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Abstract DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.

Abstract Background Cardiomyocytes (CMs) derived from human induced pluripotent stem cells (hiPSCs) by traditional methods are a mix of atrial and ventricular CMs and many other non-cardiomyocyte cells. Retinoic acid (RA) plays an important role in regulation of the spatiotemporal development of the embryonic heart. Methods CMs were derived from hiPSC (hi-PCS-CM) using different concentrations of RA (Control without RA, LRA with 0.05μM and HRA with 0.1 μM) between day 3-6 of the differentiation process. Engineered heart tissues (EHTs) were generated by assembling hiPSC-CM at high cell density in a low collagen hydrogel. Results In the HRA group, hiPSC-CMs exhibited highest expression of contractile proteins MYH6, MYH7 and cTnT. The expression of TBX5, NKX2.5 and CORIN, which are marker genes for left ventricular CMs, was also the highest in the HRA group. In terms of EHT, the HRA group displayed the highest contraction force, the lowest beating frequency, and the highest sensitivity to hypoxia and isoprenaline, which means it was functionally more similar to the left ventricle. RNAsequencing revealed that the heightened contractility of EHT within the HRA group can be attributed to the promotion of augmented extracellular matrix strength by RA. Conclusion By interfering with the differentiation process of hiPSC with a specific concentration of RA at a specific time, we were able to successfully induce CMs and EHTs with a phenotype similar to that of the left ventricle or right ventricle.

Summary: Salt fractionation is a classical approach for separating chromatin based on its differential salt solubility and physical properties. Here, we present a protocol to apply salt fractionation for genome-scale profiling of chromatin isolated from livers at different stages of aging in mice. We elaborate on the steps to isolate nuclei, digest with micrococcal nuclease, sequentially salt fractionate, purify DNA, and construct libraries for genome profiling. We also include information on a computational pipeline for data analysis.For complete details on the use and execution of this protocol, please refer to Yang et al.1 This protocol is an adaptation of the salt fractionation method of Teves and Henikoff.2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

A growing number of viruses pose significant threats to human health, impact agricultural production and compromise food safety. Minimizing the impact of viral infections demands for effective technologies that can deliver sensitive viral detection under various settings. Functional nucleic acids (FNAs) – natural or synthetic nucleic acid molecules with catalytic and/or binding properties – have been increasingly explored as key components for setting up diagnostic tests for viral detection. FNA-based viral biosensors offer distinct advantages, such as the ability to achieve sensitive viral detection in complex biological samples, ease of use, scalability, and cost-effectiveness. This mini-review will be dedicated to appraising progress made in recent years in FNA-based biosensors for diagnosing diverse human and animal viruses. We will first describe virus structures and potential biomarkers that can be utilized as the targets for FNA probe engineering. This is followed by reviewing the latest advances in two classes of FNAs - DNAzyme and DNA aptamers, with focuses on DNAzyme- and DNA aptamer-based biosensors that employ diverse signal transduction mechanisms to achieve sensitive viral detections. Finally, we will discuss current challenges in the field and suggest future research directions that can address these challenges.

Abstract Electrochemical biosensing represents a highly effective technology for detecting disease biomarkers given its high sensitivity, low and clinically relevant limit of detection, and cost effectiveness. However, in complex media such as urine, blood, sweat or saliva, biosensing performance can be significantly impacted by electrode biofouling by proteins, cells, lipids, and other matrix components. Such biofouling leads to reduced signal from the target analyte coupled with an elevated background signal, resulting in poor signal‐to‐noise ratios (SNRs), reduced sensitivity, and lower specificity. This comprehensive review describes the design of anti‐fouling polymers and peptides as a potential solution to prevent or suppress electrochemical biosensor fouling. Various anti‐fouling polymers and peptides developed for improved biosensing in complex media are summarized in the context of their mechanism(s) of anti‐fouling, methods of deposition, and practical applications. Recent advances and persistent challenges in the field are also reviewed to provide perspectives on new directions toward enhancing anti‐fouling in electrochemical biosensors.

Abstract The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit’s AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.

Despite their ubiquity, few have used traffic camera networks for social science research. Using 1,312,977 images collected from 768 London-based cameras leading up to the 2015 UK general election, this study not only demonstrates how traffic camera data can be used to effectively measure same-day turnout, but we also provide ways such data can be used to assess political behavior more broadly. Such automated enumeration is especially important in countries where official results are only returned for the current election, making it difficult for those interested in assessing turnout at lower levels of aggregation, even when those elections are next on the calendar. Although we are not the first to suggest the value of images-as-data, this study hopes to underline the importance of video-as-data, while simultaneously offering an important foundation for future research.

