OrthoRefine: automated enhancement of prior ortholog identification via synteny

BACKGROUND

Identifying orthologs continues to be an early and imperative step in genome analysis but remains a challenging problem. While synteny (conservation of gene order) has previously been used independently and in combination with other methods to identify orthologs, applying synteny in ortholog identification has yet to be automated in a user-friendly manner. This desire for automation and ease-of-use led us to develop OrthoRefine, a standalone program that uses synteny to refine ortholog identification.

RESULTS

We developed OrthoRefine to improve the detection of orthologous genes by implementing a look-around window approach to detect synteny. We tested OrthoRefine in tandem with OrthoFinder, one of the most used software for identification of orthologs in recent years. We evaluated improvements provided by OrthoRefine in several bacterial and a eukaryotic dataset. OrthoRefine efficiently eliminates paralogs from orthologous groups detected by OrthoFinder. Using synteny increased specificity and functional ortholog identification; additionally, analysis of BLAST e-value, phylogenetics, and operon occurrence further supported using synteny for ortholog identification. A comparison of several window sizes suggested that smaller window sizes (eight genes) were generally the most suitable for identifying orthologs via synteny. However, larger windows (30 genes) performed better in datasets containing less closely related genomes. A typical run of OrthoRefine with ~ 10 bacterial genomes can be completed in a few minutes on a regular desktop PC.

CONCLUSION

OrthoRefine is a simple-to-use, standalone tool that automates the application of synteny to improve ortholog detection. OrthoRefine is particularly efficient in eliminating paralogs from orthologous groups delineated by standard methods.

Pregnancy Termination and Postnatal Major Congenital Heart Defect Prevalence After Introduction of Prenatal Cardiac Screening

Importance

Prenatal cardiac screening of the first and second trimesters has had a major impact on postnatal prevalence of congenital heart defects (CHDs), rates of termination of pregnancy (TOP), and outcomes among children born alive with CHDs.

Objective

To examine the prenatal and postnatal incidence of major CHDs (ie, necessitating intervention within the first year of life), detection rate trends, rates of TOP, and the association of cardiac screening with postnatal outcomes.

Design, Settings, and Participants

In this cross-sectional study, 3827 fetuses with antenatally diagnosed major CHDs in the Czech Republic (population 10.7 million) between 1991 and 2021 were prospectively evaluated with known outcomes and associated comorbidities. Prenatal and postnatal prevalence of CHD in an unselected population was assessed by comparison with a retrospective analysis of all children born alive with major CHDs in the same period (5454 children), using national data registry. Data analysis was conducted from January 1991 to December 2021.

Main Outcomes and Measures

Prenatal detection and postnatal prevalence of major CHDs and rate of TOPs in a setting with a centralized health care system over 31 years.

Results

A total of 3 300 068 children were born alive during the study period. Major CHD was diagnosed in 3827 fetuses, of whom 1646 (43.0%) were born, 2069 (54.1%) resulted in TOP, and 112 (2.9%) died prenatally. The prenatal detection rate increased from 6.2% in 1991 to 82.8% in 2021 (P < .001). Termination of pregnancy decreased from 70% in 1991 to 43% (P < .001) in 2021. Of 627 fetuses diagnosed in the first trimester (introduced in 2007), 460 were terminated (73.3%). Since 2007, of 2066 fetuses diagnosed in the second trimester, 880 (42.6%) were terminated, resulting in an odds ratio of 3.6 (95% CI, 2.8-4.6; P < .001) for TOP in the first trimester compared with the second trimester. Postnatal prevalence of major CHDs declined from 0.21% to 0.14% (P < .001). The total incidence (combining prenatal detection of terminated fetuses with postnatal prevalence) of major CHD remained at 0.23% during the study period.

Conclusions and Relevance

In this cross-sectional study, the total incidence of major CHD did not change significantly during the 31-year study period. The prenatal detection of major CHD approached 83% in the current era. Postnatal prevalence of major CHD decreased significantly due to early TOPs and intrauterine deaths. The introduction of first trimester screening resulted in a higher termination rate in the first trimester but did not revert the overall decreasing trend of termination for CHDs in general.

An in vitro model that mimics the foreign body response in the peritoneum: Study of the bioadhesive properties of HA-based materials

A cascade of reactions known as the foreign body response (FBR) follows the implantation of biomaterials leading to the formation of a fibrotic capsule around the implant and subsequent health complications. The severity of the FBR is driven mostly by the physicochemical characteristics of implanted material, the method and place of implantation, and the degree of immune system activation. Here we present an in vitro model for assessing new materials with respect to their potential to induce a FBR in the peritoneum. The model is based on evaluating protein sorption and cell adhesion on the implanted material. We tested our model on the free-standing films prepared from hyaluronan derivatives with different hydrophobicity, swelling ratio, and rate of solubilization. The proteomic analysis of films incubated in the mouse peritoneum showed that the presence of fibrinogen was driving the cell adhesion. Neither the film surface hydrophobicity/hydrophilicity nor the quantity of adsorbed proteins were decisive for the induction of the long-term cell adhesion leading to the FBR, while the dissolution rate of the material proved to be a crucial factor. Our model thus helps determine the probability of a FBR to materials implanted in the peritoneum while limiting the need for in vivo animal testing.

ANC method: Experimental approach and recent results

The Asymptotic Normalization Coefficient (ANC) method, has proven to be useful in retrieving the direct part of the radiative capture cross section for a number of reactions of astrophysical interest. In this work, some of the latest results obtained by the AsFin2 group of the LSN-INFN (Catania) and the OJR of the NPI (Řež) will be briefly discussed.

