Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data

Genomic structural variants (SVs) constitute a significant proportion of genetic variation in the genome. The rapid development of long-reads sequencing has facilitated the detection of long-fragment SVs. There is no published study to detect SVs using long-read data from sheep. We applied a long-read mapping approach to detect SVs and characterized a total of 30,771 insertions, deletions, inversions and translocations. We identified 716, 916, 842 and 303 specific SVs in Southdown sheep, Alpine merino sheep, Qilian White Tibetan sheep and Oula sheep, respectively. We annotated these SVs and found that these SV-related genes were primarily enriched in the well-established pathways involved in the regulation of the immune system, growth and development and environmental adaptability. We detected and annotated SVs based on NGS resequencing data to validate the accuracy based on third-generation detection. Moreover, five candidate SVs were verified using the PCR method in 50 sheep. Our study is the first to use a long-reads sequencing approach to construct a novel structural variation map in sheep. We have completed a preliminary exploration of the potential effects of SVs on sheep.

The identification and characterization of genome-wide long terminal repeat retrotransposon provide an insight into elucidating the trait evolution of five Rhododendron species

Rhododendron is well-known for its beauty and colorful corolla. Although some high-quality whole-genome sequencing of Rhododendron has been completed, there is lack of studies on long terminal repeat (LTR) retrotransposons in Rhododendron, which limits our ability to elucidate the causes of genetic variations in Rhododendron species. The properties of the intact Rhododendron LTR retrotransposon were investigated at the genome-wide level. Based on the available data, the high-quality genomes from five species, i.e., R. griersonianum, R. simsii, R. henanense subsp. lingbaoense, R. mucronatum var. ripense and R. ovatum were selected as the identification targets with good assembly continuity. A total of 17,936 intact LTR retrotransposons were identified; they belong to the superfamilies Copia and Gypsy with 17 clades. The insertion time of these transposons was later than 120 million years ago, and the outbreak period was concentrated more recently than 30 million years ago. Phylogenetic analysis revealed that many LTR retrotransposons might originate from intraspecific duplication. The current evidences also suggests that most of the LTR retrotransposons were inserted in the interstitial part of the genes in R. griersonianum, R. simsii, R. henanense, and R. ovatum, and the functions of the inserted genes are mainly involved in starch metabolism and proteolysis etc. The effect of LTR retrotransposon on gene expression depends on its insertion site and activation. Highly expressed LTR retrotransposons tended to be younger. The activity of LTR retrotransposons may affect some stage-specific expression genes of flower development, such as leucine-rich repeat receptor-like kinase. The available results herein improve our knowledge of LTR retrotransposons in Rhododendron genomes and facilitate the further study of genetic variation and trait evolution in Rhododendron.

Associations of Pain and Sarcopenia with Successful Aging among Older People in China: Evidence from CHARLS

OBJECTIVES

Sarcopenia and chronic pain are geriatric syndromes that negatively impact the lives of older people. The aim of this study was to explore the relationship among sarcopenia, pain, and successful aging among older persons participating in the China Health and Retirement Longitudinal Study (CHARLS).

DESIGN

Cohort study with a 2-year follow-up.

SETTING AND PARTICIPANTS

Data were derived from 2 waves of the CHARLS, and 4280 community-dwelling participants aged ≥ 60 years were included in the study.

METHODS

Sarcopenia status was defined according to the Asian Working Group for Sarcopenia 2019 (AWGS 2019) criteria. Successful aging was defined following Rowe and Kahn's multidimensional model. Pain was assessed by a self-reported questionnaire. A generalized estimating equation (GEE) was used to examine the associations.

RESULTS

Longitudinal results demonstrated that compared with no sarcopenia, possible sarcopenia [OR (95%CI): 0.600 (0.304~1.188)] was not significantly associated with successful aging. Pain only was strongly associated with successful aging [0.388 (0.251~0.600)], whereas the association between sarcopenia only and successful aging was weaker [0.509 (0.287~0.905)]. The likelihood of being successful aging was substantially lower in the presence of coexisting sarcopenia and pain [0.268 (0.108~0.759)].

CONCLUSIONS

Both pain and sarcopenia are significant predictors for achieving successful aging among community-dwelling older adults. Early identification of sarcopenia and pain permits the implementation of treatment strategies and presents an opportunity to mitigate the risk of being unsuccessful aging.

