with 5-lux cyclic light rearing. DD-PCR analysis showed that a 283-bp expressed sequence tag (EST) was downregulated in retinas of rats raised from birth in 400-lux cyclic light. A BLAST search identified the EST as the 3'-terminal sequence of mitochondria-encoded NADH dehydrogenase subunit 3 (ND-3). Northern blot analysis showed that the EST hybridized to two mRNA transcripts, the larger of which was confirmed to encompass the adenosine triphosphate (ATP) synthase subunit 6 (ATPase-6), cytochrome c oxidase subunit III (CO-III), ND-3, and tRNA-Gly. Northern blot analysis demonstrated that CO-III and ATPase-6 were downregulated 1.8- and 2.3-fold by 400-lux cyclic light compared with 5-lux cyclic light, respectively; however, there was no change in cytochrome c oxidase subunit I and II (CO-I and -II) or in 12S ribosomal RNA (12S rRNA), a mitochondrial housekeeping gene. Western blot analysis using anti-CO-III antibody showed more CO-III protein in retinal mitochondria from dim-light-raised rats. The enzyme activity of CO was two times higher in retinal homogenates from dim-light-raised rats than those from bright-light-raised rats. In situ hybridization using a (35)S-labeled CO-III probe showed that the CO-III transcript was present and downregulated in most of the retinal layers of bright-light-reared animals. CONCLUSIONS: Rearing in cyclic light at 400-lux downregulates the expression of ATPase-6, CO-III, and ND-3 compared with rearing in 5-lux cyclic light. The authors hypothesize that these changes are adaptive responses to light stress that provide neuroprotection to retinal cells by elevating the level of stress-related factors and reducing the level of oxidized cytochrome c, the form that activates the apoptotic cascade of cell death.

Adaptation, Ocular↗
PubMed2000

Identification of c-myc responsive genes using rat cDNA microarray.

c-Myc functions through direct activation or repression of transcription. Using cDNA microarray analysis, we have identified c-Myc-responsive genes by comparing gene expression profiles between c-myc null and c-myc wild-type rat fibroblast cells and between c-myc null and c-myc null cells reconstituted with c-myc. From a panel of 4400 cDNA elements, we found 198 genes responsive to c-myc when comparing wild-type or reconstituted cells with the null cells. The plurality of the named c-Myc-responsive genes that were up-regulated, including 30 ribosomal protein genes, are involved in macromolecular synthesis and metabolism, suggesting a major role of c-Myc in the regulation of protein synthetic and metabolic pathways. When ectopically overexpressed, c-Myc induced a different and smaller set of c-Myc-responsive genes as compared with the physiologically expressed c-Myc condition. Thus, these results from expression profiling suggest a new primary function for c-Myc and raise the possibility that the physiological and transforming functions of c-myc may be separable.

Animals↗
PubMed2002

[Comparative study of PCR-based Cryptosporidium discriminating techniques with a review of the literature].

We identified the species or genotypes of the six Cryptosporidium isolates from patients and C. parvum strain HNJ-1 using the seven previously described species-differentiation and genotyping PCR protocols for detection of Cryptosporidium parasites. In addition, we also discussed about the usefulness of these PCR-based protocols on the basis of the reports previously published. Cryptosporidium diagnostic fragment was amplified by PCR with each primer pair, targeting the 18S ribosomal RNA (18SrRNA), Cryptosporidium oocyst wall protein (COWP). Heat shock protein 70 (HSP70), Polythreonine (Poly-T), Thrombospondin related adhesive protein of Cryptosporidium-1 (TRAP-C1), and unknown gene locus, in all isolates from patients and the strain HNJ-1. The RFLP profiles of 18SrRNA, COWP, HSP70, Poly-T, and TRAP-C1 PCR products in all isolates from patients were found to be the same among isolates, and were correspondent to those of C. parvum human genotype. While the RFLP profiles of HNJ-1 were strictly different from those of isolates from patients, and were correspondent to C. parvum cattle genotype. In addition, nucleotide sequences in 18 SrRNA gene of all isolates from patients and HNJ-1 were found to be identical to that of C. parvum, human or cattle genotype, respectively. Therefore, the isolates from patients and HNJ-1 were identified as C. parvum human and cattle genotype, respectively. According to the reports related to the PCR-based protocols applied in the present study, RFLP profiles targeting the HSP70, Poly-T, TRAP-C1 genes had been revealed in only a few species or genotypes, but those of 18SrRNA and COWP genes were in all species and genotypes. However, we supposed that it was difficult to distinguish between human or cattle genotype and other species or genotypes by RFLP profiles of 18SrRNA or COWP because the RFLP profiles of human or cattle genotype were identical or similar to those of other species or genotypes. On the other hand, it has been known that the nucleotide sequences in 18SrRNA or COWP gene are different among Cryptosporidium species and/or genotypes. Therefore, the direct sequencing method targeting the variable regions which can be used to distinguish among Cryptosporidium species, as well as the genotypes within C. parvum in either 18SrRNA or COWP gene is the most useful tool for accurate identification of Cryptosporidium isolates.

