Phenotypical Characteristics of the Biological Properties of Staphylococci Withdrawn From Patients with Allergic Dermatitis

Atopic dermatitis, eczema, allergic dermatitis occupy the main place among dermatoses, where the allergic component is leading in the onset and development of the disease. The most common complication of allergic dermatitis is the attachment of a secondary pyococcus infection, which is associated with a decrease in the antimicrobial resistance of the skin surface. Therapy of infectious lesions is complicated by the increasing resistance of the main pathogens of pyoderma - Staphylococcus aureus and Staphylococcus epidermidis - to widely used antibiotics.The aim of the research: to determine the phenotypic features of staphylococci extracted from patients with allergic dermatitis to assess their pathogenic potential.Materials and methods. The object of the study was 369 staphylococcus isolates removed from affected and intact skin sections of patients with allergic dermatitis, as well as from representative skin sections of healthy individuals undergoing inpatient treatment at the Department of Dermatology of “Institute of Dermatology and Venereology of NAMS of Ukraine”. Biochemical identification and biological properties of staphylococci were determined using methods of classical bacteriology.Results. As a result of the conducted researches, it is established that the complex of phenotypic traits of the removed staphylococcus cultures indicates the presence in the pathogen of factors related to the resistance of the host protection mechanisms and determines the intensity of the alterative action of the infectant in relation to the host organism, the phenotypic manifestation of the studied factors was higher in the staphylococcus isolates removed from the affected skin areas of patients with allergic dermatitis. Conclusions. The level and frequency of phenotypic expression of pathogenicity factors are more pronounced in microorganisms obtained from patients from affected and intact areas compared to controls, which confirms their pathogenetic role in the burden of the disease, which in turn can be used as an auxiliary differential diagnosis criterion

From Monograph to International Movement: Music Assisted Learning Across the Life Span for Students with Autism Spectrum and Related Disorders

