Origin of Enhancement of Orbital Magnetic Moment in SiO2-Coated Fe3O4 Nanocomposites Studied by X-ray Magnetic Circular Dichroism.

In this study, magnetic Fe3O4 nanoparticles (NPs) were dispersed uniformly by varying the thickness of the SiO2 coating, and their electronic and magnetic properties were investigated. X-ray diffraction confirmed the structural configuration of monophase inverse-spinel Fe3O4 NPs in nanometer size. Scanning electron microscopy revealed the formation of proper nonporous crystallite particles with a clear core-shell structure with silica on the surface of Fe3O4 NPs. The absorption mechanism studied through the zeta potential indicates that SiO2-coated Fe3O4 nanocomposites (SiO2@Fe3O4 NCs) possess electrostatic interactions to control their agglomeration in stabilizing suspensions by providing a protective shield of amorphous SiO2 on the oxide surface. High-resolution transmission electron microscopy images demonstrate a spherical morphology having an average grain diameter of ∼11-17 nm with increasing thickness of SiO2 coating with the addition of a quantitative presence and proportion of elements determined through elemental mapping and electron energy loss spectroscopy studies. Synchrotron-based element-specific soft X-ray absorption spectroscopy and X-ray magnetic circular dichroism (XMCD) techniques have been involved in the bulk-sensitive total fluorescence yield mode to understand the origin of magnetization in SiO2@Fe3O4 NCs. The magnetization hysteresis of Fe3O4 was determined by XMCD. At room temperature, the magnetic coercivity (Hc) is as high as 1 T, which is about 2 times more than the value of the thin film and about 5 times more pronounced than that of NPs. For noninteracting single-domain NPs with the Hc spread from 1 to 3 T, the Stoner-Wohlfarth model provided an intriguing explanation for the hysteresis curve. These curves determine the different components of Fe oxides present in the samples that derive the remnant magnetization involved in each oxidation state of Fe and clarify which Fe component is responsible for the resultant magnetism and magnetocrystalline anisotropy based on noninteracting single-domain particles.

The significance of eighteen rice genotypes on arsenic accumulation, physiological response and potential health risk.

Rice is an important food crop that is susceptible to arsenic (As) contamination under paddy soil conditions depending on As uptake characteristics of the rice genotypes. Here we unveiled the significance of eighteen (fine and coarse) rice genotypes against As accumulation/tolerance, morphological and physiological response, and antioxidant enzymes-enabled defense pathways. Arsenic significantly affected rice plant morphological and physiological attributes, with relatively more impacts on fine compared to coarse genotypes. Grain, shoot, and root As uptake were lower in fine genotypes (0.002, 0.020, and 0.032 mg pot-1 DW, respectively) than that of coarse (0.031, 0.60, and 1.2 mg pot-1 DW, respectively). Various biochemical (pigment contents, hydrogen peroxide, lipid peroxidation) and defense (antioxidant enzymes) plant parameters indicated that the fine genotypes, notably Kainat and Basmati-385, possessed the highest As tolerance. Arsenic-induced risk indices exhibited greater hazard quotient (up to 1.47) and carcinogenic risk (up to 0.0066) for coarse genotypes compared to the fine ones, with the greatest risk for KSK-282. This study elaborates the pivotal role of genotypic variation among rice plants in As accumulation, which is crucial for mitigating the associated human health risk. Further research is required on molecular aspects, e.g., genetic sequencing, to examine rice genotypes variation in defense mechanisms to As contamination.

Imaging non-collinear antiferromagnetic textures via single spin relaxometry.

Antiferromagnetic materials are promising platforms for next-generation spintronics owing to their fast dynamics and high robustness against parasitic magnetic fields. However, nanoscale imaging of the magnetic order in such materials with zero net magnetization remains a major experimental challenge. Here we show that non-collinear antiferromagnetic spin textures can be imaged by probing the magnetic noise they locally produce via thermal populations of magnons. To this end, we perform nanoscale, all-optical relaxometry with a scanning quantum sensor based on a single nitrogen-vacancy (NV) defect in diamond. Magnetic noise is detected through an increase of the spin relaxation rate of the NV defect, which results in an overall reduction of its photoluminescence signal under continuous laser illumination. As a proof-of-concept, the efficiency of the method is demonstrated by imaging various spin textures in synthetic antiferromagnets, including domain walls, spin spirals and antiferromagnetic skyrmions. This imaging procedure could be extended to a large class of intrinsic antiferromagnets and opens up new opportunities for studying the physics of localized spin wave modes for magnonics.

Knowledge and practices of primary care physicians on the current referral system of diabetic retinopathy in Islamabad and Rawal-Pindi, Pakistan.

