Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been co...Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.展开更多
Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres, Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chr...Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres, Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chromosomes were observed in the progeny of a Chinese Spring-lmperial rye 3R addition line. An unstable multicentric chromosome was found in the progeny of a 6R/6D substitution line. Drastic variation of terminal heterochromatin including movement and disappearance of terminal heterochromatin occurred in the progeny of wheat- rye addition line 3R, and the 5RS ditelosomic addition line. Highly stable minichromosomes were observed in the progeny ofa monosomic 4R addition line, a ditelosomic 5RS addition line and a 6R/6D substitution line. Minichromosomes, with and without the FISH signals for telomeric DNA （TTTAGGG）n, derived from a monosomic 4R addition line are stable and transmissible to the next generation. The results indicated that centromeres and terminal heterochromatin can be profoundly altered in wheat-rye hybrid derivatives.展开更多
Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and...Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.展开更多
We present the numerical simulation results of a model granular assembly formed by spherical particles with tIertzian interaction subjected to a simple shear in the athermal quasi-static limit. The stress-strain curve...We present the numerical simulation results of a model granular assembly formed by spherical particles with tIertzian interaction subjected to a simple shear in the athermal quasi-static limit. The stress-strain curve is shown to separate into smooth, elastic branches followed by a subsequent plastic event. Mode analysis shows that the lowest-frequency vibrational mode is more localized, and eigenvalues and participation ratios of low- frequency modes exhibit similar power-law behavior as the system approaches plastic instability, indicating that the nature of plastic events in the granular system is also a saddle node bifurcation. The analysis of projection and spatial structure shows that over 75% contributions to the non-affine displacement field at a plastic instability come from the lowest-frequency mode, and the lowest-frequency mode is strongly spatially correlated with local plastic rearrangements, inferring that the lowest-frequency mode could be used as a predictor for future plastic rearrangements in the disordered system jammed marginally.展开更多
From a mixture of α-,β-and y-himachalenes extracted from waste wood of Atlas cedar(Cedrus atlantica),cadalene(1,6-dimethyl-4-isopropylnaphthalene)and iso-cadalene(1,6-dimethyl-3-isopropylnaphthalene)were produced in...From a mixture of α-,β-and y-himachalenes extracted from waste wood of Atlas cedar(Cedrus atlantica),cadalene(1,6-dimethyl-4-isopropylnaphthalene)and iso-cadalene(1,6-dimethyl-3-isopropylnaphthalene)were produced in two steps with up to 71%±5%yield through the ar-himachalene intermediate using I2 and/or AlCl3 as reagents.The selectivity is shown to sharply depend on the operating conditions:while I2/AlCl3 in dichloromethane promotes the formation of cadalene,the formation of iso-cadalene is favored in the presence of AlCl3 in cyclohexane.The bicyclic aromatic compounds were thus obtained through unique rearrangements involving sequential C—C bond cleavage/fo rmation and hydride transfer processes.In the absence of AlCl3 or I2,dihydrocurcumene was also found to be formed with up to 70%selectivity.A tentative mechanism is proposed and discussed.展开更多
Chromosomal fragile sites (CFSs) are loci or regions susceptible to spontaneous or induced occurrence of gaps, breaks and rearrangements. In this work, we studied the data of 4535 patients stored at DECIPHER (Database...Chromosomal fragile sites (CFSs) are loci or regions susceptible to spontaneous or induced occurrence of gaps, breaks and rearrangements. In this work, we studied the data of 4535 patients stored at DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources). We mapped fragile sites to chromosomal bands and divided the 23 chromosomes into fragile and non-fragile sites. The frequency of rearrangements at the chromosomal location of clones found to be deleted or duplicated in the array/CGH analysis, provided by DECIPHER, was compared in Chromosomal Fragile Sites vs. non-Fragile Sites of the human genome. The POSSUM Web was used to complement this study. The results indicated 1) a predominance of rearrangements in CFSs, 2) the absence of statistically significant difference between the frequency of rearrangements in common CFSs vs. rare CFSs, 3) a predominance of deletions over duplications in CFSs. These results on constitutional chromosomal rearrangements are evocative of the findings previously reported by others relatively to cancer supporting the current line of evidence and suggesting that a common mechanism can underlie the generation of constitutional and somatic rearrangements. The combination of insights obtained from our results and their interrelationships can indicate strategies by which the mechanisms can be targeted with preventive medical interventions.展开更多
