Twelve toll-like receptor (TLR) genes in the family Equidae - comparative genomics, selection and evolution

Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.

Supernumerary Marker Chromosome Identified in Asian Elephant (Elephas maximus)

We identified a small, supernumerary marker chromosome (sSMC) in two phenotypically normal Asian elephants (Elephas maximus): a female (2n = 57,XX,+mar) and her male offspring (2n = 57,XY,+mar). sSMCs are defined as structurally abnormal chromosomes that cannot be identified by conventional banding analysis since they are usually small and often lack distinct banding patterns. Although current molecular techniques can reveal their origin, the mechanism of their formation is not yet fully understood. We determined the origin of the marker using a suite of conventional and molecular cytogenetic approaches that included (a) G- and C-banding, (b) AgNOR staining, (c) preparation of a DNA clone using laser microdissection of the marker chromosome, (d) FISH with commercially available human painting and telomeric probes, and (e) FISH with centromeric DNA derived from the centromeric regions of a marker-free Asian elephant. Moreover, we present new information on the location and number of NORs in Asian and savanna elephants. We show that the metacentric marker was composed of heterochromatin with NORs at the terminal ends, originating most likely from the heterochromatic region of chromosome 27. In this context, we discuss the possible mechanism of marker formation. We also discuss the similarities between sSMCs and B chromosomes and whether the marker chromosome presented here could evolve into a B chromosome in the future.

The natural cytotoxicity receptor (NCR) genes in the family Felidae

Natural killer (NK) cells belong to the innate immune system. The germline-encoded natural killer cell receptors represent activating and inhibitory receptors regulating multiple NK cell activities. The natural cytotoxicity receptors (NCRs) are activating natural cytotoxicity triggering receptors 1, 2 and 3 (NKp46, NKp44, and NKp30), encoded by the genes NCR1, NCR2, and NCR3, respectively. NCRs may be expressed in different cell types engaged in mechanisms of innate and adaptive immunity. The family Felidae, comprising the domestic cat and a wide variety of free-ranging species represents a well-suited model for biomedical and evolutionary studies. We characterized the NCR1, NCR2 and NCR3 genes in a panel of felid species. We confirmed the presence of potentially functional genes NCR1, NCR2 and NCR3 in all species. All three genes are conserved within the family and are similar to other phylogenetically related mammalian families. The NCR1 and NCR2 phylogenetic trees based on both nucleotide and protein sequences corresponded to the current zoological taxonomy, with some exceptions suggesting effects of different selection pressures in some species. Highly conserved NCR3 sequences did not allow a robust phylogenetic analysis. Most interspecific differences both at the nucleotide and protein level were found in NCR2. Within species, the most polymorphic CDS was detected in NCR1. Selection analyses indicated the effects of purifying selection on individual amino acid sites in all three genes. In stray cats, a rather high intraspecific diversity was observed. This article is protected by copyright. All rights reserved.

The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors

The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition - the bacteriome and have commonly overlooked the fungal fraction - the mycobiome. To further understand the factors that shape the gut mycobiome of primates and mycobiome-bacteriome interactions, we sequenced 16 S rRNA and ITS2 markers in fecal samples of four different nonhuman primate species and three human groups under different subsistence patterns (n = 149). The results show that gut mycobiome composition in primates is still largely unknown but highly plastic and weakly structured by primate phylogeny, compared with the bacteriome. We find significant gut mycobiome overlap between captive apes and human populations living under industrialized subsistence contexts; this is in contrast with contemporary hunter-gatherers and agriculturalists, who share more mycobiome traits with diverse wild-ranging nonhuman primates. In addition, mycobiome-bacteriome interactions were specific to each population, revealing that individual, lifestyle and intrinsic ecological factors affect structural correspondence, number, and kind of interactions between gut bacteria and fungi in primates. Our findings indicate a dominant effect of ecological niche, environmental factors, and diet over the phylogenetic background of the host, in shaping gut mycobiome composition and mycobiome-bacteriome interactions in primates.

Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae

Background

The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family.

Results

Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3.

Conclusions

The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.

Comparative Study of the Bush Dog (Speothos venaticus) Karyotype and Analysis of Satellite DNA Sequences and Their Chromosome Distribution in Six Species of Canidae

The bush dog (Speothos venaticus, 2n = 74) is a near threatened species taxonomically classified among South American canids. We revised the bush dog karyotype and performed a comparative sequence analysis of satellite and satellite-like DNAs in 6 canids: the bush dog, domestic dog (Canis familiaris, 2n = 78), grey wolf (C. lupus, 2n = 78), Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54+B), red fox (Vulpes vulpes, 2n = 34+B), and arctic fox (V. lagopus, 2n = 48-50) to specify the species position among Canidae. Using FISH with painting and BAC probes, we found that the distribution of canid evolutionarily conserved chromosome segments in the bush dog karyotype is similar to that of the domestic dog and grey wolf. The bush dog karyotype differs by 2 acrocentric chromosome pairs formed by tandem fusions of the canine (29;34) and (26;35) orthologues. An interstitial signal of the telomeric probe was observed in the (26;35) fusion site in the bush dog indicating a recent evolutionary origin of this rearrangement. Sequences and hybridisation patterns of satellite DNAs were compared, and a phylogenetic tree of the 6 canid species was constructed which confirmed the bush dog position close to the wolf-like canids, and apart from the raccoon dog and foxes.

