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  • Investigation of important biochemical compounds from selected freshwater macroalgae and their role in agriculture

    Shah, Zahir; Badshah, Syed Lal; Iqbal, Arshad; Shah, Zamarud; Emwas, Abdul-Hamid M.; Jaremko, Mariusz (Chemical and Biological Technologies in Agriculture, Springer Science and Business Media LLC, 2022-01-15) [Article]
    Background Freshwater macroalgae possess a number of important secondary metabolites. They are an unexplored source of medicinal compounds. In this study, three freshwater macroalgae—$\textit{Chara vulgaris}$, $\textit{Cladophora glomerata}$ and $\textit{Spirogyra crassa}$—were collected from the river Swat and the river Kabul in the Charsadda district of Khyber Pakhtunkhwa, Pakistan. To assess the role of freshwater macroalgae in agriculture, various experiments were performed on their extracts. Methanolic extract of the three macroalgae were first analyzed through gas chromatography–mass spectrometry (GC–MS) for the presence of important medicinal secondary metabolites. The methanol based macroalgae extracts were tested for antibacterial, insecticidal, cytotoxic and phytotoxic activities. Results Initially, the algae were dried, crushed and treated with methanol for the extraction of secondary metabolites. The GC–MS results contained several important long chain fatty acids and other related long-chain hydrocarbons, such as alkanes and alkenes. Several benzene derivatives were also detected during the course of the investigation. Several of these compounds have established roles in the treatment of human ailments and can be supplied to farm animals. For example, phenylephrine is a decongestant, dilates pupils, increases blood pressure and helps in relieving hemorrhoids. Hexahydropseudoionone has uses in perfumes and other cosmetics. Several essential oils were also detected in the methanolic extract of the three macroalgae that can be utilized in various industrial products. Bioassays showed that these algal extracts—especially the $\textit{Spirogyra}$ sp. extract—contain moderate to maximum bioactivity. Conclusions Macroalgae possess important secondary metabolites with medicinal properties. These secondary metabolites can be used as biopesticides, plant growth enhancers, and remedies for various diseases in farm animals and for the control of weeds. They can be further explored for isolation and purification of useful biochemical compounds.
  • Underestimated PAH accumulation potential of blue carbon vegetation: Evidence from sedimentary records of saltmarsh and mangrove in Yueqing Bay, China.

    Huang, Runqiu; Zhang, Chunfang; Xu, Xiangrong; Jin, Runjie; Li, Dan; Christakos, George; Xiao, Xi; He, Junyu; Agusti, Susana; Duarte, Carlos M.; Wu, Jiaping (The Science of the total environment, Elsevier BV, 2022-01-13) [Article]
    Sediments of blue carbon vegetation are becoming a sink of natural and anthropogenic pollutants, such as polycyclic aromatic hydrocarbons (PAHs). However, the extent to which PAHs are accumulated and varied in blue carbon sediments, and the impact of blue carbon vegetation on the accumulation and retention capacity of PAHs, have been poorly explored. This study examines the sedimentary records of PAHs in profiles from mangrove plantations, saltmarsh, and mudflat in Ximen Island and Maoyan Island of Yueqing Bay, China. The existence of blue carbon vegetation provides a sheltered environment for the accelerated burial of sediment and OC. Decadal PAH sedimentation records show staged changes characterized by the emission of PAHs and colonization of blue carbon vegetation, reflecting the accelerated burial of PAHs in sediments by blue carbon vegetation colonization. In addition, the colonization of blue carbon vegetation contributes to the shift of PAH compositions in sediments. This study provides new insights into the underestimated PAH accumulation potential and retention capacity of blue carbon vegetation and the corresponding underlying sediments, supporting the environmental benefits of blue carbon vegetation.
  • Rice domestication.

