Biomedical subjects

Zhijie Liu

Publications and source records attributed to Zhijie Liu.

12 recordsLinked to original sources

PubMed2006

Coordination between CCR7- and CCR9-mediated chemokine signals in prevascular fetal thymus colonization.

Thymus seeding by T-lymphoid progenitor cells is a prerequisite for T-cell development. However, molecules guiding thymus colonization and their roles before and after thymus vascularization are unclear. Here we show that mice doubly deficient for chemokine receptors CCR7 and CCR9 were defective specifically in fetal thymus colonization before, but not after, thymus vascularization. The defective prevascular fetal thymus colonization was followed by selective loss of the first wave of T-cell development generating epidermal Vgamma3(+) gammadelta T cells. Unexpectedly, CCL21, a CCR7 ligand, was expressed not by Foxn1-dependent thymic primordium but by Gcm2-dependent parathyroid primordium, whereas CCL25, a CCR9 ligand, was predominantly expressed by Foxn1-dependent thymic primordium, revealing the role of the adjacent parathyroid in guiding fetal thymus colonization. These results indicate coordination between Gcm2-dependent parathyroid and Foxn1-dependent thymic primordia in establishing CCL21/CCR7- and CCL25/CCR9-mediated chemokine guidance essential for prevascular fetal thymus colonization.

Animals↗

PubMed2006

A point-process model for rapid identification of post-translational modifications.

Post-translational modifications (PTMs) are very important to biological function, and yet are notoriously difficult to detect and identify, especially in a high-throughput manner. Most of the existing approaches rely on exhaustive searches which are highly time consuming and thus are currently limited to handling of a few types of PTMs. In this paper, we present a point-process model that aims to find the optimal mass shifts to maximize the spectra alignment between an experimental MS/MS spectrum and a candidate theoretical spectrum, through cross-correlation calculation, yields a rapid search for all types of PTMs in a blind mode, i.e., without giving the types of the searching PTMs in advance. The test results show that our new approach's performance is comparable to or better than the other blind search methods, but is more efficient computationally and simpler in its concept.

Algorithms↗

PubMed2005

Mapping of orthologous genes in the context of biological pathways: An application of integer programming.

Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene mapping, which often leads to suboptimal mapping results because sequence-similarity information alone does not contain sufficient information for accurate identification of orthology relationship. Here we present an algorithm for pathway mapping across microbial genomes. The algorithm takes into account both sequence similarity and genomic structure information such as operons and regulons. One basic premise of our approach is that a microbial pathway could generally be decomposed into a few operons or regulons. We formulated the pathway-mapping problem to map genes across genomes to maximize their sequence similarity under the constraint that the mapped genes be grouped into a few operons, preferably coregulated in the target genome. We have developed an integer-programming algorithm for solving this constrained optimization problem and implemented the algorithm as a computer software program, p-map. We have tested p-map on a number of known homologous pathways. We conclude that using genomic structure information as constraints could greatly improve the pathway-mapping accuracy over methods that use sequence-similarity information alone.

Algorithms↗

PubMed2005

Molecular phylogenetic studies on an unnamed bovine Babesia sp. based on small subunit ribosomal RNA gene sequences.

The 18S small subunit ribosomal RNA (18S rRNA) gene of an unnamed Babesia species (designated B. U sp.) was sequenced and analyzed in an attempt to distinguish it from other Babesia species in China. The target DNA segment was amplified by polymerase chain reaction (PCR). The PCR product was ligated to the pGEM-T Easy vector for sequencing. It was found that the length of the 18S rRNA gene of all B. U sp. Kashi 1 and B. U sp. Kashi 2 was 1699 bp and 1689 bp. Two phylogenetic trees were, respectively, inferred based on 18S rRNA sequence of the Chinese bovine Babesia isolates and all of Babesia species available in GenBank. The first tree showed that B. U sp. was situated in the branch between B. major Yili and B. bovis Shannxian, and the second tree revealed that B. U sp. was confined to the same group as B. caballi. The percent identity of B. U sp. with other Chinese Babesia species was between 74.2 and 91.8, while the percent identity between two B. U sp. isolates was 99.7. These results demonstrated that this B. U sp. is different from other Babesia species, but that two B. U sp. isolates obtained with nymphal and adultal Hyalomma anatolicum anatolicum tick belong to the same species.

