Clonality and allelotype analyses of focal nodular hyperplasia compared with hepatocellular adenoma and carcinoma

AIM： To identify clonality and genetic alterations in focal nodular hyperplasia （FNH） and the nodules derived from it. METHODS： Twelve FNH lesions were examined. Twelve hepatocellular adenomas （HCAs） and 22 hepatocellular carcinomas （HCCs） were used as references. Nodules of different types were identified and isolated from FNH by microdissection. An X-chromosome inactivation assay was employed to describe their clonality status. Loss of heterozygosity （LOH） was detected, using 57 markers, for genetic alterations.RESULTS： Nodules of altered hepatocytes （NAH）, the putative precursors of HCA and HCC, were found in all the FNH lesions. Polyclonality was revealed in 10 FNH lesions from female patients, and LOH was not detected in any of the six FNH lesions examined, the results apparently showing their polyclonal nature. In contrast, monoclonality was demonstrated in all the eight HCAs and in four of the HCCs from females, and allelic imbalances were found in the HCAs （9/9） and HCCs （15/18）, with chromosomal arms 11p, 13q and 17p affected in the former, and 6q, 8p, 11p, 16q and 17p affected in the latter lesions in high frequencies （≥ 30%）. Monodonality was revealed in 21 （40%） of the 52 microdissected NAH, but was not found in any of the five ordinary nodules. LOH was found in all of the 13 NAH tested, being highly frequent at six loci on 8p, 11p, 13q and 17p. CONCLUSION： FNH, as a whole, is polyclonal, but some of the NAH lesions derived from it are already neoplastic and harbor similar allelic imbalances as HCAs.

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.

Distribution and clonality of peripheral blood TCR Vα subfamily T cells in patients with acute promyelocytic leukemia

Objective： To investigate the distribution and clonality of TCR Va subfamily T cells in patients with acute promyelocytic leukemia （APL）. Methods： The complementary determining region 3 （CDR3） of TCR Va 29 subfamily genes in peripheral blood mononuclear cells from 9 APL patients were amplified using RT-PCR. The positive products were further analyzed to identity the clonality of T cells by GeneScan technique. Results： One to seven of TCR Va subfamilies could be detected in peripheral blood T cells from 9 cases with APL, the frequent expression of Va subfamilies predominated in Vα3 and Va19. Clonal expanded T cells could be detected in 8 APL patients, which predominant used Va3, Va26 or Va27 （3 out of 8 cases）. However, almost all Va subfamilies with polyclonal expansion could be detected in peripheral blood T cells from 10 cases of normal individuals. Conclusion： Remarkable skew distribution and clonal expansion of TCR Va subfamilies T cells is the common feature in patients with APL. Clonal expansion of T cells might reflect a response in host to APL cell associated antigen, whether these expanded T cells have the ability for specific cytotoxicity against APL cells, remains an open question.

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.

Belowground Bud Bank Is Insensitive to Short-Term Nutrient Addition in the Meadow Steppe of Inner Mongolia

Human activities and industrialization have significantly increased soil nutrients,such as nitrogen(N)and phos-phorus(P),profoundly impacting the composition and structure of plant community,as well as the ecosystem functions,especially in nutrient-limited ecosystems.However,as the key propagule pool of perennial grasslands,how belowground bud bank and its relationship with aboveground vegetation respond to short-term changes in soil nutrients was still unclear.In this study,we conducted a short-term(2021–2022)soil fertilization experiment with N addition(10 g N m^(-2) yr^(-1))and P addition(5 g N m^(-2) yr^(-1))in the meadow steppe of Inner Mongolia,China,to explore the responses of belowground bud bank,aboveground shoot population and their relationships(represented by the ratio of bud to shoot density-meristem limitation index(MLI))for the whole community and three plant functional groups(perennial rhizomatous grasses-PR,perennial bunchgrasses-PB,and perennial forbs-PF)to nutrient addition.The short-term nutrient addition had no significant influences on belowground bud density,aboveground shoot density,and MLI of the whole plant community.Plant functional groups showed different responses to soil fertilization.Specifically,N addition significantly increased the bud density and shoot density of PR,especially in combination with P addition.N addition reduced the shoot density of PF but had no influence on its bud density and MLI.Nutrient addition had significant effects on the three indicators of PB.Our study indicates that the belowground bud bank and its relationship with aboveground vegetation in temperate meadow steppe are insensitive to short-term soil fertilization,but plant functional groups exhibit specific responses in terms of population regeneration,which implies that plant community composition and ecosystem functions will be changed under the ongoing global change.