https://remix.berklee.edu/able-assembly-conference/1020/thumbnail.jp

Improving Single Cell ‘Omics Methods for Investigating Microbial Dark Matter

Die überwiegende Mehrheit des mikrobiellen Lebens ist unentdeckt und wenig erforscht, da sie bisher noch nicht erfolgreich kultiviert werden konnten. Wir bezeichnen sie daher als mikrobielle dunkle Materie (microbial dark matter, MDM). MDM hat hohes biotechnologisches Potential, z.B. für die Nutzung nachhaltiger Energiequellen, zur biologischen Sanierung kontaminierter Böden, oder für medizinische Anwendungen. Der Einsatz kulturunabhängiger Methoden zur Untersuchung von Mikroorganismen in der Natur, die Metagenomik und Metatranskriptomik, hat unser Verständnis von MDM erheblich verbessert. Allerdings ist es mit diesen Methoden immer noch schwierig, einzelne Spezies bioinformatisch zu analysieren, insbesondere von Organismen mit geringer Häufigkeit in komplexen Habitaten. Stammvariationen, die falsche Zuordnung von Sequenzen, insbesondere mobiler genetische Elemente sowie sich stark wiederholende Sequenzregionen sind nur einige der Probleme, mit denen z.B. die Metagenomik konfrontiert ist. Auch bei der Metatranskriptomik führen die phänotypische Heterogenität der Zellen und die Diversität der mikrobiellen Gemeinschaften zu komplexen Transkriptionsprofilen, die nicht vollständig zugeordnet werden können. Daher wurden die Einzelzellgenomik (single cell genomics, SCG) und die Einzelzelltranskriptomik (single cell transcriptomics, SCT), die zusammen als Einzelzell-\u27omics (SC \u27omics) bezeichnet werden, entwickelt, um die Nachteile der Metagenomik und Metatranskriptomik zu überwinden. Die Anwendung von SCG hat sich zu einem wichtigen Instrument für die Erweiterung unseres Wissens über MDM entwickelt, beispielsweise durch die jüngste Entdeckung mehrerer neuer Phyla, von denen es derzeit nur sogenannte single amplified genomes (SAGs) gibt. Vollständige SAGs von vielen Mikroorganismen, insbesondere von solchen mit geringer Abundanz, sind jedoch aufgrund der vielen technischen Herausforderungen und der hohen Kosten selten. Auch die SCT ist mit den vielen Herausforderungen der Arbeit mit RNA konfrontiert, wie z. B. der kurzen Halbwertszeit von mRNA und geringen Genexpression, weshalb sie in der Mikrobiologie noch nicht häufig angewendet wird. Daher haben sich die hohen Erwartungen an mikrobielle SC \u27omics noch nicht vollständig erfüllen können. In einem typischen SCG-Arbeitsablauf können die Zellen nach der Probenentnahme vor der Einzelzellisolierung mit Fluoreszenzfarbstoffen markiert werden. Nach der Isolierung werden die Zellen lysiert und das Genom anschließend amplifiziert, gefolgt von der Sequenzierung und bioinformatischen Datenanalyse. In dieser Arbeit wurden die Schritte der Zellmarkierung, Isolierung, Lyse und Ganzgenom-Amplifikation (whole genome amplifikation, WGA) verbessert, um die Methodik zu verbessern. Zunächst wurde ein Ansatz zur gezielten Zellmarkierung entwickelt, der die Anreicherung von Mikroorganismen mit geringer Häufigkeit aus Umweltproben ermöglichte. Dieser Ansatz half bei der Entdeckung neuer Phylogenien und Stoffwechseln von Mikroorganismen die in geringer Abundanz vorkommen und die andernfalls durch konventionelle Metagenomik übersehen worden wären. Darüber hinaus trägt dieser Ansatz dazu bei, die Kosten für SCG zu senken, da nun nicht mehr Zehntausende von Einzelzellen sequenziert werden müssen, um seltene Mikroorganismen zu analysieren. Als nächstes wurden die Schritte der Zellisolierung und Zelllyse verbessert, um sowohl physische Zellschäden als auch den DNA-Abbau zu minimieren, was den Erfolg des nachgeschalteten Genom-Amplifikationsschritts erhöht. Für den WGA-Schritt wurde ein Ansatz zur Volumenreduzierung systematisch getestet und etabliert, um die Homogenität und Vollständigkeit der Genomabdeckung deutlich zu verbessern. Dies Ergebnisse der Versuche zeigen, dass eine weitere Volumenreduzierung in den nL oder pL Bereich nicht erforderlich. Die Kosten der WGA konnten um 97,5 % gesenkt werden konnten, was den Durchsatz von SCG erhöhen und die Verwendung dieses Ansatzes in weiteren Forschungsgruppen positiv beeinflussen dürfte. Da SCG allein nur Informationen über die Phylogenie, genetische Struktur und das Stoffwechselpotenzial, nicht aber über die tatsächliche Aktivität einer Zelle liefert, wurde in dieser Arbeit eine mikrobielle SCT-Pipeline entwickelt, um die individuellen Funktionen der Zelle in einer Gemeinschaft besser zu verstehen. Derzeit gibt es nur sehr wenige Methoden für mikrobielle SCT, und die, die es gibt, bleiben aufgrund ihrer schwierigen Anwendung und geringen Zugänglichkeit außerhalb ihrer jeweiligen Arbeitsgruppen weitgehend ungenutzt. Daher wurden in dieser Studie Änderungen und Verbesserungen an einer eukaryotischen Einzelzell-RNA-Sequenzierungsmethode (RNA-seq) vorgenommen, um ihre Anwendung bei Prokaryoten zu ermöglichen. Es wurde festgestellt, dass der Zusatz von Dithiothreitol (DTT) im Lysepuffer wahrscheinlich die DNase I hemmt, was zu einer DNA Kontamination führt. Die hier vorgestellten Einzelzell-RNA-seq-Ergebnisse zeigten zuverlässige Transkriptionsprofile im Vergleich zu RNA-seq-Ergebnissen aus der gesamten Probe. Dies wurde auch durch ein Proof-of-Principle-Experiment bestätigt, bei dem hitzeschockbehandelte und unbehandelte Escherichia coli Zellen verglichen wurden. Darüber hinaus wurden in den Einzelzelldaten im Vergleich zur Populations-Analyse Hinweise auf einzigartige Reaktionen bei der Synthese von Sekundärmetaboliten und der CRISPR-Cas-Editierung gefunden, was die Bedeutung der Untersuchung der Heterogenität seltener funktioneller Subpopulationen auf Einzelzellebene unterstreicht. Insgesamt wird erwartet, dass die verbesserten SCG- und SCT-Methoden, die in dieser Arbeit etabliert wurden, eine breitere Anwendung für ein besseres Verständnis der MDM-Diversität und -Funktion in der Umwelt ermöglichen

Derivative based global sensitivity measures

The method of derivative based global sensitivity measures (DGSM) has recently become popular among practitioners. It has a strong link with the Morris screening method and Sobol' sensitivity indices and has several advantages over them. DGSM are very easy to implement and evaluate numerically. The computational time required for numerical evaluation of DGSM is generally much lower than that for estimation of Sobol' sensitivity indices. This paper presents a survey of recent advances in DGSM concerning lower and upper bounds on the values of Sobol' total sensitivity indices $S\_{i}^{tot}$. Using these bounds it is possible in most cases to get a good practical estimation of the values of $S\_{i}^{tot}$. Several examples are used to illustrate an application of DGSM

Influence of backreaction of electric fields and Schwinger effect on inflationary magnetogenesis