Genetic Basis of Dorper Sheep (Ovis aries) Revealed by Long-Read De Novo Genome Assembly

Dorper sheep (Ovis aries) (DPS), developed in the 1930s by crossing Dorset Horn and Blackhead Persian sheep in South Africa, is a world-famous composite breed for mutton production. The genetic basis underlying this breed is yet to be elucidated. Here, we report the sequencing and assembly of a highly contiguous Dorper sheep genome via integration of Oxford Nanopore Technology (ONT) sequencing and Hi-C (chromatin conformation capture) approaches. The assembled genome was around 2.64 Gb with a contig N50 of 73.33 Mb and 140 contigs in total. More than 99.5% of the assembled sequences could be anchored to 27 chromosomes and they were annotated with 20,450 protein-coding genes. Allele-specific expression (ASE) genes of Dorper sheep were revealed through ASE analysis and they were involved in the immune system, lipid metabolism, and environmental adaptation. A total of 5,701 and 456 allelic sites were observed in the SNP and indels loci identified from relevant whole-genome resequencing data. These allelic SNP and INDEL sites were annotated in 1,002 and 294 genes, respectively. Moreover, we calculated the number of variant sites and related genes derived from the maternal and paternal ancestors, revealing the genetic basis of outstanding phenotypic performance of Dorper sheep. In conclusion, this study reports the first reference genome of Dorper sheep and reveals its genetic basis through ASE. This study also provides a pipeline for mining genetic information of composite breeds, which has an implication for future hybrid-breeding practices.

The Transcriptional Cell Atlas of Testis Development in Sheep at Pre-Sexual Maturity

Sheep testes undergo a dramatic rate of development with structural changes during pre-sexual maturity, including the proliferation and maturation of somatic niche cells and the initiation of spermatogenesis. To explore this complex process, 12,843 testicular cells from three males at pre-sexual maturity (three-month-old) were sequenced using the 10× Genomics Chromium^TM single-cell RNA-seq (scRNA-seq) technology. Nine testicular somatic cell types (Sertoli cells, myoid cells, monocytes, macrophages, Leydig cells, dendritic cells, endothelial cells, smooth muscle cells, and leukocytes) and an unknown cell cluster were observed. In particular, five male germ cell types (including two types of undifferentiated spermatogonia (A_pale and A_dark), primary spermatocytes, secondary spermatocytes, and sperm cells) were identified. Interestingly, A_pale and A_dark were found to be two distinct states of undifferentiated spermatogonia. Further analysis identified specific marker genes, including UCHL1, DDX4, SOHLH1, KITLG, and PCNA, in the germ cells at different states of differentiation. The study revealed significant changes in germline stem cells at pre-sexual maturation, paving the way to explore the candidate factors and pathways for the regulation of germ and somatic cells, and to provide us with opportunities for the establishment of livestock stem cell breeding programs.

Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep

Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 795 sheep populations comprising 27 breeds with two wool types, measuring the population differentiation index (Fst), nucleotide diversity (θπ ratio), and extended haplotype homozygosity among populations (XP-EHH) to detect the selective signatures of hair sheep and fine-wool sheep. The top 5% of the Fst and θπ ratio values, and values of XP-EHH < −2 were considered strongly selected SNP sites. Annotation showed that the PRX, SOX18, TGM3, and TCF3 genes related to hair follicle development and wool shedding were strongly selected. Our results indicated that these methods identified important genes related to hair follicle formation, epidermal differentiation, and hair follicle stem cell development, and provide a meaningful reference for further study on the molecular mechanisms of economically important traits in sheep.

Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep

To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the “HIBLUP” package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h²) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.

Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep

BACKGROUND

The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits.

RESULTS

A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263).

CONCLUSION

This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding.

Correction: Largely enhanced thermoelectric effect and pure spin current in silicene-based devices under hydrogen modification

Correction for 'Largely enhanced thermoelectric effect and pure spin current in silicene-based devices under hydrogen modification' by G. Qiao et al., Nanoscale, 2020, 12, 277-288, DOI: 10.1039/C9NR07541K.

Genomic Prediction of Additive and Dominant Effects on Wool and Blood Traits in Alpine Merino Sheep

Dominant genetic effects may provide a critical contribution to the total genetic variation of quantitative and complex traits. However, investigations of genome-wide markers to study the genomic prediction (GP) and genetic mechanisms of complex traits generally ignore dominant genetic effects. The increasing availability of genomic datasets and the potential benefits of the inclusion of non-additive genetic effects in GP have recently renewed attention to incorporation of these effects in genomic prediction models. In the present study, data from 498 genotyped Alpine Merino sheep were adopted to estimate the additive and dominant genetic effects of 9 wool and blood traits via two linear models: (1) an additive effect model (MAG) and (2) a model that included both additive and dominant genetic effects (MADG). Moreover, a method of 5-fold cross validation was used to evaluate the capability of GP in the two different models. The results of variance component estimates for each trait suggested that for fleece extension rate (73%), red blood cell count (28%), and hematocrit (25%), a large component of phenotypic variation was explained by dominant genetic effects. The results of cross validation demonstrated that the MADG model, comprising additive and dominant genetic effects, did not display an apparent advantage over the MAG model that included only additive genetic effects, i.e., the model that included dominant genetic effects did not improve the capability for prediction of the genomic model. Consequently, inclusion of dominant effects in the GP model may not be beneficial for wool and blood traits in the population of Alpine Merino sheep.

Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep

Adaptation to high-altitude hypoxia is essential for domestic animals, such as yak, Tibetan chicken, and Tibetan sheep, living on high plateaus, as it ensures efficient oxygen absorption and utilization. Red blood cells are the primary medium for transporting oxygen in the blood. However, little is known about the genetic mechanism of erythrocyte traits. Genome-wide association studies (GWASs) based on single markers or haplotypes have identified potential mechanisms for genetic variation and quantitative traits. To identify loci associated with erythrocyte traits, we performed a GWAS based on the method of the single marker and haplotype in 498 Alpine Merino sheep for six erythrocyte traits: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV). Forty-two significant single-nucleotide polymorphisms (SNPs) associated with the six erythrocyte traits were detected by means of a single-marker GWAS, and 34 significant haplotypes associated with five erythrocyte traits were detected by means of haplotype analysis. We identified six genes (DHCR24, SPATA9, FLI1, PLCB1, EFNB2, and SH2B3) as potential genes of interest via gene function annotations, location, and expression variation. In particular, FLI1 and PLCB1 were associated with hematopoiesis and erythropoiesis, respectively. These results provide a theoretical basis for analyzing erythrocyte traits and high-altitude hypoxia adaptation in Alpine Merino sheep and will be a useful reference for future studies of plateau-dwelling livestock.

The complete mitochondrial genome sequence and phylogenetic analysis of Alpine Merino sheep (Ovis aries)

Alpine Merino sheep is one of the most important fine-wool sheep breeds in China. In this study, we present the complete mitogenome of Alpine Merino sheep for the first time. The genome has a length of 16,619bp, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). Phylogenetically, the Alpine Merino sheep is closer to Oula Tibetan sheep and Tashkurgan sheep. This report provided new data for the phylogeny of Alpine Merino sheep.

[Three-dimensional finite element analysis of cantilever fixed bridge supported by implants with mandibular central incisor]

Objective: To investigate effect of the contact surface between the bridge and the adjacent teeth on the stress distribution of the implant and bone tissue and the displacement of the prosthesis in the cantilever fixed implant bridge restoring missing mandibular central incisors. Methods: Two-dimensional images of the mandible and dentition in healthy adults were obtained using CT data. A three-dimensional finite element model of cantilever fixed bridge supported by implants with mandibular central incisor was established by computer reconstruction technique.The contact surface between the bridge and the adjacent natural tooth was designed as "oval" and "trapezoid". The "trapezoid" has a slightly smaller median diameter on the labial side and a slightly larger medial diameter on the lingual side. Loading of 120 N was applied on the tangential margin of the middle line of the long axis of the bridge 41. The direction was set at 0°, which was parallel to the long axis of the tooth and downward. The buccal to lingual and downward angles were 30°, 45° and 60°, respectively, perpendicular to the long axis of the tooth and 90° to the lingual side.The stress distribution of the implant and surrounding bone tissue and the displacement of the prosthesis were compared between the two models. Results: Under axial and buccolingual loading, the maximum equivalent stress peak in the implant and surrounding bone tissue in the cantilever with trapezoidal contact surface design and the maximum displacement of the prosthesis were lower. Moreover, the distribution of stress was more balanced and the concentration range of stress was smaller. With the loading angle increasing, this trend was more obvious. When loading angle increased to 90°, the maximum equivalent stress and the maximum displacement of the elliptic contact surface model implant and surrounding bone tissue were 196 and 101 MPa and 0.196 mm, respectively, while the trapezoidal contact surface model were 157 and 72 MPa and 0.164 mm, respectively. Conclusions: The trapezoidal contact surface of the bridge and the adjacent teeth in the cantilever fixed bridge supported by implants with mandibular central incisor is beneficial to reduce the impact of the leverage on the implant and surrounding bone tissue.

A case report regarding general anesthesia management of a patient with pulmonary vein stenosis that underwent balloon dilatation and stent implantation

RATIONALE

Pulmonary vein stenosis (PVS) is a rare cardiovascular deformity that can lead to high mortality if left untreated. Patients frequently experience multiple complications such as hemoptysis, pulmonary hypertension, bronchial venous rupture and cardiac insufficiency. Currently, pulmonary vein stenosis balloon dilatation (stent implantation) is the only treatment, and this can be performed under local or general anesthesia. However, a case report on the general anesthesia management of PVS has not been previously reported. In this case report, we discuss anesthetic considerations in patients with PVS, focusing specifically on perioperative airway and circulatory management as well as the risk evaluation, and the appropriate effective management of all potential complications intraoperatively.

