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Chromatin immunoprecipitation (ChIP) is an important technique for characterizing protein-DNA binding in vivo. One drawback of ChIP-based techniques is the lack of cell type-specificity when profiling complex tissues. To overcome this limitation, we developed SpyChIP to identify cell type-specific transcription factor (TF) binding sites in native physiological contexts without tissue dissociation or nuclei sorting. SpyChIP takes advantage of a specific covalent isopeptide bond that rapidly forms between the 15-amino acid SpyTag and the 17-kDa protein SpyCatcher. In SpyChIP, the target TF is fused with SpyTag by genome engineering, and an epitope tagged SpyCatcher is expressed in cell populations of interest, where it covalently binds to SpyTag-TF. Cell type-specific ChIP is obtained by immunoprecipitating chromatin prepared from whole tissues using antibodies directed against the epitope-tagged SpyCatcher. Using Spy-ChIP, we identified the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two distinct cell types of the Drosophila haltere imaginal disc. Our results revealed extensive region-specific Ubx-DNA binding events, highlighting the significance of cell type-specific ChIP and the limitations of whole-tissue ChIP approaches. Analysis of Ubx::SpyChIP results provided insights into the relationship between chromatin accessibility and Ubx-DNA binding, as well as different mechanisms Ubx employs to regulate its downstream cis-regulatory modules. In addition to SpyChIP, we suggest that SpyTag-SpyCatcher technology, as well as other protein pairs that form covalent isopeptide bonds, will facilitate many additional in vivo applications that were previously impractical. [ABSTRACT FROM AUTHOR]

To increase the speed of information flow and storage capacity in electronic devices laser can be used to carry information instead of electric current. Since the photon is faster than electrons, one expects information to be transmitted very fast through the internet when photons replace electrons. This requires searching for chips that act as capacitors, inductors or resistors. To do this Maxwell's equation for the electric field intensity beside the electron equation of motion were used. The electron is assumed to vibrate naturally inside a frictional medium in the presence of a local electric and magnetic fields. These equations have been used to find a useful expression for the absorption coefficient. The absorption coefficient was found to be dependent on the laser and natural frequencies beside the coefficient of friction in addition to the internal electric and magnetic fields. These parameters can be fine-tuned to make the chip act as a capacitor, inductor or resistor. The laser intensity decreases when the absorption coefficient inecreases. Thus, the absorption coefficient acts as an electic resistor. Therefore, if the absorption coefficient inecreases upon decreasing the frequency the chip acts as a capacitor. But when the absorption coefficient inecreases when the laser frequency inreases the chip acts as an inductor. In the case that the absorption coefficient inecreases with the concentration of the carriers it acts in this situation as a resistor. For magnetic materials with magnetic flux density that cancels the frictional force, when the laser frequency is equal nearly to the atom’s natural frequency the material acts as an inductor. But when the frictional force is low with the internal and external electric fields in phase, the material acts as a capacitor. However, it acts as a resistor for negligible natural frequency, when no electric dipoles exist and when the internal magnetic field force balance the frictional force.

[Display omitted] [ABSTRACT FROM AUTHOR]

Intracellular bacteria that reside within a host cell use a variety of strategies to exploit this unique niche. While these organisms are technically challenging to study in the context of an infected host cell, recent advances have led to an improved understanding of how the intracellular environment impacts bacterial gene expression. We recently demonstrated that chromatin immunoprecipitation (ChIP) can be used to quantify transcription factor binding in the obligate intracellular pathogen Chlamydia trachomatis within infected cells. Furthermore, we showed it was possible to experimentally modulate transcription factor binding while simultaneously measuring changes in transcription. Here we discuss these findings as well as other recent work that has used ChIP to study intracellular pathogens within infected cells. We also discuss technical considerations associated with this approach and its possible future applications.

The endoplasmic reticulum (ER)-anchored hepatic cytochromes P450 (P450s) are enzymes that metabolize endo- and xenobiotics i.e. drugs, carcinogens, toxins, natural and chemical products. These agents modulate liver P450 content through increased synthesis or reduction via inactivation and/or proteolytic degradation, resulting in clinically significant drug-drug interactions. P450 proteolytic degradation occurs via ER-associated degradation (ERAD) involving either of two distinct routes: Ubiquitin (Ub)-dependent 26S proteasomal degradation (ERAD/UPD) or autophagic lysosomal degradation (ERAD/ALD). CYP3A4, the major human liver/intestinal P450, and the fast-turnover CYP2E1 species are degraded via ERAD/UPD entailing multisite protein phosphorylation and subsequent ubiquitination by gp78 and CHIP E3 Ub-ligases. We are gaining insight into the nature of the structural determinants involved in CYP3A4 and CYP2E1 molecular recognition in ERAD/UPD [i.e. K48-linked polyUb chains and linear and/or "conformational" phosphodegrons consisting either of consecutive sequences on surface loops and/or disordered regions, or structurally-assembled surface clusters of negatively charged acidic (Asp/Glu) and phosphorylated (Ser/Thr) residues, within or vicinal to which, Lys-residues are targeted for ubiquitination]. Structural inspection of select human liver P450s reveals that such linear or conformational phosphodegrons may indeed be a common P450-ERAD/UPD feature. By contrast, although many P450s such as the slow-turnover CYP2E1 species and rat liver CYP2B1 and CYP2C11 are degraded via ERAD/ALD, little is known about the mechanism of their ALD-targeting. On the basis of our current knowledge of ALD-substrate targeting, we propose a tripartite conjunction of K63-linked Ub-chains, P450 structural "LIR" motifs and selective cellular "cargo receptors" as plausible P450-ALD determinants.