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.

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.

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.

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.

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.

Architectural Plasticity in Response to Soil Moisture in the Stoloniferous Herb, Duchesnea indica

Architectural plasticity of clonal plants may enhance exploitation of soil moisture heterogeneity by the plants. The plasticity of clonal architecture in response to soil moisture in the stoloniferous herb, Duchesnea indica Focke, was investigated in an experiment with different soil moisture contents as treatments, i.e. 40%, 60%, 80%, 100% of the maximum moisture content of soil (MMCS). As soil moisture content increased, the spacer length, ramet density, branching intensity and branching angle of D. indica plants changed by quadratic curve. And the optimum habitat for the plants was at 80% of the MMCS. This architectural plasticity in D. indica was simulated through the Dynamic Logistic Model. The imitative effect was statistically satisfactory. Its architectural plasticity observed here may allow the species to show foraging behavior in its habitat where soil moisture is patchily distributed.

Effect of Light Intensity and Nutrient Availability on Clonal Growth and Clonal Morphology of the Stoloniferous Herb Halerpestes ruthenica

In a greenhouse experiment plasticity of clonal growth and clonal morphology of the stoloniferous rosette herb Halerpestes nahenica Ovcz. in response to differing levels of light intensity and nutrient availability was studied. Total plant dry weight, leaf area of primary ramets, total number of ramets and of stolons, and total stolon length were significantly reduced, while specific internode length and specific petiole length significantly increased under deep shading (6.25% of high light intensity, 5.3% of full daylight) or under low nutrient availability. Under low nutrient availability, mean stolon internode length of H. ruthenica was significantly larger while branching intensity and number of ramets smaller than those under high nutrient availability. These responses are consistent with the foraging model of clonal plants, indicating that H. nahenica is able to forage nutrients through the plastic responses of clonal growth and clonal. morphology when it grows in heterogeneous environments. However, under deep shading, both mean stolon internode length and mean petiole length were significantly reduced, which disagrees with the findings of many other stoloniferous herbs in response to low or medium levels of shading (ca. 13%-75% of high light intensity, >10% of full daylight), suggesting that under deep shading stoloniferous herbs may not forage light through the plastic responses of spacer length. Many traits such as total plant dry weight, total number and length of stolons, total length of secondary and tertiary stolons. total number of ramets, leaf area of primary ramets and branching intensity were markedly influenced by the interaction effect of light intensity and nutrient availability. Under high light intensity nutrient availability affected these traits more pronouncedly, however under low light intensity nutrient availability either did not affect or affected less markedly on these traits, indicating that fight intensity had significant effect on nutrient foraging in H. nahenica. Under deep shading or low nutrient availability, H. ruthenica may increase its mean stolon internode length by means of thinning stolon internodes (i.e., an increase in specific internode length), which provides it with more chance to escape from resource-poor sites.

