A simplified procedure to determine the optimal rate of freezing biological systems

The effect of several cell-level parameters on the predicted optimal cooling rate B(opt) of an arbitrary biological system has been studied using a well-defined water transport model. An extensive investigation of the water transport model revealed three key cell level parameters: reference permeability of the membrane to water L(pg), apparent activation energy E(Lp), and the ratio of the available surface area for water transport to the initial volume of intracellular water (SA/WV). We defined B(opt) as the "highest" cooling rate at which a predefined percent of the initial water volume is trapped inside the cell (values ranging from 5% to 80%) at a predefined end temperature (values ranging from -5 degrees C to -40 degrees C). Irrespective of the choice of the percent of initial water volume trapped and the end temperature, an exact and linear relationship exists between L(pg), SA/WV, and B(opt0. However, a nonlinear and inverse relationship is found between E(Lp) and B(opt). Remarkably, for a variety of biological systems a comparison of the published experimentally determined values of B(opt) agreed quite closely with numerically predicted B(opt) values when the model assumed 5% of initial water is trapped inside the cell at a temperature of -15 degrees C. This close agreement between the experimental and model predicted optimal cooling rates is used to develop a generic optimal cooling rate chart and a generic optimal cooling rate equation that greatly simplifies the prediction of the optimal rate of freezing of biological systems.     

Radiosurgery dose reduction for brain metastases on immunotherapy (RADREMI): A prospective phase I study protocol

IntroductionUp to 20% of patients with brain metastases treated with immune checkpoint inhibitor (ICI) therapy and concomitant stereotactic radiosurgery (SRS) suffer from symptomatic radiation necrosis. The goal of this study is to evaluate Radiosurgery Dose Reduction for Brain Metastases on Immunotherapy (RADREMI) on six-month symptomatic radiation necrosis rates.MethodsThis study is a prospective single arm Phase I pilot study which will recruit patients with brain metastases receiving ICI delivered within 30 days before SRS. All patients will be treated with RADREMI dosing, which involves SRS doses of 18 Gy for 0−2 cm lesions, 14 Gy for 2.1−3 cm lesions, and 12 Gy for 3.1−4 cm lesions. All patients will be monitored for six-month symptomatic radiation necrosis (defined as a six-month rate of clinical symptomatology requiring steroid administration and/or operative intervention concomitant with imaging findings consistent with radiation necrosis) and six-month local control. We expect that RADREMI dosing will significantly reduce the symptomatic radiation necrosis rate of concomitant SRS + ICI without significantly sacrificing the local control obtained by the present RTOG 90−05 SRS dosing schema. Local control will be defined according to the Response Assessment in Neuro-Oncology (RANO) criteria.DiscussionThis study is the first prospective trial to investigate the safety of dose-reduced SRS in treatment of brain metastases with concomitant ICI. The findings should provide fertile soil for future multi-institutional collaborative efficacy trials of RADREMI dosing for this patient population.Trial RegistrationClinicaltrials.gov identifier: NCT04047602 (registration date: July 25, 2019).     

Comparative analysis of methods to determine DNA methylation levels of a tumor-related microRNA gene

Quantifying levels of DNA methylation in tumors is a useful approach for the identification of potential tumor suppressors and to find biomarkers that can be used as prognostic or therapeutic indicators. In the current study, we compared three methods commonly used for quantifying DNA methylation—bisulfite pyrosequencing, quantitative methylation-specific PCR (Q-MSP), and MethyLight—by focusing on the CpG island of the gene encoding the microRNA-34b and microRNA-34c (miR-34b/c); aberrant regulation of this miR is associated with various human malignancies, including gastric cancer. Standard curve analysis using control DNA samples demonstrated the highest quantitative accuracy in Q-MSP analysis. We also carried out methylation analysis using gastric mucosa specimens obtained from gastric cancer patients. We found a high correlation between methylation levels determined by Q-MSP and those determined by MethyLight (R² = 0.952), whereas the results of bisulfite pyrosequencing and the other two methods were less well correlated (R² = 0.864 and R² = 0.804 for Q-MSP and MethyLight, respectively). This may reflect possible PCR bias in the pyrosequencing technique, which we show can be corrected for by applying a cubic approximate equation to the original data. Thus, although results obtained by the different DNA methylation analysis techniques are largely comparable, an appropriate correction may be necessary for stringent comparison.     