AIM:To study the diagnostic value of immunoglobulin heavy chain(IgH)and T-cell receptorγ (TCR-γ)gene monoclonal rearrangements in primary gastric lymphoma(PGL).METHODS:A total of 48 patients with suspected PGL at ou...AIM:To study the diagnostic value of immunoglobulin heavy chain(IgH)and T-cell receptorγ (TCR-γ)gene monoclonal rearrangements in primary gastric lymphoma(PGL).METHODS:A total of 48 patients with suspected PGL at our hospital were prospectively enrolled in this study from January 2009 to December 2011.The patients were divided into three groups(a PGL group,a gastric linitis plastica group,and a benign gastric ulcer group)based on the pathological results(gastric mucosal specimens obtained by endoscopy or surgery)and follow-up.Endoscopic ultrasonography(EUS)and EUSguided biopsy were performed in all the patients.The tissue specimens were used for histopathological examination and for IgH and TCR-γ gene rearrangement polymerase chain reaction analyses.RESULTS:EUS and EUS-guided biopsy were successfully performed in all 48 patients.In the PGL group(n=21),monoclonal IgH gene rearrangements were detected in 14(66.7%)patients.A positive result for each set of primers was found in 12(57.1%),8(38.1%),and 4(19.0%)cases using FR1/JH,FR2/JH,and FR3/JH primers,respectively.Overall,12(75%)patients with mucosal-associated lymphoid tissue lymphoma(n=16)and 2(40%)patients with diffuse large B-cell lymphoma(n=5)were positive for monoclonal IgH gene rearrangements.No patients in the gastric linitis plastica group(n=17)and only one(10%)patient in the benign gastric ulcer group(n=10)were positive for a monoclonal IgH gene rearrangement.No TCRgene monoclonal rearrangements were detected.The sensitivity of monoclonal IgH gene rearrangements was 66.7%for a PGL diagnosis,and the specificity was96.4%.In the PGL group,8(100%)patients with stage IIE PGL(n=8)and 6(46.1%)patients with stage IE PGL(n=13)were positive for monoclonal IgH gene rearrangements.CONCLUSION:IgH gene rearrangements may be associated with PGL staging and may be useful for the diagnosis of PGL and for differentiating between PGL and gastric linitis plastica.展开更多
Acquired immune deficiency syndrome (AIDS)-related lymphoma (ARL) remains the main cause of AIDS-related deaths in the highly active anti-retroviral therapy (HAART) era. Recently, rearrangement of MYC is associated wi...Acquired immune deficiency syndrome (AIDS)-related lymphoma (ARL) remains the main cause of AIDS-related deaths in the highly active anti-retroviral therapy (HAART) era. Recently, rearrangement of MYC is associated with poor prognosis in patients with diffuse large B-cell lymphoma. Here, we report a rare case of gastrointestinal (GI)-ARL with MYC rearrangements and coinfected with Epstein-Barr virus (EBV) infection presenting with various endoscopic findings. A 38-yearold homosexual man who presented with anemia and was diagnosed with an human immunodeficiency virus infection for the first time. GI endoscopy revealed multiple dish-like lesions, ulcerations, bloody spots, nodular masses with active bleeding in the stomach, erythematous flat lesions in the duodenum, and multiple nodular masses in the colon and rectum. Magnified endoscopy with narrow band imaging showed a honeycomb-like pattern without irregular microvessels in the dish-like lesions of the stomach. Biopsy specimens from the stomach, duodenum, colon, and rectum revealed diffuse large B-cell lymphoma concomitant with EBV infection that was detected by high tissue EBV-polymerase chain reaction levels and Epstein-Barr virus small RNAs in situ hybridization. Fluorescence in situ hybridization analysis revealed a fusion between the immunoglobulin heavy chain (IgH) and c-MYC genes, but not between the IgH and BCL2 loci. After 1-mo of treatment with HAART and R-CHOP, endoscopic appearance improved remarkably, and the histological features of the biopsy specimens revealed no evidence of lymphoma. However, he died from multiple organ failure on the 139 th day after diagnosis. The cause of his poor outcome may be related to MYC rearrangement. The GI tract involvement in ARL is rarely reported, and its endoscopic findings are various and may be different from those in non-AIDS GI lymphoma; thus, we also conducted a literature review of GI-ARL cases.展开更多
Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mit...Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mitogenomic data sets from GenBank, we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae. The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement. Except for the genus Babina, the monophyly of each genus was well supported. The genus Amnirana occupied the most basal position among the Ranidae. The [Lithobates ＋ Rana] was the closest sister group of Odorrana. The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high, with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types. Some taxa owned their unique gene rearrangement characteristics, which had significant implication for their phylogeny analysis. All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.展开更多
Numerous aspects of the water oxidation mechanism in photosystemⅡhave not been fully elucidated,especially the O-O bond formation pathway.However,a body of experimental evidences have identified the O5 and W2 ligands...Numerous aspects of the water oxidation mechanism in photosystemⅡhave not been fully elucidated,especially the O-O bond formation pathway.However,a body of experimental evidences have identified the O5 and W2 ligands of the oxygen-evolving complex as the highly probable substrate candidates.In this work,we studied O-O bond formation between O5 and W2 based on the native Mn4 Ca cluster by density functional calculations.Structural rearrangements before the formation of the S_(4) state were found as a prerequisite for O-O bond formation between O5 and W2,regardless if the suggested pathways involving the typical Mnl(Ⅳ)-O·species or the recently proposed Mn4(Ⅶ)(O)2 species.Possible alternatives for the S2→S_(3) and S_(3)→S_(4) transitions accounting for such required rearrangements are discussed.These findings reflect that the structural flexibility of the Mn4 Ca cluster is essential to allow structural rearrangements during the catalytic cycle.展开更多
