Nanopore sequencing reveals full-length Tropomyosin 1 isoforms and their regulation by RNA-binding proteins during rat heart development

Alternative splicing (AS) contributes to the diversity of the proteome by producing multiple isoforms from a single gene. Although short-read RNA-sequencing methods have been the gold standard for determining AS patterns of genes, they have a difficulty in defining full-length mRNA isoforms assembled using different exon combinations. Tropomyosin 1 (TPM1) is an actin-binding protein required for cytoskeletal functions in non-muscle cells and for contraction in muscle cells. Tpm1 undergoes AS regulation to generate muscle versus non-muscle TPM1 protein isoforms with distinct physiological functions. It is unclear which full-length Tpm1 isoforms are produced via AS and how they are regulated during heart development. To address these, we utilized nanopore long-read cDNA sequencing without gene-specific PCR amplification. In rat hearts, we identified full-length Tpm1 isoforms composed of distinct exons with specific exon linkages. We showed that Tpm1 undergoes AS transitions during embryonic heart development such that muscle-specific exons are connected generating predominantly muscle-specific Tpm1 isoforms in adult hearts. We found that the RNA-binding protein RBFOX2 controls AS of rat Tpm1 exon 6a, which is important for cooperative actin binding. Furthermore, RBFOX2 regulates Tpm1 AS of exon 6a antagonistically to the RNA-binding protein PTBP1. In sum, we defined full-length Tpm1 isoforms with different exon combinations that are tightly regulated during cardiac development and provided insights into the regulation of Tpm1 AS by RNA-binding proteins. Our results demonstrate that nanopore sequencing is an excellent tool to determine full-length AS variants of muscle-enriched genes.     

外源SNP对干旱胁迫下不同马铃薯品种叶片抗氧化酶活性的影响

以正常水分状态、轻度干旱胁迫、中度干旱胁迫和重度干旱胁迫下的马铃薯抗旱品种‘底西瑞’和干旱敏感品种‘大西洋’ 植株为材料,于现蕾期采用0（对照）和0.01 mmol·L^-1 SNP分别喷施各处理植株,对不同处理下2个品种的植株形态、叶片超氧阴离子和H₂O₂含量以及抗氧化酶活性进行比较分析,探讨外源SNP对干旱状态下马铃薯的生理应答机制,为马铃薯的抗旱栽培提供新的技术理论支持。结果显示：（1）SNP喷施对重度水分胁迫下马铃薯植株的正常生长具有一定的保护作用。（2）在干旱胁迫条件下,马铃薯叶片POD活性在品种‘底西瑞’中增加而在品种‘大西洋’中降低,超氧阴离子含量和H₂O₂含量以及CAT和APX活性在各品种中均增加,但超氧阴离子含量和H₂O₂含量增加程度与胁迫程度无关。（3）抗旱品种‘底西瑞’在干旱胁迫下的超氧阴离子含量低于干旱敏感品种‘大西洋’,而其POD、CAT和APX活性则高于‘大西洋’; 0.01 mmol·L^-1SNP处理未改变马铃薯叶片中超氧阴离子和H₂O₂含量随土壤水分的变化趋势,但改变了‘大西洋’叶片中SOD、POD、CAT活性以及‘底西瑞’叶片中APX活性的变化趋势。（4）外源喷施0.01 mmol·L^-1SNP降低了‘底西瑞’在中度和重度胁迫下以及‘大西洋’在轻度和中度胁迫下超氧阴离子含量,提高了干旱胁迫下‘底西瑞’和‘大西洋’的POD和APX活性。研究表明,POD、CAT和APX可作为马铃薯水分胁迫下的应答以及品种抗旱性的筛选指标,外源SNP可通过诱导增强干旱胁迫下马铃薯的抗氧化酶活性来提高其抗旱性。     

The Modified Sequential Treatment Regimen Containing Levofloxacin for Helicobacter pylori Eradication in Turkey