High-resolution melt analysis of DNA methylation to discriminate semen in biological stains

The goal of this study was to develop a method for the detection of semen in biological stains using high-resolution melt (HRM) analysis and DNA methylation. To perform this task, we used an epigenetic locus that targets a tissue-specific differentially methylated region for semen. This specific locus, ZC3H12D, contains methylated CpG sites that are hypomethylated in semen and hypermethylated in blood and saliva. Using this procedure, DNA from forensic stains can be isolated, processed using bisulfite-modified polymerase chain reaction (PCR), and detected by real-time PCR with HRM capability. The method described in this article is robust; we were able to obtain results from samples with as little as 1 ng of genomic DNA. Samples inhibited by humic acid still produced reliable results. Furthermore, the procedure is specific and will not amplify non-bisulfite-modified DNA. Because this process can be performed using real-time PCR and is quantitative, it fits nicely within the workflow of current forensic DNA laboratories. As a result, it should prove to be a useful technique for processing trace evidence samples for serological analysis.     

A contribution to the problem of the concept “biological clock” (part I)

Summary In the first parts of this study on the concept of the biological clock it has been investigated how it is used in the field of biorhythmology. The analysis of the contents of the concept is preceded by a survey of the current research in this field.There are two general hypotheses with respect to the ultimate origin of rhythmic phenomena: the Endogenous Timer Hypothesis and the Exogenous Timer Hypothesis. Within the Endogenous Timer Hypothesis two contrasting viewpoints with respect to the structure of the biological clock can be distinguished, which have been called: the Discrete Entity view, and the Organizational view.It has been shown that in the application of the general clock-idea upon the organism a logical distortion is present. The organism is conceived tobe a clock and tohave a clock simultaneously.In anticipation of the analysis of the explanatory value of the concept of the biological clock in part II, it has been put forward that in a number of cases time-measurement can be considered as a superfluous (redundant) element in the explanation of the phenomena involved.Finally it has been demonstrated that in the case of the Exogenous Timer Hypothesis the concept of the biological clock is not relevant. The Exogenous Timer Hypothesis has been compared with the Endogenous Timer Hypothesis with respect to the criterion of the principle of parsimony, orOccam's razor.List of rhythmological terms autonomous system not under the influence of a periodic source of energy,i.e. selfsustained and free oscillations - non-autonomous system under the influence of a periodic source of energy,i.e. forced oscillations whether in active or passive systems - period time after which a definite phase of the oscillation reoccurs - frequency reciprocal of period - phase instantaneous state of an oscillation within a period, represented by the value of the variable and all its time derivatives - phase angle value of the abscissa corresponding to a point of the curve (phase) given either in radians, in degrees or in other fractions of the whole period. It can be given in units of time, if the length of the period is stated - synchronization state in which two or more oscillations have the same frequency due to mutual or unilateral influences - entrainment coupling of a self-sustained oscillation to a Zeitgeber (forcing oscillation) with the result that either both oscillations have the same frequency (synchronization) or that the frequencies are integral multiples (frequency-demultiplication): possible only within limited ranges of frequencies - Zeitgeber that forcing oscillation which entrains a biological rhythm - free-running rhythms selfsustained oscillations under constant conditions - response-curve indicates, in biology, how the amount and the sign of a phase shift, induced by a single stimulus, depends on the phase in which the stimulus is applied     

A role for poly(ADP-ribosyl)ation in DNA methylation.

The aberrant DNA methylation of promoter regions of housekeeping genes leads to gene silencing. Additional epigenetic events, such as histone methylation and acetylation, also play a very important role in the definitive repression of gene expression by DNA methylation. If the aberrant DNA methylation of promoter regions is the starting or the secondary event leading to the gene silencing is still debated. Mechanisms controlling DNA methylation patterns do exist although they have not been ultimately proven. Our data suggest that poly(ADP-ribosyl)ation might be part of this control mechanism. Thus an additional epigenetic modification seems to be involved in maintaining tissue and cell-type methylation patterns that when formed during embryo development, have to be rigorously conserved in adult organisms.     

