ALLELIC VARIATIONS OF SOS, HVNHX AND SDO GENES IN SOME BARLEY (Hordeum Vulgare L.) GENOTYPES

This study has been carried out at the Biotechnology Lab., Department of Field Crops, Faculty of Agriculture, Damascus University during the growing season 2019 - 2020, in order to detect the variations of SOS, HVNHX and SDO genes in different barley genotypes. Clear variations in the SOS, HVNHX and SDO genes, which are responsible for salinity tolerance were found among the investigated genotypes. It has been found that the variation in the amplicon size between loci per gene was very high in some cases, while there was a high degree of symmetry in other cases, and could be easily distinguished on 2% Agarose gel. The PCR results for the SOS genes (SOS1, SOS2, SOS3), HVNHX genes (HVNHX1, HVNHX2, HVNHX3) and SDO genes (Cu/Zn SODII, Cu/Zn SODI, CAT, GRI , APXIII) have shown only one morphological pattern in most of the studied genotypes, while revealed two patterns for the SOS3 gene, but the rest of genes (HVNHX1, HVNHX2, HVNHX3 Cu/Zn SODI, CAT) exhibited only one morphological pattern. The SOS3 was superior in the number of polymorphic patterns, as the number of total patterns was 14 in all the studied genotypes, but the Cu/Zn SODI showed the least number of polymorphic patterns with only 1 pattern, while the largest number (7 patterns) was detected in the genotype (H9), but the two genotypes Fourat9 and Fourat7 showed only one polymorphic pattern.

Cutaneous Manifestations in Confirmed COVID-19 Patients: A Systematic Review

There have been increasing reports of skin manifestations in COVID-19 patients. We conducted a systematic review and included manuscripts describing patients with positive RT-PCR coronavirus testing from nasopharyngeal swabs who also developed cutaneous manifestations. A total of 655 patients were selected, with different types of skin rashes: Erythematous maculopapular (n = 250), vascular (n = 146), vesicular (n = 99), urticarial (n = 98), erythema multiforme/generalized pustular figurate erythema/Stevens-Johnson syndrome (n = 22), ocular/periocular (n = 14), polymorphic pattern (n = 9), generalized pruritus (n = 8), Kawasaki disease (n = 5), atypical erythema nodosum (n = 3), and atypical Sweet syndrome (n = 1). Chilblain-like lesions were more frequent in the younger population and were linked to a milder disease course, while fixed livedo racemosa and retiform purpura appeared in older patients and seemed to predict a more severe prognosis. For vesicular rashes, PCR determined the presence of herpesviruses in the vesicle fluid, which raised the possibility of herpesvirus co-infections. The erythema-multiforme-like pattern, generalized pustular figurate erythema and Stevens-Johnson syndrome were most frequently linked to hydroxychloroquine intake. A positive PCR determination of SARS-COV-2 from conjunctival swabs suggest that eye discharge can also be contagious. These cutaneous manifestations may aid in identifying otherwise asymptomatic COVID-19 carriers in some cases or predict a more severe evolution in others.

Genetic polymorphism and natural selection of circumsporozoite protein in Myanmar Plasmodium vivax

Background Circumsporozoite surface protein (CSP) of malaria parasites has been recognized as one of the leading vaccine candidates. Clinical trials of vaccines for vivax malaria incorporating Plasmodium vivax CSP (PvCSP) have demonstrated their effectiveness in preventing malaria, at least in part. However, genetic diversity of pvcsp in the natural population remains a major concern. Methods A total of 171 blood samples collected from patients infected with Plasmodium vivax in Myanmar were analysed in this study. The pvcsp was amplified by polymerase chain reaction, followed by cloning and sequencing. Polymorphic characteristics and natural selection of pvcsp population in Myanmar were analysed using DNASTAR, MEGA6 and DnaSP programs. The polymorphic pattern and natural selection of publicly accessible global pvcsp sequences were also comparatively analysed. Results Myanmar pvcsp sequences were divided into two subtypes VK210 and VK247 comprising 143 and 28 sequences, respectively. The VK210 subtypes showed higher levels of genetic diversity and polymorphism than the VK247 subtypes. The N-terminal non-repeat region of pvcsp displayed limited genetic variations in the global population. Different patterns of octapeptide insertion (ANKKAEDA in VK210 and ANKKAGDA in VK247) and tetrapeptide repeat motif (GGNA) were identified in the C-terminal region of global pvcsp population. Meanwhile, the central repeat region (CRR) of Myanmar and global pvcsp, both in VK210 and VK247 variants, was highly polymorphic. The high level of genetic diversity in the CRR has been attributed to the different numbers, types and combinations of peptide repeat motifs (PRMs). Interestingly, 27 and 5 novel PRMs were found in Myanmar VK210 and VK247 variants, respectively. Conclusion Comparative analysis of the global pvcsp population suggests a complex genetic profile of pvcsp in the global population. These results widen understanding of the genetic make-up of pvcsp in the global P. vivax population and provide valuable information for the development of a vaccine based on PvCSP.

Assessment of genetic diversity among poplar (Populus deltoides Marsh.) clones from India using RAPD markers.

Here we determined the genetic diversity among 19 Populus deltoides clones collected from forest nurseries of four districts of Haryana State. All of these were raised in the farm area of the Department of Forestry, and the leaf samples from the young plants of different clones of poplar were collected for molecular analysis. The extraction method (CTAB), DNA purification and, PCR reaction conditions were standardized to obtain genetic diversity. Out of the 30 RAPD markers used in this study, only 11 showed polymorphic pattern and showed a total of 94 alleles. Out of these, 59 were polymorphic, and 35 were monomorphic. An average number of alleles amplified was 8.54. The genetic similarity value calculated varied from 0.20 to 0.73 for 19 Poplar clones. The maximum similarity value (0.73) was observed between clone FRIAM 100 and W32, indicating FRIAM 100 and W32 to be most closely related genotypes. Despite low number of alleles that detected polymorphism, RAPD analysis indicated that there is high genetic diversity among Populus deltoides clones analyzed in this study. Since poplar is a crucial commercial agroforestry tree of Haryana state, this type of genetic characterization of the planting material is a pre-requisite to ensure a broader genetic base of the species.

Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions

The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.

GHRL gene-based genotyping of ovine and caprine breeds reveals highly polymorphic intronic sequences in Awassi sheep with several RNA motifs

Background The current study was conducted to identify the genetic polymorphism of ghrelin (GHRL) gene of sheep and goats, as well as to determine whether these polymorphisms were associated with the evolutionary genetic differences in the involved species. This study was performed on 233 sheep and 91 goats. Two genetic loci of 113 bp and 262 bp partially spanning over exon 2/intron 2 and intron 4/exon 5 of GHRL gene respectively were amplified and genotyped using polymerase chain reaction–single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods. Results The SSCP banding pattern of 262-bp locus indicated the presence of four diplotypes (BC, BB, AC, and AB) in Awassi sheep, three diplotypes (BC, BB, and AB) in Karadi sheep, and only two diplotypes (BC and BB) in all goats’ samples. The current study detected several novel SNPs in the ovine–caprine populations as well as two SNPs that are observed only in sheep, including intron4:119 C>A and intron4:123 T>G. The phylogenetic analysis revealed that the observed diplotypes resided within ovine sequences and were closely related to caprine counterparts. Computational analyses indicated the presence of various intronic RNA motifs. However, all these motifs were gathered in Awassi breed. Conclusion It is stated that the intron 4 is highly diverse amongst goats and sheep as well as within sheep with a particular emphasis on Awassi. This genetic peculiarity may in turn suggest a high polymorphic pattern of this breed in comparison with other related counterparts.

Analysis of genetic diversity of Ficus carica L. (Moraceae) collection using simple sequence repeat (SSR) markers

Modern technologies and accurate information on genetic diversity and structure are contributing to improve the plant breeding, in particular for all the minor species with a lack of data. Genetic diversity of 139 different Ficus carica L. genotypes collected from Italy and Croatia, and divided into two subgroups: uniferous (only main crop) and biferous (breba and main crop), was investigated using 49 microsatellite markers. A total of 70 alleles were generated, of which 64 (91.4%) showed a polymorphic pattern indicating high level of genetic diversity within the studied collection. The mean heterozygosity over the 64 single locus microsatellites was 0.33 and the expected and observed averaged variance were 16.50 and 184.08, respectively. The 139 fig genotypes formed two clusters in the PCoA analysis, suggesting a division between Italian and Croatian genotypes. Moreover, the fig accessions could be divided into two main clusters based on the STRUCTURE analysis according to the biological type, uniferous or biferous, with partly overlapping varieties. In conclusion, our results demonstrated that molecular markers were able to discriminate among genotypes and useful for the authentication of fig tree varieties (homonymies and synonymies).

Characterisation of KiSS1R gene and Non genetic factors affecting reproductive traits in Indian goats

This study was undertaken to explore the genetic polymorphism in the KiSS1R (GPR54) gene from 80 Black Bengal, 50 Ganjam and 20 Raighar goat. Each of the sampled goats was recorded for its reproductive traits. The genomic DNA was isolated from the collected blood samples. The target 3’ UTR comprising of 246 bp fragment of KiSS1R gene was successfully amplified using the specific primer. Amplified samples were subjected for HRM analysis followed by sequencing. The nucleotide sequence alignment with the retrieved DNA sequence from NCBI BLAST confirmed absence of polymorphic pattern in KiSS1R gene in 3’ UTR. However, in the studied populations breed had significant effect on littersize, kidding interval and age at sexual maturity. It was found that age at sexual maturity and kidding interval were the highest in Ganjam goat population as compared to Raighar and Black Bengal goat population. Litter size was found highest in Black Bengal goat.

Identification of point mutation in TLR2 gene and its association with mastitis in water buffalo

Mastitis is an economically important disease causing great loss to dairy sector owing to its negative effect on production. Its multi factorial etiology makes it difficult to use prophylactic methods for control. Identification of genetic resistance mechanisms and selection for it is a potential strategy for mastitis control. The present study was done in 101 Murrah buffaloes to find the common causative agents of mastitis in buffaloes, to identify variants in exon 2 and 3' UTR of TLR 2 gene and to study their association with intramammary infection. The microbiological examination revealed Staphylococcus aureus to be most common causative organism followed by Streptococcus agalactiae. PCR-RFLP using Sau3AI and HpyCH4V for exon 2 and 3' UTR respectively resulted in polymorphic pattern for exon2, while 3' UTR resulted in monomorphic pattern. PCR RFLP Sau3AI genotypes of TLR2 exon 2 were found to be highly associated with mastitis resistance. AA genotype was found to be least susceptible, while AB genotype was found most frequent among affected buffaloes.

TLR6 Gene Polymorphism, Sequence Analysis, and Phylogenetic Tree in Susscrofa

TLRs (Toll like receptors) gene have a very important role in early defense against invading pathogens, still we do not have sufficient literature available about them specially TLR6 gene in swine. The current study deals with the characteristic polymorphic, sequencing and evolutionary pattern of TLR6 gene in swine. SSCP based amplification and polymorphic pattern of TLR6 gene, with the eight primers showed different polymorphism. Further, the evolutionary pattern of TLR6 gene was studied through phylogenetic tree analysis. Conclusively, the current comparative phylogenetic and polymorphic analysis of vertebrate TLR6 gene in swine provided informative insights into the process of gene evolution.