Identification of six potato virus Y isolates from Saudi Arabia

Six potato virus Y (PVY) were isolated from 20 potato plants (Solanum tuberosum sp. tuberosum L.) from the Riyadh region of Saudi Arabia showing leaf systemic symptoms (necrotic spots and mild mosaicism). 16 virus-infected plants gave positive indirect enzyme-linked immunosorbent assay (ELISA) results with PVY commercial antiserum. Electron microscopy revealed the presence of rod-shaped particles (300 × 17 nm). Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) indicated the 34 kDa viral coat protein and agarose gel of the immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) products indicated the 800 bp cp gene. The sequences were aligned together, narrowed to six (one PVY-N and five PVY-O isolates) and then aligned with all published worldwide PVY cp sequences. The highest similarity index among the six isolates was shown between PVY-saudi-O1 and PVY-saudi-O4 (99.9%), while the least involved PVY-saudi-N and PVY-saudi-O3 (99.1%). The phylogenetic analysis of the cp gene nucleotide sequence revealed a cluster of PVY-saudi-N and the Egyptian strain GU980964. The results indicate the need for more sensitive detection of the virus in the imported seeds or tubers from countries, especially in the Middle East like Egypt, to avoid high threat to the Saudi potato trade.Key words: Reverse transcription-polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), coat protein (CP), sequence alignment, similarity index

Complete Sequences of Organelle Genomes from the Medicinal Plant Rhazya Stricta (Apocynaceae) and Contrasting Patterns of Mitochondrial Genome Evolution Across Asterids

Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. Results: The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Conclusions: Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution among angiosperms. The genomic data have enabled a rigorous examination of the gene transfer events. Rhazya is unique among the eight sequenced asterids in the types of events that have shaped the evolution of its mitochondrial genome. Furthermore, the organelle genomes of R. stricta provide valuable genomic resources for utilizing this important medicinal plant in biotechnology applications.King Abdulaziz UniversityIntegrative Biolog

Revisiting the Second Law and Weak Cosmic Censorship Conjecture in High-Dimensional Charged-AdS Black Hole: an Additional Assumption

The verification of the second law of black hole mechanics and the WCCC in the context of enthalpy as mass of the black hole and its related thermodynamic properties has not been tested through a vast number of literature in the recent past. Such studies are of great physical importance as they provide us with a large number of information regarding the thermodynamics and the dynamics of AdS black hole systems. We invest the prior limited surveys of such analysis to investigate the WCCC for the $D$- dimensional asymptotically AdS-charged black holes characterized by its mass ($M$), electric charge ($Q$), and AdS radius ($l$) under the absorption of scalar particles of charge $q$. We examine the WCCC by analyzing the energy-momentum condition of the electrically charged particles as absorbed by the black holes. We prove that the conjecture is well verified irrespective of whether the initial black hole configurations are extremal or non-extremal by changing its charge, the AdS radius, and their variations. We show that the first law and the WCCC are valid for all spacetime dimensions ($D$) independent of the choice of the parameters characterizing the black holes. But to verify the second law in the extremal and non-extremal configurations one has to be very cautious as it gets strongly affected by the choices of the values of the black hole parameters and their variations... In the context of the extended phase space, taking the grand canonical potential into account allow us to obtain the missing information about the variation of the cosmological constant necessary to construct the extended phase space, namely the notion of the black hole pressure, and which is absent in the previous literature so far.Comment: 51 pages and 32 figures. Text improved and references update

Topology of Born-Infeld-AdS Black Hole Phase Transition

The thermodynamic criticality of the AdS black holes serves as an important structure during the thermal phase transition. This paper discusses about the critical points and their topology during thermal phase transitions of the Born-Infeld AdS black holes. We make such investigations using two different topological approaches, namely, using Duan's topological current $\phi$-mapping theory, and the off-shell free energy. Within Duan's formalism, we observe that for a given value of the Born-Infeld parameter $b$, there exists an associated electric charge parameter $Q$, which is highly sensitive to the topological phase transitions. This way we examine the connections of the first-order phase transition and the topological nature of the critical points. We find that the topological nature has a possible breakdown in certain parametric ranges. In effect, we determine the unconventional and the conventional phase critical points as the creation (topologically vortex) and annihilation (topologically anti-vortex) points (pairs). As the second approach, we call the off-shell free energy to determine the topological classes: of which one corresponds to the AdS-Schwarzschild black hole phases, while the other provides a possible topological phase transition. Here we also reveal a novel phase transition between two unstable phases, namely, the unstable small black hole and the intermediate black holes. For a certain parametric values of the Born-Infeld parameter and the pressure, we also study the different topological descriptions that inevitably correspond to the AdS-Reissner-Nordstr\Ddot{o}m black hole phases. As a consistency check of the critical points during the topological phase transitions, we study the vortex/anti-vortex annihilation thermodynamics from local as well as global thermodynamic viewpoint.Comment: 48 pages and 32 figures, references update

Molecular generation and characterization of an efficient recombinant vaccine for avian influenza A/H5N8 in Saudi Arabia

Purpose: To characterize a highly pathogenic avian influenza (HPAI) H5N8 for engineering recombinant 6-+ 2 vaccine strain based on reverse genetic technology. Methods: A total of 135 swab samples from various birds were collected from different parts of Saudi Arabia as part of an influenza surveillance activity. The samples were checked for influenza virus infection using reverse transcriptase-polymerase chain reaction (RT-PCR). Furthermore, Avian influenza H5N8 (A/chicken/KSA/1-NRC/2018), was used for the generation of H5N8 vaccine strain. The vaccine was tested on specific pathogen-free (SPF) chicken purchased from a local market. Results: The results indicate that the candidate vaccine (rgH5N8/KSA) induced specific neutralizing antibodies in chicken, and thereby protected the chickens from subsequent infections of H5N8. Conclusion: The study reinforces the development of a vaccine against avian influenza H5N8 virus isolated in Saudi Arabia, suggesting its possible application against the influenza virus associated with bird fl