Studies on the biological role of DNA methylation: V. The pattern of E.coli DNA methylation.

The distribution of the methylatable sites GATC and CCATGG was studied by analyzing the molecular average size of restriction fragments of E. coli DNA. Both sites were found to be randomly distributed, reflecting a random pattern of methylation. The methylation pattern of specific sequences such as the origin of replication and rRNA genes has been studied in wild type E. coli and a methylation deficient (dam- dcm-) mutant. These sequences were found to be methylated in wild type cells and unmethylated in the mutant indicating that there is no effect of the state of methylation of these sequences on their expression. Analysis of the state of methylation of GATC sites in newly replicating DNA using the restriction enzyme Dpn I (cleaves only when both strands are methylated) revealed no detectable hemimethylated DNA suggesting that methylation occurs at the replication fork. Taking together the results presented here and previously published data (5), we arrive at the conclusion that the most likely function of E. coli DNA methylations is probably in preventing nuclease activity.     

Quantification of DNA methylation in electrofluidics chips (Bio-COBRA)

Alterations of normal gene expression patterns are a hallmark of human cancers. It is now clear that the dysregulation of epigenetic modifications of the DNA and surrounding histones contributes to aberrant gene silencing, thus being major participants not only in the progression but also the initiation of the disease phenotype. The best-studied epigenetic modification is DNA methylation, which converts cytosine to 5-methylcytosine. Aberrant hypermethylation of the promoter is frequently observed in cancer and is generally associated with gene silencing. Currently, accurate and reproducible quantification of DNA methylation remains challenging. Here, we describe Bio-COBRA, a modified protocol for Combined Bisulfite Restriction Analysis (COBRA), that incorporates an electrophoresis step in microfluidics chips. Microfluidics technology involves the handling of small amounts of liquid in miniaturized systems. In the life sciences, microfluidics usually entails the scaling down of at least one application, such as electrophoresis, to chip format, which often results in increased efficiency and reliability. Bio-COBRA provides a platform for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. Its sensitivity and reproducibility also makes it a tool for the analysis of DNA methylation in clinical samples. The Bio-COBRA assay can be performed on 12 samples in less than 1 h. If the protocol is started at the DNA isolation step, however, approximately 48 h would be required to complete the entire procedure.     

Studies on the biological role of DNA methylation. II. Role of phiX174 DNA methylation in the process of viral progeny DNA synthesis.

In vivo inhibition of bacteriophage phiX174 DNA methylation by nicotinamide resulted in the accumulation of replicative intermediates with multiple-genome length single-stranded "tails". These abnormal replicative intermediates could not be chased into viral single-stranded circular DNA. The effect of nicotinamide on phage maturation and accumulation of abnormal replicative intermediates could be reversed by washing out the inhibitor. The results suggest that the single methyl group present in the viral DNA serves as a recognition site for a specific endonuclease, probably the gene A protein product, that is responsible for the excision of the single-stranded one-genome long viral DNA, before final maturation of the virus occurs.     

Understanding the role of DNA methylation in successful biological invasions: a review

Biological invasions provide a unique opportunity to investigate rapid adaptation and evolution as the introduced taxa adapt to biogeographic contexts or habitats in which they have not evolved. The capacity of populations to evolve is generally thought to be constrained by their existing heritable genetic variation, which is usually associated with variation in genomic DNA nucleotide sequences. However, there is increasing acceptance that a range of mechanisms—collectively termed ‘epigenetics’ can alter gene function and affect ecologically important traits. Epigenetic processes may mediate adaptive phenotypic plasticity and provide heritable variation on a finer timescale than DNA sequence-based mutations. This review focuses on DNA methylation, a well-studied epigenetic mechanism known to be associated with biological adaptation to environmental stress. We explore the role of DNA methylation in characterising the adaptive potential of invasive species. We also provide an overview of studies focused on DNA methylation and invasive species to date, and identify knowledge gaps and potential ways to advance understanding of epigenetic-based adaptation. A summary of the literature suggests that DNA methylation could play a key role in the success of invasive species. Introduced populations with reduced genetic diversity often display increased DNA methylation variation in comparison with native populations, which could create phenotypic diversity when it is most required. Recent data show that DNA methylation could contribute to adaptation through both phenotypic plasticity and heritable variation, particularly through clonal reproduction. From a methodological perspective, recent advances in molecular techniques provide an exciting opportunity to explore the functional relevance of DNA methylation to successful biological invasions. Gaining a greater understanding of the adaptive and evolutionary processes that contribute to invasion success is critical for preventing and managing the future introduction, establishment and spread of invasive species.     