Context: The use of herbal compounds is a comparatively safer alternative to synthetic compounds for periodontal therapy. Aim: This study aims to investigate effect of extracts from pomegranate in a chip and gel form on periodontitis following scaling and root planing in adult periodontitis patients. Settings and Design: An in vivo prospective study. Materials and Methods: Thirty patients of adult periodontitis with initial pocket depth ≥4 mm were enrolled into the research and divided randomly into three groups, (10 in every group). After baseline examination, scaling root planing of tooth was achieved. Then subgingival application of medicated chips in Group 1, gel in Group 2, and placebo in Group 3 was done. Plaque index, gingival index, probing pocket depth, and relative attachment ranges were recorded at baseline, 21 days and 45 days. Statistical Analysis Used: Analysis of variance test. Results: The study confirmed significant improvements of plaque index ratings in Group 1 at day 21. It showed significant improvements of gingival index scores, probing pocket depth, and clinical attachment at day 21 and 45. Gingival index rankings and probing pocket depth were extensively elevated altogether in three groups at day 21 and 45. Relative attachment degree was extensively raised in Group 1 and Group 2 at day 21 and day 45 and in Group 3 at day 45. The relative attachment degrees confirmed significance at day 21 between Group 1 and Group 2, and Group 1 and Group 3. Conclusion: Pomegranate extracts in chip and gel shape may offer additionally advantages to scaling and root planing for remedy of periodontal pockets.

Zinc finger proteins (ZFPs) are widely involved in plant growth and abiotic stress responses, however, few of these proteins have been functionally characterized in tree species. In this study, we cloned and characterized the BpSZA1 gene encoding a C2H2-type ZFP from Betula platyphylla. BpSZA1 is a transcription factor localized in the nucleus, with a transcription activation domain located at the N-terminus. BpSZA1 was predominantly expressed in stems and was induced by salt. We generated transgenic birch lines displaying overexpression (OE) or RNAi silencing (Ri) of BpSZA1 and exposed these along with wild-type birch seedlings to salinity. Phenotypic and physiological parameters such as superoxide dismutase, peroxisome, H2O2 content, proline content, water loss rate, and malondialdehyde content were examined. Overexpression of BpSZA1 in birch conferred increased salt tolerance. Chromatin immunoprecipitation-qPCR and RNA-seq showed that BpSZA1 binds to the GAGA-motif in the promoter of downstream target genes including BpAPX1 , BpAPX2 , BpCAT , and Bp6PGDH to activate their transcription. BpSZA1 also participates in abscisic acid (ABA) biosynthesis, proline biosynthesis, and the ABA/jasmonic acid pathway to enhance the salt stress of B. platyphylla. [ABSTRACT FROM AUTHOR]

Cancer genomes have long been known to carry a high number of somatic mutations distributed across many genes. However, recent sequencing studies have unveiled that non-cancerous cells also carry a considerable number of somatic mutations, which are acquired continuously through the lifespan. Accordingly, the pathophysiological relevance of somatic mutagenesis beyond cancer has become a topic of intensive research. Human genetic studies and experiments in mice have shown that some somatic mutations in the hematopoietic system provide a competitive advantage to the mutant cell and allow its clonal expansion. This phenomenon, termed clonal hematopoiesis, is typically driven by mutations in known oncogenes and tumor suppressor genes, and it is associated with a higher risk of hematological malignancies. Unexpectedly, accumulating genetic and experimental evidence strongly suggest that clonal hematopoiesis, at least when driven by certain mutations, also contributes causally to the development of cardiovascular disease and, therefore, represents a new cardiovascular risk factor. While clonal hematopoiesis is relatively common in healthy individuals, especially among the elderly, it is particularly frequent in cancer patients and survivors. Hence, it has emerged as a candidate contributor to the increased risk of cardiovascular complications in cancer patients. This review summarizes our current understanding of the connection between clonal hematopoiesis and cardiovascular disease, with a special focus on the available evidence linking clonal hematopoiesis to cardiovascular disorders that are frequent in cancer patients and survivors. • Somatic mutations that drive clonal hematopoiesis represent a new cardiovascular risk factor. • Clonal hematopoiesis is particularly common in elderly individuals and cancer patients. • Some clonal hematopoiesis-related mutations contribute directly to cardiovascular disease. • Cytotoxic therapies facilitate clonal hematopoiesis driven by mutations in DNA damage response genes. [ABSTRACT FROM AUTHOR]

Clonal haematopoiesis (CH) is a phenomenon whereby somatic mutations confer a fitness advantage to haematopoietic stem and progenitor cells (HSPCs) and thus facilitate their aberrant clonal expansion. These mutations are carried into progeny leucocytes leading to a situation whereby a substantial fraction of an individual's blood cells originate from the HSPC mutant clone. Although this condition rarely progresses to a haematological malignancy, circulating blood cells bearing the mutation have the potential to affect other organ systems as they infiltrate into tissues under both homeostatic and disease conditions. Epidemiological and clinical studies have revealed that CH is highly prevalent in the elderly and is associated with an increased risk of cardiovascular disease and mortality. Recent experimental studies in murine models have assessed the most commonly mutated 'driver' genes associated with CH, and have provided evidence for mechanistic connections between CH and cardiovascular disease. A deeper understanding of the mechanisms by which specific CH mutations promote disease pathogenesis is of importance, as it could pave the way for individualized therapeutic strategies targeting the pathogenic CH gene mutations in the future. Here, we review the epidemiology of CH and the mechanistic work from studies using murine disease models, with a particular focus on the strengths and limitations of these experimental systems. We intend for this review to help investigators select the most appropriate models to study CH in the setting of cardiovascular disease. [ABSTRACT FROM AUTHOR]

Somatic mutations in hematopoietic stem cells are common with aging and can result in expansion of clones harboring mutations, termed clonal hematopoiesis. This results in an increased risk of blood cancers but has also been linked with chronic inflammatory disease states. In recent years, clonal hematopoiesis has been established to have a causative role in atherogenesis and cardiovascular disease. Additionally, as the effector cells have been identified to be immune cells, there is ongoing interest in assessing whether dysregulated immune function plays a role in other chronic inflammatory conditions such as rheumatologic disease. Here, we summarize current understanding of clonal hematopoiesis with a focus on cardiovascular disease and inflammation while outlining the potential, yet unexplored, relationship between clonal hematopoiesis and autoimmune disease. [ABSTRACT FROM AUTHOR]

