Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites.

Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.

Proton-controlled molecular ionic ferroelectrics.

Molecular ferroelectric materials consist of organic and inorganic ions held together by hydrogen bonds, electrostatic forces, and van der Waals interactions. However, ionically tailored multifunctionality in molecular ferroelectrics has been a missing component despite of their peculiar stimuli-responsive structure and building blocks. Here we report molecular ionic ferroelectrics exhibiting the coexistence of room-temperature ionic conductivity (6.1 × 10-5 S/cm) and ferroelectricity, which triggers the ionic-coupled ferroelectric properties. Such ionic ferroelectrics with the absorbed water molecules further present the controlled tunability in polarization from 0.68 to 1.39 µC/cm2, thermal conductivity by 13% and electrical resistivity by 86% due to the proton transfer in an ionic lattice under external stimuli. These findings enlighten the development of molecular ionic ferroelectrics towards multifunctionality.

A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation.

Epigenetic mechanisms are essential to establish and safeguard cellular identities in mammals. They dynamically regulate the expression of genes, transposable elements and higher-order chromatin structures. Consequently, these chromatin marks are indispensable for mammalian development and alterations often lead to disease, such as cancer. Bivalent promoters are especially important during differentiation and development. Here we used a genetic screen to identify new regulators of a bivalent repressed gene. We identify BEND3 as a regulator of hundreds of bivalent promoters, some of which it represses, and some of which it activates. We show that BEND3 is recruited to a CpG-containg consensus site that is present in multiple copies in many bivalent promoters. Besides having direct effect on the promoters it binds, the loss of BEND3 leads to genome-wide gains of DNA methylation, which are especially marked at regions normally protected by the TET enzymes. DNA hydroxymethylation is reduced in Bend3 mutant cells, possibly as consequence of altered gene expression leading to diminished alpha-ketoglutarate production, thus lowering TET activity. Our results clarify the direct and indirect roles of an important chromatin regulator, BEND3, and, more broadly, they shed light on the regulation of bivalent promoters.

A genome-wide screen reveals new regulators of the 2-cell-like cell state.

In mammals, only the zygote and blastomeres of the early embryo are totipotent. This totipotency is mirrored in vitro by mouse '2-cell-like cells' (2CLCs), which appear at low frequency in cultures of embryonic stem cells (ESCs). Because totipotency is not completely understood, we carried out a genome-wide CRISPR knockout screen in mouse ESCs, searching for mutants that reactivate the expression of Dazl, a gene expressed in 2CLCs. Here we report the identification of four mutants that reactivate Dazl and a broader 2-cell-like signature: the E3 ubiquitin ligase adaptor SPOP, the Zinc-Finger transcription factor ZBTB14, MCM3AP, a component of the RNA processing complex TREX-2, and the lysine demethylase KDM5C. All four factors function upstream of DPPA2 and DUX, but not via p53. In addition, SPOP binds DPPA2, and KDM5C interacts with ncPRC1.6 and inhibits 2CLC gene expression in a catalytic-independent manner. These results extend our knowledge of totipotency, a key phase of organismal life.

Correction: Highly active spherical amorphous MoS2: facile synthesis and application in photocatalytic degradation of rose bengal dye and hydrogenation of nitroarenes.

[This corrects the article DOI: 10.1039/C5RA19442C.].

Additive manufacturing of eco-friendly building insulation materials by recycling pulp and paper.

Thermal insulation materials by recycling pulp and paper wastes play an important role in environmental sustainability of green buildings. As society is pursuing the goal of zero carbon emissions, it is highly desirable to use eco-friendly materials and manufacturing technologies for building insulation envelopes. Here we report additive manufacturing of flexible and hydrophobic insulation composites from recycled cellulose-based fibers and silica aerogel. The resultant cellulose-aerogel composites exhibit thermal conductivity of 34.68 mW m-1 K-1, mechanical flexibility with a flexural modulus of 429.21 MPa, and superhydrophobicity with water contact angle of 158.72°. Moreover, we present the additive manufacturing process of recycled cellulose aerogel composites, providing enormous potential for high energy efficiency and carbon-sequestration building applications.

Targeted Nanopore Resequencing and Methylation Analysis of LINE-1 Retrotransposons.

