Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure.

As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.

Evidence of housing instability identified by addresses, clinical notes, and diagnostic codes in a real-world population with substance use disorders.

Introduction: Housing instability is a social determinant of health associated with multiple negative health outcomes including substance use disorders (SUDs). Real-world evidence of housing instability is needed to improve translational research on populations with SUDs. Methods: We identified evidence of housing instability by leveraging structured diagnosis codes and unstructured clinical data from electronic health records of 20,556 patients from 2017 to 2021. We applied natural language processing with named-entity recognition and pattern matching to unstructured clinical notes with free-text documentation. Additionally, we analyzed semi-structured addresses containing explicit or implicit housing-related labels. We assessed agreement on identification methods by having three experts review of 300 records. Results: Diagnostic codes only identified 58.5% of the population identifiable as having housing instability, whereas 41.5% are identifiable from addresses only (7.1%), clinical notes only (30.4%), or both (4.0%). Reviewers unanimously agreed on 79.7% of cases reviewed; a Fleiss' Kappa score of 0.35 suggested fair agreement yet emphasized the difficulty of analyzing patients having ambiguous housing situations. Among those with poisoning episodes related to stimulants or opioids, diagnosis codes were only able to identify 63.9% of those with housing instability. Conclusions: All three data sources yield valid evidence of housing instability; each has their own inherent practical use and limitations. Translational researchers requiring comprehensive real-world evidence of housing instability should optimize and implement use of structured and unstructured data. Understanding the role of housing instability and temporary housing facilities is salient in populations with SUDs.

Xylazine-involved fatal overdoses and localized geographic clustering: Cook County, IL, 2019-2022.

BACKGROUND: Xylazine, a veterinary analgesic sedative, is circulating in the illicit drug markets of at least 23 states including Illinois. We conducted a geographic analysis to better identify the spatial distribution of xylazine-involved fatal overdoses in Cook County, IL. METHODS: Cook County Medical Examiner Office's (CCMEO) publicly available data was used to identify xylazine-involved fatal overdoses from January 1, 2019, to June 30, 2022. Xylazine-positive (cases) to xylazine-negative groups with drug mixtures involving fentanyl, alcohol and stimulants (controls) were matched on age, race, sex, and year of death. Ripley's K-function was used to examine the likelihood of case clustering compared to controls with the Bernoulli spatial scan deployed to identify specific geographic clusters. RESULTS: Almost all (94.4%) xylazine-positive overdoses contained fentanyl. Using coordinate-based matching, we found that approximately 3% of xylazine overdose incidents were co-located with other overdoses. Xylazine cases clustered to from 0 to 16.1 miles (max=10.6 miles). Results of the Bernoulli spatial scan varied by control group with two high-risk clusters found relative to alcohol and stimulants and a low-risk cluster relative to fentanyl. Differences in co-occurring drugs were found between xylazine and fentanyl groups like the absolute number of drugs (4.6v 3.4, p<0.0001) and fentanyl analog types. CONCLUSIONS: Xylazine fatal overdose incident locations exhibited localized clustering relative to fentanyl overdoses but clusters were not precisely detected at these scales. Even so, our results, especially relative to repeat overdose micro "hot spots", offer insight on targeting harm reduction and other services at the neighborhood-level.

Substance use disorders and social determinants of health from electronic medical records obtained during Kentucky's "triple wave".

Social determinants of health (SDOH) play a critical role in the risk of harmful drug use. Examining SDOH as a means of differentiating populations with multiple co-occurring substance use disorders (SUDs) is particularly salient in the era of prevalent opioid and stimulant use known as the "Third Wave". This study uses electronic medical records (EMRs) from a safety net hospital system from 14,032 patients in Kentucky from 2017 to 2019 in order to 1) define three types of SUD cohorts with shared/unique risk factors, 2) identify patients with unstable housing using novel methods for EMRs and 3) link patients to their residential neighborhood to obtain quantitative perspective on social vulnerability. We identified patients in three cohorts with statistically significant unique risk factors that included race, biological sex, insurance type, smoking status, and urban/rural residential location. Adjusting for these variables, we found a statistically significant, increasing risk gradient for patients experiencing unstable housing by cohort type: opioid-only (n = 7385, reference), stimulant-only (n = 4794, odds ratio (aOR) 1.86 95 % confidence interval (CI): 1.66-2.09), and co-diagnosed (n = 1853, aOR = 2.75, 95 % CI: 2.39 to 3.16). At the neighborhood-level, we used 8 different measures of social vulnerability and found that, for the most part, increasing proportions of patients with stimulant use living in a census tract was associated with more social vulnerability. Our study identifies potentially modifiable factors that can be tailored by substance type and demonstrates robust use of EMRs to meet national goals of enhancing research on social determinants of health.

