The epigenome under pressure: On regulatory adaptation to chronic stress in the brain.

Chronic stress (CS) can have long-lasting consequences on behavior and cognition, that are associated with stable changes in gene expression in the brain. Recent work has examined the role of the epigenome in the effects of CS on the brain. This review summarizes experimental evidence in rodents showing that CS can alter the epigenome and the expression of epigenetic modifiers in brain cells, and critically assesses their functional effect on genome function. It discusses the influence of the developmental time of stress exposure on the type of epigenetic changes, and proposes new lines of research that can help clarify these changes and their causal involvement in the impact of CS.

Remembering through the genome: the role of chromatin states in brain functions and diseases.

Chromatin is the physical substrate of the genome that carries the DNA sequence and ensures its proper functions and regulation in the cell nucleus. While a lot is known about the dynamics of chromatin during programmed cellular processes such as development, the role of chromatin in experience-dependent functions remains not well defined. Accumulating evidence suggests that in brain cells, environmental stimuli can trigger long-lasting changes in chromatin structure and tri-dimensional (3D) organization that can influence future transcriptional programs. This review describes recent findings suggesting that chromatin plays an important role in cellular memory, particularly in the maintenance of traces of prior activity in the brain. Inspired by findings in immune and epithelial cells, we discuss the underlying mechanisms and the implications for experience-dependent transcriptional regulation in health and disease. We conclude by presenting a holistic view of chromatin as potential molecular substrate for the integration and assimilation of environmental information that may constitute a conceptual basis for future research.

Implementing Rounding Checklists in a Pediatric Oncologic Intensive Care Unit.

Standardized rounding checklists during multidisciplinary rounds (MDR) can reduce medical errors and decrease length of pediatric intensive care unit (PICU) and hospital stay. We added a standardized process for MDR in our oncologic PICU. Our study was a quality improvement initiative, utilizing a four-stage Plan-Do-Study-Act (PDSA) model to standardize MDR in our PICU over 3 months, from January 2020 to March 2020. We distributed surveys to PICU RNs to assess their understanding regarding communication during MDR. We created a standardized rounding checklist that addressed key elements during MDR. Safety event reports before and after implementation of our initiative were retrospectively reviewed to assess our initiative's impact on safety events. Our intervention increased standardization of PICU MDR from 0% to 70% over three months, from January 2020 to March 2020. We sustained a rate of zero for CLABSI, CAUTI, and VAP during the 12-month period prior to, during, and post-intervention. Implementation of a standardized rounding checklist may improve closed-loop communication amongst the healthcare team, facilitate dialogue between patients' families and the healthcare team, and reduce safety events. Additional staffing for resource RNs, who assist with high acuity patients, has also facilitated bedside RN participation in MDR, without interruptions in clinical care.

Understanding excited state properties of host materials in OLEDs: simulation of absorption spectrum of amorphous 4,4-bis(carbazol-9-yl)-2,2-biphenyl (CBP).

4,4-Bis(carbazol-9-yl)-2,2-biphenyl (CBP) is widely used as a host material in phosphorescent organic light-emitting diodes (PhOLEDs). In the present study, we simulate the absorption spectra of CBP in gas and condensed phases, respectively, using the efficient time-dependent long-range corrected tight-binding density functional theory (TD-LC-DFTB). The accuracy of the condensed-phase absorption spectra computed using the structures obtained from classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) simulations is examined by comparison with the experimental absorption spectrum. It is found that the TD-LC-DFTB gas-phase spectrum is in good agreement with the GW-BSE spectrum, indicating TD-LC-DFTB is an accurate and robust method in calculating the excitation energies of CBP. For the condensed-phase spectrum, we find that the electrostatic embedding has a minor influence on the excitation energy. Computing accurate absorption spectra is a particular challenge since static and dynamic disorders have to be taken into account. The static disorder results from the molecular packing in the material, which leads to molecule deformations. Since these structural changes sensitively impact the excitation energies of the individual molecules, a proper representation of this static disorder indicates that a reasonable structural model of the material has been generated. The good agreement between computed and experimental absorption spectra is therefore an indicator for the structural model developed. Concerning dynamic disorder, we find that molecular changes occur on long timescales in the ns-regime, which requires the use of fast computation approaches to reach convergence. The structural models derived in this work are the basis for future studies of charge and exciton transfer in CBP and related materials, also concerning the degradation mechanisms of CBP-based PhOLEDs.

Pain and Analgesia in Children with Cancer after Hemipelvectomy: A Retrospective Analysis.

