Sequence Mutation of Exon 7 of Badh2 Gene and Aroma Identification of Fragrant Rice Varieties

In this study,we performed amplificaion and sequence analysis of exon7 of gene Badh2 of 12 fragrant rice materials,and identified the aroma of fragrant rice materials by the method of seed chewing and KOH soaking,so as to analyze the sequence mutation of exon 7 in the Badh2 gene of rice material and its corresponding relation with the flavor character.The results showed that an 8 bp deletion(aaaa--t---ggc)and a mutation of SNP(g→t)in exon 7 of Badh2 gene were found in 10 materials,including Xiangnuo,Lvjinxiang,Meixiangzhan 2,Huaxiang,Yuexiangxuan 1,Hongyuxiang,Meixiangxuan 1,Baxiangxuan 1,Taixiangxuan 1,Taixiangxuan 2.This mutation was consistent with the mutation of EU155083 sequence in GenBank and was reported for the first time in Chinese rice materials.In these 10 fragrant rice materials with mutation,Huaxiang and Meixiangxuan 1 were identified as the heterozygote genotype,and Hongyuxiang was identified as non-fragrant rice,so the sequence mutation in exon 7 of Badh2 gene in fragrant rice materials did not correspond to aroma traits one by one;and 7 materials were identified as fragrant rice,and the brown rice of Meixiangzhan 2 and Yuexiangyuan 1 had sweet taste.The results could provide a reference for the research on the genetic mechanism of rice aroma character and the promotion of fragrant rice varieties.

The mutation sequence of earth resistivity and earthquakes

Large amount of practically-observed iata were analyzed hased on the principles of fracture mechanics, and it was found that the mutation of earth resistivity was, to a certain extent, corrrelated with the rupture of media. Among the mutation sequences before most strong and moderate earthquakes had generally a relatively obvious maximum mutation. An approximately linear relation was found between the interval from starting of the maximum mutation to the occurrence of an earthquake and the magnitude and the epicentral distance of the earthquake. Furthermore, such a mutation showed a tendency to radiate from the epicenter to the peripheral areas. It is thus thought to be possible to use the mutation sequence to predict earthquakes. Finally, the paper also unfolds discussions on a number of practical problems in the earthquake prediction practice.

Nef Mutations in Long-term Non-progressors from Former Plasma Donors Infected with HIV-1 Subtype B in China

Objective To study the specific amino acid variation in Nef that may be related to disease progression after infection with HIV-1 subtype B, a predominant strain circulating in China, and to determine whether changes in Nef secondary structure may influence different stages of AIDS development based on the concept that the Nef gene of HIV infection dramatically alter the severity of viral infection and virus replication and disease progression, and that long-term non-progressors （LTNP） of HIV infection are commonly associated with either a deletion of the Nef gene or the defective Nef alleles. Methods The study subjects were divided into LTNPI（n=14）, LTNP2 （n=16） and slow progressor （SP, n=19） groups for mutational analysis of the Nef sequence. The data were obtained by using Bioedit, MEGA, Anthewin and SAS software. Results Residues in Nef TA48/49 and K151 occurred more frequently in the LTNP group while AA48/49 was more frequently observed in the SP group. Of the differences observed in the secondary structure comparison using Nef consensus sequences of these three groups, one was roughly corresponding to the Nef48/49 mutation site. Conclusion TA48/49, Kiss, and AA48/49 in the Nef gene might be associated with the different stages of HIV infection, and there may be a link between the Nef secondary structure and the progression of HIV- 1 infection.

