Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence.

S-adenosylmethionine (SAM) is the methyl-donor substrate for DNA and histone methyltransferases that regulate epigenetic states and subsequent gene expression. This metabolism-epigenome link sensitizes chromatin methylation to altered SAM abundance, yet the mechanisms that allow organisms to adapt and protect epigenetic information during life-experienced fluctuations in SAM availability are unknown. We identified a robust response to SAM depletion that is highlighted by preferential cytoplasmic and nuclear mono-methylation of H3 Lys 9 (H3K9) at the expense of broad losses in histone di- and tri-methylation. Under SAM-depleted conditions, H3K9 mono-methylation preserves heterochromatin stability and supports global epigenetic persistence upon metabolic recovery. This unique chromatin response was robust across the mouse lifespan and correlated with improved metabolic health, supporting a significant role for epigenetic adaptation to SAM depletion in vivo. Together, these studies provide evidence for an adaptive response that enables epigenetic persistence to metabolic stress.

A MicroRNA Approach to Evaluating Elevated Prostate Cancer Risk in Cancer-Free Men.

Objective criteria are required for prostate cancer (PCa) risk assessment, treatment decisions, evaluation of therapy, and initial indications of recurrence. Circulating microRNAs were utilized as biomarkers to distinguish PCa patients from cancer-free subjects or those encountering benign prostate hyperplasia. A panel of 60 microRNAs was developed with established roles in PCa initiation, progression, metastasis, and recurrence. Utilizing the FirePlex® platform for microRNA analysis, we demonstrated the efficacy and reproducibility of a rapid, high-throughput, serum-based assay for PCa biomarkers that circumvents the requirement for extraction and fractionation of patient specimens supporting feasibility for expanded clinical research and diagnostic applications.

Exploring Patients' Trust from a New Perspective. A Text-Analysis Study.

The concept of trust has been extensively studied within the field of medicine. Yet, a list of factors that clearly influence patients' trust is still under debate. Moreover, the methodological approaches found in literature have been reported to be lacking in their assessments and measurements of trust relationships in the medical field although trust between a patient and medical provider has been proven to increase adherence and improve health outcomes. Hence, adding data to this debate and exploring a reliable method to explore the construct of trust is relevant. This study collects new evidence of the most salient indicators of patient trust by using a narrative approach and highlighting the potential of this method in collecting indicators that could be used to build training that aims to increase patients' trust. We used the Linguistic Inquiry and Word Count software for text analysis to examine the spontaneous narrations of episodes of trust and distrust within the doctor-patient relationship with a sample of 82 adult patients. Results demonstrate the role of the emotional aspects of the doctor-patient relationship. Data highlights the importance of doctors' benevolence toward patients, and positive emotions seem to be deeply connected with any experience of trust, which leads patients to feel more secure. Methods are presented to use these insights to construct mechanisms that establish medical trust and allow providers to implement effective interventions.

Discovery and Mechanism of Small Molecule Inhibitors Selective for the Chromatin-Binding Domains of Oncogenic UHRF1.

Chromatin abnormalities are common hallmarks of cancer cells, which exhibit alterations in DNA methylation profiles that can silence tumor suppressor genes. These epigenetic patterns are partly established and maintained by UHRF1 (ubiquitin-like PHD and RING finger domain-containing protein 1), which senses existing methylation states through multiple reader domains, and reinforces the modifications through recruitment of DNA methyltransferases. Small molecule inhibitors of UHRF1 would be important tools to illuminate molecular functions, yet no compounds capable of blocking UHRF1-histone binding in the context of the full-length protein exist. Here, we report the discovery and mechanism of action of compounds that selectively inhibit the UHRF1-histone interaction with low micromolar potency. Biochemical analyses reveal that these molecules are the first inhibitors to target the PHD finger of UHRF1, specifically disrupting histone H3 arginine 2 interactions with the PHD finger. Importantly, this unique inhibition mechanism is sufficient to displace binding of full-length UHRF1 with histones in vitro and in cells. Together, our study provides insight into the critical role of the PHD finger in driving histone interactions, and demonstrates that targeting this domain through a specific binding pocket is a tractable strategy for UHRF1-histone inhibition.

Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1.

Eukaryotic chromatin is a highly dynamic structure with essential roles in virtually all DNA-dependent cellular processes. Nucleosomes are a barrier to DNA access, and during DNA replication, they are disassembled ahead of the replication machinery (the replisome) and reassembled following its passage. The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. Therefore, CAF-1 is important for the establishment and propagation of chromatin structure. The molecular mechanism by which CAF-1 mediates H3-H4 deposition has remained unclear. However, recent studies have revealed new insights into the architecture and stoichiometry of the trimeric CAF-1 complex and how it interacts with and deposits H3-H4 onto substrate DNA. The CAF-1 trimer binds to a single H3-H4 dimer, which induces a conformational rearrangement in CAF-1 promoting its interaction with substrate DNA. Two CAF-1•H3-H4 complexes co-associate on nucleosome-free DNA depositing (H3-H4)2 tetramers in the first step of nucleosome assembly. Here, we review the progress made in our understanding of CAF-1 structure, mechanism of action, and how CAF-1 contributes to chromatin dynamics during DNA replication.

Understanding demand for, and feasibility of, centre-based child-care for poor urban households: a mixed methods study in Dhaka, Bangladesh.

BACKGROUND: Centre-based child-care has potential to provide multiple health and development benefits to children, families and societies. With rapid urbanisation, increasing numbers of low-income women work with reduced support from extended family, leaving a child-care vacuum in many low- and middle-income countries. We aimed to understand perceptions of, and demand for, centre-based child-care in Dhaka, Bangladesh among poor, urban households, and test the feasibility of delivering sustainable centre-based child-care. METHODS: We used sequential mixed methods including a household survey (n = 222) and qualitative interviews with care-givers (n = 16), community leaders (n = 5) and policy-makers (n = 5). We co-produced and piloted a centre-based child-care model over ten-months, documenting implementation. A co-design focus group with mothers, parents' meetings, and qualitative interviews with child-care centre users (n = 5), non-users (n = 3), ex-users (n = 3) and staff (2) were used to refine the model and identify implementation issues. RESULTS: We found 24% (95% CI: 16,37%) of care-givers reported turning-down paid work due to lack of child-care and 84% (95% CI:74, 91%) reported wishing to use centre-based child-care and were willing to pay up to 283 Takka (~$3.30) per month. Adjusted odds of reported need for child-care among slum households were 3.8 times those of non-slum households (95% CI: 1.4, 10). Implementation highlighted that poor households needed free child-care with food provided, presenting feasibility challenges. Meta-inference across quantitative and qualitative findings identified the impact of the urban environment on child-care through long working hours, low social capital and fears for child safety. These influences interacted with religious and social norms resulting in caution in using centre-based child-care despite evident need. CONCLUSION: Sustainable provision of centre-based care that focuses on early childhood development requires subsidy and careful design sensitive to the working lives of poor families, particularly women and must respond to the dynamics of the urban environment and community values. We recommend increased research and policy focus on the evaluation and scale-up of quality centre-based child-care, emphasising early-childhood development, to support low-income working families in urban areas.

Attack rate and prey preference of Lasioseius subterraneous and Protogamasellus mica on four nematode species.

