Biomedical subjects

Jing Hou

Publications and source records attributed to Jing Hou.

16 recordsLinked to original sources

PubMed2026

Halolitoreus marinus gen. nov., sp. nov. and Halolitoreus rarus sp. nov., halophilic archaea isolated from diverse coastal tidal flats, and proposal of the novel family Halolitoreaceae fam. nov. in the order Halobacteriales within the class Halobacteria.

Coastal tidal flats represent dynamic saline environments that harbor largely unexplored haloarchaeal communities. In this study, amplicon sequencing, metagenomic analyses, and cultivation-based approaches revealed substantial haloarchaeal diversity in tidal flats from four provinces of eastern China despite their relatively low salinity. Five haloarchaeal strains, designated YSMS36T, DYSN1, QDMS2, CMSO5T, and ZSTT2, were isolated from diverse tidal flats. Theses strains shared 16S rRNA gene sequence similarities of 92.1-92.2% with their closest validly named relative, Salinilacihabitans rarus AD-4T. Phylogenetic analyses based on 16S rRNA and rpoB' gene sequences showed that the five strains formed a distinct and well-supported monophyletic lineage, separated from currently recognized members of the class Halobacteria. Average amino acid identity (AAI), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) values between these five strains and the related Halobacteria representatives were 49.3-62.7%, 66.9-74.9%, and 16.2-29.5%, respectively, and well below the accepted thresholds for species and genus delineation. Phylogenomic analyses further supported their placement within a novel family of the order Halobacteriales. Based on phylogenetic, genomic, chemotaxonomic, and phenotypic analyses, these five strains represent two novel species of a novel genus within a novel family. The names, Halolitoreaceae fam. nov., Halolitoreus marinus gen. nov., sp. nov., and Halolitoreus rarus sp. nov. are herein proposed.

Coastal tidal flat↗

PubMed2026

Stepwise allelic trajectory of ETP2 underlies trade-off between UVB tolerance and submergence adaptation in Arabidopsis thaliana.

Strong UVB radiation critically restricts plant growth, yield, and distribution, while mechanisms enabling adaptation to intense UVB remain unclear. Here, we uncover that the F-box ubiquitin E3 ligase UVBT1 (also known as ETP2) is indispensable for UVB tolerance in A. thaliana. In the high-altitude Tibet accession, a distinctive 166-bp deletion in ETP2 promoter leads to the complete absence of the W-box element, thereby eliminating WRKY36-mediated transcriptional repression. This results in elevated ETP2 levels, which degrade EIN2 and activate the protective anthocyanin/flavonoid pathway. Conversely, in low-altitude accessions, which are often exposed to lower UVB and higher precipitation conditions, WRKY36-mediated repression of ETP2 stabilizes EIN2 and WRKY22, endowing the plants with submergence tolerance. Notably, aside from the Tibet-accession-specific 166-bp deletion, the geographical distribution of the promoter allelic shift from C to G near the ETP2 W-box within the 166-bp region is tightly associated with UVB radiation with increasing altitudes for the other global accessions. This allelic change also enhances WRKY36-mediated repression of ETP2, suggesting an additional stepwise adaptation process. This work thus defines the WRKY36-ETP2-EIN2/WRKY22 module as a key regulator of UVB tolerance and submergence adaptation, potentially enabling A. thaliana to adapt to environments with varying UVB and precipitation conditions.

Arabidopsis↗

PubMed2026

Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov., halophilic archaea from coastal tidal flats, a saline lake, and a marine solar saltern.

