Reformulation of an extant ATPase active site to mimic ancestral GTPase activity reveals a nucleotide base requirement for function

Hydrolysis of nucleoside triphosphates releases similar amounts of energy. However, ATP hydrolysis is typically used for energy-intensive reactions, whereas GTP hydrolysis typically functions as a switch. SpoIVA is a bacterial cytoskeletal protein that hydrolyzes ATP to polymerize irreversibly during Bacillus subtilis sporulation. SpoIVA evolved from a TRAFAC class of P-loop GTPases, but the evolutionary pressure that drove this change in nucleotide specificity is unclear. We therefore reengineered the nucleotide-binding pocket of SpoIVA to mimic its ancestral GTPase activity. SpoIVAGTPase functioned properly as a GTPase but failed to polymerize because it did not form an NDP-bound intermediate that we report is required for polymerization. Further, incubation of SpoIVAGTPase with limiting ATP did not promote efficient polymerization. This approach revealed that the nucleotide base, in addition to the energy released from hydrolysis, can be critical in specific biological functions. We also present data suggesting that increased levels of ATP relative to GTP at the end of sporulation was the evolutionary pressure that drove the change in nucleotide preference in SpoIVA.

Genomic Investigation of the Coronavirus Disease-2019 Outbreak in the Republic of Korea

The South Korean government effectively contained the coronavirus disease-2019 (COVID-19) outbreak primarily associated with the Shincheonji religious group. We conducted SARS-CoV-2 whole genome sequencing of 66 cases to investigate connections among the initial South Korean cases and the Shincheonji outbreak. We assessed the accuracy of genomic investigation by comparing the whole genome sequences with comprehensive contact tracing records. Five transmission clusters were estimated among the 15 initial cases. The six close-contact cases and two potential exposure pairs identified by contact tracing showed two or fewer nucleotide base differences. Additionally, we identified two transmission clusters from the Shincheonji outbreak that were phylogenetically distinct from the initial clusters, sharing common G11083T, G26144T, and C14805T markers. The strain closest to the two Shincheonji clusters was identified from a pair of identical sequences isolated from a couple who traveled from Wuhan to Milano. Our findings provide insights into the origins of community spread of COVID-19.

Activity-specificity trade-off gives PI5P4Kβ a nucleotide preference to function as a GTP-sensing kinase

SummaryMost kinases function with ATP. However, contrary to the prevailing dogma, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) utilizes GTP as a primary phosphate donor with a unique binding mode for GTP. Although PI5P4Kβ is evolved from a primordial ATP-utilizing enzyme, PI4P5K, how PI5P4Kβ evolutionarily acquired the GTP preference to function as a cellular GTP sensor remains unclear. In this study, we show that the short nucleotide base-recognition motif, TRNVF, is responsible for the GTP binding of PI5P4Kβ, and also confers onto PI5P4Kβ an unexpected specificity that extends to inosine triphosphate (ITP) and xanthosine triphosphate (XTP). A mutational study with GTP analogues suggests that the extended specificity is an obligatory consequence to the acquisition of GTP-dependent activity. However, as the cellular concentrations of ITP and XTP are typically negligible, PI5P4Kβ can still function as a GTP sensor, suggesting that the cellular physiological conditions leave room for the functional evolution of PI5P4Kβ.

The Polymorphic Gene of Single Nucleotide Polymorphism (SNP) of Phytoene Synthase (PSY) to Characterize Carotenoids Yellow Root Cassava

Cassava (Manihot esculenta Crantz.) is a carbohydrate sources containing a limited amount of micronutrients, but some genotypes contain β-carotene as the precursor of vitamin A in the storage roots and leaves. Improvement of β-caroteneand minerals such as Fe / Zn content of cassava’s nutrition is mostly through by biofortification program. The storage root of β-carotene recognized by a yellow or yellowish color while the apical shoots with red to purplish. β-carotenein carotenoid biosynthetic pathway is an expression of the phytoene synthase (PSY) gene. The MePSY2 gene, one of the three MePSY family is the key gene to characterize carotenoids related gene in cassava. In this study, sequencing of the two cassava fulllenght PSY genomic DNA was carried out in conserved areas in the PSY gene region (PSY1 and PSY2) from the DNA of the cassava leaves. Adira1, Carvita25 and Ubi Kuning are yellow root storage genotypes (K1, K2 and K3) while Adira4 and Menti are white root storage genotypes (P1 and P2). Carvita25 is induced somaclonal variant of the Adira4 genotype. Contiq and consensus of nucleotide base sequences from the five cassava genotypes and CM3306-4 cultivars (acc GU111715.1) as references were analysed using the lasergene DNASTAR sequence analysis program. The results of the alignment of the base sequence constituent of the MePSY2 gene showed that the PSY2 gene with amplified genome length was 2,380 base pairs (bp) consisting of 1,140 bp exon region and 1,240 bp intron region. In the conserved coding region, there was a difference of one nucleotide base, that is, base C in two white tuber cassava genotypes replaced with A in three yellow tuber cassava genotypes in the 1.485 base (C1.485A). The SNP converts the amino acid (aa) alanine (A) to aspartic acid (D) at the 191th (A191D). Single Nucleotide polymorphism in conserved coding region can be used further as carotenoid marker for plant breeding of yellow root cassava. Keywords: β carotene, PSY gene, polymorphic gene SNP, yellow root cassava.

