This paper firstly introduces the concept, method and current research of molecular phylogeography and then discusses its application in the study of geoherbs. The relativity between three genetic differentiation patterns of plant inferred by molecular phylogeography (i.e. allopatric fragmentation, restricted gene flow with isolation by distance and range expansion) and the formation of genuine character is analysed. Molecular authentication of geoherbs based on molecular phylogeography has the advantage of former molecular identification at technology and knowing genetic differentiation of geoherbs. Using molecular phylogeography for study on changing history of geoherbs habitat is also explicated. The problem of germplasm degeneration in cultural geoherbs could be effectively resolved by molecular phylogeography method. The application of molecular phylogeography in these subjects opens up prospects for study on geoherbs by using the principle and method of molecular phylogeography.
Ecosystem ; Gene Flow ; Geography ; Phylogeny ; Plants, Medicinal ; classification ; genetics

Isolation-with-migration (IM) models have become popular for explaining population divergence in the presence of migrations. Bayesian methods are commonly used to estimate IM models, but they are limited to small data analysis or simple model inference. Recently three methods, IMa3, MIST, and AIM, resolved these limitations. Here, we describe the major problems addressed by these three software and compare differences among their inference methods, despite their use of the same standard likelihood function.
Bayes Theorem ; Gene Flow ; Likelihood Functions ; Phylogeny ; Statistics as Topic

Hematopoietic stem cells (HSC) maintain homeostatic hematopoiesis via their multi-lineage differentiation and self-renewal potentials. HSC can be enriched and purified by flow cytometry relying on their cell surface markers and functional characteristics, however, these methods can not meet the need for deep analysis of HSC biological property and function because of the poor purity. Recent studies have successfully purified and tracked HSC using specifically expressed genes, which can enhance the purification efficiency of HSC, thus provide a better tool for the in-vivo study of HSC. This review summarizes the new techniques and discusses their advantages and disadvantages.
Cell Differentiation ; Flow Cytometry ; Gene Expression ; Hematopoiesis ; Hematopoietic Stem Cells

Granulocyte-specific antigens, such as NA1, NA2, NBI, NB2, NC1, NDI, NE1, are a group of antigens specifically expresesed only on the granulocytes. Antibodies against these are involved in some clinical disorders such as alloimmune neonatal neutropenia(ANN), autoimmune neutropenia(AIN), and transfusion-related acute lung injury(TRALI). We investigated the frequencies of NA1, NA2, NB1, and Mart antigens among Koreans by the granulocyte indirect immunofluorescence test employing flow cytometry. The subjects were 105 Koreans(male 65, female 40), whose mean age was 31.7+/-8.2 years (range 16~57). The antigen and gene frequencies were as follows, NA1, 0.78, 0.53, NA2, 0.75, 0.50, NB1 0.86, 0.62, and Mart, 1.00, 1.00, respectively. The proportions of NB 1 -positive granulocytes among NB 1-positive individuals were variable(range, 27~100%). Through this study, the authors procured granunlocyte-specifiic antigen papnel, which is essential in the identification of causative antibody(-ies) in immune neutropenias.
Antibodies ; Female ; Flow Cytometry ; Fluorescent Antibody Technique, Indirect ; Gene Frequency ; Granulocytes ; Humans ; Lung ; Neutropenia

The study aims at evaluating genetic diversity and medicinal quality of cultivated germplasm in Rehmannia glutinosa, and providing theoretical guidance for screening excellent germplasm. The genetic diversity of 21 species of R. glutinosa were analyzed by SRAP molecular markers, and the catalpol and verbascoside was determined by HPLC. The mass fraction of catalpol and verbascoside in R. glutinosa germplasm were respectively in the range of 2.393%-6.519% and 0.063%-0.478%, the germplasm 14, 16, 15 and 20 germplasm, witch catalpol and verbascoside content was higher. A total of 57 bands were produced by 10 primer, among which 40 polymorphic bands were polymorphic bands, and the percentage of polymorphic loci was 8.77%-54.39%, the Nei's genetic diversity index (H) was 0.374 1, Shannon's polymorphism information index (I) was 0.546 6. Gst and gene flow Nm were 0.608 8 and 0.321 3, respectively. Based on the genetic uniformity, 21 species of germplasm were grouped into 2 categories. The genetic diversity level of R. glutinosa was medium low. The comprehensive consideration of the genetic diversity and the content inculde catalpol and verbascoside, germplasm 7 and germplasm 18 could be used as the preferred materials for the cultivation of reticulum. Germplasm 15 and 16 can be used as the preservation and breeding object of rhubarb germplasm.
Animals ; Gene Flow ; Genetic Variation ; Phylogeny ; Plant Breeding ; Plants, Medicinal ; genetics ; Rehmannia ; genetics