The influence of technological and design factors on rotary turning by multifaceted cutters is investigated. Semiempirical formulas are proposed to determine the best machining conditions. By optimizing the duration and conditions of machining, the cutting force and temperature in the cutting zone may be decreased, and disintegration of the chip may be improved. [ABSTRACT FROM AUTHOR]

Background: Restrictive state laws aimed at immigrants can have unintended consequences for health insurance coverage of United States citizens in immigrant families due to both actual barriers created by the laws and perceived barriers among immigrants. Increasing numbers of children in the U.S. are part of immigrant families, and these children are more likely to be living in poverty than their counterparts in native families. Immigrant restrictive policies could lead to reduced access to Medicaid and CHIP even for citizen children in immigrant families. Methods: Using data from the Current Population Survey's (CPS) March Supplement, linear probability models with difference-in-differences (DD) estimates compare probability of enrollment in Medicaid/CHIP among low-income U.S. citizen children in immigrant families and low-income children in native families and U.S. citizen children in immigrant families in states that did not adopt restrictive legislation, in order to estimate the impact of restrictive state laws aimed at immigrants. An additional model explores the effect of mother's citizenship on enrollment among all immigrant families in states with and without restrictive legislation. Results: Results suggest a significant chilling effect where the magnitude of the effect varies according to family demographics and by the types of laws being passed. Immigrant restrictive social welfare laws being adopted have a strong negative effect on U.S. citizen children in immigrant families' enrollment in Medicaid/CHIP, a 5.5 percentage point reduction in coverage. Among the subsample of only immigrant families, results point toward a global chilling effect created by an overall restrictive policy environment. All immigrant restrictive related laws, including those aimed at education, job restriction, identification access, and social welfare restrictions have a significant and negative impact on access to public insurance for U.S. citizen children with non-citizen mothers. Conclusions: This research shows that the unintended consequence of restrictive state legislation aimed at immigrants is the reduction in access to Medicaid and CHIP by low-income U.S. citizen children living in immigrant families. Reduced access to health insurance can increase unmet medical needs for an already vulnerable group. [ABSTRACT FROM AUTHOR]

Clonal hematopoiesis of indeterminate potential (CHIP) is an age‐associated phenomenon characterized by clonal expansion of blood cells harboring somatic mutations in hematopoietic genes, including DNMT3A, TET2, and ASXL1. Clinical evidence suggests that CHIP is highly prevalent and associated with poor prognosis in solid‐tumor patients. However, whether blood cells with CHIP mutations play a causal role in promoting the development of solid tumors remained unclear. Using conditional knock‐in mice that express CHIP‐associated mutant Asxl1 (Asxl1‐MT), we showed that expression of Asxl1‐MT in T cells, but not in myeloid cells, promoted solid‐tumor progression in syngeneic transplantation models. We also demonstrated that Asxl1‐MT–expressing blood cells accelerated the development of spontaneous mammary tumors induced by MMTV‐PyMT. Intratumor analysis of the mammary tumors revealed the reduced T‐cell infiltration at tumor sites and programmed death receptor‐1 (PD‐1) upregulation in CD8+ T cells in MMTV‐PyMT/Asxl1‐MT mice. In addition, we found that Asxl1‐MT induced T‐cell dysregulation, including aberrant intrathymic T‐cell development, decreased CD4/CD8 ratio, and naïve‐memory imbalance in peripheral T cells. These results indicate that Asxl1‐MT perturbs T‐cell development and function, which contributes to creating a protumor microenvironment for solid tumors. Thus, our findings raise the possibility that ASXL1‐mutated blood cells exacerbate solid‐tumor progression in ASXL1‐CHIP carriers. [ABSTRACT FROM AUTHOR]

It is known that the development of foci of chronic inflammation usually accompanies body aging. In these foci, senescent cells appear with a pro-inflammatory phenotype that helps maintain inflammation. Their removal with the help of senolytics significantly improves the general condition of the body and, according to many indicators, contributes to rejuvenation. The cells of the immune system participate in the initiation, development, and resolution of inflammation. With age, the human body accumulates mutations, including the cells of the bone marrow, giving rise to the cells of the immune system. We assume that a number of such mutations formed with age can lead to the appearance of "naive" cells with an initially pro-inflammatory phenotype, the migration of which to preexisting foci of inflammation contributes not to the resolution of inflammation but its chronicity. One of such cell variants are monocytes carrying mitochondrial mutations, which may be responsible for comorbidity and deterioration in the prognosis of the course of pathologies associated with aging, such as atherosclerosis, arthritis, osteoporosis, and neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

Perioperative neurocognitive disorders (PND) commonly occur in elderly patients, and isoflurane could be a risk factor. During the pathogenesis of neurodegeneration, the ubiquitin–proteasome system (UPS) participates in the process of aging, which affects synaptic plasticity and synaptic function. However, whether UPS is involved in the etiology of PND is unclear. In this study, we examined the expression change of ubiquitin E3 ligase protein carboxyl-terminus of Hsc70-interacting protein (CHIP) and the function turbulence of UPS in isoflurane-exposed aged mouse to illustrate the role of UPS in PND. Neurodegenerative behavioral changes were shown in isoflurane-exposed aged mice and correlated with neuropathological changes manifested with reduced number of intersections and spine density in the cortex. Ubiquitin function was decreased while the apoptosis was activated, and CHIP protein expression decline altered synapsin expression and phosphorylation associated with the neurodegeneration in isoflurane-induced PND. Aging was the big important factor. And it remained consistent with the synapsin phosphorylation/dephosphorylation level changes in CHIP knock-down N2a cells. Per our observation, the decline in CHIP protein expression and synaptic degeneration might reveal the reason for synaptic degeneration in the underlying pathogenesis of PND caused by isoflurane. [ABSTRACT FROM AUTHOR]