AIM: To assess the current knowledge and practices in diabetic eye care and referral system regarding diabetic retinopathy (DR) in health centers of Islamabad and Rawal-Pindi. METHODS: A cross-sectional study was carried out in 4 government and private health centers in Rawalpindi-Islamabad from May 2018 to Oct. 2018. A total of 38 Primary Care Physicians (general practitioners, family physicians, and internists) were recruited out of which data for 2 were either not returned, or were missing partially. Data were collected through a 27-item consented & validated, multiple-choice questionnaire based on physician characteristics, knowledge and practice of diabetic eye care and challenges faced due current DR referral system. Descriptive analyses for all variables were performed including, mean and standard deviation. Analytical analyses were also conducted to study association between different study variables. RESULTS: Mean scores of knowledge for general practitioners, family physicians, and internists were 41.7%, 42.0% and 46.6% respectively. A lack of knowledge, and suboptimal practices were observed regarding signs, symptoms, screening, testing, evaluation and referral of DR regardless of physicians' specialty, or years in practice. Lack of expertise regarding direct ophthalmoscopy, interpretation of findings, and referral to an ophthalmologist were noted. Physicians who performed consultation and counselling according to patients' needs referred more patients to an ophthalmologist than those who restricted their consultation to a fixed amount of time and had more patients per unit time (P=0.01). Physicians who had taken care of less than 5 number of patients with DR marked less incorrect answers with no significantly greater number or correct answers compared to physicians who had taken care of more than 5 number of patients with DR (P=0.044). An association of more than 5 patients with DR taken care of with more need based patient consultation and counselling was also noted (P=0.017). An evaluation of the current referral system for DR revealed major loopholes in the health care infrastructure, proper guidelines, properly functioning equipment, check and balances, and lack of guidance to physicians regarding acquiring and updating knowledge regarding DR. CONCLUSION: Lack of updated and adequate knowledge, practices among primary care physicians, and suboptimal diabetic eye care and referral system have contributed to late presentation of DR. Interventions are needed to improve current diabetic eye care, and knowledge and practices of primary care physicians.

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency.

Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5' overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.

Kinetics and Fidelity of the Repair of Cas9-Induced Double-Strand DNA Breaks.

The RNA-guided DNA endonuclease Cas9 is a powerful tool for genome editing. Little is known about the kinetics and fidelity of the double-strand break (DSB) repair process that follows a Cas9 cutting event in living cells. Here, we developed a strategy to measure the kinetics of DSB repair for single loci in human cells. Quantitative modeling of repaired DNA in time series after Cas9 activation reveals variable and often slow repair rates, with half-life times up to ∼10 hr. Furthermore, repair of the DSBs tends to be error prone. Both classical and microhomology-mediated end joining pathways contribute to the erroneous repair. Estimation of their individual rate constants indicates that the balance between these two pathways changes over time and can be altered by additional ionizing radiation. Our approach provides quantitative insights into DSB repair kinetics and fidelity in single loci and indicates that Cas9-induced DSBs are repaired in an unusual manner.

TRIM28 is an Epigenetic Barrier to Induced Pluripotent Stem Cell Reprogramming.

Since the discovery of induced pluripotent stem cells there has been intense interest in understanding the mechanisms that allow a somatic cell to be reprogrammed back to a pluripotent state. Several groups have studied the alterations in gene expression that occur as somatic cells modify their genome to that of an embryonic stem cell. Underpinning many of the gene expression changes are modifications to the epigenetic profile of the associated chromatin. We have used a large-scale shRNA screen to identify epigenetic modifiers that act as barriers to reprogramming. We have uncovered an important role for TRIM28 in cells resisting transition between somatic and pluripotent states. TRIM28 achieves this by maintaining the H3K9me3 repressed state and keeping endogenous retroviruses (ERVs) silenced. We propose that knockdown of TRIM28 during reprogramming results in more plastic H3K9me3 domains, dysregulation of genes nearby H3K9me3 marks, and up regulation of ERVs, thus facilitating the transition through reprogramming. Stem Cells 2017;35:147-157.

High-throughput assessment of context-dependent effects of chromatin proteins.

BACKGROUND: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation. RESULTS: Recruitment to over 1000 genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing reporter genes. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by twofold. In regions marked by a H3K36me3-rich chromatin signature, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a. CONCLUSIONS: The multiplexed tethered reporter assay should be applicable to a large number of chromatin proteins and will be a useful tool to dissect combinatorial regulatory interactions in chromatin.

Comparison of microcoils and polyvinyl alcohol particles in selective microcatheter angioembolization of non variceal acute gastrointestinal hemorrhage.

