De novo assembly, functional annotation, and marker development of Asian pear (Pyrus pyrifolia) fruit transcriptome through massively parallel sequencing

This study investigated the Asian pear transcriptome using the RNA-Seq normalized fruit cDNA library to create a transcriptomic resource for unigene and marker discovery. Following the removal of lowquality reads, 127,085,054 trimmed reads were assembled de novo to yield 37,649 non-redundant unigenes with an average length of 599 bp. Alternative splicing events were detected in 4121 contigs. A total of 30,560 single nucleotide polymorphisms (SNPs) and 7443 simple sequence repeat (SSR) makers were obtained. Approximately 21,449 (56.9%) unigenes were categorized into three gene ontology groups; 3682 (9.8%) were classified into 25 cluster of orthologous groups; and 10,451 (27.8%) were assigned to six Kyoto Encyclopedia of Genes and Genomes pathways. Differentially expressed genes were investigated using the reads per kilobase of the exon model per million reads methodology. A total of 546 unigenes showed significant differences in expression levels at different fruit developmental stages. Gene ontology categories associated with various aspects, including carbohydrate metabolic processes, transmembrane transport, and signal transduction, were enriched with genes with divergent expressions. These Pyrus pyrifolia transcriptome data provide a rich resource for the discovery and identification of new genes. Furthermore, the numerous putative SSRs and SNPs detected in this study will be important resources for the future development of a linkage map or of marker-assisted breeding programs for the Asian pear.

Low level measurement of (60)Co by gamma ray spectrometry using γ-γ coincidence

This paper presents the latest development of the laboratory to measure the natural and artificial massic activities in environmental samples. The measurement method of coincident emitters by gamma-gamma coincidence using an anti-Compton device and its digital electronics is described. Results obtained with environmental samples are shown. Despite its low efficiency, this method decreases detection limits of (60)Co for certain samples compared to conventional gamma-ray spectrometry due to its very low background.

Reciprocal positive regulation between Cx26 and PI3K/Akt pathway confers acquired gefitinib resistance in NSCLC cells via GJIC-independent induction of EMT

Gefitinib efficiency in non-small-cell lung cancer (NSCLC) therapy is limited due to development of drug resistance. The molecular mechanisms of gefitinib resistance remain still unclear. In this study, we first found that connexin 26 (Cx26) is the predominant Cx isoform expressed in various NSCLC cell lines. Then, two gefitinib-resistant (GR) NSCLC cell lines, HCC827 GR and PC9 GR, from their parental cells were established. In these GR cells, the results showed that gefitinib resistance correlated with changes in cellular EMT phenotypes and upregulation of Cx26. Cx26 was detected to be accumulated in the cytoplasm and failed to establish functional gap-junctional intercellular communication (GJIC) either in GR cells or their parental cells. Ectopic expression of GJIC-deficient chimeric Cx26 was sufficient to induce EMT and gefitinib insensitivity in HCC827 and PC9 cells, while knockdown of Cx26 reversed EMT and gefitinib resistance in their GR cells both in vitro and in vivo. Furthermore, Cx26 overexpression could activate PI3K/Akt signaling in these cells. Cx26-mediated EMT and gefitinib resistance were significantly blocked by inhibition of PI3K/Akt pathway. Specifically, inhibition of the constitutive activation of PI3K/Akt pathway substantially suppressed Cx26 expression, and Cx26 was confirmed to functionally interplay with PI3K/Akt signaling to promote EMT and gefitinib resistance in NSCLC cells. In conclusion, the reciprocal positive regulation between Cx26 and PI3K/Akt signaling contributes to acquired gefitinib resistance in NSCLC cells by promoting EMT via a GJIC-independent manner.

Type II deiodinase polymorphisms and serum thyroid hormone levels in patients with mild cognitive impairment