Plant parasitic nematodes are common and important global pests, causing over US$150 billion in crop losses across the agricultural sector worldwide. Meloidogyne javanica and Pratylenchus zeae are two of the most damaging plant-parasitic nematodes and there are limited options for their control. We evaluated the potential of a large (Lasioseius subterraneous) and a small (Protogamasellus mica) mesostigmatan mite as biological control agents of plant-parasitic nematodes. We tested the attack rate and reproductive potential of these two mite species on four nematode species: M. javanica (eggs), Pra. zeae (adults) and two microbivorous nematodes, Mesorhabditis sp. and Aphelenchus avenae (adults for both species). Each mite/nematode combination (1 mite:100 nematodes) was tested in six replicate arenas. In a separate trial, each mite species was presented with 50 A. avenae and 50 Pra. zeae in the same arena to determine prey preference. Both mite species significantly reduced the abundance of all nematode species used in the trials when compared to nematode-only controls. Lasioseius subterraneous consumed all available M. javanica eggs within 72 h. The larger mite had a significantly higher overall attack rate than the smaller mite, each consuming an average of 96 and 72 nematodes, respectively, within 72 h. However, both mites had a similar reproductive rate. Protogamasellus mica displayed a positive preference towards the plant parasitic nematode Pra. zeae over the fungal feeding A. avenae whereas L. subterraneous did not display a prey preference. Our results highlight the potential of these two predators to control plant parasitic nematodes, although further trials under field conditions are needed.

Effects of a mulch layer on the assemblage and abundance of mesostigmatan mites and other arthropods in the soil of a sugarcane agro-ecosystem in Australia.

Sugarcane farmers can utilise a soil conservation technique called green cane trash blanketing, a form of mulching that can increase plant productivity through a number of channels, e.g., via altering soil physical, chemical and biological characteristics, and influence soil arthropod assemblages. Predatory mites (Mesostigmata) are important components of soil communities because they can control populations of other soil-dwelling pest species. Our aim was to characterise mulch-influenced predatory Mesostigmata community assemblages in sugarcane soils in Queensland, Australia. We found that application of a mulch layer significantly increased the abundance of Mesostigmata, and oribatid mites and collembolans, in soils. Furthermore, we observed that the assemblages of Mesostigmata in soil covered by mulch were significantly different to those in bare soil; and the assemblages of Mesostigmata changed over time. The assemblages of Mesostigmata, but not Oribatida or collembolans, were significantly different in soil under mulch depending on whether the mulch was freshly laid, or decomposing. Our results show that the use of mulch, specifically the green cane trash blanket, can increase overall microarthropod abundance including Mesostigmata. This is likely due to increased habitat complexity and changing resource availability.

Vehicle Emissions as an Important Urban Ammonia Source in the United States and China.

Ammoniated aerosols are important for urban air quality, but emissions of the key precursor NH3 are not well quantified. Mobile laboratory observations are used to characterize fleet-integrated NH3 emissions in six cities in the U.S. and China. Vehicle NH3:CO2 emission ratios in the U.S. are similar between cities (0.33-0.40 ppbv/ppmv, 15% uncertainty) despite differences in fleet composition, climate, and fuel composition. While Beijing, China has a comparable emission ratio (0.36 ppbv/ppmv) to the U.S. cities, less developed Chinese cities show higher emission ratios (0.44 and 0.55 ppbv/ppmv). If the vehicle CO2 inventories are accurate, NH3 emissions from U.S. vehicles (0.26 ± 0.07 Tg/yr) are more than twice those of the National Emission Inventory (0.12 Tg/yr), while Chinese NH3 vehicle emissions (0.09 ± 0.02 Tg/yr) are similar to a bottom-up inventory. Vehicle NH3 emissions are greater than agricultural emissions in counties containing near half of the U.S. population and require reconsideration in urban air quality models due to their colocation with other aerosol precursors and the uncertainties regarding NH3 losses from upwind agricultural sources. Ammonia emissions in developing cities are especially important because of their high emission ratios and rapid motorizations.

Comparative Evaluation of AmpliVue HSV 1+2 Assay with ELVIS Culture for Detecting Herpes Simplex Virus 1 (HSV-1) and HSV-2 in Clinical Specimens.

The AmpliVue HSV 1+2 assay was compared to the ELVIS HSV ID and D(3) Typing Culture System for the qualitative detection and differentiation of herpes simplex virus 1 (HSV-1) and HSV-2 DNA in 1,351 cutaneous and mucocutaneous specimens. Compared to ELVIS, AmpliVue had sensitivities of 95.7 and 97.6% for detecting HSV-1 and HSV-2, respectively. Following arbitration of discordant results by an independent molecular method, the AmpliVue assay had a resolved sensitivity and specificity of 99.2 and 99.7%, respectively, for both HSV-1 and HSV-2, whereas ELVIS had a resolved sensitivity of 87.1% for HSV-1 and 84.5% for HSV-2.

