Seroepidemiology of herpes simplex virus in Yogyakarta, Indonesia

Sera from 487 individuals in Yogyakarta, Indonesia, were tested for antibodies to herpes simplex virus (HSV) by a passive hemagglutination method. Age-specific incidence rates for antibodies to HSV were calculated. For sera from persons other than prostitutes, in the age group from 10 to 19, the positive rate was 48% but in the age group higher than 20, it was more than 87%. Fifty of 59 pregnant women (85%) were positive. The positive rate and the distribution of antibody levels in prostitutes were higher than in the general population.     

A Prospective Study: Current Problems in Radiotherapy for Nasopharyngeal Carcinoma in Yogyakarta,Indonesia

Introduction

Nasopharyngeal carcinoma (NPC) has a high incidence in Indonesia. Previous study in Yogyakarta revealed a complete response of 29% and a median overall survival of less than 2 years. These poor treatment outcome are influenced by the long diagnose-to-treatment interval to radiotherapy (DTI) and the extended overall treatment time of radiotherapy (OTT). This study reveals insight why the OTT and DTI are prolonged.

Method

All patients treated with curative intent radiotherapy for NPC between July 2011 until October 2012 were included. During radiotherapy a daily diary was kept, containing information on DTI, missed radiotherapy days, the reason for missing and length of OTT.

Results

Sixty-eight patients were included. The median DTI was 106 days (95% CI: 98−170). Fifty-nine patients (87%) finished the treatment. The median OTT for radiotherapy was 57 days (95% CI: 57–65). The main reason for missing days was an inoperative radiotherapy machine (36%). Other reasons were patient’s poor condition (21%), public holidays (14%), adjustment of the radiation field (7%), power blackout (3%), inoperative treatment planning system (2%) and patient related reasons (9%). Patient’s insurance type was correlated to DTI in disadvantage for poor people.

Conclusion

Yogyakarta has a lack of sufficient radiotherapy units which causes a delay of 3–4 months, besides the OTT is extended by 10–12 days. This influences treatment outcome to a great extend. The best solution would be creating sufficient radiotherapy units and better management in health care for poor patients. The growing economy in Indonesia will expectantly in time enable these solutions, but in the meantime solutions are needed. Solutions can consist of radiation outside office hours, better maintenance of the facilities and more effort from patient, doctor and nurse to finish treatment in time. These results are valuable when improving cancer care in low and middle income countries.     

Bacteriophage T5 Mutants Carrying Deletions in tRNA Gene Region

A new series of heat-stable (st) mutants of bacteriophage T5, which contains deletions in the tRNA gene region, has been isolated. An accurate mapping of the deletion boundaries for more than 30 mutants of phage T5 has been carried out. As a result of the analysis of nucleotide sequences flanking the deleted regions in wild-type phage DNA, it has been shown that they all contain short, direct repeats of different lengths (2–35 nucleotide residues), and that only one repetition is retained in the mutant phage DNA. On the basis of the obtained results, it was suggested that deletion mutants of the phage T5 are formed as a result of illegal recombination occurring with the participation of short repeats in DNA (SHDIR). Based on the example of two mutants, it has been shown that the resistance to thermal inactivation depends on the size of the deleted region.     

黄石爬鮡外周血液指标特征的观察

黄石爬鮡（Euchiloglanis kishinouyei）属于较为原始的高原鱼类。通过生化分析仪测定红细胞数及血红蛋白含量,Wright’s染色及细胞化学方法,即过碘酸雪夫（PAS）、酚氧化酶（PO）、苏丹黑B（SBB）和过氧化物（POX）染色,观察其外周血细胞的显微结构及细胞化学特征。黄石爬鮡的红细胞数为（0.55 ± 0.06）×1012 个/L,血红蛋白含量为（73.00 ± 5.57） g/L;血细胞中红细胞占98.03%,且其细胞体积较大,白细胞中血栓细胞占比例最多,为37.06%,异嗜性粒细胞最少,为9.64%,异嗜性粒细胞分为Ⅰ型、Ⅱ型和Ⅲ型。细胞化学染色显示,红细胞均呈阴性,白细胞存在染色特性差异,其中白细胞过碘酸雪夫（PAS）染色均为阳性,过氧化物（POX）染色除I型和III型异嗜性粒细胞外均为阴性。     