We investigated type II deiodinase (DIO2) polymorphisms and serum thyroid hormone levels in subjects with mild cognitive impairment (MCI) in a Uygur population. We studied the DIO2 Thr92Ala (rs225014) and ORFa-Gly3Asp (rs12885300) polymorphisms of 129 unrelated MCI cases and 131 matched controls. All subjects were genotyped using SNaPshot SNP genotyping assays. Serum thyroid hormone levels were measured by radioimmunoassay. Levels of serum triiodothyronine and thyroxine in the MCI group were significantly lower than those in the control group. Genotype and allele frequencies in the DIO2 gene between the MCI and control groups were not significantly different. There was no association in genotype and allele frequencies of Thr92Ala between genders in both groups. ORFa-Gly3Asp genotype and allele frequencies were significantly different in patients and controls by gender. The Asp allele was less frequent among male MCI patients compared to controls (odds ratio = 0.471, 95% confidence interval = 0.261-0.848). However, female Asp carriers were more frequent among MCI patients than among controls (odds ratio = 2.842, 95% confidence interval = 1.326-6.09). Serum levels of triiodothyronine and thyroxine were lower in individuals of the Ala/Ala genotype than in those with the Thr/Thr or Thr/Ala genotype. Serum levels of triiodothyronine were lower in male Gly/Gly carriers than in Gly/Asp or Asp/Asp carriers. Decreased serum levels of triiodothyronine and thyroxine may influence the incidence of MCI in the Uygur population. DIO2 gene polymorphisms may play a role in the incidence of MCI in male patients.

Identification and characterisation of tobacco microRNA transcriptome using high-throughput sequencing

MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in numerous biological processes in plants. In this study, we investigate miRNAs in Honghua Dajinyuan, an agronomically important species of tobacco in China. Here, we report a comprehensive analysis of miRNA expression profiles in the leaf, stem and root using a high-throughput sequencing approach. A total of 165 miRNAs, representing 55 conserved families, and 50 novel miRNAs, representing 19 families, were identified in three libraries. In addition, 12 miRNAs were randomly selected from a differentially expressed conserved miRNA family in three libraries with expression alterations and subjected to qRT-PCR validation. Of these, the expression level of nta-miR167d is highly enriched in the leaf tissue. In addition, the expression level of nta-miR319a is prominently enriched in the stem, while nta-miR160c is highly enriched in the root. Moreover, the target prediction showed that most of the targets coded for transcription factors that are involved in cellular and metabolic processes. GO analysis showed that most of the targets were involved in organelle function, served binding functions, and take part in cellular and metabolic processes. This study helps shed new light on understanding the role of miRNAs in different parts of the tobacco plant and adds a significant number of novel miRNAs to the tobacco miRNA transcriptome.

Effects of estrogen intervention on the biomechanical characteristics of serum SOD, MDA, and middle cerebral artery in aged female rats

OBJECTIVE

This study aims to study the biological and biomechanical characteristics of the middle cerebral artery (MCA) in aged and estrogen-intervened aged rats, thereby providing biomechanical basis for clinics.

MATERIALS AND METHODS

Thirty 18-month-old Sprague Dawley (SD) rats, 30 18-month-old estrogen-intervened SD rats, and 30 four-month-old SD rats were studied. The estrogen-intervened rats were given estradiol benzoate on the fifth feeding day. Thirty-four days after the feeding, the serum of each rat was obtained. The radioimmunoassay was performed for the content determination of serum E2, ER, malondialdehyde (MDA), and superoxide dismutase (SOD). The tensile test was performed to evaluate the MCA of each rat.

RESULTS

Through the estrogen intervention, the serum contents of E2, ER, SOD, and MDA in old rats were restored to normal levels. The maximum stress, maximum strain, and elastic limit of the MCA in the aged estrogen-intervened rat group were greater than those of the non-intervened aged rat group, with a significant difference (p < 0.05). The elastic modulus in the aged estrogen-intervened rat group was less than that of the non-intervened aged rat group, with a significant difference (p < 0.05).

CONCLUSION

E2 intervention can improve the flexibility, toughness, and compliance of MCA in aged rats.

Highly regioselective and alternating copolymerization of carbonyl sulfide with phenyl glycidyl ether

Polymer structures containing sulfur atoms can provide enhancement of important polymer properties compared to their oxygen-containing counterparts.

Changes in the metabolism of chondroitin sulfate glycosaminoglycans in articular cartilage from patients with Kashin-Beck disease

OBJECTIVES

To identify changes in the expression patterns of enzymes involved in chondroitin sulfate (CS) glycosaminoglycan (GAG) metabolism in articular cartilage proteoglycan (PG) isolated from adolescent patients with Kashin-Beck disease (KBD).

METHODS

Samples of articular cartilage were divided into two groups: Control samples (from five normal children), and KBD samples (from five KBD children) aged 3-12 years old. The morphology and pathology of hand joint cartilage were examined by histochemical staining. The localization and expression patterns of enzymes involved in CS GAG metabolism (i.e., PAPS synthetase 2 (PAPSS2), PAPS transporter 1 (PAPST1), Carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferases 15 (CHST15), Arylsulfatase B (ARSB) and N-acetylgalactosamine-6-sulfate sulfatase (GALNS)) were performed using immuno-histochemical analyses. Positive immunostaining in articular cartilage was semi-quantified.