Effect of Cyclic Heat Stress on Hypothalamic Oxygen Homeostasis and Inflammatory State in the Jungle Fowl and Three Broiler-Based Research Lines.

Heat stress (HS) is devastating to poultry production sustainability due its detrimental effects on performance, welfare, meat quality, and profitability. One of the most known negative effects of HS is feed intake depression, which is more pronounced in modern high-performing broilers compared to their ancestor unselected birds, yet the underlying molecular mechanisms are not fully defined. The present study aimed, therefore, to determine the hypothalamic expression of a newly involved pathway, hypoxia/oxygen homeostasis, in heat-stressed broiler-based research lines and jungle fowl. Three populations of broilers (slow growing ACRB developed in 1956, moderate growing 95RB from broilers available in 1995, and modern fast growing MRB from 2015) and unselected Jungle fowl birds were exposed to cyclic heat stress (36°C, 9 h/day for 4 weeks) in a 2 × 4 factorial experimental design. Total RNAs and proteins were extracted from the hypothalamic tissues and the expression of target genes and proteins was determined by real-time quantitative PCR and Western blot, respectively. It has been previously shown that HS increased core body temperature and decreased feed intake in 95RB and MRB, but not in ACRB or JF. HS exposure did not affect the hypothalamic expression of HIF complex, however there was a line effect for HIF-1α (P = 0.02) with higher expression in JF under heat stress. HS significantly up regulated the hypothalamic expression of hemoglobin subunits (HBA1, HBBR, HBE, HBZ), and HJV in ACRB, HBA1 and HJV in 95RB and MRB, and HJV in JF, but it down regulated FPN1 in JF. Additionally, HS altered the hypothalamic expression of oxygen homeostasis- up and down-stream signaling cascades. Phospho-AMPKThr172 was activated by HS in JF hypothalamus, but it decreased in that of the broiler-based research lines. Under thermoneutral conditions, p-AMPKThr172 was higher in broiler-based research lines compared to JF. Ribosomal protein S6K1, however, was significantly upregulated in 95RB and MRB under both environmental conditions. HS significantly upregulated the hypothalamic expression of NF-κB2 in MRB, RelB, and TNFα in ACRB, abut it down regulated RelA in 95RB. The regulation of HSPs by HS seems to be family- and line-dependent. HS upregulated the hypothalamic expression of HSP60 in ACRB and 95RB, down regulated HSP90 in JF only, and decreased HSP70 in all studied lines. Taken together, this is the first report showing that HS modulated the hypothalamic expression of hypoxia- and oxygen homeostasis-associated genes as well as their up- and down-stream mediators in chickens, and suggests that hypoxia, thermotolerance, and feed intake are interconnected, which merit further in-depth investigations.

Ileal microbial composition in genetically distinct chicken lines reared under normal or high ambient temperatures.

