Epidemiology and Azole Resistance of Clinical Isolates of Aspergillus fumigatus from a Large Tertiary Hospital in Ningxia, China.

Purpose: The objective of this study was to determine the clinical distribution, in vitro antifungal susceptibility and underlying resistance mechanisms of Aspergillus fumigatus (A. fumigatus) isolates from the General Hospital of Ningxia Medical University between November 2021 and May 2023. Methods: Antifungal susceptibility testing was performed using the Sensititre YeastOne YO10, and isolates with high minimal inhibitory concentrations (MICs) were further confirmed using the standard broth microdilution assays established by the Clinical and Laboratory Standards Institute (CLSI) M38-third edition. Whole-Genome Resequencing and RT-qPCR in azole-resistant A. fumigatus strains were performed to investigate the underlying resistance mechanisms. Results: Overall, a total of 276 A. fumigatus isolates were identified from various clinical departments, showing an increasing trend in the number of isolates over the past 3 years. Two azole-resistant A. fumigatus strains (0.72%) were observed, one of which showed overexpression of cyp51A, cyp51B, cdr1B, MDR1/2, artR, srbA, erg24A, and erg4B, but no cyp51A mutation. However, the other strain harbored two alterations in the cyp51A sequences (L98H/S297T). Therefore, we first described two azole-resistant clinical A. fumigatus strains in Ningxia, China, and reported one azole-resistant strain that has the L98H/S297T mutations in the cyp51A gene without any tandem repeat (TR) sequences in the promoter region. Conclusions: This study emphasizes the importance of enhancing attention and surveillance of azole-resistant A. fumigatus, particularly those with non-TR point mutations of cyp51A or non-cyp51A mutations, in order to gain a better understanding of their prevalence and spread in the region.

Characterization of integrons, extended spectrum beta lactamases and genetic diversity among uropathogenic Escherichia coli isolates from Kerman, south east of Iran.

Background and Objectives: The study aimed to investigate the distribution of genes encoding integrons, extended spectrum beta-lactamase (ESBL) in E. coli isolated from UTIs, as well as the genetic diversity among the isolates. Materials and Methods: E. coli isolates were recovered from the patients with UTI in Kerman Iran. Antibiotic susceptibility was done according to CLSI guidelines. The presence of ESBL genes and integrons was evaluated using PCR. PCR and sequencing were applied for the evaluation of cassette content of integrons. Genotyping of the isolates was performed by multiple-locus variable-number tandem repeat analysis (MLVA). Results: Imipenem was the most effective antibiotic, while the highest resistance was observed to streptomycin. In total 40.2% of isolates were ESBL producers. Of 69 integron-positive isolates, 59 only had class I integrons, 4 only had class II integrons and 6 had both types. The most common gene cassette found within class I integrons was dfrA17-aadA5 (n=27). The E. coli isolates were divided into 16 MLVA clusters. Conclusion: The current study demonstrated the simultaneous presence of class I integrons and ESBLs involved in the resistance of UPEC isolates to antibacterial agents. Our finding also revealed that the E. coli isolates belonged to diverse clones.

Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset.

African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has had serious effects on the global pig industry. Virus genome sequencing and comparison play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Although more than 140 ASFV genome sequences have been deposited in the public databases, the genome-wide diversity of ASFV remains unclear. Here we prepared a curated dataset of ASFV genome sequences by filtering genomes with sequencing errors as well as duplicated genomes. A total of 123 ASFV genome sequences were included in the dataset, representing 10 genotypes collected between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in differentiating closely related ASFV isolates, and drew new clues in the classification of some ASFV isolates. Genome-wide diversity of ASFV genomes was explored by pairwise sequence similarity comparison and ORF distribution comparison. Tandem repeat sequences were found widely distributed and highly varied in ASFV genomes. Structural variation and highly variable poly G or poly C tracts also contributed to the genome diversity. This study expanded our knowledge on the patterns of genetic diversity and evolution of ASFV, and provided valuable information for diagnosis improvement and vaccine development.

Genomic Basis of Occurrence of Cryptic Resistance among Oxacillin- and Cefoxitin-Susceptible mecA-Positive Staphylococcus aureus.