Five novel halophilic archaeal strains, designated DTA46T, DTA98T, HHNYT27T, N11T, and SY-15T, were isolated from diverse saline environments across various regions of China. Amplicon and metagenome analyses revealed that three amplicon reads were affiliated with strains DTA46T, HHNYT27T, and N11T while two MAGs related to strains N11T and SY-15T. The sequence similarities among these five strains and current species of the genus Halorubrum were 93.1%-99.1% and 86.0%-95.9% judged by 16S rRNA and rpoB' genes, respectively. Phylogenomic and comparative genomic analyses revealed their close affiliation with Halorubrum. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between these strains and existing Halorubrum species ranged from 74.9%-93.6%, 22.3%-58.3%, and 68.3%-93.7%, respectively. All are below the recommended thresholds for species delineation, which supports their classification as novel taxa. The growth characteristics of strains DTA46T, DTA98T, HHNYT27T, N11T, and SY-15T were determined as follows: temperature range 20-60 °C (optima: 35, 37-42, 37, 35, and 42 °C), NaCl concentration 1.4-5.5 M (optima: 2.6, 3.1, 3.1, 3.1, and 5.1 M), and pH range 5.5-9.5 (optima: 8.0, 8.0, 7.0, 7.5, and 7.0). Based on the polyphasic characterization integrating phenotypic, chemotaxonomic, phylogenetic, and phylogenomic evidence, strains DTA46T, DTA98T, HHNYT27T, N11T, and SY-15T are proposed to represent five novel species of the genus Halorubrum, for which the names Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov. are designated, respectively.

Phylogeny↗

PubMed2024

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast.

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein coexpression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship.

Saccharomyces cerevisiae↗

PubMed2006

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria.

BACKGROUND: Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features. RESULTS: The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts. CONCLUSION: In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our findings are consistent with the notion that since the light energy absorption, transfer and conversion is highly efficient even in photosynthetic bacteria, the further improvements in photosynthetic efficiency in higher plants may rely on changes in metabolic network properties.

Arabidopsis↗

PubMed2006

Double-deformable-mirror adaptive optics system for phase compensation.

Two kinds of algorithm for an adaptive optics (AO) system that uses two deformable mirrors (DMs), one with large stroke and the other with high spatial frequency, to correct different aberrations are described. The algorithms are based on modal method and direction-gradient method, respectively. Numerical simulations for the algorithms have been made. The simulation results indicate that the two DMs in the AO system can correct different aberrations with different characteristics, and the closed-loop performance of a double-DM AO system will be almost the same as that of an AO system that uses a single DM with an ideal stroke.

Journal Article↗

PubMed2006

[Temporal and spatial distribution characteristics and indicator effects of Corbicula fluminea in coastal flat of Changjiang estuary].

Corbicula fluminea is a kind of macrobenthos commonly seen in the coastal wetland ecosystem of Changjiang estuary. This paper studied the temporal and spatial distribution characteristics of its population density and biomass, and analyzed the heavy metals concentrations in its body and in suspended particles and sediments. The results showed that the distribution of C. fluminea was discrepant in different seasons, sampling sites, and even, sampling sections of same sampling site. The population density and biomass of C. fluminea were higher in spring and autumn but lower in summer, and higher in mid-tidal flat than in low and high flats of Chongming. Its annual average population density and biomass was the maximal in Xupu. C. fluminea had definite accumulation ability to copper and zinc, but not to lead and chromium. There was a significant negative correlation between the lead concentrations in C. fluminea and sediments.

Animals↗

PubMed2005

Expression, purification and molecular modeling of recombinant fibrinogenase [IV], a metalloproteinase from Deinakistrodon acutus venom.

A novel metalloproteinase, recombinant fibrinogenase IV (rFIV(a)), was expressed and purified from Deinakistrodon acutus venom. It was a single chain protein with an apparent molecular weight 27 kDa and an isoeletric point of pH 7.1. RFIV(a) cleaved preferentially the Aalpha-chain and also cleaved Bbeta, gamma-chains of fibrinogen when the incubation time was prolonged. The proteolytic activity was inhibited by EDTA, l-cysteine, and DTT, indicating rFIV(a) was a metalloproteinase requiring disulfide bonds for its activity. It kept above 85% of the initial activity from pH 4.5-11, showed an equal maximum activity at the temperature range from 30 to 50 degrees C, and was inactivated by Zn2+, Cu2+ and Cd2+. Homology modeling of rFIV(a) showed that two highly conserved disulfide bonds (Cys159-Cys164 and Cys117-Cys197) was maintained from its structure, and it exhibited the characteristic conserved motif H142E143XXH146XXGXXH152, whose three histidine residues were involved in binding of the catalytically essential zinc ion. This work demonstrates the expression, purification and characterization of recombinant fibrinogenase IV, which belongs to class P-I metalloproteinase from D. acutus venom.