Clinical and Molecular Characterization of Patients with Distal 11q Deletions

Jacobsen syndrome is caused by segmental aneusomy for the distal end of the long arm of chromosome 11. Typical features include mild to moderate psychomotor retardation, trigonocephaly, facial dysmorphism, cardiac defects, and thrombocytopenia, though none of these features are invariably present. To define the critical regions responsible for these abnormalities, we studied 17 individuals with de novo terminal deletions of 11q. The patients were characterized in a loss-of-heterozygosity analysis using polymorphic dinucleotide repeats. The breakpoints in the complete two-generation families were localized with an average resolution of 3.9 cM. Eight patients with the largest deletions extending from 11q23.3 to 11qter have breakpoints, between D11S924 and D11S1341. This cytogenetic region accounts for the majority of 11q⁻ patients and may be related to the FRA11B fragile site in 11q23.3. One patient with a small terminal deletion distal to D11S1351 had facial dysmorphism, cardiac defects, and thrombocytopenia, suggesting that the genes responsible for these features may lie distal to D11S1351. Twelve of 15 patients with deletion breakpoints as far distal as D11S1345 had trigonocephaly, while patients with deletions distal to D11S912 did not, suggesting that, if hemizygosity for a single gene is responsible for this dysmorphic feature, the gene may lie distal to D11S1345 and proximal to D11S912.     

Molecular Definition of the 22q11 Deletions in Velo-Cardio-Facial Syndrome

Velo-cardio-facial syndrome (VCFS) is a common genetic disorder among individuals with cleft palate and is associated with hemizygous deletions in human chromosome 22q11. Toward the molecular definition of the deletions, we constructed a physical map of 22q11 in the form of overlapping YACs. The physical map covers >9 cM of genetic distance, estimated to span 5 Mb of DNA, and contains a total of 64 markers. Eleven highly polymorphic short tandem-repeat polymorphic (STRP) markers were placed on the physical map, and 10 of these were unambiguously ordered. The 11 polymorphic markers were used to type the DNA from a total of 61 VCFS patients and 49 unaffected relatives. Comparison of levels of heterozygosity of these markers in VCFS patients and their unaffected relatives revealed that four of these markers are commonly hemizygous among VCFS patients. To confirm these results and to define further the breakpoints in VCFS patients, 15 VCFS individuals and their unaffected parents were genotyped for the 11 STRP markers. Haplotypes generated from this study revealed that 82% of the patients have deletions that can be defined by the STRP markers. The results revealed that all patients who have a deletion share a common proximal breakpoint, while there are two distinct distal breakpoints. Markers D22S941 and D22S944 appear to be consistently hemizygous in patients with deletions. Both of these markers are located on a single nonchimeric YAC that is 400 kb long. The results also show that the parental origin of the deleted chromosome does not have any effect on the phenotypic manifestation     

Molecular Genetics of the Brown (B)-Locus Region of Mouse Chromosome 4. I. Origin and Molecular Mapping of Radiation- and Chemical-Induced Lethal Brown Deletions

Over a period of many years, germ-cell mutagenesis experiments using the mouse specific-locus test have generated numerous radiation- and chemical-induced alleles of the brown (b; Tyrp1) locus in mouse chromosome 4. We describe here the origin, maintenance and initial molecular characterization of 28 b mutations that are prenatally lethal when homozygous. Each of these mutations is deleted for Tyrp1 sequences, and each of 25 mutations tested further is deleted for at least one other locus defined by molecular clones previously found to be closely linked to b by interspecific backcross analysis. A panel of DNAs from mice carrying a lethal b mutation and a Mus spretus chromosome 4 was used in the fine structure mapping of these molecularly defined loci. The deletional nature of each of these prenatally lethal mutations is consistent with the hypothesis that the null phenotype at b has an effect only on the quality (color) of eumelanin produced in melanocytes. The resulting deletion map provides a framework on which to build future molecular-genetic and biological analyses of this region of mouse chromosome 4.     

