Diversity of culturable moderately halophilic and halotolerant bacteria in a marsh and two salterns a protected ecosystem of Lower Loukkos (Morocco)

To study the biodiversity of halophilic bacteria in a protected wetland located in Loukkos (Northwest, Morocco), a total of 124 strains were recovered from sediment samples from a marsh and salterns. 120 isolates (98%) were found to be moderately halophilic bacteria; growing in salt ranges of 0.5 to 20%. Of 124 isolates, 102 were Gram-positive while 22 were Gram negative. All isolates were identified based on 16S rRNA gene phylogenetic analysis and characterized phenotypically and by screening for extracellular hydrolytic enzymes. The Gram-positive isolates were dominated by the genus Bacillus (89%) and the others were assigned to Jeotgalibacillus, Planococcus, Staphylococcus and Thalassobacillus. The Gram negative isolates were dominated by the genus Vibrio (41%) and the others were assigned to Halomonas, Psychrobacter, Marinobacterium, Pseudoalteromonas, Salinivibrio and Photobacterium. The growth of strains obtained under different physico-chemical conditions and the screening for hydrolytic enzymes showed a high diversity even within the same species

Development of specific primers for the detection of HVA1 from barley in transgenic durum wheat by polymerase chain reaction (PCR) technology

Genetic transformation is a widely employed tool in both basic research and commercial plant breeding programs. Its application requires that transgenes be stably integrated and expressed in the plant genome. When transgenic plants are developed, it is essential to determine which plants contain the transgene. Detection methods are usually based on amplification of the target transgene. This paper describes a development of detection method based on conventional and real time polymerase chain reaction (PCR) for simultaneous detection of barley HVA1 transgene and its transcript in transformed durum wheat. Since there exist a high homology between the barley HVA1 gene and the wheat gene, development of a specific sets of primers is needed for PCR-based characterizations, and the study of the transgene. Based on the alignment of the two genes sequences obtained from public databases, several primers were designed to detect and distinguish between the transformed and non-transformed plants. Real time PCR has been employed because of its inherent sensitivity and quantitative nature. It has been possible to design the following primers pairs F2/MMR, F2/R10 and F14/R10 as highly specific and suitable for the detection of HVA1 DNA by conventional and real-time PCR. Nonetheless, the primers used were allowed to reach high efficiencies and did not show any cross-reactivity with DNAs extracted from various plants. The sensitivity achieved was 6.4 pg. The primer pair F2/R10 was considered as highly specific for the detection of both DNA and mRNA of the HVA1 by real-time PCR. The assays proved to be accurate, specific, sensitive and sufficiently reproducible for further application in high-throughput molecular characterization of transgenic lines.Keywords: HVA1, durum wheat, transgenic plant, real time polymerase chain reaction (PCR), droughtAfrican Journal of Biotechnology, Vol. 13(4), pp. 581-592, 22 January, 201

Identification of Differentially Expressed Genes by cDNA-AFLP Technique in Response to Drought Stress in Triticum durum