BACKGROUND: Heat stress (HS) has negative effects on poultry productivity, health and welfare resulting in economic losses. Broiler chickens are particularly susceptible to HS due to their high metabolic rate and rapid growth. The commensal intestinal bacterial populations have an important physiological role in the host and could ameliorate the negative effect of HS on the host. Thus, the aim of this study was to compare changes in the ileal (IL) microbiota in four different broiler lines during HS. RESULTS: Day-old broiler chicks from Giant Jungle Fowl (JF), Athens Canadian Random Bred (ACRB), 1995 Random Bred (L1995), and Modern Random Bred (L2015) lines were raised under thermoneutral (TN) conditions until day (d) 28. On d 29 birds were subjected to TN (24 °C) or chronic cyclic HS (8 h/d, 36 °C) condition till d 56. On d 56 two birds per pen were euthanized, and IL luminal content (IL-L) and mucosal scrapings (IL-M) were collected for bacterial DNA isolation. Libraries were constructed using V3-V4 16S rRNA primers and sequenced using MiSeq. DNA sequences were analyzed using QIIME2 platform and SILVA 132 database for alpha and beta diversity, and taxonomic composition, respectively. Functional property of microbiota was predicted using the PICRUSt 2 pipeline and illustrated with STAMP software. Shannon index was significantly elevated in IL-M under HS. ß-diversity PCoA plots revealed separation of microbial community of L2015-TN from JF-TN, JF-HS, ACRB-TN, and ACRB-HS in the IL-M. PERMANOVA analysis showed a significant difference between microbial community of L1995-HS compared to ACRB-HS and JF-TN, L1995-TN compared to ACRB-HS and JF-TN, L2015-HS compared to ACRB-HS and ACRB-TN, L2015-HS compared to JF-TN, L2015-TN compared to ACRB-HS and JF-TN, and ACRB-HS compared to JF-TN in the IL-L. The impact of HS on microbial composition of IL-M was more prominent compared to IL-L with 12 and 2 taxa showing significantly different relative abundance, respectively. Furthermore, differences in microbiota due to the genetic line were more prominent in IL-M than IL-L with 18 and 8 taxa showing significantly different relative abundance, respectively. Unlike taxonomy, predicted function of microbiota was not affected by HS. Comparison of L2015 with JF or ACRB showed significant changes in predicted function of microbiota in both, IL-M and IL-L. Differences were most prominent between L2015 and JF; while there was no difference between L2015 and L1995. CONCLUSIONS: These data indicate the genetic line × temperature effect on the diversity and composition of IL microbiota. Moreover, the data showcase the effect of host genetics on the composition of IL microbiota and their predicted function. These data are of critical importance for devising nutritional strategies to maintain GIT microbial balance and alleviate the negative effects of HS on broiler chickens' performance and health.

SNP-based breeding for broiler resistance to ascites and evaluation of correlated production traits.

BACKGROUND: The goal of this study was to evaluate marker-assisted selection (MAS) in broiler chickens using previously mapped gene regions associated with ascites syndrome incidence. The second-generation MAS products were assessed for impact on ascites phenotype and whether there were associated changes in important production traits. Previously, we used whole genome resequencing (WGR) to fine-map 28 chromosomal regions as associated with ascites phenotype in our experimental ascites broiler line (Relaxed, REL) based on a hypobaric chamber challenge. Genotypes for single nucleotide polymorphisms (SNPs) in mapped regions on chromosomes 2 and 22, were used for MAS in our REL line. After two generations, birds homozygous for the genotypes associated with resistance for both chromosomal regions were established. The MAS F2 generation was then compared to the REL line for ascites susceptibility and 25 production traits. RESULTS: Selection based on SNPs in the carboxypeptidase Q (CPQ, Gga2) and leucine rich repeat transmembrane neuronal 4 (LRRTM4, Gga22) gene regions resulted in a sex- and simulated altitude- dependent reduction of ascites incidence in two F2 cohorts of the MAS line. Comparisons of the F2 MAS and REL lines for production traits when reared at ambient pressure found no significant negative impacts for feed intake (FI), feed conversion ratio (FCR), or deboned part yields for either sex for two F2 cohorts. There were, however, improvements in the MAS for full-trial body weight gain (BWG), FCR, absolute and relative tender weights, and relative drumstick weight. CONCLUSIONS: These results validate the mapping of the 28 chromosomal regions and demonstrate that fine mapping by WGR is an effective strategy for addressing a complex trait; it also stands as the first successful SNP-based selection program against a complex disease trait, such as ascites. The MAS line is comparable and, in some instances, superior, in growth performance to the REL control while being more resistant to ascites. This study indicates that MAS based on WGR can provide significant breeding potential in agricultural systems.

Opioid Overdoses Increase at Home During the COVID-19 Stay-At-Home Order Period in Cook County, Illinois.