The giant roundworm Ascaris infects pigs and people worldwide and causes serious diseases. The taxonomic relationship between Ascaris suum and Ascaris lumbricoides is still unclear. The purpose of the present study was to investigate the genetic diversity and population genetic structure of 258 Ascaris specimens from humans and pigs from 6 sympatric regions in Ascaris-endemic regions of China using existing simple sequence repeat data. The microsatellite markers showed a high level of allelic richness and genetic diversity in the samples. Each of the populations demonstrated excess homozygosity (Ho < He, Fis > 0). According to a genetic differentiation index (Fst=0.0593), there was a high-level of gene flow in the Ascaris populations. A hierarchical analysis on molecular variance revealed remarkably high levels of variation within the populations. Moreover, a population structure analysis indicated that Ascaris populations fell into 3 main genetic clusters, interpreted as A. suum, A. lumbricoides, and a hybrid of the species. We speculated that humans can be infected with A. lumbricoides, A. suum, and the hybrid, but pigs were mainly infected with A. suum. This study provided new information on the genetic diversity and population structure of Ascaris from human and pigs in China, which can be used for designing Ascaris control strategies. It can also be beneficial to understand the introgression of host affiliation.
Ascaris lumbricoides ; Ascaris suum ; Ascaris ; China ; Gene Flow ; Genetic Structures ; Genetic Variation ; Humans ; Microsatellite Repeats ; Swine

OBJECTIVETo elucidate the effect of FasL gene expression on the proliferation and apoptosis of hypoxic rectal carcinoma cells.

METHODSThe normoxic expression level of FasL in HR-8348 subtype cells (HR-8348(B), HR-8348(L), HR-8348(F) and HR-8348(As)) with different invasive power were verified by Western blot. Hypoxia models for HR-8348(B), HR-8348(L), HR-8348(F) and HR-8348(As) were constructed with chemical modeling, then the FasL levels in all groups at 12 h after hypoxia were quantitated by Western blot. Distribution of different cell life cycles was determined with flow cytometry. Cell reproductive activities were detected with MTT method, and cell apoptosis was assessed with TUNEL.

RESULTSFasL protein was pigmentized at the position of 40,000 by Western blot, and the expression level of FasL was significantly higher in HR-8348(F) cells than those in HR-8348(B), HR-8348(L) and HR-8348(As) cells(F=361.149, P<0.01) in normoxia. At 12 h after hypoxia, the FasL level was also significantly higher in HR-8348(F) cells than those in other groups(F=278.766, P<0.01), but was not markedly different as compared to themselves in normoxia(t=1.762, P>0.05). The proliferation index was significantly higher in HR-8348(F)(60.43+/-3.72) than those in HR-8348(B)(40.01+/-3.30), HR-8348(L)(41.30+/-4.06) and HR-8348(As) cells(35.87+/-4.39), respectively (F=39.477,P<0.01). However, both inhibition rate of proliferation and apoptotic index were remarkably lower in HR-8348(F)(17.30+/-1.98 and 13.10+/-1.04) than those in HR-8348(B)(33.70+/-4.33 and 21.60+/-1.31), HR-8348(L)(34.20+/-3.92 and 20.10+/-1.15), and HR-8348(As)(38.00+/-4.55 and 23.90+/-1.23), respectively(F=28.811 and 76.462, respectively, P<0.01).

