Few tools of gene editing have been developed in Bacillus licheniformis at present. In order to enrich the tools, an FLP/FRT gene editing system that can repeatedly use a single selectable marker was constructed in Bacillus licheniformis, and the system was verified by knocking out an alpha amylase gene (amyL), an protease gene (aprE) and knocking in an exogenous Vitreoscilla hemoglobin gene (vgb). First, knock-out plasmids pNZTT-AFKF of amyL and pNZTT-EFKF of aprE were constructed using thermosensitive plasmid pNZT1 as a carrier. The two knock-out plasmids contained respective homology arms, resistance genes and FRT sites. Then the knock-out plasmids were transformed into Bacillus licheniformis and the target genes were replaced by respective deletion cassette via twice homologous exchange. Finally, an expression plasmid containing FLP recombinase reading frane was introduced and mediated the excision of resistance marker. In order to expand the practicability of the system, knock-in plasmid pNZTK-PFTF-vgb was constructed, with which knock-in of vgb at pflB site was carried out successfully. The results showed that amyL and aprE were successfully knocked out and the marker kanamycin cassette exactly excised. The activities of amylase and protease of deletion mutants were reduced by 95.3% and 80.4% respectively. vgb was successfully knocked in at pflB site and the marker tetracycline cassette excised. The expression of integrated vgb was verified via real-time PCR. It is the first time to construct an FLP/FRT system for gene editing in Bacillus licheniformis, which could provide an effective technical means for genetic modification.
Bacillus licheniformis ; Gene Editing ; Plasmids ; Sequence Deletion

To investigate the frequency of RHD 1227A allele in Rh negative population and random population, an AS-PCR (allele specific-polymerase chain reaction) method was employed to detect RHD 1227A allele. RHD gene copy was determined by D zygosity test and RHD exon 9 nucleotide sequence analysis. The results showed that among 143 Rh negative donors, forty-one RHD 1227A allele carriers were detected, and 8 (19.51%) out of which were RhCCdee, 32 (78.05%) were RhCcdee, and 1 (2.44%) was RhCcdEe. Thirty-five Rh negative RHD 1227A carriers had RHD gene deletion, and the remaining carriers were RHD 1227A homozygous. Seven (1.43%) individuals were detected with RHD 1227A allele among 489 random donors. They were all G/A heterozygous at RHD 1227 site. Serological test indicated that they were normal Rh positive phenotype. It is concluded that the frequency of RHD 1227A allele is 16.43% among Rh negative population and 0.72% among the random population.
Asian Continental Ancestry Group ; genetics ; Base Sequence ; China ; Chromosome Deletion ; Cloning, Molecular ; Gene Deletion ; Gene Frequency ; genetics ; Humans ; Molecular Sequence Data ; Polymorphism, Genetic ; Rh-Hr Blood-Group System ; genetics ; immunology ; Sequence Analysis, DNA

OBJECTIVETo study the mechanisms of dystrophin gene deletion by cloning and sequencing the junction fragment of dystrophin gene with exons 3 to 5 deletion.

METHODSPCR was performed to verify dystrophin gene exons 3 to 5 deletion in a patient with Duchenne muscular dystrophy. A PCR-based genome-walking method was used to localize the breakpoint in introns 2 and 5, and the deletion-junction fragment was directly amplified by PCR approach with forward and reverse primers annealing to a DNA sequence as close as possible to the breakpoint in the introns 2 and 5. The sequencing result of the deletion-junction fragment was compared with the normal intron sequences.

RESULTSA sequence of 2113 bp containing the junction fragment was obtained. The 5' breakpoint was located in SINE/Alu element of intron 2, and the 3' breakpoint was located in the unique sequence near the sequence TTTAAA. The breakpoints were associated with a strong topoisomerase II cleavage site. A 26-bp fragment was inserted into the breakpoint and formed 3 duplications (GGCTTATATTTAA) of 13 bp around the deletion-junction fragment.

CONCLUSIONRepeat sequence and strong topoisomerase II cleavage site around the breakpoint may predispose double-strand DNA breaks and recombination, which, in addition to the nonhomologous end-joining mechanism, may contribute as important factors to the gene deletion.