Animals↗
PubMed2003

Profiling, comparison and validation of gene expression in gastric carcinoma and normal stomach.

Gastric carcinoma is the fourth most common cause of cancer death worldwide but its molecular biology is poorly understood. We catalogued the genes expressed in two gastric adenocarcinomas and normal stomach, using serial analysis of gene expression (SAGE), and compared the profiles on-line with other glandular epithelia. Candidates were validated by Northern blotting and immunohistochemistry. A total of 29 480 transcripts, derived from 10 866 genes, were identified. In all, 1% of the genes were differentially expressed (>/=fivefold difference plus P-value </=0.01) between cancers and normal stomach. The most abundant transcripts included ribosomal and mitochondrial proteins, of which most were upregulated in the tumours, as were other widely expressed genes including transcription factors, signalling molecules (serine/threonine protein kinases), thymosin beta 10 and collagenase I. Transcripts abundant in normal stomach were functionally important, including gastrin, immunoglobulin alpha, lysozyme, MUC5, pS2 and pepsinogens, which were among 55 gastric-specific genes. Many transcripts were minimally characterized or new, some cancer-associated genes reflected their intestinal morphology, and some normal gastric genes had previously been considered as pancreatic carcinoma markers. The gastric carcinoma profiles resembled other tumours', supporting the existence of common cancer-associated targets. These data provide a catalogue from which to develop markers for better diagnosis and therapy of gastric carcinoma.

Blotting, Northern↗
PubMed1975

Polyribosomal structures inactive for protein synthesis present in erythroid cells during terminal stages of differentiation.

During the terminal stages of differentiation nucleated erythroid cells from the fetal mouse synthesize hemoglobin at a lower rate because after the last cycle of cell division about half of their polyribosomal structures are rendered inactive for protien synthesis though they maintain their aggregated shape. Partially inactive polyribosomes are tested in comparison with normal polyribosomes for the capacity to support polypeptide chain synthesis in cell-free conditions. The following observations are made: a) no difference is found for the profile on sucrose density gradients; b) partially inactive polyribosomes carry growing polypeptide chains in reduced amounts in comparison with active polyribosomes; c) partially inactive polyribosomes are not capable to release "run off" 80 S ribosomal monomers and to dissociate to active ribosomal subunits. These data are interpreted as the evidence for a block of chain termination producing inactivation of polyribosomes during the late maturation of nucleated erythroid cells.

Animals↗
PubMed2001

Analysis of alterations in gene expression after amplification of recombinant genes in CHO cells.

Dihydrofolate reductase (DHFR) based amplification of recombinant genes using increasing concentrations of methotrexate (MTX) is a common method to establish CHO cell lines producing high amounts of the desired protein. Once, cell lines with highly amplified target genes and good expression rates are isolated, further characterization of their transcriptional pattern is intended to clarify the question what other factors are elevated, as a prerequisite or consequence of recombinant protein production. In order to define genes which are upregulated in a cell line that shows high production rates, we have investigated alterations in gene expression which occur beside amplification of the recombinant genes. For this purpose, the suppression subtractive hybridization method was used to create a cDNA library enriched for differentially expressed sequences in the recombinant antibody producing CHO cell line versus the original counterpart. Differential expression was confirmed by Northern blotting and Northern ELISA. In addition to the expected recombinant genes, we have identified 5 transcripts which are upregulated in the recombinant cell line. One sequence has not been found in existing data bases, the others revealed to be genes involved in protein synthesis and regulation of transcription. Furthermore, an alternatively spliced, non-functional form of the DHFR mRNA was detected, suggesting a dramatic increase of the selection pressure exerted by MTX.

Animals↗
PubMed2003

Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice.