PATIENT CONCERNS

A 58-year-old male patient was admitted because of coughing rusty sputum for during 2 years as well as experiencing dyspnea and chest distress after exertion or exercising. The difficulty breathing and chest distress had been going on for a year. This patient had undergone circumferential pulmonary vein isolation twice during the last 2 years.

DIAGNOSES

Based on the transthoracic echocardiography and computed tomography, this patient's diagnosis was considered as pulmonary vein stenosis, pulmonary hypertension (secondary), and pulmonary arteriovenous thrombosis.

INTERVENTIONS

We considered that such severe patients with PVS require respiratory and circulatory supports and perhaps emergency surgical interventions. Henceforth, we administered general anesthesia to the patient and had extracorporeal membrane oxygenation (ECMO) on standby.

OUTCOMES

The duration of the surgery was approximately 4 hours, the intraoperative vital signs were stable, no pericardial effusion was observed postoperatively, the blood flow in the pulmonary vein stent was smooth, and the patient was discharged 7 days later following rehabilitation.

LESSONS

This surgical procedure involving respiratory and circulatory supports requires the involvement of different medical personnel such as interventionists, anesthesiologists, and surgeons. Therefore, multidisciplinary cooperation under general anesthesia will undoubtedly benefit such patients.

Prognostic significance of overexpressed long non-coding RNA TUG1 in patients with clear cell renal cell carcinoma

OBJECTIVE

The long non-coding RNAs (lncRNAs) study has gradually become one of the hot topics in the field of RNA biology. However, little is known about the pathological role of lncRNA TUG1 in clear cell renal cell carcinoma (ccRCC) patients. This study attempted to investigate the association of lncRNA TUG1 expression with progression and prognosis in ccRCC patients.

PATIENTS AND METHODS

Using qRT-PCR, the expression of TUG1 was measured in 203 ccRCC tissues and 45 adjacent non-cancerous tissues. Then, the relationships between TUG1 level and the clinicopathological factors of patients with ccRCC were analyzed. The prognostic significance was evaluated using Kaplan-Meier and Cox regression analyses.

RESULTS

The relative level of TUG1was significantly higher in ccRCC tissues compared to the adjacent non-tumor tissues (p < 0.01). Furthermore, TUG1 was associated significantly with histological grade, tumor stage, lymph node metastasis and distant metastasis (all p < 0.05). Interestingly, Kaplan-Meier analysis showed that higher TUG1 expression levels were associated with a shorter overall survival (p < 0.001) in ccRCC patients. Cox proportional hazards analysis showed that high TUG1 expression was an independent prognostic marker of poor outcome.

CONCLUSIONS

These findings suggested that TUG1 may act as a tumor promoter in ccRCC and could serve as a potential therapeutic target for this tumor.

Basal Tumor Cell Isolation and Patient-Derived Xenograft Engraftment Identify High-Risk Clinical Bladder Cancers

Strategies to identify tumors at highest risk for treatment failure are currently under investigation for patients with bladder cancer. We demonstrate that flow cytometric detection of poorly differentiated basal tumor cells (BTCs), as defined by the co-expression of CD90, CD44 and CD49f, directly from patients with early stage tumors (T1-T2 and N0) and patient-derived xenograft (PDX) engraftment in locally advanced tumors (T3-T4 or N+) predict poor prognosis in patients with bladder cancer. Comparative transcriptomic analysis of bladder tumor cells isolated from PDXs indicates unique patterns of gene expression during bladder tumor cell differentiation. We found cell division cycle 25C (CDC25C) overexpression in poorly differentiated BTCs and determined that CDC25C expression predicts adverse survival independent of standard clinical and pathologic features in bladder cancer patients. Taken together, our findings support the utility of BTCs and bladder cancer PDX models in the discovery of novel molecular targets and predictive biomarkers for personalizing oncology care for patients.