The time evolution of oxygen plasma treated polystyrene(PS)surfaces was investigated upon storing them in theair under controlled humidity conditions.The methods of water contact angle,X-ray photoelectron spectroscopy...The time evolution of oxygen plasma treated polystyrene(PS)surfaces was investigated upon storing them in theair under controlled humidity conditions.The methods of water contact angle,X-ray photoelectron spectroscopy(XPS),sumfrequency generation(SFG)vibrational spectroscopy,and atomic force microscopy(AFM)were used to infer the surfaceproperties and structure.Chemical groups containing oxygen were formed on the PS surface with the plasma treatment,demonstrated by water contact angle and XPS.The surface polarity decayed markedly on time,as assessed by steady increasein the water contact angle as a function of storage time,from zero to around 60°.The observed decay is interpreted as arisingfrom surface rearrangement processes to burying polar groups away from the uppermost layer of the surfaces,which is incontact with air.On the other hand,XPS results show that the chemical composition in the first 3 nm surface layer isunaffected by the surface aging,and the depth profile of oxygen is essentially the same with time.A possible change of PSsurface roughness was examined by AFM,and it showed that the increase of water contact angle during surface aging couldnot be attributed to surface roughness.Thus,it is concluded that surface aging is attributable to surface reorganization andthe motion of oxygen containing groups is confined within the XPS probing depth.SFG spectroscopy,which is intrinsicallyinterface-specific,was used to detect the chemical structure of PS surface at the molecular level after various aging times.The results are interpreted as follows.During the aging of the plasma treated PS surfaces,the oxygen containing groupsundergo reorientation processes toward the polymer bulk and/or parallel to the surface,while the CH_2 moiety stands up onthe PS surface.Our results indicate that the surface configuration changes do not require large length scale segmentalmotions or migration of macromolecules.Motions that are responsible for surface configuration changes could be relativelysmall rotational motions.The aging behaviors under different relative humidity conditions were shown to be similar from18% to 91%,whereas the kinetics of surface polarity decays were faster in higher relative humidity.Here,the surfacerearrangement of polystyrene films that were previously treated by oxygen plasma and aged,and was investigated in terms ofcontact angle after the water immersion.The contact angles of the water-immersed samples were found to change andapproach the initial values before the immersion asymptotically.展开更多
The gene rearrangement of βand γchain of T-cell receptors (TCR) was detected in 13 cases of non-Hodgkin's lymphoma with T-cell immunophenotype with Southern blot and PCR. Clonally rearranged.TCR βgene was seen ...The gene rearrangement of βand γchain of T-cell receptors (TCR) was detected in 13 cases of non-Hodgkin's lymphoma with T-cell immunophenotype with Southern blot and PCR. Clonally rearranged.TCR βgene was seen in 11 cases out of the 13 and rearranged TCR γgene in 12. These facts suggest that clonal rearrangement of antigen receptors is a sensitive and specific marker to establish the T-cell monoclonality and lineage and a useful adjunct to morphological diagnosis and immunophenotyping.展开更多
Skeleton diversity is an important feature of compound libraries and plays a key role in the success of biological screening.Ligand-controlled divergent synthesis can transform the same substrate into different molecu...Skeleton diversity is an important feature of compound libraries and plays a key role in the success of biological screening.Ligand-controlled divergent synthesis can transform the same substrate into different molecular skeletons,which not only can endow compound libraries with diverse biological activities but also reveal new catalytic modes,and therefore has received extensive attention.Herein,we disclose a Ni-catalyzed,ligand-controlled switchable skeletal rearrangement reaction of acryloyl o-bromobenzamides and activated alkenes.In this protocol,modification of the ligand backbone allows the conversion of the same starting material into four structurally distinct scaffolds of pharmacological importance.Specifically,the use of terpyridine ligand favors the 6-exo cyclization and subsequent 1,2-acyl/Ni dyotropic rearrangement to generate highly functionalized cyclohexenols,while the sterically hindered ^(iPr)PDI ligand facilitates the 6-exo cyclization and subsequent 1,2-aryl/Ni dyotropic rearrangement to form highly functionalized cycloheptenols.Furthermore,isoquinoline-1,3-diones were obtained through alkene diarylation in the absence of additional activated alkenes.More strikingly,the bidentate ligand promotes nucleophilic addition of the aryl halides to the amide carbonyl,followed by 1,4-acyl transfer and cross-coupling to afford 2-benzazepin-5-ones.展开更多