Retrotransposition of LINE-1 (L1) elements represents a major source of insertional polymorphisms in mammals, and their mutagenic activity is restricted by silencing mechanisms, such as DNA methylation. Despite a very high level of sequence identity between copies, their internal sequence contains small nucleotide polymorphisms (SNPs) that can alter their activity. Such internal SNPs can also appear in different alleles of a given L1 locus. Given their repetitive nature and relatively long size, short-read sequencing approaches have limited access to L1 internal sequence or DNA methylation state. Here, we describe a targeted method to specifically sequence more than a hundred L1-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. Our protocol, modified from the nanopore Cas9 targeted sequencing (nCATS) strategy, provides a full and haplotype-resolved L1 sequence and DNA methylation levels. It introduces a streamlined and multiplex approach to synthesize guide RNAs and a quantitative PCR (qPCR)-based quality check during library preparation for cost-effective L1 sequencing. More generally, this method can be applied to any type of transposable elements and organisms.

An Unusual Case of a Dematiaceous Fungus with an Exclusive Cerebral Involvement After ABO-Incompatible Renal Transplantation.

BACKGROUND Cladophialophora carrionii was detected postoperatively in a cerebral space-occupying lesion of a patient who had undergone ABO-incompatible renal transplantation. The infection was successfully treated with oral terbinafine and itraconazole. CASE REPORT An otherwise healthy 46-year-old man underwent ABO-incompatible renal transplantation. Postoperatively, he was hemodynamically stable and the graft was functioning well. Within 2 weeks, the patient developed clinical depression, followed by seizures and left-side hemiparesis. There were no skin findings. Radiological investigation showed 2 space-occupying lesions in the brain parenchyma. The patient's condition improved after partial frontal lobectomy and microsurgical abscess evacuation, with a short course of liposomal amphotericin B and a combination of oral terbinafine and itraconazole. Microbiological examination of the pus showed growth of C. carrionii, which predominantly causes subcutaneous mycoses. CONCLUSIONS It is very rare for melanized fungal infections to cause an exclusively cerebral disease without any skin involvement. Furthermore, among established cases, C. carrionii is a very rarely detected pathogen.

Participatory design for selection of icons to represent daily activities of living for a vision-based rehabilitation-cum-assistance system for locked-in patients.

Purpose: The majority of rehabilitation systems for locked-in patients are used for therapeutic purposes. However, round-the-clock assistance and support are essential after discharge from hospitals or nursing homes. This inspired us to develop a round-the-clock rehabilitation-cum-assistance system operated by eye gazes of locked-in patients. To do this, we aimed to identify the essential daily activities of living for locked-in patients and represent these activities using the most universally acceptable icons/images on the interface for the rehabilitation-cum-assistance system.Method: Activities were selected from available conventions and literature with advice from a local physiotherapy centre. Simple arithmetic averages and weighted averages of recognition rates for different icons representing different daily activities were calculated as per ISO 3864. Universal acceptability of the icons was compared based on responses from 72 locked-in patients across five different age groups. The final icons or images were then selected.Results: Three icons were categorized as identifiable with overall average recognition rates above 66.7%. Icons with average recognition rates 30-60% were considered to have "medium" recognisability and 21 icons were in this category. The average recognition rates of six icons were below 30% and were not acceptable. An overall recognition efficiency of 91% was achieved for participants from all age groups.Conclusions: The most preferred and unambiguous icons or images representing the essential daily activities of living were identified for use on the interface of our rehabilitation-cum-assistance system for round-the-clock operation.Implications for rehabilitationPerforming some of the daily activities by locked-in patients himself/herself is essential for self-independence as well as measures the level of regular improvement.Assistive technologies have huge potential for application for the purpose, especially the vision-based systems.Present technology is useful for development of a vision-based rehabilitation-cum-assistance system for 24 × 7 assistance for the locked-in patients.A new approach for real-time, user-based field evaluation of icons representing daily activities of living using statistical method of averaging of the recognition rates.

Advanced catalytic performance of amorphous MoS2 for degradation/reduction of organic pollutants in both individual and simultaneous fashion.

A cluster [(S2)2Mo(S2)2Mo(S2)2], has been used to synthesise molybdenum sulfide microparticles (MPs) by solvothermal treatments under inert environment. During synthesis, surfactants i.e. oleylamine and dodecanthiol take part in chief role in shaping the morphology of MPs into ultrathin nano-fibre, and nano-rod. MPs have been characterized by X-ray diffraction analysis, energy dispersive X-ray spectroscopy, transmission electron microscopy and UV-vis spectroscopic techniques. The optical spectral data reveals a simultaneous presence of direct and indirect band gap in both MoS2. The material emerges as an effective catalyst towards the mineralization of different cationic dyes (rhodamine B and methylene blue) and anionic dye (rosebngal). These MPs have also been effectively used for the simultaneous degradations of different dyes in the same reaction mixture which make further highlighted the catalytic performances of MoS2. The above kinetics of the decomposition processes were examined and found to follow the pseudo-first-order reaction model. The plausible mechanism has been explained by comparing the position of conduction band levels of MoS2 (measured by Mott-schotky and touc's plot) and potential value of borohydride. We have also investigated the active species behind the degradation of dyes by using different scavengers. The new catalyst was also effective for the degradation of mixture of dyes to the same extent as it was in case of individual.

