Nucleotide Sequence Differences Research Articles

Characterization of Amniotic Fluid Ureaplasma Species from Pregnancies Complicated by Preterm Prelabor Rupture of Membranes.

The main aim of this study was to determine expanded sequence types (eSTs) of Ureaplasma species (U. spp.). DNA isolated from the amniotic fluid of pregnancies complicated by preterm prelabor rupture of membranes (PPROM) using an expanded multilocus sequence typing scheme. Additionally, the study sought to examine whether phylogenetic subgroups of U. spp. DNA differ with respect to maternal demographic and clinical parameters and selected aspects of short-term neonatal morbidity. This retrospective cohort study was focused on singleton pregnancies complicated by PPROM occurring between the gestational ages of 24+0 and 36+6 weeks, where amniocentesis was conducted to assess the intra-amniotic environment and the presence of U. spp. DNA in the amniotic fluid samples was confirmed. The stored aliquots of U. spp. DNA were used to assess differences in nucleotide sequences in six U. spp. genes (ftsH, rpL22, valS, thrS,ureG, and mba-np1) using the eMLST scheme. The expanded multilocus sequence typing scheme was performed in 73 samples of U. spp. DNA isolated from pregnancies complicated by PPROM. In total, 33 different U. spp. DNA eSTs were revealed, 21 (#20, 233-244, 248-251, 253, 255, 259, and 262) of which were novel. The most frequently identified eST was #41, identified in 18% (13/73) of the aliquots. Based on their genetic relationships, the U. spp. DNA was divided into two clusters and four subgroups [cluster I (U. parvum): A, 43% (n = 31); B, 15% (n = 11); and C, 26% (n = 19); cluster II (U. urealyticum): 1; 16% (n = 12)]. Cluster II had a higher rate of polymicrobial findings than cluster I (58% vs 16%; p = 0.005), while subgroup A had the highest rate of concomitant Mycoplasma hominis in the amniotic fluid samples (66%; p = 0.04). In conclusion, Ureaplasma spp. DNA obtained from PPROM consisted of 33 different eSTs of U. spp. DNA. No differences in maternal and neonatal characteristics were found among the phylogenetical subgroups of U. spp. DNA, except for a higher rate of polymicrobial amniotic fluid findings in those with U. urealyticumand the concomitant presence of M. hominis in the amniotic fluid in those with the presence of U. parvum.

New Insights into Polymorphisms in Candidate Genes Associated with Incidence of Postparturient Endometritis in Ossimi Sheep (Ovis aries)

This study examined the genes related to immunity, metabolism, and antioxidants that may interact with the prevalence of postpartum endometritis in Ossimi sheep. We used fifty endometritis-positive Ossimi sheep and fifty that appeared to be normal. For the purpose of taking blood samples, each ewe had its jugular vein pierced. Nucleotide sequence differences for the immunological (alpha-2-macroglobulin, toll-like receptor 2, transforming growth factor beta, interleukin 1 receptor-associated kinase 3, high-mobility group box 1, Fc alpha and Mu receptor, and inducible nitric oxide synthase), metabolic (ADAM metallopeptidase with thrombospondin type 1 motif 20, potassium sodium-activated channel subfamily T member 2, Mitogen-activated protein kinase kinase kinase 4, FKBP prolyl isomerase 5, and relaxin family peptide receptor 1), and antioxidant (superoxide dismutase, catalase, NADH: ubiquinone oxidoreductase subunit s5, and Heme oxygenase-1) genes were found among sheep with endometritis and those in good condition utilizing PCR-DNA sequencing. Fisher’s exact test revealed a significant difference in the probability of dispersal of all significant nucleotide changes between ewe groups with and without endometritis (p ˂ 0.01). In endometritis ewes, there was a considerable up-regulation of the expression levels of A2M, TLR2, IRAK3, HMGB1, FCAMR, iNOS, ADAMTS20, KCNT2, MAP3K4, FKBP5, RXFP1, and HMOX1. Conversely, there was a down-regulation of the genes that encode TGF-β, SOD, CAT, and NDUFS5. The kind of marker and its frequency in postparturient endometrtits significantly impacted the transcript levels of the indicators under analysis. The results validate that nucleotide changes and gene manifestation outlines in these candidates are significant predictors of the prevalence of endometritis in sheep.