A paucity of data exists centering on the pain experience of children following hemipelvectomy performed for primary bone and soft tissue sarcomas. In this study, we aimed to describe the incidence, severity, and evolution of perioperative pain and function in pediatric oncology patients undergoing hemipelvectomy, and, additionally, we sought to detail the analgesic regimens used for these patients perioperatively. A retrospective chart review was conducted, studying cancer patients, aged 21 years and under, who underwent hemipelvectomy at MD Anderson Cancer Center (MDACC) from 2018 to 2021. Primary outcomes included the evolution of pain throughout the perioperative course, as well as the route, type, dose, and duration of analgesic regimens. Eight patients were included in the analysis. The mean age at operation was 13 ± 2.93 years. All patients received opioids and acetaminophen. The mean pain scores were highest on post-operative day (POD)0, POD5, and POD 30. The mean opioid use was highest on POD5. A total of 75% of patients were noted to be ambulating after hemipelvectomy. The mean time to ambulation was 5.33 ± 2.94 days. The combination of acetaminophen with opioids, as well as adjunctive regional analgesia, non-steroidal anti-inflammatory drugs, gabapentin, and/or ketamine in select patients, appeared to be an effective analgesic regimen, and functional outcomes were excellent in 75% of patients.

Epigenetic Inheritance: Impact for Biology and Society-recent progress, current questions and future challenges.

Epigenetic inheritance has emerged as a new research discipline that aims to study the mechanisms underlying the transmission of acquired traits across generations. Such transmission is well established in plants and invertebrates but remains not well characterized and understood in mammals. Important questions are how life experiences and environmental factors induce phenotypic changes that are passed to the offspring of exposed individuals, sometimes across several successive generations, what is the contribution of germ cells and what are the consequences for health and disease. These questions were recently discussed at the symposium Epigenetic Inheritance: Impact for Biology and Society organized every 2 years in Zürich, Switzerland. This review provides a summary of the research presented during the symposium and discusses current important questions, perspectives and challenges for the field in the future.

Retrospective Review of Flexible Bronchoscopy in Pediatric Cancer Patients.

The use of flexible bronchoscopy (FB) with bronchoalveolar lavage (BAL) to diagnose and manage pulmonary complications has been shown to be safe in adult cancer patients, but whether its use is safe in pediatric cancer patients remains unclear. Thus, to describe the landscape of FB outcomes in pediatric cancer patients and to help define the populations most likely to benefit from the procedure, we undertook a retrospective review of FBs performed in patients younger than 21 years treated at our institution from 2002 to 2017. We found that a greater volume of total fluid instilled during BAL was significantly associated with increased probabilities of positive BAL culture (p=0.042), positive bacterial BAL culture (p=0.037), and positive viral BAL culture (p=0.0496). In more than half of the FB cases, findings resulted in alterations in antimicrobial treatment. Our study suggests that for pediatric cancer patients, FB is safe, likely provides diagnostic and/or therapeutic benefits, and has implications for treatment decisions.

In-Nucleus Hi-C in Drosophila Cells.

The genome is organized into topologically associating domains (TADs) delimited by boundaries that isolate interactions between domains. In Drosophila, the mechanisms underlying TAD formation and boundaries are still under investigation. The application of the in-nucleus Hi-C method described here helped to dissect the function of architectural protein (AP)-binding sites at TAD boundaries isolating the Notch gene. Genetic modification of domain boundaries that cause loss of APs results in TAD fusion, transcriptional defects, and long-range topological alterations. These results provided evidence demonstrating the contribution of genetic elements to domain boundary formation and gene expression control in Drosophila. Here, the in-nucleus Hi-C method has been described in detail, which provides important checkpoints to assess the quality of the experiment along with the protocol. Also shown are the required numbers of sequencing reads and valid Hi-C pairs to analyze genomic interactions at different genomic scales. CRISPR/Cas9-mediated genetic editing of regulatory elements and high-resolution profiling of genomic interactions using this in-nucleus Hi-C protocol could be a powerful combination for the investigation of the structural function of genetic elements.

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis.

As phosphorus is one of the most limiting nutrients in many natural and agricultural ecosystems, plants have evolved strategies that cope with its scarcity. Genetic approaches have facilitated the identification of several molecular elements that regulate the phosphate (Pi) starvation response (PSR) of plants, including the master regulator of the transcriptional response to phosphate starvation PHOSPHATE STARVATION RESPONSE1 (PHR1). However, the chromatin modifications underlying the plant transcriptional response to phosphate scarcity remain largely unknown. Here, we present a detailed analysis of changes in chromatin accessibility during phosphate starvation in Arabidopsis thaliana root cells. Root cells undergo a genome-wide remodeling of chromatin accessibility in response to Pi starvation that is often associated with changes in the transcription of neighboring genes. Analysis of chromatin accessibility in the phr1 phl2 double mutant revealed that the transcription factors PHR1 and PHL2 play a key role in remodeling chromatin accessibility in response to Pi limitation. We also discovered that PHR1 and PHL2 play an important role in determining chromatin accessibility and the associated transcription of many genes under optimal Pi conditions, including genes involved in the PSR. We propose that a set of transcription factors directly activated by PHR1 in Pi-starved root cells trigger a second wave of epigenetic changes required for the transcriptional activation of the complete set of low-Pi-responsive genes.

