非综合征型多数牙先天缺失家系中PAX9新突变的研究及PAX9突变导致非综合征型先天缺牙基因型—表型分析

目的 在中国多个非综合征型先天缺牙家系中鉴定PAX9突变,并研究PAX9突变导致非综合征型先天缺牙的基因型—表型关系,为先天缺牙基因诊断提供依据。方法 收集自2018年至2023年期间于河北医科大学口腔医院就诊的44例非综合征型多数牙缺失患者。采集先证者及其核心家系成员外周血进行全外显子组测序(WES),并用Sanger测序验证其突变,通过生物信息学工具对突变体进行了致病性分析和功能预测。在PubMed等检索出与先天缺牙相关PAX9突变的55篇文章共232例患者,分析PAX9突变基因型—表型关系。结果 在中国家庭中发现了一个新的PAX9基因移码突变c.447delG (p.Pro150Argfs*62)和一个已报道的PAX9基因错义突变c.406C>T (p.Gln136*)。通过生物信息学分析和三维结构建模,预测发现该移码突变具有致病性,突变导致PAX9蛋白提前终止,结构与功能受损严重。总结PAX9基因型—表型关系发现,携带PAX9突变的非综合征型先天缺牙患者最容易缺失第二磨牙。结论 发现非综合征型先天缺牙新的PAX9基因移码突变c.447delG(p.Pro150Argfs*62),扩展先天缺牙PAX9突变谱。非综合征型先天缺牙PAX9突变最易感牙位为第二磨牙,PAX9突变导致的乳牙缺失均为乳磨牙缺失。

Noonan综合征发病机制的研究进展

Noonan综合征(NS)是一种遗传异质性疾病,大约80%的NS发病机制与丝裂原活化蛋白激酶信号传导通路(RAS-MAPK)有关的基因突变相关,然而有近20%NS个体的潜在遗传病因尚无法解释,且各基因致病机制尚不清楚。目前尚无有效治疗NS的方案,仅以对症治疗为主。深入了解NS各基因的致病机制及相关的基因型—表型有助于找到潜在的治疗靶点。文章对NS发病机制做一综述,为治疗提供更多的研究方向。

Study on Genetic Diversity of Agronomic Traits and Genetic Relationships among Core Collections of Bitter Gourd

[Objective] This study aimed to investigate the genetic diversity of agronomic traits and genetic relationships among core collections of bitter gourd.[Method] Total 141 germplasms of bitter gourd were selected,and the genetic diversity of 13 agronomic traits was analyzed.In addition,total 46 core collections of bitter gourd were employed,and their genetic relationships were analyzed based on the phenotypic values and genotypic values of 5 agronomic traits,respectively.[Result] The genetic diversity analysis of agronomic traits showed that the genetic diversity indexes of the 4 qualitative traits of bitter gourd germplasms ranged from 0.46 to 1.34;the distribution of the 9 quantitative traits data was more dispersed with average coefficient of variation of 20.02%.The genetic relationship analysis showed that based on the phenotypic values and genotypic values of the 5 quantitative traits,the genetic distances among the 46 core collections of bitter gourd were different.Based on the genotypic values,the genetic distances among the 46 bitter gourd core collections ranged from 0.84 to 10.71.The 46 germplasms were divided into 17 groups with the rescaled distance of 8.5,which further classified the relationships among different germplasms.[Conclusion] This study will lay a solid foundation for the effective utilization of core collections and new variety breeding in bitter gourd.

