GSA-Human: Genome Sequence Archive for Human.

The Genome Sequence Archive for Human (GSA-Human) is a data repository specialized for human genetic related data derived from biomedical researches, and also supports the data collection and management of National Key Research and Development Projects. GSA-Human has a data security management strategy according to the national regulations of human genetic resources. It provides two different models of data access: Open-access and Controlled-access.

An online coronavirus analysis platform from the National Genomics Data Center.

Since the first reported severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in December 2019, coronavirus disease 2019 (COVID-19) has become a global pandemic, spreading to more than 200 countries and regions worldwide. With continued research progress and virus detection, SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate. To meet the need for fast analysis of these genome sequences, the National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB) has established an online coronavirus analysis platform, which includes assembly, BLAST alignment, genome annotation, variant identification, and variant annotation modules.

[Database resources of the reference genome and genetic variation maps for the Chinese population].

With the implementation of the international human genome project and 1000 genome project, hundreds of Chinese individual genome sequences have been published. Establishing a high-precision Chinese population reference genome and identifying the unique genome variations are fundamental for future precision medicine research in China. To further meet the needs of scientific management and deep mining on the rapidly growing Chinese genomic data, Beijing Institute of Genomics, Chinese Academy of Sciences, has developed a Virtual Chinese Genome Database (VCGDB, http://bigd.

Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle.

An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancylactation-involution cycle (PL cycle) during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy (day 12 of pregnancy), lactation (day 14 of lactation), and involution (day 7 of involution). The pregnancy-, lactation- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs (ncRNAs), respectively.

A scenario on the stepwise evolution of the genetic code.

It is believed that in the RNA world the operational (ribozymes) and the informational (riboscripts) RNA molecules were created with only three (adenosine, uridine, and guanosine) and two (adenosine and uridine) nucleosides, respectively, so that the genetic code started uncomplicated. Ribozymes subsequently evolved to be able to cut and paste themselves and riboscripts were acceptive to rigorous editing (adenosine to inosine); the intensive diversification of RNA molecules shaped novel cellular machineries that are capable of polymerizing amino acids-a new type of cellular building materials for life. Initially, the genetic code, encoding seven amino acids, was created only to distinguish purine and pyrimidine; it was later expanded in a stepwise way to encode 12, 15, and 20 amino acids through the relief of guanine from its roles as operational signals and through the recruitment of cytosine.

Homology modeling and PAPS ligand (cofactor) binding study of bovine phenol sulfotransferase.

In order to understand the mechanisms of ligand binding and the interaction between the ligand and the bovine phenol sulfotransferase, (bSULT1A1, EC 2.8.2.

Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase.

Although the GSK3/SHAGGY-like kinase is a highly conserved serine/threonine kinase implicated in many signaling pathways in eukaryotes, the lack of knowledge of its three-dimensional (3D) structure has hindered efforts to understand the binding specificities of substrate and catalytic mechanism. To understand the structure-activity relationships, the protein 3D structure was built by using homology modeling based on the known X-ray diffraction structure of Glycogen synthase kinase-3beta (Gsk3beta) and the model structure was further refined using unrestrained molecular dynamics simulations. The research indicates that the general 3D organization of the GSK3/SHAGGY-like kinase is a typical kinase family and comprises an N-terminal domain of beta-sheet and a larger C-terminal domain mainly constituted by alpha-helix.

Homology modeling and molecular dynamics studies of a novel C3-like ADP-ribosyltransferase.

The novel C3-like ADP-ribosyltransferase is produced by a Staphylococcus aureus strain that especially ADP-ribosylates RhoE/Rnd3 subtype proteins, and its three-dimensional (3D) structure has not known. In order to understand the catalytic mechanism, the 3D structure of the protein is built by using homology modeling based on the known crystal structure of exoenzyme C3 from Clostridium botulinum (1G24). Then the model structure is further refined by energy minimization and molecular dynamics methods.

Theoretical study on the rate constants for the C2H5 + HBr --> C2H6 + Br reaction.

The reaction C(2)H(5) + HBr --> C(2)H(6) + Br has been theoretically studied over the temperature range from 200 to 1400 K. The electronic structure information is calculated at the BHLYP/6-311+G(d,p) and QCISD/6-31+G(d) levels. With the aid of intrinsic reaction coordinate theory, the minimum energy paths (MEPs) are obtained at the both levels, and the energies along the MEP are further refined by performing the single-point calculations at the PMP4(SDTQ)/6-311+G(3df,2p)//BHLYP and QCISD(T)/6-311++G(2df,2pd)//QCISD levels.

Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl.

The multiple channel reaction H + CH(3)CH(2)Cl --> products has been studied by the ab initio direct dynamics method. The potential energy surface information is calculated at the MP2/6-311G(d,p) level of theory. The energies along the minimum energy path are further improved by single-point energy calculations at the PMP4(SDTQ)/6-311+G(3df,2p) level of theory.

DFT and ab initio direct dynamics studies on the hydrogen abstraction reactions of chlorine atoms with CH(4-n)F(n) (n = 1-3).

A direct dynamics study is carried out for the hydrogen abstraction reactions Cl + CH(4-n)F(n) (n = 1-3) in the temperature range of 200-1,000 K. The minimum energy paths (MEPs) of these reactions are calculated at the BH&H-LYP/6-311G(d,p) level, and the energies along the MEPs are further refined at the QCISD(T)/6-311+G(2df,2p) and QCISD(T)/6-311+G(d,p) (single-point) level. The rate constants obtained by using the improved canonical variational transition state theory incorporating small-curvature tunneling correction (ICVT/SCT) are in good agreement with the available experimental results.

Direct ab initio dynamics study on the rate constants and kinetic isotope effect for the reactions of H atoms with GeDn(CH3)4-n (n = 1-4).

Direct ab initio dynamic calculations are performed on the reactions of atomic hydrogen with GeD(n)(CH(3))(4-n) (n = 1-4) over the temperature range 200-2000 K at the PMP4SDTQ/6-311 +G(3df,2p)//MP2/6-31 +G(d) (for n = 2-4) and G2//MP2/6-31 +G(d) (for n = 1) levels. The corresponding k(H)/k(D) ratios are then calculated in order to determine the kinetic isotope effect for the four reactions. For the simplest GeD(4) +H reaction, the only one that has available experimental data, the calculated canonical variational transition state theory incorporates small-curvature tunneling correction (CVT/SCT) thermal rate constants, and the k(H)/k(D) values are in good agreement with the experimental values within the experimental temperature range 293-550 K.