Insoluble hyaluronan films obtained by heterogeneous crosslinking with iron(III) as resorbable implants

We present water-insoluble hyaluronan films crosslinked by trivalent iron developed as potential resorbable implants. The films were crosslinked by sorption of ferric salt into solid HA films in water/2-propanol bath. These heterogeneously crosslinked films (het-FeHA) remained tough and dimensionally stable when rehydrated in saline. In contrast, films prepared by drying the well-known homogeneous ferric hyaluronate gels (hom-FeHA) softened upon rehydration and expanded rapidly. Differences between hom-FeHA and het-FeHA result from polymer network topology (dominant inter- or intra-molecular crosslink, respectively). Moreover, Mössbauer spectroscopy of het-FeHA revealed diiron complexes, while iron in the hom-FeHA was present exclusively as γ-FeOOH nanoparticles or amorphous FeOOH. The biocompatibility tests of het-FeHA did not show any adverse effect and the sample disintegrated within one day when implanted in mice peritoneum. In conclusion, we developed implantable hyaluronan-based free-standing film with minimal swelling that can be resorbed quickly enough to avoid induction of foreign-body reaction.

ANC experiments for nuclear astrophysics

Among the indirect methods to determine nuclear cross-section present in literature, the so-called Asymptotic Normalization Coefficient (ANC) has proven to be useful in retrieving the direct part of a radiative capture cross-section in reactions of interest for astrophysics. In this work, the method will be presented, and some results obtained in collaboration between NPI CAS and INFN-LNS will be presented.

Neonatal pneumonia caused by Trichomonas vaginalis

Neonatal pneumonia is mostly bacterial and other etiology is considered less frequently. We report a case of newborn whose neonatal pneumonia has not improved, despite the aggressive ventilation regime and empiric antibiotic therapy. A special sample from the respiratory tract was collected for PCR examination. The test confirmed the presence of Trichomonas vaginalis. Antibiotic therapy was extended to include metronidazole. Targeted antibiotic therapy, which lasted for 28 days, improved the condition and the patient was discharged in a stabilized condition to home care on the 44th day of life. We demonstrate the need to consider atypical pathogens in the case of infections that do not respond to conventional therapy. The multiplex real-time PCR technique was used to detect the DNA of the pathogen. Targeted antibiotic therapy is the result of pathogen identification.

The Neutrons for Science Facility at SPIRAL-2

The neutrons for science (NFS) facility is a component of SPIRAL-2, the new superconducting linear accelerator built at GANIL in Caen (France). The proton and deuteron beams delivered by the accelerator will allow producing intense neutron fields in the 100 keV-40 MeV energy range. Continuous and quasi-mono-kinetic energy spectra, respectively, will be available at NFS, produced by the interaction of a deuteron beam on a thick Be converter and by the 7Li(p,n) reaction on thin converter. The pulsed neutron beam, with a flux up to two orders of magnitude higher than those of other existing time-of-flight facilities, will open new opportunities of experiments in fundamental research as well as in nuclear data measurements. In addition to the neutron beam, irradiation stations for neutron-, proton- and deuteron-induced reactions will be available for cross-sections measurements and for the irradiation of electronic devices or biological cells. NFS, whose first experiment is foreseen in 2018, will be a very powerful tool for physics, fundamental research as well as applications like the transmutation of nuclear waste, design of future fission and fusion reactors, nuclear medicine or test and development of new detectors.

Effects of pure plant secondary metabolites on methane production, rumen fermentation and rumen bacteria populations in vitro

In this study, the effects of seven pure plant secondary metabolites (PSMs) on rumen fermentation, methane (CH₄ ) production and rumen bacterial community composition were determined. Two in vitro trials were conducted. In trial 1, nine concentrations of 8-hydroxyquinoline, α-terpineol, camphor, bornyl acetate, α-pinene, thymoquinone and thymol were incubated on separate days using in vitro 24-hr batch incubations. All compounds tested demonstrated the ability to alter rumen fermentation parameters and decrease CH₄ production. However, effective concentrations differed among individual PSMs. The lowest concentrations that reduced (p < .05) CH₄ production were as follows: 8 mg/L of 8-hydroxyquinoline, 120 mg/L of thymoquinone, 240 mg/L of thymol and 480 mg/L of α-terpineol, camphor, bornyl acetate and α-pinene. These concentrations were selected for use in trial 2. In trial 2, PSMs were incubated in one run. Methane was decreased (p < .05) by all PSMs at selected concentrations. However, only 8-hydroxyquinoline, bornyl acetate and thymoquinone decreased (p < .05) CH₄ relative to volatile fatty acids (VFAs). Based on denaturing gradient gel electrophoresis analysis, different PSMs changed the composition of bacterial communities to different extents. As revealed by Ion Torrent sequencing, the effects of PSMs on relative abundance were most pronounced in the predominant families, especially in Lachnospiraceae, Succinivibrionaceae, Prevotellaceae, unclassified Clostridiales and Ruminococcaceae. The CH₄ production was correlated negatively (-.72; p < .05) with relative abundance of Succinivibrionaceae and positively with relative abundance of Ruminococcaceae (.86; p < .05). In summary, this study identified three pure PSMs (8hydroxyquinoline, bornyl acetate and thymoquinone) with potentially promising effects on rumen CH₄ production. The PSMs tested in this study demonstrated considerable impact on rumen bacterial communities even at the lowest concentrations that decreased CH₄ production. The findings from this study may help to elucidate how PSMs affect rumen bacterial fermentation.