Suša je najveći abiotički uzročnik smanjenog uroda žitarica. Da bi se poboljšala tolerancija biljaka na sušu neophodno je identificirati različito eksprimirane gene te razumijeti njihovu aktivnost u uvjetima stresa. Transkriptomika je učinkovita metoda analize molekularnih mehanizama u uvjetima abiotičkog stresa. Za identifikaciju smo gena odgovornih za otpornost na sušu pomoću metode cDNA-AFLP ispitali prisutnost mRNA u kontrolnim uzorcima te listovima durum pšenice izloženim vodnom stresu. Uspješno smo sekvencionirali 76 fragmenata gena dobivenih transkripcijom. Većina transkripata, identificiranih pomoću baze podataka BLAST, pripadaju skupinama gena koji imaju ulogu u metabolizmu, prijenosu energije, staničnoj biosintezi, obrani stanica, transdukciji signala, regulaciji transkripcije, razgradnji proteina te prijenosu tvari. Ekspresija je tih gena potvrđena pomoću metode qRT-PCR, koristeći deset odabranih uzoraka gena. Dobiveni bi rezultati mogli pridonijeti razumijevanju staničnih mehanizama koji aktiviraju različite skupine gena u koordiniranom odgovoru na manjak vode. Identifikacijom gena što reagiraju na stres dobiveni su podaci korisni za razvoj tehnika oplemenjivanja, pomoću kojih se može povećati otpornost durum pšenice na sušu.Drought is the single largest abiotic stress factor leading to reduced crop yields. The identification of diff erentially expressed genes and the understanding of their functions in environmentally stressful conditions are essential to improve drought tolerance. Transcriptomics is a powerful approach for the global analysis of molecular mechanisms under abiotic stress. To identify genes that are important for drought tolerance, we analyzed mRNA populations from untreated and drought-stressed leaves of Triticum durum by cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique. Overall, 76 transcript-derived fragments corresponding to differentially induced transcripts were successfully sequenced. Most of the transcripts identified here, using basic local alignment search tool (BLAST) database, were genes belonging to different functional categories related to metabolism, energy, cellular biosynthesis, cell defense, signal transduction, transcription regulation, protein degradation and transport. The expression patterns of these genes were confirmed by quantitative reverse transcriptase real-time polymerase chain reaction (qRT-PCR) based on ten selected genes representing different patterns. These results could facilitate the understanding of cellular mechanisms involving groups of genes that act in coordination in response to stimuli of water deficit. The identification of novel stress-responsive genes will provide useful data that could help develop breeding strategies aimed at improving durum wheat tolerance to field stress

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Immobilization of Bacillus licheniformis using Fe3O4@SiO2 nanoparticles for the development of bacterial bioreactor

International audienceIn the biotechnology field, nanoparticles with a strong magnetic moment can bring attractive and novel potentialities. They are detectable, manipulable, stimulable by a magnetic field and they could be applied as nano-tracers for medical imaging and nano-vectors for transporting therapeutic agents to a target. For our part, we applied Fe3O4 nanoparticles to immobilize bacteria of Moroccan strains in order to develop bacterial bioreactor. For this aim, we got through the synthesis and characterization of magnetite Fe3O4 nanoparticles by co-precipitation in basic medium. The obtained nanoparticles were encapsulated in silica by sol-gel process. The results of this step allowed us to use Fe3O4@SiO2 nanoparticles to immobilize Bacillus licheniformis by adsorption and separate it magnetically. The principle of this system gives us the opportunity to develop a bacterial bioreactor for industrial applications

Extraction of high quality DNA from seized Moroccan cannabis resin (Hashish).

The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish) free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004) adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR) amplification of tetrahydrocannabinolic acid (THCA) synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish) resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances

Prevalence of resistance to integrase strand-transfer inhibitors (INSTIs) among untreated HIV-1 infected patients in Morocco

Abstract Objective The integrase strand-transfer inhibitors (INSTIs) are an important class in the arsenal of antiretroviral drugs designed to block the integration of HIV-1 cDNA into the host DNA through the inhibition of DNA strand transfer. In this study for the first time in Morocco, the complete HIV-1 integrase gene was analysed from newly diagnosed patients to evaluate the prevalence of natural polymorphisms and INSTIs resistance-associated mutations in the integrase gene. Results The 864pb IN coding region was successfully sequenced from plasma sample for 77 among 80 antiretroviral naïve patients. The sequences were interpreted for drug resistance according to the Stanford algorithm. Sixty samples were HIV-1 subtype B (78%), fourteen CRF02_AG (18%), two subtype C and one subtype A. Overall 81 of 288 (28%) amino acid IN positions presented at least one polymorphism each. We found 18 (36.73%), 42 (25.76%) and 21 (27.27%) of polymorphic residues assigned to the N-Terminal Domain, Catalytic Core Domaine and the C-Terminal Domain positions respectively. Primary INSTIs resistance mutation were absent, however secondary mutations L74IM, T97A were detected in four samples (5.2%). These results demonstrate that untreated HIV-1 infected Moroccans will be susceptible to INSTIs

DNA yield and purity of isolated DNA from the eight cannabis resin samples using Wagner and adapted CTAB protocol (all DNA were re-dissolve in 100 µl sterile deionised water).

<p>DNA yield and purity of isolated DNA from the eight cannabis resin samples using Wagner and adapted CTAB protocol (all DNA were re-dissolve in 100 µl sterile deionised water).</p