The oxacillin- and cefoxitin-susceptible mecA-positive Staphylococcus aureus is a novel "stealth" methicillin-resistant S. aureus (MRSA) type. Here, we sequenced the whole genome of two oxacillin- and cefoxitin-susceptible mecA-positive MRSA isolates from breast abscesses in a lactating woman and a nasal swab of a healthy student in Guangzhou for investigating the mechanism underlying its occurrence. The reversion of these isolates was selected by exposure to sub-MICs of cefoxitin with or without mupirocin. The mecA expression of both parental strains and their revertants was determined, and the whole genome of the revertants was sequenced. Comparative whole-genome analyses performed for both strains revealed that mecA of the clinical strain was mutated by a single-bp insertion at the 262nd position in the tandem repeat region of the gene, and this mutation that led to the formation of a premature stop codon. The colonizing strain was mutated by a novel G-to-A base substitution in the second promoter region (-35 bp) of mecA. The mecA expression level of strain 697 revertant was 37 times higher than that of the parental strain. Although the mecA expression level was even higher for parental strain 199 compared with that for its revertant, its cDNA sequence contained a single-bp insertion. Collectively, both the missense and single substitution mutations of the second promoter of mecA could render MRSA isolates as "stealth" MRSA, thereby emphasizing the importance of combining phenotype tests with mecA or penicillin-binding protein 2a detection for the identification of MRSA. IMPORTANCE The oxacillin- and cefoxitin-susceptible mecA-positive Staphylococcus aureus is a novel type of "stealth" methicillin-resistant S. aureus (MRSA), which is difficult to be detected using conventional methods. To investigate the genomic basis of their occurrence, we sequenced the whole genome of two previously recovered oxacillin- and cefoxitin-susceptible mecA-positive MRSA isolates from breast abscesses in a lactating woman and a nasal swab of a healthy student in Guangzhou. Complete SCCmec structure was absent except for mecA in clinical isolate 199. Additionally, a novel single-base pair insertion was observed in the clinical strain, which resulted in premature termination and a frameshift mutation. The colonizing isolate 697 had a Scc-mec-type IVa, and the second promoter region (-35 bp) of mecA was mutated by a novel G-to-A base substitution. The reversion of oxacillin- and cefoxitin-susceptible mecA-positive S. aureus to resistant MRSA isolates was selected by exposure to subminimum inhibitory cefoxitin with or without mupirocin.

Efficacy of chemotherapy combined with sorafenib for FLT3-ITD-positive acute myeloid leukemia / 中国基层医药

Objective:To investigate the effect of chemotherapy combined with sorafenib on the prognosis of FLT3 internal tandem duplication (FLT3-ITD)-positive acute myeloid leukemia and to find a more effective treatment.Methods:The clinical data of 60 patients who were newly diagnosed with acute myeloid leukemia and who received treatment in The Second Affiliated Hospital of Qiqihar Medical University from January 2015 to January 2017 were retrospectively analyzed. The patients were divided into three groups according to whether they were positive for FLT3-ITD and the treatment method they used. The observation group (FLT3-ITD-positive, n = 19) were treated with sorafenib based on routine chemotherapy. The control group 1 (FLT3-ITD-positive, n = 21) was treated only with routine chemotherapy. The control group 2 (FLT3-ITD-negative, n = 20) was treated only with routine chemotherapy. After the first and fourth courses of treatment, clinical efficacy was compared among the three groups. Results:After the first course of treatment, the complete remission rate in control group 2 was 50.0% (10/20), which was significantly higher than 15.8% (3/19) in the observation group and 4.8% (1/21) in the control group 1 ( H = 13.39, P < 0.05). After the fourth course of treatment, the complete remission rate in the observation group, control group 2, and control group 1 was 63.2% (12/19), 60.0% (12/20), and 4.8% (1/21), respectively, and the differences were statistically significant ( H = 19.21, P < 0.05). Four-year follow-up results showed that the median survival time in the observation group, control group 1, and control group 2 was 36.63, 24.15, and 45.00 months respectively. The event-free survival in the observation group, control group 1, and control group 2 was 18.00, 9.82, and 24.90 months, respectively. The median survival time and the event-free survival in the control group 2 were significantly longer than those in the observation group and control group 1 ( χ2 = 19.93, 23.04, both P < 0.001). Conclusion:Chemotherapy combined with sorafenib for treating newly-diagnosed FLT3-ITD-positive acute myeloid leukemia can provide comprehensive benefits and have advantages for survival over chemotherapy without sorafenib and chemotherapy alone.

