ANALYSIS OF T CELL CLONALITY BY CDR3 SIZE OF T-CELL ANTIGEN RECEPTOR Vβ REPERTOIRE IN HCL AND c-ALL

Objective: To analyze the distribution and clonality of TCR Vβ subfamily T cells in hairy cell leukemia (HCL) and common-acute lymphoblastic leukemia (c-ALL). Methods: Peripheral blood mononuclear cell samples from 3 cases of HCL and 1 case of c-ALL were investigated for analysis of complementarity determining region 3 (CDR3) size of T cell receptor Vβ repertoire using reverse transcriptase-polymerase chain reaction (RT-PCR). The products were further analyzed by genescan to identify T cell clonality. Results: Some Vβ subfamily PCR products from 4 patients contained monopeak (monoclone) or a dominant peak (oligoclone). In contrast, multipeak (polyclone) distributions were found in all Vβ subfamily PCR products from normal control cases. Conclusion: T cell clonal expansion may be found in HCL and c-ALL cases that may indicate a host response directed against leukemia related antigen. In addition, it may be useful to detect the minimal residual disease.

Clonality analysis of neuroendocrine cells in gastric adenocarcinoma

AIM:To achieve a better understanding of the origination of neuroendocrine(NE)cells in gastric adenocarcinoma.METHODS:In this study,120 cases of gastric adenocarcinoma were obtained.First,frozen section-immunohistochemistrical samples were selected from a large quantity of neuroendocrine cells.Second,laser capture microdissection was used to get target cells from gastric adenocarcinoma and whole genome amplification was applied to get a large quantity of DNA for further study.Third,genome-wide microsatellite abnormalities[microsatellite instability(MSI),loss of heterozygosity (LOH)]and p53 mutation were detected by polymerase chain reaction(PCR)-single-strand conformation polymer-phism-silver staining and PCR-sequencing in order to identify the clonality of NE cells.RESULTS:The total incidence rate of MSI was 27.4%,while LOH was 17.9%.Ten cases had a highest concordance for the two types of cells.The other samples had similar microsatellite changes,except for cases 7 and10.Concordant p53 mutations exhibited in sample 4,14,21 and 27,and there were different mutations between two kinds of cells in case 7.In case 17,mutation took place only in adenocarcinoma cells.p53 mutation was closely related with degree of differentiation,tumor-node-metastasis stage,vessel invasion and lymph node metastasis.In brief,NE and adenocarcinoma cells showed the same MSI,LOH or p53 mutation in most cases(27/30).In the other three cases,different MSI,LOH or p53 mutation occurred.CONCLUSION:NE and the gastric adenocarcinoma cells may mainly derive from the same stem cells,but the remaining cases showing different origin needs further investigation.

Reproductive height determines the loss of clonal grasses with nitrogen enrichment in a temperate grassland

Tall clonal grasses commonly display competitive advantages with nitrogen(N)enrichment.However,it is currently unknown whether the height is derived from the vegetative or reproductive module.Moreover,it is unclear whether the height of the vegetative or reproductive system regulates the probability of extinction and colonization,and determines species diversity.In this study,the impacts on clonal grasses were studied in a field experiment employing two frequencies(twice a year vs.monthly)crossing with nine N addition rates in a temperate grassland,China.We found that the N addition decreased species frequency and increased extinction probability,but did not change the species colonization probability.A low frequency of N addition decreased species frequency and colonization probability,but increased extinction probability.Moreover,we found that species reproductive height was the best index to predict the extinction probability of clonal grasses in N-enriched conditions.The low frequency of N addition may overestimate the negative effect from N deposition on clonal grass diversity,suggesting that a higher frequency of N addition is more suitable in assessing the ecological effects of N deposition.Overall,this study illustrates that reproductive height was associated with the clonal species extinction probability under N-enriched environment.

