Genomic Pathogen Typing Using Solid-State Nanopores

In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based “fingerprints” of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.     

Circulating MiRNA-122 Levels Are Associated with Hepatic Necroinflammation and Portal Hypertension in HIV/HCV Coinfection

BackgroundIntroduction of combined antiretroviral therapy (cART) has improved survival of HIV infected individuals, while the relative contribution of liver-related mortality increased. Especially in HIV/HCV-coinfected patients hepatic fibrosis and portal hypertension represent the main causes of liver-related morbidity and mortality. Circulating miRNA-122 levels are elevated in HIV patients and have been shown to correlate with severity of liver injury. However, the association of miRNA-122 levels and hepatic fibrosis and portal hypertension remains to be explored in HIV/HCV coinfection.MethodsFrom a total of 74 (31% female) patients with HIV/HCV coinfection were included. Serum levels of miRNA-122 were analyzed by quantitative polymerase chain reaction (PCR) and normalized to SV-40 spike-in RNA. Hepatic venous pressure gradient (HVPG) was measured in 52 (70%) patients and the fibrosis stage was determined in 63 (85%) patients using transient elastography.ResultsThe levels of circulating miRNA-122 were increased in HIV/HCV coinfected patients and significantly correlated with the alanine aminotransferase (ALT) (r_s = 0.438; p<0.001) and aspartate transaminase AST values (r_s = 0.336; p = 0.003), but not with fibrosis stage (p = n.s.). Interestingly, miRNA-122 levels showed an inverse correlation with hepatic venous pressure gradient (HVPG) (r_s = −0.302; p = 0.03).ConclusionElevated miRNA-122 levels are associated with liver injury, and with low HVPG. Though, miRNA-122 levels are not suitable to predict the degree of fibrosis, they might function as indicators for portal hypertension in HIV/HCV coinfected patients.     

Effects of N-acetyl-l-cysteine on bleomycin induced oxidative stress in malignant testicular germ cell tumors

Testicular cancer is a very common cancer in males aged 15–44 years. Bleomycin is used in chemotherapy regimens in the treatment of patients having testicular germ-cell tumor. Bleomycin generates oxygen radicals, induces oxidative cleavage of DNA strand and induces apoptosis in cancer cells. There is no study in the literature investigating effects of N-Acetyl-l-Cysteine (NAC) on bleomycin-induced oxidative stress in testicular germ cell tumors. For this reason, we studied effects of NAC on oxidative stress produced in wild-type NTera-2 and p53-mutant NCCIT testis cancer cells incubated with bleomycin and compared the results with H₂O₂ which directly produces oxidative stress. We determined protein carbonyl content, thiobarbituric acid reactive substances (TBARS), glutathione (GSH), 8-isoprostane, lipid hydroperoxide levels and total antioxidant capacity in both testicular cancer cells. Bleomycin and H₂O₂ significantly increased 8-isoprostane, TBARS, protein carbonyl and lipid hydroperoxide levels in NTera-2 and NCCIT cells. Bleomycin and H₂O₂ significantly decreased antioxidant capacity and GSH levels in both cell lines. Co-incubation with NAC significantly decreased lipid hydroperoxide, 8-isoprostane, protein carbonyl content and TBARS levels increased by bleomycin and H₂O₂. NAC enhanced GSH levels and antioxidant capacity in the NTera-2 and NCCIT cells. It can be concluded that NAC diminishes oxidative stress in human testicular cancer cells induced by bleomycin and H₂O₂.     

An overview of biodiversity and conservation status of steppes of the Anatolian Biogeographical Region

The Anatolian Biogeographical Region is unique in the Palearctic realm, with high plant and butterfly species richness and populations of globally threatened birds, mammals and herptiles (amphibians and reptiles). It is a place of diverse land-use practices, dating back to the earliest farming practices in the world. Among 10,930 species of vascular plants, birds, butterflies, mammals and herptiles distributed in Turkey, we identified 1130 living predominantly in steppic environments and being classified either as threatened, near-threatened or data deficient at the national level, if not globally. A total of 28 effective protected areas were present in the region, covering 1.5 % of the 391,597 km² land area. Only 16.2 % of the threatened and near-threatened species (n = 809) were distributed within the protected area network, ranging from 94.1 % for birds to as low as 12.9 % for vascular plants. The total area of steppe and steppe forest vegetation has been reduced by at least 44 % of its former extent due to diverse habitat destructive activities. The most significant threats arise from unsustainable agricultural activities including overgrazing, conversion to croplands and afforestation. To maintain steppe diversity, we propose a “to-do list”, including mainstreaming biodiversity, effective implementation of Turkey’s Rangeland Act, conducting effective environmental impact assessments, establishing an effective site network for steppe biodiversity conservation and filling gaps in scientific knowledge.     