Genotype phenotype classification of hepatocellular adenoma

Studies that compare tumor genotype with phenotype have provided the basis of a new histological/molecular classification of hepatocellular adenomas. Based on two molecular criteria （presence of a TCFI/HNF1α or β-catenin mutation）, and an additional histological criterion （presence or absence of an inflammatory infiltrate）, subgroups of hepatocellular adenoma can be defined and distinguished from focal nodular hyperplasia. Analysis of 96 hepatocellular adenomas performed by a French collaborative network showed that they can be divided into four broad subgroups： the first one is defined by the presence of mutations in TCF1 gene inactivating the hepatocyte nuclear factor 1 （HNF1α）, the second by the presence of β-catenin activating mutations; the category without mutations of HNF1α or β-catenin is further divided into 2 subgroups depending on the presence or absence of inflammation. Therefore, the approach to the diagnosis of problematic benign hepatocytic nodules may be entering a new era directed by new molecular information. It is hoped that immunohistological tools will improve significantly diagnosis of liver biopsy in our ability to distinguish hepatocellular adenoma from focal nodular hyperplasia （FNH）, and to delineate clinically meaningful entities within each group to define the best clinical management. The optimal care of patients with a liver nodule will benefit from the recent knowledge coming from molecular biology and the combined expertise of hepatologists, pathologists, radiologists, and surgeons.

Inheritance of Seed Color and Luster in Mungbean(Vigna radiata)

The inheritance of seed color and seed luster of mungbean was studied by using accessions/varieties with different seed color,black (Bkck),green (KPS1) and green (KPS2).In KPS2×Bkck combination,the p2 seed color was shiny black.The F3 data indicated the following genotype:3B-for black seed color,and 1 bb for green seed color.Plant purple petiole gene and black seed color gene were very close linkage.There was no segregation between them.Perhaps the same gene B controlled the color of purple petiole.Moreover in KPS1X Bkck combination F3 seed color popuktion showed a wide rang of phenotypic variability.Perhaps seed luster was controlled by more than two genes.

Clinical presentation and genotype of hepatitis delta in Karachi

AIM： To assess the clinical presentation and genotypes of delta hepatitis in local population. METHODS： In this prospective study, 39 consecutive patients who were positive for HBsAg and hepatitis D virus （HDV） antibody were included. The patients were divided in two groups on the basis of presence or absence of HDV RNA and a comparative study was done. Genotype of HDV was determined in PCR positive patients. RESULTS： Overall there is male dominance, in which 34 patients out of 39 （87.2%） were male. Twenty （51%） patients were from the adjacent areas of three provinces; Sindh, Punjab and Balochistan indicating the higher prevalence of delta hepatitis in this mid region of Pakistan. Patients of all age groups were affected with delta hepatitis （median 31.5 years, range 12-75）. HDV RNA was detectable in 23 patients （59%）. All the HDV strains belonged to genotype I. HBV DNA was detectable only in 3 cases who were also HBeAg and HDV RNA positive. Patients with detectable HDV RNA were younger than patients with undetectable RNA; mean age 29.7±12.8 years vs 36.8±15.2. There were no statistically significant differences in the clinical presentation and routine biochemical profile of patients with detectable or undetectable HDV RNA. Clinical cirrhosis was present in 19 （49%） patients; 12 with detectable RNA and 7 with undetectable HDV RNA （P = 0.748）. Decompensated disease was seen in eight patients; five and three respectively from each group. Four patients with undetectable RNA and two patients with detectable RNA had normal ALT and ultrasound abdomen. CONCLUSION： HDV may infect at any age, usually young adult males. Genotype I is prevalent. With time some of the patients become HDV RNA negative or asymptomatic carrier. Most of the patients have suppressed HBV DNA replication. Significant numbers of patients have cirrhosis.