Clonal hematopoiesis:a shared risk factor for cardiovascular diseases and tumors

Clonal hematopoiesis(CH)is a clonally expanded population of hematopoietic stem cells carrying somatic mutations that differentiate through multilineage hematopoiesis to form terminally differentiated mature hematopoietic cells carrying markers of the clonal mutation.Genes integral to critical cellular processes such as epigenetic regulation,DNA damage response,and inflammation frequently carry these mutations.Clonal hematopoiesis becomes increasingly prevalent with age and is associated with an increased risk of hematological tumors and some nonhematological conditions.Recent insights have revealed that the mutations driving CH are not only implicated in hematologic neoplasms but also possess the potential to influence cardiovascular pathogenesis.Here,we reviewed up-to-date findings about the roles of CH in cardiovascular diseases and tumors and explored the clinical significance of CH,as well as look forward to future related studies,so as to provide valuable references for future research and clinical practice.

Clonality: A New Marker for Gastric Cancer Survival

Continuous efforts have been made to identify molecular markers for the prognosis of gastric cancer, the second leading cause of cancer death accounting for 10% of cancer mortality worldwide （Ferlay et al., 2010; Chen et al., 2013）. Studies using candidate gene approach, GWAS （genome-wide asso- ciation study）, and expression profiling have reported markers significantly associated with gastric cancer survival （Luo et al., 2011; Kang et al., 2014; Song et al., 2014）, and these markers have contributed to the clinical prediction of patients＇ outcome. However, gastric cancer is a highly heterogeneous disease etiologically, clinically, and pathologically. In this sense, it is plausible that single markers like DNA sequence variation, or gene/microRNA expression cannot fully reflect the heterogeneous survival of gastric cancer.

A Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis

Objective A core genome multilocus sequence typing(cgMLST)scheme to genotype and identify potential risk clonal groups(CGs)in Proteus mirabilis.Methods In this work,we propose a publicly available cgMLST scheme for P.mirabilis using chew BBACA.In total 72 complete P.mirabilis genomes,representing the diversity of this species,were used to set up a cgMLST scheme targeting 1,842 genes,635 unfinished(contig,chromosome,and scaffold)genomes were used for its validation.Results We identified a total of 205 CGs from 695 P.mirabilis strains with regional distribution characteristics.Of these,159 unique CGs were distributed in 16 countries.CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes.Nine virulence genes(papC,papD,papE,papF,papG,papH,papI,papJ,and papK)related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20.These CGs require attention due to potential risks.Conclusion This research innovatively performs high-resolution molecular typing of P.mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline(chewBBACA).We found that the CGs of P.mirabilis showed regional distribution differences.We expect that our research will contribute to the establishment of cgMLST for P.mirabilis.

Comparison of genetic impact on growth and wood traits between seedlings and clones from the same plus trees of Pinus koraiensis

To evaluate the relationships among clones and open pollinated families from the same plus trees and to select elite breeding materials,growth,and wood characteristics of 33-year-old Pinus korainsis clones and families were measured and analyzed.The results show that growth and wood characters varied significantly.The variation due to clonal effects was higher than that of family effects.The ratio of genetic to phenotypic coefficient of variation of clones in growth and wood traits was above 90%,and the repeatability of these characteristics was more than 0.8,whereas the ratio of genetic to phenotypic coefficient of variation of families was above 90%.The broad-sense heritability of all characteristics exceeded 0.4,and the narrow-sense family heritability of growth traits was less than 0.3.Growth characteristics were positively correlated with each other,but most wood properties were weakly correlated in both clones and families.Fiber length and width were positively correlated between clones and families.Using the membership function method,eleven clones and four families were selected as superior material for improved diameter growth and wood production,and two families from clonal and open-pollinated trees showed consistently better performance.Generally,selection of the best clones is an effective alternative to deployment of families as the repeatability estimates from clonal trees were higher than narrow-sense heritability estimates from open pollinated families.The results provide valuable insight for improving P.koraiensis breeding programs and subsequent genetic improvement.