CONCLUSIONThe expression enhancement of intracellular FasL in rectal carcinoma in hypoxia can lead to accelerated proliferation and reduced apoptosis of cells, which will promote tumor cells to adapt microenvironmental hypoxia.

Apoptosis ; Cell Hypoxia ; Cell Line, Tumor ; Cell Proliferation ; Fas Ligand Protein ; genetics ; Flow Cytometry ; Gene Expression Regulation, Neoplastic ; Humans

In this study, 31 Notopterygium incisum populations were analyzed using ITS sequences to investigate the genetic structure. The results showed that: the ITS region ranged in size from 634 to 635 bp and base composition was with high G + C content of 57.8%. Thirty-one polymorphic sites were detected from 402 sequences of 31 populations of N. incisum, and the proportion of polymorphic sites was 4.88%, in which parsimony informative sites were up to 12. And 31 haplotypes were identified based on these polymorphic sites. Molecular variance analysis (AMOVA) indicated that high genetic differentiation (57%) existed among population, and gene flow was low (N(m) = 0.38) among populations. Phylogenetic relationships of 31 haplotypes were analyzed using NJ method with N. forbesiias an out-group. Phylogenetic analysis showed that 31 haplotypes from different populations mixed together and did not form distinct geographically separated clades.
Apiaceae ; classification ; genetics ; Base Sequence ; China ; DNA, Intergenic ; genetics ; Gene Flow ; Genetic Variation ; Molecular Sequence Data ; Phylogeny

Inflammation can be a causative factor for carcinogenesis or can result from a consequence of cancer progression. Moreover, cancer therapeutic interventions can also induce an inflammatory response. Various inflammatory parameters are used to assess the inflammatory status during cancer treatment. It is important to select the most optimal biomarker among these parameters. Additionally, suitable biomarkers must be examined if there are no known parameters. We briefly reviewed the published literature for the use of inflammatory parameters in the treatment of patients with cancer. Most studies on inflammation evaluated the correlation between host characteristics, effect of interventions, and clinical outcomes. Additionally, the levels of C-reactive protein, albumin, lymphocytes, and platelets were the most commonly used laboratory parameters, either independently or in combination with other laboratory parameters and clinical characteristics. Furthermore, the immune parameters are classically examined using flow cytometry, immunohistochemical staining, and enzyme-linked immunosorbent assay techniques. However, gene expression profiling can aid in assessing the overall peri-interventional immune status. The checklists of guidelines, such as STAndards for Reporting of Diagnostic accuracy and REporting recommendations for tumor MARKer prognostic studies should be considered when designing studies to investigate the inflammatory parameters. Finally, the data should be interpreted after adjusting for clinically important variables, such as age and cancer stage.
Biomarkers ; C-Reactive Protein ; Carcinogenesis ; Checklist ; Enzyme-Linked Immunosorbent Assay ; Flow Cytometry ; Gene Expression Profiling ; Humans ; Immune System ; Inflammation ; Lymphocytes

OBJECTIVETo study the effects of HIV Tat protein on CCR5 expression of monocytes and HIV infection in monocytes.

METHODSMembrane expression of CCR5 on monocytes was analyzed by flow cytometry. Stimulated with HIV Tat protein, monocytes were infected with monocyte-tropic HIV(Ba-L) and HIV gag p24 level in the supernatant was measured by ELISA methods.

RESULTSHIV Tat protein increased CCR5 expression in human monocytes,which was inhibited by rabbit anti-Tat polyclonal antibody. Tat protein also increased p24 level after monocyte-tropic HIV-1(Ba-L) infected monocytes.

CONCLUSIONTat increases CCR5 expression and HIV-1 infection in monocytes, which indicates that HIV Tat might be a key protein in HIV-1 infection.

Flow Cytometry ; Gene Products, tat ; pharmacology ; HIV ; HIV Infections ; metabolism ; Humans ; Monocytes ; metabolism ; Receptors, CCR5 ; biosynthesis ; genetics ; tat Gene Products, Human Immunodeficiency Virus