[Analysis of cell free fetal DNA fragmentation rate in pregnant women during the course of gravidit]

AIM OF STUDY

To assess cell free fetal DNA (cffDNA) fragmentation rate in pregnant women during the course of gravidity.

STUDY DESIGN

QF PCR efficiency in cffDNA and quantitative analyses in particular cffDNA molecular size fractions.

SETTING

The study was performed at Department of Medical Genetics and Fetal Medicine, University Hospital Olomouc.

METHOD

1. 363 plasma DNA samples from women in different week of pregnancy (from 4th w.g. to 37th w.g.) were tested for QF PCR efficiency in particular STRs and AMELX/Y. 2. Size fractionated cff DNA (150-300 bp, 300-500 bp, 500-760 bp) was quantified by QF PCR in 91 pregnant women (from 9th w.g. to 40th w.g.). 3. Size fractionated cff DNA from male fetuses was quantified by real time PCR (SRY/internal control) in 22 pregnant women (from 9th w.g. to 36th w.g.).

RESULTS

1. QF PCR efficiency decreased from longer to shorter molecules. 2. The only 500 -760 bp fraction showed cffDNA increase in relation to week of gravidity. 3. Indirect relation between amount of cffDNA and week of gravidity was found in 150-300 bp fraction by Real-time PCR.

CONCLUSION

Assembling of all 3 approaches indicates increase of longer cffDNA molecules during the gravidity while level of the short cffDNA molecule fragments probably remains from the approximately 9th w.g. the same.

[Noninvasive fetal sex detection from maternal plasma in pregnant women]

OBJECTIVE

Objective of our study was optimization of noninvasive fetal sex detection from maternal plasma in pregnant women.

STUDY DESIGN

Molecular DNA quantitative analyses in gonosomal loci.

SETTING

The study was performed at Department of Medical Genetics and Fetal Medicine, University Hospital Olomouc.

METHODS

Together 475 DNA samples isolated from maternal plasma in different weeks of pregnancy ranging from 4th w.g. to 37th w.g. Y chromosomal sequences in AMELY and TSPY were tested by refined quantitative fluorescent PCR using capillary electrophoresis.

RESULTS

The method is able to distinguish 1% of Y chromosomal sequences of artificial mixtures. Investigation and assessment in cell free fetal DNA samples achieved 4.05% of false positivity and 7.15% of false negativity in Y sequence detection.

CONCLUSION

Established method allows detecting fetal sex with high sensitivity and specificity. The method is possible to use also for quantitative purposes.

[Paternity testing based on the analysis of DNA and its revision]

Paternity testing is nowadays mostly based on the analysis of DNA short tandem repeats (STR). Number and selection of STR loci differ according to identification kit producers and also particular laboratories. This article refers a revision of formerly excluded paternity. The cause of the mismatch was revealed by the enlargement of STR loci panel and reciprocal evaluation of samples and paternity was on the contrary confirmed. Different possibilities of failures, their consequences and preventions are also discussed.

[Rapid detection of most frequent chromosomal aneuploidies by the multiplex QF PCR method in the first trimester of pregnancy]

OBJECTIVE

Rapid detection of most frequent aneuploidies by the multiplex QF PCR method in non-cultured samples of chorial tissue. Summarized results of QF PCR method applied in the management of care of pregnant women in the first trimester of pregnancy.

TYPE OF STUDY

An original contribution.

SETTING

Institute of Medical Genetics and Fetal Medicine, Faculty Hospital and Medical Faculty, Palacky University Olomouc.

METHODS

The samples of chorial tissue were obtained from 101 pregnant women. Non-cultured samples were processed by the multiplex QF PCR method. STR loci of chromosomes 13, 18, 21 and X and Y were analyzed. These markers were amplified in two separate multiplex PCR reactions under the same conditions and subjected to fragmentation analysis in capillary electrophoresis.

RESULTS

All 101 analyzed samples of chorial tissue were successfully amplified. In this group, 16 pathologies of the fetuses were detected by the multiplex QF PCR method. Triploidy was detected in two cases, trisomy of chromosome 21--Down syndrome was found in seven cases, and trisomy of chromosome 18--Edwards syndrome was found in six cases and monosomy of gonosome X--the Turner' s syndrome was revealed once.