Genetical Study of Mutation in Maternal-fetal ABO Incompatibility

This study looked into a family involving a rare mother-child ABO blood type inconsistency and explored its genetic and molecular basis. In the family, the mother had type AB blood and the father was blood type B and they gave birth to a baby of blood type O. Their blood types were phenotypically identified by using different techniques, including micro-column gel test, immune inhibition test, absorption and elution tests. The sequences of all 7 exons of ABO allele from the core family members were determined by using PCR and clone-based sequencing. The loci of mutated gene were compared against normal human genes. The result showed that the mother＇s erythrocytes were agglutinable with monoclonal anti-A antibody（2＋） and had agglutination reaction with anti-B antibody（4＋）. The mother＇s serum registered agglutination action with standard blood type A cells. The findings showed an ABO inconsistency. When domestic antibodies were used, the mother＇s erythrocytes yielded agglutination reaction with humanized anti-B serum（4＋） and anti-B monoclonal antibody but were non-agglutinable with humanized anti-A serum and anti-A monoclonal antibody. Upon absorption and elution, the titer of anit-A antibody was 128 both before and after the absorption test, with no significant difference found between pre- and post-absorption values. Our results confirmed that the mother＇s allelic gene was type B and contained type A. The father＇s blood type was type B, and son＇s blood type was type O. Clone-based sequencing revealed that the mother carried a heterozygous gene of B101.01（nt A640→G）/O01, which contained an M214→V mutation that could express a weak expression of antigen A, resulting in blood type AB. However, their son did not have the M214→V mutation, which yielded a false ABO-inconsistency between him and his mother. We were led to conclude that type B gene with a M214→V mutation can encode both antigen B and weak antigen B that can lead to false ABO-inconsistencies.

Whole exome sequencing identifies an AMBN missense mutation causing severe autosomal-dominant amelogenesis imperfecta and dentin disorders

Tooth development is a complex process that involves precise and time-dependent orchestration of multiple genetic, molecular,and cellular interactions. Ameloblastin(AMBN, also named "amelin" or "sheathlin") is the second most abundant enamel matrix protein known to have a key role in amelogenesis. Amelogenesis imperfecta(AI [MIM: 104500]) refers to a genetically and phenotypically heterogeneous group of conditions characterized by inherited developmental enamel defects. The hereditary dentin disorders comprise a variety of autosomal-dominant genetic symptoms characterized by abnormal dentin structure affecting either the primary or both the primary and secondary teeth. The vital role of Ambn in amelogenesis has been confirmed experimentally using mouse models. Only two cases have been reported of mutations of AMBN associated with non-syndromic human AI. However, no AMBN missense mutations have been reported to be associated with both human AI and dentin disorders.We recruited one kindred with autosomal-dominant amelogenesis imperfecta(ADAI) and dentinogenesis imperfecta/dysplasia characterized by generalized severe enamel and dentin defects. Whole exome sequencing of the proband identified a novel heterozygous C-T point mutation at nucleotide position 1069 of the AMBN gene, causing a Pro to Ser mutation at the conserved amino acid position 357 of the protein. Exfoliated third molar teeth from the affected family members were found to have enamel and dentin of lower mineral density than control teeth, with thinner and easily fractured enamel, short and thick roots, and pulp obliteration. This study demonstrates, for the first time, that an AMBN missense mutation causes non-syndromic human AI and dentin disorders.

Gene targeted and immune therapies for nodal and gastrointestinal follicular lymphomas

Follicular lymphoma(FL)is the most common indolent B-cell lymphoma(BCL)globally.Recently,its incidence has increased in Europe,the United States,and Asia,with the number of gastrointestinal FL cases expected to increase.Genetic abnormalities related to t(14;18)translocation,BCL2 overexpression,NF-κB pathway-related factors,histone acetylases,and histone methyltransferases cause FL and enhance its proliferation.Meanwhile,microRNAs are commonly used in diagnosing FL and predicting patient prognosis.Many clinical trials on novel therapeutics targeting these genetic abnormalities and immunomodulatory mechanisms have been conducted,resulting in a marked improvement in therapeutic outcomes for FL.Although developing these innovative therapeutic agents targeting specific genetic mutations and immune pathways has provided hope for curative options,FL treatment has become more complex,requiring combinatorial therapeutic regimens.However,optimal treatment combinations have not yet been achieved,highlighting the importance of a complete understanding regarding the pathogenesis of gastrointestinal FL.Accordingly,this article reviews key research on the molecular pathogenesis of nodal FL and novel therapies targeting the causative genetic mutations.Moreover,the results of clinical trials are summarized,with a particular focus on treating nodal and gastrointestinal FLs.