We study the generation of electromagnetic fields during inflation when the conformal invariance of Maxwell's action is broken by the kinetic coupling $f^{2}(\phi)F_{\mu\nu}F^{\mu\nu}$ of the electromagnetic field to the inflaton field $\phi$. We consider the case where the coupling function $f(\phi)$ decreases in time during inflation and, as a result, the electric component of the energy density dominates over the magnetic one. The system of equations which governs the joint evolution of the scale factor, inflaton field, and electric energy density is derived. The backreaction occurs when the electric energy density becomes as large as the product of the slow-roll parameter $\epsilon$ and inflaton energy density, $\rho_{E}\sim \epsilon \rho_{\rm inf}$. It affects the inflaton field evolution and leads to the scale-invariant electric power spectrum and the magnetic one which is blue with the spectral index $n_{B}=2$ for any decreasing coupling function. This gives an upper limit on the present-day value of observed magnetic fields below $10^{-22}\,{\rm G}$. It is worth emphasizing that since the effective electric charge of particles $e_{\rm eff}=e/f$ is suppressed by the coupling function, the Schwinger effect becomes important only at the late stages of inflation when the inflaton field is close to the minimum of its potential. The Schwinger effect abruptly decreases the value of the electric field, helping to finish the inflation stage and enter the stage of preheating. It effectively produces the charged particles, implementing the Schwinger reheating scenario even before the fast oscillations of the inflaton. The numerical analysis is carried out in the Starobinsky model of inflation for the powerlike $f\propto a^{\alpha}$ and Ratra-type $f=\exp(\beta\phi/M_{p})$ coupling functions.Comment: 21 pages, 8 figure

Rethinking Juvenile Rehabilitation: Presumptive Waiver and Alternative Sentencing in Indiana

Indiana’s juvenile justice system, like all systems of juvenile justice, is premised on rehabilitation. And while Indiana is far from an outdated, overly punitive system, there are several tangible opportunities for improvement. Indiana enacted an alternative sentencing scheme for juvenile offenders waived into adult court in 2013, but alternative sentencing has not been implemented in an effective manner yet. Furthermore, Indiana’s statutory system of waiver contains several aspects that are inconsistent with, or simply fail to account for, modern social science understandings. This Comment seeks to expound upon relevant social science principles within the context of juvenile justice in order to bring to light many of the considerations that form the basis of a developmentally focused system. The Comment will bring to light twenty-first century literature on adolescent brain development and explain how youth behavioral tendencies can be better understood in light of this research. The Comment then takes an in-depth look at Indiana’s system of “presumptive waiver” and its alternative sentencing scheme. Throughout this analysis, the Comment will highlight serious problems and inconsistencies within these statutory schemes. The Comment will conclude with four concrete reform proposals that seek to enhance Indiana’s system of waiver and alternative sentencing by making changes informed by developmental social science principles. These reform proposals are not unrealistic, system-rocking changes made for political grandstanding and internet clickbait. They are real proposals that can be effectively and immediately implemented without large-scale disruption. This Comment will demonstrate that these proposals should be taken into serious consideration by the Indiana legislature

Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics

Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment

Microbial single-cell omics: the crux of the matter

Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies

Magnetogenesis in Higgs-Starobinsky inflation

In the framework of mixed Higgs-Starobinsky inflation, we consider the generation of Abelian gauge fields due to their nonminimal coupling to gravity (in two different formulations of gravity -- metric and Palatini). We couple the gauge-field invariants $F_{\mu\nu}F^{\mu\nu}$ and $F_{\mu\nu}\tilde{F}^{\mu\nu}$ to an integer power of the scalar curvature $R^n$ in Jordan frame and, treating these interactions perturbatively, switch to the Einstein frame where they lead to effective kinetic and axial couplings between gauge fields and inflaton. We determine the power spectra, energy densities, correlation length, and helicality of the generated gauge fields for different values of the nonminimal coupling constants and parameter $n$. We analytically estimate the spectral index $n_{B}$ of the magnetic power spectrum and show that for $n>1$ it is possible to get the scale-invariant or even red-tilted spectrum for a wide range of modes that implies larger correlation length of the generated fields. On the other hand, the magnitude of these fields typically decreases in time becoming very small in the end of inflation. Thus, it is difficult to obtain both large magnitude and correlation length of the gauge field in the frame of this model.Comment: 20 pages, 7 figures, submitted to Phys. Rev.

The Future of HCV Therapy: NS4B as an Antiviral Target

Chronic hepatitis C virus (HCV) infection is a major worldwide cause of liver disease, including cirrhosis and hepatocellular carcinoma. It is estimated that more than 170 million individuals are infected with HCV, with three to four million new cases each year. The current standard of care, combination treatment with interferon and ribavirin, eradicates the virus in only about 50% of chronically infected patients. Notably, neither of these drugs directly target HCV. Many new antiviral therapies that specifically target hepatitis C (e.g. NS3 protease or NS5B polymerase inhibitors) are therefore in development, with a significant number having advanced into clinical trials. The nonstructural 4B (NS4B) protein, is among the least characterized of the HCV structural and nonstructural proteins and has been subjected to few pharmacological studies. NS4B is an integral membrane protein with at least four predicted transmembrane (TM) domains. A variety of functions have been postulated for NS4B, such as the ability to induce the membranous web replication platform, RNA binding and NTPase activity. This review summarizes potential targets within the nonstructural protein NS4B, with a focus on novel classes of NS4B inhibitors