CONCLUSIONS

The multiplex QF PCR method is an indispensable part of the screening of the first trimester and provides a rapidly available and reliable result in the examined patients.

[Prenatal diagnostics of tuberous sclerosis based on causal mutation knowledge]

BACKGROUND

Tuberous sclerosis is an autosomal-dominant disease characterised by development of benign growth - hamartomas in different organs. Disorder is caused by mutations affecting either of the tumor-suppressor genes, TSC1 or TSC2. Quest for causing mutations is very difficult due to their random distribution over the genes.

METHODS AND RESULTS

Article refers on accomplishment of the first tuberous sclerosis prenatal diagnostics in Czech Republic based on knowledge of causing mutation. Foetal DNA sample, obtained in 13th week from Q435X family pregnant woman, was analyzed by DGGE method.

CONCLUSIONS

Examination excluded presence of tested TSC1 gene defect in an offspring.

[Analysis of free foetal DNA in maternal plasma using STR loci]

BACKGROUND

Problems of maternal and foetal genotype differentiation of maternal plasma in pregnant women are solved generally by real-time systems. In this case the specific probes are used to distinguish particular genotype. Mostly gonosomal sequences are utilised to recognise the male foetus. This work describes possibilities in free foetal DNA detection and quantification by STR.

METHODS AND RESULTS

Artificial genotype mixtures ranging from 0,2 % to 100 % to simulate maternal and paternal genotypes and 27 DNA samples from pregnant women in different stage of pregnancy were used for DNA quantification and detection. Foetal genotype was confirmed by biological father genotyping. The detection was performed in STR from 21st chromosome Down syndrome (DS) responsible region by innovated (I) QF PCR which allows to reveal and quantify even very rare DNA mosaics. The STR quantification was assessed in artificial mixtures of genotypes and discriminability of particular genotypes was on the level of few percent. Foetal DNA was detected in 74 % of tested samples.

CONCLUSIONS

The IQF PCR application in quantification and differentiation between maternal and foetal genotypes by STR loci could have importance in non-invasive prenatal diagnostics as another possible marker for DS risk assessment.

CHEMICAL IMMOBILIZATION OF CAPTIVE AARDVARK (ORYCTEROPUS AFER)

Four aardvarks (Orycteropus afer) were anesthetized over a 6-yr period. They were sedated using detomidine (0.13+/-0.025 mg/kg i.m.; 0.12-0.14 mg/kg) and anesthetized with detomidine (0.12+/-0.025 mg/kg i.m.; 0.09-0.18 mg/kg) followed by ketamine (6.3+/-1.68 mg/kg i.m.; 4.3-8.2 mg/kg). Effects of anesthesia were reversed by atipamezole (0.065+/-0.013 mg/kg i.m.; 0.05-0.09 mg/kg). The detomidine-ketamine combination produced smooth anesthesia, excellent muscle relaxation, and was suitable for routine diagnostic and therapeutic interventions (blood collection, radiologic examinations, minor surgery).

TOXOPLASMOSIS IN NILGAIS (BOSELAPHUS TRAGOCAMELUS) AND A SAIGA ANTELOPE (SAIGA TATARICA)

Three captive female nilgais (Boselaphus tragocamelus) either showed late-term abortion or their newborn calves died within 2 days of birth. Toxoplasma gondii DNA was demonstrated in the brain and liver of each fetus and in one of the two neonates by single-stage polymerase chain reaction (PCR) with TGR1E and by seminested PCR with B1 gene. Retrospectively, antibodies titers > or =640 to T. gondii by indirect fluorescence were found in the sera of all three female and one male nilgais. No other cause of abortion was detected. Fatal toxoplasmosis was also diagnosed in one captive, adult female saiga antelope (Saiga tatarica), which died suddenly. Toxoplasma gondii was detected in the liver, lung, spleen, kidney, and intestine. An unusual finding was the presence of numerous tissue cysts in the liver of this animal. Toxoplasmosis was confirmed by PCR with TGR1E and immunohistochemically. Toxoplasmic hepatitis and pneumonia were considered to be the primary causes of death.

[Angiomyolipoma--its role in prenatal diagnosis of tuberous sclerosis]

Tuberous sclerosis (TSC) is a frequent hereditary autosomal-dominant disease characterised by hamartomas developing in many organs. The disorder is caused by mutations affecting either of the tumor-suppressor genes, TSC1 and TSC2. Tumorogenesis is triggered by the loss of second functional gene copy, mostly accompanied by loss of heterozygosity (LOH) of flanking polymorphic markers. Search for causing mutations is very laborious, time consuming and low effective. Prenatal diagnosis is often hampered by lack of detection of causing mutation. Detection of LOH in hamartomatous tissue suggests which gene is involved in particular case of disease and specifies which of homologous chromosomes carries germinal mutation. Examination of LOH is useful for prenatal diagnostics especially when time is lacking due to patient's pregnancy or in case of mutation screening failure.

