Calotropis procera is a wild plant species in the family Apocynaceae that is able to grow in harsh, arid and heat stressed conditions. Understanding how this highly adapted plant persists in harsh ...environments should inform future efforts to improve the hardiness of crop and forage plant species. To study the plant response to droμght and osmotic stress, we treated plants with polyethylene glycol and NaCl and carried out transcriptomic and metabolomics measurements across a time-course of five days.
We identified a highly dynamic transcriptional response across the time-course including dramatic changes in inositol signaling, stress response genes and cytokinins. The resulting metabolome changes also involved sharp increases of myo-inositol, a key signaling molecule and elevated amino acid metabolites at later times.
The data generated here provide a first glimpse at the expressed genome of C. procera, a plant that is exceptionally well adapted to arid environments. We demonstrate, through transcriptome and metabolome analysis that myo-inositol signaling is strongly induced in response to drought and salt stress and that there is elevation of amino acid concentrations after prolonged osmotic stress. This work should lay the foundations of future studies in adaptation to arid environments.
Outbreaks of Middle East respiratory syndrome (MERS) raise questions about the prevalence and evolution of the MERS coronavirus (CoV) in its animal reservoir. Our surveillance in Saudi Arabia in 2014 ...and 2015 showed that viruses of the MERS-CoV species and a human CoV 229E–related lineage co-circulated at high prevalence, with frequent co-infections in the upper respiratory tract of dromedary camels. Including a betacoronavirus 1 species, we found that dromedary camels share three CoV species with humans. Several MERS-CoV lineages were present in camels, including a recombinant lineage that has been dominant since December 2014 and that subsequently led to the human outbreaks in 2015. Camels therefore serve as an important reservoir for the maintenance and diversification of the MERS-CoVs and are the source of human infections with this virus.
Nanoparticles (NPs) are new inspiring clinical targets that have emerged from persistent efforts with unique properties and diverse applications. However, the main methods currently utilized in their ...production are not environmentally friendly. With the aim of promoting a green approach for the synthesis of NPs, this review describes eco-friendly methods for the preparation of biogenic NPs and the known mechanisms for their biosynthesis. Natural plant extracts contain many different secondary metabolites and biomolecules, including flavonoids, alkaloids, terpenoids, phenolic compounds and enzymes. Secondary metabolites can enable the reduction of metal ions to NPs in eco-friendly one-step synthetic processes. Moreover, the green synthesis of NPs using plant extracts often obviates the need for stabilizing and capping agents and yields biologically active shape- and size-dependent products. Herein, we review the formation of metallic NPs induced by natural extracts and list the plant extracts used in the synthesis of NPs. In addition, the use of bacterial and fungal extracts in the synthesis of NPs is highlighted, and the parameters that influence the rate of particle production, size, and morphology are discussed. Finally, the importance and uniqueness of NP-based products are illustrated, and their commercial applications in various fields are briefly featured.
Nanoparticles (NPs) are new inspiring clinical targets that have emerged from persistent efforts with unique properties and diverse applications.
The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three gene phylogenetic ...dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton.
Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome ...(mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae).
Phylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae).
This study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.
The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 diagnosis is crucial for effective medical intervention and transmission control. RT-PCR is the most ...sensitive/specific, but requires costly equipment and trained personnel in centralized laboratories, which are inaccessible to resource-limited areas. Antigen rapid tests enable point-of-care (POC) detection but are significantly less sensitive/specific. CRISPR-Cas systems are compatible with isothermal amplification and dipstick readout, enabling sensitive/specific on-site testing. However, improvements in sensitivity and workflow complexity are needed to spur clinical adoption. We outline the mechanisms/strategies of major CRISPR-Cas systems, evaluate their on-site diagnostic capabilities, and discuss future research directions.
CRISPR-based detection systems are poised to emerge as the next-generation point-of-care (POC) diagnostic platform, and have the potential to marry the advantages of RT-PCR (sensitive/specific) and rapid test kits (RTKs) (fast turnaround, user-friendly).These systems also circumvent the deficiencies of both RT-PCR (long turnaround, equipment/trained user requirement) and RTKs (low sensitivity).These POC platforms play a crucial role for effective medical intervention and transmission control of infectious diseases such as COVID-19.For these systems to be widely adopted clinically, developments have been made to enhance the thermal compatibility of CRISPR with isothermal amplification assays, towards a one-step, one-pot platform.