DNA Polymorphisms and mRNA Levels of Immune Biomarkers as Candidates for Inflammatory Postpartum Disorders Susceptibility in Italian Buffaloes.

The immunological genes that may interact with inflammatory postpartum diseases in Italian buffaloes were examined in this study. A total number of 120 female Italian buffaloes (60 normal and 60 with inflammatory reproductive diseases) were employed. Each buffalo's jugular vein was pierced to get five milliliters of blood. To obtain whole blood and extract DNA and RNA, the blood was placed within tubes containing sodium fluoride or EDTA anticoagulants. The immunological (IKBKG, LGALS, IL1B, CCL2, RANTES, MASP2, HMGB1, and S-LZ) genes' nucleotide sequence differences between healthy buffaloes and buffaloes affected by inflammatory reproductive diseases were found by employing PCR-DNA sequencing. According to Fisher's exact test (p ˂ 0.01), there were noticeably different probabilities of all major nucleotide changes spreading among buffalo groups with and without reproductive problems. Buffaloes were significantly more likely to express the examined genes when they had inflammatory reproductive diseases. The outcomes might support the significance of these markers' nucleotide variations and gene expression patterns as indicators of the prevalence of inflammatory reproductive disorders and provide a workable buffalo management policy.

LOSS OF HAEMAGGLUTINATION ACTIVITY OF AN INFECTIOUS BRONCHITIS VIRUS AFTER ATTENUATION

Avian infectious bronchitis virus (IBV) has been reported to acquire haemagglutination (HA) activity after treatment with neuraminidase, which depends on the IBV S1 protein. The purpose of this study was to test the IBV HA activity and its relationship to the S1 sequences. A wild strain of IBV, 2575/98 possessed HA activity after neuraminidase treatment. On the contrary, its attenuated strain through 75 chicken embryo passages did not. The nucleotide sequence differences in S1 genes before and after attenuation were C166A and G280T, resulting in amino acid changes of P56T and A94S. The S1 and S genes of the wild strain were cloned and expressed in a baculovirus (B) expression system. To test the relationship between HA activity and the S sequence changes after attenuation, the two nucleotide residues were mutated. The HA activity of those recombinant baculoviruses (rBs) was tested. The results showed that rB containing S gene from wild strain possesses the HA activity, that containing S gene with C166A mutation shows partial HA but that containing G280T mutation shows no any HA activity. Thus, a Taiwan IBV strain 2575/98 loses its HA activity after attenuation and this loss might be related to amino acid changes of P56T and A94S in the IBV S protein.

Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence.

All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.

Complete mitochondrial genome of a golden orb-web spider Trichonephila clavata (Chelicerata, Arachnida) from South Korea

The mitochondrial genome of a golden orb-web spider Trichonephila clavata (L. Koch, 1878) from South Korea is determined and characterized in detail, which is the second mitochondrial genome reported from this species: the first was published from the Chinese sample by Pan et al. (2016). It was 14,436 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and one control region (CR). It has a base composition of 35.99% for ‘A,’ 14.88% for ‘G,’ 9.09% for ‘C,’ and 40.04% for ‘T.’ Comparing the South Korean and Chinese mitochondrial genomes, we observed 8% nucleotide sequence differences between their CRs, caused by the different numbers and sorts of possessed tandem repeats, suggesting a promising molecular marker to distinguish South Korean individuals from Chinese ones. The phylogenetic trees using the maximum likelihood (ML) method were reconstructed with nucleotides (without 3rd codon position) and amino acids from 13 PCGs, respectively, which consistently confirmed that T. clavata (Subfamily Nephilinae) from South Korea and China are clustered together, distinctly separated from the other subfamily Araneinae in the monophyletic family Araneidae.

Biotypic and genotypic diversity in Pasteurella canis isolated from host animals and humans: differences in trehalose fermentation and nucleotide sequences encoding trehalose-6-phosphate hydrolase (treC).