26Mg target for nuclear astrophysics measurements

Two nuclear reactions of astrophysical interest, 26Mg(3He,d)27Al and 26Mg(d,p)27Mg, were measured for extraction of the Asymptotic Normalization Coefficients. Investigation of the target composition is presented, as well as the effects that showed up during analysis of the in-beam data obtained on CANAM accelerators in the Nuclear Physics Institute of the Czech Academy of Sciences (NPI CAS).

[Hantavirus causing fatal haemorrhagic fever in the Czech Republic]

Hantaviruses are RNA viruses of the family Bunyaviridae. Their hosts are mammals of the orders rodents (voles, rats, mice), insectivores (shrews, moles), and chiroptera (bats). Hantaviruses are present in many areas of Europe, the Americas, Asia, and Africa. In the Czech Republic, the occurrence of five species of hantaviruses has been reported (Dobrava/Belgrade, Puumala, Tula, Seewis, and Asikkala), with the first three of them causing human diseases. Although the course of hantavirus infections can be very serious, there is a low awareness of these diseases, even among health professionals, and hantavirus is often not considered in the diagnosis. A case history is reported of a patient who developed hantavirus haemorrhagic fever with renal syndrome (HFRS) with fatal outcome. The patient presented with typical clinical signs, but the correct diagnosis was only made at post mortem.

[Evaluation of prophylactic precautions after exposure to biological materials]

OBJECTIVES

Study of transmission rates of hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) and effect of HBV vaccination after parenteral exposure to biological materials.

PATIENTS AND METHODS

This was a retrospective study of 879 individuals (419 health care professionals and 460 persons from the general population) after blood and body fluid exposure examined at the Clinic of Infectious Diseases in Ostrava from 1999 to 2013. HBsAg, anti-HBs, anti-HBc, anti-HCV, anti-HIV, bilirubin, and ALT were tested in exposed patients and known sources at the baseline and, except anti-HBc, after 3, 6, and 12 months. Susceptible persons were vaccinated against HBV and screened for anti-HBs after 1-2 months. Antiretroviral prophylaxis was provided if reasonable.

RESULTS

At the baseline, 42 exposed persons were HBV positive, six were HCV positive, and none was HIV positive. During the follow-up, no new HBsAg positivity was detected in exposed individuals, although 25 of 837 susceptible persons were exposed to HBsAg-positive sources. After vaccination, protective anti-HBs were detected in 707 (84.7%) of 837 susceptible persons and in 709 (97.8%) of 725 persons with known post-vaccination response. Fifty-six of 873 persons had been exposed to HCV-positive sources and HCV transmission was shown in three (two health care professionals) of them. No HIV transmission was observed, although 11 of 879 individuals had been exposed to HIV-positive sources, with antiretroviral prophylaxis provided to nine of them.

CONCLUSIONS

Contemporary post-exposure prophylactic precautions in the Czech Republic can be considered as adequate for the prevention of HBV and HIV, but health care professionals in particular are at risk of HCV transmission.

[The use of electron microscopy and virus isolation in the diagnosis of aseptic neuroinfections]

OBJECTIVE

In aseptic neuroinfections, the etiology is usually known in 50-70% of cases. The aim was to increase the rates using electron microscopy (EM) and virus isolation in cell cultures.

MATERIAL AND METHODS

The prospective study included 34 patients with aseptic neuroinfections hospitalized at the Department of Infectious Diseases in Ostrava fromJuly to November 2012. EM examined cerebrospinal fluid of all patients and virus isolation in tissue cultures was performed in all cerebrospinal fluid samples. Cerebrospinal fluid was examined by polymerase chain reaction for enteroviruses in 30 patients and for herpes simplex virus 1 and 2 in 29 patients. Detection of antibodies against Borrelia burgdorferi and tick-borne encephalitis was performed in all 34 patients.

RESULTS

Possible etiological agents were discovered in 31 out of 34 patients (91%), with one agent being found in 23 patients (68%) and two agents being detected in 8 patients (24%). EM revealed the agents in 26 patients and virus isolation was successful in 10 patients. EM was the only method to identify 10 agents. A group of 23 patients with a single agent detected included 14 patients with enteroviral meningitis, 4 patients with Lyme borreliosis and 4 patients with tick-borne encephalitis; EM detected an undefined virus in the last patient. An unusual group of 8 patients with two agents detected comprised 5 patients with enteroviruses and spirochetes, 2 patients with tick-borne encephalitis and undefined viruses and 1 patient with a spirochete and an undetermined virus.

CONCLUSION

EM can aid in explaining the etiology of aseptic neuroinfections. However, the clinical interpretation of results remains problematic, such as detection of unknown viruses or two possible agents in 8 out of 34 patients.