A Scalable and Distributed Mechanism for DNA Databases by Aggregate Queries

The matter of sharing unique individual genomic grouping courses of action without giving the security of their data to help vast scale biomedical research ventures. Regardless, extends the results in different types. This approach is demonstrated powerful in keeping up the protection requirement against antagonistic server. We present a cryptographic security for questions that permits playing out most widely recognized DNA based personality. The limit is more affordable than figuring in current dispersed registering assessing plans. This point is spurred by the way that capacity is less expensive than calculation in current distributed computing evaluating plans. In addition, encoding the information makes it workable for us to deal with more extravagant arrangement of the inquiries the coordinating between the inquiry and grouping of the database, including: (1) A certain is the quantity that matches between question images and a succession; (2) Consistent OR matches where a question image is permitted to coordinate a subset of the letters in order along these lines making it conceivable to deal with (as an uncommon case) a "not equivalent to" necessity for an inquiry image ("not a G"); (3) Bolster for the expanded letter set of nucleotide base codes that envelops ambiguities in DNA groupings; (4) Inquiries that determine the quantity of events of every sort of image in the predetermined arrangement positions. (5) A begin question whose answer is "yes" if the quantity of matches surpasses a question indicated edge. (6) All inquiry composes we can conceal appropriate responses from the unscrambling server, with the goal that just the customer takes in the appropriate response. (7) The customer deterministically adapts just the question's answer, with the exception of inquiry compose (v) where we measure the (simple little) factual spillage to customer of real check.

Kajian Variasi Sekuens Interspesies dan Filogeni Kelelawar Pteropus sp. Menggunakan Gen COI

Penelitian ini bertujuan untuk menganalisis variasi interspesies kelelawar Pteropus sp. dan menjelaskan hubungan filogeni Pteropus sp. dengan spesies Pteropus lain yang terdata di GenBank berdasarkan Gen COI. Analisis sekuens menggunakan Geneious v5.6.4 dan menunjukkan adanya variasi interspesies sekuens gen COI pada ketiga sampel Pteropus sp. yang ditunjukkan oleh adanya perbedaan 5 pasang basa nukleotida pada urutan sekuens sampel nomor 157, 160, 421, 427 dan 652 dengan jarak genetik 0,006. Filogeni Ke-3 sampel kelelawar Pteropus sp. dengan spesies Pteropus lain dilakukan menggunakan MEGAX. Hasil filogeni menunjukkan bahwa sampel yang diteliti merupakan kelelawar dari genus Pteropus tetapi belum dapat dipastikan spesiesnya, karena ketika pohon filogeni dikonstruksikan membentuk satu klaster sendiri. Penjelasan dari proses tersebut adalah penyortiran garis keturunan yang tidak lengkap dan terjadinya hibridisasi, serta diduga bahwa primer yang digunakan kurang mampu dalam membedakan variasi intrespesies terhadap kelelawar genus PteropusThis study aimed to analyze the interspecificvariations of bats from Pteropus sp. and describethe phylogenetic relationship of Pteropus sp. with other Pteropus species recorded inGenBank based on the COI gene. Sequenceanalysis by Geneious v5.6.4 showed interspecificvariations of COI gene sequences in all threesamples of Pteropus sp. which was indicated byvariations in 5 nucleotide base pairs in thesequences number 157, 160, 421, 427 and 652with 0.006 of genetic distance value. Phylogeneticof the 3 bat samples of Pteropus sp. with otherPteropus species was carried out by MEGAX.Phylogenetic analyses showed that the samplesstudied are bats of the genus Pteropus, but theexact species cannot be determined because thesamples were grouped in the same cluster duringphylogenetic tree construction. The most probable explanation for this observation is hybridization between two different Pteropus spesies and also it is assumed that the primersused are not capable to distinguish interspecificvariations of the bats from the Pteropus genusPenelitian ini bertujuan untuk menganalisis variasi interspesies kelelawar Pteropus sp. dan menjelaskan hubungan filogeni Pteropus sp. dengan spesies Pteropus lain yang terdata di GenBank berdasarkan Gen COI. Analisis sekuens menggunakan Geneious v5.6.4 dan menunjukkan adanya variasi interspesies sekuens gen COI pada ketiga sampel Pteropus sp. yang ditunjukkan oleh adanya perbedaan 5 pasang basa nukleotida pada urutan sekuens sampel nomor 157, 160, 421, 427 dan 652 dengan jarak genetik 0,006. Filogeni Ke-3 sampel kelelawar Pteropus sp. dengan spesies Pteropus lain dilakukan menggunakan MEGAX. Hasil filogeni menunjukkan bahwa sampel yang diteliti merupakan kelelawar dari genus Pteropus tetapi belum dapat dipastikan spesiesnya, karena ketika pohon filogeni dikonstruksikan membentuk satu klaster sendiri. Penjelasan dari proses tersebut adalah penyortiran garis keturunan yang tidak lengkap dan terjadinya hibridisasi, serta diduga bahwa primer yang digunakan kurang mampu dalam membedakan variasi intrespesies terhadap kelelawar genus Pteropus