The biotypic and genotypic features of Pasteurella canis isolated from dogs, cats, and humans were clarified by repetitive sequence-based fingerprinting and nucleotide sequences encoding trehalose-6-phosphate hydrolase (treC). Thirty P. canis and 48 P. multocida isolates were collected from dogs, cats, and humans to perform biotyping. The genotyping of P. canis by fingerprinting was followed by dendrogram construction. The whole-genome sequences (WGSs) were searched for the enzyme-coding nucleotide sequences around the main and adjacent loci constituting the operon. Full-length nucleotide sequences encoding the enzyme were determined using polymerase chain reaction and direct sequencing. Biotypic results were compared to the dendrogram and nucleotide sequence data. We observed a difference in trehalose fermentation with a positivity rate of 46.7%. Two (A-1/A-2) and three (B-1/B-2/B-3) clades were located on the dendrograms generated based on two repetitive sequence-based fingerprinting techniques, showing no association between trehalose fermentation and the clades. Based on the WGSs, two variants of the gene, namely, a 1,641 bp gene treC and a pseudogene (1,335 bp) of treC with its first 306 nucleotides deleted, were observed. Trehalose-positive isolates harbored treC, whereas trehalose-negative isolates lacked treC with or without the pseudogene. Our observations suggest biotypic and genotypic diversity among the P. canis isolates from animal and human hosts, with respect to trehalose fermentation and treC nucleotide sequences. This is the first report on the diversity of treC nucleotide sequences among these isolates.

Rapid and sensitive amplicon-based genome sequencing of SARS-CoV-2.

As SARS-CoV-2 variants of concern emerged, the genome sequencing of SARS-CoV-2 strains became more important. In this study, SARS-CoV-2 was sequenced using amplicon-based genome sequencing with MinION. The primer panel used in this study consisted of only 11 primer panels and the size of the amplicons was approximately 3 kb. Full genome sequences were obtained with a hundred copies of the SARS-CoV-2 genome, and 92.33% and 75.39% of the genome sequences were obtained with 10 copies of the SARS-CoV-2 genome. The few differences in nucleotide sequences originated from mutations in laboratory cultures and/or mixed nucleotide sequences. The quantification of the SARS-CoV-2 genomic RNA was done using RT-ddPCR methods, and the level of LoD indicated that this sequencing method can be used for any RT-qPCR positive clinical sample. The sequencing results of the SARS-CoV-2 variants and clinical samples showed that our methods were very reliable. The genome sequences of five individual clinical samples were almost identical, and the analysis of the sequence variance showed that most of these nucleotide substitutions were observed in the genome sequences of the other clinical samples, indicating this amplicon-based whole-genome sequencing method can be used in various clinical fields.

Genetic Variability of Some Tomato Yellow Leaf Curl Virus Isolates and the Effect of the Virus on the Tomato (Solanum lycopersicom L.) Plant Content of Some Mineral Elements

This study was conducted to isolate and identify three isolates of Tomato yellow leaf curl virus (TYLCV), infecting tomato, using polymerase chain reaction technology (PCR) and determining the nucleotide sequences produced by PCR- amplified products to determine the genetic similarity and differences amongst the virus isolates. It also aimed to analyze the plant content of mineral elements: magnesium, calcium, sodium, and potassium to determine the effect of the virus on the plant content of these elements. The laboratory experiments mentioned in this study were carried out in the Plant Virology Laboratory of the Plant Protection Department at the College of Agriculture/ Karbala University. Analysis of the mineral elements was carried out in the Soil Laboratory, College of Agriculture/ University of Kufa. A greenhouse experiment was also carried out to investigate the response of some tomato genotypes against TYLCV during the agricultural season 2018-2019. Results of PCR amplification by the CP-F and CP-R primer pair revealed the possibility of amplifying a 789bp product from each TYLCV isolate isolated from some farms located in some desert areas in Najaf and Karbala governorates. Analysis of the sequences resulting from the PCR-amplified products obtained from the viral isolates (5, 8, and 10) by BLAST Basic Local Alignment Search Tool (BLAST) indicated that all these viral isolates diagnosed in this study belong to TYLCV. TYLCV isolates 5 and 8 obtained from Najaf province had a 100% similarity in the sequences of PCR-amplified products amplified from the TYLCV coat protein. These isolates gave a difference (96%) in the coat protein nucleotide sequence of the virus isolate 10. Furthermore, analysis of some mineral elements in plants infected with TYLCV showed a decrease in the concentrations of magnesium and calcium and an increase in the concentrations of elements sodium and potassium with a significant difference from their normal concentrations in the non-infected plants.