    Fornasiero, Alice; Wing, Rod Anthony; Ronald, Pamela (Current biology : CB, Elsevier BV, 2022-01-11) [Article]
    Rice is a staple food crop for more than one-third of the global population (, of which 90% live at or near the poverty line. Thus, rice genetic improvement is important for global food security and is critical for enhancing socioeconomic benefits and reducing the environmental impacts of agriculture. In continued efforts to address the long-standing problem of food security and sustainable agriculture, scientists are utilizing genes from diverse varieties of rice to improve the resilience of rice to pests, diseases and environmental stress. This Primer describes the history of rice domestication, the importance of wild relatives of rice for crop improvement, and the domestication of wild species of rice not previously planted by farmers - a new approach called neodomestication.
  • In Vitro and In Silico Approaches for the Evaluation of Antimicrobial Activity, Time-Kill Kinetics, and Anti-Biofilm Potential of Thymoquinone (2-Methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione) against Selected Human Pathogens

    Qureshi, Kamal A.; Imtiaz, Mahrukh; Parvez, Adil; Rai, Pankaj K.; Jaremko, Mariusz; Emwas, Abdul-Hamid M.; Bholay, Avinash D.; Fatmi, Muhammad Qaiser (Antibiotics, MDPI AG, 2022-01-10) [Article]
    Thymoquinone (2-methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione; TQ), a principal bioactive phytoconstituent of Nigella sativa essential oil, has been reported to have high antimicrobial potential. Thus, the current study evaluated TQ’s antimicrobial potential against a range of selected human pathogens using in vitro assays, including time-kill kinetics and anti-biofilm activity. In silico molecular docking of TQ against several antimicrobial target proteins and a detailed intermolecular interaction analysis was performed, including binding energies and docking feasibility. Of the tested bacteria and fungi, S. epidermidis ATCC 12228 and Candida albicans ATCC 10231 were the most susceptible to TQ, with 50.3 ± 0.3 mm and 21.1 ± 0.1 mm zones of inhibition, respectively. Minimum inhibitory concentration (MIC) values of TQ are in the range of 12.5–50 µg/mL, while minimum biocidal concentration (MBC) values are in the range of 25–100 µg/mL against the tested organisms. Time-kill kinetics of TQ revealed that the killing time for the tested bacteria is in the range of 1–6 h with the MBC of TQ. Anti-biofilm activity results demonstrate that the minimum biofilm inhibitory concentration (MBIC) values of TQ are in the range of 25–50 µg/mL, while the minimum biofilm eradication concentration (MBEC) values are in the range of 25–100 µg/mL, for the tested bacteria. In silico molecular docking studies revealed four preferred antibacterial and antifungal target proteins for TQ: D-alanyl-D-alanine synthetase (Ddl) from Thermus thermophilus, transcriptional regulator qacR from Staphylococcus aureus, N-myristoyltransferase from Candida albicans, and NADPH-dependent D-xylose reductase from Candida tenuis. In contrast, the nitroreductase family protein from Bacillus cereus and spore coat polysaccharide biosynthesis protein from Bacillus subtilis and UDP-N-acetylglucosamine pyrophosphorylase from Aspergillus fumigatus are the least preferred antibacterial and antifungal target proteins for TQ, respectively. Molecular dynamics (MD) simulations revealed that TQ could bind to all four target proteins, with Ddl and NADPH-dependent D-xylose reductase being the most efficient. Our findings corroborate TQ’s high antimicrobial potential, suggesting it may be a promising drug candidate for multi-drug resistant (MDR) pathogens, notably Gram-positive bacteria and Candida albicans.
  • Digital E. coli Counter: A Microfluidics and Computer Vision-Based DNAzyme Method for the Isolation and Specific Detection of E. coli from Water Samples

    Rauf, Sakandar; Tashkandi, Nouran Abdulatif; De Oliveira Filho, José Ilton; Oviedo-Osornio, Claudia Iluhí; Danish, Muhammad S.; Hong, Pei-Ying; Salama, Khaled N. (Biosensors, MDPI AG, 2022-01-10) [Article]
    Biological water contamination detection-based assays are essential to test water quality; however, these assays are prone to false-positive results and inaccuracies, are time-consuming, and use complicated procedures to test large water samples. Herein, we show a simple detection and counting method for E. coli in the water samples involving a combination of DNAzyme sensor, microfluidics, and computer vision strategies. We first isolated E. coli into individual droplets containing a DNAzyme mixture using droplet microfluidics. Upon bacterial cell lysis by heating, the DNAzyme mixture reacted with a particular substrate present in the crude intracellular material (CIM) of E. coli. This event triggers the dissociation of the fluorophore-quencher pair present in the DNAzyme mixture leading to a fluorescence signal, indicating the presence of E. coli in the droplets. We developed an algorithm using computer vision to analyze the fluorescent droplets containing E. coli in the presence of non-fluorescent droplets. The algorithm can detect and count fluorescent droplets representing the number of E. coli present in the sample. Finally, we show that the developed method is highly specific to detect and count E. coli in the presence of other bacteria present in the water sample.
  • Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat

    Silva, Paula; Evers, Byron; Kieffaber, Alexandria; Wang, Xu; Brown, Richard; Gao, Liangliang; Fritz, Allan K.; Crain, Jared; Poland, Jesse (Cold Spring Harbor Laboratory, 2022-01-06) [Preprint]
    Barley yellow dwarf (BYD) is one of the major viral diseases of cereals. Phenotyping BYD in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species. The objectives of this study were to, i) evaluate the use of high-throughput phenotyping (HTP) from unmanned aerial systems to improve BYD assessment and selection, ii) identify genomic regions associated with BYD resistance, and iii) evaluate genomic prediction models ability to predict BYD resistance. Up to 107 wheat lines were phenotyped during each of five field seasons under both insecticide treated and untreated plots. Across all seasons, BYD severity was lower with the insecticide treatment and plant height (PTHTM) and grain yield (GY) showed increased values relative to untreated entries. Only 9.2% of the lines were positive for the presence of the translocated segment carrying resistance gene $\textit{Bdv2}$ on chromosome 7DL. Despite the low frequency, this region was identified through association mapping. Furthermore, we mapped a potentially novel genomic region for resistance on chromosome 5AS. Given the variable heritability of the trait (0.211 0.806), we obtained relatively good predictive ability for BYD severity ranging between 0.06 0.26. Including $\textit{Bdv2}$ on the predictive model had a large effect for predicting BYD but almost no effect for PTHTM and GY. This study was the first attempt to characterize BYD using field-HTP and apply GS to predict the disease severity. These methods have the potential to improve BYD characterization and identifying new sources of resistance will be crucial for delivering BYD resistant germplasm.
  • Thymosin β4 Is an Endogenous Iron Chelator and Molecular Switcher of Ferroptosis

    Lachowicz, Joanna; Pichiri, Gius; Piludu, Marco; Fais, Sara; Orrù, Germano; Congiu, Terenzio; Piras, Monica; Faa, Gavino; Fanni, Daniela; Torre, Gabriele; Lopez, Xabier; Chandra, Kousik; Szczepski, Kacper; Jaremko, Lukasz; Ghosh, Mitra; Emwas , Abdul-Hamid; Castagnola, Massimo; Jaremko, Mariusz; Hannappel, Ewald; Coni, Pierpaolo (International Journal of Molecular Sciences, Research Square Platform LLC, 2022-01-04) [Article]
    Thymosin β4 (Tβ4) was extracted forty years agofrom calf thymus. Since then, it has been identified as a G-actin binding protein involved in blood clotting, tissue regeneration, angiogenesis, and anti-inflammatory processes. Tβ4 has also been implicated in tumor metastasis and neurodegeneration. However, the precise roles and mechanism(s) of action of Tβ4 in these processes remain largely unknown, with the binding of the G-actin protein being insufficient to explain these multi-actions. Here we identify for the first time the important role of Tβ4 mechanism in ferroptosis, an iron-dependent form of cell death, which leads to neurodegeneration and somehow protects cancer cells against cell death. Specifically, we demonstrate four iron2+ and iron3+ binding regions along the peptide and show that the presence of Tβ4 in cell growing medium inhibits erastin and glutamate-induced ferroptosis in the macrophage cell line. Moreover, Tβ4 increases the expression of oxidative stress-related genes, namely BAX, hem oxygenase-1, heat shock protein 70 and thioredoxin reductase 1, which are downregulated during ferroptosis. We state the hypothesis that Tβ4 is an endogenous iron chelator and take part in iron homeostasis in the ferroptosis process. We discuss the literature data of parallel involvement of Tβ4 and ferroptosis in different human pathologies, mainly cancer and neurodegeneration. Our findings confronted with literature data show that controlled Tβ4 release could command on/off switching of ferroptosis and may provide novel therapeutic opportunities in cancer and tissue degeneration pathologies
  • Heterotrophic Bacterioplankton Growth and Physiological Properties in Red Sea Tropical Shallow Ecosystems With Different Dissolved Organic Matter Sources