Introduction: Stay-at-home orders during the COVID-19 pandemic decreased population mobility to reduce SARS-CoV-2 infection rates. We empirically tested the hypothesis that this public health measure was associated with a higher likelihood of opioid- and stimulant-involved deaths occurring in homes located in Cook County, Illinois. Methods: The stay-at-home period was from March 21, 2020 to May 30, 2020. We analyzed overdose data from the Cook County Medical Examiner's Office using a death location description from case investigations categorized as home, medical, motel, scene, and other. Two groups of decedents were defined as either having an opioid or stimulant listed in the primary cause of death field. We modeled a weekly time series to detect changes in deaths (number) and trends during segmented time periods. Chi-square or Fisher's exact and adjusted logistic regression was used for testing the differences between the stay-at-home and a 13-week preceding period. Results: There were 4,169 and 2,012 opioid- and stimulant-involved deaths, respectively, from 2018 to 2020. Both groups were demographically similar: 75% male, 52% White, and aged 45 years (mean). In the 13 weeks before stay-at-home orders, 51% of opioid-involved deaths occurred in homes, which increased to 59% (p<0.0001) during the 10 weeks of the order and decreased back to 51% in the 18 weeks after the order expired. For stimulant-involved deaths, 51% were residential immediately before the orders, with a nonsignificant increase to 52% during the stay-at-home period. Before the pandemic, there were 20 deaths/week, increasing to 37 deaths/week (p<0.0001) during stay-at-home enactment. Deaths involving fentanyl among the opioid-involved group increased from 76% to 89%, whereas those involving heroin decreased from 55% to 37%. The adjusted OR for opioid-involved fatal overdoses occurring at home during this period compared with that occurring the 13 weeks before was 1.37 (95% CI=1.05, 1.79). Conclusions: The likelihood of a death occurring at home, especially for people using opioids, increased during the stay-at-home order period. Findings have implications for mitigating overdose risks during social isolation.

Effects of Cyclic Chronic Heat Stress on the Expression of Nutrient Transporters in the Jejunum of Modern Broilers and Their Ancestor Wild Jungle Fowl.

Heat stress (HS) has been reported to disrupt nutrient digestion and absorption in broilers. These effects may be more prominent in fast-growing chickens due to their high metabolic activity. However, the underlying molecular mechanisms are not yet fully elucidated. Hence, the current study aimed to evaluate the effect of chronic HS on jejunal nutrient transport in slow- (Athens Canadian Random Bred, ACRB from 1950), moderate- (The 1995 random bred, 95RAN), rapid- (modern broilers, modern random bred, MRB) growing birds and their ancestor wild jungle fowl (JF). One-day male chicks (n = 150/line) were placed by line in environmentally controlled chambers and kept under the same industry-standard environmental conditions until d28. On d29, an 8-h daily cyclic HS (36°C) was applied to half of the chambers, which lasted until d55, while keeping the rest under thermal neutral (TN, 24°C) conditions. Jejunum tissues were collected for morphology assessment and molecular analysis of carbohydrate-, amino acid-, and fatty acid-transporters. MRB exhibited the highest body weight (BW) followed by 95RAN under both conditions. HS decreased feed intake (FI) in MRB and 95RAN, which resulted in lower BW compared to their TN counterparts; however, no effect was observed in ACRB and JF. MRB showed a greater villus height (VH) to crypt depth (CD) ratio under both environmental conditions. Molecular analyses showed that glucose transporter (GLUT) 2, 5, 10, and 11 were upregulated in MRB compared to some of the other populations under TN conditions. HS downregulated GLUT2, 10, 11, and 12 in MRB while it increased the expression of GLUT1, 5, 10, and 11 in JF. GLUT2 protein expression was higher in JF compared to ACRB and MRB under TN conditions. It also showed an increase in ACRB but no effect on 95RAN and MRB under HS conditions. ACRB exhibited greater expression of the EAAT3 gene as compared to the rest of the populations maintained under TN conditions. HS exposure did not alter the gene expression of amino acid transporters in MRB. Gene expression of CD36 and FABP2 was upregulated in HS JF birds. Protein expression of CD36 was downregulated in HS JF while no effect was observed in ACRB, 95RAN, and MRB. Taken together, these data are the first to show the effect of HS on jejunal expression of nutrient transporters in three broiler populations known to represent 70 years of genetic progress in the poultry industry and a Red Jungle Fowl population representative of the primary ancestor of domestic chickens.

Focal Atrial Tachycardia Originating From the Right Atrial Appendage Masquerading as Inappropriate Sinus Tachycardia.

Focal atrial tachycardia arising from the right atrial appendage (RAAT) may be misdiagnosed as sinus tachycardia. The electrocardiogram from this case demonstrates a negative notched P-wave in leads V1 and V2 during RAAT compared with a beat of sinus rhythm. RAAT was confirmed and eliminated with mapping and ablation. (Level of Difficulty: Advanced.).

Histological Analysis and Gene Expression of Satellite Cell Markers in the Pectoralis Major Muscle in Broiler Lines Divergently Selected for Percent 4-Day Breast Yield.