Characterization of infectious laryngotracheitis virus isolates from laying hens during 2019-2020 outbreaks in Tamil Nadu, India.

Infectious laryngotracheitis (ILT) is an acute respiratory disease in chickens that is a serious threat to poultry-producing countries worldwide. In the present study, we isolated and characterized infectious laryngotracheitis (ILTV) virus isolates by sequencing and restriction fragment length polymorphism analysis of PCR-amplified products (PCR-RFLP). A total of 26 ILTV outbreaks were investigated that occurred between 2019 and 2020 in flocks that had not been vaccinated against ILTV. ILTV was isolated by cultivating tracheal samples in embryonated chicken eggs, which showed multiple opaque pock lesions and thickening of the chorioallantoic membrane after 120 hours of infection. The ILTV isolates were identified and characterized by PCR and sequencing a portion of the ICP4 and TK genes. Phylogenetic analysis based on the ICP4 region showed that the sequences clustered with chicken-embryo-origin vaccine-like strains. Sequence analysis of the ICP4 region differentiated chicken-embryo-origin (CEO), tissue-culture-origin (TCO), and field ILTV strains, with significant differences in nucleotide and amino acid sequences. Furthermore, PCR-RFLP analysis of the TK gene showed that the patterns were identical to those obtained with low-virulence and vaccine strains. In conclusion, sequencing of a portion of the ICP4 region of ILTV allowed differentiation of ILTV field, CEO, and TCO vaccine strains. In this study, CEO-vaccine-like strains were found to be the cause of ILTV outbreaks between 2019 and 2020 in Tamil Nadu in southern India.

Exploration of Cytochrome P450 Structure and Function in In Silico Assays for Toxicity

Cytochrome P450 (CYP or P450) enzymes are known for their role in detoxifying xenobiotics and may at times cause toxicity. CYP1A1gene polymorphisms have been linked to susceptibility risks of various cancers and neoplasms, including bladder cancer. The aim of the study was to use bioinformatics tools to examine structural differences in CYP1A1 wild type and isoforms 2 and 3. Protein sequences of selected CYPs were retrieved from the NCBI protein databank and GenPept. Sequence homologies were searched for by BLAST, and by multiple sequence alignments. Protein structural characteristics such as ligand binding and secondary structure prediction were analyzed by Phyre. The CYPIA1 wild type and isoforms had 33 % variation in their amino acid residues and binding sites. The predicted binding sites for the first 6 amino acid residues were similar between the wild type and isoform two; however, the average distances from the ligands differed. The predicted secondary structure of the CYP1A1 isoform 3 exhibited the widest difference from the wild type in the percentage of disordered helix (17%), alpha helix (66%), beta strand (3%) and trans‐membrane domains (12%). Differences in nucleotide sequence between the CYP1A1 wild type and isoforms caused a change in the protein structure which further altered the trans‐membrane topology and ligand binding potential of the protein. These findings indicate structural deficits among the three Cytochrome P450 isoforms, suggesting the possible conferment of risks to toxicity and associated diseases.

Comparative analyses of the mitochondrial genomes of the cattle tick Rhipicephalus microplus clades A and B from China.

The cattle tick (Rhipicephalus microplus) is one of the most common ticks parasitizing livestock, causing diseases as the vector of pathogens. In this study, we amplified and sequenced the complete mitochondrial (mt) genome of R. microplus from Hainan province of China and compared it with that of R. microplus from Guizhou province of China. The mt genome sequence of R. microplus from Hainan isolate was 15,163bp in size, which was significantly longer (299bp) than R. microplus from Guizhou isolate. Nucleotide sequence difference in the entire mt genome except for non-coding region was 5.6% between R. microplus from Hainan and Guizhou isolates. For the 13 protein-coding genes, this comparison revealed the sequence differences of nucleotide (3.8-10.1%) and amino acid (1.2-17.3%). Phylogenetic analysis of R. microplus indicated that R. microplus from Hainan isolate clustered in clade A, and R. microplus from Guizhou isolate clustered in clade B. Taken together, the findings support the recent proposal the existence of two lineages (clades A and B) of R. microplus in China.