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In the traditional micromilling (TMM) of Inconel718 alloy, due to the influence of material plasticity and size effect, relatively large burr will be produced. In order to hinder the burr forming in micromilling, ultrasonic vibration in feed direction is applied to the workpiece to complete vibration cutting. Combined with trajectory simulation and cutting experiment, the burr formation mechanism of TMM and ultrasonic vibration assisted micromilling (UVAMM) was studied. The results show that when the ratio of amplitude (A) to feed per tooth (ƒz) is greater than 0.5, continuous cutting changes to intermittent cutting in the vibration cutting process. The fractured area with dimples on the burr increases with the increase of amplitude. Compared with TMM, UVAMM improves chip breaking ability, facilitates the propagation of burr crack, and effectively inhibits the formation of burr. When the chip breaking condition is reached, the burr shape is usually tearing or flocculent. Under the conditions of low speed (n), large ƒz, and large A, the burr suppression is more obvious. [ABSTRACT FROM AUTHOR]

Despite the numerous advantages of microchip implants, their adoption remains low in the public sector. We conducted a cross-sectional survey to identify concerns and expectations about microchip implants among potential users. A total of 179 United States adults aged 18–83 years responded to two qualitative questions that were then analyzed using the thematic analysis technique. The identified codes were first categorized and then clustered to generate themes for both concerns and expectations. The prevalence of each theme was calculated across various demographic factors. Concerns were related to data protection, health risks, knowledge, negative affect, ease of use, metaphysical dilemmas, monetary issues, and negative social impact. Expectations included medical and non-medical uses, dismissal of microchips, technical advances, human enhancement, regulations, and affordability. The prevalence of concerns and benefits differed by immigration status and medical conditions. Informed by our findings, we present a modification to the Technology Acceptance Model for predicting public's behavioral intention to use subcutaneous microchips. We discuss the five newly proposed determinants and seven predictor variables of this model by surveying the literature. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the ongoing COVID-19 (coronavirus disease-2019) outbreak and has unprecedentedly impacted the public health and economic sector. The pandemic has forced researchers to focus on the accurate and early detection of SARS-CoV-2, developing novel diagnostic tests. Among these, microfluidic-based tests stand out for their multiple benefits, such as their portability, low cost, and minimal reagents used. This review discusses the different microfluidic platforms applied in detecting SARS-CoV-2 and seroprevalence, classified into three sections according to the molecules to be detected, i.e., (1) nucleic acid, (2) antigens, and (3) anti-SARS-CoV-2 antibodies. Moreover, commercially available alternatives based on microfluidic platforms are described. Timely and accurate results allow healthcare professionals to perform efficient treatments and make appropriate decisions for infection control; therefore, novel developments that integrate microfluidic technology may provide solutions in the form of massive diagnostics to control the spread of infectious diseases. [ABSTRACT FROM AUTHOR]

Hard machining is a process which has become highly recommended in manufacturing industry to replace grinding and perform production. The important technological parameters that determine this process are tool wear, machined surface roughness, cutting force and morphology of the removed chip. In this work, an attempt has been made to analyse the morphology and form of chip removed during turning of hardened steel AISI 1045 (40HRC) with mixed ceramic tool type CC650. Using a Taguchi plan L9, whose factors are cutting speed and feed rate with three levels for each. Macroscopic and microscopic results of chip morphology were correlated with these two cutting parameters additional to surface roughness. Sufficient experimental results were obtained using the mixed ceramic tool when turning of hardened steel AISI 1045 (40HRC) at high cutting speeds. Roughness of machined surface confirmed that it is influenced by feed rate. Chips show a sawtooth shape for all combinations of the experimental plan used. The chip form changed with cutting parameters variation and given an important indicator of suraface quality for industriel. Having the indicators on the surface quality from simple control of chip without stopping machining give an important advantage in order to maximize production and reduce costs.

Abstract Background In 2019, Kaya-Okur et al. reported on the cleavage under targets and tagmentation (CUT&Tag) technology for efficient profiling of epigenetically modified DNA fragments. It was used mainly for cultured cell lines and was especially effective for small samples and single cells. This strategy generated high-resolution and low-background-noise chromatin profiling data for epigenomic analysis. CUT&Tag is well suited to be used in plant cells, especially in tissues from which small samples are taken, such as ovules, anthers, and fibers. Results Here, we present a CUT&Tag protocol step by step using plant nuclei. In this protocol, we quantified the nuclei that can be used in each CUT&Tag reaction, and compared the efficiency of CUT&Tag with chromatin immunoprecipitation with sequencing (ChIP-seq) in the leaves of cotton. A general workflow for the bioinformatic analysis of CUT&Tag is also provided. Results indicated that, compared with ChIP-seq, the CUT&Tag procedure was faster and showed a higher-resolution, lower-background signal than did ChIP. Conclusion A CUT&Tag protocol has been refined for plant cells using intact nuclei that have been isolated.

Zinc finger proteins (ZFPs) are widely involved in plant growth and abiotic stress responses, however, few of these proteins have been functionally characterized in tree species. In this study, we cloned and characterized the BpSZA1 gene encoding a C2H2-type ZFP from Betula platyphylla. BpSZA1 is a transcription factor localized in the nucleus, with a transcription activation domain located at the N-terminus. BpSZA1 was predominantly expressed in stems and was induced by salt. We generated transgenic birch lines displaying overexpression (OE) or RNAi silencing (Ri) of BpSZA1 and exposed these along with wild-type birch seedlings to salinity. Phenotypic and physiological parameters such as superoxide dismutase, peroxisome, H2O2 content, proline content, water loss rate, and malondialdehyde content were examined. Overexpression of BpSZA1 in birch conferred increased salt tolerance. Chromatin immunoprecipitation-qPCR and RNA-seq showed that BpSZA1 binds to the GAGA-motif in the promoter of downstream target genes including BpAPX1, BpAPX2, BpCAT, and Bp6PGDH to activate their transcription. BpSZA1 also participates in abscisic acid (ABA) biosynthesis, proline biosynthesis, and the ABA/jasmonic acid pathway to enhance the salt stress of B. platyphylla.