Plagiogrammaceae, a poorly described family of diatoms, are common inhabitants of the shallow marine littoral zone, occurring either in the sediments or as epiphytes. Previous molecular phylogenies ...of the Plagiogrammaceae were inferred but included only up to six genera: Plagiogramma, Dimeregramma, Neofragilaria, Talaroneis, Psammogramma and Psammoneis. In this paper, we describe a new plagiogrammoid genus, Orizaformis, obtained from Bohai Sea (China) and present molecular phylogenies of the family based on three and four genes (nuclear-encoded large and small subunit ribosomal RNAs and chloroplast-encoded rbcL and psbC). Also included in the new phylogenies is Glyphodesmis. The phylogenies suggest that the Plagiogrammaceae is composed of two major clades: one consisting of Talaroneis, Orizaformis and Psammoneis, and the second of Glyphodesmis, Psammogramma, Neofragilaria, Dimeregramma and Plagiogramma. In addition, we describe three new species within established genera: Psammoneis obaidii, which was collected from the Red Sea, Saudi Arabia; and Neofragilaria stilus and Talaroneis biacutifrons from the Mozambique Channel, Indian Ocean, and illustrate two new combination taxa: Neofragilaria anomala and Neofragilaria lineata. Our observations suggest that the biodiversity of the family is strongly needed to be researched, and the phylogenetic analyses provide a useful framework for future studies of Plagiogrammaceae.
Background Inherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C > T ...transitions resulting from spontaneous deamination of 5'-methylcytosine. Methods Here, we have investigated the potential role of MBD4 in regulating DNA methylation levels using genome-wide transcriptome and methylome analyses. Additionally, we have elucidated its function through a series of in vitro experiments. Results Here we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity. Conclusions Our data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and underscores its critical role in safeguarding against methylation damage. Furthermore, it illustrates how MBD4 functions in normal and pathological conditions. Keywords: MBD4, MLH1, Mismatch repair, Cancer, DNA methylation
Many years back, during Islamic civilization, truffle (Kama'ah) was mentioned by Prophet Muhammed (PBUH) to be well recognized as a therapeutic for eye diseases. (“In the Sahihain, it is narrated ...that the Prophet said: “The Kama'ah (truffle) is among the manna (which is a food mentioned in the Qura'n, Surah al-Baqarah), and its water (extract or juice) cures the eye diseases”). Truffles represent a large group of soil fungi belonging to Ascomycota, Basidiomycota, and Zygomycota. Because of their exceptionally profitable protein, fat, polysaccharide, carbohydrate, ash, mineral, phenolic and other organic molecule contents, truffles have been appreciated as food, nutritional and therapeutic sources for many years.
The main aim of this review is to highlight a comprehensive compile of truffles traditional uses, mycochemistry, pharmacological properties and nutritional value with special focus on desert truffles. Such review represents a good candidate reference for future truffle research.
In this review, we discuss the traditional aspects of truffles with reference to Prophetic Traditional Medicine (al-Tibb al-Nabawi) to cure aliments such as trachoma. The use of truffles is justified by many recent research findings with regards to their anti-inflammatory, anti-bacterial, anti-oxidant, and anti-cancer properties. Although the molecular mechanism and functions of the different truffle species have been intensively studied, we look forward to translating these traditional remedies into preclinical and clinical applications.
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•During Islamic civilization, truffle (Kama'ah) was mentioned by Prophet Muhammed (PBUH) to be therapeutic for eye diseases.•Truffles have been appreciated as food, nutritional and therapeutic sources for many years.•The recent studies have shown that truffles have many biological activities, i.e., anti-oxidants, anti-cancer, cytotoxic, anti-microbial, and anti-inflammatory activities.•The traditional uses of truffles should be translated clinical application.
The present study has tested the biodiesel potential of two hyper lipid producing strains Chlorella sp. and Scenedesmus sp. in terms of biomass yield, quantity and quality of lipid and fatty acid ...composition. Biomass yield of Chlorella sp. and Scenedesmus sp. was 1.26 and 1.33 g/L, respectively on day 18 and 20. The lipid content and lipid productivity of Chlorella sp. and Scenedesmus sp. was estimated to be 21.3, 26.5% and 12.33, 14.74 mg/L/d, respectively. Notably, relative abundance of lipid types in both the strains revealed >60% neutral lipids followed by glycolipids and phospholipids in minimal level. Central composite design based optimization revealed 69 and 65.4% FAME yield from Chlorella sp. and Scenedesmus sp. at 3% sulphuric acid and 65 °C reaction temperature. Eventually, higher levels of saturated fatty acids (~45%) and monounsaturated fatty acids (~34%) and make Scenedesmus sp. a promising parent material for workable biodiesel production.
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•Biodiesel potentials of oleaginous Chlorella sp. and Scenedesmus sp. were compared.•21.3 and 26.5% lipids obtained from Chlorella sp. and Scenedesmus sp. respectively.•Both strains had higher abundance of neutral lipids (>60%) over other lipid types.•CCD showed 69% FAME yield from Scenedesmus sp. at 3% H2SO4 and 65 °C.•Oleic, palmitoleic, and palmitic acids present in higher levels in Scenedesmus sp.
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