Amino Acid Sequence↗

PubMed2005

Crystal structure of a non-hemorrhagic fibrin(ogen)olytic metalloproteinase complexed with a novel natural tri-peptide inhibitor from venom of Agkistrodon acutus.

Thrombotic occlusive diseases pose a great threat to human health. Thrombolytic agents are in widespread use for the dissolution of arterial and venous pathologic thrombi in these kinds of diseases. Snake venom metalloproteinases (SVMPs) can act directly on fibrin/fibrinogen and are therefore potential candidates for therapeutic use against thrombotic occlusive diseases. In this study, we have determined the crystal structure of FII, a novel non-hemorrhagic SVMP isolated from Anhui Agkistrodon acutus snake venom by molecular replacement. The structure reveals that FII is a member of the P-I class SVMPs. The Zn2+ ion essential for hydrolytic activity is found in the active site and is tetrahedrally co-ordinated by three histidine residues and water molecule. Unambiguous electron density for a tri-peptide with sequence KNL is also found located near the active site. Biochemical evidences show that the tri-peptide KNL can inhibit the enzymatic activity of FII.

Amino Acid Sequence↗

PubMed2005

Crystallization and preliminary X-ray studies of a non-haemorrhagic fibrin(ogen)olytic metalloproteinase from the venom of Agkistrodon acutus.

A non-haemorrhagic fibrin(ogen)olytic metalloproteinase from the venom of Agkistrodon acutus has been crystallized by the hanging-drop method. The crystals belong to space group P3(1)21, with unit-cell parameters a = b = 80.57, c = 66.77 A and one molecule in the asymmetric unit. X-ray diffraction data were collected to 1.86 A resolution.

Agkistrodon↗

PubMed2004

Time-sharing wave-front-sensing adaptive optics.

Based on the concept of common-path/common-mode adaptive optics, the time-sharing wave-front-sensing adaptive optics system contains only one Hartmann-Shack (H-S) wave-front sensor, which detects two aberrations in the beam path alternately. After data fusion of the two aberrations, the actuator voltage of the deformable mirror (DM) is obtained. How the disturbances of the slope data and the response matrix influence the DM's actuator voltage in the data fusion methods is discussed, and the effective upper limits are given. Feasible data fusion methods are tested, and experiments verify that the performance of the system is good. The time-sharing technique is limited in sampling rate and is suitable only for corrections of slowly changing phases, because the H-S wave-front sensor's sampling frequency must be adequate for the alternate detection of two aberrations.

Journal Article↗

PubMed2003

Population survey of CCR5 delta32, CCR5 m303, CCR2b 64I, and SDF1 3'A allele frequencies in indigenous Chinese healthy individuals, and in HIV-1-infected and HIV-1-uninfected individuals in HIV-1 risk groups.

