Complete chloroplast genomes of Vachellia nilotica and Senegalia senegal : Comparative genomics and phylogenomic placement in a new generic system

Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica and Senegalia senegal. Therefore, sequencing the chloroplast (cp) genomes of these species and determining their phylogenetic placement via conserved genes may help to validate the taxonomy. Hence, we sequenced the cp genomes of V. nilotica and S. senegal, and the results showed that the sizes of the genomes are 165.3 and 162.7 kb, respectively. The cp genomes of both species comprised large single-copy regions (93,849~91,791 bp) and pairs of inverted repeats (IR; 26,093~26,008 bp). The total numbers of genes found in the V. nilotica and S. senegal cp genomes were 135 and 132, respectively. Approximately 123:130 repeats and 290:281 simple sequence repeats were found in the S. senegal and V. nilotica cp genomes, respectively. Genomic characterization was undertaken by comparing these genomes with those of 17 species belonging to related genera in Fabaceae. A phylogenetic analysis of the whole genome dataset and 56 shared genes was undertaken by generating cladograms with the same topologies and placing both species in a new generic system. These results support the likelihood of identifying segregate genera from Acacia with phylogenomic disposition of both V. nilotica and S. senegal in the subfamily Mimosoideae. The current study is the first to obtain complete genomic information on both species and may help to elucidate the genome architecture of these species and evaluate the genetic diversity among species.publishedVersio

In silico data mining of large-scale databases for the virtual screening of human interleukin-2 inhibitors

Interleukin-2 (IL-2) is involved in the activation and differentiation of T-helper cells. Uncontrolled activated T cells play a key role in the pathophysiology by stimulating inflammation and autoimmune diseases like arthritis, psoriasis and Crohn’s disease. T cells activation can be suppressed either by preventing IL-2 production or blocking the IL-2 interaction with its receptor. Hence, IL-2 is now emerging as a target for novel therapeutic approaches in several autoimmune disorders. This study was carried out to set up an effective virtual screening (VS) pipeline for IL-2. Four docking/scoring approaches (FRED, MOE, GOLD and Surflex-Dock) were compared in the re-docking process to test their performance in producing correct binding modes of IL-2 inhibitors. Surflex-Dock and FRED were the best in predicting the native pose in its top-ranking position. Shapegauss and CGO scoring functions identified the known inhibitors of IL-2 in top 1, 5 and 10 % of library and differentiated binders from non-binders efficiently with average AUC of > 0.9 and > 0.7, resp. The applied docking protocol served as a basis for the VS of a large database that will lead to the identification of more active compounds against IL-2

Comparative chloroplast genomics of endangered Euphorbia species : Insights into hotspot divergence, repetitive sequence variation, and phylogeny.

Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genomes of two species, E. larica and E. smithii, of the genus Euphorbia through next-generation sequencing and perform a comparative analysis with nine related genomes in the family. The results revealed that the cp genomes had similar quadripartite structure, gene content, and genome organization with previously reported genomes from the same family. The size of cp genomes ranged from 162,172 to 162,358 bp with 132 and 133 genes, 8 rRNAs, 39 tRNA in E. smithii and E. larica, respectively. The numbers of protein-coding genes were 85 and 86, with each containing 19 introns. The four-junction regions were studied and results reveal that rps19 was present at JLB (large single copy region and inverted repeat b junction) in E. larica where its complete presence was located in the IRb (inverted repeat b) region in E. smithii. The sequence comparison revealed that highly divergent regions in rpoC1, rpocB, ycf3, clpP, petD, ycf1, and ndhF of the cp genomes might provide better understanding of phylogenetic inferences in the Euphorbiaceae and order Malpighiales. Phylogenetic analyses of this study illustrate sister clades of E. smithii with E. tricullii and these species form a monophyletic clade with E. larica. The current study might help us to understand the genome architecture, genetic diversity among populations, and evolutionary depiction in the genera.publishedVersio

Ramsay Hunt Syndrome Associated with Varicella-Zoster Virus Encephalitis in a Child

