An LC-MS/MS-based platform for the quantification of multiple amyloid beta peptides in surrogate cerebrospinal fluid.

Introduction: The accurate quantification of amyloid beta (Aβ) peptides in cerebrospinal fluid (CSF) is crucial for Alzheimer's disease (AD) research, particularly in terms of preclinical and biomarker studies. Traditional methods, such as the enzyme-linked immunosorbent assay (ELISA), have limitations. These include high costs, labor intensity, lengthy processes, and the possibility of cross-reactivity.

Quantification of cell-free circulating mitochondrial DNA copy number variation in hepatocellular carcinoma.

Objective: Hepatocellular carcinoma is the most common primary malignant liver tumor. Mitochondrial DNA copy number has been shown to be associated with various malignancies. However, there has not been any study on the absolute quantification of mtDNA copy number in hepatocellular carcinoma.

The production and characterization of SARS-CoV-2 RNA reference material.

SARS-CoV-2 in vitro transcribed RNA reference materials (RM), UME RM 2019 and UME RM 2020, were produced by Scientific and Technological Research Council of Turkey (TUBITAK), National Metrology Institute (UME), to be used as a quality control material for SARS-CoV-2 measurements, in liquid-frozen and lyophilized forms, respectively. These RNA RMs include ten internationally recommended SARS-CoV-2 target gene fragments (Pasteur-RdRp-IP2, Pasteur-RdRp-IP4, Charite-E, Charite-RdRp, CDC-N1, CDC-N2, China CDC-ORF1ab, China CDC-N, Hong Kong-ORF1b, and Hong Kong-N) for virus detection and one human gene fragment (RNase P) as an internal control. Two different platforms, RT-qPCR and RT-ddPCR, were used to characterize UME RM 2019 (UME RM 2020 was only characterized with RT-qPCR).

Thermal Proteome Profiling and Meltome Analysis of a Thermophilic Bacterial Strain, ARTRW1: Toward Industrial Applications.

Thermophilic microorganisms that thrive in extreme environments are of great importance because they express heat-resistant enzymes with the potential to serve as biocatalysts in industrial applications. Thermal proteome profiling (TPP) is a multiplexed quantitative mass spectrometry method for analyses of structural information and melting behavior of thousands of proteins, simultaneously determining the thermal denaturation profiles of each protein. We report, in this study, TPP applied to a thermophilic bacterial proteome, a recently isolated strain of named as ARTRW1.

Whole-Genome Sequence of Geobacillus thermoleovorans ARTRW1, Isolated from Armutlu Geothermal Spring, Turkey.

The thermophilic microorganism ARTRW1 was isolated from water samples collected in the Armutlu hot spring in Turkey. Here, the whole-genome sequence and its annotations are reported.

Comparison of Volumetric and Bead-Based Counting of CD34 Cells by Single-Platform Flow Cytometry.

Background: Over 2,000 people a year in the United Kingdom need a bone marrow or blood stem cell transplant. It is important to accurately quantify the hematopoietic stem cells to predict whether the transplant will be successful in replenishing the immune system. However, they are present at low frequency, which complicates accurate quantification.

Oligomer based real-time detection of microorganisms producing nuclease enzymes.

In this study, we provide a method using fluorescently labeled oligonucleotides for the diagnosis of microorganisms producing nucleases in real time, while growing them in culture media. The detection of such microorganisms was possible in a short period of time, as short as 10 minutes up to a maximum of 8 hours, depending on the bacterial density. We also showed the suitability of this new method for determination of minimum inhibitory concentration (MIC) in culture media in a very short period of time, compared to conventional methods.

Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine.

Background: Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use.

Screening of Hallucinogenic Compounds and Genomic Characterisation of 40 Anatolian Salvia Species.

Introduction: Salvia, an important and widely available member of Lamiaceae family. Although comparative analysis on secondary metabolites in several Salvia species from Turkey has been reported, their hallucinogenic chemicals have not been screened thoroughly.

Objective: This study provides LC-MS/MS analysis of 40 Salvia species for screening their psychoactive constituents of salvinorin A and salvinorin B.

International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction.

Enumeration-based determination of DNA copy-concentration was assessed through an international comparison among national metrology institutes (NMIs) and designated institutes (DIs). Enumeration-based quantification does not require a calibration standard thereby providing a route to "absolute quantification", which offers the potential for reliable value assignments of DNA reference materials, and International System of Units (SI) traceability to copy number 1 through accurate counting. In this study, 2 enumeration-based methods, flow cytometric (FCM) counting and the digital polymerase chain reaction (dPCR), were compared to quantify a solution of the pBR322 plasmid at a concentration of several thousand copies per microliter.

Inter-laboratory assessment of different digital PCR platforms for quantification of human cytomegalovirus DNA.

Quantitative PCR (qPCR) is an important tool in pathogen detection. However, the use of different qPCR components, calibration materials and DNA extraction methods reduces comparability between laboratories, which can result in false diagnosis and discrepancies in patient care. The wider establishment of a metrological framework for nucleic acid tests could improve the degree of standardisation of pathogen detection and the quantification methods applied in the clinical context.

Proteomic Analysis of Kidney Preservation Solutions Prior to Renal Transplantation.

One of the main issues in kidney transplantation is the optimal functional preservation of the organ until its transplantation into the appropriate recipient. Despite intensive efforts, the functional preservation period remains limited to hours. During this time, as a result of cellular injury, various proteins, peptides, and other molecules are released by the organ into the preservation medium.

Comparison of DNA extraction methods for meat analysis.