Macrophages are a heterogeneous class of innate immune cells that offer a primary line of defense to the body by phagocytizing pathogens, digesting them, and presenting the antigens to T and B cells to initiate adaptive immunity. Through specialized pro-inflammatory or anti-inflammatory activities, macrophages also directly contribute to the clearance of infections and the repair of tissue injury. Macrophages are distributed throughout the body and largely carry out tissue-specific functions. In skeletal muscle, macrophages regulate tissue repair and regeneration; however, the characteristics of these macrophages are not yet fully understood, and their involvement in skeletal muscle aging remains to be elucidated. To investigate these functions, it is critical to efficiently isolate macrophages from skeletal muscle with sufficient purity and yield for various downstream analyses. However, methods to prepare enriched skeletal muscle macrophages are scarce. Here, we describe in detail an optimized method to isolate skeletal muscle macrophages from mice. This method has allowed the isolation of CD45+/CD11b+ macrophage-enriched cells from young and old mice, which can be further used for flow cytometric analysis, fluorescence-activated cell sorting (FACS), and single-cell RNA sequencing.

Tissue-resident macrophages represent a group of highly responsive innate immune cells that acquire diverse functions by polarizing toward distinct subpopulations. The subpopulations of macrophages that reside in skeletal muscle (SKM) and their changes during aging are poorly characterized. By single-cell transcriptomic analysis with unsupervised clustering, we found 11 distinct macrophage clusters in male mouse SKM with enriched gene expression programs linked to reparative, proinflammatory, phagocytic, proliferative, and senescence-associated functions. Using a complementary classification, membrane markers LYVE1 and MHCII identified four macrophage subgroups: LYVE1−/MHCIIhi (M1-like, classically activated), LYVE1+/MHCIIlo (M2-like, alternatively activated), and two new subgroups, LYVE1+/MHCIIhi and LYVE1−/MHCIIlo. Notably, one new subgroup, LYVE1+/MHCIIhi, had traits of both M2 and M1 macrophages, while the other new subgroup, LYVE1−/MHCIIlo, displayed strong phagocytic capacity. Flow cytometric analysis validated the presence of the four macrophage subgroups in SKM and found that LYVE1− macrophages were more abundant than LYVE1+ macrophages in old SKM. A striking increase in proinflammatory markers (S100a8 and S100a9 mRNAs) and senescence-related markers (Gpnmb and Spp1 mRNAs) was evident in macrophage clusters from older mice. In sum, we have identified dynamically polarized SKM macrophages and propose that specific macrophage subpopulations contribute to the proinflammatory and senescent traits of old SKM.

2D transition metal dichalcogenides (TMDCs) are promising materials for device applications owing to their electronic, optical, and material properties varying with the number of monolayers. Synthesis of large area crystalline TMDC thin films is still challenging with techniques such as exfoliation and chemical vapor growth owing to the uncontrollability of deposition area and high temperature growths with toxic precursors, respectively. Pulsed laser deposition (PLD) is a technique that can overcome these challenges owing to stoichiometric layer by layer growth control by optimizing the growth parameters. In this study, we optimize parameters such as temperature, post-growth annealing, inert gas pressure, and substrate–target distance during PLD growth of MoS2 to obtain uniform and highly crystalline thin films on an ∼1 in.2 substrate. The optimized growth conditions are 800 °C with a 30 min post-growth annealing at a laser fluence of 2.2 J/cm2 with a substrate–target distance of 5 cm and 0.5 mTorr of argon partial pressure. An RMS roughness of 0.17 nm was obtained for 3 nm (4 monolayers) thick MoS2 films with a thin film conductivity of ∼4000 S/m.

Many of the features associated with senescence appear steadily over time before cells stop dividing.

Adult stem cells undergo both replicative and chronological aging in their niches, with catastrophic declines in regenerative potential with age. Due to repeated environmental insults during aging, the chromatin landscape of stem cells erodes, with changes in both DNA and histone modifications, accumulation of damage, and altered transcriptional response. A body of work has shown that altered chromatin is a driver of cell fate changes and a regulator of self-renewal in stem cells and therefore a prime target for juvenescence therapeutics. This review focuses on chromatin changes in stem cell aging and provides a composite view of both common and unique epigenetic themes apparent from the studies of multiple stem cell types.

Summary: The SWI/SNF chromatin remodeling complex is highly conserved from yeast to human, and aberrant SWI/SNF complexes contribute to human disease. The Snf5/SMARCB1/INI1 subunit of SWI/SNF is a tumor suppressor frequently lost in pediatric rhabdoid cancers. We examined the effects of Snf5 loss on the composition, nucleosome binding, recruitment, and remodeling activities of yeast SWI/SNF. The Snf5 subunit is shown by crosslinking-mass spectrometry (CX-MS) and subunit deletion analysis to interact with the ATPase domain of Snf2 and to form a submodule consisting of Snf5, Swp82, and Taf14. Snf5 promotes binding of the Snf2 ATPase domain to nucleosomal DNA and enhances the catalytic and nucleosome remodeling activities of SWI/SNF. Snf5 is also required for SWI/SNF recruitment by acidic transcription factors. RNA-seq analysis suggests that both the recruitment and remodeling functions of Snf5 are required in vivo for SWI/SNF regulation of gene expression. Thus, loss of SNF5 alters the structure and function of SWI/SNF. : Mutation of SWI/SNF chromatin remodeling complex subunits contributes to cancer and neurological disorders. Sen et al. report that loss of the Snf5 subunit alters the architecture and function of SWI/SNF in a yeast model system. These findings may reflect changes that occur in pediatric rhabdoid tumors with mutated Snf5. Keywords: Chromatin remodeling, SWI/SNF, Snf5, SMARCB1, BAF47, INI1