Current guidelines, rarely if at all, address decision-making for revascularization when bypass surgery is not a possibility for high-risk cases. Patients who are surgically turned down are routinely excluded from clinical trials, even though they remain symptomatic. Furthermore, the reasons for surgical ineligibility are often times not captured in standardized risk models. There is no data regarding health status outcomes following PCI procedures in these patients and the ultimate question remains whether the benefits of PCI outweigh its risks in this controversial subpopulation. When CHIP (Complex High risk Indicated Percutaneous coronary interventions) is selected for these very complex individuals, there is no unanimity regarding the goals for interventional revascularization (for instance, the ambition to achieve completeness of revascularization vs. more targeted or selective PCI). The recognition that, worldwide, these patients are becoming increasingly prevalent and increasingly commonplace in the cardiac catheterization labs, along with the momentum for more complex interventional procedures and expanding skillsets, gives us a timely opportunity to better examine the outcomes for these patients and inform clinical decision-making.

Aging is characterized by increased mortality, functional decline, and exponential increases in the incidence of diseases such as cancer, stroke, cardiovascular disease, neurological disease, respiratory disease, etc. Though the role of aging in these diseases is widely accepted and considered to be a common denominator, the underlying mechanisms are largely unknown. A significant age-related feature observed in many population cohorts is somatic mosaicism, the detectable accumulation of somatic mutations in multiple cell types and tissues, particularly those with high rates of cell turnover (e.g., skin, liver, and hematopoietic cells). Somatic mosaicism can lead to the development of cellular clones that expand with age in otherwise normal tissues. In the hematopoietic system, this phenomenon has generally been referred to as “clonal hematopoiesis of indeterminate potential” (CHIP) when it applies to a subset of clones in which mutations in driver genes of hematologic malignancies are found. Other mechanisms of clonal hematopoiesis, including large chromosomal alterations, can also give rise to clonal expansion in the absence of conventional CHIP driver gene mutations. Both types of clonal hematopoiesis (CH) have been observed in studies of animal models and humans in association with altered immune responses, increased mortality, and disease risk. Studies in murine models have found that some of these clonal events are involved in abnormal inflammatory and metabolic changes, altered DNA damage repair and epigenetic changes. Studies in long-lived individuals also show the accumulation of somatic mutations, yet at this advanced age, carriership of somatic mutations is no longer associated with an increased risk of mortality. While it remains to be elucidated what factors modify this genotype-phenotype association, i.e., compensatory germline genetics, cellular context of the mutations, protective effects to diseases at exceptional age, it points out that the exceptionally long-lived are key to understand the phenotypic consequences of CHIP mutations. Assessment of the clinical significance of somatic mutations occurring in blood cell types for age-related outcomes in human populations of varied life and health span, environmental exposures, and germline genetic risk factors will be valuable in the development of personalized strategies tailored to specific somatic mutations for healthy aging.

Perioperative neurocognitive disorders (PND) commonly occur in elderly patients, and isoflurane could be a risk factor. During the pathogenesis of neurodegeneration, the ubiquitin–proteasome system (UPS) participates in the process of aging, which affects synaptic plasticity and synaptic function. However, whether UPS is involved in the etiology of PND is unclear. In this study, we examined the expression change of ubiquitin E3 ligase protein carboxyl-terminus of Hsc70-interacting protein (CHIP) and the function turbulence of UPS in isoflurane-exposed aged mouse to illustrate the role of UPS in PND. Neurodegenerative behavioral changes were shown in isoflurane-exposed aged mice and correlated with neuropathological changes manifested with reduced number of intersections and spine density in the cortex. Ubiquitin function was decreased while the apoptosis was activated, and CHIP protein expression decline altered synapsin expression and phosphorylation associated with the neurodegeneration in isoflurane-induced PND. Aging was the big important factor. And it remained consistent with the synapsin phosphorylation/dephosphorylation level changes in CHIP knock-down N2a cells. Per our observation, the decline in CHIP protein expression and synaptic degeneration might reveal the reason for synaptic degeneration in the underlying pathogenesis of PND caused by isoflurane.

Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.

Aluminum alloy materials are very difficult to break in the processing process; chip accumulation leads to poor processing stability. In this paper, a coated composite micro–textured tool is presented. The influence of coated composite micro–textured tool on chip shape and cutting force under the same cutting parameters is studied. Firstly, the combination of cutting force and cutting temperature is optimized based on cutting test. Secondly, combined with the finite element simulation technology, three kinds of composite micro–texture tools are tested to determine the same cutting parameters, tools and workpiece materials, and optimize the composite micro–texture combination from the angle of chip shape, cutting temperature and cutting force. Finally, on the basis of optimizing the microstructure combination, the optimization of the cutting performance of aluminum alloy by coating material is studied. It was found that the chip was more easily broken in the composite microstructure when two tools were used. The cutting force decreased by 25% and the cutting temperature decreased by 9.09% compared with the non–micro–texture tools. The cutting temperature and cutting force decreased by 3% and 4.99% compared with those of uncoated composite microstructure.