Nucleoporin 88 expression in hepatitis B and C virus-related liver diseases

AIM: To investigate the expression of nucleoporin 88 (Nup88) in hepatitis B virus (HBV) and C virus (HCV)-related liver diseases. METHODS: We generated a new monoclonal Nup88 antibody to investigate the Nup88 protein expression by immunohistochemistry (IHC) in 294 paraffin-embedded liver specimens comprising all stages of hepatocellular carcinogenesis. In addition, in cell culture experiments HBV-positive (HepG2.2.15 and HB611) and HBV-negative (HepG2) hepatoma cell lines were tested for the Nup88 expression by Western-immunoblotting to test data obtained by IHC.RESULTS: Specific Nup88 expression was found in chronic HCV hepatitis and unspecific chronic hepatitis, whereas no or very weak Nup88 expression was detected in normal liver. The Nup88 expression was markedly reduced or missing in mild chronic HBV infection and inversely correlated with HBcAg expression. Irrespective of the HBV- or HCV-status, increasing Nup88 expression was observed in cirrhosis and dysplastic nodules, and Nup88 was highly expressed in hepatocellular carcinomas. The intensity of Nup88 expression significantly increased during carcinogenesis (P < 0.0001) and correlated with dedifferentiation (P < 0.0001). Interestingly, Nup88 protein expression was significantly downregulated in HBV-positive HepG2.2.15 (P < 0.002) and HB611 (P < 0.001) cell lines as compared to HBV-negative HepG2 cells. CONCLUSION: Based on our immunohistochemical data, HBV and HCV are unlikely to influence the expression of Nup88 in cirrhotic and neoplastic liver tissue, but point to an interaction of HBV with the nuclear pore in chronic hepatitis. The expression of Nup88 in nonneoplastic liver tissue might reflect enhanced metabolic activity of the liver tissue. Our data strongly indicate a dichotomous role for Nup88 in non-neoplastic and neoplastic conditions of the liver.

Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis

Carotenoids play an important role in many physiological processes in plants and the phytoene desaturase gene （PDS3） encodes one of the important enzymes in the carotenoid biosynthesis pathway. Here we report the identification and analysis of a T-DNA insertion mutant of PDS3 gene. Functional complementation confirmed that both the albino and dwarfphenotypes ofthepds3 mutant resulted from functional disruption of the PDS3 gene. Chloroplast development was arrested at the proplastid stage in thepds3 mutant. Further analysis showed that high level ofphytoene was accumulated in the pds3 mutant. Addition of exogenous GA3 could partially rescue the dwarf phenotype, suggesting that the dwarf phenotype ofthepds3 mutant might be due to GA deficiency. Microarray and RT-PCR analysis showed that disrupting PDS3 gene resulted in gene expression changes involved in at least 20 metabolic pathways, including the inhibition of many genes in carotenoid, chlorophyll, and GA biosynthesis pathways. Our data suggest that the accumulated phytoene in the pds3 mutant might play an important role in certain negative feedbacks to affect gene expression of diverse cellular pathways.

Phenotypic and Genotypic Comparison of Vibrio in Seawater Fish from Batam and Mataram, Indonesia

Grouper and snapper are the potential fishery commodity in Indonesia with a high economic value, as well as an export commodity. A common disease in grouper and snapper aquaculture is vibriosis. Vibriosis is a disease caused by bacteria of the genus Vibrio. The aim of study was to compare between phenotypic and genotypic identification of Vibrio isolated from Batam and Mataram, Indonesia. Bacteria were isolated from anterior kidney and eye of fish, then grown in thiosulfate-citrate-bile salts-sucrose （TCBS） and incubated in room temperature （25-28 ~C） for 24 h, and identified using morphology and biochemical test. Bacterial isolates were extracted, amplified and sequenced on 16S rRNA region. Phylogenetic tree of bacteria was constructed using neighbor-joining and maximum-parsimony methods. The phenotypic identification was found six isolates of Vibrio from Batam, such as K alginolyticus, V. carchariae, K damselae, V. fluvialis, V. furnissii and K parahaemolyticus. Three isolates were found from Mataram, such as 1I. alginolyticus, V. carchariae and V. fluvialis. Blast analysis showed isolates of V. alginolyticus_btm and V. carchariae_btm homolog to V. parahaemolyticus strain DAHMV3; isolates of V. damselae_btm and K alginolyticus_mtr homolog to V. neocaledonicus strain MS1; isolates of V. parahaemolyticus__btm and V. furnisii_btm homolog with Photobacterium damselae subsp, damselae strain： 04Ya311 and isolate of K fluvialis_mtr homolog to V. azureus strain MMRF532, respectively. All phenotypic identification was not supported by molecular identification on 16S rRNA region. It was suggested that phenotypic identification should be supported by molecular examination, especially in identification of Vibrio species.