[Immunomodulatory effect of adriamycin in mouse 4T1 model of breast cancer].

To explore the immunomodulatory effect of adriamycin on 4T1 breast cancer. We used a tandem mass tag-based quantitative proteomic method to detect differential proteins in breast cancer tissues, and multiple bioinformatics databases to analyze the differentially expressed proteins in the proteome. Also, we used enzyme-linked immunosorbent assay to detect the effects of adriamycin on helper T cells 1 and 2 in breast cancer tissues, and flow cytometry to detect CD4+ T cells, CD8+ T cells and regulatory T cells. We discovered the immunomodulatory targets of adriamycin in differential proteins. In total 170 differential proteins were significantly up-regulated, whereas 58 were markedly down-regulated. In addition, 73 proteins were involved in immune regulation. Kyoto encyclopedia of genes and genomes enriched important protein pathways related to cytokines and factor receptors, interleukin 17 pathway and cancer transcriptional regulatory pathways. These pathways and important differential proteins related to immunomodulatory functions were ultimately regulated by adriamycin on CD4+ T cells, CD8+ T cells and regulatory T cells, thereby affecting the prognosis of breast cancer. Moreover, adriamycin significantly increased interleukin 2, CD4+ T and CD8+ T (P<0.01) and markedly reduced regulatory T cells (P<0.05). The function of adriamycin against triple-negative breast cancer was closely related to the immunoregulation process of the differential proteins Ighm, Igkc, S100A8, S100A9 and Tmsb4x. Adriamycin could regulate the content of helper T cells 1 cytokines, CD4+ T and CD8+ T lymphocytes in breast cancer and reduce the number of regulatory T cells to produce immunomodulatory effects.

Immunomodulatory effect of adriamycin in mouse 4T1 model of breast cancer / 生物工程学报

To explore the immunomodulatory effect of adriamycin on 4T1 breast cancer. We used a tandem mass tag-based quantitative proteomic method to detect differential proteins in breast cancer tissues, and multiple bioinformatics databases to analyze the differentially expressed proteins in the proteome. Also, we used enzyme-linked immunosorbent assay to detect the effects of adriamycin on helper T cells 1 and 2 in breast cancer tissues, and flow cytometry to detect CD4+ T cells, CD8+ T cells and regulatory T cells. We discovered the immunomodulatory targets of adriamycin in differential proteins. In total 170 differential proteins were significantly up-regulated, whereas 58 were markedly down-regulated. In addition, 73 proteins were involved in immune regulation. Kyoto encyclopedia of genes and genomes enriched important protein pathways related to cytokines and factor receptors, interleukin 17 pathway and cancer transcriptional regulatory pathways. These pathways and important differential proteins related to immunomodulatory functions were ultimately regulated by adriamycin on CD4+ T cells, CD8+ T cells and regulatory T cells, thereby affecting the prognosis of breast cancer. Moreover, adriamycin significantly increased interleukin 2, CD4+ T and CD8+ T (P<0.01) and markedly reduced regulatory T cells (P<0.05). The function of adriamycin against triple-negative breast cancer was closely related to the immunoregulation process of the differential proteins Ighm, Igkc, S100A8, S100A9 and Tmsb4x. Adriamycin could regulate the content of helper T cells 1 cytokines, CD4+ T and CD8+ T lymphocytes in breast cancer and reduce the number of regulatory T cells to produce immunomodulatory effects.

Peptides derived from Kex2-processed repeat proteins are widely distributed and highly diverse in the Fungi kingdom.