Ramsay Hunt Syndrome (RHS) is a triad of peri-auricular pain, ipsilateral facial nerve palsy and vesicular rash around the ear pinna. It is caused by reactivation of varicella-zoster virus (VZV) that lies dormant in the geniculate ganglia. It can be complicated by VZV encephalitis rarely. We report the case of an 8-year-old previously healthy boy who presented to a tertiary care hospital in Muscat, Oman in 2021 with fever, progressive left ear pain, vesicular rash around his ear pinna and left-sided facial nerve palsy. His course was complicated by VZV encephalitis where he was managed with IV acyclovir and IV corticosteroids. He improved significantly and was asymptomatic with a normal neurology examination at the 6-months follow-up. Keywords: Varicella Zoster Virus; Ramsay Hunt Syndrome; Encephalitis; Children

Modified Le Fort I Osteotomy and Genioplasty for Management of Severe Dentofacial Deformity in β-Thalassaemia Major: Case report and review of the literature

β-thalassaemia major is an autosomal recessive form of haemoglobinopathy that is characterised by complete lack of production of the β-chains resulting in multiple complications that include severe anaemia, failure to thrive and skeletal abnormalities. Facial deformities induced by β-thalassaemia major are rare and are very challenging to treat from a surgical point of view. We report a 33-year-old female patient with β-thalassaemia major who presented to the Dental & Maxillofacial Surgery Department, Sultan Qaboos University Hospital, Muscat, Oman, in 2017 with gross dentofacial skeletal deformity contributing to her psychosocial issues. The facial deformity was corrected surgically by excision of the enlarged maxilla, modified Le Fort I osteotomy and advancement genioplasty. This case highlights the pre-operative preparation, surgical management, encountered complications and treatment outcome within 24 months of follow-up.Keywords: Beta-Thalassaemia; Thalassaemia Major; Cooley's Anemia; Le Fort Osteotomy; Genioplasty; Dentofacial Deformities; Case Report; Oman

Transcriptomic analysis of Dubas bug (Ommatissus lybicus Bergevin) infestation to Date Palm

publishedVersio

Comparative chloroplast genomics of endangered euphorbia species: Insights into hotspot divergence, repetitive sequence variation, and phylogeny

Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genomes of two species, E. larica and E. smithii, of the genus Euphorbia through next-generation sequencing and perform a comparative analysis with nine related genomes in the family. The results revealed that the cp genomes had similar quadripartite structure, gene content, and genome organization with previously reported genomes from the same family. The size of cp genomes ranged from 162,172 to 162,358 bp with 132 and 133 genes, 8 rRNAs, 39 tRNA in E. smithii and E. larica, respectively. The numbers of protein-coding genes were 85 and 86, with each containing 19 introns. The four-junction regions were studied and results reveal that rps19 was present at JLB (large single copy region and inverted repeat b junction) in E. larica where its complete presence was located in the IRb (inverted repeat b) region in E. smithii. The sequence comparison revealed that highly divergent regions in rpoC1, rpocB, ycf3, clpP, petD, ycf1, and ndhF of the cp genomes might provide better understanding of phylogenetic inferences in the Euphorbiaceae and order Malpighiales. Phylogenetic analyses of this study illustrate sister clades of E. smithii with E. tricullii and these species form a monophyletic clade with E. larica. The current study might help us to understand the genome architecture, genetic diversity among populations, and evolutionary depiction in the genera

Microbiome Variation Across Populations of Desert Halophyte Zygophyllum qatarensis

Microbial symbionts play a significant role in plant health and stress tolerance. However, few studies exist that address rare species of core-microbiome function during abiotic stress. In the current study, we compared the microbiome composition of succulent dwarf shrub halophyte Zygophyllum qatarensis Hadidi across desert populations. The results showed that rhizospheric and endosphere microbiome greatly varied due to soil texture (sandy and gravel). No specific bacterial amplicon sequence variants were observed in the core-microbiome of bulk soil and rhizosphere, however, bacterial genus Alcaligenes and fungal genus Acidea were abundantly distributed across root and shoot endospheres. We also analyzed major nutrients such as silicon (Si), magnesium, and calcium across different soil textures and Z. qatarensis populations. The results showed that the rhizosphere and root parts had significantly higher Si content than the bulk soil and shoot parts. The microbiome variation can be attributed to markedly higher Si – suggesting that selective microbes are contributing to the translocation of soluble Si to root. In conclusion, low core-microbiome species abundance might be due to the harsh growing conditions in the desert – making Z. qatarensis highly selective to associate with microbial communities. Utilizing rare microbial players from plant microbiomes may be vital for increasing crop stress tolerance and productivity during stresses