[Prospects and applications of innovated quantitative fluorescent PCR (IQF PCR) in analyses of genetic mosaics using gonosomal sequences]

BACKGROUND

Quantification of fluorescence labelled PCR products on capillary electrophoresis (QF PCR) has limits primarily in the possibility of more sensitive analyses to detect minority cell lines and small time related variations. PCR efficiency and human factor affect measuring error and reproducibility of results in these cases. The aim of this work was to assess and optimise of innovated (I)QF PCR in quantification of Y sequences in gonosomal mosaics.

METHODS AND RESULTS

Artificially prepared Y/X mosaics were tested and quantified by IQF PCR, which replaces real-time PCR. Comparison of relative fluorescence to PCR cycles in different Y/X dilutions was plotted on the graphs. Calibration curve for Y sequences quantification was set by the analyses of ratio of Y/X fluorescent signals. An empirical formula was created for the rare mosaic calculation.

CONCLUSIONS

QF PCR refined by manual real-time PCR eliminates limits of QF PCR and specifies quantitative analyses based on PCR. The outstanding feature of IQF PCR is its high sensitivity and accuracy in quantification of Y/X gonosomal mosaics.

[Microdeletion of the azoospermia factor as one of the causes of male infertility]

One of the possible causes of male infertility is microdeletion of the Y chromosome in the Yq11.23 region--named the azoospermia factor. These deletions are associated with azoospermia or severe oligozoospermia. In these cases, testicular histopathological findings comprise a wide spectrum, from total absence of germ cells, through arrest of their maturation to decreased sperm production. Most Y-chromosome microdeletions arise de novo but transmission from the father is also possible, either by the natural way or by assisted reproduction. In relation to the assisted reproduction, the relationship between the Y-deletions and presence of spermatozoa in testis, fertilization capability and embryo quality were examined. Heredity of the deleted Y chromosome is holandric and therefore all sons of males with deletions will carry the same defect and will probably have fertility problems. Another negative influence of deletions on a man's health has not yet been identified.

[Analysis of specific sequences in female patients with Turner syndrome--initial study]

BACKGROUND

DNA sequences from chromosome Y can cause gonadoblastoma development in patients with Turner syndrome (TS). Estimated risk is about 30%. The aim of the study is detection of Y-sequences of DNA level, calculation of mosaicism and its cytogenetic location. Clinical result of the study is the recommendation to gonadectomy of proved positive patients.

METHODS AND RESULTS

Samples from 110 patients were collected. The PCR method and analysis of products on agarose gel was compared with analysis of DNA fragments from quantitative fluorescent (QF) PCR on capillary electrophoresis. The loci DYZ3, AMGX/Y and SRY were used for detection. The method QF PCR was effected for DYZ3 and AMGX/Y loci. The positive cases were examined by FISH method. Five (4.5%) and 3 (2.7%) positive cases were detected in DYZ3 and SRY resp. loci by electrophoresis on agarose gel. Seventeen (15.5%) and 7 (6.4%) positive cases were detected in DYZ3 and AMGX/Y resp. by capillary electrophoresis. The estimated mosaicism ranged from 1:5 to 1:100,000.

CONCLUSIONS

QG PCR is the most sensitive method for diagnostics of Y-sequences. Simultaneously the incidence of Y-positive cells can be estimated. The positive cases with marker in karyotype were confirmed by FISH.

[Early fetal karyotyping and its role in prenatal diagnosis]

OBJECTIVE

Shift of indicated invasive examination in prenatal diagnostics towards the earlier phases of pregnancy with preservation of quality of cytogenetic detection.

DESIGN

Cytogenetic and molecular-cytogenetic analysis of the chorionic villi after long term culture.

SETTING

Department of Medical Genetics and Foetal Medicine, Faculty of Medicine, Palacky University Olomouc, Faculty Hospital in Olomouc.

METHODS

Cultivation of fibroblasts developing from chorionic villi after enzymatic or mechanical disintegration and their karyotyping. Using fluorescent in situ hybridisation to identify the most common chromosomal aneuploidies and to determine gonosomes in indicated cases.

RESULTS

Testing and optimisation of long term culture method and its routine use. Method was utilised so far in 12 patients and successfulness was 83%. Additional fluorescent in situ hybridisation was performed in 6 cases.

CONCLUSION

Using long term culture method of chorionic villi as reliable and routine tool in prenatal diagnostics.