BACKGROUND: Recently, a gene cluster responsible for biosynthesis of ustiloxin in Aspergillus flavus was identified as the first case of a ribosomally synthesized and post-translationally modified peptide (RiPP) synthetic pathway in Ascomycota. RiPPs are biosynthesized from precursor peptides, which are processed to produce the RiPP backbone (core peptides) for further modifications such as methylation and cyclization. Ustiloxin precursor peptide has two distinctive features: a signal peptide for translocation into the endoplasmic reticulum and highly repeated core sequences cleaved by Kex2 protease in the Golgi apparatus. On the basis of these characteristics, the ustiloxin-type RiPP precursor peptides or Kex2-processed repeat proteins (KEPs) in strains belonging to the Fungi kingdom were computationally surveyed, in order to investigate the distribution and putative functions of KEPs in fungal ecology. RESULTS: In total, 7878 KEPs were detected in 1345 of 1461 strains belonging to 8 phyla. The average number of KEPs per strain was 5.25 in Ascomycota and 5.30 in Basidiomycota, but only 1.35 in the class Saccharomycetes (Ascomycota) and 1.00 in the class Tremellomycetes (Basidiomycota). The KEPs were classified into 838 types and 2560 stand-alone ones, which had no homologs. Nearly 200 types were distributed in more than one genus, and 14 types in more than one phylum. These types included yeast α-mating factors and fungal pheromones. Genes for 22% KEPs were accompanied by genes for DUF3328-domain-containing proteins, which are indispensable for cyclization of the core peptides. DUF3328-domain-containing protein genes were located at an average distance of 3.09 genes from KEP genes. Genes for almost all (with three exceptions) KEPs annotated as yeast α-mating factors or fungal pheromones were not accompanied by DUF3328-domain-containing protein genes. CONCLUSION: KEPs are widely distributed in the Fungi kingdom, but their repeated sequences are highly diverse. From these results and some examples, a hypothesis was raised that KEPs initially evolved as unmodified linear peptides (e.g., mating factors), and then those that adopted a modified cyclic form emerged (e.g., toxins) to utilize their strong bioactivity against predators and competitive microorganisms.

Male patient 46,XX SRY-negative and unambiguous genitalia: A case report / Paciente masculino con cariotipo 46 XX negativo para el gen SRY y sin ambigüedad genital: reporte de un caso

In most cases, male sexual differentiation occurs with SRY gene mediation. However, exceptional genotypes have been identified, as shown in this paper. This was a male adult patient seen at the Servicio de Paternidades, Instituto de Genética, Universidad Nacional de Colombia. The following procedures were carried out: Amelogenin gene and short tandem repeat analyses using human identification commercial kits, conventional karyotype, SRY fluorescent in situ hybridization, PCR analysis for Y chromosome microdeletions, clinical evaluation, and genetic counseling. We present an adult male with unambiguous genitalia, karyotype 46,XX, and an SRY negative and ZFY positive molecular profile. The diagnosis of nonsyndromic 46,XX testicular disorder of sex development (DSD) -a rare genetic condition- was established. Only 20 % of similarly diagnosed patients are SRY negative and exhibit diverse molecular profiles. Until now, available evidence seems to indicate that, even in the absence of SRY, the ZFY factor is involved in male sexual differentiation.

En la mayoría de los casos, la diferenciación sexual masculina ocurre con la participación del gen SRY. Sin embargo, se pueden presentar otros genotipos excepcionales, como en el caso que se presenta en este reporte. Se trata de un paciente adulto de sexo masculino atendido en el Servicio de Paternidades del Instituto de Genética de la Universidad Nacional de Colombia. Se le hicieron los análisis del gen de la amelogenina y de repeticiones cortas en tándem (Short Tandem Repeat, STR) específicas para el gen SRY con estuches comerciales de identificación humana, así como los de cariotipo convencional e hibridación in situ fluorescente del SRY, y el estudio de microdeleciones del cromosoma Y mediante reacción en cadena de la polimerasa (PCR). Se le hizo la evaluación clínica y se le brindó asesoramiento genético. El paciente no presentaba ambigüedad genital, su cariotipo era 46 XX, y el perfil molecular era negativo para el gen SRY y positivo para el ZFY. Se le diagnosticó un trastorno de diferenciación sexual 46 XX testicular no sindrómico, una rara condición genética. Solo el 20 % de los pacientes con este diagnóstico son negativos para SRY y exhiben perfiles moleculares diversos. La información disponible parece indicar que el ZFY está relacionado con la diferenciación sexual masculina, aún en ausencia del gen SRY.