Phenotypic Plasticity in Response to the Heterogeneous Water Supplyin the Rhizomatous Grass Species, Calamagrostis epigejosin the Mu Us Sandy Land of China

Calamagrostis epigejos (L.) Roth. is a perennial grass with slender and long rhizome segments between interconnected neighbor ramets. To investigate the phenotypic plasticity in response to the heterogeneous soil water supply, ramet pairs of the species were subjected to heterogeneous water supply by which either mother ramets or daughter ramets were in high or low soil water supply, respectively, in the Maowusu (Mu Us) Sandy Land of Nei Mongol. The results showed that the phenotypic characteristics of the individual ramets of C epigejos were greatly influenced by the heterogeneous water supply. The ramets treated with high water supply significantly produced more new rhizomes and more offspring (ramets), and accumulated more shoot biomass, and allocated more biomass to their shoots than those treated with low water supply. In comparison with the daughter ramets in homogeneous soil water supply, phenotypic characteristics, in terms of new rhizome growth, the production of new offspring, and the biomass allocation pattern, of the daughter ramets within the pairs of the species were not significantly changed, no matter that high or low soil water supply to mother ramets. The phenotypic responses of mother ramets to soil water supply were similar to those of daughter ramets. From these results, it is inferred that the interconnected ramets of C epigejos response phenotypically to their local soil water rather than to the soil water experienced by the interconnected ramets. The interconnected ramets of C epigejos might be independent of each other in water relationship, although they are physically interconnected with rhizome segments. The physiological independence of interconnected ramets might facilitate the risk spreading and thus enhance the genet survivorship under the frequent drought stresses in Mu Us Sandland.

Liver cell adenoma:A case report with clonal analysis and literature review

We report a case of liver cell adenoma （LCA） in a 33-year-old female patient with special respect to its clonality status, pathogenic factors and differential diagnosis. The case was examined by histopathology, immunohistochemistry and a clonality assay based on X-chromosomal inactivation mosaicism in female somatic tissues and polymorphism at androgen receptor focus. The clinicopathological features of the reported cases from China and other countries were compared. The lesion was spherical, sizing 2 cm in its maximal dimension. Histologically, it was composed of cells arranged in cords, most of which were two-cell-thick and separated by sinusoids. Focal fatty change and excessive glycogen storage were observed. The tumor cells were round or polygonal in shape, resembling the surrounding parenchymal cells. Mitosis was not found. No portal tract, central vein or ductule was found within the lesion. The tumor tissue showed a positive reaction for cytokeratin （CK） 18, but not for CK19, vimentin, estrogen and progesterone receptors. Monoclonality was demonstrated for the lesion, confirming the diagnosis of an LCA. Clonality analysis is helpful for its distinction from focal nodular hyperplasia.K

Analysis on age structure of Zoysia japonica (Poaceae) population

The age-structure of natural population of Zoysia japonica in Xiuyan County of Liaoning Province was studied by generational method. The results showed that the highest tiller age class was three, but 1st age class tillers held dominant posi-tion with proportions over 95% in each month during the growing seasons. The 2nd age class and 3rd age class tillers were minority in the population. So Z. japonica population was an expanding population. The zero age class buds on the rhizomes were dominant in buds age structures. The proportion of buds to tillers on quantity in each month was about 30% to 40% and reached the highest at the end of September. The increasing of buds proportion before dormancy guaranteed the quantity of tillers in the next spring. The biomass of 1st age class tillers changed with time. The biomass kept increasing from April to July and reached the highest at the end of July and then decreased.

OPTIMIZATION OF AIRPORT TAXIING PLANNING DURING CONGESTED HOURS BASED ON IMMUNE CLONAL SELECTION ALGORITHM

In order to ease congestion and ground delays in major hub airports, an aircraft taxiing scheduling optimization model is proposed with schedule time as the object function. In the new model, the idea of a classical job shop-schedule problem is adopted and three types of special aircraft-taxi conflicts are considered in the constraints. To solve such nondeterministic polynomial time-complex problems, the immune clonal selection algorithm（ICSA） is introduced. The simulation results in a congested hour of Beijing Capital International Airport show that, compared with the first-come-first-served（FCFS） strategy, the optimization-planning strategy reduces the total scheduling time by 13.6 min and the taxiing time per aircraft by 45.3 s, which improves the capacity of the runway and the efficiency of airport operations.

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.