Studies on the phenotypic and genotypic characteristics of SA14 wild Japanese encephalitis virus and its attenuated viruses

The aim of this study was to explore the molecular basis for the attenuation of the Japanese encephalitis vires （JEV） vaccine strain SA14-14-2. The virulence of SA14 wild Japanese encephalitis virus （JEV） and its several attenuated viruses was tested by intracerebral （i. c. ） or intraperitonial （i. p. ） inoculation of 10-12 g mice. The stability of neumattenuation was tested by one passage in suckling mouse brain. The E protein genes of those viruses were amplified by PCR, sequenced and compared. Three attenuated virus strains, SA14-14-2 vaccine virus, SA14-9-7 and SA14-5-3, did not exhibit lethal infections by i.c. or i.p. inoculation of 10-12 g mice and revert to the virulence. The other virus strain, SA14-12- 1-7, showed no neuminvasiveness by i.p. inoculation but residual neurovimlence by i.c. inoculation and reverted to high virulence after one brain passage. Comparison of the E protein gene sequences of the five virus strains indicated that there were differences of twelve nucleotides and eight amino acids between the parent strain SA14 and vaccine strain SA14-14-2, of which six amino acids （E-107, E-176, E-439, E-138, E-279, E-315） exhibited changes common to those of SA14-9-7 and SA14-5-3, three substitutions common to SA14-12-1-7. Two amino acid substitutions at the sites E177 （T→A） and E264 （Q→H） are unique to the SA14-14-2 vaccine virus. The results suggest that the mutations of E-107 （Leu→Phe）, E- 176 （Ile→Val）, and E-439 （Lys→Arg） may contribute for the attenuation of neuminvasiveness and partially for the attenuation of neumvirulence, the mutations of E-138, E-279, E-315 may not only critical to the neumattenuation but also to its stability.

The Hemochromatosis Distribution in Matera Province： A New SNP to Explain the Low Genotype-Phenotype Correlation

The present study aims to investigate the genotype-phenotype correlation of the hereditary hemochromatosis （HH）, a genetic disorder of iron metabolism, in Matera province （Basilicata, Italy）. Integrating both epidemiological and molecular approaches, the authors studied： （a） the frequency of the HH main mutations; （b） the association between mutations and HH cases. The majority of patients with HH are homozygous for the C282Y mutation of the HFE gene. A second mutation （H63D） is more widely distributed and its connection with HH isn＇t clear, but a low penetrance is attributed to this variant. The population-based study consists of three steps： （1） determination of iron biochemical parameters, （2） genetic test, and （3） sequencing of HFE gene and bioinformatics studies. A case report is presented in a 41-year-old male （genotype： H63D/wt） with biochemical and clinical evidences of HH, in absence of secondary iron overload factors. In the cohort of studied patients （150M：62F）, there are 18 homozygous patients; H63D/H63D genotype is found in 11 cases. In the heterozygous group, H63D/wt is the predominant genotype （61/68 subjects）. All the H63D/wt residents in the same village （Mont.） show altered biochemical parameter levels. In our case study, a substitution localized into the HFE promoter （nt225A 〉 C） is found. Results show that the H63D genotype is responsible for most cases of HH. The peculiar clinical manifestation found in Mont. suggests a founder effect. In our case, the iron overload is related to a presence of an undetected mutation, critical for the transcriptional regulation of the HFE gene.