Reverse transcription followed by real-time quantitative polymerase chain reaction (RT Q-PCR) is useful for the systematic measurement of plant physiological changes in gene expression. The validity of using 18S rRNA and three housekeeping genes, glyceraldehyde-3-phosphate dehydrogenase, actin, and tubulin, was tested as a reference of RT Q-PCR. Under various growth stages of etiolated seedlings, different cultivars, and various times after UV-irradiation treatment, expression level of 18S rRNA correlated with total RNA suggesting the uniformity of RT Q-PCR efficiencies among samples. Relative expressions of housekeeping genes varied among samples and independently of experimental conditions, up to two-fold, signifying generally constant fraction of mRNA in total RNA. Results indicate 18S rRNA was the most reliable reference gene for RT Q-PCR of total RNA.

Actins↗
PubMed2005

Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.

We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this "diauxic shift." Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift.

Aerobiosis↗
PubMed2003

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

MOTIVATION: Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many other areas in bioinformatics probabilistic models have proven to be both more realistic and powerful than parsimony models. For instance, they allow for assessing solution reliability and consideration of alternative solutions in a uniform way. There is also an added benefit in making model assumptions explicit and therefore making model comparisons possible. For orthology analysis, uncertainty has recently been addressed using parsimonious reconciliation combined with bootstrap techniques. However, until now no probabilistic methods have been available. RESULTS: We introduce a probabilistic gene evolution model based on a birth-death process in which a gene tree evolves 'inside' a species tree. Based on this model, we develop a tool with the capacity to perform practical orthology analysis, based on Fitch's original definition, and more generally for reconciling pairs of gene and species trees. Our gene evolution model is biologically sound (Nei et al., 1997) and intuitively attractive. We develop a Bayesian analysis based on MCMC which facilitates approximation of an a posteriori distribution for reconciliations. That is, we can find the most probable reconciliations and estimate the probability of any reconciliation, given the observed gene tree. This also gives a way to estimate the probability that a pair of genes are orthologs. The main algorithmic contribution presented here consists of an algorithm for computing the likelihood of a given reconciliation. To the best of our knowledge, this is the first successful introduction of this type of probabilistic methods, which flourish in phylogeny analysis, into reconciliation and orthology analysis. The MCMC algorithm has been implemented and, although not yet being in its final form, tests show that it performs very well on synthetic as well as biological data. Using standard correspondences, our results carry over to allele trees as well as biogeography.

Algorithms↗
PubMed2003

Poultry digestive microflora biodiversity as indicated by denaturing gradient gel electrophoresis.

Populations of digestive microflora in chickens change with age and are affected by diet, stressors, and performance enhancers. Culturing techniques used to profile a bacterial community inadvertently select for some organisms while excluding others. Several molecular-based techniques have been used to profile mixed microbial populations on the basis of DNA extracted from the entire community. Denaturing gradient gel electrophoresis was used in the present study to examine PCR-amplified fragments (amplicons) of a 16S ribosomal DNA variable region from predominant digestive bacteria. The objective of the study was to examine changes in digestive microbial communities of developing Leghorn chicks and molted Leghorn hens. Dendrograms of amplicon patterns indicated approximately 51% similarity between cecal bacteria composition in Leghorn chicks less than 20 d old and chicks greater than 20 d old. Cecal communities in Leghorn chicks given a competitive exclusion culture exhibited 21% correlation at all ages with those in control chicks. Nonmolted and molted hens had 40% similarity between cecal communities, whereas diets with low calcium (0.8% wt/wt) and excess zinc (2,800 mg/kg) lessened population differences (90% similarity). Results indicated the potential usefulness of the molecular-based denaturing gradient gel electrophoresis to monitor changes in digestive bacterial communities in chickens.

Aging↗
PubMed1980

Age-related alterations of the proximal axon segment in lamina IIIab-pyramidal cells of the human isocortex. A Golgi and fine structural study.

In the human isocortex preferably the pyramidal cells of layer IIIab are subjected to a conspicuous age-related alteration in that they develop spindle-shaped enlargements of their proximal axon segment. In Golgi impregnations such IIIab-pyramidal cells with an axon dilatation do not display obvious alterations in the ramification or spine density of their dendrites. Electron microscopically different degrees of this alteration can be recognized; beginning with a cone-shaped and slight dilatation and culminating in a giant spindle-shaped enlargement of the proximal axon segment. The fasciculated microtubules normally characterizing the initial segment are pushed aside or are lacking. Lipofuscin granules, RER cisterns and ribosome rosettes penetrate into the dilatation. The axolemma of those parts of the axon segment in the vicinity of which lipofuscin granules can be encountered lacks a dense axolemmal undercoating. As concerns the adjacent profiles of the dilatation there are no obvious alterations in comparison to a normal proximal axon segment. A slender process arises distally from the dilatation showing the morphological characteristics of the axon initial segment.

Aged↗