Pseudoscardovia suis gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of wild pigs (Sus scrofa)

Seventeen fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from the digestive tract of wild pigs (Sus scrofa). Most of them were identified as Bifidobacterium boum according to sequences of 16S rRNA gene. Two strains isolated from the small intestine content had unusual morphology of cells in comparison with bifidobacteria. Cells growing in liquid anaerobic media were regular shaped rods arranged mostly in pairs. These isolates showed relatively low 16S rRNA gene sequence similarities (maximum identity of 94%) to members of the family Bifidobacteriaceae. Nevertheless, phylogenetic analyses of 16S rRNA, hsp60 and xfp gene sequences revealed that these strains are more related to recently described Neoscardovia, Aeriscardovia and other scardovial genera, than to Bifidobacterium species. Partial gene sequences of other phylogenetic markers showed low (65.8-89.5%) similarities to genome sequences of bifidobacteria and Gardnerella vaginalis. The major fatty acids detected in cells of the representative strain DPTE4(T) were C(16:0), C(18:1), C(14:0). The peptidoglycan type of the DPTE4(T) strain was A3βl-Orn(l-Lys)-l-Ser(l-Ala)-l-Ala(2). Polar lipid analysis revealed two phosphoglycolipids and phospholipids, a glycolipid and diphosphatidylglycerol. The results of phylogenetic, genotypic and phenotypic analyses support the proposal of a novel taxa, Pseudoscardovia suis gen. nov., sp. nov. (type strain=DPTE4(T)=DSM 24744(T)=CCM 7942(T)).

The presence of bifidobacteria in social insects, fish and reptiles

The occurrence and species distribution of bifidobacteria in the digestive tract of important representatives of social insects such as ants, bees, wasps and bumblebees as well as the incidence of bifidobacteria in fecal samples of several species of vertebrates represented mainly by reptiles was assigned by culture-independent method based on DGGE and real time PCR. Bifidobacteria were present in the gut of most social insects--honey bees, wasps, cockroaches and bumblebees, except for ants. In honey bees, where the counts of bifidobacteria ranged from 2 to 8% of the total bacteria, the most common species seemed to be Bifidobacterium indicum. Proportion of bifidobacteria was found in broad range from 0.1 to 35-37% in wasps and cockroaches; the variance of bifidobacteria in bumblebees was lower, ranging from 1 to 7% of total bacterial count. Among studied vertebrates, the detectable presence of bifidobacteria was found only in trout (1.1%) and geckos (0.2%), but large amount of these bacteria was observed in Vietnamese box turtle, where bifidobacteria represented nearly one-fourth (22%) of total bacterial counts.

Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract

Our previous study, based primarily on PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing, focused on the isolation of four bifidobacterial groups from the digestive tract of three bumblebee species. In that study, we proposed that these isolated groups potentially represented novel species of the family Bifidobacteriaceae. One of the four, Bifidobacterium bombi, has been described recently. Strains representing two of the other groups have been classified as members of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA and heat-shock protein 60 (hsp60) gene sequences. Analysis of 16S rRNA gene sequence similarities revealed that the isolates of the first group were affiliated to Bifidobacterium asteroides YIT 11866(T), B. indicum JCM 1302(T) and B. coryneforme ATCC 25911(T) (96.2, 96.0 and 95.9 % sequence similarity, respectively), together with other bifidobacteria showing lower sequence similarity. Additional representatives of the second group were found to be affiliated to Bifidobacterium minimum YIT 4097(T) and B. coryneforme ATCC 25911(T) (96.0 and 96.3 % sequence similarity) and also to other bifidobacteria with lower sequence similarity. These results indicate that the isolates of the two groups belong to novel species within the genus Bifidobacterium. This observation was further substantiated by the results of partial sequencing of hsp60. On the basis of phylogenetic and phenotypic analyses and analysis of 16S rRNA and partial hsp60 gene sequences, we propose two novel species, Bifidobacterium actinocoloniiforme sp. nov. (type strain LISLUCIII-P2(T)  = DSM 22766(T)  = CCM 7728(T)) and Bifidobacterium bohemicum sp. nov. (type strain JEMLUCVIII-4(T)  = DSM 22767(T)  = CCM 7729(T)).

[Retreatment with peginterferon plus ribavirin in chronic hepatitis C patients: our own experiences]

Retreatment with peginterferon plus ribavirin was initiated in 26 patients with hepatitis C virus genotype 1b infection (17 relapsers after the first course of therapy, 9 non-responders). So far, retreatment has been completed in 19 patients, one patient achieved a sustained virologic response, and 3 patients were relapsers. Therapy was discontinued in 14 patients (9 non-responders) because of a lack of a treatment response, and in 1 patient due to adverse effects. Retreatment is a new chance for patients with chronic hepatitis C infection. However successful outcome is rare especially in non-responders.

The design of oligonucleotide primers for the universal amplification of the N-acetylglucosaminidase gene (nag1) in Chytridiomycetes with emphasis on the anaerobic Neocallimastigales

The common feature of all chytridiomycetous fungi, aerobic as well as anaerobic, is an abundance of chitin in their cell wall. The genes coding for chitinases have therefore been widely used as phylogenetic markers in ascomycetes. As their utility for Chytridiomycetes has not been determined we chose the gene encoding an enzyme involved in chitin degradation and energy metabolism, the beta-(1,4)-N-acetylglucosaminidase (nag1). Primer pair Nag-forward and Nag-reverse was used to create PCR product from 5 strains of anaerobic and 7 strains of aerobic chytrids. However, Blast search of sequenced amplicons showed that these primers are specific only for fungus Emericella nidulans. Amino acid alignment of Nag1 proteins of fungal, protozoal and bacterial origin available in GenBank database was therefore performed. Five amino acid regions were found to be conserved enough to serve as a suitable domain for the design of a set of primers for the universal amplification of the nag1 gene in the Neocallimastigales fungi.

[Lamivudine therapy in patients with severe acute hepatitis B]

OBJECTIVES

Fulminant hepatitis develops in 1 % of patients with acute hepatitis B. Lamivudine therapy in patients with severe acute hepatitis B probably reduces their risk of fulminant hepatitis but experience with this type of treatment is still limited.