The aim of this study is to determine in indigenous Chinese ethnic groups the frequencies of the chemokine (SDF1 3'A) and chemokine receptors (CCR5 delta32, CCR5 m303, and CCR2b 64I) HIV-1/AIDS restriction alleles. The study includes two cohorts; the first comprised 3165 indigenous healthy subjects representing eight ethnic groups: Han (n = 1406), Uygur (n = 316), Mongolia (n = 134), Hui (n = 386), Tibetan (n = 330), Zhuang (n = 378), Dai (n = 101), and Jingbo (n =114). The second cohort consisted of 330 HIV-1-infected (86 subjects infected by sexual transmission and 198 subjects infected by HIV-1-contaminated blood or by sharing injection equipment; the remaining 46 subjects said nothing about HIV-1 transmission) and 474 HIV-1-uninfected Han Chinese belonging to one of two HIV-1 high-risk groups: intravenous drug users (n = 215) and individuals with sexually transmitted diseases (n = 259). Genotypes for the four genes were obtained using PCR (CCR5 delta32) or PCR-restriction fragment length polymorphism. Randomly selected amplified PCR products were further confirmed by direct DNA sequencing. The variant allele frequencies were determined to be 0% to 3.48% for CCR5 delta32, 0% for CCR5 m303, 16.23% to 28.79% for CCR2b 64I, and 17.70% to 27.76% for SDF1 3'A in Chinese healthy individuals from eight ethnic groups. These findings show that allele frequencies differ among the eight Chinese ethnic groups for CCR5 delta32, CCR2b 64I, and SDF1 3'A and that the CCR5 m303 and CCR5 delta32 mutant alleles were absent or infrequent in Chinese, which may be helpful for studies of specific anti-HIV-1 vaccine trials and coreceptor inhibitor drug targets in Chinese populations. Furthermore, we observed no significant differences in allele or genotypic frequencies between HIV-1-infected and HIV-1-uninfected groups from the Han ethnic group. Our finding is the first reporting that there is likely no effect of the examined polymorphisms in our study on HIV-1 transmission in the Chinese Han population, However, the genetic effects of these and other AIDS-modifying polymorphisms on the pathogenesis and clinical outcome of HIV-1/AIDS diseases is under investigation in Chinese populations.

Adult↗

PubMed2003

[Single nucleotide polymorphism loci of HIV-1 coreceptor CCR5 gene in Chinese Han people].

OBJECTIVE: To investigate the single nucleotide polymorphism(SNP) loci of HIV-1 coreceptor CCR5 gene in Chinese Han people. METHODS: The coding region of CCR5 was amplified using 2 pairs of primers and the PCR products of all 42 healthy subjects were sequenced by 4 different primers. The results of sequencing were analyzed by DNAstar in search of SNP loci. RESULTS: Six SNP loci were discovered in the coding region of CCR5, among them four SNPs, i.e. 184A-->G, 503G-->T, 688G-->A and 999G-->T, cause amino acids changes and two SNPs are nonsense mutations. One cytosine deletion at the 894nt results in frame shift mutation and prematured termination. 184A-->G, 503G-->T and 999G-->T were found in Chinese Han people for the first time. The allelic frequencies of mutant 184G, 503T and 999T alleles were 1.1%, 21.1% and 10.0% in healthy Hans, respectively. The population distribution of G503T markedly deviated from Hardy-Weinberg equilibrium. CONCLUSION: The SNP loci in the coding region of CCR5 in Chinese Han people has its own characteristics, which is not consistent with those of Japanese and obviously different from those of Caucasian and African.

Adult↗

PubMed2003

[Polymorphism of CXCR4 coding region of human immunodeficiency virus-1 in Chinese Han people].

OBJECTIVE: To study the polymorphism of human immunodeficiency virus (HIV)-1 coreceptor CXCR4 in Chinese Han ethnic group for AIDS prevention and treatment. METHODS: Totally 48 individuals were enrolled into the study. CXCR4 (cDNA No-AF147204) was cloned by PCR amplification using 2 pairs of primers, then sequenced using sequencing primers. The results of the same sequencing primers were analyzed by DNAstar software to find and identify single nucleotide polymorphism (SNP) sites. RESULTS: Totally 7 SNPs were found in the coding region of CXCR4, among them 3 were synonymous mutation (C-->T at loci 129, 426 and 968), 3 were missense mutation (C-->T at locus 38, A-->T at locus 90, and A-->C at locus 712) and 1 was stop mutation (C-->T at 106, which converted the codon for glutamic acid into stop codon). CONCLUSIONS: The polymorphism of CXCR4 coding region in Chinese Han is probably different from that of the other ethnic groups. Six of the 7 SNPs were discovered for the first time. Their influences on AIDS progression are worthy of studying.