PCR-based SNP Markers for Sex Identification in Date Palm (Phoenix dactylifera L.) cv. KL1

The date palm (Phoenix dactylifera L.) is a valuable commercial plant in the Arecaceae family. It is a sweet, edible fruit containing a lot of nutrients including carbs, sugar, protein, and potassium. Maejo 36 or KL1 is a Thai date palm with excellent fresh fruit quality that is mostly grown in Thailand's northern and northeastern areas. The main issue with date palm farming is that there is no reliable way to discriminate between male and female seedlings prior to flowering, which takes 3 - 5 years after planting. An increase in the number of female date palm plants in commercial orchards may increase in date production and profitable investment. The present research aims to develop Single Nucleotide Polymorphisms (SNP) markers for the sex identification of date palm cv. KL1. The SNP markers were designed by analysis of nucleotide sequence difference from GenBank (accession number GL746268.1). The results revealed that SNP primers; PH02F - PdaNu01 (PdaNU02 or PdaNU03) - PdaNU05 used in multiplex PCR technique can precisely distinguish the sex of date palm by generating 2 different sizes of PCR-products in male plants, and only 1 size of PCR-product in female plants. This research indicates that SNP markers with multiplex-PCR technique are a high potential method for identifying the sex of date palm cv. KL1 may be used to increase female plants for cultivation at the seedling stage, which is highly beneficial for commercial date palm production. HIGHLIGHTS Date palm is currently an economic fruits crops in Thailand The sex of date palm can be identified by phenotype in flowering stage until five years after planting The amplicon patterns in male and female date palm generated by SNP marker are applicable to predict their genders at an early seedling stage The use of SNP marker is highly beneficial for commercial date palm production GRAPHICAL ABSTRACT

3D printed hydrophobic barriers in a paper-based biosensor for point-of-care detection of dengue virus serotypes

Paper-based biosensor is one of the most commonly used platforms for point-of-care testing (POCT). Among these platforms, microfluidic paper-based analytical devices (μPADs) have the most versatile designs due to the different hydrophobic barrier patterns and layers of the devices. In addition, μPADs can also be used in combination with other biosensor platforms to improve the performance of the device. Simple and convenient methods for fabricating low-cost and design-adjustable hydrophobic barriers on paper are one of the most challenging aspects for creating μPADs. This work demonstrated a simple technique for using the common polylactic acid (PLA) filament and wax filament to create hydrophobic barriers on paper for μPADs using a commercialized 3D printer. As a proof of concept, the papers with 3D printed PLA barrier were used in combination with a fluidic chip in a prototype biosensor, in which the barrier paper housed four cell-free reactions and the fluidic chip achieved sample delivery to the reactions in the device. Our designed prototype was capable of discriminating dengue virus serotypes based on small nucleotide sequence differences. The proposed combination of 3D-printed barrier paper and fluidic chip provides a versatile platform for rapid prototyping of POCT with possible compatibility with various detection systems.

Isolation, sequencing of the HvnHID gene and its role in the purple-grain colour development in Tibetan hulless barley

2-hydroxyisoflavanone dehydratase (HID) plays an important role in isoflavone biosynthesis. In this study, HID was isolated from the seeds of the purple-grained Tibetan hulless barley variety Nerumuzha and the white-grained variety Kunlun 10. The HvnHID gene includes the 981 bp open reading frame and encodes a protein of 327 amino acids. It has a typical Abhydrolase_3 domain (78–306) and belongs to the carboxylesterase (CXE) family of the Abhydrolase_3 (α/β hydrolase) superfamily. There are eight nucleotide differences in the HvnHID coding sequence and two amino acid differences (one in the Abhydrolase_3 domain) between Nerumuzha and Kunlun 10. The HvnHID of hulless barley has the closest relationship with the HID in Hordeum vulgare, and the most distant relationship in Panicum hallii. At the early-mid stage of the seed colour development, the HvnHID expression levels in the purple and black seeds were significantly higher than in the white and blue ones (P < 0.01). During the seed colour development of purple-grained hulless barley, the expression of the key genes (HvnF3'H, HvnDRF, HvnANT1, and HvnGT) in the anthocyanidin biosynthetic pathway increased significantly, while the HvnHID expression decreased significantly (P < 0.01). Thus, it is likely that HvnHID negatively regulates the anthocyanidin biosynthesis. This result provides an important basis for further study of the biological functions of HvnHID in the anthocyanidin biosynthetic pathway.

