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PubMed2002

Degradation of 2,7-dichlorodibenzo-p-dioxin by wood-rotting fungi, screened by dioxin degrading ability.

One hundred thirty-six strains of wood-rot fungi (74 strains, 66 species of 19 genera, and 62 unidentified strains) were screened for the dibenzo-p-dioxin (DD) decreasing activity. It was observed that 20% of additional DD (1 micromol) disappeared in the cultures of eight strains belonging to four genera (Aleurodiscus (one strain), Ceriporia (one strain), Phanerochaete (one strain), Phlebia (five strains)) and four unidentified strains. These 12 fungal strains were used for the examination of the degradation of [U-14C]2,7-dichlorodibenzo-p-dioxin (2,7-diCDD). The fungi unidentified strain MZ-227, Phlebia sp. MG-60 and Phlebia lindtneri showed higher cumulative 14CO2 evolution rates than the other nine fungi. MZ-227, Phlebia sp. MG-60, and P. lindtneri converted 250 nmol of 2,7-diCDD to 196, 155 and 149 nmol of 14CO2, respectively, during a 30-day incubation period

Biodegradation, Environmental↗
PubMed1984

Ethanol from Whey: Continuous Fermentation with a Catabolite Repression-Resistant Saccharomyces cerevisiae Mutant.

An alternative method for the conversion of cheese whey lactose into ethanol has been demonstrated. With the help of continuous-culture technology, a catabolite repression-resistant mutant of Saccharomyces cerevisiae completely fermented equimolar mixtures of glucose and galactose into ethanol. The first step in this process was a computer-controlled fed-batch operation based on the carbon dioxide evolution rate of the culture. In the absence of inhibitory ethanol concentrations, this step allowed us to obtain high biomass concentrations before continuous fermentation. The continuous anaerobic process successfully incorporated a cell-recycle system to optimize the fermentor productivity. Under conditions permitting a low residual sugar concentration (</=1%), maximum productivity (13.6 g liter h) was gained from 15% substrate in the continuous feed at a dilution rate of 0.2 h. Complete fermentation of highly concentrated feed solutions (20%) was also demonstrated, but only with greatly diminished fermentor productivity (5.5 g liter h).

Journal Article↗
PubMed1985

Effect of seeding during thermophilic composting of sewage sludge.

The effect of seeding on the thermophilic composting of sewage sludge was examined by measuring the changes in CO2 evolution rates and microbial numbers. Although the succession of thermophilic bacteria and thermophilic actinomycetes clearly reflected the effect of seeding, no clear difference was observed in the overall rate of composting or quality of the composted product.

Bacteria↗
PubMed1985

Effect of temperature on composting of sewage sludge.

The effect of temperature on the composting reaction of sewage sludge was investigated at 50, 60, and 70 degrees C. The total amount of CO(2) evolved and the final conversion of volatile matter were maximum at 60 degrees C., suggesting that the optimal temperature for composting was around 60 degrees C. The specific CO(2) evolution rate (moles of CO(2) evolved per hour per viable cell) was maximum at 70 degrees C. The isolated thermophilic bacterium which was dominant at 60 degrees C but did not grow at 70 degrees C showed that the rate of O(2) consumption measured on the agar plate at 70 degrees C was four times higher than that at 60 degrees C. This showed that the energy yielded from catabolism is rather uncoupled with the anabolism at 70 degrees C in the metabolism of microorganisms indigenous in the compost. A higher respiratory quotient was observed at 70 degrees C than at any other temperature.

Journal Article↗
PubMed1982

Nucleotide sequence of a cloned woodchuck hepatitis virus genome: comparison with the hepatitis B virus sequence.