In this paper we extend the notion of rearrangement of nonnegative functions to the setting of Carnot groups. We define rearrangement with respect to a given family of anisotropic balls Br , or equivalently with respe...In this paper we extend the notion of rearrangement of nonnegative functions to the setting of Carnot groups. We define rearrangement with respect to a given family of anisotropic balls Br , or equivalently with respect to a gauge‖x‖, and prove basic regularity properties of this construction. If u is a bounded nonnegative real function with compact support, we denote by u*its rearrangement. Then, the radial function u* is of bounded variation. In addition, if u is continuous then u* is continuous, and if u belongs to the horizontal Sobolev space W 1,ph , then Dhu*(x)/Dh( ‖x‖ )| is in Lp. Moreover, we found a generalization of the inequality of P(o)lya and Szeg(o) ∫|Dhu*|p/Dh(‖x‖)|pdx≤C ∫|Dhu|pdx,where p ≥ 1.展开更多
Flow through a narrow bent channel may induce topological rearrangements in a twodimensional monodispersed dry liquid foam.We use the Cellular Potts Model to simulate a foam under a variable driving force in order to ...Flow through a narrow bent channel may induce topological rearrangements in a twodimensional monodispersed dry liquid foam.We use the Cellular Potts Model to simulate a foam under a variable driving force in order to investigate the strain-rate response from these rearrangements.We observe a set of foams’behaviors ranging from elastic,viscoelastic to fluid regime.Bubble’s topological rearrangements are localized and their cumulative rearrangements change linearly with time,thus nonavalanches critical behavior is found.The strain-rate affects the rate of topological rearrangements,its dependence on the drag force is nonlinear,obeying a Herschel–Bulkley-like relationship below the foam’s flow point.展开更多
In this paper we study linear secret sharing schemes by monotone span programs, according to the relation between realizing access structures by linear secret sharing schemes and computing monotone Boolean functions b...In this paper we study linear secret sharing schemes by monotone span programs, according to the relation between realizing access structures by linear secret sharing schemes and computing monotone Boolean functions by monotone span programs. We construct some linear secret sharing schemes. Furthermore, we study the rearrangements of access structures that is very important in practice.展开更多
Some of the most extreme genome wide rearrangements are found in ciliates, which are unique in possessing both germline micronucleus and somatic macronucleus in every cell/organism. A series of DNA rearrangement event...Some of the most extreme genome wide rearrangements are found in ciliates, which are unique in possessing both germline micronucleus and somatic macronucleus in every cell/organism. A series of DNA rearrangement events, including DNA elimination, chromosomal fragmentation, gene unscrambling and alternative processing, happen during macronuclear development. To assess the molecular evolution of macronuclear and germline-limited sequences in different cryptic species of Chilodonella uncinata, we characterized the actin, α-tubulin and β-tubulin genes in the micronucleus and macronucleus genomes of USA-SC2 strain and compared them with other strains(i.e. cryptic species). Three main results are:(i) rearrangement patterns between germline and soma are conserved for each gene among the cryptic species of C. uncinata;(ii) in contrast, the germlinelimited regions are highly divergent in sequence and length among the cryptic species;(iii) pointer shifting is frequent among the cryptic species. We speculate that pointer sequences may serve as the buffer between the conserved macronuclear destined sequences and rapidly-evolving internal eliminated sequences. The data combined with previous studies demonstrate the plasticity of gene rearrangement among different groups of ciliates and add to the growing data for the role of genome rearrangements in species differentiation.展开更多
Most eukaryotes employ a variety of mechanisms to defend the integrity of their genome by recognizing and silencing parasitic mobile nucleic acids.However,recent studies have shown that genomic DNA undergoes extensive...Most eukaryotes employ a variety of mechanisms to defend the integrity of their genome by recognizing and silencing parasitic mobile nucleic acids.However,recent studies have shown that genomic DNA undergoes extensive rearrangements,including DNA elimination,fragmentation,and unscrambling,during the sexual reproduction of ciliated protozoa.Non-coding RNAs have been identified to program and regulate genome rearrangement events.In Paramecium and Tetrahymena,scan RNAs(scnRNAs)are produced from micronuclei and transported to vegetative macronuclei,in which scnRNA elicits the elimination of cognate genomic DNA.In contrast,Piwi-interacting RNAs(piRNAs)in Oxytricha enable the retention of genomic DNA that exhibits sequence complementarity in macronuclei.An RNA interference(RNAi)-like mechanism has been found to direct these genomic rearrangements.Furthermore,in Oxytricha,maternal RNA templates can guide the unscrambling process of genomic DNA.The non-coding RNA-directed genome rearrangements may have profound evolutionary implications,for example,eliciting the multigenerational inheritance of acquired adaptive traits.展开更多
基金CAs Youth Interdisciplinary Team(JCTD-2022-06)the National Nature Science Foundation of China(31870209).
文摘Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.