Individual hosts carry H. pylori isolates with different cagA features - motifs and copy number.

H. pylori strains with different genetic contents may infect different or an individual human host. Genetic diversity of cagA is thought to contribute to differences in H. pylori strains pathogenicity. In this study, diversity of cagA genotype, EPIYA motif and copy number was assessed in H. pylori single colonies isolated from individual patients. Gastric biopsies from 14H. pylori-positive dyspeptic patients were cultured on selective brucella blood agar and incubated at 37°C under microaerobic conditions. Four single colonies were obtained from each biopsy subculture on brucella blood agar under similar incubation condition. Presence of cagA and types of EPIYA motifs was determined by polymerase chain reaction (PCR) and cagA copy number by quantitative real-time (RT) PCR. Single colonies of 5 patients showed no variation in cagA genotype, EPIYA motif and copy number. Out of the remaining 9 patients, 1 patient showed presence or absence of cagA gene, 2 patients had mixed EPIYA motifs, 2 patients had different cagA copy number, 1 patient showed absence or presence of cagA and mixed motifs, 2 patients had cagA genes with different nucleotide sequences, 1 patient showed presence or absence of cagA and difference in cagA nucleotide sequence. Four isolates that contained multiple copies of cagA, carried EPIYA-ABC motif. Genetic diversity of cagA among single colonies isolated from individual patients represents evidence that gastric mucosa of every individual is colonized with a specific and heterogeneous population of H. pylori. Future studies on patients in different disease groups may elucidate the role of mixed populations of H. pylori in development of gastric diseases.

Polymorphisms in hormone-sensitive lipase and leptin receptor genes and their association with growth traits in Barki lambs.

Background and Aim:Marker-assisted selection has many advantages over conventional selection in animal breeding. The candidate gene approach has been applied to identify genetic markers associated with economically important traits in livestock. This study was established to investigate variation in the hormone-sensitive lipase (HSL) and leptin receptor (LEPR) genes, and their association with growth traits in Barki lambs.Materials and Methods:Records for birth weight (BW), pre-weaning average daily gain (ADG1), weaning weight (WW), post-weaning average daily gain (ADG2), and marketing weight (MW) were obtained from 247 Barki lambs. Polymerase chain reaction–single-stranded conformational polymorphism analyses were used to detect variation in exon 9 of HSL and exon 19 of LEPR. General linear models were used to test for associations between the variation in ovine HSL and LEPR, and growth traits.Results:The SSCP banding patterns for HSL showed three variants (H1, H2, and H3), which contained two nucleotide-sequence differences (c.1865C>T and c.2038T>C). Two SSCP banding patterns (L1 and L2) were observed for LEPR and these contained two nucleotide-sequence differences (c.2800G>A and c.2978C>G). The HSL genotype showed no effect on the studied traits. The LEPR genotype was proven to have significant effects (p<0.05) on ADG2 and MW. The presence of the L1 variant was associated (p<0.01) with decreased ADG2 and MW.Conclusion:The finding of an association between LEPR gene variation and growth rate after weaning in Barki lambs warrants efforts to improve this trait.

Genetic variants of the BMP2 and GDF9 genes and their associations with reproductive performance traits in Barki ewes