The complete nucleotide sequence of a woodchuck hepatitis virus genome cloned in Escherichia coli was determined by the method of Maxam and Gilbert. This sequence was found to be 3,308 nucleotides long. Potential ATG initiator triplets and nonsense codons were identified and used to locate regions with a substantial coding capacity. A striking similarity was observed between the organization of human hepatitis B virus and woodchuck hepatitis virus. Nucleotide sequences of these open regions in the woodchuck virus were compared with corresponding regions present in hepatitis B virus. This allowed the location of four viral genes on the L strand and indicated the absence of protein coded by the S strand. Evolution rates of the various parts of the genome as well as of the four different proteins coded by hepatitis B virus and woodchuck hepatitis virus were compared. These results indicated that: (i) the core protein has evolved slightly less rapidly than the other proteins; and (ii) when a region of DNA codes for two different proteins, there is less freedom for the DNA to evolve and, moreover, one of the proteins can evolve more rapidly than the other. A hairpin structure, very well conserved in the two genomes, was located in the only region devoid of coding function, suggesting the location of the origin of replication of the viral DNA.

Amino Acid Sequence↗
PubMed2005

A Sabin 3-derived poliovirus recombinant contained a sequence homologous with indigenous human enterovirus species C in the viral polymerase coding region.

Outbreaks of poliomyelitis caused by circulating vaccine-derived polioviruses (cVDPVs) have been reported in areas where indigenous wild polioviruses (PVs) were eliminated by vaccination. Most of these cVDPVs contained unidentified sequences in the nonstructural protein coding region which were considered to be derived from human enterovirus species C (HEV-C) by recombination. In this study, we report isolation of a Sabin 3-derived PV recombinant (Cambodia-02) from an acute flaccid paralysis (AFP) case in Cambodia in 2002. We attempted to identify the putative recombination counterpart of Cambodia-02 by sequence analysis of nonpolio enterovirus isolates from AFP cases in Cambodia from 1999 to 2003. Based on the previously estimated evolution rates of PVs, the recombination event resulting in Cambodia-02 was estimated to have occurred within 6 months after the administration of oral PV vaccine (99.3% nucleotide identity in VP1 region). The 2BC and the 3D(pol) coding regions of Cambodia-02 were grouped into the genetic cluster of indigenous coxsackie A virus type 17 (CAV17) (the highest [87.1%] nucleotide identity) and the cluster of indigenous CAV13-CAV18 (the highest [94.9%] nucleotide identity) by the phylogenic analysis of the HEV-C isolates in 2002, respectively. CAV13-CAV18 and CAV17 were the dominant HEV-C serotypes in 2002 but not in 2001 and in 2003. We found a putative recombination between CAV13-CAV18 and CAV17 in the 3CD(pro) coding region of a CAV17 isolate. These results suggested that a part of the 3D(pol) coding region of PV3(Cambodia-02) was derived from a HEV-C strain genetically related to indigenous CAV13-CAV18 strains in 2002 in Cambodia.

Cambodia↗
PubMed1982

Sequelae of the initial attack of acute rheumatic fever in children from north India. A prospective 5-year follow-up study.

We determined the outcome of acute rheumatic fever in 85 children from North India who had received regular antistreptococcal prophylaxis after their first attack. By the end of the 5-year follow-up, 33 patients had rheumatic heart disease. Mitral insufficiency, the most common valvular lesion, appeared in 91% of the patients, whereas mitral stenosis developed in only 18%. Initial carditis, congestive heart failure, cardiomegaly or moderate-to-severe mitral insufficiency significantly increased the risk of rheumatic heart disease (p less than 0.001). The recurrence rate of acute rheumatic fever in children who received continuous prophylaxis was 0.006 per patient-year. Most recurrence (92%) mimicked the first attack and produced further cardiac damage in five patients with carditis and in one patient with chorea. Cardiac status during the first attack of rheumatic fever and the continuity of prophylaxis were the major determinants of outcome. Statistical comparisons disclosed that with continuous prophylaxis, the prevalence rate, evolution and clinical spectrum of the sequelae of acute rheumatic fever in children from India do not differ significantly from those in the West.

Child↗
PubMed2001

Theoretical analysis of mutation-adaptive evolutionary algorithms.

Adaptive evolutionary algorithms require a more sophisticated modeling than their static-parameter counterparts. Taking into account the current population is not enough when implementing parameter-adaptation rules based on success rates (evolution strategies) or on premature convergence (genetic algorithms). Instead of Markov chains, we use random systems with complete connections - accounting for a complete, rather than recent, history of the algorithm's evolution. Under the new paradigm, we analyze the convergence of several mutation-adaptive algorithms: a binary genetic algorithm, the 1/5 success rule evolution strategy, a continuous, respectively a dynamic (1+1) evolutionary algorithm.