Single source precursor driven phase selective synthesis of Au-CuGaS2 heteronanostructures: an observation of plasmon enhanced photocurrent efficiency.

The design of new functional metal-semiconductor heteronanostructures with improved photovoltaic efficiencies has drawn significant attention because of their unprecedented properties and potential applications. Herein, we report a phase selective synthesis of ternary CuGaS2 (wurtzite and tetragonal) by simple solution based thermal decomposition of a new binuclear single molecular precursor [Ga(acda)3Cu(PPh3)2]NO3 (acda = 2-aminocyclopentene-1-dithiocarboxylic acid, PPh3 = triphenylphosphine) where the phase selectivity has been achieved easily by changing the combination of surface active agents. Furthermore, we have extended our approach to develop a well-controlled synthetic strategy for the preparation of a Au-CuGaS2 heteronanocomposite with both the phases. A detailed microscopic study reveals that during heterostructure synthesis, an epitaxial junction has been formed at the interface of ternary CuGaS2 and metallic Au. To find out the influence of this epitaxial connectivity on the properties, we have studied the photocurrent and photoresponse behavior of the material and compared them with that of bare CuGaS2. For both the wurtzite and tetragonal phases, the Au-CuGaS2 twin structure exhibits a plasmon enhanced superior charge transport ability and an abruptly high photocurrent density compared to that of pure CuGaS2. Due to efficient charge separation by strong plasmon-exciton coupling at the interface, Au-CuGaS2 can be used as a potential candidate for photoelectrochemical applications.

Exploration of Phytoconstituents from Mussaenda roxburghii and Studies of Their Antibiofilm Effect.

In the context of ethno botanical importance with no phytochemical investigations, Mussaenda roxburghii have been investigated to explore it's phytoconstituents and studies of their antibiofilm activity. Four compounds have been isolated from the aerial parts of this plant and were characterized as 2α,3ß,19α,23-tetrahydroxyurs-12-en-28-oic acid (1), ß-sitosterol glucoside (4), lupeol palmitate (5), and myoinositol (6). All these compounds were tested for antibacterial and antibiofilm activity against Pseudomonas aeruginosa. Compound 1 exhibited three times more antibiofilm activity with minimum inhibitory concentration (MIC) at 0.74 mm compared to that of streptomycin. Molecular docking studies exhibited a very high binding affinity of 1 with P. aeruginosa quorum sensing proteins and motility associated proteins viz. LasR and PilB, PilY1, PilT, respectively. Compound 1 was also found to be non-cytotoxic against sheep RBC and murine peritoneal macrophages at selected sub-MIC doses.

piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation?

P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are small, noncoding RNAs known for silencing transposable elements (TEs) in the germline of animals. Most genomes host TEs, which are notorious for mobilizing themselves and endangering survival of the host if not controlled. By silencing TEs in the germline, piRNAs prevent harmful mutations from being passed on to the next generation. How piRNAs are generated and how they silence TEs were the focus of researchers ever since their discovery. Now a spate of recent papers are beginning to tell us that piRNAs can play roles beyond TE silencing and are involved in diverse cellular processes from mRNA regulation to development or genome rearrangement. In this review, we discuss some of these recently reported roles. Data on these new roles are often rudimentary, and the involvement of piRNAs in these processes is yet to be definitely established. What is interesting is that the reports are on animals widely separated on the phylogenetic tree of life and that piRNAs were also found outside the gonadal tissues. Some of these piRNAs map to TE sequences, prompting us to hypothesize that genomes may have co-opted the TE-derived piRNA system for their own regulation.-Sarkar, A., Volff, J.-N., Vaury, C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation?

Export of piRNA precursors by EJC triggers assembly of cytoplasmic Yb-body in Drosophila.