The relationship between human leukocyte antigen-cw6 allele and psoriasis vulgaris

Psoriasis vulgaris is chronic skin disease that is linked to genetics and immune system. The most important predisposing genetic factor is human leukocyte antigen (HLA). This study was performed to determine the relationship between HLA-Cw6 allele and psoriasis vulgaris and the changes of nucleotide base squences, using observation method with a cross sectional comparative study. Samples were selected using consecutive sampling of 30 patients with psoriasis vulgaris attending the Dermatology and STD polyclinic at DR. M. Djamil Hospital. 30 healthy volunteers were selected as controls. The subjects’ medical history was recorded followed by a dermatological examination, collection of samples, DNA isolation, then primers were designed for HLA-Cw6 allele, genes were sequencing and finally analyzed using PCR-SSP. The results were 20% of patients with psoriasis vulgaris carried HLA-Cw6 allele, while it was absent in the control group. This difference is statistically significant at the 5% level (p = 0.024). We found the changes of nucleotide base formations of HLA-Cw6. In conclusion, based on these observations, presence of the HLA-Cw6 allele is an important genetic risk factor for developing psoriasis vulgaris.

Variasi Genetik Plutella xylostella L. (Lepidoptera: Plutellidae) berdasarkan Gen Cytochrome C Oxidase I

Daerah Modoinding dan Tomohon di Sulawesi Utara, dikenal sebagai daerah penghasil sayuran kubis di Indonesia. Sayuran kubis memiliki hama utama yaitu Plutella xylostella. Penyebab serangga ini dapat bertahan hingga saat ini karena adanya sifat resistensi akibat pemberian insektisida yang berlebihan. Penelitian ini dilakukan untuk menganalisis variasi pada gen cytochrome C oxidase IPlutella xylostella yang diperoleh dari dua lokasi yang berbeda, yaitu Modoinding dan Tomohon. Analisis sekuens menunjukkan adanya perbedaan pasang basa nukleotida dari sampel yang berbeda lokasi. Selain itu, variasi juga ditunjukkan pada sampel yang diperoleh dari basis data GenBank dengan adanya perbedaan 1-14 pasang basa nukleotida dengan spesimen pada penelitian ini. Hubungan kekerabatan gen COI P. xylostella keseluruhan sampel tergolong dalam variasi intraspesies dengan nilai jarak genetik berkisar antara 0-0,022 (0-2,20%).Modoinding and Tomohon areas in North Sulawesi, are known as regions in Indonesia that produce a cabbage. The main pest of cabbage, Plutella xylostella. This insect can survive due to its resistance resulted from prolonged insecticide application. This study aims to analyze genetic variation of COI genes in P. xylostella from Modoinding and Tomohon areas. Sequence analysis showed there were differences in nucleotide base pairs between these locations. In addition, variations were also shown in samples obtained from the GenBank database with differences in 1-14 nucleotide base pairs with specimens in this study. The genetic relationship of P. xylostella COI gene in all samples was classified as intraspecific variation with genetic distance values ranging from 0-0,022 (0-2,20%).D aerah Modoinding dan Tomohon di Sulawesi Utara, dikenal sebagaidaerah penghasil sayuran kubis di Indonesia. Sayuran kubis memilikihama utama yaitu Plutella xylostella. Penyebab serangga ini dapatbertahan hingga saat ini karena adanya sifat resistensi akibat pemberianinsektisida yang berlebihan. Penelitian ini dilakukan untuk menganalisisvariasi pada gen cytochrome C oxidase I Plutella xylostella yang diperolehdari dua lokasi yang berbeda, yaitu Modoinding dan Tomohon. Analisissekuens menunjukkan adanya perbedaan pasang basa nukleotida darisampel yang berbeda lokasi. Selain itu, variasi juga ditunjukkan padasampel yang diperoleh dari basis data GenBank dengan adanyaperbedaan 1-14 pasang basa nukleotida dengan spesimen padapenelitian ini. Hubungan kekerabatan gen COI P. xylostella keseluruhansampel tergolong dalam variasi intraspesies dengan nilai jarak genetikberkisar antara 0-0,022 (0-2,20%).