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.

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.

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.

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.

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.

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.

Profiling of hepatocellular carcinoma neoantigens reveals immune microenvironment and clonal evolution related patterns

Objective: Neoantigens derived from tumor-specific genomic alterations have demonstrated great potential for immunotherapeutic interventions in cancers. However, the comprehensive profile of hepatocellular carcinoma(HCC) neoantigens and their complex interplay with immune microenvironment and tumor evolution have not been fully addressed.Methods: Here we integrated whole exome sequencing data, transcriptome sequencing data and clinical information of 72 primary HCC patients to characterize the HCC neoantigen profile, and systematically explored its interactions with tumor clonal evolution, driver mutations and immune microenvironments.Results: We observed that higher somatic mutation/neoantigen load was associated with better clinical outcomes and HCC patients could be further divided into two subgroups with distinct prognosis based on their neoantigen expression patterns. HCC subgroup with neoantigen expression probability high(NEP-H) showed more aggressive pathologic features including increased incidence of tumor thrombus(P=0.038), higher recurrence rate(P=0.029),more inclined to lack tumor capsule(P=0.026) and with more microsatellite instability sites(P=0.006). In addition,NEP-H subgroup was also characterized by higher chance to be involved in tumor clonal evolution [odds ratio(OR)=46.7, P<0.001]. Gene set enrichment analysis revealed that upregulation of MYC and its targets could suppress immune responses, leading to elevated neoantigen expression proportion in tumor cells. Furthermore, we discovered an immune escape mechanism that tumors could become more inconspicuous by evolving subclones with less immunogenicity. We observed that smaller clonal mutation clusters with higher immunogenicity in tumor were more likely to involve in clonal evolution. Based on identified neoantigen profiles, we also discovered series of neoantigenic hotspot genes, which could serve as potential actionable targets in future.Conclusions: Our results revealed the landscape of HCC neoantigens and discovered two clinically relevant subgroups with distinct neoantigen expression patterns, suggesting the neoantigen expression should be fully considered in future immunotherapeutic interventions.

权重自适应clonal选择算法及其应用研究

在求解两个目标以上的多目标优化问题时,基于Pareto支配的多目标进化算法多数需要较长的求解时间。基于固定权重的聚合函数方法求解速度快,但要确定一个适合待求解问题的合理权重是十分困难的,为了解决这一问题,将clonal选择算法与权重自适应方法相结合,提出了一种适用于多目标优化问题的权重自适应clonal选择算法。并将权重自适应clon-al选择算法应用于以等功率裕量、轧制能耗及带钢打滑概率作为优化的目标函数的三目标优化模型进行冷连轧轧制规程多目标优化。结果表明,与实际应用的轧制规程相比优化后的轧制规程使功率裕量更加均衡,打滑发生的机率变小,同时也降低了总的轧制能耗。与权重自适应遗传算法相比,该算法能更好的达到预期的优化效果。

Distribution patterns of clonal plants in the subnival belt of the Hengduan Mountains,SW China

Clonal reproduction(i.e.,production of potentially independent offspring by vegetative growth)is thought to provide plants with reproductive assurance.Thus,studying the evolution of clonal reproduction in local floras is crucial for our understanding of the adaptive mechanisms plants deploy in stressful environments such as alpine regions.In this study,we characterized clonal plant species in the subnival belt of the Hengduan Mountains(a global biodiversity hotspot with extreme environmental conditions in southwest China),in order to determine the effects of sex system,growth form,and elevational distribution on clonality.We compiled clonality data of angiosperm species belonging to 41 families in the subnival belt of the Hengduan Mountains using published information.Of the 793 species recorded in the region,47.92%(380 species)are clonal species.Both sex system and growth form had significant effects on the occurrence of clonal reproduction:unisexual species(79.79%)were more likely to be clonal than bisexual species(43.63%),and herbaceous species(51.04%)were more likely to be clonal than woody species(16.67%).Compared with non-alpine-endemic species(44.60%),alpine-endemic species(58.33%)showed a significantly higher proportion of clonal reproduction.Further logistic regression analysis showed a positive association between incidence of clonality and elevational range,indicating that species distributed at high elevations are more likely to be clonal.Furthermore,the elevational gradients in clonality were contingent on sex system or growth form.This study reveals that plants in the subnival belt of the Hengduan Mountains might optimize their probability of reproduction through clonal reproduction,a finding that adds to our growing understanding of plant's adaptations to harsh alpine environments.