Background:  Eradication rates of Helicobacter pylori have declined to unacceptable levels in recent years. New and effective treatment options are warranted both as a first and second line treatment.
Aim:  To test an effectiveness of modified sequential therapy with levofloxacin for H. pylori eradication in Turkey.
Material and Methods:  Helicobacter pylori infected dyspeptic patients were included to the study. Subjects were treated with modified sequential therapy consisting of rabeprazole 20 mg b.i.d. and amoxicillin 1 g b.i.d., for 7 days followed by rabeprazole 20 mg b.i.d, levofloxacin 500 mg q.d. and metronidazole 500 mg b.i.d for the remaining 7 days.
Results:  Sixty-three treatment naive patients and 37 previous treatment failures were enrolled to the study (59 F, 41 M, age: 21–80 years). There was five drop out. Helicobacter pylori eradication was achieved in 80 patients, intention-to-treat (ITT): 80% (95% CI: 71–87%) and per-protocol (PP): 84.2% (95% CI: 75–91%), totally. In treatment naive patients ITT and PP eradication rates were 82.5% (95% CI: 71–91%), and 86.7% (95% CI: 75–94%), respectively. As a second line treatment eradication was successful in ITT 75.7%.(95% CI: 59–88%), and PP 80% (95% CI: 63–92%).Mild side effects were reported by 8 patients (8.4%).
Conclusions:  Sequential therapy using "rabeprazole and amoxicillin 7 days followed by rabeprazole, metronidazole and levofloxacin for 7 days" is a new regimen with acceptable eradication rates in naïve patients in Turkey. Further modifications in the dose or duration of this new sequential therapy might increase its effectiveness as both first and second line treatment.     

Diagnosis of Helicobacter pylori infection and determination of clarithromycin resistance by fluorescence in situ hybridization from formalin-fixed, paraffin-embedded gastric biopsy specimens

A reliable diagnostic test for Helicobacter pylori is important in clinical practice and research. The ideal diagnostic test for H. pylori should be sensitive, specific, and cost-effective. Helicobacter pylori resistance to clarithromycin is a common reason for failure of eradication therapy. The aim of this study was to evaluate the fluorescent in situ hybridization (FISH) method to detect H. pylori and determine clarithromycin resistance in formalin-fixed, paraffin-embedded gastric biopsy specimens. One hundred seventeen gastric biopsy specimens from patients with dyspepsia were examined for the presence of H. pylori by conventional culture, FISH, and histopathological methods. A set of fluorescent-labeled oligonucleotide probes binding to either H. pylori 16S rRNA or 23S rRNA sequences were used for FISH analysis. Phenotypic antibiotic susceptibilities of the isolates were tested using the Epsilometer test method (E test). Helicobacter pylori was detected in 70 of 117 biopsy specimens by histopathological examination and FISH, whereas it was detected in 47 specimens by culturing. Histopathology and FISH techniques failed to identify H. pylori in 1 biopsy sample isolated by culture. Clarithromycin resistance was found in 11 of 46 H. pylori isolates using the E test method. All of the phenotypic resistance measurements of isolates were correlated with genotypic clarithromycin resistance. Eleven clarithromycin-resistant strains were identified by FISH. The diagnosis of H. pylori infection and the determination of clarithromycin resistance in formalin-fixed, paraffin-embedded specimens using FISH is promising because it provides a rapid, reliable, and culture-independent diagnosis.     

Development and brain delivery of chitosan-PEG nanoparticles functionalized with the monoclonal antibody OX26

The inhibition of the caspase-3 enzyme is reported to increase neuronal cell survival following cerebral ischemia. The peptide Z-DEVD-FMK is a specific caspase inhibitor, which significantly reduces vulnerability to the neuronal cell death. However, this molecule is unable to cross the blood-brain barrier (BBB) and to diffuse into the brain tissue. Thus, the development of an effective delivery system is needed to provide sufficient drug concentration into the brain to prevent cell death. Using the avidin (SA)-biotin (BIO) technology, we describe here the design of chitosan (CS) nanospheres conjugated with poly(ethylene glycol) (PEG) bearing the OX26 monoclonal antibody whose affinity for the transferrin receptor (TfR) may trigger receptor-mediated transport across the BBB. These functionalized CS-PEG-BIO-SA/OX26 nanoparticles (NPs) were characterized for their particle size, zeta potential, drug loading capacity, and release properties. Fluorescently labeled CS-PEG-BIO-SA/OX26 nanoparticles were administered systemically to mice in order to evaluate their efficacy for brain translocation. The results showed that an important amount of nanoparticles were located in the brain, outside of the intravascular compartment. These findings, which were also confirmed by electron microscopic examination of the brain tissue indicate that this novel targeted nanoparticulate drug delivery system was able to translocate into the brain tissue after iv administration. Consequently, these novel nanoparticles are promising carriers for the transport of the anticaspase peptide Z-DEVD-FMK into the brain.     