    Silva, Luis; Calleja Cortes, Maria de Lluch; Huete-Stauffer, Tamara M.; Ivetic, Snjezana; Ansari, Mohd Ikram; Viegas, Miguel; Moran, Xose Anxelu G. (Frontiers in Microbiology, Frontiers Media SA, 2022-01-03) [Article]
    Despite the key role of heterotrophic bacterioplankton in the biogeochemistry of tropical coastal waters, their dynamics have been poorly investigated in relation to the different dissolved organic matter (DOM) pools usually available. In this study we conducted four seasonal incubations of unfiltered and predator-free seawater (Community and Filtered treatment, respectively) at three Red Sea coastal sites characterized by different dominant DOM sources: Seagrass, Mangrove, and Phytoplankton. Bacterial abundance, growth and physiological status were assessed by flow cytometry and community composition by 16S rRNA gene amplicons. The Seagrass site showed the highest initial abundances (6.93 ± 0.30 × 10$^{5}$ cells mL$^{–1}$), coincident with maximum DOC concentrations (>100 μmol C L$^{–1}$), while growth rates peaked at the Mangrove site (1.11 ± 0.09 d$^{–1}$) and were consistently higher in the Filtered treatment. The ratio between the Filtered and Community maximum bacterial abundance (a proxy for top-down control by protistan grazers) showed minimum values at the Seagrass site (1.05 ± 0.05) and maximum at the Phytoplankton site (1.24 ± 0.30), suggesting protistan grazing was higher in open waters, especially in the first half of the year. Since the Mangrove and Seagrass sites shared a similar bacterial diversity, the unexpected lack of bacterial response to predators removal at the latter site should be explained by differences in DOM characteristics. Nitrogen-rich DOM and fluorescent protein-like components were significantly associated with enhanced specific growth rates along the inshore-offshore gradient. Our study confirms the hypotheses that top–down factors control bacterial standing stocks while specific growth rates are bottom-up controlled in representative Red Sea shallow, oligotrophic ecosystems.
  • CS-Cells: A CRISPR-Cas12 DNA Device to Generate Chromosome-Shredded Cells for Efficient and Safe Molecular Biomanufacturing

    Pantoja Angles, Aarón; Ali, Zahir; Mahfouz, Magdy M. (ACS Synthetic Biology, American Chemical Society (ACS), 2022-01-03) [Article]
    Synthetic biology holds great promise for translating ideas into products to address the grand challenges facing humanity. Molecular biomanufacturing is an emerging technology that facilitates the production of key products of value, including therapeutics and select chemical compounds. Current biomanufacturing technologies require improvements to overcome limiting factors, including efficient production, cost, and safe release; therefore, developing optimum chassis for biomolecular manufacturing is of great interest for enabling diverse synthetic biology applications. Here, we harnessed the power of the CRISPR-Cas12 system to design, build, and test a DNA device for genome shredding, which fragments the native genome to enable the conversion of bacterial cells into nonreplicative, biosynthetically active, and programmable molecular biomanufacturing chassis. As a proof of concept, we demonstrated the efficient production of green fluorescent protein and violacein, an antimicrobial and antitumorigenic compound. Our CRISPR-Cas12-based chromosome-shredder DNA device has built-in biocontainment features providing a roadmap for the conversion of any bacterial cell into a chromosome-shredded chassis amenable to high-efficiency molecular biomanufacturing, thereby enabling exciting and diverse biotechnological applications.
  • On the effects of CO2 atmosphere in the pyrolysis of Salicornia bigelovii