Clonal Transgenerational Effects Transmit for Multiple Generations in a Floating Plant

Environmental conditions of a parent plant can influence the performance of their clonal offspring,and such clonal transgenerational effects may help offspring adapt to different environments.However,it is still unclear how many vegetative generations clonal transgenerational effects can transmit for and whether it depends on the environmental conditions of the offspring.We grew the ancestor ramets of the floating clonal plant Spirodela polyrhiza under a high and a low nutrient level and obtained the so-called 1^(st)-generation offspring ramets of two types(from these two environments).Then we grew the 1^(st)-generation offspring ramets of each type under the high and the low nutrient level and obtained the so-called 2^(nd)-generation offspring ramets of four types.We repeated this procedure for another five times and analyzed clonal transgenerational effects on growth,morphology and biomass allocation of the 1^(st)-to the 6^(th)-generation offspring ramets.We found positive,negative or neutral(no)transgenerational effects of the ancestor nutrient condition on the offspring of S.polyrhiza,depending on the number of vegetative generations,the nutrient condition of the offspring environment and the traits considered.We observed significant clonal transgenerational effects on the 6^(th)-generation offspring;such effects occurred for all three types of traits(growth,morphology and allocation),but varied depending on the nutrient condition of the offspring environment and the traits considered.Our results suggest that clonal transgenerational effects can transmit for multiple vegetative generations and such impacts can vary depending on the environmental conditions of offspring.

Soil Moisture Rather than Soil Nutrient Regulates the Belowground Bud Bank of Rhizomatous Species Psammochloa villosa in Arid Sand Dunes

In arid and semi-arid sand dune ecosystems,belowground bud bank plays an important role in population regeneration and vegetation restoration.However,the responses of belowground bud bank size and composition to sand burial and its induced changes in soil environmental factors have been rarely studied.In arid sand dunes of Northwestern China,we investigated belowground bud bank size and composition of the typical rhizomatous psammophyte Psammochloa villosa as well as three key soil environmental factors(soil moisture,total carbon and total nitrogen)under different depths of sand burial.Total buds and rhizome buds increased significantly with increasing burial depth,whereas tiller buds first increased and then decreased,with a peak value at the depth of 20-30 cm.Soil moisture increased significantly with sand burial depth,and was positively correlated with the number of all buds and rhizome buds.Soil total carbon concentration first increased and then decreased with sand burial depth,and total nitrogen concentration was significantly lower under deep sand burial than those at shallow depths,and only the number of tiller buds was positively correlated with soil total nitrogen concentration.These results indicate that soil moisture rather than soil nutrient might regulate the belowground bud bank of P.villosa,and that clonal psammophytes could regulate their belowground bud bank in response to sand burial and the most important environmental stress(i.e.,soil moisture).These responses,as the key adaptive strategy,may ensure clonal plant population regeneration and vegetation restoration in arid sand dunes.

Acute myocardial infarction in myeloproliferative neoplasms

Myeloproliferative neoplasms(MPNs)are a heterogeneous group of hematologic malignancies characterized by an abnormal proliferation of cells of the myeloid lineage.Affected individuals are at increased risk for cardiovascular and thrombotic events.Myocardial infarction(MI)may be one of the earliest clinical manifestations of MPNs or may be a thrombotic complication that develops during the natural course of the disease.In the present review,we examine the epidemiology,pathogenesis,clinical presentation,and management of MI in MPNs based on the available literature.Moreover,we review potential biomarkers that could mediate the MI-MPNs crosstalk,from classical biochemical tests,e.g.,lactate dehydrogenase,creatine kinase and troponins,to pro-inflammatory cytokines,oxidative stress markers,and clonal hematopoiesis.

Clones or no clones：genetic structure of riparian Populus euphratica forests in Central Asia