• Two BMP2 variants and three GDF9 variants were identified in Barki ewes. • BMP2 variants were associated with TNLW and TWLW; however GDF9 variants were associated with twining rate, TNLB and TWLB. • Variation in ovine BMP2 and GDF9 affects reproductive performance traits of Barki ewes. The aim of this study was to investigate variation in the bone morphogenetic protein 2 ( BMP2 ) and growth differentiation factor 9 ( GDF9 ) genes, and ascertain whether it was associated with reproductive traits in Barki ewes. Records for conception rate of ewe, lambing number of ewe, lambing rate of ewe, twining rate of ewe, total number of lambs born per ewe (TNLB), total weight of lambs born per ewe (TWLB), total number of lambs weaned per ewe (TNLW), total weight of lambs weaned per ewe (TWLW) and ewe rearing ability were obtained for 296 Barki ewes. Polymerase chain reaction–single strand conformational polymorphism (PCR–SSCP) analyses were used to detect variation in exon 2 of BMP2 and exon 1 of GDF9 . The SSCP banding patterns for BMP2 revealed two variants ( A1 and A2 ), which contained one nucleotide sequence difference (c.962A > T). Three SSCP banding patterns ( C1 , C2 and C3 ) were observed for GDF9 and these contained two nucleotide-sequence differences (c.25C > T and c.260 G > A). Association analysis between the variation in BMP2 and GDF9 and reproductive performance traits revealed that BMP2 genotype was associated ( P < 0.05) with TNLW and TWLW, while GDF9 genotype was associated with twining rate of ewe ( P < 0.001), TNLB ( P < 0.001) and TWLB ( P < 0.05). This suggests that selection for the BMP2 and GDF9 genotypes might increase reproductive performance traits in Barki ewes.

Genetic Characterization and Pathogenicity Analysis of Recently Isolated Fowl Adenovirus 8b in Korea.

A Korean field strain of fowl adenovirus (FAdV) 8b was isolated from chickens showing high mortality. Isolated FAdV-8b strains with the hexon and fiber genes were genetically analyzed. The Korean FAdV-8b (K194/19) strain isolated in 2019 showed higher sequence identity with the FAdV-8b strain isolated in China but lower sequence identity with the Korean FAdV-8b (K187/08) strain isolated in 2008. The K194/19 strain formed a distinct subcluster within the FAdV-8b cluster in a phylogenetic tree based on hexon and fiber genes. FAdV can infect day-old chicks through vertical transmission, and so blood samples were obtained from 54-, 60-, and 63-wk-old parent chickens. FAdV-specific antibody levels were investigated with ELISA and virus neutralization (VN) tests with the K194/19 and K187/08 strains as antigens. In VN tests, all sera neutralized the K187/08 strain. However, the K194/19 strain was neutralized by sera collected from 60- and 63-wk-old chickens but not sera obtained from 54-wk-old chickens, indicating natural infection. Finally, to determine the pathogenicity of the K194/19 strain, 1-day-old and 4-wk-old specific-pathogen-free birds were infected with the K194/19 and K187/08 strains. No significant difference in pathogenicity was observed between the two strains. Although the K194/19 strain showed similar pathogenicity with the K187/08 strain, differences in nucleotide and amino acid sequences of the hexon and fiber genes may determine the evasion ability of the K187/08 neutralizing antibody, indicating the need for development of a novel FAdV vaccine.

Baltic Group Tick-Borne Encephalitis Virus Phylogeography: Systemic Inconsistency Pattern between Genetic and Geographic Distances.

Tick-Borne Encephalitis Virus (TBEV) is a dangerous arbovirus widely distributed in Northern Eurasia. The area of this pathogen changes over time. At the beginning of the 2000s, the Ixodes tick populations in Karelia increased. At the same time, the area of I. persulcatus, the main vector of the Siberian TBEV subtype, also expanded. Herein, we sequenced 10 viruses isolated from ticks collected in three locations from the Karelia region in 2008–2018. PCR positive samples were passaged in suckling mice or pig embryo kidney cells (PEK). After the second passage in suckling, mice viral RNA was isolated and E-gene fragment was sequenced. Viral sequences were expected to be similar or nearly identical. Instead, there was up to a 4.8% difference in nucleotide sequence, comparable with the most diverse viruses belonging to the Baltic subgroup in Siberian TBEV subtype (Baltic TBEV-Sib). To reveal whether this was systemic or incidental, a comprehensive phylogeographical analysis was conducted. Interestingly, viruses within each geographic region demonstrated comparable diversity to the whole Baltic TBEV-Sib. Moreover, Baltic TBEV-Sib has a distribution area limited by three ecological regions. This means that active virus mixing occurs in the vast geographic area forming one common virus pool. The most plausible explanation is the involvement of flying animals in the TBEV spread.