MATERIALS AND METHODS

Between 1999 and 2006, 17 immunocompetent patients (12 women, 5 men, age 17-83 years) with severe acute hepatitis B were treated with lamivudine. Prior to treatment, all patients had their total bilirubin values above 220 micromol/l (more than 13 mg/dl). In 9 patients, the marked increase of bilirubin levels was accompanied by aminotransferase level decrease. Sixteen patients received lamivudine at a dose of 100 mg per day; one patient was given 150 mg daily. In 12 patients, concurrent corticosteroid therapy was administered.

RESULTS

One patient developed fulminant hepatitis B and underwent successful urgent liver transplantation 5 days after the lamivudine therapy was initiated. Sixteen patients responded well to the treatment and their biochemical parameters improved rapidly. Within 3-7 months, the HBsAg was undetectable in 14 out of 15 investigated patients. Protective anti-HBs antibodies developed in 11 of them in 3-21 months. The lamivudine therapy was terminated in 12 patients and it continued for more than 1 year in 3 patients only. Four patients continue to receive lamivudine but the therapy still has not exceeded 9 months. The corticosteroid therapy was short-term; it was longer than one month in 1 of 12 patients.

CONCLUSION

Early treatment with lamivudine alone or with corticosteroids probably decreases the risk of progression to fulminant hepatitis in patients with severe acute hepatitis B.

Effect of gluten-free diet on microbes in the colon

The effect of gluten-free diet (GFD) and chitosan was evaluated in healthy individuals; GFD remarkably influenced the structure of the gut bacterial population and its metabolism. Administration of GFD and chitosan (3 g daily) significantly changed composition and metabolism of the bacterial population. Chitosan stimulated the counts of fecal chitinolytic bacteria and decreased the body mass of treated persons.

Differentiation of anaerobic polycentric fungi by rDNA PCR-RFLP

The suitability of restriction fragment length polymorphism (RFLP) analysis of the ribosomal DNA cluster for discriminating two genera of anaerobic polycentric fungi, Orpinomyces and Anaeromyces, was determined. Three PCR-amplified DNA fragments--nuclear small subunit (SSU; 18S rDNA), the nuclear large subunit (LSU; 28S rDNA) and internal transcribed spacer (ITS)--were restricted with endonucleases AluI, DraI, HinfI and MboI. Although the SSU DNA fragment could be restricted successfully by all four enzymes, no differences were observed between restriction patterns of Orpinomyces and Anaeromyces. The most polymorphic restriction pattern between Orpinomyces and Anaeromyces resulted from cleavage of LSU rDNA fragments cut by AluI and HinfI and ITS fragment cut by DraI and HinfI. Genus-specific RFLP patterns were determined for Orpinomyces and Anaeromyces genera; the results showed that the PCR-RFLP analysis of rDNA offers an easy and rapid tool for differentiation of two polycentric genera of anaerobic fungi, which could be hardly separated on the basis of morphology.

Diet-dependent shifts in ruminal butyrate-producing bacteria

The influence of a host's diet on Butyrivibrio and Pseudobutyrivibrio populations was investigated by competitive PCR. Specific primers were designed and competitive PCRs developed for both groups. Results (from 4 cows with different diets) suggested that high-fiber intake essentially increases the Butyrivibrio amounts in the rumen, whereas high-energy food additives lead to its suppression. The Pseudobutyrivibrio concentration also changed during the experiment but without any significant relation to the host's diet.

Occurrence of restriction-modification systems in ruminal butyrate-producing bacteria

Thirty-five strains of ruminal bacteria belonging to the former Butyrivibrio fibrisolvens species were screened for the presence of site-specific restriction endonuclease and modification methyltransferase activities. Seven strains possessed endonuclease activities detectable in crude cell extracts. The recognition sequences and optimal reaction conditions for seven of them were determined. Five enzymes were found to be isoschizomers of type II endonucleases (EcoRV, NsiI, AseI (2x) and SauI), one was type IIS (FokI) and two remained unknown. The optimal reaction buffer was found to be a low ionic strength buffer and all enzymes possessed sufficient activity at 39 degrees C. The presence of DNA modification among all strains was also determined. Most of the methylation activities correlated with restriction activities, yet some strains possessed unaccompanied modification methyltransferases.

Detection of cellulolytic bacteria from the human colon

The main representatives of bacteria in the human colon were investigated by specific PCR and denaturing gradient gel electrophoresis (DGGE). Prevalent in both cases were species of Bifidobacterium, Clostridium, Bacteroides, Faecalibacterium and Eubacterium. Simultaneously, cellulolytic bacteria were isolated from the human feces. The largest proportion was represented by ruminococcus-like isolates. Their presence was confirmed both by PCR and DGGE methods; the latter one was able to give more comprehensive data about the composition of bacterial population in the human colon chyme.

Determination of the cross section for nuclear reactions in complex nuclear decay chains

In the present paper decays of genetically connected nuclei are considered and equations for their independent cross sections are derived. An optimisation parameter is proposed for an experiment where spectra of the residual nuclei are studied by the induced activity method. This parameter depends on irradiation time, delay time and spectrum measurement time.