基金supported by the grants of the National High Technology Research and Development Program("863"Program) of China(No.2011AA100101)the Special Financial Grant from the China Postdoctoral Science Foundation (No.2012T50157),and 2011 Collaborative Innovation Plan of the Ministry Of Education of China
文摘Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres, Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chromosomes were observed in the progeny of a Chinese Spring-lmperial rye 3R addition line. An unstable multicentric chromosome was found in the progeny of a 6R/6D substitution line. Drastic variation of terminal heterochromatin including movement and disappearance of terminal heterochromatin occurred in the progeny of wheat- rye addition line 3R, and the 5RS ditelosomic addition line. Highly stable minichromosomes were observed in the progeny ofa monosomic 4R addition line, a ditelosomic 5RS addition line and a 6R/6D substitution line. Minichromosomes, with and without the FISH signals for telomeric DNA （TTTAGGG）n, derived from a monosomic 4R addition line are stable and transmissible to the next generation. The results indicated that centromeres and terminal heterochromatin can be profoundly altered in wheat-rye hybrid derivatives.
基金supported by the National Natural Science Foundation of China(No.31801042)the Health and Medical Research Fund(No.04152666 and No.07180576)General Research Fund(No.14115418),and Direct Grant(No.2020.052).
文摘Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.
基金Supported by the National Natural Science Foundation of China under Grant Nos 11272048 and 51239006the European Commission Marie Curie Actions under Grant No IRSES-294976
文摘We present the numerical simulation results of a model granular assembly formed by spherical particles with tIertzian interaction subjected to a simple shear in the athermal quasi-static limit. The stress-strain curve is shown to separate into smooth, elastic branches followed by a subsequent plastic event. Mode analysis shows that the lowest-frequency vibrational mode is more localized, and eigenvalues and participation ratios of low- frequency modes exhibit similar power-law behavior as the system approaches plastic instability, indicating that the nature of plastic events in the granular system is also a saddle node bifurcation. The analysis of projection and spatial structure shows that over 75% contributions to the non-affine displacement field at a plastic instability come from the lowest-frequency mode, and the lowest-frequency mode is strongly spatially correlated with local plastic rearrangements, inferring that the lowest-frequency mode could be used as a predictor for future plastic rearrangements in the disordered system jammed marginally.
文摘From a mixture of α-,β-and y-himachalenes extracted from waste wood of Atlas cedar(Cedrus atlantica),cadalene(1,6-dimethyl-4-isopropylnaphthalene)and iso-cadalene(1,6-dimethyl-3-isopropylnaphthalene)were produced in two steps with up to 71%±5%yield through the ar-himachalene intermediate using I2 and/or AlCl3 as reagents.The selectivity is shown to sharply depend on the operating conditions:while I2/AlCl3 in dichloromethane promotes the formation of cadalene,the formation of iso-cadalene is favored in the presence of AlCl3 in cyclohexane.The bicyclic aromatic compounds were thus obtained through unique rearrangements involving sequential C—C bond cleavage/fo rmation and hydride transfer processes.In the absence of AlCl3 or I2,dihydrocurcumene was also found to be formed with up to 70%selectivity.A tentative mechanism is proposed and discussed.
文摘We discovered a new approach modification Bamberger, Barton, Beckmann, Wallach, Gabriel, Hofmann, Hofmann A.W. Martius, Dimroth, Semmler-Wolff-Schroeter, Sus, Claisen, Newman-Kwart, Orlon, Pistschimuka, Robev, Smiles, Sawdey, Sommelet, Stevens, Tiemann, Fischer-Hepp, Chapman, Chattaway, Schonberg, Stieglitz Rearrangements with of phosphorous, arsine, stibine and bismuthine in organometallic chemistry. The authors have proposed a new mechanism for possible reactions.
基金partially supported by CIGMH/FCM/UNL,under the project PEST-OE/SAU/UI0009/2011CMA/FCT/UNL,under the project PEst-OE/MAT/UI0297/2011.
文摘Chromosomal fragile sites (CFSs) are loci or regions susceptible to spontaneous or induced occurrence of gaps, breaks and rearrangements. In this work, we studied the data of 4535 patients stored at DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources). We mapped fragile sites to chromosomal bands and divided the 23 chromosomes into fragile and non-fragile sites. The frequency of rearrangements at the chromosomal location of clones found to be deleted or duplicated in the array/CGH analysis, provided by DECIPHER, was compared in Chromosomal Fragile Sites vs. non-Fragile Sites of the human genome. The POSSUM Web was used to complement this study. The results indicated 1) a predominance of rearrangements in CFSs, 2) the absence of statistically significant difference between the frequency of rearrangements in common CFSs vs. rare CFSs, 3) a predominance of deletions over duplications in CFSs. These results on constitutional chromosomal rearrangements are evocative of the findings previously reported by others relatively to cancer supporting the current line of evidence and suggesting that a common mechanism can underlie the generation of constitutional and somatic rearrangements. The combination of insights obtained from our results and their interrelationships can indicate strategies by which the mechanisms can be targeted with preventive medical interventions.