Preventing adulteration of meat and meat products with less desirable or objectionable meat species is important not only for economical, religious and health reasons, but also, it is important for fair trade practices, therefore, several methods for identification of meat and meat products have been developed. In the present study, ten different DNA extraction methods, including Tris-EDTA Method, a modified Cetyltrimethylammonium Bromide (CTAB) Method, Alkaline Method, Urea Method, Salt Method, Guanidinium Isothiocyanate (GuSCN) Method, Wizard Method, Qiagen Method, Zymogen Method and Genespin Method were examined to determine their relative effectiveness for extracting DNA from meat samples. The results show that the salt method is easy to perform, inexpensive and environmentally friendly.

The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis.

Background: Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive.

An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1.

Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM)-P103.1) was performed in order to evaluate the comparability of measurements of RNA copy number ratio for multiple gene targets between two samples.

Voltammetric detection of sequence-selective DNA hybridization related to Toxoplasma gondii in PCR amplicons.

This work describes the single-use electrochemical DNA biosensor technology developed for voltammetric detection of sequence selective DNA hybridization related to important human and veterinary pathogen; Toxoplasma gondii. In the principle of electrochemical label-free detection assay, the duplex of DNA hybrid formation was detected by measuring guanine oxidation signal occured in the presence of DNA hybridization. The biosensor design consisted of the immobilization of an inosine-modified (guanine-free) probe onto the surface of pencil graphite electrode (PGE), and the detection of the duplex formation in connection with the differential pulse voltammetry(DPV) by measuring the guanine signal.

Selection of Nucleic Acid Aptamers Specific for Mycobacterium tuberculosis.

Tuberculosis (TB) remains to be a major global health problem, with about 9 million new cases and 1.4 million deaths in 2011. For the control of tuberculosis as well as other infectious diseases, WHO recommended "ASSURED" (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free, and Deliverable to the end user) diagnostic tools that can easily be maintained and used in developing countries.

Resveratrol ameliorates cisplatin-induced oxidative injury in New Zealand rabbits.

This study investigated the preventive role of resveratrol in cisplatin-induced nephrotoxicity. The study used groups of New Zealand rabbits that were treated as follows: group C (cisplatin treated), group R (resveratrol treated), group R+C (resveratrol + cisplatin treatment), and group E (control group). Kidney levels of glutathione were significantly lower in group C than in groups E and R, whereas glutathione levels in group R+C were found to be similar to the control values.

Development and validation of a generic method for quantification of collagen in food supplement tablets using liquid chromatography coupled with time-of-flight mass spectrometry.

A generic method for the quantification of type II collagen in protein-based dietary supplements is described. This quantitative analysis was conducted using liquid chromatography-electrospray ionization-time-of-flight mass spectrometry (LC-ESI-TOF MS). Compared to classical methods with the use of isotope-labeled standards, our method includes, for the first time, the quantification of hydroxyproline using histidine as an internal standard.

The effects of acute acetaminophen toxicity on hepatic mRNA expression of SOD, CAT, GSH-Px, and levels of peroxynitrite, nitric oxide, reduced glutathione, and malondialdehyde in rabbit.

We investigated the regulation of antioxidant system under acetaminophen (AAP) toxicity. Twelve male New Zealand rabbits were divided into two groups with the following treatments: Group 1 animals were intraperitoneally injected with single saline (control). Group 2 animals were treated with intraperitoneal injection of AAP at a dose of 250 mg/kg body weight.

The effects of chronic exposure to ethanol and cigarette smoke on the formation of peroxynitrite, level of nitric oxide, xanthine oxidase and myeloperoxidase activities in rat kidney.

The aim of this study was to investigate the effects of chronic ethanol intake and cigarette smoke exposure on rat kidney. The animals were divided into four experimental groups: (1) the control group (C), (2) the ethanol group (E), (3) the cigarette smoke group (CS), and (4) the cigarette smoke plus ethanol group (CS+E). Rats in E, CS and CS+E groups were treated with ethanol and/or cigarette smoke for 6 months.

G protein betagamma complex translocation from plasma membrane to Golgi complex is influenced by receptor gamma subunit interaction.

On activation of a receptor the G protein betagamma complex translocates away from the receptor on the plasma membrane to the Golgi complex. The rate of translocation is influenced by the type of gamma subunit associated with the G protein. Complementary approaches--imaging living cells expressing fluorescent protein tagged G proteins and assaying reconstituted receptors and G proteins in vitro--were used to identify mechanisms at the basis of the translocation process.

G protein betagamma11 complex translocation is induced by Gi, Gq and Gs coupling receptors and is regulated by the alpha subunit type.

G protein activation by Gi/Go coupling M2 muscarinic receptors, Gq coupling M3 receptors and Gs coupling beta2 adrenergic receptors causes rapid reversible translocation of the G protein gamma11 subunit from the plasma membrane to the Golgi complex. Co-translocation of the beta1 subunit suggests that gamma11 translocates as a betagamma complex. Pertussis toxin ADP ribosylation of the alphai subunit type or substitution of the C terminal domain of alphao with the corresponding region of alphas inhibits gamma11 translocation demonstrating that alpha subunit interaction with a receptor and its activation are requirements for the translocation.

Receptor-mediated reversible translocation of the G protein betagamma complex from the plasma membrane to the Golgi complex.

Heterotrimeric G proteins have been thought to function on the plasma membrane after activation by transmembrane receptors. Here we show that, after activation by receptors, the G protein betagamma complex selectively translocates to the Golgi. Receptor inactivation results in Gbetagamma translocating back to the plasma membrane.