The optimum processing conditions for green laver chips were determined using response surface methodology (RSM) to improve taste and reduce off-flavors by applying reaction flavor and air-frying techniques. The optimum composition ( w / w ) for the chips included 20% green laver, 20% hairtail surimi, and 60% flour. Additional ingredients included distilled water (90 mL) with GDL (3 g), NaHCO₃ (2 g), salt (1 g), sugar (12 g), roasted soybean powder (1.5 g), and reaction flavor solution (RFS, 10 mL). The mixture was kneaded, shaped, dried at 50 °C for 2 h, and air-fried at 195 °C for 80 sec. The resulting green laver chips showed overall acceptance and brittleness values of 7.00 ± 0.74 and 5.89 ± 0.59 N, respectively, with absolute residual errors of 8.43% and 7.07%. The optimum reaction flavor precursors for green laver chips were determined to be threonine (1.0 g%), proline (1.0 g%), glycine (1.4 g%), methionine (0.05 g%), and glucose (2 g%). Flavor analysis revealed that green laver chips with reaction flavor (GLCR) contained 13 alkylpyrazines with corn-like and nutty odors, and 2-acetylpyrrole, which contributed a popcorn-like odor. In contrast, green laver chips without reaction flavor (GLC) predominantly contained straight-chain aldehydes with undesirable odors. The heating process in the air fryer appeared to reduce the aldehyde content and promote pyrazine formation, significantly enhancing GLCR's flavor.

Chromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNA in vivo. The occupancy of transcription factors (TFs) from ChIP-seq agrees well with an alternative method, chromatin endogenous cleavage (ChEC-seq2). However, ChIP-seq and ChEC-seq2 reveal strikingly different patterns of enrichment of yeast RNA polymerase II (RNAPII). We hypothesized that this reflects distinct populations of RNAPII, some of which are captured by ChIP-seq and some of which are captured by ChEC-seq2. RNAPII association with enhancers and promoters - predicted from biochemical studies - is detected well by ChEC-seq2 but not by ChIP-seq. Enhancer/promoter-bound RNAPII correlates with transcription levels and matches predicted occupancy based on published rates of enhancer recruitment, preinitiation assembly, initiation, elongation, and termination. The occupancy from ChEC-seq2 allowed us to develop a stochastic model for global kinetics of RNAPII transcription which captured both the ChEC-seq2 data and changes upon chemical-genetic perturbations to transcription. Finally, RNAPII ChEC-seq2 and kinetic modeling suggests that a mutation in the Gcn4 transcription factor that blocks interaction with the NPC destabilizes promoter-associated RNAPII without altering its recruitment to the enhancer., Competing Interests: JV, BS, DB, NM, HR, NM, JB No competing interests declared, (© 2024, VanBelzen et al.)

Background: Clonal hematopoiesis of indeterminate potential (CHIP) has been shown to increase all-cause mortality and risk of cardiomyopathy in patients with solid malignancies. CHIP has also been shown to increase T cell activation in heart failure patients. It is unclear whether CHIP can affect the risk of immune checkpoint inhibitor (ICI) myocarditis in patients with cancer treated with immunotherapy., Methods: We enrolled patients with solid tumors in a prospective study, determined CHIP status at time of enrollment through blood whole exome sequencing, and assessed incidence of ICI myocarditis from time of enrollment through December 1st, 2023. We performed a competing risk cox regression to evaluate the role of CHIP in ICI myocarditis, accounting for patient demographics, cardiac comorbidities, cardiotoxic cancer therapy, and dual ICI use in our covariates. We also generated cumulative incidence curves using subdistribution hazards to evaluate development of ICI myocarditis stratified by CHIP vs no CHIP. Chart review was performed to evaluate patient co-morbidities, lab values, imaging findings and outcomes., Results: Among the 88 patients receiving ICI therapy, average age was 67 ± 14 years, of which 50% harbored CHIP variants. Among all comorbidities, including diabetes, heart failure and obstructive coronary artery disease, only coronary artery calcifications were significantly increased in patients with CHIP. There were no statistically significant differences in cancer therapy or cardiovascular drugs between patients with and without CHIP. Among examined outcomes, patients with CHIP had a statistically higher rate of ICI myocarditis (overall: 57%, CHIP: 73% (32/44), no CHIP: 41% (18/44), p = 0.003) and death (CHIP: 60%, no CHIP 31%, p = 0.011). In a multivariate competing risk analysis, CHIP status doubled the risk of developing ICI myocarditis, similar to the risk of dual ICI use (CHIP status HR 2.74, 95% CI: 1.44-5.22, p = 0.002 vs dual ICI use HR 2.39, 95% CI: 1.11-5.14, p = 0.026)., Conclusions: This study is the first to show that CHIP independently increases risk of ICI myocarditis, with implications for risk stratification of patients prior to ICI initiation and frequency of cardiac monitoring., Competing Interests: Declarations. Ethics approval and consent to participate: This prospective study was approved by the Yale University IRB and all participants were consented at time of enrollment. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Somatic mutations of hematopoietic cells in the peripheral blood of normal individuals refer to clonal hematopoiesis of indeterminate potential (CHIP), which is associated with a 0.5-1% risk of progression to hematological malignancies and cardiovascular diseases. CHIP has also been reported in Multiple Myeloma (MM) patients, but its biological relevance remains to be elucidated. In this study, high-depth targeted sequencing of peripheral blood from 76 NDMM patients revealed CHIP in 46% of them, with a variant allele frequency (VAF) ranging from ~ 1 to 34%. The most frequently mutated gene was DNMT3A, followed by TET2. More aggressive disease features were observed among CHIP carriers, who also exhibited higher proportion of high-risk stages (ISS and R-ISS 3) compared to controls. Longitudinal analyses at diagnosis and during follow-up showed a slight increase of VAFs (p = 0.058) for epigenetic (DNMT3A, TET2, and ASXL1) and DNA repair genes (TP53; p = 0.0123). A more stable frequency was observed among other genes, suggesting different temporal dynamics of CH clones. Adverse clinical outcomes, in term of overall and progression-free survivals, were observed in CHIP carriers. These patients also exhibited weakened immune T-cells and enhanced frailty, predicting greater toxicity and consequently shorter event-free survival. Finally, correlation analysis identified platelets count as biomarker for higher VAF among CHIP carriers, regardless of the specific variant. Overall, our study highlights specific biological and clinical features, paving the way for the development of tailored strategies for MM patients carrying CHIP., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Myeloproliferative neoplasms, polycythemia vera, essential thrombocytosis, and primary myelofibrosis are a unique group of clonal hematopoietic stem cell neoplasms that share somatic, gain-in-function driver mutations in JAK 2, CALR , and MPL . As a consequence, these disorders exhibit similar phenotypic features, the most common of which are the ceaseless production of normal erythrocytes, myeloid cells, platelets alone or in combination, extramedullary hematopoiesis, myelofibrosis, and a potential for leukemic transformation. In the case of polycythemia vera and essential thrombocytosis, however, prolonged survival is possible. With an incidence value in the range of 0.5-2.0/100,000, myeloproliferative neoplasms are rare disorders, but they are not new disorders, and after a century of scrutiny, their clinical features and natural histories are well-defined, though their individual management continues to be controversial. With respect to polycythemia vera, there has been a long-standing dispute between those who believe that the suppression of red blood cell production by chemotherapy is superior to phlebotomy to prevent thrombosis, and those who do not. With respect to essential thrombocytosis, there is a similar dispute about the role of platelets in veinous thrombosis, and the role of chemotherapy in preventing thrombosis by suppressing platelet production. Linked to these disputes is another: whether therapy with hydroxyurea promotes acute leukemia in disorders with a substantial possibility of longevity. The 21st century revealed new insights into myeloproliferative neoplasms with the discovery of their three somatic, gain-of-function driver mutations. Almost immediately, this triggered changes in the diagnostic criteria for myeloproliferative neoplasms and their therapy. Most of these changes, however, conflicted with prior well-validated, phenotypically driven diagnostic criteria and the management of these disorders. The aim of this review is to examine these conflicts and demonstrate how genomic discoveries in myeloproliferative neoplasms can be used to effectively complement the known phenotypic features of these disorders for their diagnosis and management.

Mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth and its dysregulation leads to a variety of human diseases. Although NPRL2, an essential component of the GATOR1 complex, is reported to effectively suppress amino acid-induced mTORC1 activation, the regulation of NPRL2 protein stability is unclear. In this study, we show that chaperon-associated ubiquitin ligase CHIP interacts with NPRL2 and promotes its polyubiquitination and proteasomal degradation. Moreover, HSP70 mediates CHIP-induced ubiquitination and degradation of NPRL2. Consistently, overexpression of HSP70 enhances whereas HSP70 depletion inhibits amino acid-induced mTORC1 activation. Accordingly, knockdown of HSP70 promotes basal autophagic flux, and inhibits cell growth and proliferation. Taken together, these results demonstrated that HSP70 is a novel activator of mTORC1 through mediating CHIP-induced ubiquitination and degradation of NPRL2., (© 2024 Federation of American Societies for Experimental Biology.)

Background and Aims: Somatic mutations in the TET2 gene that lead to clonal haematopoiesis (CH) are associated with accelerated atherosclerosis development in mice and a higher risk of atherosclerotic disease in humans. Mechanistically, these observations have been linked to exacerbated vascular inflammation. This study aimed to evaluate whether colchicine, a widely available and inexpensive anti-inflammatory drug, prevents the accelerated atherosclerosis associated with TET2-mutant CH., Methods: In mice, TET2-mutant CH was modelled using bone marrow transplantations in atherosclerosis-prone Ldlr-/- mice. Haematopoietic chimeras carrying initially 10% Tet2-/- haematopoietic cells were fed a high-cholesterol diet and treated with colchicine or placebo. In humans, whole-exome sequencing data and clinical data from 37 181 participants in the Mass General Brigham Biobank and 437 236 participants in the UK Biobank were analysed to examine the potential modifying effect of colchicine prescription on the relationship between CH and myocardial infarction., Results: Colchicine prevented accelerated atherosclerosis development in the mouse model of TET2-mutant CH, in parallel with suppression of interleukin-1β overproduction in conditions of TET2 loss of function. In humans, patients who were prescribed colchicine had attenuated associations between TET2 mutations and myocardial infarction. This interaction was not observed for other mutated genes., Conclusions: These results highlight the potential value of colchicine to mitigate the higher cardiovascular risk of carriers of somatic TET2 mutations in blood cells. These observations set the basis for the development of clinical trials that evaluate the efficacy of precision medicine approaches tailored to the effects of specific mutations linked to CH., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Cardiology.)

Competing Interests: Funding Support and Author Disclosures The authors have reported that they have no relationships relevant to the contents of this paper to disclose.

Purpose: The detection of pathogenic microorganisms plays a significant role in the diagnosis and management of pneumonia that are responsible for a substantial number of deaths worldwide. However, conventional microbiological tests (CMT) have low accuracy and are time-consuming. In this study, we aim to evaluate the clinical value of Chips for Complicated Infection Detection (CCID) in detecting pneumonia pathogens., Patients and Methods: This study was conducted at nine hospitals in China from January 2021 to September 2022. Respiratory samples from adult pneumonia patients were collected from each patient. CMT and CCID were performed in parallel to identify the pathogens., Results: A total of 245 patients were included, with 73% being elderly. CCID identified pathogenic microbes in 78.0% of patients and conventional microbiological tests (CMT) in 57.1% of the patients (p<0.001). The overall positive and negative percent agreements between CCID and CMT for pathogen detection were 90.07% and 38.46%, respectively. 38.8% of patients were diagnosed with mixed infections with at least two pathogens by CCID. Bacterial infections identified by CCID accounted for 60.0% of 245 patients, with the top 3 being Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterococcus faecium, respectively. K. pneumoniae was the most common pathogen in elderly patients, with a significantly higher prevalence compared to non-elderly patients (p = 0.0011). Among the 197 patients who had used antibiotics before sample collection, the positive rate of CCID was significantly higher than that of CMT (p < 0.001)., Conclusion: This study indicates that compared to CMT, this novel chip has significant advantages in detecting pathogens in pneumonia patients, especially in the elderly., Competing Interests: The authors report there are no competing interests to declare., (© 2024 Zhang et al.)