基金Supported by The Scientific Research Foundation of the Ministry of Health,China,the Medical and Health Science Foundation,Zhejiang Province,China,No.WKJ-2009-2-021
文摘AIM:To study the diagnostic value of immunoglobulin heavy chain(IgH)and T-cell receptorγ (TCR-γ)gene monoclonal rearrangements in primary gastric lymphoma(PGL).METHODS:A total of 48 patients with suspected PGL at our hospital were prospectively enrolled in this study from January 2009 to December 2011.The patients were divided into three groups(a PGL group,a gastric linitis plastica group,and a benign gastric ulcer group)based on the pathological results(gastric mucosal specimens obtained by endoscopy or surgery)and follow-up.Endoscopic ultrasonography(EUS)and EUSguided biopsy were performed in all the patients.The tissue specimens were used for histopathological examination and for IgH and TCR-γ gene rearrangement polymerase chain reaction analyses.RESULTS:EUS and EUS-guided biopsy were successfully performed in all 48 patients.In the PGL group(n=21),monoclonal IgH gene rearrangements were detected in 14(66.7%)patients.A positive result for each set of primers was found in 12(57.1%),8(38.1%),and 4(19.0%)cases using FR1/JH,FR2/JH,and FR3/JH primers,respectively.Overall,12(75%)patients with mucosal-associated lymphoid tissue lymphoma(n=16)and 2(40%)patients with diffuse large B-cell lymphoma(n=5)were positive for monoclonal IgH gene rearrangements.No patients in the gastric linitis plastica group(n=17)and only one(10%)patient in the benign gastric ulcer group(n=10)were positive for a monoclonal IgH gene rearrangement.No TCRgene monoclonal rearrangements were detected.The sensitivity of monoclonal IgH gene rearrangements was 66.7%for a PGL diagnosis,and the specificity was96.4%.In the PGL group,8(100%)patients with stage IIE PGL(n=8)and 6(46.1%)patients with stage IE PGL(n=13)were positive for monoclonal IgH gene rearrangements.CONCLUSION:IgH gene rearrangements may be associated with PGL staging and may be useful for the diagnosis of PGL and for differentiating between PGL and gastric linitis plastica.
基金Supported by The National Center for Global Health and Medicine
文摘Acquired immune deficiency syndrome (AIDS)-related lymphoma (ARL) remains the main cause of AIDS-related deaths in the highly active anti-retroviral therapy (HAART) era. Recently, rearrangement of MYC is associated with poor prognosis in patients with diffuse large B-cell lymphoma. Here, we report a rare case of gastrointestinal (GI)-ARL with MYC rearrangements and coinfected with Epstein-Barr virus (EBV) infection presenting with various endoscopic findings. A 38-yearold homosexual man who presented with anemia and was diagnosed with an human immunodeficiency virus infection for the first time. GI endoscopy revealed multiple dish-like lesions, ulcerations, bloody spots, nodular masses with active bleeding in the stomach, erythematous flat lesions in the duodenum, and multiple nodular masses in the colon and rectum. Magnified endoscopy with narrow band imaging showed a honeycomb-like pattern without irregular microvessels in the dish-like lesions of the stomach. Biopsy specimens from the stomach, duodenum, colon, and rectum revealed diffuse large B-cell lymphoma concomitant with EBV infection that was detected by high tissue EBV-polymerase chain reaction levels and Epstein-Barr virus small RNAs in situ hybridization. Fluorescence in situ hybridization analysis revealed a fusion between the immunoglobulin heavy chain (IgH) and c-MYC genes, but not between the IgH and BCL2 loci. After 1-mo of treatment with HAART and R-CHOP, endoscopic appearance improved remarkably, and the histological features of the biopsy specimens revealed no evidence of lymphoma. However, he died from multiple organ failure on the 139 th day after diagnosis. The cause of his poor outcome may be related to MYC rearrangement. The GI tract involvement in ARL is rarely reported, and its endoscopic findings are various and may be different from those in non-AIDS GI lymphoma; thus, we also conducted a literature review of GI-ARL cases.
基金supported by the Innovative Research Team in University of Sichuan Bureau of Education (No.14TD0002)the Scientific Research Fund of Sichuan Provincial Education Department (No.11ZA077)
文摘Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mitogenomic data sets from GenBank, we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae. The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement. Except for the genus Babina, the monophyly of each genus was well supported. The genus Amnirana occupied the most basal position among the Ranidae. The [Lithobates ＋ Rana] was the closest sister group of Odorrana. The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high, with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types. Some taxa owned their unique gene rearrangement characteristics, which had significant implication for their phylogeny analysis. All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.