    Aljaziri, Jinan; Gautam, Ribhu; Alturkistani, Sultan H.; Fiene, Gabriele; Tester, Mark A.; Sarathy, Mani (Bioresource Technology Reports, Elsevier BV, 2022-01) [Article]
    This study focuses on understanding the effects of a CO$_2$ atmosphere on the pyrolysis of $\textit{Salicornia bigelovii}$ by performing a detailed kinetic analysis and investigating the pyrolysis products. In comparison to N$_2$ pyrolysis, CO$_2$ pyrolysis increased the amounts of acids, phenols, amines/amides and N-aromatics in the bio-oil. Biochar showed a 6.5% increase in carbon and a 5.8% decrease in oxygen due to the presence of CO$_2$ in the pyrolysis atmosphere. CO$_2$ also inhibited the volatilization of certain functional groups, such as phenols, tertiary alcohols and aromatics from the biochar, and the surface area of the biochar was 12 times larger than pyrolysis in N$_2$ atmosphere. Pyrolysis in CO$_2$ led to an increase in the average apparent activation energy from 146.5 kJ mol$^{−1}$ in N$_2$ to 163.4 kJ mol$^{−1}$. The kinetic equation was found to conform to a three dimensional diffusion mechanism. Finally, the pre-exponential factor was determined for each reaction.
  • Cyclodextrins: Structural, Chemical, and Physical Properties, and Applications

    Poulson, Benjamin Gabriel; Alsulami, Qana; Sharfalddin, Abeer A.; El Agammy, Emam; Mouffouk , Fouzi; Emwas, Abdul-Hamid M.; Jaremko, Lukasz; Jaremko, Mariusz (Polysaccharides, MDPI AG, 2022) [Article]
    Due to their unique structural, physical and chemical properties, cyclodextrins and their derivatives have been of great interest to scientists and researchers in both academia and industry for over a century. Many of the industrial applications of cyclodextrins have arisen from their ability to encapsulate, either partially or fully, other molecules, especially organic compounds. Cyclodextrins are non-toxic oligopolymers of glucose that help to increase the solubility of organic compounds with poor aqueous solubility, can mask odors from foul-smelling compounds, and have been widely studied in the area of drug delivery. In this review, we explore the structural and chemical properties of cyclodextrins that give rise to this encapsulation (i.e., the formation of inclusion complexes) ability. This review is unique from others written on this subject because it provides powerful insights into factors that affect cyclodextrin encapsulation. It also examines these insights in great detail. Later, we provide an overview of some industrial applications of cyclodextrins, while emphasizing the role of encapsulation in these applications. We strongly believe that cyclodextrins will continue to garner interest from scientists for many years to come, and that novel applications of cyclodextrins have yet to be discovered
  • Computational Study of SARS-CoV-2 RNA Dependent RNA Polymerase Allosteric Site Inhibition

    Faisal, Shah; Badshah, Syed Lal; Kubra, Bibi; Sharaf, Mohamed; Emwas, Abdul-Hamid M.; Jaremko, Mariusz; Abdalla, Mohnad (2021-12-30) [Article]
    The COVID-19 pandemic has caused millions of fatalities since 2019. Despite the availability of vaccines for this disease, new strains are causing rapid ailment and are a continuous threat to vaccine efficacy. Here, molecular docking and simulations identify strong inhibitors of the allosteric site of the SARS-CoV-2 virus RNA dependent RNA polymerase (RdRp). More than one hundred different flavonoids were docked with the SARS-CoV-2 RdRp allosteric site through computational screening. The three top hits were Naringoside, Myricetin and Aureusidin 4,6-diglucoside. Simulation analyses confirmed that they are in constant contact during the simulation time course and have strong association with the enzyme’s allosteric site. Absorption, distribution, metabolism, excretion and toxicity (ADMET) data provided medicinal information of these top three hits. They had good human intestinal absorption (HIA) concentrations and were non-toxic. Due to high mutation rates in the active sites of the viral enzyme, these new allosteric site inhibitors offer opportunities to drug SARS-CoV-2 RdRp. These results provide new information for the design of novel allosteric inhibitors against SARS-CoV-2 RdRp
  • Dynamics of phytoplankton groups in three contrasting situations of the open NW Mediterranean Sea revealed by pigment, microscopy, and flow cytometry analyses