RESULTS

Reduced aggrecan staining was observed in KBD samples compared with the control samples. The percentages of positive staining for the anabolic enzymes PAPSS2, PAPST1 and CHST15 in the upper and middle zones of KBD samples were significantly lower than that found in the Controls. In contrast, the percentages of positive staining in KBD samples for the catabolic enzymes ARSB and GALNS were significantly higher than the control samples. However, the staining for all of these GAG metabolism enzymes were hardly observed in the deep zones of KBD cartilage, suggesting that significant cell death and necrosis had occurred in this region.

CONCLUSIONS

Our results indicate that alterations of enzymes involved in articular cartilage CS GAG metabolism on PGs in the articular cartilage play an important role in the onset and pathogenesis of KBD in adolescent children.

HCOOH measurements from space: TES retrieval algorithm and observed global distribution

Presented is a detailed description of the TES (Tropospheric Emission Spectrometer)-Aura satellite formic acid (HCOOH) retrieval algorithm and initial results quantifying the global distribution of tropospheric HCOOH. The retrieval strategy, including the optimal estimation methodology, spectral microwindows, a priori constraints, and initial guess information, are provided. A comprehensive error and sensitivity analysis is performed in order to characterize the retrieval performance, degrees of freedom for signal, vertical resolution, and limits of detection. These results show that the TES HCOOH retrievals (i) typically provide at best 1.0 pieces of information; (ii) have the most vertical sensitivity in the range from 900 to 600 hPa with ~2 km vertical resolution; (iii) require at least 0.5 ppbv (parts per billion by volume) of HCOOH for detection if thermal contrast is greater than 5 K, and higher concentrations as thermal contrast decreases; and (iv) based on an ensemble of simulated retrievals, are unbiased with a standard deviation of ±0.4 ppbv. The relative spatial distribution of tropospheric HCOOH derived from TES and its associated seasonality are broadly correlated with predictions from a state-of-the-science chemical transport model (GEOS-Chem CTM). However, TES HCOOH is generally higher than is predicted by GEOS-Chem, and this is in agreement with recent work pointing to a large missing source of atmospheric HCOOH. The model bias is especially pronounced in summertime and over biomass burning regions, implicating biogenic emissions and fires as key sources of the missing atmospheric HCOOH in the model.

Identification of a novel HLA-B*51 variant allele, B*51:59, in a Chinese Han individual

HLA-B*51 differs from the closest allele B*51:06:01 by nt 956 C > T (codon 171 CAC>TAC) missense mutation in exon 3.

Detection and correction of assembly errors of rice Nipponbare reference sequence

A complete and high-quality genome reference sequence of an organism provides a solid foundation for a wide research community and determines the outcomes of relevant genomic, genetic, molecular and evolutionary research. Rice is an important food crop and a model plant for grasses, and therefore was the first chosen crop plant for whole genome sequencing. The genome of the japonica representative rice variety, Nipponbare, was sequenced using a gold standard, map-based clone-by-clone strategy. However, although the Nipponbare reference sequence (RefSeq) has the best quality for existing crop genome sequences, it still contains many assembly errors and gaps. To improve the Nipponbare RefSeq, first a robust method is required to detect the hidden assembly errors. Through alignments between BAC-end sequences (BESs) embedded in the Nipponbare bacterial artificial chromosome (BAC) physical map and the Nipponbare RefSeq, we detected locations on the Nipponbare RefSeq that were inversely matched with BESs and could therefore be candidates for spurious inversions of assembly. We performed further analysis of five potential locations and confirmed assembly errors at those locations; four of them, two on chr4 and two on chr11 of the Nipponbare RefSeq (IRGSP build 5), were found to be caused by reverse repetitive sequences flanking the locations. Our approach is effective in detecting spurious inversions in the Nipponbare RefSeq and can be applied for improving the sequence qualities of other genomes as well.