Development of competitive PCR for detection of Butyrivibrio fibrisolvens in the rumen

Competitive PCR method was developed for the detection and enumeration of Butyrivibrio fibrisolvens. Sequences of 16S rDNA were obtained from our isolates (serving as a source of data for primer design) and were distinguished into nine different groups of butyrivibria. Specific primers for two distinct groups were designed with the help of BioEdit program. These primers were tested with DNA of 20 strains of ruminal B. fibrisolvens isolates. Annealing temperature 58 degrees C showed a little specificity but a better selectivity was found after raising it up to 65 degrees C. A group 1 competitive fragment of 16S rDNA of different length was constructed using restriction cutting with MspI followed by ligation; the size of the resulting fragment was cut down by 75 bp. The fragment worked in the presence of the original 16S rDNA fragment of B. fibrisolvens JK 609.

Characterizations of highly expressed genes of four fast-growing bacteria

Predicted highly expressed (PHX) genes are characterized for the completely sequenced genomes of the four fast-growing bacteria Escherichia coli, Haemophilus influenzae, Vibrio cholerae, and Bacillus subtilis. Our approach to ascertaining gene expression levels relates to codon usage differences among certain gene classes: the collection of all genes (average gene), the ensemble of ribosomal protein genes, major translation/transcription processing factors, and genes for polypeptides of chaperone/degradation complexes. A gene is predicted highly expressed (PHX) if its codon frequencies are close to those of the ribosomal proteins, major translation/transcription processing factor, and chaperone/degradation standards but strongly deviant from the average gene codon frequencies. PHX genes identified by their codon usage frequencies among prokaryotic genomes commonly include those for ribosomal proteins, major transcription/translation processing factors (several occurring in multiple copies), and major chaperone/degradation proteins. Also PHX genes generally include those encoding enzymes of essential energy metabolism pathways of glycolysis, pyruvate oxidation, and respiration (aerobic and anaerobic), genes of fatty acid biosynthesis, and the principal genes of amino acid and nucleotide biosyntheses. Gene classes generally not PHX include most repair protein genes, virtually all vitamin biosynthesis genes, genes of two-component sensor systems, most regulatory genes, and most genes expressed in stationary phase or during starvation. Members of the set of PHX aminoacyl-tRNA synthetase genes contrast sharply between genomes. There are also subtle differences among the PHX energy metabolism genes between E. coli and B. subtilis, particularly with respect to genes of the tricarboxylic acid cycle. The good agreement of PHX genes of E. coli and B. subtilis with high protein abundances, as assessed by two-dimensional gel determination, is verified. Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are also examined. The spatial distribution of PHX genes within each genome reveals clusters and significantly long regions without PHX genes.

Highly expressed and alien genes of the Synechocystis genome

Comparisons of codon frequencies of genes to several gene classes are used to characterize highly expressed and alien genes on the SYNECHOCYSTIS: PCC6803 genome. The primary gene classes include the ensemble of all genes (average gene), ribosomal protein (RP) genes, translation processing factors (TF) and genes encoding chaperone/degradation proteins (CH). A gene is predicted highly expressed (PHX) if its codon usage is close to that of the RP/TF/CH standards but strongly deviant from the average gene. Putative alien (PA) genes are those for which codon usage is significantly different from all four classes of gene standards. In SYNECHOCYSTIS:, 380 genes were identified as PHX. The genes with the highest predicted expression levels include many that encode proteins vital for photosynthesis. Nearly all of the genes of the RP/TF/CH gene classes are PHX. The principal glycolysis enzymes, which may also function in CO(2) fixation, are PHX, while none of the genes encoding TCA cycle enzymes are PHX. The PA genes are mostly of unknown function or encode transposases. Several PA genes encode polypeptides that function in lipopolysaccharide biosynthesis. Both PHX and PA genes often form significant clusters (operons). The proteins encoded by PHX and PA genes are described with respect to functional classifications, their organization in the genome and their stoichiometry in multi-subunit complexes.

Predicted highly expressed genes of diverse prokaryotic genomes

Our approach in predicting gene expression levels relates to codon usage differences among gene classes. In prokaryotic genomes, genes that deviate strongly in codon usage from the average gene but are sufficiently similar in codon usage to ribosomal protein genes, to translation and transcription processing factors, and to chaperone-degradation proteins are predicted highly expressed (PHX). By these criteria, PHX genes in most prokaryotic genomes include those encoding ribosomal proteins, translation and transcription processing factors, and chaperone proteins and genes of principal energy metabolism. In particular, for the fast-growing species Escherichia coli, Vibrio cholerae, Bacillus subtilis, and Haemophilus influenzae, major glycolysis and tricarboxylic acid cycle genes are PHX. In Synechocystis, prime genes of photosynthesis are PHX, and in methanogens, PHX genes include those essential for methanogenesis. Overall, the three protein families-ribosomal proteins, protein synthesis factors, and chaperone complexes-are needed at many stages of the life cycle, and apparently bacteria have evolved codon usage to maintain appropriate growth, stability, and plasticity. New interpretations of the capacity of Deinococcus radiodurans for resistance to high doses of ionizing radiation is based on an excess of PHX chaperone-degradation genes and detoxification genes. Expression levels of selected classes of genes, including those for flagella, electron transport, detoxification, histidine kinases, and others, are analyzed. Flagellar PHX genes are conspicuous among spirochete genomes. PHX genes are positively correlated with strong Shine-Dalgarno signal sequences. Specific regulatory proteins, e.g., two-component sensor proteins, are rarely PHX. Genes involved in pathways for the synthesis of vitamins record low predicted expression levels. Several distinctive PHX genes of the available complete prokaryotic genomes are highlighted. Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are discussed. Our methodology may be used complementary to experimental expression analysis.