Animals↗

PubMed2005

Amplification of 16S rRNA genes of Anaplasma species in China for phylogenetic analysis.

In this study, a phylogenetic tree was inferred through comparing five 16S rRNA gene sequences of four isolates of Anaplasma ovis and one of Anaplasma marginale in China with all nineteen 16S rRNA gene sequences deposited in GenBank (12 A. marginale, 3 A. ovis and 4 Anaplasma centrale derived from America, Uruguay, South Africa, Zimbabwe, Australia, Isreal and Japan). The analysis showed that all A. ovis isolated in China were separated into an A. ovis cluster, while the A. marginale in China was separated into an A. marginale cluster (see Fig. 1). This analysis demonstrated that there are at least two different Anaplasma species widespread among ruminants in North China.

Anaplasma↗

PubMed2005

Sero-epidemiological surveillance of hypodermosis in yaks and cattle in north China by ELISA.

A large-scale serological surveillance was conducted for hypodermosis in the north of China. A total of 4175 sera samples of yaks and cattle were collected from five provinces in north China that included Xinjiang, Inner Mongolia, Heilongjiang, Jiling and Gansu provinces, between 2001 and 2002, and were examined for anti-hypoderma antibody by ELISA. The results indicate that the naturally infested positive rates of Hypoderma spp. in the above provinces were 51.77%, 27.02%, 13.00%, 6.03% and 44.41%, respectively. These results suggest a significant warble fly population in the north of China. Positive sera were collected from infested cattle in Pingliang county of the Gansu province monthly between August 2001 and July 2002. These sera were used to evaluate the seasonal kinetics of anti-hypoderma antibody. The kinetics demonstrated that anti-hypoderma antibody was elevated from October to December. Thus, serological surveillances associated with low infestation rates and chemical therapy would best be performed from October to December in the region.

Animals↗

PubMed2005

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

Computational evaluation of protein-DNA interaction is important for the identification of DNA-binding sites and genome annotation. It could validate the predicted binding motifs by sequence-based approaches through the calculation of the binding affinity between a protein and DNA. Such an evaluation should take into account structural information to deal with the complicated effects from DNA structural deformation, distance-dependent multi-body interactions and solvation contributions. In this paper, we present a knowledge-based potential built on interactions between protein residues and DNA tri-nucleotides. The potential, which explicitly considers the distance-dependent two-body, three-body and four-body interactions between protein residues and DNA nucleotides, has been optimized in terms of a Z-score. We have applied this knowledge-based potential to evaluate the binding affinities of zinc-finger protein-DNA complexes. The predicted binding affinities are in good agreement with the experimental data (with a correlation coefficient of 0.950). On a larger test set containing 48 protein-DNA complexes with known experimental binding free energies, our potential has achieved a high correlation coefficient of 0.800, when compared with the experimental data. We have also used this potential to identify binding motifs in DNA sequences of transcription factors (TF). The TFs in 79.4% of the known TF-DNA complexes have accurately found their native binding sequences from a large pool of DNA sequences. When tested in a genome-scale search for TF-binding motifs of the cyclic AMP regulatory protein (CRP) of Escherichia coli, this potential ranks all known binding motifs of CRP in the top 15% of all candidate sequences.

Base Sequence↗

PubMed2004

A comparison of small-subunit ribosomal RNA gene sequences of bovine Babesia species transmitted by Haemaphysalis spp. in China.

The ribosomal small-subunit RNA gene sequences of six Chinese Babesia stocks infective to cattle, including a Babesia bigemina isolate, a B. bovis isolate, two B. ovata isolates, a Babesia sp. Wenchuan isolate and a B. major isolate, were compared and analyzed. The target DNA segment was amplified by polymerase chain reaction and the product ligated into the pGEM-T Easy vector for sequencing. The length of the 18S rRNA gene of all Babesia species involved in this study varied between 1,653 and 1,693 bp. The phylogenetic trees were inferred based on the 18S rRNA sequence of the Chinese isolates as well as other species of Babesia available in GenBank. The results showed that the B. ovata transmitted by Haemaphysalis longicornis and Babesia sp. Wenchuan isolate were confined to the same group as B. ovata Korea, with an identity among them of >96.5%, while B. major transmitted by H. punctata was situated in another branch, and identity with other bovine Babesia species was less than 92.5%. B. ovata should, therefore, be a valid species, differing from B. major according to the 18S rRNA gene sequence.