下颌单颗磨牙缺失区三维测量及数据库的建立

目的:研发三维测量软件,使用该软件对下颌非游离端单颗磨牙缺失后缺牙区相关解剖数据进行三维测量分析并建立数据库,为临床及科研提供参考依据。方法:选择50名确诊为下颌非游离端单颗磨牙缺失的成年患者,拍摄锥形束CT并运用3D-DMTC软件进行测量分析,测量缺牙区相关解剖数据。对各项结果用SPSS 21.0软件进行统计分析,并建立下颌单颗磨牙缺失后相关解剖数据库。结果:成功研发三维测量软件3D-DMTC。测得缺牙区牙槽嵴顶到下颌神经管的最近距离平均值为:15.84±2.10 mm;下颌神经管距离下颌骨颊侧壁最近距离平均值为:5.83±1.56 mm;下颌神经管距离下颌骨舌侧最近距离平均值为:3.78±1.19 mm;相邻两牙间最短距离平均值为:10.08±1.58 mm;剩余牙槽骨体积平均值为:2674.94±775.67 mm3。建立下颌单颗磨牙缺失后相关解剖数据库ADSML。结论:通过使用自主开发的测量软件测量得到相关数据并建立数据库,可辅助临床医生深入对患者颌骨的解剖情况的认识,并为临床治疗及相关科研提供参考。     

Hemoglobinopathy: Molecular Epidemiological Characteristics and Health Effects on Hakka People in the Meizhou Region,Southern China

Background

Hemoglobinopathies are the most common inherited diseases in southern China. However, there have been only a few epidemiological studies of hemoglobinopathies in Guangdong province.

Materials and Methods

Peripheral blood samples were collected from 15299 “healthy” unrelated subjects of dominantly ethnic Hakka in the Meizhou region, on which hemoglobin electrophoresis and routine blood tests were performed. Suspected cases with hemoglobin variants and hereditary persistence of fetal hemoglobin (HPFH) were further characterized by PCR, DNA sequencing, reverse dot blot (RDB) or multiplex ligation-dependent probe amplification (MLPA). In addition, 1743 samples were randomly selected from the 15299 subjects for thalassemia screening, and suspected thalassemia carriers were identified by PCR and RDB.

Results

The gene frequency of hemoglobin variants was 0.477% (73/15299). The five main subgroups of the ten hemoglobin variants were Hb E, Hb G-Chinese, Hb Q-Tahiland, Hb New York and Hb J-Bangkok. 277 cases (15.89%, 277/1743) of suspected thalassemia carriers with microcytosis (MCV<82 fl) were found by thalassemia screening, and were tested by a RDB gene chip to reveal a total of 196 mutant chromosomes: including 124 α-thalassemia mutant chromosomes and 72 β-thalassemia mutant chromosomes. These results give a heterozygote frequency of 11.24% for common α and β thalassemia in the Hakka population in the Meizhou region. 3 cases of HPFH/δβ-thalassemia were found, including 2 cases of Vietnamese HPFH (FPFH-7) and a rare Belgian ^Gγ(^Aγδβ)⁰–thalassemia identified in Chinese.

Conclusions

Our results provide a detailed prevalence and molecular characterization of hemoglobinopathies in Hakka people of the Meizhou region. The estimated numbers of pregnancies each year in the Meizhou region, in which the fetus would be at risk for β thalassemia major or intermedia, Bart’s hydrops fetalis, and Hb H disease, are 25 (95% CI, 15 to 38), 40 (95% CI, 26 to 57), and 15 (95% CI, 8 to 23), respectively.     