Adult ; Base Sequence ; Chromosome Breakage ; Cloning, Molecular ; Dystrophin ; genetics ; Exons ; genetics ; Gene Deletion ; Humans ; Male ; Molecular Sequence Data ; Muscular Dystrophies ; genetics ; pathology ; Polymerase Chain Reaction ; Sequence Analysis, DNA

Choriocarcinoma/pathology* ; Female ; Gene Deletion ; Humans ; PTEN Phosphohydrolase/genetics* ; Pregnancy ; Sequence Deletion ; Stomach Neoplasms/surgery*

The objective of this study was to elucidate the cause of the spermatogenic defect in idiopathic azoospermia and non-mosaic type of Klinefelter syndrome. Genomic DNAs from 9 cases of Korean idiopathic azoospermia and 6 of Korean non-mosaic type of Klinefelter syndrome were used for the detection of Y chromosome microdeletions by polymerase chain reaction using 60 primers. Microdeletions of the Y chromosome were found in 1 of 9 (11.1%) patients with idiopathic azoospermia, whereas none was deleted in non-mosaic type of Klinefelter syndrome. This result suggests that Y chromosome microdeletions could be one of the etiologic factors in idiopathic azoospermia.
Gene Dosage ; Human ; Klinefelter Syndrome/classification/*genetics ; Male ; Oligospermia/classification/*genetics ; Polymerase Chain Reaction ; *Sequence Deletion ; Sequence Tagged Sites ; Spermatogenesis ; X Chromosome/genetics ; Y Chromosome/*genetics

OBJECTIVETo determine microdeletion loci and the characteristic of Y chromosome azoospermia factor(AZF) associated with Chinese idiopathic azoospermia or severe oligozoospermia and hence to provide a theoretic basis for gene diagnosis of AZF microdeletion in Chinese infertility men.

METHODSThe subjects of this study included 134 cases of azoospermia and 118 severe oligozoospermia, and 210 healthy male controls. With multiplex PCR technique, an analysis of 15 sequence tag sites(STS) in AZFa, AZFb and AZFc microdeletion was performed.

RESULTSNo microdeletion was detected in controls whereas 13 STS loci microdeletions existed in cases, including sY84 and sY86 in AZFa; sY121, sY123, sY124, sY127, sY134 and sy133 in AZFb; sY152, sY242, sY254, sY255 and sY157 in AZFc. Five azoospermia patients were involved in AZFa microdeletions, 7 azoospermia and 3 severe oligozoospermia patients in AZFb, and 14 azoospermia and 18 severe oligozoospermia patients in AZFc. The prevalence rates of microdeletion in AZFa, AZFb and AZFc were 2.0%,4.0% and 12.7% respectively. The microdeletion rate showed statistically significant difference between the cases and controls.

CONCLUSIONThis study revealed an association between the microdeletion of 13 STS loci of AZF region and the idiopathic azoospermia or severe oligozoospermia in Chinese. There is no evidence to identify the genetic polymorphism of the above STS loci. The frequency and distribution characteristic of AZF microdeletion are similar to those of Caucasians. As candidate loci the 13 STS are useful in clinical gene diagnosis for the detection of AZF microdeletion in Chinese idiopathic azoospermia and severe oligozoospermia.

China ; epidemiology ; Chromosome Deletion ; Chromosomes, Human, Y ; genetics ; DNA ; genetics ; Electrophoresis, Agar Gel ; Female ; Gene Deletion ; Genetic Loci ; Humans ; Infertility, Male ; genetics ; pathology ; Male ; Molecular Epidemiology ; Oligospermia ; epidemiology ; genetics ; pathology ; Seminal Plasma Proteins ; genetics ; Sequence Tagged Sites

OBJECTIVETo detect subtelomeric rearrangement in patients with idiopathic mental retardation/developmental delays (MR/DD) and to provide new methods and evidence for the etiologic diagnosis of MR/DD in China.

METHODS1.

INCLUSION CRITERIA(1) Moderate to severe MR/DD; (2) no definite perinatal brain injury; (3) no toxication, hypoxia, infection of central nervous system and cranial trauma; (4) routine karyotyping is normal; (5) no evidence of typical inherited metabolic disorder or specific neurodegenerative disorders from cranial neuro-imaging and blood/urinary metabolic diseases screening; (6) no mutation of FMR1 gene in male patients plus one of the following criteria: (1) positive family history of MR; (2) positive family history of miscarriages and perinatal deaths; (3) abnormal growth; (4) facial and non-facial dysmorphism. 2. Multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) were applied to detect subtelomeric rearrangements in patients and their parents.

RESULTSFour cases were identified from 39 selected cases with subtelomeric rearrangements (10%), including der (2) t (2; 4) (pter; pter), 11qter del, 8pter del, and 15p11.2 del. The first two abnormalities of chromosome subtelomeric regions have not been reported yet. All these cases had some small dysmorphologies, such as microcephaly, hypertelorism, low nasal bridge, and three of them had hypotonia. One case had recurrent seizure and abnormal behavior (laughter not associated with happiness), and another case with dysgenesis of corpus callosum and septum pellucidum. Family and perinatal histories were normal for all cases. All chromosome rearrangements were de novo which were not from the parents with normal phenotype. It indicated that all these abnormal rearrangements should be responsible for the mental retardation phenotype of these patients. The phenotype of case 4 was similar to Angelman syndrome, his deletion was actually a kind of interstitial rearrangements. It will be confirmed by DNA methylation test to determine whether the deleted allele was of maternal origin.