基金financial support of this work by the Swedish Research Council(2017-00935)Swedish Energy Agency and Knut and Alice Wallenberg Foundation(KAW 2016.0072)。
文摘Numerous aspects of the water oxidation mechanism in photosystemⅡhave not been fully elucidated,especially the O-O bond formation pathway.However,a body of experimental evidences have identified the O5 and W2 ligands of the oxygen-evolving complex as the highly probable substrate candidates.In this work,we studied O-O bond formation between O5 and W2 based on the native Mn4 Ca cluster by density functional calculations.Structural rearrangements before the formation of the S_(4) state were found as a prerequisite for O-O bond formation between O5 and W2,regardless if the suggested pathways involving the typical Mnl(Ⅳ)-O·species or the recently proposed Mn4(Ⅶ)(O)2 species.Possible alternatives for the S2→S_(3) and S_(3)→S_(4) transitions accounting for such required rearrangements are discussed.These findings reflect that the structural flexibility of the Mn4 Ca cluster is essential to allow structural rearrangements during the catalytic cycle.
基金This work was funded in part by NSF(DMR-0084301)Eastman Kodak Company.
文摘The time evolution of oxygen plasma treated polystyrene(PS)surfaces was investigated upon storing them in theair under controlled humidity conditions.The methods of water contact angle,X-ray photoelectron spectroscopy(XPS),sumfrequency generation(SFG)vibrational spectroscopy,and atomic force microscopy(AFM)were used to infer the surfaceproperties and structure.Chemical groups containing oxygen were formed on the PS surface with the plasma treatment,demonstrated by water contact angle and XPS.The surface polarity decayed markedly on time,as assessed by steady increasein the water contact angle as a function of storage time,from zero to around 60°.The observed decay is interpreted as arisingfrom surface rearrangement processes to burying polar groups away from the uppermost layer of the surfaces,which is incontact with air.On the other hand,XPS results show that the chemical composition in the first 3 nm surface layer isunaffected by the surface aging,and the depth profile of oxygen is essentially the same with time.A possible change of PSsurface roughness was examined by AFM,and it showed that the increase of water contact angle during surface aging couldnot be attributed to surface roughness.Thus,it is concluded that surface aging is attributable to surface reorganization andthe motion of oxygen containing groups is confined within the XPS probing depth.SFG spectroscopy,which is intrinsicallyinterface-specific,was used to detect the chemical structure of PS surface at the molecular level after various aging times.The results are interpreted as follows.During the aging of the plasma treated PS surfaces,the oxygen containing groupsundergo reorientation processes toward the polymer bulk and/or parallel to the surface,while the CH_2 moiety stands up onthe PS surface.Our results indicate that the surface configuration changes do not require large length scale segmentalmotions or migration of macromolecules.Motions that are responsible for surface configuration changes could be relativelysmall rotational motions.The aging behaviors under different relative humidity conditions were shown to be similar from18% to 91%,whereas the kinetics of surface polarity decays were faster in higher relative humidity.Here,the surfacerearrangement of polystyrene films that were previously treated by oxygen plasma and aged,and was investigated in terms ofcontact angle after the water immersion.The contact angles of the water-immersed samples were found to change andapproach the initial values before the immersion asymptotically.
文摘The gene rearrangement of βand γchain of T-cell receptors (TCR) was detected in 13 cases of non-Hodgkin's lymphoma with T-cell immunophenotype with Southern blot and PCR. Clonally rearranged.TCR βgene was seen in 11 cases out of the 13 and rearranged TCR γgene in 12. These facts suggest that clonal rearrangement of antigen receptors is a sensitive and specific marker to establish the T-cell monoclonality and lineage and a useful adjunct to morphological diagnosis and immunophenotyping.
基金supported by the National Natural Science Foundation of China(22171215,22301225,22471203)the Hubei Provincial Outstanding Youth Fund(2022CFA092)+1 种基金the Hubei Provincial Natural Science Foundation(2023AFB034)the Guangdong Basic and Applied Basic Research Foundation(2022A1515110113)。
文摘Skeleton diversity is an important feature of compound libraries and plays a key role in the success of biological screening.Ligand-controlled divergent synthesis can transform the same substrate into different molecular skeletons,which not only can endow compound libraries with diverse biological activities but also reveal new catalytic modes,and therefore has received extensive attention.Herein,we disclose a Ni-catalyzed,ligand-controlled switchable skeletal rearrangement reaction of acryloyl o-bromobenzamides and activated alkenes.In this protocol,modification of the ligand backbone allows the conversion of the same starting material into four structurally distinct scaffolds of pharmacological importance.Specifically,the use of terpyridine ligand favors the 6-exo cyclization and subsequent 1,2-acyl/Ni dyotropic rearrangement to generate highly functionalized cyclohexenols,while the sterically hindered ^(iPr)PDI ligand facilitates the 6-exo cyclization and subsequent 1,2-aryl/Ni dyotropic rearrangement to form highly functionalized cycloheptenols.Furthermore,isoquinoline-1,3-diones were obtained through alkene diarylation in the absence of additional activated alkenes.More strikingly,the bidentate ligand promotes nucleophilic addition of the aryl halides to the amide carbonyl,followed by 1,4-acyl transfer and cross-coupling to afford 2-benzazepin-5-ones.