Chromosome landing at the bacterial blight resistance gene Xa4 locus using a deep coverage rice BAC library

Xa4 is a dominantly inherited rice gene that confers resistance to Philippine race 1 of the bacterial blight pathogen Xanthomonas oryzae pv. oryzae in rice. In order to isolate the gene by positional cloning, a bacterial artificial chromosome (BAC) library was constructed from genomic DNA isolated from an Xa4-harboring accession, IRBB56. The library contains 55,296 clones with an average insert size of 132 kb, providing 14 rice genome equivalents. Three DNA markers closely linked to Xa4 were used to screen the library. The marker RS13, a resistance gene analogue that co-segregates with Xa4, identified 18 clones, of which four and six, respectively, were simultaneously detected by the other two markers, G181 and L1044. Fingerprinting and Southern analysis indicated that these clones overlapped and define an interval spanning 420 kb. In an F2 population derived from an indica variety, IR24, and its Xa4-containing near isogenic line (NIL), IRBB4, the susceptible plants were screened in order to map the Xa4 gene genetically and physically. Out of 24 insert ends isolated from the BACs in the contig, three revealed polymorphisms between IR24 and IRBB4. Two insert ends, 56M22F and 26D24R, flanked Xa4 on each side. Based on the overlap of the BACs, six overlapping clones were considered to include the Xa4 allele, one of which, 106P13, was chosen for further investigation.

Oxidative stress and status of antioxidant enzymes in children with Kashin-Beck disease

OBJECTIVES

To clarify whether there is oxidative stress in Kashin-Beck disease (KBD) and if cartilage damage from reactive oxygen species (ROS) and oxidative stress mediate the chondral necrosis in articular cartilage of KBD.

METHODS

We recruited 64 KBD patients, 46 healthy children from severely affected KBD regions, 81 healthy children from a non-severely affected KBD endemic regions, and 91 healthy control children from a non-KBD region. Ten patients with KBD from the non-severely affected KBD regions were included in the experiment. The 2,3-DAN fluorescence technique was used to test selenium in the hair and blood. The biochemical techniques used to test the indicators of oxidative stress included thiobarbituric acid reactive substances (TBARS) levels, and antioxidant enzyme activities in serum samples. Histochemical staining was used to detect proteoglycans in cartilage sections. The 4-hydroxy-2-nonenal (4-HNE) and 8-hydroxydeoxyguanisine (8-OHdG) were localized by immunohistochemistry.

RESULTS

The levels of TBARS in serum were significantly increased in KBD children. The levels of antioxidants in serum were significantly higher in both KBD and normal children from KBD regions than in the normal children from non-KBD regions. The percentage of chondrocytes staining for 4-HNE and 8-OHdG in KBD patients was significantly higher than in controls. Staining for 4-HNE and 8-OHdG in KBD patients was prominent in all zones of articular cartilage, especially in the necrotic chondrocytes of the deep zone.

CONCLUSION

KBD is an oxidative stress-related disease, and the oxidative stress in cartilage contributes to the pathology of cartilage damage in KBD.

Emergency endovascular stent-grafting for acute type B aortic dissection with symptomatic malperfusion

AIM

The aim of this paper was to analyze the durability and efficacy of emergency thoracic endovascular aortic repair (TEVAR) for acute Stanford type B aortic dissection (TBAD) with malperfusion syndrome.

METHODS

A retrospective analysis of acute TBAD with spinal cord, kidney, viscera, and extremity malperfusion was performed. Emergency TEVAR to cover primary tear site by stent-graft was strongly suggested to included candidates. Computed tomography (CT) scans and clinical findings were carried out in diagnosis and follow-up.

RESULTS

One hundred twenty-seven TBAD patients (101 men, 46.1±11.4 year, range 34~76) who presented with acute end-organ malperfusion, including sudden paraplegia (N.=4), acute renal failure (N.=26), acute viscera ischemia (N.=61) and limb ischemia (N.=36), received aortic stent-grafting 2~48 hours after onset. Technical success was achieved in all primary TEVAR. The overall endoleak rate was 7.1% (9/127; typeI:3; typeII: 4; typeIV: 2). The 30-day mortality was 0.8% (2/127). 125 patients were followed for 19.1±14.5 (1~86) months, one patient died 50 days post-TEVAR due to myocardial infarction. Four patients required reintervention with additional stent grafts. Follow-up CT angiography showed enlargement of the true lumen and different degrees of thrombosis in the distal false lumen (complete thrombosis in 48, partial thrombosis in 52 and patency in 24).

CONCLUSION

Emergency TEVAR is an effective method to treat acute TBAD complicated with end-organ malperfusion. Covering of the proximal entry site of TBAD by stent-graft leads to flow increased in the true lumen and thrombosis of the false lumen of varying degree, which may improve end-organ perfusion and restore branch vessels patency.