Phenotypic and Genotypic Comparison of Pseudomonas stutzeri in Freshwater Fish in Indonesia

Pseudomonas stutzeri caused an outbreak of freshwater fish in Luwuk Banggai （tilapia and catfish）, Bali （tilapia）, Jambi （tilapia and catfish） and Tanjung Pinang （catfish）. The study was purposed to comprehensively identify special phenotypic and genotypic characteristics of P. stutzeri isolated from several areas in Indonesia, including its morphometric and biochemical characteristics and molecular variation. Bacteria were isolated from internal organs （kidney, ulcer and eye） of fish. They were then identified using morphology and biochemical test. DNA isolates were entirely extracted, amplified and reversed on 16S rRNA region, and further then were sequenced. Phylogenetic trees of bacteria were constructed using neighbor-joining and maximum-parsimony methods. The colony were similar, such as rod shape （Jambi, Tanjung Pinang, Bali）, bacil shape （Luwuk Banggai）, transparant in tryptic soy agar （TSA） （Luwuk Banggai）, creamy beige in glutamate starch phenol red （GSP） （Bali）, gram negative, motile, no reaction in the oxidative-fermentative test, positive result in catalase and oxidase test, negative in lysine decarboxylase and ornithine decarboxylase test and positive result in indole test; gelatin was degraded （only Bali）, urea was not degraded, no color change in Methyl-red and Voges-proskaeur （MR-VP） test; acid not produce from glucose, inositol or sucrose. Citrate was utilized by some isolates： positive （Jambi, Tanjung Pinang） and negative （Bali, Luwuk Banggai）. Results showed us that isolates of Jambi, Bali and Tanjung Pinang were monophyletic species with P. stutzeri $8 and ZH-1 comparing to gen bank. However, merely phenotypic analysis among Pseudomonas sp. was confused compared to each other.

Analysis of genotypes and phenotypes in Chinese children with tuberous sclerosis complex

Tuberous sclerosis complex(TSC) is a neurocutaneous syndrome with serious clinical presentations, an autosomal dominant genetic disorder involving multiple organs and systems. We retrospectively investigated the clinical manifestations and genotypes of 20 Chinese children with TSC to enable informed diagnostic and surveillance recommendations in China. A retrospective analysis of clinical manifestations in 20 children(7.00±5.30 years old) with TSC was conducted. A genetic testing of the genes TSC1 and TSC2 was performed in 14 children.The earliest manifestations of TSC were skin lesions(80% of patients) and seizures(75%). Fourteen of the children presented with retinal hamartomas, and 2 of these underwent eye enucleation at other hospitals through misdiagnosis. On magnetic resonance imaging, 18 children exhibited subependymal nodules, and 16 ones showed cortical nodules. 5 cases of non-renal hamartomas, 5 cases of multiple renal cysts, and 5 cases of cardiac rhabdomyomas were observed.The genotyping of TSC1 and TSC2 in 14 children revealed 11 with mutations in TSC2, 2 with mutations in TSC1, and no mutations of either gene in one patient. Eight of these observed mutations are reported here in for the first time. The illness presentations of the TSC2-mutated patients were more severe than that of patients carrying TSC1 mutations.There were differences in the mutations of TSC genes in Chinese children from those reported in other countries. The described clinical characteristics and genotyping will help pediatric neurologists to understand, diagnosis, and treat TSC.

Topological spaces via phenotype--genotype spaces

Researchers hope that establishing a notion of proximity using topology will help to clarify the biological processes underlying the evolution of living organisms. The simple model presented here, using RNA shapes, can carry over to more general and complex genotype-phenotype systems. Proximity is an important component of continuity, in both real-world and topological terms. Consequently, phenotype spaces provide an appropriate setting for modeling and investigating continuous and discontinuous evolutionary change.