Many riparian（Tugai） forests growing along rivers in arid and hyper-arid regions of Central Asia are dominated by the Euphrates poplar（Populus euphratica）. Besides generative reproduction, which is only possible upon flooding events and at a distance to the groundwater of less than 2 m, this phreatophytic tree species also reproduces vegetatively by forming clones that can cover land surface areas of several hectares. Along a gradient of groundwater distances, we investigated whether the fraction of clones in P. euphratica stands（1） increases with increasing distance to the water table;（2） is higher if supplied with water via river cut-offs; and（3） approaches 100% at a short distance to the groundwater, but at high salt concentrations in the upper soil layers, which would prevent germination and establishment of seedlings. AFLP（Amplified Fragment Length Polymorphism） analyses were conducted on leaf samples taken from mature P. euphratica trees growing at the fringes of the Taklimakan Desert in stands with different distances（2–12 m） to the groundwater at two plots at the middle and the lower reaches of the Tarim River and in a stand close to Ebinur Lake, Xinjiang, China. Genetic diversity was large among plots, but considerably smaller within plots. We found the highest genetic diversity（caused by regeneration from seeds） at plots that have a short distance to the groundwater or are supplied with additional water. There was no significant relationship between groundwater distance and clonal fraction. All investigated trees at the saline Ebinur Lake site belonged to one single clone. Our results demonstrate that the genetic pattern of this widespread species is not easily predictable even over small distances as it is a result of a complex interplay of stand history and dispersal of propagules（pollen, seeds, and vegetative diaspores） by wind and water. In conservation and restoration schemes, P. euphratica stands with a high genetic diversity and stands that grow at short distances to the water table and are regularly subjected to flooding（which favors generative over clonal reproduction） should be prioritized.

Genetic Diversity of the Pepper Pathogen <i>Phytophthora capsici</i>on Farms in the Amazonian High Jungle of Peru

Phytophthora capsici is an important oomycete pathogen of Capsicum peppers worldwide. Populations of P. capsici recovered from coastal regions in Peru were previously shown to be dominated by a single clonal lineage referred to as PcPE-1. During 2008, 219 isolates of P. capsici were collected from Capsicum pubescens (Rocoto), C. annum (Pimento), and C. baccatum (Aji) at 9 farms in the Amazonian high jungle in the areas surrounding Oxapampa, and one coastal location, Carabayllo. Two isolates of P. capsici were also recovered from Cyclanthera pedata (Caigua fruit) near one field. All isolates were characterized using a panel of eight single nucleotide polymorphism (SNP) markers that are fixed for heterozygosity in the PcPE-1 lineage. A subset of isolates was also characterized using amplified fragment length polymorphism (AFLP) markers. Nine discreet SNP multi-locus genotypes were identified, and the PcPE-1 lineage was recovered from all of the field sites. Both A1 and A2 mating types were recovered from two sites. The implications of the genotypic diversity and distribution identified in this study are discussed.

Modular growth and clonal propagation of Hippophae rhamnoides subsp, sinensis in response to irrigation intensity

A multipurpose clone plant species, Hippophae rhamniodes has the capacity for indefinite longevity, although under successive drought stress it may often decline or die across large areas. Field trials were con- ducted over 2 years to examine the effects of varied irrigation intensities on modular growth and clonal propagation in a semi-arid area. Irrigation levels included a control, as well as two, four and six times the volume of water that was typically received via local annual average precipitation. Irrigation intensity significantly influenced clonal propagation capacity （number of daughter ramets）, aboveground modular growth （height, base diameter, and crown width）, belowground modular growth included root nodule dry weight, stretching capacity of lateral roots （length of the longest lateral roots, and diameter of first-grade lateral roots）, and branching intensity of lateral roots （number of lateral roots bifurcation grade, number of first- grade lateral roots）. The modular growth and the density of daughter ramets were small under non-irrigation or low irrigation, and became larger with increased irrigation intensity. Beyond a certain threshold, however, further increases in irrigation intensity resulted in a reversion to the development. The optimal irrigation intensities for growth and propagation were 3.48-5.29 times the volume of nominal local annual average precipitation. There were effects of irrigation intensities on the positive significant correlations between aboveground and belowground modular growths, and on clonal propagation capacities. Under various water treatments, H. rhamnoides may adapt to the environment through the regulation of growth and propagation. We concluded that water shortages act to weaken the growth and propagation of H. rhamniodes plantations.