OBJECTIVES: To compare the efficacy of polyvinyl alcohol (PVA) particles with microcoils in angiembolisation of non variceal acute gastrointestinal haemorrhage. METHODS: This is a retrospective cross-sectional study of patients who underwent transcatheter angioembolization from January, 1995 to December, 2013 at Aga Khan University Hospital, Karachi. Patients were divided into two groups on basis of use of either microcoils or PVA particles and compared in terms of technical success, clinical success, re-bleeding and ischemic complication rates. Chi (χ(2)) square and Fisher's exact tests were applied and a P-value of less than 0.05 was considered statistically significant. RESULTS: Fifty seven patients underwent angioembolization. Microcoil and PVA particles embolization was performed in 63% (36/57) and 35% (20/57) cases respectively. Technical success was achieved in all cases (100%). Clinical success rate was higher in microcoils group (92%) than PVA particles group (75%) with statistically significant P value (p=0.048). Ischemic complication was seen in one case (3%) in the microcoil group, while no such complications were seen in the PVA particles group. CONCLUSION: In angioembolization of non variceal acute gastrointestinal haemorrhage microcoils are better than Polyvinyl alcohol particles with higher clinical success and lower re-bleed rates.

TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes.

Enhancers are regulatory elements that promote gene expression in a spatio-temporal way and are involved in a wide range of developmental and disease processes. Both the identification and subsequent functional dissection of enhancers are key steps in understanding these processes. Several high-throughput approaches were recently developed for these purposes; however, in almost all cases enhancers are being tested outside their native chromatin context. Until recently, the analysis of enhancer activities at their native genomic locations was low throughput, laborious and time-consuming. Here, we discuss the potential of a powerful approach, TRIP, to study the functioning of enhancers in their native chromatin environments by introducing sensor constructs directly in the genome. TRIP allows for simultaneously analyzing the quantitative readout of numerous sensor constructs integrated at random locations in the genome. The high-throughput and flexible nature of TRIP opens up potential to study different aspects of enhancer biology at an unprecedented level.

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.

Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D hotspots within the nucleus. The identified hotspots are significantly enriched for known cancer genes, and bear the expected characteristics of bona fide regulatory interactions, such as enrichment for transcription factor-binding sites. In addition, we observe a striking pattern of mutual exclusive integration. This is an indication that insertions in these loci target the same gene, either in their linear genomic vicinity or in their 3D spatial vicinity. Our findings shed new light on the repertoire of targets obtained from insertional mutagenesis screening and underline the importance of considering the genome as a 3D structure when studying effects of genomic perturbations.

Prolonged Ezh2 Depletion in Glioblastoma Causes a Robust Switch in Cell Fate Resulting in Tumor Progression.

EZH2 is frequently overexpressed in glioblastoma (GBM), suggesting an oncogenic function that could be a target for therapeutic intervention. However, reduced EZH2 activity can also promote tumorigenesis, leading to concerns about the use of EZH2 inhibitors. Here, we provide further insight about the effects of prolonged Ezh2 inhibition in glioblastoma using preclinical mouse models and primary tumor-derived human GBM cell lines. Using doxycycline-inducible shRNAs that mimic the effects of a selective EZH2 inhibitor, we demonstrate that prolonged Ezh2 depletion causes a robust switch in cell fate, including significantly enhanced proliferation, DNA damage repair, and activation of part of the pluripotency network, resulting in altered tumor cell identity and tumor progression. Short-term Ezh2 depletion significantly improved survival without the tumor progression observed upon prolonged Ezh2 depletion, suggesting that precise dosing regiments are very important. These results could be of high clinical relevance with regard to how glioblastomas should be treated with epigenetic therapies.

Using TRIP for genome-wide position effect analysis in cultured cells.

The influence of local chromatin context on gene expression can be explored by integrating a transcription reporter at different locations in the genome as a sensor. Here we provide a detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level. TRIP is based on tagging each reporter with a unique barcode, which is used for independent reporter expression analysis and integration site mapping. Compared with previous methods for studying position effects, TRIP offers a 100-1,000-fold higher throughput in a faster and less-labor-intensive manner. The entire experimental protocol takes ∼42 d to complete, with high-throughput sequencing and data analysis requiring an additional ∼11 d. TRIP was developed by using transcription reporters in mouse embryonic stem (mES) cells, but because of its flexibility the method can be used to probe the influence of chromatin context on a variety of molecular processes in any transfectable cell line.

Chromatin landscapes of retroviral and transposon integration profiles.

The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of ~ 120,000 to ~ 180,000 unselected integrations in the mouse genome for the Sleeping Beauty (SB) and piggyBac (PB) transposons, and the Mouse Mammary Tumor Virus (MMTV). We analyzed ~ 80 (epi)genomic features to generate bias maps at both local and genome-wide scales. MMTV showed a remarkably uniform distribution of integrations across the genome. More distinct preferences were observed for the two transposons, with PB showing remarkable resemblance to bias profiles of the Murine Leukemia Virus. Furthermore, we present a model where target site selection is directed at multiple scales. At a large scale, target site selection is similar across systems, and defined by domain-oriented features, namely expression of proximal genes, proximity to CpG islands and to genic features, chromatin compaction and replication timing. Notable differences between the systems are mainly observed at smaller scales, and are directed by a diverse range of features. To study the effect of these biases on integration sites occupied under selective pressure, we turned to insertional mutagenesis (IM) screens. In IM screens, putative cancer genes are identified by finding frequently targeted genomic regions, or Common Integration Sites (CISs). Within three recently completed IM screens, we identified 7%-33% putative false positive CISs, which are likely not the result of the oncogenic selection process. Moreover, results indicate that PB, compared to SB, is more suited to tag oncogenes.