CONCLUSIONSThe subtelomeric rearrangements were found in 10% patients with idiopathic MR. It indicated that subtelomeric rearrangements should be one of major reasons of MR/DD related to genetic factors. Two novel subtelomeric rearrangements were identified. These de novo rearrangements are probably disease related, because they are not inherited from their parents with normal phenotype. The detection should be carried out for all the patients with idiopathic MR/DD with unknown origin, because one cannot figure out the specific signs for subtelomeric rearrangements. Sequentially use of MLPA and FISH is a more efficient and economic method to detect the subtelomeric rearrangements.

Adolescent ; Child ; Child, Preschool ; Chromosome Structures ; DNA Probes ; Female ; Gene Rearrangement ; Humans ; In Situ Hybridization, Fluorescence ; Infant ; Intellectual Disability ; genetics ; Male ; Mutation ; Sequence Deletion ; Telomere ; genetics

UNLABELLEDTo screen and analyze the apoptosis- and proliferation-related genes in human nasopharyngeal carcinoma (NPC).

METHODSAccording to gene ontology classification, the abnormal expressions of the genes related to cell apoptosis and proliferation were identified in the NPC gene chip data. The cell apoptosis- and proliferation-related genes expressed in each of the 3 stages, as defined by the tree model for the pathogenesis and progression of NPC, were screened, and with literature review, their distribution in the tree model were analyzed.

RESULTSNineteen genes related to cell apoptosis were found in NPC, among which 9 were down-regulated (such as DNASE1L3) and located in the chromosome deletion regions, and 10 were up-regulated (such as DEDD) in the chromosome amplification regions. Twenty-one cell proliferation-related genes were identified, including 8 down-regulated genes (such as TUSC2) in the chromosome deletion regions and 13 up-regulated ones (such as EMP1) in the chromosome amplification regions. In the chromosome deletion regions, the down-regulated cell apoptosis-related genes participated mostly in inducing and regulating cell apoptosis, and the up-regulated cell proliferation-related genes in the chromosome amplification regions were mostly associated with the positive regulation of cell proliferation.

CONCLUSIONNPC occurs possibly through two pathways by inhibiting cell apoptosis or by promoting excessive cell proliferation.

Apoptosis ; genetics ; Cell Proliferation ; Chromosome Deletion ; Down-Regulation ; Gene Expression Profiling ; Humans ; Nasopharyngeal Neoplasms ; genetics ; pathology ; Oligonucleotide Array Sequence Analysis ; Up-Regulation

OBJECTIVE: To provide genetic testing for two brothers with mental retardation and epilepsy. METHODS: Array comparative genomic hybridization (aCGH) was used to detect copy number variations in the two patients, their parents and maternal grandparents. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) was utilized to delineate the deleted region in the pedigree. RESULTS: A 138 kb deletion in 15q11.2 region was detected by aCGH in both patients, which encompassed part of the UBE3A gene. MS-MLPA has narrowed down the region to exons 8 to 14 of the UBE3A gene. The same deletion was also found in their mother and grandfather. CONCLUSION The pathogenesis of this rare form of recurrent Angelman syndrome may be attributed to the partial deletion of maternal UBE3A gene.
Angelman Syndrome ; Comparative Genomic Hybridization ; DNA Copy Number Variations ; Female ; Gene Deletion ; Humans ; Male ; Sequence Deletion ; Ubiquitin-Protein Ligases

OBJECTIVETo investigate the polymorphism of mitochondrial DNA region V in Bouyei people and Miao people living in Guizhou province of China.

METHODSPolymerase chain reaction and direct sequencing were used in the study.

RESULTSOnly two kinds of polymorphism were found in Bouyei and Miao people. One was standard pattern, the other short pattern. And the frequencies of short pattern(9 bp deletion) in Bouyei and Miao people were 31.1% and 33.3% respectively.

CONCLUSIONThe polymorphisms of mitochondrial DNA region V in Bouyei people and Miao people living in Guizhou province of China are similar, but they are different from those in other people.

Base Sequence ; China ; DNA, Mitochondrial ; chemistry ; genetics ; Female ; Gene Frequency ; Humans ; Male ; Polymorphism, Genetic ; genetics ; Sequence Analysis, DNA ; Sequence Deletion