Muscle development during embryonic and early post-hatch growth is primarily through hyperplastic growth and accumulation of nuclei through satellite cell contribution. Post-hatch, muscle development transitions from hyperplasia to hypertrophic growth of muscle fibers. Commercial selection for breast yield traditionally occurs at ages targeting hypertrophic rather than hyperplastic growth. This has resulted in the production of giant fibers and concomitant challenges with regard to muscle myopathies. The current study investigates the impact of selection during the period of hyperplastic growth. It is hypothesized that selection for percentage breast yield during hyperplasia will result in an increased number of muscle cells at hatch and potentially impact muscle fiber characteristics at processing. This study characterizes the breast muscle histology of three broiler lines at various ages in the growth period. The lines include a random bred control (RAN) as well as lines which have been selected from RAN for high (HBY4) and low (LBY4) percentage 4-day breast yield. Post-rigor pectoralis major samples from six males of each line and age were collected and stored in formalin. The sample ages included embryonic day 18 (E18), post-hatch day 4 (d4), and day 56 (d56). The samples were processed using a Leica tissue processor, embedded in paraffin wax, sectioned, and placed on slides. Slides were stained using hematoxylin and eosin. E18 and d4 post-hatch analysis showed advanced muscle fiber formation for HBY4 and immature muscle development for LBY4 as compared to RAN. Post-hatch d56 samples were analyzed for fiber number, fiber diameter, endomysium, and perimysium spacing. Line HBY4 had the largest muscle fiber diameter (54.2 ± 0.96 µm) when compared to LBY4 (45.4 ± 0.96 µm). There was no line difference in endomysium spacing while perimysium spacing was higher for HBY4 males. Selection for percentage 4-day breast yield has impacted the rate and extent of muscle fiber formation in both the LBY4 and HBY4 lines with no negative impact on fiber spacing. The shift in processing age to later ages has exposed issues associated with muscle fiber viability. Selection during the period of muscle hyperplasia may impact growth rate; however, the potential benefits of additional satellite cells are still unclear.

Blood Plasma Biomarkers for Woody Breast Disease in Commercial Broilers.

Woody breast (WB) myopathy results in poor muscle quality. The increasing incidence of WB over the last several years indicates a need for improved prediction or early diagnosis. We hypothesized that the use of body fluids, including blood, may be more suitable than breast muscle tissue in developing a minimally invasive diagnostic tool for WB detection. To identify potential early-age-biomarkers that may represent the potential onset of WB, blood samples were collected from 100, 4 wks old commercial male broilers. At 8 wks of age, WB conditions were scored by manual palpation. A total of 32 blood plasma samples (eight for each group of WB and non-WB control birds at two time points, 4 wks and 8 wks) were subjected to shotgun proteomics and untargeted metabolomics to identify differentially abundant plasma proteins and metabolites in WB broilers compared to non-WB control (Con) broilers. From the proteomics assay, 25 and 16 plasma proteins were differentially abundant (p < 0.05) in the 4 and 8 wks old samples, respectively, in WB compared with Con broilers. Of those, FRA10A associated CGG repeat 1 (FRAG10AC1) showed >2-fold higher abundance in WB compared with controls. In the 8 wks old broilers, 4 and 12 plasma proteins displayed higher and lower abundances, respectively, in WB compared with controls. Myosin heavy chain 9 (MYH9) and lipopolysaccharide binding protein (LBP) showed more than 2-fold higher abundances in WB compared with controls, while transferrin (TF) and complement C1s (C1S) showed more than 2-fold lower abundances compared with controls. From the untargeted metabolomics assay, 33 and 19 plasma metabolites were differentially abundant in birds at 4 and 8 wks of age, respectively, in WB compared with controls. In 4 wks old broilers, plasma 3-hydroxybutyric acid (3-HB) and raffinose concentrations showed the highest and lowest fold changes, respectively, in WB compared with controls. The blood plasma 3-HB and raffinose concentrations were confirmed with targeted biochemical assays. Blood biomarkers, such as 3-HB and raffinose, may be suitable candidate targets in the prediction of WB onset at early ages.

Hypertrabeculation; a phenotype with Heterogeneous etiology.