PIWI-interacting RNAs (piRNAs) are effectors of transposable element (TE) silencing in the reproductive apparatus. In Drosophila ovarian somatic cells, piRNAs arise from longer single-stranded RNA precursors that are processed in the cytoplasm presumably within the Yb-bodies. piRNA precursors encoded by the flamenco (flam) piRNA cluster accumulate in a single focus away from their sites of transcription. In this study, we identify the exportin complex containing Nxf1 and Nxt1 as required for flam precursor nuclear export. Together with components of the exon junction complex (EJC), it is necessary for the efficient transfer of flam precursors away from their site of transcription. Indeed, depletion of these components greatly affects flam intra-nuclear transit. Moreover, we show that Yb-body assembly is dependent on the nucleo-cytoplasmic export of flam transcripts. These results suggest that somatic piRNA precursors are thus required for the assembly of the cytoplasmic transposon silencing machinery.

Enhanced photocatalytic performance of morphologically tuned Bi2S3 NPs in the degradation of organic pollutants under visible light irradiation.

Here in, morphologically tuned Bi2S3 NPs were successfully synthesized from a single-source precursor complex [Bi(ACDA)3] [HACDA=2-aminocyclopentene-1-dithiocarboxylic acid] by decomposing in various solvents using a simple solvothermal method. The as-obtained products were characterized by XRD, TEM, UV-vis spectroscopy and BET surface area measurements. Structural analyses revealed that the as-prepared Bi2S3 NPs can be tuned to different morphologies by varying various solvents and surfactants. The interplay of factors that influenced the size and morphology of the nanomaterials has been studied. Moreover, mastery over the morphology of nanoparticles enables control of their properties and enhancement of their usefulness for a given application. These materials emerged as a highly active visible light-driven photocatalyst towards degradation of methylene blue dye and the efficiencies are dependent on size and surface area of the NPs. In addition, photocatalytic degradation of highly toxic dichlorodiphenyltrichloroethane was studied using synthesized Bi2S3 NPs as catalyst and the rate of degradation has been found to be much better compared to that exhibited by commercial WO3. We believe that this new synthesis approach can be extended to the synthesis of other metal sulfide nanostructures and open new opportunities for device applications.

Drosophila MOF regulates DIAP1 and induces apoptosis in a JNK dependent pathway.

Histone modulations have been implicated in various cellular and developmental processes where in Drosophila Mof is involved in acetylation of H4K16. Reduction in the size of larval imaginal discs is observed in the null mutants of mof with increased apoptosis. Deficiency involving Hid, Reaper and Grim [H99] alleviated mof (RNAi) induced apoptosis in the eye discs. mof (RNAi) induced apoptosis leads to activation of caspases which is suppressed by over expression of caspase inhibitors like P35 and Diap1 clearly depicting the role of caspases in programmed cell death. Also apoptosis induced by knockdown of mof is rescued by JNK mutants of bsk and tak1 indicating the role of JNK in mof (RNAi) induced apoptosis. The adult eye ablation phenotype produced by ectopic expression of Hid, Rpr and Grim, was restored by over expression of Mof. Accumulation of Mof at the Diap1 promoter 800 bp upstream of the transcription start site in wild type larvae is significantly higher (up to twofolds) compared to mof (1) mutants. This enrichment coincides with modification of histone H4K16Ac indicating an induction of direct transcriptional up regulation of Diap1 by Mof. Based on these results we propose that apoptosis triggered by mof (RNAi) proceeds through a caspase-dependent and JNK mediated pathway.

Colorimetric estimation of human glucose level using γ-Fe2O3 nanoparticles: an easily recoverable effective mimic peroxidase.

This article reports simple, green and efficient synthesis of γ-Fe2O3 nanoparticles (NPs) (maghemite) through single-source precursor approach for colorimetric estimation of human glucose level. The γ-Fe2O3 NPs, having cubic morphology with an average particle size of 30 nm, exhibited effective peroxidase-like activity through the catalytic oxidation of peroxidase substrate 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H2O2 producing a blue-colored solution. On the basis of this colored-reaction, we have developed a simple, cheap, highly sensitive and selective colorimetric method for estimation of glucose using γ-Fe2O3/TMB/glucose-glucose oxidase (GOx) system in the linear range from 1 to 80 µM with detection limit of 0.21 µM. The proposed glucose sensor displays faster response, good stability, reproducibility and anti-interference ability. Based on this simple reaction process, human blood and urine glucose level can be monitored conveniently.

Argonaute-1 functions as a mitotic regulator by controlling Cyclin B during Drosophila early embryogenesis.