[Providing Internet-based information services at the 2nd Medical School of Charles University]

Development of the internet network at the 2nd Faculty of Medicine, Charles University from one of the first nodes of Prague Academic Network up to a complicated infrastructure with many client computers is accompanied with a corresponding development of information services available in this network. For today's users, infrastructure of the network is hidden behind the services whose technical details are not significant. The paper deals with history, current state and possible perspectives of information services (both basic as e-mail, WWW and more advanced like specialized database server, proxy, etc.) available to users at the 2nd Faculty of Medicine--taking into account the development of information technologies, networking infrastructure and the possibilities and limitations of co-operation between the faculty and its teaching hospital.

Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA

Our basic observation is that each genome has a characteristic "signature" defined as the ratios between the observed dinucleotide frequencies and the frequencies expected if neighbors were chosen at random (dinucleotide relative abundances). The remarkable fact is that the signature is relatively constant throughout the genome; i.e. , the patterns and levels of dinucleotide relative abundances of every 50-kb segment of the genome are about the same. Comparison of the signatures of different genomes provides a measure of similarity which has the advantage that it looks at all the DNA of an organism and does not depend on the ability to align homologous sequences of specific genes. Genome signature comparisons show that plasmids, both specialized and broad-range, and their hosts have substantially compatible (similar) genome signatures. Mammalian mitochondrial (Mt) genomes are very similar, and animal and fungal Mt are generally moderately similar, but they diverge significantly from plant and protist Mt sets. Moreover, Mt genome signature differences between species parallel the corresponding nuclear genome signature differences, despite large differences between Mt and host nuclear signatures. In signature terms, we find that the archaea are not a coherent clade. For example, Sulfolobus and Halobacterium are extremely divergent. There is no consistent pattern of signature differences among thermophiles. More generally, grouping prokaryotes by environmental criteria (e.g., habitat propensities, osmolarity tolerance, chemical conditions) reveals no correlations in genome signature.

A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes

We provide data and analysis to support the hypothesis that the ancestor of animal mitochondria (Mt) and many primitive amitochondrial (a-Mt) eukaryotes was a fusion microbe composed of a Clostridium-like eubacterium and a Sulfolobus-like archaebacterium. The analysis is based on several observations: (i) The genome signatures (dinucleotide relative abundance values) of Clostridium and Sulfolobus are compatible (sufficiently similar) and each has significantly more similarity in genome signatures with animal Mt sequences than do all other available prokaryotes. That stable fusions may require compatibility in genome signatures is suggested by the compatibility of plasmids and hosts. (ii) The expanded energy metabolism of the fusion organism was strongly selective for cementing such a fusion. (iii) The molecular apparatus of endospore formation in Clostridium serves as raw material for the development of the nucleus and cytoplasm of the eukaryotic cell.

Detecting alien genes in bacterial genomes

We present new methods for calculating codon bias of a group of genes or an individual gene relative to a standard gene class. This method is suitable for identifying alien (e.g., horizontally transferred) and highly expressed genes. In yeast and several bacterial genomes, highly expressed genes typically include ribosomal protein genes, elongation factors, chaperonins (heat shock proteins), and a subset of genes involved in glycolysis generally essential in exponential growth. Highly expressed genes of the Synechocystis genome feature several photosystem II genes, and highly expressed genes in several methanogens (Methanococcus jannaschii, M. thermoautotrophicum) are essential for methanogenesis. Alien genes mostly consist of ORFs of unknown function, transposases, prophage genes, and restriction/modification enzymes. Notably, nuclear ribosomal proteins of yeast are highly expressed, whereas mitochondrial ribosomal protein genes appear to be alien genes. Alien genes often occur in clusters, suggesting in these cases that transfer events entail several genes.

Comparative DNA analysis across diverse genomes

We review concepts and methods for comparative analysis of complete genomes including assessments of genomic compositional contrasts based on dinucleotide and tetranucleotide relative abundance values, identifications of rare and frequent oligonucleotides, evaluations and interpretations of codon biases in several large prokaryotic genomes, and characterizations of compositional asymmetry between the two DNA strands in certain bacterial genomes. The discussion also covers means for identifying alien (e.g. laterally transferred) genes and detecting potential specialization islands in bacterial genomes.

Codon usages in different gene classes of the Escherichia coli genome

A new measure for assessing codon bias of one group of genes with respect to a second group of genes is introduced. In this formulation, codon bias correlations for Escherichia coli genes are evaluated for level of expression, for contrasts along genes, for genes in different 200 kb (or longer) contigs around the genome, for effects of gene size, for variation over different function classes, for codon bias in relation to possible lateral transfer and for dicodon bias for some gene classes. Among the function classes, codon biases of ribosomal proteins are the most deviant from the codon frequencies of the average E. coli gene. Other classes of 'highly expressed genes' (e.g. amino acyl tRNA synthetases, chaperonins, modification genes essential to translation activities) show less extreme codon biases. Consistently for genes with experimentally determined expression rates in the exponential growth phase, those of highest molar abundances are more deviant from the average gene codon frequencies and are more similar in codon frequencies to the average ribosomal protein gene. Independent of gene size, the codon biases in the 5' third of genes deviate by more than a factor of two from those in the middle and 3' thirds. In this context, there appear to be conflicting selection pressures imposed by the constraints of ribosomal binding, or more generally the early phase of protein synthesis (about the first 50 codons) may be more biased than the complete nascent polypeptide. In partitioning the E. coli genome into 10 equal lengths, pronounced differences in codon site 3 G+C frequencies accumulate. Genes near to oriC have 5% greater codon site 3 G+C frequencies than do genes from the ter region. This difference also is observed between small (100-300 codons) and large (>800 codons) genes. This result contrasts with that for eukaryotic genomes (including human, Caenorhabditis elegans and yeast) where long genes tend to have site 3 more AT rich than short genes. Many of the above results are special for E. coli genes and do not apply to genes of most bacterial genomes. A gene is defined as alien (possibly horizontally transferred) if its codon bias relative to the average gene exceeds a high threshold and the codon bias relative to ribosomal proteins is also appropriately high. These are identified, including four clusters (operons). The bulk of these genes have no known function.

