Next generation sequencing shows diversity of Omicron sub-lineages of SARS-COV2 circulating in Jeddah, Saudi Arabia

The ever-evolving Omicron variant of the SARS-CoV-2 and its sub-lineages have prompted Saudi Arabia to continuously track circulating lineages. We focused on the presence of diverse SARS-CoV-2 circulation in Saudi Arabia and presented the whole genome sequencing study of 94 positive SARS-CoV-2 specimens procured between February and April 2022 in the city of Jeddah, Saudi Arabia. Following whole-genome sequencing, bioinformatics analysis was undertaken. The SARS-CoV-2 variant Omicron clades 21K and 21L constituted the entirety of sequenced specimens, belonging to BA.2 (n = 56) and BA.1.1 (n = 20), respectively, and low-frequency sub-lineages were BA.2.3 (n = 6), BA.1 (n = 4), BA.2.40.1 (n = 2), BA.1.14 (n = 1), BA.2.10 (n = 1), BA2.32 (n = 1), BA.2.57 (n = 1), BA2.64 (n = 1), and BA2.5 (n = 1). Mutational patterns were identified, as well as possible consequences for the spread of the virus. Comparative molecular docking of Omicron-specific Nucleocapsid protein harboring the mutations P13L, R203K, G204R, as well as S413R, and the deletions E31-, R32-, and S33- showed reduced interaction with human RIG-I protein with 8 interacting amino acid residues and 10 polar interactions, while the SARS-CoV-2 Nucleocapsid protein exhibited 15 interacting amino acid residues and 26 polar interactions. Ongoing monitoring is essential for assessing the genomic epidemiological consequences of tourist travel and pilgrimage in Jeddah and across Saudi Arabia, as well as the prompt identification of emerging variants for further investigation

Metabolomic Profiling of 13 Diatom Cultures and Their Adaptation to Nitrate-Limited Growth Conditions

<div><p>Diatoms are very efficient in their use of available nutrients. Changes in nutrient availability influence the metabolism and the composition of the cell constituents. Since diatoms are valuable candidates to search for oil producing algae, measurements of diatom-produced compounds can be very useful for biotechnology. In order to explore the diversity of lipophilic compounds produced by diatoms, we describe the results from an analysis of 13 diatom strains. With the help of a lipidomics platform, which combines an UPLC separation with a high resolution/high mass accuracy mass spectrometer, we were able to measure and annotate 142 lipid species. Out of these, 32 were present in all 13 cultures. The annotated lipid features belong to six classes of glycerolipids. The data obtained from the measurements were used to create lipidomic profiles. The metabolomic overview of analysed cultures is amended by the measurement of 96 polar compounds. To further increase the lipid diversity and gain insight into metabolomic adaptation to nitrogen limitation, diatoms were cultured in media with high and low concentrations of nitrate. The growth in nitrogen-deplete or nitrogen-replete conditions affects metabolite accumulation but has no major influence on the species-specific metabolomic profile. Thus, the genetic component is stronger in determining metabolic patterns than nitrogen levels. Therefore, lipid profiling is powerful enough to be used as a molecular fingerprint for diatom cultures. Furthermore, an increase of triacylglycerol (TAG) accumulation was observed in low nitrogen samples, although this trend was not consistent across all 13 diatom strains. Overall, our results expand the current understanding of metabolomics diversity in diatoms and confirm their potential value for producing lipids for either bioenergy or as feed stock.</p></div

Principal Component Analysis of the lipid profiles of 13 analysed cultures grown in nitrogen-replete conditions based on 142 annotated lipid analytes (32 analytes common for all samples).

<p>Each replicate is represented by a coloured abbreviation of the culture name: Ampant, <i>Amphitetras antediluviana</i>; Bidbid, <i>Biddulphia biddulphiana</i>; Cerdea, <i>Cerataulina daemon</i>; Chasim, <i>Chaetoceros simplex</i>; Eunlae, <i>Eunotogramma sp</i>.; Hemsin, <i>Hemiaulus sinensis</i>; Lepdan, <i>Leptocylindrus danicus</i>; Rhiset, <i>Rhizosolenia setigera</i>; Thafra, <i>Thalassionema frauenfeldii</i>; Tp1007, <i>Thalassiosira pseudonana</i> CCMP1007; Tp1335, <i>Thalassiosira pseudonana</i> CCMP 1335; Tw1587, <i>Thalassiosira weissflogii</i> CCMP 1587; Tweiss1336, <i>Thalassiosira weissflogii</i>.</p

Heatmap of 96 primary metabolite changes in nitrogen-depleted cultures of diatoms.

<p>A blue-white-red scale of colours represents none-to-high relative content of a polar analyte. Asterisks mark Anova p-values below 0.05 (‘*’ < 0.05; ‘**’ < 0.01; ‘***’ < 0.001). The data were clustered on basis of the Euclidean distance. Analytes not detected are marked gray. The histogram presents the density of data points. Following culture abbreviations were used: Ampant, <i>Amphitetras antediluviana</i>; Bidbid, <i>Biddulphia biddulphiana</i>; Cerdea, <i>Cerataulina daemon</i>; Chasim, <i>Chaetoceros simplex</i>; Eunlae, <i>Eunotogramma sp</i>.; Hemsin, <i>Hemiaulus sinensis</i>; Lepdan, <i>Leptocylindrus danicus</i>; Rhiset, <i>Rhizosolenia setigera</i>; Thafra, <i>Thalassionema frauenfeldii</i>; Tp1007, <i>Thalassiosira pseudonana</i> CCMP1007; Tp1335, <i>Thalassiosira pseudonana</i> CCMP 1335; Tw1587, <i>Thalassiosira weissflogii</i> CCMP 1587; Tweiss1336, <i>Thalassiosira weissflogii</i>. The “LN” suffix marks samples from low nitrogen growth conditions.</p

Heatmap of 142 lipid analytes from the nitrogen-replete cultures of diatoms.