Animals↗

PubMed2004

Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.

A flexible protein-peptide docking method has been designed to consider not only ligand flexibility but also the flexibility of the protein. The method is based on a Monte Carlo annealing process. Simulations with a distance root-mean-square (dRMS) virtual energy function revealed that the flexibility of protein side chains was as important as ligand flexibility for successful protein-peptide docking. On the basis of mean field theory, a transferable potential was designed to evaluate distance-dependent protein-ligand interactions and atomic solvation energies. The potential parameters were developed using a self-consistent process based on only 10 known complex structures. The effectiveness of each intermediate potential was judged on the basis of a Z score, approximating the gap between the energy of the native complex and the average energy of a decoy set. The Z score was determined using experimentally determined native structures and decoys generated by docking with the intermediate potentials. Using 6600 generated decoys and the Z score optimization criterion proposed in this work, the developed potential yielded an acceptable correlation of R(2) = 0.77, with binding free energies determined for known MHC I complexes (Class I Major Histocompatibility protein HLA-A(*)0201) which were not present in the training set. Test docking on 25 complexes further revealed a significant correlation between energy and dRMS, important for identifying native-like conformations. The near-native structures always belonged to one of the conformational classes with lower predicted binding energy. The lowest energy docked conformations are generally associated with near-native conformations, less than 3.0 Angstrom dRMS (and in many cases less than 1.0 Angstrom) from the experimentally determined structures.

Algorithms↗

PubMed2003

Efficacy of different dosages of ivermectin injectable against the Hypoderma spp. in yaks.

A chemotherapy trial was conducted to determine the lowest dosage of injectable preparation of ivermectin against Hypoderma spp. infestation in yaks in Tibetan areas in Tianzhu county, Gansu province, in northwest of China. One hundred and sixty yaks were randomly divided into four groups of 40 yaks for the trial. The first three groups were treated by subcutaneous injection in the neck with 0.1% ivermectin (respectively, 1, 5, 10 microg/kg body weight). The fourth group was not treated and considered as control group. All the experiments were performed in November 2000 and the animals were examined for the presence of warbles in the next March and May. The results indicated that there was no warbles found on the back of treated animal while third stage larvae were palpated on back of some of the yaks in control group. It is concluded that dosage of 1 microg/kg ivermectin injectable was sufficient to kill or stop development of larvae of Hypoderma spp. in naturally infected yaks if administrated in November.

Animals↗

PubMed2003

Beyond the rotamer library: genetic algorithm combined with the disturbing mutation process for upbuilding protein side-chains.

The disturbing genetic algorithm, incorporating the disturbing mutation process into the genetic algorithm flow, has been developed to extend the searching space of side-chain conformations and to improve the quality of the rotamer library. Moreover, the growing generation amount idea, simulating the real situation of the natural evolution, is introduced to improve the searching speed. In the calculations using the pseudo energy scoring function of the root mean squared deviation, the disturbing genetic algorithm method has been shown to be highly efficient. With the real energy function based on AMBER force field, the program has been applied to rebuilding side-chain conformations of 25 high-quality crystallographic structures of single-protein and protein-protein complexes. The averaged root mean standard deviation of atom coordinates in side-chains and veracities of the torsion angles of chi(1) and chi(1) + chi(2) are 1.165 A, 88.2 and 72.9% for the buried residues, respectively, and 1.493 A, 79.2 and 64.7% for all residues, showing that the method has equal precision to the program SCWRL, whereas it performs better in the prediction of buried residues and protein-protein interfaces. This method has been successfully used in redesigning the interface of the Basnase-Barstar complex, indicating that it will have extensive application in protein design, protein sequence and structure relationship studies, and research on protein-protein interaction.

Algorithms↗

PubMed2002

Potential of mean force for protein-protein interaction studies.

Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximately 3 A, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations.

Databases, Protein↗