Paciente masculino con cariotipo 46 XX negativo para el gen SRY y sin ambigüedad genital: reporte de un caso / Male patient 46, XX SRY -negative and unambiguous genitalia: A case report

En la mayoría de los casos, la diferenciación sexual masculina ocurre con la participación del gen SRY. Sin embargo, se pueden presentar otros genotipos excepcionales, como en el caso que se presenta en este reporte. Se trata de un paciente adulto de sexo masculino atendido en el Servicio de Paternidades del Instituto de Genética de la Universidad Nacional de Colombia. Se le hicieron los análisis del gen de la amelogenina y de repeticiones cortas en tándem (Short Tandem Repeat, STR) específicas para el gen SRY con estuches comerciales de identificación humana, así como los de cariotipo convencional e hibridación in situ fluorescente del SRY, y el estudio de microdeleciones del cromosoma Y mediante reacción en cadena de la polimerasa (PCR). Se le hizo la evaluación clínica y se le brindó asesoramiento genético. El paciente no presentaba ambigüedad genital, su cariotipo era 46 XX, y el perfil molecular era negativo para el gen SRY y positivo para el ZFY. Se le diagnosticó un trastorno de diferenciación sexual 46 XX testicular no sindrómico, una rara condición genética. Solo el 20 % de los pacientes con este diagnóstico son negativos para SRY y exhiben perfiles moleculares diversos. La información disponible parece indicar que el ZFY está relacionado con la diferenciación sexual masculina, aún en ausencia del gen SRY.

In most cases, male sexual differentiation occurs with SRY gene mediation. However, exceptional genotypes have been identified, as shown in this paper. This was a male adult patient seen at the Servicio de Paternidades, Instituto de Genética, Universidad Nacional de Colombia. The following procedures were carried out: Amelogenin gene and short tandem repeat analyses using human identification commercial kits, conventional karyotype, SRY fluorescent in situ hybridization, PCR analysis for Y chromosome microdeletions, clinical evaluation, and genetic counseling. We present an adult male with unambiguous genitalia, karyotype 46,XX, and an SRY negative and ZFY positive molecular profile. The diagnosis of nonsyndromic 46,XX testicular disorder of sex development (DSD) -a rare genetic condition- was established. Only 20 % of similarly diagnosed patients are SRY negative and exhibit diverse molecular profiles. Until now, available evidence seems to indicate that, even in the absence of SRY, the ZFY factor is involved in male sexual differentiation.

How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans.

Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions, but the new long-read methods (PacBio and Nanopore) tended to result in longer assembled satellites. Important differences exist between the assemblies resulting from the two long-read technologies, such as the sizes of long satellites. Our results also suggest that the lengths of some annotated genes with internal repeats which were assembled using Sanger sequencing are likely to be incorrect.

[Clinical application of STR genotyping diagnosis for hydatidiform mole and nonmolar gestation].

