Biomedical subjects

Jiayin Dai

Publications and source records attributed to Jiayin Dai.

9 recordsLinked to original sources

PubMed2026

DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.

SUMMARY: We developed DirectASRM, a comprehensive database for the systematic identification, integration, and annotation of allele-specific RNA modifications (ASRMs) from direct RNA sequencing data. DirectASRM enables single-base, transcript-level detection of ASRMs across multiple RNA modification types, diverse organisms and condition-specific contexts. The database further evaluates the confidence of each ASRM-SNP pair association within isoform context by jointly considering statistical evidence of allelic modification imbalance and independent support from external next-generation sequencing (NGS) - based RNA modification resources. DirectASRM also provides extensive functional annotations for ASRMs and their associated variants, including intra-sample transcript-level allele-specific expression (ASE) and allele-specific splicing, as well as additional post-transcriptional regulatory features such as miRNA binding, circRNA, RNA-protein interactions, and disease relevance. Overall, DirectASRM serves as a comprehensive resource that supports systematic investigation of the potential functional impact of genetic variants in epitranscriptomic regulation. AVAILABILITY AND IMPLEMENTATION: DirectASRM database is freely accessible at http://modinfor.com/DirectASRM/. DirectASRM pipeline is available at GitHub (https://github.com/jiayin1101/DirectASRM_pipeline) and Zenodo (DOI: https://doi.org/10.5281/zenodo.19876077).

Alleles↗

PubMed2006

The microfauna communities and operational monitoring of an activated sludge plant in China.

The composition of the microfauna community in aeration tanks at the Baoding Sewage Treatment Plant in China was analysed each week from July 2002 to July 2003. The community composition of these microfauna populations was compared with effluent quality data recorded on the same days. A total of 94 species of ciliates, 40 species of amoebae and 13 species of large flagellates were identified in the 50 samples analysed. Numbers of metazoa including rotifers, nematodes, gastrotrichs and oligochaeta were also recorded. Although, Aspidisca cicada showed the highest mean abundance and was present in 98% of the samples, factor analysis revealed, among other things, that high Vorticella convallaria and Arcella hemisphaerica populations correlated with good performance of the treatment plant, while high numbers of Litonotus obtusus indicated poor conditions for settlement of sludge. These results show some agreement with an earlier study of sewage plants in Beijing, but analysis of more plants having a diversity of input components working under a range of different operating conditions should be performed to gain a general understanding of the value of indicator species for predicting the efficiency of activated sludge plants in China.

Animals↗

PubMed2006

Perfluorooctanesulfonate and periluorooctanoate in red panda and giant panda from China.

Perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) are important perfluorochemicals (PFCs) in various applications. Recently, it has been shown that these compounds are widespread in the environment, wildlife, and humans. The giant panda and the red panda belong to the order Carnivora, but are highly specialized as bamboo feeders. Both species are considered rare and endangered. In this study, we report for the first time on levels of PFOS and PFOA in serum of the giant panda and the red panda captured in zoos and animal parks from six provinces in China. PFOS was the predominant compound in all panda samples measured (ranging from 0.80 to 73.80 microg/L for red panda and from 0.76 to 19.00 microg/L for giant panda). The PFOA level ranged from 0.33 to 8.20 microg/L for red panda, and from 0.32 to 1.56 microg/L for giant panda. There was a positive significant correlation between concentrations of PFOS and PFOA in the serum obtained from pandas. No age- or sex- related differences were observed in concentrations of the fluorochemicals in panda sera. Greater concentrations of the fluorochemicals were found for those individuals collected from zoos near urbanized or industrialized areas than for other areas. These data combined with other reported data suggest that there are large differences in distribution of perfluorinated compounds in terrestrial animals.

Age Factors↗

PubMed2006

PCDD/F, PAH and heavy metals in the sewage sludge from six wastewater treatment plants in Beijing, China.