Change in texture improvement of low-fat tofu by means of low-fat soymilk protein denaturation.

BACKGROUND: Tofu made from low-fat soy flour is a nutritional food for consumers and economically benefits the food processor. However, low-fat tofu has poor textural quality, especially insufficient firmness. Stepwise heating (heating at 75 °C, followed by holding at 95 °C) of full-fat soymilk increases gel properties. Therefore we evaluated the two-step heating of low-fat soymilk to improve tofu texture. RESULTS: The denaturation enthalpy and temperature of ß-conglycinin and glycinin were higher in low-fat tofu compared to high-fat tofu. The viscosity of low-fat soymilk and texture of tofu by one-step heating were weaker than full-fat soymilk and tofu. However, the two-step heating increased free sulfhydryl groups and viscosity of low-fat soymilk to a value higher or similar to conventional soymilk. The syneresis of low-fat tofu was reduced about 30% and hardness was higher (131.0 N) by the two-step process compared to one-step heating of full-fat tofu (101.4 N) by the one-step process. The microstructure of low-fat tofu became finer, denser and more homogeneous by the two-step heat process. CONCLUSION: Low-fat tofu produced by denaturing the two major soy proteins separately had improved textural qualities similar to full-fat tofu as a result of increased hydrophobic interactions between denatured protein molecules.

LYP inhibits T-cell activation when dissociated from CSK.

Lymphoid tyrosine phosphatase (LYP) and C-terminal Src kinase (CSK) are negative regulators of signaling mediated through the T-cell antigen receptor (TCR) and are thought to act in a cooperative manner when forming a complex. Here we studied the spatiotemporal dynamics of the LYP-CSK complex in T cells. We demonstrate that dissociation of this complex is necessary for recruitment of LYP to the plasma membrane, where it downmodulates TCR signaling. Development of a potent and selective chemical probe of LYP confirmed that LYP inhibits T-cell activation when removed from CSK. Our findings may explain the reduced TCR-mediated signaling associated with a single-nucleotide polymorphism that confers increased risk for certain autoimmune diseases, including type 1 diabetes and rheumatoid arthritis, and results in expression of a mutant LYP that is unable to bind CSK. Our compound also represents a starting point for the development of a LYP-based treatment of autoimmunity.

CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA.

Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approaches using full-length proteins in the budding yeast system. We find that the C-terminal tail of Asf1 enhances the interaction of Asf1 with CAF-1. Surprisingly, although H3/H4 also enhances the interaction of Asf1 with the CAF-1 subunit Cac2, H3/H4 forms a tight complex with CAF-1 exclusive of Asf1, with an affinity weaker than Asf1-H3/H4 or H3/H4-DNA interactions. Unlike Asf1, monomeric CAF-1 binds to multiple H3/H4 dimers, which ultimately promotes the formation of (H3/H4)(2) tetramers on DNA. Thus, transition of H3/H4 from the Asf1-associated dimer to the DNA-associated tetramer is promoted by CAF-1-induced H3/H4 oligomerization.

Development of an infection prevention and control pathway to facilitate high-throughput cataract surgery in Scotland.