Objective: To investigate the value of short tandem repeat (STR) genotyping in the diagnostic workup of molar and non-molar gestations with correlation of histological characteristics. Methods: Six hundred and fifty-six cases were selected based on clinically suspected hydropic abortion and/or molar pregnancy from July 2015 to September 2017 at Beijing Obstetrics and Gynecology Hospital. DNA was extracted from dissected chorionic villi and paired maternal endometrial FFPE tissue samples by Simplex OUP™ FFPE DNA Tissue Kit. STR genotyping was performed by PowerPlex 16 HS system. Results: DNA genotyping was informative in 649 of 656 cases, leading to identification of 215 hydatidiform mole gestations and 434 non-molar gestations. Most of non-molar gestations (375 cases, 86.4%) were diploid hydropic abortion. Various trisomy syndromes were found (53 cases, 12.2%), including trisomy 2, 3, 4, 7, 8, 13, 16 and 21. Only 2(0.5%) digynic triploid gestations were detected. Moreover, 4 cases (0.9%) of uniparental disomies (homologous or heterologous) were found. There were 196 cases with histologic diagnostic suspicious of hydatidiform moles were accurate sub-classified. Among them, 59 cases hydatidiform moles were under-diagnosed as diploid hydropic abortions, and 28 cases diploid hydropic abortions were over-diagnosed as hydatidiform moles.Compared with partial moles(PHM), there were no specific histomorphological features between the various types of non-molar gestations and partial moles for definitive diagnostic separation. There was no significant difference in the expression of p57(kip2) among PHM, trisomy and diploid hydropic abortions group (P=0.247). Conclusions: STR genotyping can distinguish non-molar gestations from early hydatidiform moles, and efficiently avoid misdiagnosis based only on histological evaluation. Therefore, using STR genotyping, not only can the overdiagnosis of non-molar pregnancy be avoided, but also individualized management can be offered to patients including monitoring of serum hCG.

[Genetic Polymorphisms of 27 Y-STR Loci in Dongxiang Population of Gansu Province].

OBJECTIVES: To investigate the genetic polymorphisms of 27 Y-STR in Dongxiang population of Gansu province, and to explore the population genetic relationship and the value of forensic application. METHODS: The genotyping of 27 Y-STR loci in 526 unrelated male individuals in Dongxiang population of Gansu province were detected by STRtyper-27Y kit. The allele frequencies and haplotype diversity were also calculated. Combining with other genetics data of 14 loci in same populations, which have been published at home and abroad, the genetic distance and clustering relationship in Dongxiang population of Gansu province were calculated. RESULTS: Totally 55 haplotypes were found in the DYS385a/b biallelic loci, 39 haplotypes in DYF387S1 loci, and 4-16 alleles in the rest 23 single copy STR loci. The GD value was from 0.453 9 （DYS391） to 0.957 5 （DYS385a/b）. Totally 471 haplotypes were observed in 27 Y-STR loci in 526 individuals, and the value of haplotypes diversity was 0.999 5. The genetic distance between Dongxiang and Tibetan populations of Gansu province was the closest （0.068 2）, while it was the longest between Dongxiang population in Gansu province and Han population in Henan province （0.084 7）. The result of dimensional analysis established upon the genetic distance was basically matched with that of the cluster analysis. CONCLUSIONS: The 27 Y-STR loci show a high genetic polymorphism in Dongxiang population of Gansu province, which has significance for the Y-STR database establishment, population genetics study and forensic practice.

Quantification and Genotyping of Trace Samples.

OBJECTIVES: To introduce real-time polymerase chain reaction （real-time PCR） into the initial sample screening, to improve the effectiveness of traditional trace sample extraction method. METHODS: Serial diluted 9947A was quantified using a Rotor-Gene Q real-time RT-PCR, and the genotype was determined with AmpFℓSTRTM IdentifilerTM Plus PCR kit. Thus a quantitative threshold model was built to obtain complete STR typing from the trace samples. In addition, 903 trace samples were used to verify the reliability. RESULTS: When the samples quality concentration was >0.03 ng/µL, the effective STR typing could be directly obtained; when the concentration was >0.01 and ≤0.03 ng/µL, the effective STR typing could be directly obtained by optimizing the PCR thermal cycle parameters （30 cycles）; and when the concentration was ≤0.01 ng/µL, no effective map could be obtained even if PCR was optimized. CONCLUSIONS: The real-time PCR quantitative threshold model is effective for the screening of trace samples.