Algorithms↗
PubMed2005

Microbial succession associated with organic matter decomposition during thermophilic composting of organic waste.

Using dog food as a model of the organic waste, thermophilic composting was carried out for 14 days at a fixed temperature of 60 degrees C. The relationship between organic matter decomposition measured by CO2 evolution during the bio-stabilization process and microbial succession expressed as the changes over time in the restriction fragment length polymorphism (RFLP) patterns of 16S rDNA sequences, of micro-organisms associated with the composting material was also examined. The CO2 evolution rate peaked on day 3 and gradually decreased until it became extremely small after day 9 of composting, indicating that vigorous organic matter decomposition ceased around this time. On the other hand, the RFLP pattern changed drastically from day 0 to day 4 or 5, then remained stable until day 7 or 8, reaching its final configuration, with little variations, after day 9 of composting. RFLP analysis therefore indicates that microbial succession continued into the later stage of composting. Nevertheless, by day 9, the rate of organic matter decomposition was so low that its influence on microbial populations could be hardly recognized by conventional methods of dilution plating. Moreover, the compost produced by day 9 showed no inhibitory effect on the growth of Komatsuna (Brassica campestris L. var. rapiferafroug), indicating that the maturity of compost is sufficient for plant growth when the rate of organic matter decomposition has become extremely low and the RFLP patterns become stable.

Bacteria↗
PubMed2006

Cloning, sequencing, and expression of the amelogenin gene in two scincid lizards.

Our knowledge of the gene coding for amelogenin, the major enamel protein, is mainly based on mammalian sequences. Only two sequences are available in reptiles. To know whether the snake sequence is representative of the amelogenin condition in squamates, we have studied amelogenin in two scincid lizards. Lizard amelogenin possesses numerous conserved residues in the N- and C-terminal regions, but its central region is highly variable, even when compared with the snake sequence. This rapid evolution rate indicates that a single squamate sequence was not representative, and that comparative studies of reptilian amelogenins might be useful to detect the residues which are really important for amelogenin structure and function. Reptilian and mammalian enamel structure is roughly similar, but no data support amelogenin being similarly expressed during amelogenesis. By performing in situ hybridization using a specific probe, we showed that lizard ameloblasts express amelogenin as described during mammalian amelogenesis. However, we have not found amelogenin transcripts in odontoblasts. This indicates that full-length amelogenin is specific to enamel matrix, at least in this lizard.

Ameloblasts↗
PubMed2003

Identification of conserved regulatory elements by comparative genome analysis.

BACKGROUND: For genes that have been successfully delineated within the human genome sequence, most regulatory sequences remain to be elucidated. The annotation and interpretation process requires additional data resources and significant improvements in computational methods for the detection of regulatory regions. One approach of growing popularity is based on the preferential conservation of functional sequences over the course of evolution by selective pressure, termed 'phylogenetic footprinting'. Mutations are more likely to be disruptive if they appear in functional sites, resulting in a measurable difference in evolution rates between functional and non-functional genomic segments. RESULTS: We have devised a flexible suite of methods for the identification and visualization of conserved transcription-factor-binding sites. The system reports those putative transcription-factor-binding sites that are both situated in conserved regions and located as pairs of sites in equivalent positions in alignments between two orthologous sequences. An underlying collection of metazoan transcription-factor-binding profiles was assembled to facilitate the study. This approach results in a significant improvement in the detection of transcription-factor-binding sites because of an increased signal-to-noise ratio, as demonstrated with two sets of promoter sequences. The method is implemented as a graphical web application, ConSite, which is at the disposal of the scientific community at http://www.phylofoot.org/. CONCLUSIONS: Phylogenetic footprinting dramatically improves the predictive selectivity of bioinformatic approaches to the analysis of promoter sequences. ConSite delivers unparalleled performance using a novel database of high-quality binding models for metazoan transcription factors. With a dynamic interface, this bioinformatics tool provides broad access to promoter analysis with phylogenetic footprinting.

