scholarly journals Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade

2012 ◽  
Vol 44 (9) ◽  
pp. 1051-1055 ◽  
Author(s):  
Shin-Ichiro Tachibana ◽  
Steven A Sullivan ◽  
Satoru Kawai ◽  
Shota Nakamura ◽  
Hyunjae R Kim ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Genome Sequences ◽  
Plasmodium Cynomolgi ◽  
Insight Into

scholarly journals Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

PLoS Biology ◽  
2018 ◽  
Vol 16 (8) ◽  
pp. e2006035 ◽  
Author(s):  
Aude Gilabert ◽  
Thomas D. Otto ◽  
Gavin G. Rutledge ◽  
Blaise Franzon ◽  
Benjamin Ollomo ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Genome Sequences

scholarly journals Pyruvate Substitutions on Glycoconjugates

2019 ◽  
Vol 20 (19) ◽  
pp. 4929 ◽  
Author(s):  
Hager ◽  
Sützl ◽  
Stefanović ◽  
Blaukopf ◽  
Schäffer
Keyword(s):  
Cell Wall ◽  
Cell Surface ◽  
Early Stage ◽  
Ring Structure ◽  
Genome Sequences ◽  
Cell Wall Component ◽  
Cellular Physiology ◽  
Associated Functions ◽  
Acid Labile ◽  
Insight Into

Glycoconjugates are the most diverse biomolecules of life. Mostly located at the cell surface, they translate into cell-specific “barcodes” and offer a vast repertoire of functions, including support of cellular physiology, lifestyle, and pathogenicity. Functions can be fine-tuned by non-carbohydrate modifications on the constituting monosaccharides. Among these modifications is pyruvylation, which is present either in enol or ketal form. The most commonly best-understood example of pyruvylation is enol-pyruvylation of N-acetylglucosamine, which occurs at an early stage in the biosynthesis of the bacterial cell wall component peptidoglycan. Ketal-pyruvylation, in contrast, is present in diverse classes of glycoconjugates, from bacteria to algae to yeast—but not in humans. Mild purification strategies preventing the loss of the acid-labile ketal-pyruvyl group have led to a collection of elucidated pyruvylated glycan structures. However, knowledge of involved pyruvyltransferases creating a ring structure on various monosaccharides is scarce, mainly due to the lack of knowledge of fingerprint motifs of these enzymes and the unavailability of genome sequences of the organisms undergoing pyruvylation. This review compiles the current information on the widespread but under-investigated ketal-pyruvylation of monosaccharides, starting with different classes of pyruvylated glycoconjugates and associated functions, leading to pyruvyltransferases, their specificity and sequence space, and insight into pyruvate analytics.

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

scholarly journals Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5],12:i:− Strains Isolated from Wild Griffon Vultures in Eastern Spain

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Clara Marin ◽  
Giuseppe D’Auria ◽  
Llúcia Martínez-Priego ◽  
Francisco Marco-Jiménez
Keyword(s):  
Salmonella Enterica ◽  
Draft Genome ◽  
Wild Animals ◽  
Genome Sequences ◽  
Host Pathogen Interactions ◽  
Content Type ◽  
Zoonotic Pathogens ◽  
Host Pathogen ◽  
Serovar Typhimurium ◽  
Insight Into

Monophasic Salmonella enterica subsp. enterica serovar Typhimurium is one of the most common zoonotic pathogens. Salmonella species reside in a wide variety of hosts, including wild animals. Thus, we report here the genome sequences of 12 monophasic S. Typhimurium strains isolated from healthy wild vultures to gain better insight into their epidemiology and host-pathogen interactions.

scholarly journals STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Albert E. Zhou ◽  
Zalak V. Shah ◽  
Katie R. Bradwell ◽  
James B. Munro ◽  
Andrea A. Berry ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Severe Malaria ◽  
Command Line ◽  
Research Groups ◽  
Genome Sequences ◽  
Amino Acid Motif ◽  
Variant Surface Antigen ◽  
Parasite Biology ◽  
Insight Into

Abstract Background RIFINs and STEVORs are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion. These two highly diverse multigene families feature multiple paralogs, making their classification challenging using traditional bioinformatic methods. Results STRIDE (STevor and RIfin iDEntifier) is an HMM-based, command-line program that automates the identification and classification of RIFIN and STEVOR protein sequences in the malaria parasite Plasmodium falciparum. STRIDE is more sensitive in detecting RIFINs and STEVORs than available PFAM and TIGRFAM tools and reports RIFIN subtypes and the number of sequences with a FHEYDER amino acid motif, which has been associated with severe malaria pathogenesis. Conclusions STRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence.

scholarly journals Complete Genome Sequences of Cellvibrio japonicus Strains with Improved Growth When Using α-Diglucosides

2019 ◽  
Vol 8 (44) ◽  
Author(s):  
Cecelia A. Garcia ◽  
Jackson A. Narrett ◽  
Jeffrey G. Gardner
Keyword(s):  
Complete Genome ◽  
Growth Characteristics ◽  
Metabolic Flexibility ◽  
Genome Sequences ◽  
Additional Insight ◽  
Content Type ◽  
Carbohydrate Degradation ◽  
Cellvibrio Japonicus ◽  
Insight Into

Cellvibrio japonicus is a saprophytic bacterium that has been studied for its substantial carbohydrate degradation capability. We announce the genome sequences of three strains with improved growth characteristics when utilizing α-diglucosides. These data provide additional insight into the metabolic flexibility of a biotechnologically relevant bacterium.

scholarly journals Genome Sequences of Three Nocardia cyriacigeorgica Strains and One Nocardia asteroides Strain

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Florian Vautrin ◽  
Emmanuelle Bergeron ◽  
Audrey Dubost ◽  
Danis Abrouk ◽  
Christophe Martin ◽  
...  
Keyword(s):  
Type Strain ◽  
Draft Genome ◽  
Nocardia Asteroides ◽  
Environmental Isolates ◽  
Genome Sequences ◽  
Content Type ◽  
Nocardia Cyriacigeorgica ◽  
Insight Into

We report four draft genome sequences of Nocardia spp. The strains are the Nocardia cyriacigeorgica DSM 44484 pathogenic type strain; two environmental isolates, Nocardia cyriacigeorgica EML446 and EML1456; and the Nocardia asteroides ATCC 19247 nonpathogenic type strain, with estimated genome sizes of 6.3 to 6.8 Mb. The study of these isolates will provide insight into physiology, evolution, and pathogenicity of Nocardia spp.

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