In order to better understand land application of sewage sludge, the characterization of heavy metals, PCDD/F and PAHs in sewage sludge was investigated from six different wastewater treatment plants (WWTP) in Beijing City, China. It was found that the total concentrations of Zn in Wujiacun (WJC) sewage sludge, and Cd and Hg in sewage sludge generated from all of the six different places are higher than Chinese regulation limit of pollutants for sludge to be used for agriculture (GB18918-2002). The levels of 16 PAHs that have been categorized as priority pollutants by US EPA in the sewage sludge samples varied from 2467 to 25923 microg/kg (dry weight), the highest values of 25923 microg/kg being found in WJC WWTP. The concentrations of Benzo[a]pyrene were as high as 6.1mg/kg dry weight in WJC sewage sludge, exceeding the maximum permitted content by GB18918-2002. Individual PAH content varies considerably with sewage samples. The ratios of anthracene to anthracene plus phenanthrene (An/178), benz[a]anthracene to benz[a]anthracene plus chrysene (BaA/228), indene[1,2,3-cd]pyrene to indene[1,2,3-cd]pyrene plus benzo[g,h,i]perylene (In/In+BP), and fluoranthene to fluoranthene plus pyrene (Fl/Fl+Py) suggest that petroleum and combustion of fossil fuel were the dominant contributions for the PAHs in sewage sludge. The concentrations of total PCDD/F in the sewage sludge ranged from 330 to 4245 pg/g d.w. The toxicity equivalent concentrations is between 3.47-88.24 pg I-TEQ according to NATO/CCMS, which is below Chinese legislation limit value proposed for land application. The PCDD/F congener/homologue profiles found in the Beijing samples indicated that the high chlorinated PCDD/F contamination might originate mainly from PCP-related source and depositional sources while the low chlorinated PCDD/F homologues could be originating from incineration or coal combustion. The major source of PCDD/Fs in Beijing sludge is still unclear.

China↗

PubMed2006

Isolation and characterization of a pseudomonas oleovorans degrading the chloroacetamide herbicide acetochlor.

To date, no pure bacterial cultures that could degrade acetochlor have been described. In this study, one strain of microorganism capable of degrading acetochlor, designated as LCa2, was isolated from acetochlor-contaminated soil. The strain LCa2 is Pseudomonas oleovorans according to the criteria of Bergey's manual of determinative bacteriology and sequence analysis of the partial 16S rRNA gene. Optimum growth temperature and pH were 35 degrees C and 8.0, respectively. The strain could degrade 98.03% of acetochlor treated at a concentration of 7.6 mg l(-1) after 7 days of incubation and could tolerate 200 mg l(-1) of acetochlor. When the acetochlor concentration became higher, the degradation cycle became longer. The acetochlor biodegradation products were identified by GC-MS based on mass spectral data and fragmentation patterns. The main plausible degradative pathways involved dechlorination, hydroxylation, N-dealkylation, C-dealkylation and dehydrogenation.

Herbicides↗

PubMed2006

Effects of an organophosphorous insecticide on survival, fecundity, and development of Hylyphantes graminicola (Sundevall) (Araneae: Linyphiidae).

Abstract-The effects of an organophosphorous insecticide, methamidophos, on fecundity and development of the spider Hylyphantes graminicola (Sundevall) (Araneae: Linyphiidae) were assessed under laboratory conditions. Susceptibility of adults of both sexes to the insecticide and its influence on fecundity of females and development of offspring were investigated. At 48 h after topical application in adults, the median lethal dose (LD50) and 10% lethal dose (LD10) were 0.35 and 0.12 microg/spider, respectively, for males and 0.52 and 0.16 microg/spider, respectively, for females. Methamidophos had detrimental effects on fecundity of females; number of eggs per clutch, total egg mass, and clutch size decreased significantly. The hatching rate of eggs from LD10-treated females was slightly higher than the rate in the controls, but the hatching rate of eggs from LD50-treated females was lower than the rate in the controls. However, no significant differences were observed in hatching time and development time across treatments. Development time of spiderlings from LD50-treated females was significantly longer than the time in the controls, and body sizes of the first spiderlings from insecticide-treated females were larger than those in the controls. However, matured offspring were smaller than those in the controls. It was concluded that methamidophos has long-term effects on H. graminicola, and that this may affect the development of spider populations in the field.