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle.

BACKGROUND: Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized. RESULTS: Here we measure changes in the spatial chromatin conformation in mouse liver using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription. We find topologically associating domains harboring circadian genes that switch assignments between the transcriptionally active and inactive compartment at different hours of the day, while their boundaries stably maintain their structure over time. To study chromatin contacts of promoters at high resolution over time, we apply promoter capture Hi-C. We find circadian gene promoters displayed a maximal number of chromatin contacts at the time of their peak transcriptional output. Furthermore, circadian genes, as well as contacted and transcribed regulatory elements, reach maximal expression at the same timepoints. Anchor sites of circadian gene promoter loops are enriched in DNA binding sites for liver nuclear receptors and other transcription factors, some exclusively present in either rhythmic or stable contacts. Finally, by comparing the interaction profiles between core clock and output circadian genes, we show that core clock interactomes are more dynamic compared to output circadian genes. CONCLUSION: Our results identify chromatin conformation dynamics at different scales that parallel oscillatory gene expression and characterize the repertoire of regulatory elements that control circadian gene transcription through rhythmic or stable chromatin configurations.

Case Discussion and Literature Review: Cancer Immunotherapy, Severe Immune-Related Adverse Events, Multi-Inflammatory Syndrome, and Severe Acute Respiratory Syndrome Coronavirus 2.

Pediatric, adolescent and young adult (AYA) patients receiving novel cancer immunotherapies may develop associated toxicities with overlapping signs and symptoms that are not always easily distinguished from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection/clinical sequelae. We describe 2 diagnostically challenging cases of SARS-CoV-2 and Multi-Inflammatory Syndrome-Adult (MIS-A), in patients with a history of acute lymphoblastic leukemia following cellular therapy administration and review evolving characterization of both the natural course of SARS-CoV-2 infection and toxicities experienced in younger cancer immunotherapy patients. Vigilant monitoring for unique presentations and epidemiologic surveillance to promptly detect changes in incidence of either condition may be warranted.

Long-Term Impact of Social Isolation and Molecular Underpinnings.

Prolonged periods of social isolation can have detrimental effects on the physiology and behavior of exposed individuals in humans and animal models. This involves complex molecular mechanisms across tissues in the body which remain partly identified. This review discusses the biology of social isolation and describes the acute and lasting effects of prolonged periods of social isolation with a focus on the molecular events leading to behavioral alterations. We highlight the role of epigenetic mechanisms and non-coding RNA in the control of gene expression as a response to social isolation, and the consequences for behavior. Considering the use of strict quarantine during epidemics, like currently with COVID-19, we provide a cautionary tale on the indiscriminate implementation of such form of social isolation and its potential damaging and lasting effects in mental health.

An Intronic Alu Element Attenuates the Transcription of a Long Non-coding RNA in Human Cell Lines.

Alu elements are primate-specific repeats and represent the most abundant type of transposable elements (TE) in the human genome. Genome-wide analysis of the enrichment of histone post-translational modifications suggests that human Alu sequences could function as transcriptional enhancers; however, no functional experiments have evaluated the role of Alu sequences in the control of transcription in situ. The present study analyses the regulatory activity of a human Alu sequence from the AluSx family located in the second intron of the long intergenic non-coding RNA Linc00441, found in divergent orientation to the RB1 gene. We observed that the Alu sequence acts as an enhancer element based on reporter gene assays while CRISPR-Cas9 deletions of the Alu sequence in K562 cells resulted in a marked transcriptional upregulation of Linc00441 and a decrease in proliferation. Our results suggest that an intragenic Alu sequence with enhancer activity can act as a transcriptional attenuator of its host lincRNA.

Novel tephritid-specific features revealed from cytological and transcriptomic analysis of Anastrepha ludens embryonic development.