Directional Filter for SAR Images Based on Nonsubsampled Contourlet Transform and Immune Clonal Selection

A directional filter algorithm for intensity synthetic aperture radar （SAR） image based on nonsubsampled contourlet transform （NSCT） and immune clonal selection （ICS） is presented. The proposed filter mainly focuses on exploiting different features of edges and noises by NSCT. Furthermore, ICS strategy is introduced to optimize threshold parameter and amplify parameter adaptively. Numerical experiments on real SAR images show that there are improvements in both visual effects and objective indexes.

Identification of portal vein tumor thrombus with an independent clonal origin in hepatocellular carcinoma via multi-omics data analysis

Objective: Multiple mechanisms underlying the development of portal vein tumor thrombus(PVTT) in hepatocellular carcinoma(HCC) have been reported recently. However, the origins of PVTT remain unknown. Increasing multi-omics data on PVTTs in HCCs have made it possible to investigate whether PVTTs originate from the corresponding primary tumors(Ts).Methods: The clonal relationship between PVTTs and their corresponding primary Ts was investigated using datasets deposited in public databases. One DNA copy number variations dataset and three gene expression datasets were downloaded for the analyses.Clonality analysis was performed to investigate the clonal relationship between PVTTs and Ts from an individual patient.Differential gene expression analysis was applied to investigate the gene expression profiles of PVTTs and Ts.Results: One out of 19 PVTTs had no clonal relationship with its corresponding T, whereas the others did. The PVTTs with independent clonal origin showed different gene expression and enrichment in biological processes from the primary Ts. Based on the unique gene expression profiles, a gene signature including 24 genes was used to identify pairs of PVTTs and primary Ts without any clonal relationship. Validation in three datasets showed that these types of pairs of PVTTs and Ts can be identified by the 24-gene signature.Conclusions: Our findings show a direct evidence for PVTT origin and consolidate the heterogeneity of PVTTs observed in clinic.The results suggest that PVTT investigation at a molecular level is clinically necessary for diagnosis and treatment.

Role of chromosomal instability and clonal heterogeneity in the therapy response of breast cancer cell lines

Objective:Chromosomal instability(CIN)is a hallmark of cancer characterized by cell-to-cell variability in the number or structure of chromosomes,frequently observed in cancer cell populations and is associated with poor prognosis,metastasis,and therapeutic resistance.Breast cancer(BC)is characterized by unstable karyotypes and recent reports have indicated that CIN may influence the response of BC to chemotherapy regimens.However,paradoxical associations between extreme CIN and improved outcome have been observed.Methods:This study aimed to 1)evaluate CIN levels and clonal heterogeneity(CH)in MCF7,ZR-751,MDA-MB468,BT474,and KPL4 BC cells treated with low doses of tamoxifen(TAM),docetaxel(DOC),doxorubicin(DOX),Herceptin(HT),and combined treatments(TAM/DOC,TAM/DOX,TAM/HT,HT/DOC,and HT/DOX)by using fluorescence in situ hybridization(FISH),and 2)examine the association with response to treatments by comparing FISH results with cell proliferation.Results:Intermediate CIN was linked to drug sensitivity according to three characteristics:estrogen receptorα(ERα)and HER2 status,pre-existing CIN level in cancer cells,and the CIN induced by the treatments.ERα+/HER2-cells with intermediate CIN were sensitive to treatment with taxanes(DOC)and anthracyclines(DOX),while ERα-/HER2-,ERα+/HER2+,and ERα-/HER2+cells with intermediate CIN were resistant to these treatments.Conclusions:A greater understanding of CIN and CH in BC could assist in the optimization of existing therapeutic regimens and/or in supporting new strategies to improve cancer outcomes.

In vitro clonal propagation of Achyranthes aspera L. and Achyranthes bidentata Blume using nodal explants

