Whole blood RNA extraction efficiency contributes to variability in RNA sequencing data sets.

Numerous methodologies are used for blood RNA extraction, and large quantitative differences in recovered RNA content are reported. We evaluated three archived data sets to determine how extraction methodologies might influence mRNA and lncRNA sequencing results. The total quantity of RNA recovered /ml of blood affects RNA sequencing by impacting the recovery of weakly expressed mRNA, and lncRNA transcripts.

A real-time PCR method to genotype mutant mouse models with altered affinity for cardiotonic steroids on the Na,K-ATPase.

The highly conserved, cardiotonic steroid binding site (also termed ouabain binding site) on the primary α subunit of Na,K-ATPase plays a receptor signaling role in a range of vital cell processes and is a therapeutic target for human disease. Mouse lines with altered affinity for cardiotonic steroids on the α1 or α2 subunit isoform of Na,K-ATPase, without any change in pump activity, were developed by the late Jerry B Lingrel and are a valuable tool for studying its physiological roles and drug actions. In one model, the normally ouabain resistant α1 isoform was rendered sensitive to ouabain binding.

Mental and Physical Health Problems as Conditions of Ex-Prisoner Re-Entry.

The article focuses on a less-discussed issue of social marginalization of people leaving penitentiaries, which is the prevalence of multifaceted health problems experienced by people in this category. It includes poor health status, resulting from, among others, poor housing conditions, harmful or risky lifestyle, and lack of access to medical services. Data from the District Inspectorate of the Prison Service in Lodz, Poland on the health conditions of inmates was accessed.

Risk Factors of Early Adolescence in the Criminal Career of Polish Offenders in the Light of Life Course Theory.

Life course theory (LCT) diagnoses childhood and adolescent factors that determine an individual's involvement in crime in the future. Farrington lists eight key correlates identified by empirical analyses of criminal careers. In this paper, we seek to discuss the inconsistencies with LCT that we observed in our three empirical studies of the criminal careers of Polish offenders.

Age-Graded Transitions and Turning Points in Polish Offenders' Criminal Careers from the Standpoint of Life Course Theory.

Both juvenile and adult criminal careers show regularities in the origins of delinquency, the dynamics of the criminal pathway, and the turning points that lead to desistance/persistence in crime. Research shows that family, education, and friendship environments contribute significantly to the individual choices that create criminal biographies. Our aim was to apply core aspects of life course theory (LCT): trajectory, the aged-graded process, transitions, institutions, and ultimately how desistance/persistence factor into explaining the criminal careers of Polish offenders.

Strategies for detecting and identifying biological signals amidst the variation commonly found in RNA sequencing data.

Background: RNA sequencing analysis focus on the detection of differential gene expression changes that meet a two-fold minimum change between groups. The variability present in RNA sequencing data may obscure the detection of valuable information when specific genes within certain samples display large expression variability. This paper develops methods that apply variance and dispersion estimates to intra-group data to identify genes with expression values that diverge from the group envelope.

Rapid processing of SARS-CoV-2 containing specimens for direct RT-PCR.

Widespread diagnostic testing is needed to reduce transmission of COVID-19 and manage the pandemic. Effective mass screening requires robust and sensitive tests that reliably detect the SARS-CoV-2 virus, including asymptomatic and pre-symptomatic infections with a low viral count. Currently, the most accurate tests are based on detection of viral RNA by RT-PCR.

Coordinated analysis of exon and intron data reveals novel differential gene expression changes.

RNA-Seq expression analysis currently relies primarily upon exon expression data. The recognized role of introns during translation, and the presence of substantial RNA-Seq counts attributable to introns, provide the rationale for the simultaneous consideration of both exon and intron data. We describe here a method for the coordinated analysis of exon and intron data by investigating their relationship within individual genes and across samples, while taking into account changes in both variability and expression level.

Let food be your medicine: nutraceutical properties of lycopene.

Currently, an increase in the awareness of a healthy lifestyle has been observed in society. People are seeking added health benefits from their dietary intake. Thus, functional foods with supplemented components that promote wellness are becoming popular.

Subclonal STAT3 mutations solidify clonal dominance.

T large granular lymphocyte leukemia (T-LGLL) is a clonal lymphoproliferative disorder that can arise in the context of pathologic or physiologic cytotoxic T-cell (CTL) responses. mutations are often absent in typical T-LGLL, suggesting that in a significant fraction of patients, antigen-driven expansion alone can maintain LGL clone persistence. We set out to determine the relationship between activating hits and CTL clonal selection at presentation and in response to therapy.

Clinical features and treatment outcomes in large granular lymphocytic leukemia (LGLL).