Effect of multiple infections with white spot syndrome virus and Vibrio anguillarum on Pacific white shrimp Litopenaeus vannamei (L.): mortality and viral replication

Multiple infections are commonly found in practical shrimp culture and may cause more serious consequences than infections by one pathogen only. Therefore, this study was conducted to evaluate the effect of multiple infections with white spot syndrome virus (WSSV) and Vibrio anguillarum on Pacific white shrimp Litopenaeus vannamei (L.), mortality, WSSV replication in vivo and host immune response. In the WSSV single-infection group (WSSV load, 2 × 10(2) copies μL(-1)), mean cumulative mortality was 29.2%. In the V. anguillarum single-infection group, cumulative mortality was 12.5% when shrimp were challenged by 10(5) CFU mL(-1) of bacteria. In the co- and super-infection groups, 37.5% and 50% cumulative mortalities, respectively, were observed at a lower bacterial concentration of 10(3) CFU mL(-1), suggesting that shrimp with multiple infections died earlier and more frequently than singly infected shrimp. WSSV load after injection was tracked over time by TaqMan quantitative PCR. WSSV load increased more rapidly in the multiple-infection groups than in the single-infection group. Additionally, mRNA expression of the genes encoding prophenoloxidase 1 and 2, which are closely involved in innate immunity in shrimp, was down-regulated more extensively in multiple-infection groups than in single-infection groups, as indicated by quantitative reverse-transcription PCR.

Biological characteristics and pathogenicity of a highly pathogenic Shewanella marisflavi infecting sea cucumber, Apostichopus japonicus

Shewanella marisflavi isolate AP629 is described as a novel pathogen of sea cucumber. The LD(50) values (14 days) in sea cucumber, mice and swordtail fish were 3.89 × 10(6) , 6.80 × 10(4) and 4.85 × 10(4) CFU g(-1) body weight, respectively. Studies on S. marisflavi were conducted, including morphology, physiological and biochemical characteristics, haemolysis, whole-cell protein and 16S rDNA gene sequence. Colonies of S. marisflavi appeared faint red on marine agar and green on thiosulphate-citrate-bile salt-sucrose media. Shewanella marisflavi had polar flagella. The cells were Gram-negative, oxidase- and catalase-positive and not sensitive to O/129. The bacterium exhibited β-haemolysis on sheep blood agar and produced H(2) S. Shewanella marisflavi survived and grew at 4-35°C, pH 6.0-9.2 and in the presence of 0-8% NaCl. The whole-cell proteins included 13 discrete bands, and proteins of molecular weight 87, 44 and 39 kDa were found in all five strains of Shewanella spp. The difference in 16S rDNA gene sequences in S. marisflavi was at the 446 bp site: S. marisflavi (KCCM 41822) - G, isolate AP629 - A. This is the first report that Shewanella is pathogenic to sea cucumber.

Genetic evolution of EGFR and the clonal origin of adenocarcinomas exhibiting various degrees of bronchioloalveolar carcinoma

e22050

Background: EGFR mutations may accumulate during multistage progression of bronchioloalveolar carcinoma (BAC), leading to heterogeneity within the tumor. Moreover, intrapulmonary emersions are the predominant sites of BAC progression in the absence of other distant metastases. In cases of emerging bilateral lung lesions during the follow-up to complete resection, the issue of how to differentiate between lesions originating from multifocal BACs or distant metastases/local recurrence is an important and unresolved issue. This study was performed to determine whether sequential adenocarcinoma with BAC features emerges in the lung field arises from a single clone or multiple clones in the same individual. Methods: Samples of adenocarcinomas exhibiting various degrees of BAC were obtained by thoracotomy. Sequential specimens were obtained on detection of novel lesions in the lung field. Genomic DNA was extracted from the specimens, and the presence of activating mutations in EGFR was analyzed by direct sequencing. Our pathological findings, sequential imaging, and EGFR sequence data were compared to monitor evidence of cancer evolution. Results: Based on an analysis of EGFR in tumor specimens from 428 lung cancer patients, fifteen cases of sequential BAC-related adenocarcinoma obtained by thoracotomy were identified. Together with alterations in BAC/adenocarcinoma components, the EGFR-TKI untreated series with at least one episode of EGFR-activating mutations represented three typical models: no significant EGFR evolution for a single clone, genetic alterations from mutant to wild-type EGFR for multifocal lesions, and a switch from wild-type to mutant EGFR, which might exhibit uncertain circumstances of cancer progression. Conclusions: Genetic analysis in conjunction with pathological and radiological diagnoses can be used to explore the origin of multifocal BAC. The single clone model indicates subsequent disease progression, whereas genetic alterations from mutations to wild-type EGFR are suggestive of secondary primary carcinoma. When additional lesions emerge after radical resection of BAC-related lung cancer, sequential tumor samples should be obtained for further evaluation.

No significant financial relationships to disclose.