Genetic Polymorphisms of 27 Y-STR Loci in Dongxiang Population of Gansu Province / 法医学杂志

OBJECTIVES@#To investigate the genetic polymorphisms of 27 Y-STR in Dongxiang population of Gansu province, and to explore the population genetic relationship and the value of forensic application.@*METHODS@#The genotyping of 27 Y-STR loci in 526 unrelated male individuals in Dongxiang population of Gansu province were detected by STRtyper-27Y kit. The allele frequencies and haplotype diversity were also calculated. Combining with other genetics data of 14 loci in same populations, which have been published at home and abroad, the genetic distance and clustering relationship in Dongxiang population of Gansu province were calculated.@*RESULTS@#Totally 55 haplotypes were found in the DYS385a/b biallelic loci, 39 haplotypes in DYF387S1 loci, and 4-16 alleles in the rest 23 single copy STR loci. The GD value was from 0.453 9 （DYS391） to 0.957 5 （DYS385a/b）. Totally 471 haplotypes were observed in 27 Y-STR loci in 526 individuals, and the value of haplotypes diversity was 0.999 5. The genetic distance between Dongxiang and Tibetan populations of Gansu province was the closest （0.068 2）, while it was the longest between Dongxiang population in Gansu province and Han population in Henan province （0.084 7）. The result of dimensional analysis established upon the genetic distance was basically matched with that of the cluster analysis.@*CONCLUSIONS@#The 27 Y-STR loci show a high genetic polymorphism in Dongxiang population of Gansu province, which has significance for the Y-STR database establishment, population genetics study and forensic practice.

Clinical application of STR genotyping diagnosis for hydatidiform mole and nonmolar gestation / 中华病理学杂志

Objective@#To investigate the value of short tandem repeat (STR) genotyping in the diagnostic workup of molar and non-molar gestations with correlation of histological characteristics.@*Methods@#Six hundred and fifty-six cases were selected based on clinically suspected hydropic abortion and/or molar pregnancy from July 2015 to September 2017 at Beijing Obstetrics and Gynecology Hospital. DNA was extracted from dissected chorionic villi and paired maternal endometrial FFPE tissue samples by Simplex OUP™ FFPE DNA Tissue Kit. STR genotyping was performed by PowerPlex 16 HS system.@*Results@#DNA genotyping was informative in 649 of 656 cases, leading to identification of 215 hydatidiform mole gestations and 434 non-molar gestations. Most of non-molar gestations (375 cases, 86.4%) were diploid hydropic abortion. Various trisomy syndromes were found (53 cases, 12.2%), including trisomy 2, 3, 4, 7, 8, 13, 16 and 21. Only 2(0.5%) digynic triploid gestations were detected. Moreover, 4 cases (0.9%) of uniparental disomies (homologous or heterologous) were found. There were 196 cases with histologic diagnostic suspicious of hydatidiform moles were accurate sub-classified. Among them, 59 cases hydatidiform moles were under-diagnosed as diploid hydropic abortions, and 28 cases diploid hydropic abortions were over-diagnosed as hydatidiform moles.Compared with partial moles(PHM), there were no specific histomorphological features between the various types of non-molar gestations and partial moles for definitive diagnostic separation. There was no significant difference in the expression of p57kip2 among PHM, trisomy and diploid hydropic abortions group (P=0.247).@*Conclusions@#STR genotyping can distinguish non-molar gestations from early hydatidiform moles, and efficiently avoid misdiagnosis based only on histological evaluation. Therefore, using STR genotyping, not only can the overdiagnosis of non-molar pregnancy be avoided, but also individualized management can be offered to patients including monitoring of serum hCG.

Quantification and Genotyping of Trace Samples / 法医学杂志

Objective To introduce real-time polymerase chain reaction (real-time PCR) into the initial sample screening, to improve the effectiveness of traditional trace sample extraction method.Methods Serial diluted 9947A was quantified using a Rotor-Gene Q real-time RT-PCR, and the genotype was determined with AmpF?STRTMIdentifilerTMPlus PCR kit.Thus a quantitative threshold model was built to obtain complete STR typing from the trace samples.In addition, 903 trace samples were used to verify the reliability.Results When the samples quality concentration was＞0.03 ng/μL, the effective STR typing could be directly obtained;when the concentration was＞0.01 and≤0.03 ng/μL, the effective STR typing could be directly obtained by optimizing the PCR thermal cycle parameters (30 cycles);and when the concentration was≤0.01 ng/μL, no effective map could be obtained even if PCR was optimized.Conclusion The real-time PCR quantitative threshold model is effective for the screening of trace samples.