Increased DNA damage in patients with complete hydatidiform mole

The pathologic mechanisms underlying the gestational trophoblastic diseases are largely unexplored, but are thought to involve oxidative damage to the maternal vasculature and also to the placenta. In this study we have assessed the plasma levels of total antioxidant response (TAR) and the levels of endogenous DNA damage--determined by the comet assay--in peripheral blood lymphocytes from 13 women with complete hydatidiform mole (CHM) and compared these with those of 12 healthy pregnant controls and 10 healthy non-pregnant controls. Significantly lower mean levels of plasma TAR were found in patients with CHM compared with healthy pregnant controls (1.08+/-0.29 versus 1.17+/-0.14 mmol Trolox Eq/L, p<0.05) and with healthy non-pregnant controls (1.08+/-0.29 versus 1.38+/-0.12 mmol Trolox Eq/L, p<0.05). Significantly higher mean levels of endogenous DNA damage were observed in patients with CHM than in healthy pregnant controls (234.5+/-50.74 versus 125.7+/-45.4 AU, p<0.05) or in healthy non-pregnant controls (234.5+/-50.74 versus 104.0+/-49.6 AU, p<0.05). We observed an inverse correlation between the plasma TAR and the levels of endogenous DNA damage (r=-0.64, p<0.01), in that the levels of oxidative damage to the DNA were found to parallel the decrease in the plasma TAR in the CHM group. These results reveal a relationship between the extracellular and intracellular (as reflected by damage to the DNA) levels of oxidation. Our observations suggest that there is a link between the increased levels of oxidative stress and the increase in endogenous DNA damage seen in patients with CHM, as compared with those seen in normal pregnancy. However, the nature of this link, and whether it is direct or indirect, remains to be explored.     

Efficient cleavage of ribosome-associated poly(A)-binding protein by enterovirus 3C protease

Poliovirus (PV) causes a rapid and drastic inhibition of host cell cap-dependent protein synthesis during infection while preferentially allowing cap-independent translation of its own genomic RNA via an internal ribosome entry site element. Inhibition of cap-dependent translation is partly mediated by cleavage of an essential translation initiation factor, eIF4GI, during PV infection. In addition to cleavage of eIF4GI, cleavage of eIF4GII and poly(A)-binding protein (PABP) has been recently proposed to contribute to complete host translation shutoff; however, the relative importance of eIF4GII and PABP cleavage has not been determined. At times when cap-dependent translation is first blocked during infection, only 25 to 35% of the total cellular PABP is cleaved; therefore, we hypothesized that the pool of PABP associated with polysomes may be preferentially targeted by viral proteases. We have investigated what cleavage products of PABP are produced in vivo and the substrate determinants for cleavage of PABP by 2A protease (2A(pro)) or 3C protease (3C(pro)). Our results show that PABP in ribosome-enriched fractions is preferentially cleaved in vitro and in vivo compared to PABP in other fractions. Furthermore, we have identified four N-terminal PABP cleavage products produced during PV infection and have shown that viral 3C protease generates three of the four cleavage products. Also, 3C(pro) is more efficient in cleaving PABP in ribosome-enriched fractions than 2A(pro) in vitro. In addition, binding of PABP to poly(A) RNA stimulates 3C(pro)-mediated cleavage and inhibits 2A(pro)-mediated cleavage. These results suggest that 3C(pro) plays a major role in processing PABP during virus infection and that the interaction of PABP with translation initiation factors, ribosomes, or poly(A) RNA may promote its cleavage by viral 2A and 3C proteases.     

Gossypol Interferes with Both Type I and Type II Topoisomerase Activities Without Generating Strand Breaks

A considerable number of agents with chemotherapeutic potentials reported over the past years were shown to interfere with the reactions of DNA topoisomerases, the essential enzymes that regulate conformational changes in DNA topology. Gossypol, a naturally occurring bioactive phytochemical is a chemopreventive agent against various types of cancer cell growth with a reported activity on mammalian topoisomerase II. The compounds targeting topoisomerases vary in their mode of action; class I compounds act by stabilizing covalent topoisomerase-DNA complexes resulting in DNA strand breaks while class II compounds interfere with the catalytic function of topoisomerases without generating strand breaks. In this study, we report Gossypol as the interfering agent with type I topoisomerases as well. We also carried out an extensive set of assays to analyze the type of interference manifested by Gossypol on DNA topoisomerases. Our results strongly suggest that Gossypol is a potential class II inhibitor as it blocked DNA topoisomerase reactions with no consequently formed strand breaks.