Left ventricular hypertrabeculation (LVHT) is a phenotype with multiple etiologies and variable clinical presentation and significance. It is characterized by a 2-layer myocardium with an enlarged trabecular layer and a thinner compacted layer. The prevalence has been increasing due to advances in cardiac imaging. Initial attention was focused on the congenital noncompaction syndrome, and the presence of LVHT was always attributed to this etiology. However, due to the lack of consensus diagnostic criteria, LVHT has now been reported in a broad spectrum of cardiomyopathies, congenital heart diseases, monogenetic disorders, neuromuscular diseases, and even healthy individuals. LVHT is often associated with systolic dysfunction, arrhythmias, and thromboembolic events. Given the etiologic heterogeneity, the prognosis and outcomes are primarily determined by comorbidities, and treatment is dictated by known guidelines. We present hypertrabeculation (HT) as a phenotype and discuss the varied landscape in the classification, etiology, diagnosis, and management of the condition.

Hypoxia further exacerbates woody breast myopathy in broilers via alteration of satellite cell fate.

Woody breast (WB) condition has created a variety of challenges for the global poultry industry. To date, there are no effective treatments or preventative measures due to its unknown (undefined) etiology. Several potential mechanisms including oxidative stress, fiber-type switching, cellular damage, and altered intracellular calcium levels have been proposed to play a key role in the progression of the WB myopathy. In a previous study, we have shown that WB is associated with hypoxia-like status and dysregulated oxygen homeostasis. As satellite cells (SC) play a pivotal role in muscle fiber repair and remodeling under stress conditions, we undertook the present study to determine satellite cell fate in WB-affected birds when reared in either normoxic or hypoxic conditions. Modern random bred broilers from 2015 (n = 200) were wing banded and reared under standard brooding practices for the first 2 wk post-hatch. At 15 d, chicks were divided in 2 body weight-matched groups and reared to 6 wk in either control local altitude or hypobaric chambers with simulated altitude of 6,000 ft. Birds were provided ad libitum access to water and feed, according to the Cobb recommendations. At 6 wk of age, birds were processed and scored for WB, and breast samples were collected from WB-affected and unaffected birds for molecular analyses (n = 10/group). SCs were isolated from normal breast muscle, cultured in vitro, and exposed to normoxia or hypoxia for 2 h. The expression of target genes was determined by qPCR using 2-∆∆Ct method. Protein distribution and expression were determined by immunofluorescence staining and immunoblot, respectively. Data were analyzed by the Student's t test with significance set at P < 0.05. Multiple satellite cell markers, myogenic factor (Myf)-5 and paired box (PAX)-7 were significantly decreased at the mRNA and protein levels in the breast muscle from WB-affected birds compared to their unaffected counterparts. Lipogenic-and adipogenic-associated factors (acetyl-CoA carboxylase, ACCα; fatty acid synthase, FASN, malic enzyme, ME; and ATP citrate lyase, ACLY) were activated in WB-affected birds. These data were supported by an in vitro study where hypoxia decreased the expression of Myf5 and Pax7, and increased that of ACCα, FASN, ME, and ACLY. Together, these data indicate that under hypoxic condition, SC change fate by switching from a myogenic to an adipogenic program, which explains at least partly, the etiology of the WB myopathy.

Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function.

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.

Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions.

BACKGROUND: Microbial endocrinology, which is the study of neuroendocrine-based interkingdom signaling, provides a causal mechanistic framework for understanding the bi-directional crosstalk between the host and microbiome, especially as regards the effect of stress on health and disease. The importance of the cecal microbiome in avian health is well-recognized, yet little is understood regarding the mechanisms underpinning the avian host-microbiome relationship. Neuroendocrine plasticity of avian tissues that are focal points of host-microbiome interaction, such as the gut and lung, has likewise received limited attention. Avian in vivo models that enable the study of the neuroendocrine dynamic between host and microbiome are needed. As such, we utilized Japanese quail (Coturnix japonica) that diverge in corticosterone response to stress to examine the relationship between stress-related neurochemical concentrations at sites of host-microbe interaction, such as the gut, and the cecal microbiome. RESULTS: Our results demonstrate that birds which contrast in corticosterone response to stress show profound separation in cecal microbial community structure as well as exhibit differences in tissue neurochemical concentrations and structural morphologies of the gut. Changes in neurochemicals known to be affected by the microbiome were also identified in tissues outside of the gut, suggesting a potential relationship in birds between the cecal microbiome and overall avian physiology. CONCLUSIONS: The present study provides the first evidence that the structure of the avian cecal microbial community is shaped by selection pressure on the bird for neuroendocrine response to stress. Identification of unique region-dependent neurochemical changes in the intestinal tract following stress highlights environmental stressors as potential drivers of microbial endocrinology-based mechanisms of avian host-microbiome dialogue. Together, these results demonstrate that tissue neurochemical concentrations in the avian gut may be related to the cecal microbiome and reveal the Japanese quail as a novel avian model in which to further examine the mechanisms underpinning these relationships. Video abstract.