Effect of Lichong decoction on expression of Bcl-2 and Bcl-2-associated X protein mRNAs in hysteromyoma model rat

OBJECTIVE:To study on effects of Lichong decoction on expression of apoptosis-controlling genes,Bcl-2 and Bcl-2-associated X protein(Bax) mRNAs in hysteromyoma tissue of the hysteromyoma model rat.METHODS:Fifty Wistar female rats were randomly divided into a normal group,a model group,a Lichong decoction group,a Guizifuling capsule group and a Mifepristone group.The hysteromyoma rat model was established by intraperitoneal injection of exogenous estrin and progestogens.Pathological examination of uterine tissue,uterine coefficient and uterine transverse diameter were made under optic microscope and expressions of Bcl-2 and Bax mRNAs in uterine tissue in the groups were detected with real-time fluorescent quantitative polymerase chain reaction(PCR) technique.RESULTS:After treatment,under microscope it was found that in the Lichong decoction group myometrium thinned,muscle fiber slightly overgrowth or long and thin,regular arrangement,inserting phenomenon of inner circular muscle and external longitudinal muscle was occasionally or not seen in the Lichong decoction group.The uterine coefficient and the uterine transverse diameter significantly decreased(P<0.01),and Bcl-2 mRNA expression significantly decreased(P<0.01) and Bax mRNA expression significantly increased in hysteromyoma tissue(P<0.01) in the Lichong decoction group as compared with the model group.CONCLUSION:Therapeutic effects of Lichong decoction on hysteromyoma is related with decrease of Bcl-2 mRNA expression and increase of Bax mRNA expression.

Phenotype-genotype correlation with Sanger sequencing identified retinol dehydrogenase 12(RDH12) compound heterozygous variants in a Chinese family with Leber congenital amaurosis

Background： Leber congenital amaurosis （LCA） is a group of clinically and genetically heterogeneous retinal dystrophy. To date, 22 genes are known to be responsible for LCA, and some specific phenotypic features could provide significant prognostic information for a potential genetic etiology. This study is to identify gene variants responsible for LCA in a Chinese family using direct Sanger sequencing, with the help of phenotype-genotype correlations. Methods： A Chinese family with six members including two individuals affected with t.CA was studied. All pa- tients underwent a complete ophthalmic examination. Based on phenotype-genotype correlation, direct Sanger sequencing was performed to identify the candidate gene on all family members and normal controls. Targeted next-generation sequencing was used to exclude other known LCA genes. Results： By Sanger sequencing, we identified two novel missense variants in the retinol dehydrogenase 12 （RDH12） gene： a c. 164C〉A transversion predicting a p.T55K substitution, and a c.535C〉G transversion predicting a p.H179D substitution. The two affected subjects carried both RDH12 variants, while their parents and offspring carried only one of heterozygous variants, showing complete cosegregation of the variants. The compound heterozygous variants were not present in 600 normal controls Besides, the RDH12 variants were confirmed by targeted next-generation sequencing. Conclusions： The RDH12 compound heterozygous variants might be the cause of the LCA family. Our study adds to the molecular spectrum of RDH12-related retinopathy and offers an effective example of the power of phenotype-genotype correlations in molecular diagnosis of LCA.

Information schema constructs for instantiation and composition of system manifestation features

Complementing our previous publications, this paper presents the information schema constructs （ISCs） that underpin the programming of specific system manifestation feature （SMF） orientated information management and composing system models. First, we briefly present （1） the general process of pre-embodiment design with SMFs, （2） the procedures of creating genotypes and phenotypes of SMFs, （3） the specific procedure of instantiation of phenotypes of SMFs, and （4） the procedure of system model management and processing. Then, the chunks of information needed for instantiation of phenotypes of SMFs are discussed, and the ISCs designed for instantiation presented. Afterwards, the information management aspects of system modeling are addressed. Methodologically, system modeling involves （1） placement of phenotypes of SMF in the modeling space, （2） combining them towards the desired architecture and operation, （3） assigning values to the parameters and checking the satisfac- tion of constraints, and （4） storing the system model in the SMFs-based warehouse database. The final objective of the reported research is to develop an SMFs-based toolbox to support modeling of cyber-physical systems （CPSs）.