Objective:To develop the reproducible in vitro propagation protocols for the medicinally important plants viz.,Achyranthes aspera(A.aspera)L.and Achyranthes bidentata(A.bidentata)Blume using nodal segments as explants.Methods:Young shoots of A.aspera and A.bidentata were harvested and washed with running tap water and treated with 0.1%bavistin and rinsed twice with distilled water.Then the explants were surface sterilized with 0.1%(w/v)HgCl_2 solutions for I min.After rinsing with sterile distilled water for 3-4 times,nodal segments were cut into smaller segments(1 cm)and used as the explants.The explants were placed horizontally as well as vertically on solid basal Murashige and Skoog(MS)medium supplemented with 3%sucrose,0.6%(w/v)agar(HiMedia,Mumbai)and different concentration and combination of 6-benzyl amino purine(BAP),kinetin(Kin),naphthalene acetic acid(NAA)and indole acetic acid(IAA)for direct regeneration.Results:Adventitious proliferation was obtained from A.aspera and A.bidentata nodal segments inoculated on MS basal medium with 3%sucrose and augmented with BAP and Kin with varied frequency.MS medium augmented with 3.0 mg/L of BAP showed the highest percentage(93.60±0.71)of shootlets formation for A.aspera and(94.70±0.53)percentages for A.bidentata.Maximum number of shoots/explants(10.60±0.36)for A.aspera and(9.50±0.56)for A.bidentata was observed in MS medium fortified with 5.0 mg/L of BAP.For A.aspera,maximum mean length(5.50±0.34)of shootlets was obtained in MS medium augmented with 3.0 mg/L of Kin and for A.bidentata(5.40±0.61)was observed in the very same concentration.The highest percentage,maximum number of rootlets/shootlet and mean length of rootlets were observed in 1/2 MS medium supplemented with 1.0 mg/L of 1BA.Seventy percentages of plants were successfully established in polycups.Sixty eight percentages of plants were well established in the green house condition.Sixty five percentages of plants were established in the field.Conclusions:The results have shown that use of nodal buds is an alternative reproducible and dependable method for clonal propagation of A.aspera and A.bidentata.The high rate of direct shoot-root multiplication and their high rate of post-hardening survival indicate that this protocol can he easily adopted for commercial large scale cultivation.

Feasibility Study of Parameter Identification Method Based on Symbolic Time Series Analysis and Adaptive Immune Clonal Selection Algorithm

The feasibility of a parameter identification method based on symbolic time series analysis (STSA) and the adaptive immune clonal selection algorithm (AICSA) is studied. Data symbolization by using STSA alleviates the effects of harmful noise in raw acceleration data. The effect of the parameters in STSA is theoretically evaluated and numerically verified. AICSA is employed to minimize the error between the state sequence histogram (SSH) that is transformed from raw acceleration data by STSA. The proposed methodology is evaluated by comparing it with AICSA using raw acceleration data. AICSA combining STSA is proved to be a powerful tool for identifying unknown parameters of structural systems even when the data is contaminated with relatively large amounts of noise.

Role of Clonal Integration among Different Environmental Conditions (A Review)

Most of the ecosystems are dominated by clonal species. The most unique feature of clonal plants is their capability for clonal integration (translocation of vital resources among connected ramets), implying that integration may play an essential role in their success. However, a general effect of clonal integration on plant performance is lacking. We conducted a text review on the effects of clonal integration on different habitats and species. Overall, clonal integration increased performance of clonal plants in different habitats. However clonal integration has also some limitations under stressful environments. Benefits of clonal integration may lack somehow when environmental stress increases. But connected ramets placed in unfavorable patches benefited more from integration compared to severed ramet placed in nutrient rich patches. Climate change and temperature increase have positive effects on biomass of clonal species.

Comparative drug susceptibility study of five clonal strains of Trichomonas vaginalis in vitro

Objective:To produce comparative data on a group of Trichomonas vaginalis clonal strains with varied drug responses using identical methods and materials.Methods:Five clonal strains of Trichomonas vaginalis were isolated from reference strain using agar plate technique.The variability of growth kinetic and susceptibility of clonal strain to metronidazole,tinidazole, satranidazole and nitazoxanide were observed in 96 well microlilre plate.Results:Among these clonal strains there was a good correlation between rates of growth with the relative susceptibility of the strains to drugs in vitro.Regarding metronidazole,tinidazole and satranidazole susceptibility,different degrees of susceptibility were determined.However,no difference in nitazoxanide susceptibility was found between the clonal strain tested and a reference strain. Conclusions:This is the first description of biological variability in clonal stock of Trichomonas vaginalis.Different degrees of drug susceptibility were determined among clonal strains tested. Further studies will be necessary to ascertain the importance of this variability in clinical infection.

Discrimination of clonal origin patterns for molecular pathological diagnosis of RHCC/MHCC

Objective:The high post-operative recurrence of hepatocellular carcinoma(RHCC)and multinodular hepatocellular carcinoma(MHCC)seriously limit the surgical efficacy of HCC.Theoretically,RHCC/MHCC arise from either residual tumor cells or novel clone-derived tumor cells which have a great impact on designing personalized therapies and the evaluation of clinical long-term outcome.