High-resolution measurements of small field beams using polymer gels

Small field sizes are increasingly becoming important in radiotherapy particularly since the introduction of intensity-modulated radiation therapy (IMRT) techniques. It is normally a challenging task to reliably measure the delivered dose and to determine its distribution in a medium for such small fields using conventional-type dosimeters such as gas ionisation chambers. Recently, attempts have been made to use films, but they are not tissue equivalent, they measure the dose only in two dimensions and they are not as responsive to radiations. In the present work, polyacrylamide gel (PAG) dosimeters are employed to measure the dose and its distribution in three dimensions for very small field sizes, such as those typically used in stereotactic radiosurgery. Field sizes of 6 x 6 and 18 x 18 mm in width are investigated. The results show an agreement with radiochromic film and ionisation diode measurements, with some variation in measured doses near the edge of the field, where the gel data decreases more rapidly than the other methods.

[A clinical trial of oxymatrine in treating chronic viral hepatitis type B]

OBJECTIVE

To investigate the therapeutic effect of oxymatrine on chronic viral hepatitis type B.

METHODS

303 patients were randomly allocated either to a treatment group or a control group. The treatment group consisted of 253 patients treated with intravenous or intra-muscular injection of oxymatrine and oral oxymatrine capsule. Oral tiopronin was used in the control group.

RESULTS

At the end of treatment, the rate of normal ALT was similar among the different groups. The rate of normal ALT was 53.3% - 58.3% in the three oxymatrine groups six months after the end of treatment. It was higher than that of the tiopronin group (P < 0.05). After a follow up of six months, the rate of negative HBeAg was 30.0% - 40.9% in the three oxymatrine groups. It was higher than that of the tiopronin group (16.7%). The rate of negative HBV DNA was 39.2% - 49.5% in the three oxymatrine groups. It was also higher than that of the tiopronin group.

CONCLUSION

Oxymatrine can improve the liver function and increase the negative rate of HBeAg and HBV DNA in the patients with chronic hepatitis B. The therapeutic effect of oxymatrine will persist after the cessation of administration.

Mixture component effects on the in vitro dermal absorption of pentachlorophenol

Interactions between chemicals in a mixture and interactions of mixture components with the skin can significantly alter the rate and extent of percutaneous absorption, as well as the cutaneous disposition of a topically applied chemical. The predictive ability of dermal absorption models, and consequently the dermal risk assessment process, would be greatly improved by the elucidation and characterization of these interactions. Pentachlorophenol (PCP), a compound known to penetrate the skin readily, was used as a marker compound to examine mixture component effects using in vitro porcine skin models. PCP was administered in ethanol or in a 40% ethanol/60% water mixture or a 40% ethanol/60% water mixture containing either the rubefacient methyl nicotinate (MNA) or the surfactant sodium lauryl sulfate (SLS), or both MNA and SLS. Experiments were also conducted with 14C-labelled 3,3',4,4'-tetrachlorobiphenyl (TCB) and 3,3',4,4',5-pentachlorobiphenyl (PCB). Maximal PCP absorption was 14.12% of the applied dose from the mixture containing SLS, MNA, ethanol and water. However, when PCP was administered in ethanol only, absorption was only 1.12% of the applied dose. There were also qualitative differences among the absorption profiles for the different PCP mixtures. In contrast with the PCP results, absorption of TCB or PCB was negligible in perfused porcine skin, with only 0.14% of the applied TCB dose and 0.05% of the applied PCB dose being maximally absorbed. The low absorption levels for the PCB congeners precluded the identification of mixture component effects. These results suggest that dermal absorption estimates from a single chemical exposure may not reflect absorption seen after exposure as a chemical mixture and that absorption of both TCB and PCB are minimal in this model system.

[Clinical application and evaluation of polymerase chain reaction-microwell plate hybridization assay in the detection of Mycobacterium tuberculosis]

OBJECTIVE

To evaluate the clinical application and feasibility of polymerase chain reaction-microwell plate hybridization assay in the detection of Mycobacterium tuberculosis.

METHODS

1130 specimens with strong suspicion for mycobacterium tuberculosis were collected from the hospitals and were detected by fast bacilli stain, culture, PCR-electrophoresis and PCR-microwell plate hybridization respectively. The laboratory results were analyzed in combination with the symptoms and signs of patients and the observations on treatment. Also detected were 100 samples from the clinically evidenced non-tuberculosis patients.

RESULTS

In the 100 samples collected from the patients without tuberculosis, the PCR-hybridization method and culture method did not detect Mycobacterium tuberculosis, but the fast bacilli stain method and PCR-electrophoresis method brought out one and two false-positive results respectively. The results of testing the 1030 clinical samples which probably contained Mycobacterium tuberculosis demonstrated that the PCR-hybridization method had the highest positive rate (481/1030) among the four methods, and the positive rates of the other three methods were PCR-electrophoresis (406/1030), culture (365/1030) and fast bacilli stain (256/1030) in proper order. The chi-square test showed that there were significant difference between the PCR-hybridization method and the other three methods respectively (P < 0.0083 or P < 0.0017).