Process optimization of ultrasound-assisted curcumin nanoemulsions stabilized by OSA-modified starch.

This study reports on the process optimization of ultrasound-assisted, food-grade oil-water nanoemulsions stabilized by modified starches. In this work, effects of major emulsification process variables including applied power in terms of power density and sonication time, and formulation parameters, that is, surfactant type and concentration, bioactive concentration and dispersed-phase volume fraction were investigated on the mean droplet diameter, polydispersity index and charge on the emulsion droplets. Emulsifying properties of octenyl succinic anhydride modified starches, that is, Purity Gum 2000, Hi-Cap 100 and Purity Gum Ultra, and the size stability of corresponding emulsion droplets during the 1 month storage period were also investigated. Results revealed that the smallest and more stable nanoemulsion droplets were obtained when coarse emulsions treated at 40% of applied power (power density: 1.36 W/mL) for 7 min, stabilized by 1.5% (w/v) Purity Gum Ultra. Optimum volume fraction of oil (medium chain triglycerides) and the concentration of bioactive compound (curcumin) dispersed were 0.05 and 6 mg/mL oil, respectively. These results indicated that the ultrasound-assisted emulsification could be successfully used for the preparation of starch-stabilized nanoemulsions at lower temperatures (40-45 °C) and reduced energy consumption.

Applications of DNA integrating elements: Facing the bias bully.

Retroviruses and DNA transposons are an important part of molecular biologists' toolbox. The applications of these elements range from functional genomics to oncogene discovery and gene therapy. However, these elements do not integrate uniformly across the genome, which is an important limitation to their use. A number of genetic and epigenetic factors have been shown to shape the integration preference of these elements. Insight into integration bias can significantly enhance the analysis and interpretation of results obtained using these elements. For three different applications, we outline how bias can affect results, and can potentially be addressed.

Patient communication in radiology: current status of breaking bad news among radiologists and radiology trainees in Pakistan.

Breaking bad news can be an intimidating task for any physician. The aim of this study was to record the practices of breaking bad news to the patients by Pakistani radiologists and trainees. The radiologists and trainees attending the 26th National Radiological Conference in October 2010 in Karachi, Pakistan, were surveyed. The response rate was 76%. The respondents included residents (51%), private practicing radiologists (28%), academic radiologists (13%), and other trainees (8%). Most of the academic radiologists communicated with their patients. The daily frequency of breaking bad news by residents was noted, which was highest in the public teaching hospitals (71%). For severe abnormalities such as malignancy, 50% residents, 55% of the academic radiologists and 74% of the private practicing radiologists were very uncomfortable in disclosure of results. Differences in frequency of communication with patients were noticed with both different training levels, and different settings of practice in a developing country.

Chromatin position effects assayed by thousands of reporters integrated in parallel.

Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here, we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ∼1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for crosstalk between neighboring genes and estimate that enhancers can influence gene expression on average over ∼20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.

Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors.

Cancer develops through a multistep process in which normal cells progress to malignant tumors via the evolution of their genomes as a result of the acquisition of mutations in cancer driver genes. The number, identity and mode of action of cancer driver genes, and how they contribute to tumor evolution is largely unknown. This study deployed the Mouse Mammary Tumor Virus (MMTV) as an insertional mutagen to find both the driver genes and the networks in which they function. Using deep insertion site sequencing we identified around 31000 retroviral integration sites in 604 MMTV-induced mammary tumors from mice with mammary gland-specific deletion of Trp53, Pten heterozygous knockout mice, or wildtype strains. We identified 18 known common integration sites (CISs) and 12 previously unknown CISs marking new candidate cancer genes. Members of the Wnt, Fgf, Fgfr, Rspo and Pdgfr gene families were commonly mutated in a mutually exclusive fashion. The sequence data we generated yielded also information on the clonality of insertions in individual tumors, allowing us to develop a data-driven model of MMTV-induced tumor development. Insertional mutations near Wnt and Fgf genes mark the earliest "initiating" events in MMTV induced tumorigenesis, whereas Fgfr genes are targeted later during tumor progression. Our data shows that insertional mutagenesis can be used to discover the mutational networks, the timing of mutations, and the genes that initiate and drive tumor evolution.