Variation among poplar clones for growth and crown traits under field conditions at two sites of North-western India

We evaluated the growth and crown traits of 36 poplar clones at two distinct agro-climatic regions of Punjab （Ludhiana and Bathinda） in northwestern India, following randomized block design with three replications and plot size of four trees. Significant differences among clones （p〈0.001） were observed for diameter at breast height （DBH）, tree height, volume, crown width and number of branches under both the site conditions. Clones ‘G-3’, ‘25-N’ and ‘41-N’ at Ludhiana and ‘G-3’, ‘RD-01’ and ‘S7C8’ at Bathinda were found to be superior for volume production. All growth and crown traits registered significantly higher values at Ludhiana in comparison to those at Bathinda. Clone site interaction was also significant （p〈0.001）. For volume, clones ‘L-62/84’, ‘113520’, ‘25-N’ and ‘S4C2’ witnessed huge fluctuations in ranking between sites. The correlations between growth traits were positive and highly significant （p〈0.001） at both sites. The clonal mean heritability was moderate for DBH and volume both at Ludhiana （0.61–0.66） and Bathinda （0.61–0.62）. Across sites, the genetic advance was the highest for volume （49.76%） and the lowest （6.50%） in case of height.

Combined hepatocellular and cholangiocarcinoma originating from the same clone:a pathomolecular evidence-based study

Background:Combined hepatocellular and cholangiocarcinoma(CHC) is a unique subtype of liver cancer comprising both hepatocellular carcinoma(HCC) and intrahepatic cholangiocarcinoma(ICC);however,its cellular origin remains unclear.The purpose of this study was to investigate the clinicopathologic features and the clonal relationship between HCC and ICC in 34 patients with CHC.Methods:The clinicopathologic features and prognosis of the 34 CHC patients were compared with those of 29 patients with separated HCC and ICC(5HC).Loss of heterozygosity(LOH) at 10 highly polymorphic microsatellite markers was detected in 16 CHC and 10 SHC tissues for determination of the clonal origin of CHC.Expression of hepatocyte markers[hepatocyte paraffin 1(Hep Par 1) and glypican 3(GPC3)]and cholangiocyte markers[cytokeratin(CK)7 and 19]in tumor tissues was examined by immuno histochemical analysis.Results:In the 16 CHC specimens,the difference in LOH patterns between HCC and ICC was less than 30%,suggesting the same clonal origin of HCC and ICC.Consistent with this finding,immunohistochemical analysis revealed that hepatocyte markers(Hep Par 1 and GPC3) and cholangiocyte markers(CK7 and CK19) were simultaneously expressed in both the HCC and ICC components in 52.9%of CHC specimens,suggesting that the two components shared a similar phenotype with hepatic progenitor cells(HPCs).On the contrary,in all 10 SHC cases,the difference in LOH patterns between the HCC and ICC components was greater than 30%,suggesting different clonal origins of HCC and ICC.Overall survival and disease-free survival were shorter for patients with CHC than for patients with SHC(P < 0.05).Conclusions:Our results suggest that the HCC and ICC components of CHC may originate from the same clone,having the potential for dual-directional differentiation similar to HPCs.CHC tended to exhibit the biological behaviors of both HCC and ICC,which may enhance the infiltrative capacity of tumor cells,leading to poor clinical outcomes for patients with CHC.

Cytokines in the BALB/c mouse testis in various conditions

Aim: To investigate whether testosterone, estrogens, vasectomy, experimental cryptorchidism, varicocele or agingwould induce changes in the cytokine environment of the mouse testis. Methods: In adult male BALB/c mice,testosterone implants, estradiol benzoate, vasectomy, unilateral cryptorchidism, unilateral varicocele were adminis-tered/performed. The mice were followed up for different periods of time and were then sacrificed with testes incisedfor examination. The control mice received the vehicle or sham-operation. Results: IL-10 was present in Leydigcells of nearly every testis and IL-10 + macrophages in 39% of testes. IL-6 was found in the testes of intact adultmice, mice treated with testosterone for 70 days, cryptorchid testes and sham-operated testes. Conclusion: Resultssuggest that IL-10 might be involved in the generation of the immunologically privileged microenvironment in the testis.(Asian J Androl 2001 Mar; 3: 9-19)

Fine-scale genetic structure of Eremosparton songoricum and implication for conservation

Eremosparton songoricum (Litv.) Vass. is a clonal shrub that reproduces both asexually by under-ground rhizomes and sexually by seeds. It is now a rare species with a narrow distribution in fragmented habitat patches in the Gurbantunggut Desert of Xinjiang, China. The objective of this study was to determine the spatial pattern or structure of genetic variation within population. The within-populations genetic structure of E. songoricum in a plot (10 m×10 m) was analyzed using inter simple sequence repeats (ISSR) markers. Correlograms of Moran’s I showed significant positive value was about 7 m, but changed into a negative correlation with the increase of distance, indicating strong genetic structure. The natural character of clonal reproduction, restricted seed and pollen dispersal were the main factors of influencing the spatial pattern. The knowledge of clonal structures within populations was crucial for understanding evolutionary processes and ecological adaptation. This study provided basic data for the conservation and management of E. songoricum, especially for sampling strategies for ex situ conservation.