CONCLUSION

PCR-Hybridization method is specific, sensitive, accurate and fast in detecting mycobacterium tuberculosis; it is worthy to be used clinically.

Dermal absorption and tissue disposition of 3,3',4, 4'-tetrachlorobiphenyl (TCB) in an ex-vivo pig model: assessing the impact of dermal exposure variables

TCB is one of the dioxin-like polychlorinated biphenyls (PCBs). This research was designed to help assess the risk of occupational and environmental TCB exposure. To evaluate exposure variables' effects on dermal absorption and cutaneous disposition, 14C-TCB (40 microg/cm(2)) in acetone, methylene chloride, a water-acetone mixture, and a soil-based mixture were applied in an ex-vivo pig-skin-flap model (n = 4-5/treatment). Dermal absorption (0.11-0.66%, 8 hr) and penetration (1.14-2.48%) varied according to exposure conditions. Acetone and methylene chloride vehicles differed in absorption profiles and skin penetration patterns but were similar in absorption amounts. Adding water to the acetone did not change absorption but did alter the penetration pattern. The non-occluded soil-based mixture showed more absorption than did the liquid vehicles (p<0.05), but occlusion significantly (p<0.05) decreased that absorption (0.66-->0.29%, 8 hr) and penetration (2.48-->1.11%). In conclusion, dermal absorption data from liquid-organic or aqueousorganic mixtures may underestimate the risk of exposure to TCB-contaminated soil.

[Virus interaction in HBV and HCV super infection]

OBJECTIVE

To investigate virus interaction in HBV and HCV superinfection.

METHODS

The changes of serum markers of 30 patients with HBV and HCV superinfetion were observed. Meanwhile, mutation of HBV precore region at nt 1,896 and the amount of TNF alpha and IL-6 in sera were also investigated.

RESULTS

Compared with HBV or HCV single infection, positive rates of HBeAg, HBV DNA and HCV RNA in superinfectim were lower, positive rates of anti-HBe was higher, the average titers of HBsAg, anti-HBcIgG and anti-HCV were significantly lower, too. In some patients, HBsAg were seronegatively convested. Occurrence rate of HBV precore region mutation at nt1896 and levels of TNF alpha and IL-6 in sera were higher in super infection than those in single infection.

CONCLUSION

Interference existed between HBV and HCV superinfection, conversion from HBeAg to anti-HBe was not only due to the suppression by HCV but also to the mutation of HBV precore region, and HCV may be a reason causing HBV precore region mutation through increasing the pressure of the body's immunosystem.

Clinical implications of the correlation between coenzyme Q10 and vitamin B6 status

The endogenous biosynthesis of the quinone nucleus of coenzyme Q10 (CoQ10) from tyrosine is dependent on adequate vitamin B6 nutriture. Lowered blood and tissue levels of CoQ10 have been observed in a number of clinical conditions. Many of these clinical conditions are most prevalent among the elderly. Kalen et al. have shown that blood levels of CoQ10 decline with age. Similarly, Kant et al. have shown that indicators of vitamin B6 status also decline with age. Blood samples were collected from 29 patients who were not currently being supplemented with either CoQ10 or vitamin B6. Mean CoQ10 concentrations was 1.1 +/- 0.3 micrograms/ml of blood. Mean specific activities of EGOT was 0.30 +/- 0.13 mumol pyruvate/hr/10(8) erythrocytes and the mean percent saturation of EGOT with PLP was 78.2 +/- 13.9%. Means for all parameters were within normal ranges. Strong positive correlation was found between CoQ10 and the specific activity of EGOT (r = 0.5787, p < 0.001) and between CoQ10 and the percent saturation of EGOT with PLP (r = 0.4174, p < 0.024). Studies are currently in progress to determine the effect of supplementation with vitamin B6 of blood CoQ10 levels. It appears prudent to recommend that patients receiving supplemental CoQ10 be concurrently supplemented with vitamin B6 to provide for better endogenous synthesis of CoQ10 along with the exogenous CoQ10.