<p>A blue-red scale of colours represents low-to-high relative content of any given analyte. The data were clustered on basis of the Euclidean distance. Analytes not detected are marked gray. Following abbreviations were used: Ampant, <i>Amphitetras antediluviana</i>; Bidbid, <i>Biddulphia biddulphiana</i>; Cerdea, <i>Cerataulina daemon</i>; Chasim, <i>Chaetoceros simplex</i>; Eunlae, <i>Eunotogramma sp</i>.; Hemsin, <i>Hemiaulus sinensis</i>; Lepdan, <i>Leptocylindrus danicus</i>; Rhiset, <i>Rhizosolenia setigera</i>; Thafra, <i>Thalassionema frauenfeldii</i>; Tp1007, <i>Thalassiosira pseudonana</i> CCMP1007; Tp1335, <i>Thalassiosira pseudonana</i> CCMP 1335; Tw1587, <i>Thalassiosira weissflogii</i> CCMP 1587; Tweiss1336, <i>Thalassiosira weissflogii</i>.</p

Heatmap of 142 annotated lipids measured in nitrogen-replete and nitrogen-depleted cultures of diatoms.

<p>A blue-red scale of colours represents low-to-high relative content of any given analyte. The data were clustered on basis of the Euclidean distance. Analytes not detected are marked gray. Following culture abbreviations were used: Ampant, <i>Amphitetras antediluviana</i>; Bidbid, <i>Biddulphia biddulphiana</i>; Cerdea, <i>Cerataulina daemon</i>; Chasim, <i>Chaetoceros simplex</i>; Eunlae, <i>Eunotogramma sp</i>.; Hemsin, <i>Hemiaulus sinensis</i>; Lepdan, <i>Leptocylindrus danicus</i>; Rhiset, <i>Rhizosolenia setigera</i>; Thafra, <i>Thalassionema frauenfeldii</i>; Tp1007, <i>Thalassiosira pseudonana</i> CCMP1007; Tp1335, <i>Thalassiosira pseudonana</i> CCMP 1335; Tw1587, <i>Thalassiosira weissflogii</i> CCMP 1587; Tweiss1336, <i>Thalassiosira weissflogii</i>. The “LN” suffix marks samples from low nitrogen growth conditions.</p

New Insights into Plagiogrammaceae (Bacillariophyta) Based on Multigene Phylogenies and Morphological Characteristics with the Description of a New Genus and Three New Species

<div><p>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: <i>Plagiogramma</i>, <i>Dimeregramma</i>, <i>Neofragilaria</i>, <i>Talaroneis</i>, <i>Psammogramma</i> and <i>Psammoneis</i>. In this paper, we describe a new plagiogrammoid genus, <i>Orizaformis</i>, 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 <i>rbc</i>L and <i>psb</i>C). Also included in the new phylogenies is <i>Glyphodesmis</i>. The phylogenies suggest that the Plagiogrammaceae is composed of two major clades: one consisting of <i>Talaroneis</i>, <i>Orizaformis</i> and <i>Psammoneis</i>, and the second of <i>Glyphodesmis</i>, <i>Psammogramma</i>, <i>Neofragilaria</i>, <i>Dimeregramma</i> and <i>Plagiogramma</i>. In addition, we describe three new species within established genera: <i>Psammoneis obaidii</i>, which was collected from the Red Sea, Saudi Arabia; and <i>Neofragilaria stilus</i> and <i>Talaroneis biacutifrons</i> from the Mozambique Channel, Indian Ocean, and illustrate two new combination taxa: <i>Neofragilaria anomala</i> and <i>Neofragilaria lineata</i>. 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.</p></div

Maximum likelihood phylogeny of 26 strains of Plagiogrammacean diatoms (with bootstrap values at nodes) was inferred from four markers (LSU, SSU rDNA, <i>rbc</i>L and <i>psb</i>C).

<p>Taxa (<i>Neofragilaria stilus</i>, <i>Orizaformis holarctica</i> and <i>Psammoneis obaidii</i>) in bold are newly described species. Support values lower than 50% were omitted. The outgroup <i>Asterionella formosa</i> was removed from the tree.</p

<i>Neofragilaria stilus</i>, TEM.

<p>Cultured material SZCZM116. (a) Entire valve in valve view. (b) Detail of the apex. (c) Enlarged view of Fig 9a. (d) A closed girdle band.</p

<i>Neofragilaria stilus</i>, LM (a-b) and SEM (f-g).

<p>Cultured material SZCZM116. (a) Zigzag colony linked by valve corners, frustule rectangular in girdle view, two plastids per cell. (b) Cleaned material in valve view, linear to lanceolate, robust striae. (c) Exterior view of natural sample, showing elaborate cribra and marginal spines. (d) Interior view of natural sample, a robust sternum, rimoportulae absent. (e) Exterior view in culture, showing corroded cribra and slit-like areolae in the apical pore field. (f) Interior view, rimoportulae absent. (g) Chain colony in girdle view and plain girdle bands.</p