Large granular lymphocytic leukemia (LGLL) represents a clonal/oligoclonal lymphoproliferation of cytotoxic T and natural killer cells often associated with STAT3 mutations. When symptomatic, due to mostly anemia and neutropenia, therapy choices are often empirically-based, because only few clinical trials and systematic studies have been performed. Incorporating new molecular and flow cytometry parameters, we identified 204 patients fulfilling uniform criteria for LGLL diagnoses and analyzed clinical course with median follow-up of 36 months, including responses to treatments.

Inter-Individual Differences in RNA Levels in Human Peripheral Blood.

Relatively little is known about the range of RNA levels in human blood. This report provides assessment of peripheral blood RNA level and its inter-individual differences in a group of 35 healthy humans consisting of 25 females and 10 males ranging in age from 50 to 89 years. In this group, the average total RNA level was 14.

[Internal capsule integrity and its sex-related structural differences in early-onset schizophrenia - diffusion tensor imaging study].

Objectives: In schizophrenia, the most repeatable DTI findings concern reduced FA in temporal and frontal lobes with associated abnormalities in connecting neural fibers. The goal of study was to evaluate the differences in FA of the internal capsule in EOS-patients and healthy controls and to place emphasis on the sex as a potential factor determining a predominant pathological pattern of described changes.

Methods: 30 EOS patients and 30 healthy controls were studied using DTI.

[Lycopene--occurrence, properties and applications].

Natural products from plants, fungi and higher animals are valuable sources of attractive alternatives for therapeutics. One of them, lycopene is a bright red carotene found in several fruits and vegetables. Tomato, tomato-based sauces and juices are the most abundant sources of this compound for human.

Preparation of RNA from tissues and cells.

Most procedures for isolating RNA from eukaryotic cells involve lysing and denaturing cells to liberate total nucleic acids. Additional steps are then required to remove DNA. The first basic protocol describes hot phenol extraction of RNA; the method eliminates or minimizes DNA contamination by the shearing of DNA.

Guanidine methods for total RNA preparation.

Three different methods for RNA preparation using guanidine are presented in this unit--a single-step isolation method employing liquid-phase separation to selectively extract total RNA from tissues and cultured cells and two methods that rely on a CsCl step gradient to isolate total RNA.

The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on.

Since its introduction, the 'single-step' method has become widely used for isolating total RNA from biological samples of different sources. The principle at the basis of the method is that RNA is separated from DNA after extraction with an acidic solution containing guanidinium thiocyanate, sodium acetate, phenol and chloroform, followed by centrifugation. Under acidic conditions, total RNA remains in the upper aqueous phase, while most of DNA and proteins remain either in the interphase or in the lower organic phase.

DNA extraction from small blood volumes and the processing of cellulose blood cards for use in polymerase chain reaction.

This article describes two procedures for the purification of genomic DNA from small blood volumes of whole blood using DNAzol BD. In the first procedure, DNA is isolated from 1-20 microL of whole blood using a fast and simple protocol that is appropriate for the simultaneous extraction of a large number of samples. The isolated DNA is suitable for gel electrophoresis and polymerase chain reaction (PCR).

DNAzol: a reagent for the rapid isolation of genomic DNA.

In this report, we present DNAzol, a patent-pending DNA isolation reagent containing guanidine thiocyanate and a detergent mixture. It is a complete, nontoxic and ready-to-use reagent for the isolation of genomic DNA from various biological sources. In the DNAzol protocol, a biological sample is homogenized (or lysed) in DNAzol, and the DNA is precipitated with ethanol, washed and dissolved in 8 mM NaOH.

Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity.

The ratio of absorbance at 260 and 280 nm (the A260/280 ratio) is frequently used to assess the purity of RNA and DNA preparations. Data presented in this report demonstrate significant variability in the RNA A260/280 ratio when different sources of water were used to perform the spectrophotometric determinations. Adjusting the pH of water used for spectrophotometric analysis from approximately 5.

Short technical reports. Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources.

A modification of the TRI Reagent procedure has been elaborated for isolation of RNA from polysaccharide- and proteoglycan-rich material. In the modified procedure, RNA is precipitated from the aqueous phase by the combined action of isopropanol and a high-salt concentration. Under these conditions, RNA is effectively precipitated while contaminating polysaccharides and proteoglycans remain in the soluble form.

One-hour downward capillary blotting of RNA at neutral pH.

This report describes a setup for the downward capillary blotting of RNA with the use of 10 x SSC as a transfer solution. The setup is composed of a stack of blotting papers, hybridization membrane, and agarose gel. Two layers of blotting paper connect the stack with two reservoirs containing transfer solution.

A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples.

This report describes a new method for simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. The method is based on the use of a reagent containing phenol and guanidine thiocyanate. A biological sample is homogenized in the reagent and the simultaneous isolation of RNA, DNA and proteins is accomplished in a single step by a liquid-phase separation.