The ubiquitin-proteasome system is crucial for proteostasis, particularly during proteotoxic stress. The interaction between heat shock protein (HSP) 70 and the ubiquitin ligase CHIP plays a key role in this process. Our study investigates the Caenorhabditis elegans orthologs HSP-1 and CHN-1, demonstrating that HSP-1 binding decreases CHN-1 E3 ligase activity, aligning with the inhibitory effects observed in human HSP70-CHIP interactions. To explore the physiological significance of this inhibition, we utilized the HSP-1 EEYD mutant, which binds CHN-1 without reducing its activity, expressed in C. elegans. Our results reveal that the HSP-1-CHN-1 interaction is critical for maintaining germline integrity under heat stress by preventing excessive turnover of essential reproductive proteins. In HSP-1 EEYD nematodes, this protective mechanism is impaired, leading to disrupted stress-induced apoptosis, which is restored by CHN-1 depletion. Additionally, proteomic analysis identified DAF-18/PTEN as a potential CHN-1 substrate, which becomes destabilized when CHN-1 activity is not downregulated by HSP-1 during stress. Depleting DAF-18 significantly compromises the reproductive benefits observed from CHN-1 knockout in HSP-1 EEYD mutants, suggesting that the maintenance of DAF-18 plays a role in the observed phenotypes. These findings highlight the importance of HSP-1 in regulating CHN-1 E3 ligase activity to preserve germline function under stress conditions., Competing Interests: Conflict of interest The authors declare no conflict of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The increased sensitivity of novel DNA sequencing techniques has made it possible to identify somatic mutations in small circulating clones of haematopoietic stem cells. When the mutation affects a 'driver' gene, the mutant clone gains a competitive advantage and has the potential to expand over time, a phenomenon referred to as clonal haematopoiesis (CH), which is emerging as a new risk factor for various non-haematological conditions, most notably cardiovascular disease (e.g. heart failure). Dilated cardiomyopathy (DCM) is a form of non-ischaemic heart failure that is characterized by a heterogeneous aetiology. The first evidence is arising that CH plays an important role in the disease course in patients with DCM, and a strong association of CH with multiple aetiologies of DCM has been described (e.g. inflammation, chemotherapy, and atrial fibrillation). The myocardial inflammation induced by CH may be an important trigger for DCM development for an already susceptible heart, e.g. in the presence of genetic variants, environmental triggers, and comorbidities. Studies investigating the role of CH in the pathogenesis of DCM are expected to increase rapidly. To move the field forward, it will be important to report the methodology and results in a standardized manner, so results can be combined and compared. The accurate measurement of CH in patients with DCM can provide guidance of specific (anti-inflammatory) therapies, as mutations in the CH driver genes prime the inflammasome pathway., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Cardiology.)

Introduction: Clonal hematopoiesis of indeterminate potential (CHIP) and dementia disproportionately burden patients with chronic kidney disease (CKD). The association between CHIP and cognitive impairment in CKD patients is unknown., Methods: We conducted time-to-event analyses in up to 1452 older adults with CKD from the Chronic Renal Insufficiency Cohort who underwent CHIP gene sequencing. Cognition was assessed using four validated tests in up to 6 years mean follow-up time. Incident cognitive impairment was defined as a test score one standard deviation below the baseline mean., Results: Compared to non-carriers, CHIP carriers were markedly less likely to experience impairment in attention (adjusted hazard ratio [HR] [95% confidence interval {CI}] = 0.44 [0.26, 0.76], p = 0.003) and executive function (adjusted HR [95% CI] = 0.60 [0.37, 0.97], p = 0.04). There were no significant associations between CHIP and impairment in global cognition or verbal memory., Discussion: CHIP was associated with lower risks of impairment in attention and executive function among CKD patients., Highlights: Our study is the first to examine the role of CHIP in cognitive decline in CKD. CHIP markedly decreased the risk of impairment in attention and executive function. CHIP was not associated with impairment in global cognition or verbal memory., (© 2024 The Author(s). Alzheimer's & Dementia published by Wiley Periodicals LLC on behalf of Alzheimer's Association.)

Clonal hematopoiesis of indeterminate potential (CHIP) describes recurrent somatic gene mutations in the blood of healthy individuals, associated with higher risk for hematological malignancies and higher all-cause mortality by cardiovascular disease. CHIP increases with age and is more common in adult patients after chemotherapy or radiation for cancer. Furthermore, in some adult patients undergoing autologous stem cell transplantation (ASCT) or thereafter, CHIP has been identified. In children and adolescents, it remains unclear how cellular stressors such as cytotoxic therapy influence the incidence and expansion of CHIP. We conducted a retrospective study on 33 pediatric patients mostly with solid tumors undergoing ASCT for presence of CHIP. We analyzed CD34+ selected peripheral blood stem cell grafts after several cycles of chemotherapy, prior to cell infusion, by next-generation sequencing including 18 "CHIP-genes". Apart from a somatic variant in TP53 in one patient no other variants indicative of CHIP were identified. As a CHIP-unrelated finding, germline variants in CHEK2 and in ATM were identified in two and four patients, respectively. In conclusion, we could not detect "typical" CHIP variants in our cohort of pediatric cancer patients undergoing ASCT. However, more studies with larger patient numbers are necessary to assess if chemotherapy in the pediatric setting contributes to an increased CHIP incidence and at what time point.

Transcription factor (TF) gene knockout or knockdown experiments provide comprehensive downstream effects on gene regulation. However, distinguishing primary direct effects from secondary effects remains challenging. To assess the direct effect of TF binding events, we present a protocol for establishing a doxycycline (Dox)-inducible CRISPRd system in human pluripotent stem cells (hPSCs). We describe the steps for establishing CRISPRd host hPSCs, designing and preparing single-guide RNA (sgRNA) expression lentivirus vectors, generating CRISPRd hPSCs transduced with sgRNAs, and analyzing CRISPRd TF-block effects by chromatin immunoprecipitation (ChIP)-qPCR. For complete details on the use and execution of this protocol, please refer to Matsui et al. 1 ., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)