Algorithms↗
PubMed2001

Evidence from action and fluorescence spectra that UV-induced violet-blue-green fluorescence enhances leaf photosynthesis.

We assessed the contribution of UV-induced violet-blue-green leaf fluorescence to photosynthesis in Poa annua, Sorghum halepense and Nerium oleander by measuring UV-induced fluorescence spectra (280-380 nm excitation, 400-550 nm emission) from leaf surfaces and determining the monochromatic UV action spectra for leaf photosynthetic O2-evolution. Peak fluorescence emission wavelengths from leaf surfaces ranged from violet (408 nm) to blue (448 nm), while excitation peaks for these maxima ranged from 333 to 344 nm. Action spectra were developed by supplementing monochromatic radiation from 280 to 440 nm, in 20 nm increments, to a visible nonsaturating background of 500 mumol m-2 s-1 photosynthetically active radiation and measuring photosynthetic O2-evolution rates. Photosynthetic rates tended to be higher with the 340 nm supplement than with higher or lower wavelength UV supplements. Comparing photosynthetic rates with the 340 nm supplement to those with the 400 nm supplement, the percentage enhancement in photosynthetic rates at 340 nm ranged from 7.8 to 9.8%. We suspect that 340 nm UV improves photosynthetic rates via fluorescence that provides violet-blue-green photons for photosynthetic energy conversion because (1) the peak excitation wavelength (340 nm) for violet-blue-green fluorescence from leaves was also the most effective UV wavelength at enhancing photosynthetic rates, and (2) the magnitude of photosynthetic enhancements attributable to supplemental 340 nm UV was well correlated (R2 = 0.90) with the apparent intensity of 340 nm UV-induced violet-blue-green fluorescence emission from leaves.

Magnoliopsida↗
PubMedDate not supplied

Molecular epidemiologic typing systems of bacterial pathogens: current issues and perspectives.

The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s)? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission) and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection). Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

Bacterial Typing Techniques↗
PubMed2003

Hepatitis C virus clearance: the enigma of failure despite an impeccable survival strategy.

Infection with human hepatitis C virus (HCV) as a result of a bilateral process of host-virus interactions. There are factors on both sides that contribute to clearance and to chronicity. Virus strategy to survive is built on several basic features. The first, recently recognized, is a wide cell tropism. HCV can infect not only hepatocytes, but also cells of immune system (B-cells, monocytes, macrophages, dendritic cells), epithelium, and immunologically privileged sites such as the central nervous system. Dendritic cells and platelets can also be passive virus carriers. Possibilities of virus clearance or abortive inapparent HCV infection at the stage of adsorption are considered. The second feature is rapid error-prone replication that leads to accumulation within one host of multiple virus variants (quasispecies). Viral heterogeneity could be multiplied by recombination of HCV genomic/subgenomic RNA molecules. Quasispecies nature gives virus an advantage in adaptation to varying host environment including availability of permissive cells, the presence of innate and adaptive immune response, and antiviral treatment. Analysis of HCV polymorphisms and their evolution rates may pinpoint the molecular (sequence) correlates of HCV clearance. The third feature is the capacity to modify or adapt host milieu. HCV core, envelope E2 and nonstructural NS2, NS3, NS5A proteins seem to hold a grip over the host cellular functions by down-regulating processes unfavorable and up-regulating processes favorable for virus replication and persistence. The relevance of the latter interactions to HCV infection outcome remains to be demonstrated. This review discusses recent developments in this area of HCV research.

Antiviral Agents↗
PubMed1998

Measurement of autolysis in submerged batch cultures of Penicillium chrysogenum.

