Imprinted X chromosome inactivation at the gamete-to-embryo transition

In mammals, dosage compensation involves two parallel processes: (1) X inactivation, which equalizes X chromosome dosage between males and females, and (2) X hyperactivation, which upregulates the active X for X-autosome balance. The field currently favors models whereby dosage compensation initiates "de novo" during mouse development. Here, we develop "So-Smart-seq" to revisit the question and interrogate a comprehensive transcriptome including noncoding genes and repeats in mice. Intriguingly, de novo silencing pertains only to a subset of Xp genes. Evolutionarily older genes and repetitive elements demonstrate constitutive Xp silencing, adopt distinct signatures, and do not require Xist to initiate silencing. We trace Xp silencing backward in developmental time to meiotic sex chromosome inactivation in the male germ line and observe that Xm hyperactivation is timed to Xp silencing on a gene-by-gene basis. Thus, during the gamete-to-embryo transition, older Xp genes are transmitted in a "pre-inactivated" state. These findings have implications for the evolution of imprinting.

Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in Permissive Lung Cells

Chromatin conformation capture followed by next-generation sequencing in combination with large-scale polymer simulations (4DHiC) produces detailed information on genomic loci interactions, allowing for the interrogation of 3D spatial genomic structures. Here, Hi-C data was acquired from the infection of fetal lung fibroblast (MRC5) cells with α-coronavirus 229E (CoV229E). Experimental Hi-C contact maps were used to determine viral-induced changes in genomic architecture over a 48-hour time period following viral infection, revealing substantial alterations in contacts within chromosomes and in contacts between different chromosomes. To gain further structural insight and quantify the underlying changes, we applied the 4DHiC polymer simulation method to reconstruct the 3D genomic structures and dynamics corresponding to the Hi-C maps. The models successfully reproduced experimental Hi-C data, including the changes in contacts induced by viral infection. Our 3D spatial simulations uncovered widespread chromatin restructuring, including increased chromosome compactness and A-B compartment mixing arising from infection. Our model also suggests increased spatial accessibility to regions containing interferon-stimulated genes upon infection with CoV229E, followed by chromatin restructuring at later time points, potentially inducing the migration of chromatin into more compact regions. This is consistent with previously observed suppression of gene expression. Our spatial genomics study provides a mechanistic structural basis for changes in chromosome architecture induced by coronavirus infection in lung cells.

Variable expression of MECP2, CDKL5, and FMR1 in the human brain: Implications for gene restorative therapies

MECP2, CDKL5, and FMR1 are three X-linked neurodevelopmental genes associated with Rett, CDKL5-, and fragile-X syndrome, respectively. These syndromes are characterized by distinct constellations of severe cognitive and neurobehavioral anomalies, reflecting the broad but unique expression patterns of each of the genes in the brain. As these disorders are not thought to be neurodegenerative and may be reversible, a major goal has been to restore expression of the functional proteins in the patient's brain. Strategies have included gene therapy, gene editing, and selective Xi-reactivation methodologies. However, tissue penetration and overall delivery to various regions of the brain remain challenging for each strategy. Thus, gaining insights into how much restoration would be required and what regions/cell types in the brain must be targeted for meaningful physiological improvement would be valuable. As a step toward addressing these questions, here we perform a meta-analysis of single-cell transcriptomics data from the human brain across multiple developmental stages, in various brain regions, and in multiple donors. We observe a substantial degree of expression variability for MECP2, CDKL5, and FMR1 not only across cell types but also between donors. The wide range of expression may help define a therapeutic window, with the low end delineating a minimum level required to restore physiological function and the high end informing toxicology margin. Finally, the inter-cellular and inter-individual variability enable identification of co-varying genes and will facilitate future identification of biomarkers.

Site-specific R-loops induce CGG repeat contraction and fragile X gene reactivation

Here, we describe an approach to correct the genetic defect in fragile X syndrome (FXS) via recruitment of endogenous repair mechanisms. A leading cause of autism spectrum disorders, FXS results from epigenetic silencing of FMR1 due to a congenital trinucleotide (CGG) repeat expansion. By investigating conditions favorable to FMR1 reactivation, we find MEK and BRAF inhibitors that induce a strong repeat contraction and full FMR1 reactivation in cellular models. We trace the mechanism to DNA demethylation and site-specific R-loops, which are necessary and sufficient for repeat contraction. A positive feedback cycle comprising demethylation, de novo FMR1 transcription, and R-loop formation results in the recruitment of endogenous DNA repair mechanisms that then drive excision of the long CGG repeat. Repeat contraction is specific to FMR1 and restores the production of FMRP protein. Our study therefore identifies a potential method of treating FXS in the future.

Long non-coding RNAs: definitions, functions, challenges and recommendations

Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.