Evolution of Tandem Repeat Satellite Sequences in Two Closely Related Caenorhabditis Species. Diminution of Satellites in Hermaphrodites.

The availability of the genome sequence of the unisexual (male-female) Caenorhabditis nigoni offers an opportunity to compare its non-coding features with the related hermaphroditic species Caenorhabditis briggsae; to understand the evolutionary dynamics of their tandem repeat sequences (satellites), as a result of evolution from the unisexual ancestor. We take advantage of the previously developed SATFIND program to build satellite families defined by a consensus sequence. The relative number of satellites (satellites/Mb) in C. nigoni is 24.6% larger than in C. briggsae. Some satellites in C. nigoni have developed from a proto-repeat present in the ancestor species and are conserved as an isolated sequence in C. briggsae. We also identify unique satellites which occur only once and joint satellite families with a related sequence in both species. Some of these families are only found in C. nigoni, which indicates a recent appearance; they contain conserved adjacent 5' and 3' regions, which may favor transposition. Our results show that the number, length and turnover of satellites are restricted in the hermaphrodite C. briggsae when compared with the unisexual C. nigoni. We hypothesize that this results from differences in unequal recombination during meiotic chromosome pairing, which limits satellite turnover in hermaphrodites.

Development of a Fluorescence Multiplex Amplification System with 24 Y-STR Loci.

OBJECTIVES: To establish a novel multiplex amplification system which comprises 24 Y-STR loci. METHODS: otal 24 Y-STR gene loci, concluding DYS531, DYS630, DYS622, DYS552, DYS510, DYS449, DYS459a/b, DYS446, DYS443, DYS635, DYS587, DYS527a/b, DYS460, Y-GATA-A10, DYS520, DYS557, DYS522, DYS481, DYS570, DYS385a/b, DYS444, were chosen for establishing the fluorescence multiplex amplification system. The specificity, identity, sensitivity, balance of the amplification, anti-interference and accuracy of the system were detected and the gene diversity was investigated in the population of Guangdong. RESULTS: No band was found in nonhuman and female samples that were tested by the established multiplex amplification system. The same genotyping results were obtained from different tissues of the same person. Complete profiles could be obtained from more than 0.1 ng of the standard sample 9948. The loss of alleles was found when the common inhibitors such as hemoglobin and calcium ion were added 120-200 µmol/L and 1.5-2.0 mmol/L respectively to the system which with a strong anti-interference to the indigo, humic acid and EDTA. The typing of 24 Y-STR system could give the reliable results when 146 unrelated male individuals were detected and compared with the Yfiler system parallelly. The haplotype diversity （HD） of the population in Guangdong reached 0.999 72 that was better than the result retained from Yfiler system, which the HD was 0.998 58. CONCLUSIONS: The fluorescence amplification system with 24 Y-STR loci established in present study has a wildly application prospect and can be used for cases inspection, paternity tests and Y-STR database construction.

Population Difference Analysis of Allele Frequencies of 24 Y-STR Loci.

OBJECTIVES: To investigate the population genetic polymorphisms of 24 Y-STR loci in unrelated individuals in Eastern Chinese Han population, and to compare the difference of Han group between Eastern China and Guangdong. METHODS: The population genetics of 24 Y-STR loci in 268 unrelated Han individuals from Eastern China were analyzed by GFS 24 Y-STR amplification kit. The allele frequencies in Eastern Chinese Han population were compared with the data in Guangdong Han population, and the difference analysis between two groups was performed. RESULTS: Among the 24 Y-STR loci of 268 unrelated Han individuals from Eastern China, 235 alleles and 267 haplotypes were observed. GD value ranged from 0.564 9 to 0.966 8. The difference between 12 loci （DYS622, DYS552, DYS443, et al.） of Han population in Eastern China and in Guangdong was statistically significance. CONCLUSIONS: GFS 24Y STR amplification system shows favorable polymorphisms, which can be used in patrilineal genetic relationship identification.