INTRODUCTION: Cataract surgery offers significant improvement to quality of life for patients with cataracts. However, there are growing waiting lists and challenges in providing this type of surgery in a timely manner. Feedback from stakeholders had previously indicated infection prevention and control (IPC) as a potential barrier to high-throughput surgery. Antimicrobial Resistance and Healthcare Associated Infection Scotland was asked to support the implementation of high-throughput cataract surgery aimed at addressing these challenges. AIM: To develop an IPC pathway to facilitate high-throughput surgery. This would be based on best practice, and would address any barriers identified by stakeholders. METHODS: A short life working group with input from key stakeholders, including clinical teams, was established. A rapid literature review was also undertaken. RESULTS: An agreed patient pathway was developed, with the aim of helping to facilitate high-throughput surgery. Pre-, intra- and postoperative phases were considered. Where literature was unavailable, expert/consensus opinion was utilized. Facilities for high-throughput surgery were also considered, including the Jack and Jill theatre arrangement which lends itself well to this concept. CONCLUSION: Through collaboration with stakeholders, an IPC pathway was developed to facilitate high-throughput cataract surgery and address any potential IPC barriers to implementation. The process and the output described could be utilized to develop similar pathways for other surgeries that lend themselves well to high throughput, improving quality of life for patients and reducing waiting times. This study highlights the importance of establishing surveillance for postoperative endophthalmitis following implementation.

Selective ablation of differentiated cells permits isolation of embryonic stem cell lines from murine embryos with a non-permissive genetic background.

Embryonic stem (ES) cells enable the engineering of precise modifications to the mouse genome by gene targeting. Although there are reports of cultured cell contributions to chimaeras in golden hamster, rat and pig, definitive ES cell lines which contribute to the germline have not been demonstrated in any species but mouse. Among mouse strains, genetic background strongly affects the efficiency of ES isolation, and almost all ES lines in use are derived from strain 129 (refs 1,4,5) or, less commonly, C57BL/6 (refs 6-8). The CBA strain is refractory to ES isolation and there are no published reports of CBA-derived ES lines. Hence, CBA mice may provide a convenient model of ES isolation in other species. In ES derivation it is critical that the primary explant be cultured for a sufficient time to allow multiplication of ES cell progenitors, yet without allowing extensive differentiation. Thus, differences in ES derivation between mouse strains may reflect differences in the control of ES progenitor cells by other lineages within the embryo. Here we describe a strategy to continuously remove differentiated cells by drug selection, which generates germline competent ES lines from genotypes that are non-permissive in the absence of selection.

STAMP-Based Digital CRISPR-Cas13a for Amplification-Free Quantification of HIV-1 Plasma Viral Loads.

Quantification of HIV RNA in plasma is critical for identifying the disease progression and monitoring the effectiveness of antiretroviral therapy. While RT-qPCR has been the gold standard for HIV viral load quantification, digital assays could provide an alternative calibration-free absolute quantification method. Here, we reported a Self-digitization Through Automated Membrane-based Partitioning (STAMP) method to digitalize the CRISPR-Cas13 assay (dCRISPR) for amplification-free and absolute quantification of HIV-1 viral RNAs. The HIV-1 Cas13 assay was designed, validated, and optimized. We evaluated the analytical performances with synthetic RNAs. With a membrane that partitions ∼100 nL of reaction mixture (effectively containing 10 nL of input RNA sample), we showed that RNA samples spanning 4 orders of dynamic range between 1 fM (∼6 RNAs) to 10 pM (∼60k RNAs) could be quantified as fast as 30 min. We also examined the end-to-end performance from RNA extraction to STAMP-dCRISPR quantification using 140 µL of both spiked and clinical plasma samples. We demonstrated that the device has a detection limit of approximately 2000 copies/mL and can resolve a viral load change of 3571 copies/mL (equivalent to 3 RNAs in a single membrane) with 90% confidence. Finally, we evaluated the device using 140 µL of 20 patient plasma samples (10 positives and 10 negatives) and benchmarked the performance with RT-PCR. The STAMP-dCRISPR results agree very well with RT-PCR for all negative and high positive samples with Ct < 32. However, the STAMP-dCRISPR is limited in detecting low positive samples with Ct > 32 due to the subsampling errors. Our results demonstrated a digital Cas13 platform that could offer an accessible amplification-free quantification of viral RNAs. By further addressing the subsampling issue with approaches such as preconcentration, this platform could be further exploited for quantitatively determining viral load for an array of infectious diseases.