Targeting RNA with small molecules: lessons learned from Xist RNA

Although more than 98% of the human genome is noncoding, nearly all drugs on the market target one of about 700 disease-related proteins. However, an increasing number of diseases are now being attributed to noncoding RNA and the ability to target them would vastly expand the chemical space for drug development. We recently devised a screening strategy based upon affinity-selection mass spectrometry and succeeded in identifying bioactive compounds for the noncoding RNA prototype, Xist. One such compound, termed X1, has drug-like properties and binds specifically to the RepA motif of Xist in vitro and in vivo. Small-angle X-ray scattering analysis reveals that X1 changes the conformation of RepA in solution, thereby explaining the displacement of cognate interacting protein factors (PRC2 and SPEN) and inhibition of X-chromosome inactivation. In this Perspective, we discuss lessons learned from these proof-of-concept experiments and suggest that RNA can be systematically targeted by drug-like compounds to disrupt RNA structure and function.

The EUFOREA pocket guide for chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is known to affect around 5 % of the total population, with major impact on the quality of life of those severely affected (1). Despite a substantial burden on individuals, society and health economies, CRS often remains underdiagnosed, under-estimated and under-treated (2). International guidelines like the European Position Paper on Rhinosinusitis and Nasal Polyps (EPOS) (3) and the International Consensus statement on Allergy and Rhinology: Rhinosinusitis 2021 (ICAR) (4) offer physicians insight into the recommended treatment options for CRS, with an overview of effective strategies and guidance of diagnosis and care throughout the disease journey of CRS.

Selective Xi reactivation and alternative methods to restore MECP2 function in Rett syndrome

The human X-chromosome harbors only 4% of our genome but carries over 20% of genes associated with intellectual disability. Given that they inherit only one X-chromosome, males are more frequently affected by X-linked neurodevelopmental genetic disorders than females. However, despite inheriting two X-chromosomes, females can also be affected because X-chromosome inactivation enables only one of two X-chromosomes to be expressed per cell. For Rett syndrome and similar X-linked disorders affecting females, disease-specific treatments have remained elusive. However, a cure may be found within their own cells because every sick cell carries a healthy copy of the affected gene on the inactive X (Xi). Therefore, selective Xi reactivation may be a viable approach that would address the root cause of various X-linked disorders. Here, we discuss Rett syndrome and compare current approaches in the pharmaceutical pipeline to restore MECP2 function. We then focus on Xi reactivation and review available methods, lessons learned, and future directions.

Denaturing cross-linking immunoprecipitation to identify footprints for RNA-binding proteins

The isolation of protein-RNA complexes in the “denaturing cross-linked RNA immunoprecipitation” (dCLIP) protocol is based on biotin-tagging proteins of interest, UV cross-linking RNA to protein in vivo, RNase protection assay, and isolating RNA-protein complexes under denaturing conditions over a streptavidin column. Insofar as conventional antibody-based CLIP assays have been challenging to apply to Polycomb complexes, dCLIP has been applied successfully and yields small RNA footprints from which de novo motif analysis can be performed to identify RNA binding motifs.

For complete details on the use and execution of this protocol, please refer to Rosenberg et al. (2017).

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dCLIP biotags a protein of interest to identify cross-linked RNA interactors in vivo

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Biotin-streptavidin purification system enables denaturing washing conditions

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dCLIP is successfully applied to chromatin-modifying protein complexes

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dCLIP allows high-resolution mapping of RNA binding sites and de novo motif analysis

Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

Chromosome loops shift dynamically during development, homeostasis, and disease. CCCTC-binding factor (CTCF) is known to anchor loops and construct 3D genomes, but how anchor sites are selected is not yet understood. Here, we unveil Jpx RNA as a determinant of anchor selectivity. Jpx RNA targets thousands of genomic sites, preferentially binding promoters of active genes. Depleting Jpx RNA causes ectopic CTCF binding, massive shifts in chromosome looping, and downregulation of >700 Jpx target genes. Without Jpx, thousands of lost loops are replaced by de novo loops anchored by ectopic CTCF sites. Although Jpx controls CTCF binding on a genome-wide basis, it acts selectively at the subset of developmentally sensitive CTCF sites. Specifically, Jpx targets low-affinity CTCF motifs and displaces CTCF protein through competitive inhibition. We conclude that Jpx acts as a CTCF release factor and shapes the 3D genome by regulating anchor site usage.

Revealing RCOR2 as a regulatory component of nuclear speckles

Background

Nuclear processes such as transcription and RNA maturation can be impacted by subnuclear compartmentalization in condensates and nuclear bodies. Here, we characterize the nature of nuclear granules formed by REST corepressor 2 (RCOR2), a nuclear protein essential for pluripotency maintenance and central nervous system development.

Results

Using biochemical approaches and high-resolution microscopy, we reveal that RCOR2 is localized in nuclear speckles across multiple cell types, including neurons in the brain. RCOR2 forms complexes with nuclear speckle components such as SON, SRSF7, and SRRM2. When cells are exposed to chemical stress, RCOR2 behaves as a core component of the nuclear speckle and is stabilized by RNA. In turn, nuclear speckle morphology appears to depend on RCOR2. Specifically, RCOR2 knockdown results larger nuclear speckles, whereas overexpressing RCOR2 leads to smaller and rounder nuclear speckles.