The process of cellular autolysis was studied in an industrial strain of Penicillium chrysogenum by a range of methods, including assessment of biomass decline, NH+4 release, changes in culture apparent viscosity, and by means of a quantitative assessment of changes in micromorphology using a computerized image analysis system. The pattern of total intracellular proteolytic and beta-1, 3-glucanolytic activity in the culture was also examined. The overall aim was to identify a suitable method, or methods, for examining the extent of autolysis in fungal cultures. Autolysis was studied in submerged batch processes, where DOT was maintained above 40% saturation (non-O2-limited), and, under O2-limited conditions. Both N and O2 limitation promoted extensive culture autolysis. Image analysis techniques were perhaps the most sensitive method of assessing the progress of autolysis in the culture. Autolytic regions within some hyphae were apparent even during growth phase, but became much more widespread as the process proceeded. The early stages of autolysis involved continued energy source consumption, increased carbon dioxide evolution rate, degradation of penicillin, and decreased broth filterability. Later stages involved widespread mycelial fragmentation, with some regrowth (cryptic growth) occurring in non-O2-limited cultures. Intracellular proteolytic activity showed two peaks, one during the growth phase, and the other during autolysis. Autolysis was also associated with a distinct peak in beta-1,3-glucanolytic activity, indicating that degradation of cell wall matrix polymers may be occurring during autolysis in this strain of P. chrysogenum.

Biomass↗
PubMed2000

[Familial myopathy with desmin storage seen as a granulo-filamentar, electron-dense material with mutation of the alphaB-cristallin gene].

Two familial cases of a myopathy remarkable by the presence of a granulo-filamentar, electron dense material were reported in 1978. In a second step, in 1988, it was demonstrated that this material contained an abnormally-phosphorylated desmin. During the last twenty years, the occurrence of new cases in this family confirmed the autosomal dominant inheritance of the disease, and made it potentially informative for molecular genetics studies. This allowed first to map the disease on chromosome11q21-23, and afterwards to identify a mutation within a gene coding for a chaperone protein, alphaBcrystallin. An extensive clinical, pathological and genetic study of this princeps family is herein reported in detail. First, it showed the possible detection of histopathological changes in presymptomatic patients. Second, it allowed to demonstrate the simultaneous occurrence of both alphaBcrystallin and desmin in the granulo-filamentar aggregates. Third, this study provided a precise knowledge of the evolution rate of the disease. The analysis of similar observations reported in the literature clearly shows the clinical, pathological and genetic heterogeneity of this new neuro-muscular disorder.

Actin Cytoskeleton↗
PubMed2000

[The effect of aryloxyaminopropanol substances on the photosynthetic activity of chloroplasts in Spinacia oleracea L].

The effect of 18 compounds of the aryloxyaminopropanol type--potential beta-adrenolytics (differing each from other by modifications in the hydrophilic and lipophilic part of the molecule) on the inhibition of oxygen evolution rate in spinach chloroplasts has been investigated. The compounds with n-octyloxymethyl and n-nonyloxymethyl group in position 3 of aromatic ring were found to exhibit the highest inhibitory activity (IC50 = 67, resp. 120 mumol dm-3). The compounds containing a heterocycle or the dimethylamino group in the hydrophilic part of the molecule and with propoxymethyl group on the aromatic ring were not active. Using EPR spectroscopy it was found that the studied compounds interact with Z+/D+ intermediates, i.e. tyrosine radicals TyrZ and TyrD situated in D1 and D2 proteins on the donor side of photosystem 2. Higher concentrations of the studied inhibitors cause release of Mn2+ ions from the oxygen evolving complex which is situated in photosystem 2. The interaction of the tested compounds with chlorophyll occurring in the photosynthetic centres has been confirmed by fluorescence measurements as well.

Adrenergic beta-Antagonists↗
PubMed1998

Construction of the gyrB Database for the Identification and Classification of Bacteria.

Nucleotide sequences of small-subunit rRNA (16S rRNA) are most commonly used for the identification and characterization of bacteria and their complex communities. However, 16S rRNA evolves slowly and is often not very convenient to resolve bacterial strains at the species level. We have therefore attempted to develop a rapid and more convenient system for bacterial identification using the gyrB gene sequences. We chose the gyrB gene, because (i) it is rarely transmitted horizontally, (ii) its molecular evolution rate is higher than that of 16S rRNA, and (iii) the gene is distributed ubiquitously among bacterial species. We PCR-amplified the 1.2 kb-long gyrB segments from about 1,000 bacterial species by using degenerate primers and determined their nucleotide sequences. The resultant data have been assembled into the gyrB database accessible via WWW.

Journal Article↗