    Latasa, Mikel; Scharek, Renate; Moran, Xose Anxelu G.; Gutiérrez-Rodríguez, Andrés; Emelianov, Mikhail; Salat, Jordi; Vidal, Montserrat; Estrada, Marta (Progress in Oceanography, Elsevier BV, 2021-12-24) [Article]
    A detailed study of phytoplankton composition and dynamics was carried out during three contrasting situations (cruises F1, F2, and F3) in the northwestern (NW) Mediterranean Sea. Haptophytes, diatoms, and green algae dominated in F1, during the spring bloom, with high nutrients and high phytoplankton biomass. In F2, the post-bloom situation with a still weak stratification and lower nutrient concentrations, we found a high spatial variability. Stations were clearly dominated by either Synechococcus, haptophytes or cryptophytes; with Synechococcus reaching the highest abundance (4 × 105 cells mL−1, 60% of the integrated chlorophyll a) reported to date for the open Mediterranean Sea. Cryptophytes accumulated close to the surface in very shallow mixed layer stations. In late summer, F3 revealed a fully developed stratification with low nutrients and a marked deep chlorophyll maximum (DCM). Prochlorococcus was present only during this cruise, mainly in deep layers together with haptophytes and pelagophytes, while haptophytes and Synechococcus dominated the upper mixed layer. Flow cytometry (FCM) and pigment-based abundance estimates for Prochlorococcus, Synechococcus and cryptophytes were well correlated, as happened also between small picoeukaryotes (FCM) and green algae (pigments), and between large picoeukaryotes (FCM) and haptophytes (pigments). Dinoflagellate abundance by microscopy and by pigments did not agree well, probably due to the presence of heterotrophic forms or because they contained pigments other than peridinin, the standard dinoflagellate marker. The decrease in size of the FCM large picoeukaryotes group with depth was presumably related to the increasing contribution of pelagophytes, with smaller cells than haptophytes, the other main component of this fraction. Cell size increase of Prochlorococcus and Synechococcus with depth suggests vertical segregation of genotypes or photoadaptation. The groups' ecological preferences are presented with respect to depth and nutrient concentrations. Synechococcus and cryptophytes occupied shallow layers; diatoms, green algae and Prochlorococcus showed a tendency for deep layers and pelagophytes for even deeper layers, while haptophyte and dinoflagellate allocations were less clear. As for nutrients, the maximum relative contributions of green algae and especially diatoms occurred when dissolved inorganic phosphorus (DIP) concentrations were highest, of Prochlorococcus, dinoflagellates and pelagophytes when lowest, and of Synechococcus and cryptophytes when DIP concentrations were low but not minimal. The contribution of haptophytes did not show a relationship with DIP concentration. These results from individual groups stand as significant exceptions to the general relationship between phytoplankton cell size and nutrient availability.
  • The Combined Effects of Ocean Acidification and Heavy Metals on Marine Organisms: A Meta-Analysis

    Jin, Peng; Zhang, Jiale; Wan, Jiaofeng; Overmans, Sebastian; Gao, Guang; Ye, Mengcheng; Dai, Xiaoying; Zhao, Jingyuan; Xiao, Mengting; Xia, Jianrong (Frontiers in Marine Science, Frontiers Media SA, 2021-12-23) [Article]
    Ocean acidification (OA) may interact with anthropogenic pollutants, such as heavy metals (HM), to represent a threat to marine organisms and ecosystems. Here, we perform a quantitative meta-analysis to examine the combined effects of OA and heavy metals on marine organisms. The results reveal predominantly additive interactions (67%), with a considerable proportion of synergistic interactions (25%) and a few antagonistic interactions (8%). The overall adverse effects of heavy metals on marine organisms were alleviated by OA, leading to a neutral impact of heavy metals in combination with OA. However, different taxonomic groups showed large variabilities in their responses, with microalgae being the most sensitive when exposed to heavy metals and OA, and having the highest proportion of antagonistic interactions. Furthermore, the variations in interaction type frequencies are related to climate regions and heavy metal properties, with antagonistic interactions accounting for the highest proportion in temperate regions (28%) and when exposed to Zn (52%). Our study provides a comprehensive insight into the interactive effects of OA and HM on marine organisms, and highlights the importance of further investigating the responses of different marine taxonomic groups from various geographic locations to the combined stress of OA and HM.
  • Comprehensive insights into performance of water gap and air gap membrane distillation modules using hollow fiber membranes