The influence of carboxylic acid functionalized multi-walled carbon nanotubes (cMWCNTs) content on the properties of polystyrene (PS) nanocomposite (NC) films was investigated. The NC films were produced by a simple sonication assisted solvent blending technique. The interaction between the matrix (PS) and well dispersed filler (cMWCNT) was evaluated by different techniques involving Fourier transform infrared spectroscopy, Raman spectroscopy and X-Ray diffraction. Morphological images of the NCs were collected from Transmission electron microscopy. The thermal characteristics of the PS were found to be improved by the incorporation of the cMWCNTs, which was evident from the Thermogravimetric analysis (TGA) data. The thermal degradation activation energy evaluated by Coats-Redfern method and integral procedural decomposition temperature determined by Doyle's method supported the thermal stability proposed by TGA of the NCs. The reaction mechanism of thermal degradation of neat PS and respective NCs was successfully predicted using Criado method. The rheological properties and hardness were found to be upgraded by the inclusion of nanotubes to the PS matrix.

The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.

Communication is used for more than just passing on information from one person to another. It is often used as a tool to facilitate the participation of people in developmental activities. Such form of communication is known as development communication. According to Everett Rogers "Development communication refers to the uses to which communication are put in order to further development." It can thus be said to be an approach to communication which provides communities with information they can use in bettering their lives. Development communication has two primary roles, i.e. Transforming role, as it steps social change in the direction of the hygiene taste of today's generation in this competitive market and a socializing role by seeking to maintain some of the established values of the society. Media plays an important role in development communication through circulation of knowledge, providing forum for discussion of issues, teach ideas, skills for a better life and create a base of consensus for stability of the state . From the early stages of the introduction of the media in India various attempts were made to exploit their potential for development purposes. The history of development communication in India can be traced to 1940's when radio broadcast was done in different languages to promote development communication through various programmes, like-Programs for Rural Audience, Educational Programs and Family Welfare Programs. Today television in our country is also used as a medium for social education, weapon against ignorance and awareness among the people, through is difference programs like Educational Television (ETV), Countrywide Classroom (CWC), Teleconferencing etc. Experiments in Satellite technology has been conducted in recent years to bring about Social change and development. This has been done in the form of SITE Program and Kheda Communication Projects. New Technologies have also been put to serious use for development communication. New technologies like mobile, website and internet are interactive in nature. Interactivity, instant feedback and persuasion capability are used to rope in common person into the process of development. Today government has different websites and call centers that provide instant information or answers queries to questions of development. Right from its inception, development communication has been pursued by all kinds of media, both traditional and new. However, sadly enough, it had been put into more theoretical use. Its possibilities, people's change of demand and opportunities have not been d to its limit to get an overall success. Both the strength and weakness of the media and the message and access of people to these medium should be considered to achieve success in real sense and not only in pen and paper. [ABSTRACT FROM AUTHOR]

Despite recent advances in characterizing the regulation of histone H3 lysine 4 (H3-K4) methylation at the GAL1 gene by the H2B-K123-specific deubiquitinase activity of Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-acetyltransferase)-associated Ubp8p, our knowledge on the general role of Ubp8p at the SAGA-dependent genes is lacking. For this study, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation (ChIP) assay, we have analyzed the role of Ubp8p in the regulation of H3-K4 methylation at three other SAGA-dependent yeast genes, namely, PHO84, ADH1, and CUP1. Like that at GAL1, H3-K4 methylation is increased at the PHO84 core promoter in the UBP8 deletion mutant. We also show that H3-K4 methylation remains invariant at the PHO84 open reading frame in the Δ ubp8 mutant, demonstrating a highly localized role of Upb8p in regulation of H3-K4 methylation at the promoter in vivo. However, unlike that at PHO84, H3-K4 methylation at the two other SAGA-dependent genes is not controlled by Ubp8p. Interestingly, Ubp8p and H3-K4 methylation are dispensable for preinitiation complex assembly at the core promoters of these genes. Our ChIP assay further demonstrates that the association of Ubp8p with SAGA is mediated by Sgf11p, consistent with recent biochemical data. Collectively, the data show that Ubp8p differentially controls H3-K4 methylation at the SAGA-dependent promoters, revealing a complex regulatory network of histone methylation in vivo. [ABSTRACT FROM AUTHOR]