Intratumoral functional heterogeneity and chemotherapy

Intratumoral heterogeneity including genetic and nongenetic mechanisms refers to biological differences amongst malignant cells originated within the same tumor.Both,cell differentiation hierarchy and stochasticity in gene expression and signaling pathways may result in phenotypic differences of cancer cells.Since a tumor consists of cancer cell clones that display distinct behaviours,changes in clonal proliferative behavior may also contribute to the phenotypic variability of tumor cells.There is a need to reveal molecular actions driving chemotherapeutic resistance in colon cancer cells.In general,it is widely hypothesized that therapeutic resistance in colorectal cancer is a consequence of the preferential survival of cancer stem cells.However,recent data regarding colorectal cancer suggest that resistance to anticancer therapy and post-therapeutic tumor reappearence could be related to variations of clonal dynamics.Understanding the interaction of genetic and nongenetic determinants influencing the functional diversity and therapy response of tumors should be a future direction for cancer research.

Clonal Selection Based Memetic Algorithm for Job Shop Scheduling Problems

A clonal selection based memetic algorithm is proposed for solving job shop scheduling problems in this paper. In the proposed algorithm, the clonal selection and the local search mechanism are designed to enhance exploration and exploitation. In the clonal selection mechanism, clonal selection, hypermutation and receptor edit theories are presented to construct an evolutionary searching mechanism which is used for exploration. In the local search mechanism, a simulated annealing local search algorithm based on Nowicki and Smutnicki＇s neighborhood is presented to exploit local optima. The proposed algorithm is examined using some well-known benchmark problems. Numerical results validate the effectiveness of the proposed algorithm.

Effect of mini-cutting size on adventitious rooting and morphophysiological quality of Ilex paraguariensis plantlets

As the energizing and therapeutic effects of infusions of mate(Ilex paraguariensis A.St.-Hil)leaves are increasingly recognized,rising global consumption is also increasing the demand for plantlets with high genetic and morphological qualities.Mini-cuttings are an alternative for clonal plantlets;however,more details are needed on factors that affect the success of this technique.Here,toward maximizing production,we evaluated adventitious rooting competence of mini-cuttings of different sizes and the morphophysiological quality of the resultant plantlets.Small(one bud;length up to 2.5 cm),medium(multiple buds;length 2.6–5.0 cm),and large(multiple buds;length 5.1–10.0 cm)mini-cuttings were planted in a mixture of commercial substrate,vermiculite,and coarse sand(1:1:1 v:v:v),grown in a humidity chamber,then evaluated after 45,60,75,and 90 days for survival,percentage of callus and shoot formation,number and length of shoots,percentage of rooted cuttings,and number and length of roots.Any rooted mini-cuttings were then cultivated in commercial substrate and subsurface soil(2:1 v:v)and evaluated after 30,60,90 and 120 days of cultivation for morphophysiology of the plantlets,percentage of survival,number of leaves,shoot height,stem diameter,and ratio of shoot height to stem diameter.After 120 days,the plantlets were evaluated for the ratio of shoot and root dry mass,total length,surface area,total volume,and mean diameter of roots and Dickson quality index.Adventitious rooting of the mini-cuttings and the morphophysiological quality of the plantlets were not influenced by the size of the vegetative propagule.Therefore,single-bud mini-cuttings have similar adventitious rooting competence,and result in plantlets with adequate morphophysiological quality,based upon leaf development,shoot height,stem diameter and length,and surface area,volume and diameter of roots.Single-bud mini-cuttings up to 2.5 cm long can thus be used to maximize production of mate plantlets by mini-cuttings.