    Im, Baek-Gyu; Francis, Lijo; Santosh, Ravichandran; Kim, Woo-Seung; Ghaffour, NorEddine; Kim, Young-Deuk (Desalination, Elsevier BV, 2021-12-22) [Article]
    A commercially available microporous polypropylene hollow fiber membranes were employed for air gap and water gap membrane distillation (i.e., AGMD and WGMD, respectively) processes. In both configurations, the outer surface of commercially available dense polypropylene hollow fibers was used as the condensing surface of the permeate. The performance levels of the AGMD and WGMD processes utilizing microporous polyvinylidene fluoride membranes fabricated in-house were compared with those using polypropylene membranes. Under the given specific operating conditions, the maximum mean permeation flux values in AGMD and WGMD using polypropylene hollow fiber membranes were approximately 24 and 27 kg/m2h, respectively. In addition, theoretical studies on AGMD and WGMD using the designed hollow fiber module configuration were performed. The predicted results were found to well agree with the experimental results, thus verifying their validity. Moreover, parametric studies were conducted to identify the optimum evaporation-to-condensation surface area ratio (i.e., optimum numbers of hollow fiber membranes and hollow fiber condensers) in terms of specific energy consumption.
  • Cement and oil refining industries as the predominant sources of trace metal pollution in the Red Sea: A systematic study of element concentrations in the Red Sea zooplankton.

    Cai, Chunzhi; Devassy, Reny Palliparambil; El-Sherbiny, Mohsen M; Agusti, Susana (Marine pollution bulletin, Elsevier BV, 2021-12-16) [Article]
    The Red Sea is exposed to metals from a large variety of natural and anthropogenic sources. In this study, we analyzed 19 common element concentrations in 14 Red Sea zooplankton samples using inductively coupled plasma-optical emission spectrometry (ICP-OES). The average metal or metalloid concentrations of the Red Sea zooplankton were: Ca > Sr > Fe > Al > Zn > As > Cu > Mn > Cr > Mo > Ni > Pb > Cd. The As, Ca, and Cu concentrations significantly increased with increasing latitude, while Cd concentrations decreased (p 
  • Exploring the Diversity and Regulation of Apocarotenoid Metabolic Pathways in Plants

    Zheng, Xiongjie; Yang, Yu; Al-Babili, Salim (Frontiers in Plant Science, Frontiers Media SA, 2021-12-10) [Article]
    In plants, carotenoids are subjected to enzyme-catalyzed oxidative cleavage reactions as well as to non-enzymatic degradation processes, which produce various carbonyl products called apocarotenoids. These conversions control carotenoid content in different tissues and give rise to apocarotenoid hormones and signaling molecules, which play important roles in plant growth and development, response to environmental stimuli, and in interactions with surrounding organisms. In addition, carotenoid cleavage gives rise to apocarotenoid pigments and volatiles that contribute to the color and flavor of many flowers and several fruits. Some apocarotenoid pigments, such as crocins and bixin, are widely utilized as colorants and additives in food and cosmetic industry and also have health-promoting properties. Considering the importance of this class of metabolites, investigation of apocarotenoid diversity and regulation has increasingly attracted the attention of plant biologists. Here, we provide an update on the plant apocarotenoid biosynthetic pathway, especially highlighting the diversity of the enzyme carotenoid cleavage dioxygenase 4 (CCD4) from different plant species with respect to substrate specificity and regioselectivity, which contribute to the formation of diverse apocarotenoid volatiles and pigments. In addition, we summarize the regulation of apocarotenoid metabolic pathway at transcriptional, post-translational, and epigenetic levels. Finally, we describe inter- and intraspecies variation in apocarotenoid production observed in many important horticulture crops and depict recent progress in elucidating the genetic basis of the natural variation in the composition and amount of apocarotenoids. We propose that the illustration of biochemical, genetic, and evolutionary background of apocarotenoid diversity would not only accelerate the discovery of unknown biosynthetic and regulatory genes of bioactive apocarotenoids but also enable the identification of genetic variation of causal genes for marker-assisted improvement of aroma and color of fruits and vegetables and CRISPR-based next-generation metabolic engineering of high-value apocarotenoids.
  • Recent Update on UV Disinfection to Fulfill the Disinfection Credit Value for Enteric Viruses in Water