Strand compositional asymmetry in bacterial and large viral genomes

Several bacterial genomes exhibit preference for G over C on the DNA leading strand extending from the origin of replication to the ter-region in the genomes of Escherichia coli, Mycoplasma genitalium, Bacillus subtilis, and marginally in Haemophilus influenzae, Mycoplasma pneumoniae, and Helicobacter pylori. Strand compositional asymmetry is not observed in the cyanobacterium Synechocystis sp. genome nor in the archaeal genomes of Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Archaeoglobus fulgidus. A strong strand compositional asymmetry is observed in beta-type but not alpha- or gamma-type human herpesviruses featuring G > C downstream of oriL and C > G upstream of oriL. Dinucleotide relative abundances (i.e., dinucleotide representations normalized by the component nucleotide frequencies) are consonant with respect to the leading and lagging strands. Strand compositional asymmetry may reflect on differences in replication synthesis of the leading versus lagging strand, on differences between template and coding strand associated with transcription-coupled repair mechanisms, on differences in gene density between the two strands, on differences in residue and codon biases in relation to gene function, expression level, or operon organization, or on differences in single or context-dependent base mutational rates. The absence of strand asymmetry in the archaeal genomes may reflect the presence of multiple origins of replication.

Compositional differences within and between eukaryotic genomes

Eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. Comparisons within and between species sample sequences are based on the profile of dinucleotide relative abundance values (The profile is rho*XY = f*XY/f*Xf*Y for all XY, where f*X denotes the frequency of the nucleotide X and f*XY denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complement). Previous studies with respect to prokaryotes and this study document that profiles of different DNA sequence samples (sample size >/=50 kb) from the same organism are generally much more similar to each other than they are to profiles from other organisms, and that closely related organisms generally have more similar profiles than do distantly related organisms. On this basis we refer to the collection (rho*XY) as the genome signature. This paper identifies rho*XY extremes and compares genome signature differences for a diverse range of eukaryotic species. Interpretations on the mechanisms maintaining these profile differences center on genome-wide replication, repair, DNA structures, and context-dependent mutational biases. It is also observed that mitochondrial genome signature differences between species parallel the corresponding nuclear genome signature differences despite large differences between corresponding mitochondrial and nuclear signatures. The genome signature differences also have implications for contrasts between rodents and other mammals, and between monocot and dicot plants, as well as providing evidence for similarities among fungi and the diversity of protists.

Compositional biases of bacterial genomes and evolutionary implications

We compare and contrast genome-wide compositional biases and distributions of short oligonucleotides across 15 diverse prokaryotes that have substantial genomic sequence collections. These include seven complete genomes (Escherichia coli, Haemophilus influenzae, Mycoplasma genitalium, Mycoplasma pneumoniae, Synechocystis sp. strain PCC6803, Methanococcus jannaschii, and Pyrobaculum aerophilum). A key observation concerns the constancy of the dinucleotide relative abundance profiles over multiple 50-kb disjoint contigs within the same genome. (The profile is rhoXY* = fXY*/fX*fY* for all XY, where fX* denotes the frequency of the nucleotide X and fY* denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complementary sequence.) On the basis of this constancy, we refer to the collection [rhoXY*] as the genome signature. We establish that the differences between [rhoXY*] vectors of 50-kb sample contigs of different genomes virtually always exceed the differences between those of the same genomes. Various di- and tetranucleotide biases are identified. In particular, we find that the dinucleotide CpG=CG is underrepresented in many thermophiles (e.g., M. jannaschii, Sulfolobus sp., and M. thermoautotrophicum) but overrepresented in halobacteria. TA is broadly underrepresented in prokaryotes and eukaryotes, but normal counts appear in Sulfolobus and P. aerophilum sequences. More than for any other bacterial genome, palindromic tetranucleotides are underrepresented in H. influenzae. The M. jannaschii sequence is unprecedented in its extreme underrepresentation of CTAG tetranucleotides and in the anomalous distribution of CTAG sites around the genome. Comparative analysis of numbers of long tetranucleotide microsatellites distinguishes H. influenzae. Dinucleotide relative abundance differences between bacterial sequences are compared. For example, in these assessments of differences, the cyanobacteria Synechocystis, Synechococcus, and Anabaena do not form a coherent group and are as far from each other as general gram-negative sequences are from general gram-positive sequences. The difference of M. jannaschii from low-G+C gram-positive proteobacteria is one-half of the difference from gram-negative proteobacteria. Interpretations and hypotheses center on the role of the genome signature in highlighting similarities and dissimilarities across different classes of prokaryotic species, possible mechanisms underlying the genome signature, the form and level of genome compositional flux, the use of the genome signature as a chronometer of molecular phylogeny, and implications with respect to the three putative eubacterial, archaeal, and eukaryote domains of life and to the origin and early evolution of eukaryotes.