A method to determine the available UV-C dose for the decontamination of filtering facepiece respirators

Aims: To develop a method to assess model‐specific parameters for ultraviolet‐C (UV‐C, 254 nm) decontamination of filtering facepiece respirators (FFRs). Methods and Results: UV‐C transmittance was quantified for the distinct composite layers of six N95 FFR models and used to calculate model‐specific α‐values, the percentage of the surface UV‐C irradiance available for the internal filtering medium (IFM). Circular coupons, excised from the FFRs, were exposed to aerosolized particles containing MS2 coliphage and treated with IFM‐specific UV‐C doses ranging from 38 to 4707 J m^?2. Models exposed to a minimum IFM dose of 1000 J m^?2 demonstrated at least a 3 log reduction (LR) in viable MS2. Model‐specific exposure times to achieve this IFM dose ranged from 2 to 266 min. Conclusions: UV‐C transmits into and through FFR materials. LR of MS2 was a function of model‐specific IFM UV‐C doses. Significance and Impact of the Study: Filtering facepiece respirators are in high demand during infectious disease outbreaks, potentially leading to supply shortages. Reuse of disposable FFRs after decontamination has been discussed as a possible remediation strategy, but to date lacks supporting scientific evidence. The methods described here can be used to assess the likelihood that UV‐C decontamination will be successful for specific FFR models.     

Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus)

Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24–35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.     

DNA methylation alterations of upland cotton (Gossypium hirsutum) in response to cold stress

DNA methylation plays an important role in regulating gene expression in plants. In the experiment, we studied effects of cold on DNA methylation variation in upland cotton. Using the methylation-sensitive amplified polymorphism procedure, we chose 66 pairs of selective amplification primers to assess the status and levels of cytosine methylation. The hemimethylation of the external cytosine and the full methylation of the internal cytosine were scored. As a result, cold triggered the demethylation of hemimethylated or internally full methylated cytosine. With the prolongation of cold treatment, the demethylation loci increased and the methylation loci decreased. Nevertheless, this change could be reverted when cotton was subsequently recovered under normal temperature. In addition, 29 polymorphic bands that appeared in the electrophoretogram were sequenced. By homologous alignment analysis, most of these 29 fragments were identified as genes or DNA clones involved in abiotic stress response. The variation in methylation loci existed at both coding and non-coding regions. Furthermore, the expression of the abiotic stress-related genes, GhCLSD (Seq21), GhARK (Seq22), GhARM (Seq15, Seq18, Seq19 and Seq21) and GhTPS (Seq8), were tested. The results revealed that cold treatment induced down-regulation of GhCLSD, GhARK and GhARM, but up-regulated the expression of GhTPS. These changes were in accordance with the alteration of DNA methylation. Thus, cold may affect the gene expression via changing the methylation status in the cytosine nucleotide.     

A quantitative structure-activity relationship (QSAR) study on glycan array data to determine the specificities of glycan-binding proteins

Advances in glycan array technology have provided opportunities to automatically and systematically characterize the binding specificities of glycan-binding proteins. However, there is still a lack of robust methods for such analyses. In this study, we developed a novel quantitative structure-activity relationship (QSAR) method to analyze glycan array data. We first decomposed glycan chains into mono-, di-, tri- or tetrasaccharide subtrees. The bond information was incorporated into subtrees to help distinguish glycan chain structures. Then, we performed partial least-squares (PLS) regression on glycan array data using the subtrees as features. The application of QSAR to the glycan array data of different glycan-binding proteins demonstrated that PLS regression using subtree features can obtain higher R(2) values and a higher percentage of variance explained in glycan array intensities. Based on the regression coefficients of PLS, we were able to effectively identify subtrees that indicate the binding specificities of a glycan-binding protein. Our approach will facilitate the glycan-binding specificity analysis using the glycan array. A user-friendly web tool of the QSAR method is available at http://bci.clemson.edu/tools/glycan_array.