    Augsburger, Nicolas; Rachmadi, Andri Taruna; Zaouri, Noor A.; Lee, Yunho; Hong, Pei-Ying (Environmental Science & Technology, American Chemical Society (ACS), 2021-12-09) [Article]
    Ultraviolet (UV) radiation alone or in combination with other oxidation processes is increasingly being considered for water disinfection because of stringent regulatory requirements for pathogen inactivation. To fulfill this requirement, an appropriate UV dose or fluence (mJ/cm2) is applied to combat enteric viruses in surface or treated water. There is a need for a cumulative review on the effectiveness of current and emerging UV technologies against various types of human enteric viruses. We extracted the kinetics data from 52 selected experimental studies on enteric virus inactivation using low pressure (LP-UV), medium pressure (MP-UV), UV-LED, and advanced oxidation processes (AOPs) and applied a simple linear regression analysis to calculate the range of UV fluence (mJ/cm2) needed for 4-log10 inactivation. The inactivation of adenoviruses with LP-UV, MP-UV, and UV/H2O2 (10 mg/L) required the highest fluence, which ranged from 159 to 337, 45, and 115 mJ/cm2, respectively. By contrast, when using LP-UV, the inactivation of other enteric viruses, such as the Caliciviridae and Picornaviridae family and rotavirus, required fluence that ranged from 19 to 69, 18 to 43, and 38 mJ/cm2, respectively. ssRNA viruses exhibit higher sensitivity to UV radiation than dsRNA and DNA viruses. In general, as an upgrade to LP-UV, MP-UV is a more promising strategy for eliminating enteric viruses compared to AOP involving LP-UV with added H2O2 or TiO2. The UV-LED technology showed potential because a lower UV fluence (at 260 and/or 280 nm wavelength) was required for 4-log10 inactivation compared to that of LP-UV for most strains examined in this critical review. However, more studies evaluating the inactivation of enteric viruses by means of UV-LEDs and UV-AOP are needed to ascertain these observations.
  • Molecular basis of parental contributions to the behavioural tolerance of elevated pCO$_2$ in a coral reef fish

    Monroe, Alison; Schunter, Celia Marei; Welch, Megan J.; Munday, Philip L.; Ravasi, Timothy (Proceedings of the Royal Society B: Biological Sciences, The Royal Society, 2021-12-08) [Article]
    Knowledge of adaptive potential is crucial to predicting the impacts of ocean acidification (OA) on marine organisms. In the spiny damselfish, $\textit{Acanthochromis polyacanthus}$, individual variation in behavioural tolerance to elevated pCO$_2$ has been observed and is associated with offspring gene expression patterns in the brain. However, the maternal and paternal contributions of this variation are unknown. To investigate parental influence of behavioural pCO$_2$ tolerance, we crossed pCO$_2$-tolerant fathers with pCO$_2$-sensitive mothers and vice versa, reared their offspring at control and elevated pCO$_2$ levels, and compared the juveniles' brain transcriptional programme. We identified a large influence of parental phenotype on expression patterns of offspring, irrespective of environmental conditions. Circadian rhythm genes, associated with a tolerant parental phenotype, were uniquely expressed in tolerant mother offspring, while tolerant fathers had a greater role in expression of genes associated with histone binding. Expression changes in genes associated with neural plasticity were identified in both offspring types: the maternal line had a greater effect on genes related to neuron growth while paternal influence impacted the expression of synaptic development genes. Our results confirm cellular mechanisms involved in responses to varying lengths of OA exposure, while highlighting the parental phenotype's influence on offspring molecular phenotype.
  • MAVRICS: A Robust and Safe Magnetic Nanoparticle based RNA Extraction Method Compatible with Phenol-chloroform Inactivated Infectious Samples

    Li, Mo; Ramos Mandujano, Gerardo (ZappyLab, Inc., 2021-12-08) [Protocol]
    Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method called Magneticnanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities.

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