The role of Ago-1 in microRNA (miRNA) biogenesis has been thoroughly studied, but little is known about its involvement in mitotic cell cycle progression. In this study, we established evidence of the regulatory role of Ago-1 in cell cycle control in association with the G2/M cyclin, cyclin B. Immunostaining of early embryos revealed that the maternal effect gene Ago-1 is essential for proper chromosome segregation, mitotic cell division, and spindle fiber assembly during early embryonic development. Ago-1 mutation resulted in the up-regulation of cyclin B-Cdk1 activity and down-regulation of p53, grp, mei-41, and wee1. The increased expression of cyclin B in Ago-1 mutants caused less stable microtubules and probably does not produce enough force to push the nuclei to the cortex, resulting in a decreased number of pole cells. The role of cyclin B in mitotic defects was further confirmed by suppressing the defects in the presence of one mutant copy of cyclin B. We identified involvement of 2 novel embryonic miRNAs--miR-981 and miR--317-for spatiotemporal regulation of cyclin B. In summary, our results demonstrate that the haploinsufficiency of maternal Ago-1 disrupts mitotic chromosome segregation and spindle fiber assembly via miRNA-guided control during early embryogenesis in Drosophila. The increased expression of cyclin B-Cdk1 and decreased activity of the Cdk1 inhibitor and cell cycle checkpoint proteins (mei-41 and grp) in Ago-1 mutant embryos allow the nuclei to enter into mitosis prematurely, even before completion of DNA replication. Thus, our results have established a novel role of Ago-1 as a regulator of the cell cycle.

Drosophila MOF controls Checkpoint protein2 and regulates genomic stability during early embryogenesis.

BACKGROUND: In Drosophila embryos, checkpoints maintain genome stability by delaying cell cycle progression that allows time for damage repair or to complete DNA synthesis. Drosophila MOF, a member of MYST histone acetyl transferase is an essential component of male X hyperactivation process. Until recently its involvement in G2/M cell cycle arrest and defects in ionizing radiation induced DNA damage pathways was not well established. RESULTS: Drosophila MOF is highly expressed during early embryogenesis. In the present study we show that haplo-insufficiency of maternal MOF leads to spontaneous mitotic defects like mitotic asynchrony, mitotic catastrophe and chromatid bridges in the syncytial embryos. Such abnormal nuclei are eliminated and digested in the yolk tissues by nuclear fall out mechanism. MOF negatively regulates Drosophila checkpoint kinase 2 tumor suppressor homologue. In response to DNA damage the checkpoint gene Chk2 (Drosophila mnk) is activated in the mof mutants, there by causing centrosomal inactivation suggesting its role in response to genotoxic stress. A drastic decrease in the fall out nuclei in the syncytial embryos derived from mof¹/+; mnkp6/+ females further confirms the role of DNA damage response gene Chk2 to ensure the removal of abnormal nuclei from the embryonic precursor pool and maintain genome stability. The fact that mof mutants undergo DNA damage has been further elucidated by the increased number of single and double stranded DNA breaks. CONCLUSION: mof mutants exhibited genomic instability as evidenced by the occurance of frequent mitotic bridges in anaphase, asynchronous nuclear divisions, disruption of cytoskeleton, inactivation of centrosomes finally leading to DNA damage. Our findings are consistent to what has been reported earlier in mammals that; reduced levels of MOF resulted in increased genomic instability while total loss resulted in lethality. The study can be further extended using Drosophila as model system and carry out the interaction of MOF with the known components of the DNA damage pathway.

The role of MOF in the ionizing radiation response is conserved in Drosophila melanogaster.

In Drosophila, males absent on the first (MOF) acetylates histone H4 at lysine 16 (H4K16ac). This acetylation mark is highly enriched on the male X chromosome and is required for dosage compensation in Drosophila but not utilized for such in mammals. Recently, we and others reported that mammalian MOF, through H4K16ac, has a critical role at multiple stages in the DNA damage response (DDR) and double-strand break repair pathways. The goal of this study was to test whether mof is similarly required for the response to ionizing radiation (IR) in Drosophila. We report that Drosophila mof mutations in males and females, as well as mof knockdown in SL-2 cells, reduce post-irradiation survival. MOF depletion in SL-2 cells also results in an elevated frequency of metaphases with chromosomal aberrations, suggesting that MOF is involved in DDR. Mutation in Drosophila mof also results in a defective mitotic checkpoint, enhanced apoptosis, and a defective p53 response post-irradiation. In addition, IR exposure enhanced H4K16ac levels in Drosophila as it also does in mammals. These results are the first to demonstrate a requirement for MOF in the whole animal IR response and suggest that the role of MOF in the response to IR is conserved between Drosophila and mammals.