Analysis of Deletions in SMN1, SMN2, and NAIPGenes in Spinal Muscular Atrophy Patients from the Northwestern Region of Russia

Polymerase chain reaction with subsequent SSCP (single-strand DNA conformational polymorphism) and restriction (BselI restriction endonuclease) analyses were used to type the DNA samples of affected individuals and their relatives from 23 Russian families with high risk of spinal muscular atrophy (SMA) residing in the northwestern region of Russia. Deletions of exon 7 of the SMN1gene were found in 96% of the individuals examined. The frequency of homozygous deletion of exons 7 and 8 of the SMN1gene was 65%. The frequency of homozygous isolated deletion of the SMN1gene exon 7 among the SMA patients was 4.3%. Homozygous deletion of exon 5 of the NAIPgene was found in 22% of SMA patients. In SMA patients, a total of seven deletion types involving the SMN1, NAIP, and SMN2genes were detected. Deletion of exons 7 and 8 of the SMN1gene was the most common mutation associated with SMA in patients from the northwestern Russia.     

Loss of an Essential Function of Escherichia coli by Deletions in the thyA Region

In an attempt to obtain deletions in the thyA gene, an abnormal lysogen of lambda having the prophage inserted between the thyA and lysA genes was induced, and the surviving cured cells were examined for Thy(-) and Lys(-) mutants. In nearly 10,000 cured cells, 184 Lys(-) but no Thy(-) mutants were found. At the same time, the induced lambda phage contained an approximately equivalent number of lambdathyA(+) and lambdalysA(+) transducing particles. By contrast, in a strain with the genotype F' thyA(-)lysA(+)/ thyA(+)lysA(+), induction of the abnormal lambda lysogen gave rise to many Thy(-) mutants in the cells cured of the prophage. In these Thy(-) mutants it was not possible to eliminate the episome with acridine orange, although the episome could be removed in control cultures with a thyA(+) allele in the resident gene. Therefore, it was suggested that deletion of a gene in the region of the chromosome from the position of the insertion of the lambda prophage through the thyA gene caused loss of an essential and diffusible function.     

Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java,Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein

International Microbiology - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new virus responsible for the COVID-19 pandemic. The emergence of the new SARS-CoV-2 has been...     

Deletions, fusions and domain rearrangements.

The techniques of protein engineering are proving to be powerful analytical tools for the study of the structure and function of complex multidomain proteins. In particular, the overexpression of individual functional modules is providing proteins for three-dimensional structural analyses. Progress is also being made in the design and construction of novel multidomain proteins with potential therapeutic applications.     

Molecular Genetics of the Brown (B)-Locus Region of Mouse Chromosome 4. II. Complementation Analyses of Lethal Brown Deletions

Numerous new mutations at the brown (b) locus in mouse chromosome 4 have been recovered over the years in germ-cell mutagenesis experiments performed at the Oak Ridge National Laboratory. A large series of radiation- and chemical-induced b mutations known to be chromosomal deletions, and also known to be prenatally lethal when homozygous, were analyzed by pairwise complementation crosses as well as by pseudodominance tests involving flanking loci defined by externally visible phenotypes. These crosses were designed to determine the extent of each deletion on the genetic and phenotype map of the chromosomal region surrounding the b locus; the crosses also provided basic data that assigned deletions to complementation groups and defined four new loci associated with aberrancies in normal development. Specifically, the pseudodominance tests identified deletions that include the proximally mapping whirler (wi) and the distally mapping depilated (dep) genes, thereby bracketing these loci defined by visible developmental abnormalities with landmarks (deletion breakpoints) that are easily identified on the physical map. Furthermore, the complementation crosses, which were supplemented with additional crosses that allowed determination of the gross time of lethality of selected deletions, defined four new loci required for normal development. Homozygous deletion of one of these loci (b-associated fitness, baf) results in a runting syndrome evident during postnatal development; deletion of one locus [l(4)2Rn] causes death in the late gestation/neonatal period; and deletion of either of two loci [l(4)1Rn or l(4)3Rn] results in embryonic death, most likely in pre-, peri- or postimplantation stages. The placement of these new functionally defined loci on the evolving molecular map of the b region should be useful for continuing the analysis of the roles played in development by genes in this segment of chromosome 4.     