Risk factors for lymph node metastasis and survival of patients with nonampullary duodenal carcinoid tumors treated with endoscopic therapy versus surgical resection: analysis of the Surveillance, Epidemiology, and End Results program.

BACKGROUND AND AIMS: Endoscopic therapy (ET) has been used to treat nonampullary duodenal neuroendocrine tumors (NAD-NETs) ≤10 mm in size, but data on long-term outcomes are limited. In addition, management of 11- to 19-mm NAD-NETs is not well defined because of variable estimates of risk of metastasis. We aimed to determine the prevalence and risk factors of metastasis of NAD-NETs ≤19 mm and evaluate the long-term survival of patients after ET as compared with radical surgery. METHODS: The Surveillance Epidemiology and End Result database was used to identify 1243 patients with T1-2 histologically confirmed NAD-NETs ≤19 mm in size. Cancer-specific survival (CSS) and overall survival (OS) were calculated. RESULTS: Overall, 4.8% of cases had metastasis at the time of diagnosis, with lower prevalence in ≤10-mm lesions (3.1%) versus 11- to 19-mm lesions (11.7%, P < .001). The risk factors for metastases included invasion to the muscularis propria (odds ratio, 25.95; 95% confidence interval, 9.01-76.70), age <65 years (odds ratio, 1.93), submucosal involvement (odds ratio, 3.1), and 11 to 19 mm in size (vs ≤10 mm). In patients with well- to moderately differentiated T1-2N0M0 NAD-NETs ≤19 mm confined to the mucosa/submucosa who underwent ET or surgery, the 5-year CSS was 100%. The 5-year OS was similar between the ≤10-mm and 11- to 19-mm groups (86.6% vs 91.0%, P = .31) and the ET and surgery groups (87.4% vs 87.5%, P = .823). CONCLUSIONS: In NAD-NETs, invasion to the muscularis propria is the strongest risk factor for metastasis. In the absence of metastasis, in lesions with well/moderate differentiation and without muscle invasion, ET is adequate for NAD-NETs ≤10 mm and is a viable option for 11- to 19-mm lesions.

Femoral Derotation Osteotomy Improves Hip and Spine Function in Patients With Increased or Decreased Femoral Torsion.

PURPOSE: To evaluate the outcomes of proximal femoral derotation osteotomy (PFDO) on the hip and spine function of patients with abnormal femoral torsion. METHODS: This retrospective study included patients who underwent PFDO to treat increased or decreased femoral torsion between July 2014 and February 2019. The exclusion criteria were: previous fracture, fixation of slipped capital femoral epiphysis or osteotomy in the ipsilateral femur; PFDO associated to varus or valgus osteotomy; Tönnis grade 2 or 3 osteoarthritis; and PFDO performed to treat knee abnormalities. Hip function was assessed through the modified Harris Hip Score (mHHS). A subgroup of consecutive patients with low back pain before the PFDO and operated after 2017 had the spine function assessed through the Oswestry disability index (ODI). RESULTS: A total of 37 hips (34 patients) were studied: 15 hips with increased femoral torsion and 22 with decreased femoral torsion. Eight patients were male and 26 were female. The average age at PFDO was 33 years (range, 15-54 years). At a mean follow-up of 24 months (range, 12-65 months), the mean mHHS improved from 58.1 ± 14.3 before PFDO to 82 ± 15.6 at the most recent follow-up (P < .001). Improvement in the mHHS above the minimum clinically important difference (MCID) was observed in 33 hips (89%). In the subgroup of 14 consecutive patients with ODI available, the ODI improved from a mean of 45% ± 16% before the PFDO to 22% ± 17% at the most recent follow-up (P = .001). Nine (64.3%) of the 14 patients presented improvement in the ODI above the MCID. Revision procedure with a larger intramedullary nail was necessary in 2 hips to treat nonunion. CONCLUSION: Proximal femoral derotation osteotomy improves the hip and spine function in patients with increased or decreased femoral torsion and nonarthritic hips. LEVEL OF EVIDENCE: Level IV, therapeutic case series.