Acute myeloid leukemia in the era of precision medicine:recent advances in diagnostic classification and risk stratification

Acute myeloid leukemia(AML) is a genetically heterogeneous myeloid malignancy that occurs more commonly in adults, and has an increasing incidence, most likely due to increasing age. Precise diagnostic classification of AML requires clinical and pathologic information, the latter including morphologic, immunophenotypic, cytogenetic and molecular genetic analysis. Risk stratification in AML requires cytogenetics evaluation as the most important predictor, with genetic mutations providing additional necessary information. AML with normal cytogenetics comprises about 40%-50% of all AML, and has been intensively investigated. The currently used 2008 World Health Organization classification of hematopoietic neoplasms has been proposed to be updated in2016, also to include an update on the classification of AML, due to the continuously increasing application of genomic techniques that have led to major advances in our knowledge of the pathogenesis of AML. The purpose of this review is to describe some of these recent major advances in the diagnostic classification and risk stratification of AML.

Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach

In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.

Genetic Analysis of the PKHD1 Gene with Long-rang PCR Sequencing

PKHD1 gene mutations are found responsible for autosomal recessive polycystic kidney disease（ARPKD）. However, it is inconvenient to detect the mutations by common polymerase chain reaction（PCR） because the open reading frame of PKHD1 is very long. Recently, long-range（LR） PCR is demonstrated to be a more sensitive mutation screening method for PKHD1 by directly sequencing. In this study, the entire PKHD1 coding region was amplified by 29 reactions to avoid the specific PCR amplification of individual exons, which generated the size of 1 to 7 kb products by LR PCR. This method was compared to the screening method with standard direct sequencing of each individual exon of the gene by a reference laboratory in 15 patients with ARPKD. The results showed that a total of 37 genetic changes were detected with LR PCR sequencing, which included 33 variations identified by the reference laboratory with standard direct sequencing. LR PCR sequencing had 100% sensitivity, 96% specificity, and 97.0% accuracy, which were higher than those with standard direct sequencing method. In conclusion, LR PCR sequencing is a reliable method with high sensitivity, specificity and accuracy for detecting genetic variations. It also has more intronic coverage and lower cost, and is an applicable clinical method for complex genetic analyses.

Exome sequencing identifies compound heterozygous PKHD1 mutations as a cause of autosomal recessive polycystic kidney disease

Background Autosomal recessive polycystic kidney disease （ARPKD） is a rare inherited disease, which is a disorder with multiple organ involvement, mainly the kidney and liver. It is caused by mutations in the PKHD1 gene. Here, we reported the clinical characteristics of a case with ARPKD and analyze the genetic features of this patient as well as of his father using targeted exome sequencing and Sanger sequencing. Methods Genomic DNA was extracted from peripheral blood leukocytes obtained from a patient with ARPKD. The mutations were identified using exome sequencing and confirmed by Sanger sequencing. Results The patient was diagnosed as ARPKD based on ultrasonography and abdominal computed tomography which showed polycystic changes, multiple calcinosis of both kidneys, and multiple dilated bile ducts of the liver. Compound heterozygous PKHD1 gene mutations A979G and G5935A, which lead to substitution of an asparagine for an aspartate at amino acid 327 （N327D） and a glycine for an arginine at amino acid 1979 （G1979R） respectively, were identified using targeted exome sequencing and confirmed by Sanger sequencing for the patient. In addition, the father of the patient was identified to be a carrier of heterozygous A979G mutation of this gene. Conclusions We identified that the compound heterozygous PKHD1 gene mutations are the molecular basis of the patient with ARPKD. Targeted exome sequencing is suitable for genetic diagnosis of single-gene inherited diseases like ARPKD in which the pathogenic gene is a large.

Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblasti

B-cell precursor acute lymphoblastic leukemia(BCP-ALL)is characterized by genetic alterations with high heterogeneity.Precise subtypes with distinct genomic and/or gene expression patterns have been recently revealed using high-throughput sequencing technology.Most of these profiles are associated with recurrent non-overlapping rearrangements or hotspot point mutations that are analogous to the established subtypes,such as DUX4 rearrangements,MEF2D rearrangements,ZNF384/ZNF362 rearrangements,NUTM1 rearrangements,BCL2/MYC and/or BCL6 rearrangements,ETV6-RUNX1-like gene expression,PAX5alt(diverse PAX5 alterations,including rearrangements,intragenic amplifications,or mutations),and hotspot mutations PAX5(p.Pro80Arg)with biallelic PAX5 alterations,IKZF1(p.Asn159Tyr),and ZEB2(p.His1038Arg).These molecular subtypes could be classified by gene expression patterns with RNA-seq technology.Refined molecular classification greatly improved the treatment strategy.Multiagent therapy regimens,including target inhibitors(e.g.,imatinib),immunomodulators,monoclonal antibodies,and chimeric antigen receptor T-cell(CAR-T)therapy,are transforming the clinical practice from chemotherapy drugs to personalized medicine in the field of risk-directed disease management.We provide an update on our knowledge of emerging molecular subtypes and therapeutic targets in BCP-ALL.

Conformer Analysis of a Biological G-Quadruplex Element in the Human c-MYC Promoter by Native Polyacrylamide Gel Electrophoresis

The G-quadruplexes undergo complex folding and conformation exchanges.G-quadruplex stability is substantially influenced by sequence,bufer and temperature.Mutational analysis together with nuclear magnetic resonance spectroscopy(NMR),X-ray crystallography and circular dichroism spectroscopy has been proved to be a powerful approach for G-quadruplex structural analysis.Herein,we used DNA sequence mutation and native polyacrylamide gel electrophoresis to investigate the topology and conformations of a G-quadruplex model molecule Pu18 found in the human c-MYC promoter.The guanines(G6,G9 or G18)which were not contributable to G-tetrad formation in c-MYC Pu18 sequence were mutated to thymine or adenine.We screened the buffer and temperature of gel electrophoresis for Pu18.Gel electrophoresis showed that two of the four conformers of c-MYC Pu18 in 100 mM K+buffer were resolved,which was in accordance with the conformations as determined by the 1 H NMR spectra in previous studies.This technique is expected as a general methodology for its easy operation and low cost to facilitate uncovering more yet unidentified G-quadruplex folds and functions,with the assistance of other analytical methods like NMR,X-ray crystallography and circular dichroism spectroscopy.

Clinical applications of MARSALA for preimplantation genetic diagnosis of spinal muscular atrophy

Conventional PCR methods combined with linkage analysis based on short tandem repeats （STRs） or Karyomapping with single nucleotide polymorphism （SNP） arrays, have been applied to preimplantation genetic diagnosis （PGD） for spinal muscular atrophy （SMA）, an autosome recessive disorder. However, it has limitations in SMA diagnosis by Karyomapping, and these methods are unable to distinguish wild- type embryos with carriers effectively. Mutated allele revealed by sequencing with aneuploidy and linkage analyses （MARSALA） is a new method allowing embryo selection by a one-step next-generation sequencing （NGS） procedure, which has been applied in PGD for both autosome dominant and X-linked diseases in our group previously. In this study, we carried out PGD based on MARSALA for two carrier families with SMA affected children. As a result, one of the couples has given birth to a healthy baby free of mutations in SMA-causing gene. It is the first time that MARSALA was applied to PGD for SMA, and we can distinguish the embryos with heterozygous deletion （carriers） from the wild-type （normal） ones accurately through this NGS-based method. In addition, direct mutation detection allows us to identify the affected embryos （homozygous deletion）, which can be regarded as probands for linkage analysis, in case that the affected family member is absent, In the future, the NGS-based MARSALA method is expected to be used in PGD for all monogenetic disorders with known pathogenic gene mutation.

Genetic studies of schizophrenia:an update

Schizophrenia（SCZ） is a complex and heterogeneous mental disorder that affects about 1% of global population. In recent years,considerable progress has been made in genetic studies of SCZ. A number of common variants with small effects and rare variants with relatively larger effects have been identifi ed. These variants include risk loci identifi ed by genome-wide association studies,rare copy-number variants identifi ed by comparative genomic analyses,and de novo mutations identified by high-throughput DNA sequencing. Collectively,they contribute to the heterogeneity of the disease. In this review,we update recent discoveries in the fi eld of SCZ genetics,and outline the perspectives of future directions.