Impact of a multipronged approach to reduce the incidence of Clostridioides difficile infections in hospitalized patients.

BACKGROUND: Effective approaches to reduce Clostridioides difficile infections (CDI) in hospitalized patients are needed. We report data from 3 years preceding and 3 years following interventions that proved successful, with detailed analysis of all cases the first year after implementation. METHODS: Interventions included a nursing protocol to identify cases present on admission by asking if the patient had 1 or more liquid stools in the last 24 hours, and a 2-step testing algorithm with samples positive by polymerase chain reaction (PCR) for the C. difficile toxin gene reflexing to an enzyme immunoassay (EIA) for the toxin antigen. RESULTS: Healthcare-associated infections due to CDI fell from ∼160 in each of the preceding 3 years to <65 in each of the subsequent 3 years (P < .001), while the ratio of observed-to-expected hospital-onset cases diminished to ∼0.50 (P < .02). In the first year, 395 samples were PCR(+), but only 118 (29.9%) of these were EIA(+). 55 (46.6%) of the PCR(+)/EIA(+) samples were from hospital day 1 or 2 and classified as present on admission. The mean time from stool collection to report of PCR results was ∼7.5 hours, and the EIA took on average only 68 additional minutes to be reported. CONCLUSIONS: The number of incident CDI cases can be dramatically decreased by implementing an admission screening question and a 2-step testing algorithm.

Nucleotides and phosphorylation bi-directionally modulate Ca2+/calmodulin-dependent protein kinase II (CaMKII) binding to the N-methyl-D-aspartate (NMDA) receptor subunit GluN2B.

The Ca(2+)/calmodulin (CaM)-dependent protein kinase II (CaMKII) and the NMDA-type glutamate receptor are key regulators of synaptic plasticity underlying learning and memory. Direct binding of CaMKII to the NMDA receptor subunit GluN2B (formerly known as NR2B) (i) is induced by Ca(2+)/CaM but outlasts this initial Ca(2+)-stimulus, (ii) mediates CaMKII translocation to synapses, and (iii) regulates synaptic strength. CaMKII binds to GluN2B around S1303, the major CaMKII phosphorylation site on GluN2B. We show here that a phospho-mimetic S1303D mutation inhibited CaM-induced CaMKII binding to GluN2B in vitro, presenting a conundrum how binding can occur within cells, where high ATP concentration should promote S1303 phosphorylation. Surprisingly, addition of ATP actually enhanced the binding. Mutational analysis revealed that this positive net effect was caused by four modulatory effects of ATP, two positive (direct nucleotide binding and CaMKII T286 autophosphorylation) and two negative (GluN2B S1303 phosphorylation and CaMKII T305/6 autophosphorylation). Imaging showed positive regulation by nucleotide binding also within transfected HEK cells and neurons. In fact, nucleotide binding was a requirement for efficient CaMKII interaction with GluN2B in cells, while T286 autophosphorylation was not. Kinetic considerations support a model in which positive regulation by nucleotide binding and T286 autophosphorylation occurs faster than negative modulation by GluN2B S1303 and CaMKII T305/6 phosphorylation, allowing efficient CaMKII binding to GluN2B despite the inhibitory effects of the two slower reactions.

Histone transfer among chaperones.

The eukaryotic processes of nucleosome assembly and disassembly govern chromatin dynamics, in which histones exchange in a highly regulated manner to promote genome accessibility for all DNA-dependent processes. This regulation is partly carried out by histone chaperones, which serve multifaceted roles in co-ordinating the interactions of histone proteins with modification enzymes, nucleosome remodellers, other histone chaperones and nucleosomal DNA. The molecular details of the processes by which histone chaperones promote delivery of histones among their many functional partners are still largely undefined, but promise to offer insights into epigenome maintenance. In the present paper, we review recent findings on the histone chaperone interactions that guide the assembly of histones H3 and H4 into chromatin. This evidence supports the concepts of histone post-translational modifications and specific histone chaperone interactions as guiding principles for histone H3/H4 transactions during chromatin assembly.