Occurrence and Molecular Identification of Anisakis Dujardin, 1845 from Marine Fish in Southern Makassar Strait,Indonesia

Anisakis spp. (Nematoda: Anisakidae) parasitize a wide range of marine animals, mammals serving as the definitive host and different fish species as intermediate or paratenic hosts. In this study, 18 fish species were investigated for Anisakis infection. Katsuwonus pelamis, Euthynnus affinis, Caranx sp., and Auxis thazard were infected with high prevalence of Anisakis type I, while Cephalopholis cyanostigma and Rastrelliger kanagurta revealed low prevalence. The mean intensity of Anisakis larvae in K. pelamis and A. thazard was 49.7 and 5.6, respectively. A total of 73 Anisakis type I larvae collected from K. pelamis and A. thazard were all identified as Anisakis typica by PCR-RFLP analysis. Five specimens of Anisakis from K. pelamis and 15 specimens from A. thazard were sequenced using ITS1-5.8S-ITS2 region and 6 specimens from A. thazard and 4 specimens from K. pelamis were sequenced in mtDNA cox2 region. Alignments of the samples in the ITS region showed 2 patterns of nucleotides. The first pattern (genotype) of Anisakis from A. thazard had 100% similarity with adult A. typica from dolphins from USA, whereas the second genotype from A. thazard and K. pelamis had 4 base pairs different in ITS1 region with adult A. typica from USA. In the mtDNA cox2 regions, Anisakis type I specimens from A. thazard and K. pelamis showed similarity range from 94% to 99% with A. typica {"type":"entrez-nucleotide","attrs":{"text":"AB517571","term_id":"283379497","term_text":"AB517571"}}AB517571/{"type":"entrez-nucleotide","attrs":{"text":"DQ116427","term_id":"74229655","term_text":"DQ116427"}}DQ116427. The difference of 4 bp nucleotides in ITS1 regions and divergence into 2 subgroups in mtDNA cox2 indicating the existence of A. typica sibling species in the Makassar Strait.     

Molecular phylogeny of Dipterocarpaceae in Indonesia based on chloroplast DNA

In order to construct a molecular phylogeny of Indonesian Dipterocarpoideae (Dipterocarpaceae), PCR-RFLP of the chloroplast regions rbcL, petB, psbA, psaA, and trnL-F was performed with seven restriction enzymes in 129 samples including 58 species from nine genera. In the strict consensus tree with Monotes kerstingii as outgroup Indonesian Dipterocarpaceae were divided into two major clades. One clade (bootstrap value=71) consisted of Upuna, Cotylelobium, Anisoptera, Vatica, Dipterocarpus (tribe Dipterocarpeae, bootstrap value=83) and Dryobalanops (tribe Shoreae, bootstrap value=99) in a basal position. The second clade consisted of Hopea, Parashorea, and Shorea (tribe Shoreae) with 95% bootstrap support. Tribe Dipterocarpeae is monophyletic, tribe Shoreae is polyphyletic since Dryobalanops is sister to tribe Dipterocarpeae. In the neighbour-joining tree the sister group position of Dryobalanops to tribe Dipterocarpeae is not supported by the bootstrap analysis. Alternatively, we used Upuna borneensis as outgroup. The effect of outgroup selection on tree topology, taxonomic classification and the interpretation of character evolution is discussed.