[Scale-up preparation of hydrophobic interaction chromatographic packing materials based on inorganic matrix]

Based on inorganic matrix controlled pore glass (CPG) and macro-pore silica sphere, by using polyethylene glycol (PEG 1000) as a ligand, a preparation method of hydrophobic interaction chromatographic (HIC) packing material was improved by adding a proper catalyst during the bonding process. The packing material can be synthesized in a scale-up batch, for example 150g for each batch, both for analytical and preparative columns. The retention of proteins, such as cytochrome C (Cyt-C), chymotrypsingen-A (Chy-A), lysozyme (Lys) and ribonuclease(Rnase), is increased with the increasing of (NH4)2SO4 concentration in the eluant 2.5 mol/L of salt concentration for the mobile phase was chosen by considering the separation efficiency and equipment life. After comparing the effect of pH for the retention of proteins it is found that the proteins are well separated at pH 7. The time of linear gradient elution program was optimized in considering the separation efficiency and speed. It is better to take 30 minutes of the gradient program for the separation. Six standard proteins can be well separated with the high-performance HIC column in the linear gradient elution program from 2.5 to 0 mol/L of (NH4)2SO4 in 50 mmol/L of phosphate buffer solution within 30 minutes. Cyt-C, Rnase, Lys and Chy-A can be separated by the HIC column based on CPG matrix. Six proteins, Cyt-C, Rnase, Lys, Chy-A, insulin(Ins) and lipase (Lip) can be well separated on the column based on silica matrix with gradient elution program. The recovery of trypsin detected with BAEE method is over 95% after purification with the HIC column.

Serologic association between human papillomavirus type 16 infection and esophageal cancer in Shaanxi Province, China

BACKGROUND

The existence of large geographic variations in the prevalence of esophageal cancer in some countries, such as China, indicates that environmental risk factors may be important in the development of this disease. Some studies have implicated genital-mucosal strains of human papillomaviruses (HPVs) in the etiology of this cancer.

PURPOSE

We conducted a case-control study in Shaanxi Province, China, an area with a population at high risk for esophageal cancer, to assess the association of this disease with infection by HPV type 16 (HPV16), the most common cancer-associated genital-mucosal HPV type.

METHODS

Ninety individuals with esophageal cancer and 121 cancer-free control subjects were identified among the patients in two hospitals in Xi'an, Shaanxi Province. The control subjects were matched to the case patients on the basis of age and sex. Blood specimens were drawn from all study subjects, and serum was isolated by routine methods. The presence of HPV16 antibodies in serum samples was determined by use of an enzyme-linked immunosorbent assay (ELISA) that used baculovirus-derived HPV16 virus-like particles as the antigen. A similar ELISA that used bovine papillomavirus type 1 (BPV1) virus-like particles as the antigen controlled for the specificity of HPV16 seroreactivity. Data from the HPV16 and the BPV1 assays were normalized with respect to results obtained in each assay with a control serum of known HPV16 seroreactivity. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to examine the association between HPV16 seroreactivity and esophageal cancer. Reported P values are two-sided.

RESULTS

The mean seroreactivity to HPV16 virus-like particles was significantly higher for the cancer patients than for the control subjects (mean value +/- standard deviation = 0.85 +/- 0.22 versus 0.74 +/- 0.18; P<.0001). When the cancer patients and control subjects were compared by sex and age groups, the differences in mean seroreactivity remained statistically significant. The difference in mean seroreactivity to BPV1 virus-like particles between cancer patients and control subjects was not statistically significant (0.81 +/- 0.28 versus 0.88 +/- 0.32; P = .12); this result was not altered when sex and age groups were compared. By use of a cutoff point for HPV16 seropositivity that was established in studies of cervical neoplasia, 24% of the cancer patients were seropositive compared with 7% of the control subjects, yielding a sex- and age-adjusted OR of 4.5 (95% CI = 1.8-11.9). In general, the OR for esophageal cancer increased with increasing HPV16 seroreactivity.

CONCLUSIONS AND IMPLICATIONS

HPV16 infection may be a risk factor for esophageal cancer. Further studies of the association between HPV16 infection and the incidence of esophageal cancer are needed.

[Overexpression of P53 and its risk factors in esophageal cancer in urban areas of Xian]

OBJECTIVE

To investigate the risk factors of esophageal cancer (EC) in urban areas of Xi'an, and to correlate these risk factors with overexpression of P53 in EC.

METHODS

A hospital-based case-control study was performed. All cases (89) and controls (97) were permanent residents in urban areas of Xi'an. Tumor tissues and normal tissues adjacent to tumors of 65 cases, and 24 available normal esophageal tissues of controls were detected by P53 overexpression via immunohistochemical method.

RESULTS

Smoking and family history of EC were significantly associated with EC in Xi'an inhabitants. OR was 3.26 and 10.48, respectively. The laboratory findings indicated that P53 positive stain in Ec was 52.3% (34/65) and 6.1% (4/65) in normal tissues adjacent to tumor, but no positive stain was found in normal esophageal tissues of controls. Moreover, the results showed that P53 overexpression was closely related to smoking and family history of EC. OR was 3.89 and 17.28, respectively.

CONCLUSION

These findings suggest that smoking and family history of EC are important risk factors for EC, and the alteration of P53 gene may be related to smoking and inherited factor.