基金supported in part by NSF(Grant No.DMS-9970687)SECTyP-UNCuyo,Argentina(Res.3853/16-R)
文摘In this paper we extend the notion of rearrangement of nonnegative functions to the setting of Carnot groups. We define rearrangement with respect to a given family of anisotropic balls Br , or equivalently with respect to a gauge‖x‖, and prove basic regularity properties of this construction. If u is a bounded nonnegative real function with compact support, we denote by u*its rearrangement. Then, the radial function u* is of bounded variation. In addition, if u is continuous then u* is continuous, and if u belongs to the horizontal Sobolev space W 1,ph , then Dhu*(x)/Dh( ‖x‖ )| is in Lp. Moreover, we found a generalization of the inequality of P(o)lya and Szeg(o) ∫|Dhu*|p/Dh(‖x‖)|pdx≤C ∫|Dhu|pdx,where p ≥ 1.
基金supported by the Goiás Research Foundation-FAPEG.
文摘Flow through a narrow bent channel may induce topological rearrangements in a twodimensional monodispersed dry liquid foam.We use the Cellular Potts Model to simulate a foam under a variable driving force in order to investigate the strain-rate response from these rearrangements.We observe a set of foams’behaviors ranging from elastic,viscoelastic to fluid regime.Bubble’s topological rearrangements are localized and their cumulative rearrangements change linearly with time,thus nonavalanches critical behavior is found.The strain-rate affects the rate of topological rearrangements,its dependence on the drag force is nonlinear,obeying a Herschel–Bulkley-like relationship below the foam’s flow point.
文摘In this paper we study linear secret sharing schemes by monotone span programs, according to the relation between realizing access structures by linear secret sharing schemes and computing monotone Boolean functions by monotone span programs. We construct some linear secret sharing schemes. Furthermore, we study the rearrangements of access structures that is very important in practice.
基金supported by the Natural Science Foundation of China (31772428)Young Elite Scientists Sponsorship Program by CAST (2017QNRC001)+1 种基金Fundamental Research Funds for the Central Universities (201841013) to Feng Gaothe AREA award from the National Institutes of Health (1R15GM11317701) to Laura A. Katz
文摘Some of the most extreme genome wide rearrangements are found in ciliates, which are unique in possessing both germline micronucleus and somatic macronucleus in every cell/organism. A series of DNA rearrangement events, including DNA elimination, chromosomal fragmentation, gene unscrambling and alternative processing, happen during macronuclear development. To assess the molecular evolution of macronuclear and germline-limited sequences in different cryptic species of Chilodonella uncinata, we characterized the actin, α-tubulin and β-tubulin genes in the micronucleus and macronucleus genomes of USA-SC2 strain and compared them with other strains(i.e. cryptic species). Three main results are:(i) rearrangement patterns between germline and soma are conserved for each gene among the cryptic species of C. uncinata;(ii) in contrast, the germlinelimited regions are highly divergent in sequence and length among the cryptic species;(iii) pointer shifting is frequent among the cryptic species. We speculate that pointer sequences may serve as the buffer between the conserved macronuclear destined sequences and rapidly-evolving internal eliminated sequences. The data combined with previous studies demonstrate the plasticity of gene rearrangement among different groups of ciliates and add to the growing data for the role of genome rearrangements in species differentiation.
基金supported by grants from the National Basic Research Program of China(2011CBA01103)the National Natural Science Foundation of China(31171254)the Fundamental Research Funds for Central Universities(WK2060190018)
文摘Most eukaryotes employ a variety of mechanisms to defend the integrity of their genome by recognizing and silencing parasitic mobile nucleic acids.However,recent studies have shown that genomic DNA undergoes extensive rearrangements,including DNA elimination,fragmentation,and unscrambling,during the sexual reproduction of ciliated protozoa.Non-coding RNAs have been identified to program and regulate genome rearrangement events.In Paramecium and Tetrahymena,scan RNAs(scnRNAs)are produced from micronuclei and transported to vegetative macronuclei,in which scnRNA elicits the elimination of cognate genomic DNA.In contrast,Piwi-interacting RNAs(piRNAs)in Oxytricha enable the retention of genomic DNA that exhibits sequence complementarity in macronuclei.An RNA interference(RNAi)-like mechanism has been found to direct these genomic rearrangements.Furthermore,in Oxytricha,maternal RNA templates can guide the unscrambling process of genomic DNA.The non-coding RNA-directed genome rearrangements may have profound evolutionary implications,for example,eliciting the multigenerational inheritance of acquired adaptive traits.