Adult↗

PubMed2003

[Distribution of HIV-1 coreceptor CX3CR1 allelic polymorphisms in general population, HIV-1 high-risk group and HIV-1 carriers of Chinese indigenous Han and Uygur people].

OBJECTIVE: To investigate the V249I and T280M allelic polymorphisms of human immunodeficiency virus (HIV) coreceptor CX3CR1 in HIV-1 infected and uninfected population of Chinese indigenous Han and Uygur people and to probe the association between I249-M280 haplotype and HIV-1 susceptibility as well as AIDS progression. METHODS: Genomic DNA of 223 Uygur subjects and 316 Han subjects were purified from PBMC. I249 and M280 allelic frequencies were identified by polymerase chain reaction (PCR)/nest polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. All data were tested by chi(2) or u statistics analysis. RESULTS: Allelic frequencies of I249 and M280 were 16.1% and 13.3% in Uygur people, and 3.3% and 2.4% in Han people. No obvious difference existed between three groups of either ethnic group. However the allelic frequencies of HIV infected population were higher than those of general population, and those of general population higher than those of HIV-1 high-risk group. There was a strong linkage between I249 and M280 (P almost zero). CONCLUSIONS: I249 mutation was the sine qua non of M280 mutation, and most I249 alleles were accompanied by M280. The frequency of I249-M280 haplotype in Uygur population (13.3%) was adjacent to Caucasian people (15.8%), and that of I249-T280 haplotype (2.8%) was obviously lower than Caucasian people (12.5%); while both of them in Han people were much lower (0.9% and 2.4%). I249-M280 haplotype could accelerate AIDS progression according to Faure et al, while might be associated with HIV-1 susceptibility.

Alleles↗

PubMed2002

[Identification of new mutant sites and 894C deletion variant genotyping of HIV-1 coreceptor CCR5 in indigenous Chinese populations].

OBJECTIVE: To investigate the new single nucleotide polymorphism (SNP) sites of HIV-1 coreceptor CCR5 gene and conduct genotyping of CCR5-894C deletion allele in Chinese populations. METHODS: The full length fragment of CCR5 gene coding region was amplified by PCR amplification and sequenced in 45 healthy subjects from Han ethnic group. The sequencing data was analyzed by using DNAstar software for identification of new SNP sites. Furthermore, the genotyping of CCR5-894C deletion variant was performed by PCR-RFLP assay in 627 indigenous Chinese individuals including HIV-1 carriers, HIV-1 high risk population of STDs or IDUs as well as normal contrast. RESULTS: Totally six SNPs and one cytosine base deletion at the 894 nucleotide of CCR5 gene coding region were found in forty five Chinese Han subjects. Four SNPs, i.e. 184A-->G, 503G-->T, 668G-->A, 999G-->T, cause alteration of corresponding amino acids in CCR5 protein and two SNPs are nonsense mutations. The 894C deletion mutation results in a frame shift mutation of CCR5 gene. Among the six SNPs identified, the three sites 184A-->G, 503G-->T, 999G-->T were firstly reported only in Chinese people. The allelic frequencies of mutant 184G, 503T and 999T alleles were 1.1%, 21.1% and 10.0% in Han healthy subjects, respectively. PCR-RFLP assay showed the frequencies of CCR5-894C deletion alleles are 1.11%, 0.53% and 0% for Chinese Han, Tibetan and Mongolian healthy individuals, respectively. There was not significant different of the frequencies of CCR5-894C deletion allele among HIV-1 high risk populations, HIV-1 carries and healthy subjects. CONCLUSION: The subjects from Chinese Han group has its own distinctive SNP sites in the HIV-1 coreceptor CCR5 gene, three new SNPs (184A-->G, 503G-->T, 999G-->T) were firstly identified. Taking together, the significance and implication of these distinctive SNP sites and the 894C deletion mutation in the pathogenesis of HIV/AIDS disease need to be further studied.

Amino Acid Sequence↗