Anastrepha ludens is a major pest of fruits including citrus and mangoes in Mexico and Central America with major economic and social impacts. Despite its importance, our knowledge on its embryonic development is scarce. Here, we report the first cytological study of embryonic development in A. ludens and provide a transcriptional landscape during key embryonic stages. We established 17 stages of A. ludens embryogenesis that closely resemble the morphological events observed in Drosophila. In addition to the extended duration of embryonic development, we observed notable differences including yolk extrusion at both poles of the embryo, distinct nuclear division waves in the syncytial blastoderm and a heterochronic change during the involution of the head. Characterization of the transcriptional dynamics during syncytial blastoderm, cellular blastoderm and gastrulation, showed that approximately 9000 different transcripts are present at each stage. Even though we identified most of the transcripts with a role during embryonic development present in Drosophila, including sex determination genes, a number of transcripts were absent not only in A. ludens but in other tephritids such as Ceratitis capitata and Bactrocera dorsalis. Intriguingly, some A. ludens embryo transcripts encode proteins present in other organisms but not in other flies. Furthermore, we developed an RNA in situ hybridization protocol that allowed us to obtain the expression patterns of genes whose functions are important in establishing the embryonic body pattern. Our results revealed novel tephritid-specific features during A. ludens embryonic development and open new avenues for strategies aiming to control this important pest.

In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila.

Chromosomes are organized into high-frequency chromatin interaction domains called topologically associating domains (TADs), which are separated from each other by domain boundaries. The molecular mechanisms responsible for TAD formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by architectural proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence of the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila.

Seguimiento a pacientes con enfermedad por reflujo gastroesofágico posterior a fundiplicatura de NISSEN laparoscópica intervenidos en el Instituto Salvadoreño del Seguro Social / Follow-up of patients with gastroesophageal reflux disease after laparoscopic NISSEN fundiplication operated at the Instituto Salvadoreño del Seguro Social

La enfermedad por reflujo gastroesofágico (ERGE) fue reconocida como problema clínico importante y se identificó como causa de esofagitis, su prevalencia ha sido estimada en base a la presencia de síntomas típicos y atípicos. La cirugía antirreflujo (CAR), asociada a la introducción de la técnica laparoscópica y sus ventajas han permitido la expansión de la fundiplicatura laparoscópica estableciéndose como el estándar de oro en el manejo quirúrgico de ERGE. Se proponen actividades de promoción, prevención, detección, diagnóstico y tratamiento para pacientes con diagnóstico de ERGE con la finalidad de identificar aquellos candidatos para CAR. El protocolo de seguimiento para pacientes con ERGE tiene como objetivo evaluar la calidad de vida posterior a la realización de CAR en todos los pacientes intervenidos en el Instituto Salvadoreño del Seguro Social.

Enhancer RNAs: Insights Into Their Biological Role.

Enhancers play a central role in the transcriptional regulation of metazoans. Almost a decade ago, the discovery of their pervasive transcription into noncoding RNAs, termed enhancer RNAs (eRNAs), opened a whole new field of study. The presence of eRNAs correlates with enhancer activity; however, whether they act as functional molecules remains controversial. Here we review direct experimental evidence supporting a functional role of eRNAs in transcription and provide a general pipeline that could help in the design of experimental approaches to investigate the function of eRNAs. We propose that induction of transcriptional activity at enhancers promotes an increase in its activity by an RNA-mediated titration of regulatory proteins that can impact different processes like chromatin accessibility or chromatin looping. In a few cases, transcripts originating from enhancers have acquired specific molecular functions to regulate gene expression. We speculate that these transcripts are either nonannotated long noncoding RNAs (lncRNAs) or are evolving toward functional lncRNAs. Further work will be needed to comprehend better the biological activity of these transcripts.

Management guidelines for paediatric patients receiving chimeric antigen receptor T cell therapy.

In 2017, an autologous chimeric antigen receptor (CAR) T cell therapy indicated for children and young adults with relapsed and/or refractory CD19+ acute lymphoblastic leukaemia became the first gene therapy to be approved in the USA. This innovative form of cellular immunotherapy has been associated with remarkable response rates but is also associated with unique and often severe toxicities, which can lead to rapid cardiorespiratory and/or neurological deterioration. Multidisciplinary medical vigilance and the requisite health-care infrastructure are imperative to ensuring optimal patient outcomes, especially as these therapies transition from research protocols to standard care. Herein, authors representing the Pediatric Acute Lung Injury and Sepsis Investigators (PALISI) Network Hematopoietic Stem Cell Transplantation (HSCT) Subgroup and the MD Anderson Cancer Center CAR T Cell Therapy-Associated Toxicity (CARTOX) Program have collaborated to provide comprehensive consensus guidelines on the care of children receiving CAR T cell therapy.

Asmic: An Exceptional Building Block for Isocyanide Alkylations.

Asmic addresses the long-standing challenge of alkylating isocyanides, providing access to isocyanides with diverse substitution patterns. The o-anisylsulfanyl group serves a critical dual role by facilitating deprotonation-alkylation and providing a latent nucleophilic site through an unusual arylsulfanyl-lithium exchange.