Effects of Carvacrol on Sister Chromatid Exchanges in Human Lymphocyte Cultures

Carvacrol is a predominant aromatic compound in oil of oregano. It has naturally remarkable antibacterial, antiviral, antifungal and antiparasital effects. In this study, genotoxic and antigenotoxic activities of carvacrol were investigated by the in vitro sister chromatid exchange (SCE) assay on human peripheral blood lymphocytes. The genotoxicity test was performed with carvacrol in two donors. On the other hand, inhibitory effect of carvacrol was tested in the presence of mitomycin C (MMC) in the same assay. According to data, all doses of carvacrol did not increase the formation of SCE, whereas it inhibited the rate of SCE induced by MMC. In conclusion, carvacrol exhibited a significant antigenotoxic activity in mammalian cells, indicating its potential for use as an antigenotoxic agent.     

Natural Variation in the Drosophila melanogaster Clock Gene Period Modulates Splicing of Its 3′-Terminal Intron and Mid-Day Siesta

Drosophila melanogaster exhibits circadian (≅24 hr) regulated morning and evening bouts of activity that are separated by a mid-day siesta. Increases in daily ambient temperature are accompanied by a progressively longer mid-day siesta and delayed evening activity. Presumably, this behavioral plasticity reflects an adaptive response that endows D. melanogaster with the ability to temporally optimize daily activity levels over a wide range of physiologically relevant temperatures. For example, the shift in activity towards the cooler nighttime hours on hot days might minimize the risks associated with exposure to mid-day heat, whereas on cold days activity is favored during the warmer daytime hours. These temperature-induced shifts in the distribution of daily activity are partly based on the thermal sensitive splicing of an intron found in the 3′ untranslated region (UTR) of the circadian clock gene termed period (per). As temperature decreases, splicing of this 3′-terminal intron (termed dmpi8) is gradually increased, which is causally linked to a shorter mid-day siesta. Herein we identify several natural polymorphisms in the per 3′ UTR from wild-caught populations of flies originating along the east coast of the United States. Two non-intronic closely spaced single nucleotide polymorphisms (SNPs) modulate dmpi8 splicing efficiency, with the least efficiently spliced version associated with a longer mid-day siesta, especially at lower temperatures. Although these SNPs modulate the splicing efficiency of dmpi8 they have little to no effect on its thermal responsiveness, consistent with the notion that the suboptimal 5′ and 3′ splice sites of the dmpi8 intron are the primary cis-acting elements mediating temperature regulation. Our results demonstrate that natural variations in the per gene can modulate the splicing efficiency of the dmpi8 intron and the daily distribution of activity, providing natural examples for the involvement of dmpi8 splicing in the thermal adaptation of behavioral programs in D. melanogaster.     

Beneficial Effects of Ibuprofen on Pentylenetetrazol-induced Convulsion

Neurochemical Research - Ibuprofen is a non-steroidal anti-inflammatory drug (NSAID) that is commonly used as an anti-inflammatory, anti-pyretic, and analgesic. Although some studies have focused...     

Ultrafast liquid chromatographic analysis of erdosteine in human plasma based on fluorimetric detection and precolumn derivatization with 4‐bromomethyl‐7‐methoxycoumarin: Application to pharmacokinetic studies

In this study, a new analytical method for erdosteine (ERD) in plasma based on high‐performance liquid chromatography and a fluorimetric detector, is presented. Precolumn derivatization of ERD with 4‐bromomethyl‐7‐methoxy coumarin (BrMmC) and dibenzo‐18‐crown‐6‐ether as a reaction catalyst led to the production of a fluorescent compound. ERD was monitored by fluorescence with an excitation wavelength λ_ext. = 325 nm and emission wavelength λ_em. = 390 nm. Optimum reaction conditions were carefully studied and optimized. A chromatographic procedure was performed using a C18 column of 150 × 4.6 mm and 3 μm particle size and a mobile phase consisting of methanol:acetonitrile:water (30:30:40, v/v/v) under a flow rate of 0.5 ml min^?1. A calibration plot was established covering analyte concentration range 0.2–3.0 μg ml^?1; the detection limit was 0.015 μg ml^?1 and quantification limit was 0.05 μg ml^?1. Mean recovery was 87.33% and relative standard deviation was calculated to be less than 4.4%. The developed method was successfully used to determine pharmacokinetic preparations of ERD subsequent to administration of a 900 mg dose capsule to a healthy 40‐year‐old woman volunteer.