Animals↗

PubMed2004

Interplay between site-specific mutations and cyclic nucleotides in modulating DNA recognition by Escherichia coli cyclic AMP receptor protein.

Mutagenesis of various amino acids in Escherichia coli cyclic AMP receptor protein (CRP) has been shown to modulate protein compressibility and dynamics [Gekko et al. (2004) Biochemistry 43, 3844-3852]. Cooperativity of cAMP binding to CRP and the apparent DNA binding affinity are perturbed [Lin and Lee (2002) Biochemistry 41, 11857-11867]. The aim of this study is to explore the effects of mutation on the surface chemistry of CRP and to define the consequences of these changes in affecting specific DNA sequence recognition by CRP. Furthermore, the role of the interplay between mutation and specific identity of the bound cyclic nucleotide in this DNA recognition was explored. In the current study, effects of eight site-specific mutations (K52N, D53H, S62F, T127L, G141Q, L148R, H159L, and K52N/H159L) on DNA recognition of four sequences (Class I (site PI of lac), Class II (site PI of gal), and synthetic sequences that are hybrids of Classes I and II sites) modulated by three different cyclic nucleotides (cAMP, cCMP, and cGMP) were investigated. All mutations altered the surface chemistry of CRP as evidenced by the change in elution properties of these proteins from different matrixes. While T127L, S62F, K52N, and H159L exhibited unexpected behavior under combinations of specific experimental conditions, such as the identity of bound cyclic nucleotide and DNA sequence, in general, results showed that the affinities of CRP for DNA were sequence-dependent, increasing in the order of lacgal26 < gal26 < lac26 < gallac26 for all the mutants in the presence of 200 microM cAMP. The apparent association constants significantly increased in the order of no cyclic nucleotide approximately cGMP < cCMP < cAMP for all the examined DNA sequences. Linear correlation between the DeltaG for CRP-DNA complex formation and the cooperativity energy for cAMP binding was observed with gallac26, gal26, and lacgal26; however, the slope of this linear correlation is DNA sequence dependent. Structural information was presented to rationalize the interplay between CRP sequence and cyclic nucleotides in defining the recognition of DNA sequences.

Base Sequence↗

PubMed2004

Structure and protein design of a human platelet function inhibitor.

Hematophagous arthropods secrete a salivary apyrase that inhibits platelet activation by catabolizing ADP released from damaged tissues and blood cells. We report the X-ray crystal structures of a human enzyme of the soluble apyrase family in its apo state and bound to a substrate analog. The structures reveal a nucleotide binding domain comprising a five-blade beta propeller, binding determinants of the substrate and the active site, and an unusual calcium binding site with a potential regulatory function. Using a comparative structural biology approach, we were able to redesign the human apyrase so as to enhance its ADPase activity by more than 100-fold. The engineered enzyme is a potent inhibitor of platelet aggregation and may serve as the basis for the development of a new class of antithrombotic agents.

Amino Acid Sequence↗

PubMed2003

Zinc-mediated helix capping in a triple-helical protein.

Specific sequence signals at alpha-helix termini can assist protein folding by punctuating and cueing secondary structural elements in the final native conformation. Here we report the crystallization of a 56-residue alanine-containing peptide, denoted Ala-10(56), in the presence of Zn(2+). The 1.7 A crystal structure shows that Ala-10(56) forms a parallel trimeric coiled coil with three zinc ions anchoring distinct capping conformations at the amino-terminal ends of the three helices. In each polypeptide chain, the free alpha-amino nitrogen and carbonyl oxygen of the amino-terminal Ser residue coordinate to a Zn(2+) ion to form a five-membered chelate, and the syn-unidentate interaction of the Asp7 side chain with the Zn(2+) cation leads to the formation of a unique docking arrangement for helix capping. Moreover, the coordination of the zinc ion involves a neighboring trimer molecule in the crystal. Consequently, the crystal contacts are stabilized by carboxylate-Zn(2+) interactions between four Ala-10(56) trimers in the crystal lattice. The observed synergy between the protein-zinc ion recognition and the helix-packing arrangements would contribute to the conformational specificity of the Ala-10(56) trimer.

Amino Acid Sequence↗