Conclusion

Our study suggests that RCOR2 is a regulatory component of the nuclear speckle bodies, setting this co-repressor protein as a factor that controls nuclear speckles behavior.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13072-021-00425-4.

Effect of a Swing-Assist Knee Prosthesis on Stair Ambulation

This paper describes stair ambulation control and functionality of a semi-powered knee prosthesis that supplements nominally passive prosthesis behavior with swing-phase assistance. A set of stair ascent and descent controllers are described. The controllers were implemented in a semi-powered prosthesis prototype, and the prospective benefits of swing assist in stair ambulation were assessed on a group of three participants with unilateral, transfemoral amputation, relative to their respective daily-use prostheses. Results indicate that ambulation with the semi-powered knee resulted in improved stair ascent gait symmetry when compared to the participants' passive daily-use devices, and increased similitude to healthy stair ascent movement.

A disproportionate impact of G9a methyltransferase deficiency on the X chromosome

In this study from Szanto et al., the authors investigated the role of G9a, a histone methyltransferase responsible for the dimethylation of histone H3 at lysine 9 (H3K9me2) that plays key roles in transcriptional silencing of developmentally regulated genes, in X-chromosome inactivation (XCI). They found a female-specific function of G9a and demonstrate that deleting G9a has a disproportionate impact on the X chromosome relative to the rest of the genome, and show RNA tethers G9a for allele-specific targeting of the H3K9me2 modification and the G9a–RNA interaction is essential for XCI.

G9a is a histone methyltransferase responsible for the dimethylation of histone H3 at lysine 9 (H3K9me2). G9a plays key roles in transcriptional silencing of developmentally regulated genes, but its role in X-chromosome inactivation (XCI) has been under debate. Here, we uncover a female-specific function of G9a and demonstrate that deleting G9a has a disproportionate impact on the X chromosome relative to the rest of the genome. G9a deficiency causes a failure of XCI and female-specific hypersensitivity to drug inhibition of H3K9me2. We show that G9a interacts with Tsix and Xist RNAs, and that competitive inhibition of the G9a-RNA interaction recapitulates the XCI defect. During XCI, Xist recruits G9a to silence X-linked genes on the future inactive X. In parallel on the future Xa, Tsix recruits G9a to silence Xist in cis. Thus, RNA tethers G9a for allele-specific targeting of the H3K9me2 modification and the G9a-RNA interaction is essential for XCI.

The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis

CTCF is a key organizer of the 3D genome. Its specialized paralog, BORIS, heterodimerizes with CTCF but is expressed only in male germ cells and in cancer states. Unexpectedly, BORIS-null mice have only minimal germ cell defects. To understand the CTCF-BORIS relationship, mouse models with varied CTCF and BORIS levels were generated. Whereas Ctcf+/+Boris+/+, Ctcf+/-Boris+/+, and Ctcf+/+Boris-/- males are fertile, Ctcf+/-Boris-/- (Compound Mutant; CM) males are sterile. Testes with combined depletion of both CTCF and BORIS show reduced size, defective meiotic recombination, increased apoptosis, and malformed spermatozoa. Although CM germ cells exhibit only 25% of CTCF WT expression, chromatin binding of CTCF is preferentially lost from CTCF-BORIS heterodimeric sites. Furthermore, CM testes lose the expression of a large number of spermatogenesis genes and gain the expression of developmentally inappropriate genes that are "toxic" to fertility. Thus, a combined action of CTCF and BORIS is required to both repress pre-meiotic genes and activate post-meiotic genes for a complete spermatogenesis program.

Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation

Depletion of architectural factors globally alters chromatin structure but only modestly affects gene expression. We revisit the structure-function relationship using the inactive X chromosome (Xi) as a model. We investigate cohesin imbalances by forcing its depletion or retention using degron-tagged RAD21 (cohesin subunit) or WAPL (cohesin release factor). Cohesin loss disrupts the Xi superstructure, unveiling superloops between escapee genes with minimal effect on gene repression. By contrast, forced cohesin retention markedly affects Xi superstructure, compromises spreading of Xist RNA-Polycomb complexes, and attenuates Xi silencing. Effects are greatest at distal chromosomal ends, where looping contacts with the Xist locus are weakened. Surprisingly, cohesin loss creates an Xi superloop, and cohesin retention creates Xi megadomains on the active X chromosome. Across the genome, a proper cohesin balance protects against aberrant inter-chromosomal interactions and tempers Polycomb-mediated repression. We conclude that a balance of cohesin eviction and retention regulates X inactivation and inter-chromosomal interactions across the genome.

Tryptophan requirement of first-cycle commercial laying hens in peak egg production

An experiment was conducted to evaluate the digestible tryptophan (Trp) requirement of laying hens from 22 to 34 wk of age. A total of 252 Hy-line W-36 laying hens were selected at 16 wk of age and allocated by weight (P = 0.90) to 7 dietary treatments resulting in 12 replicate cages of 3 birds for each treatment. A Trp-deficient basal diet was formulated using corn, corn gluten meal, and soybean meal for each of the 3 dietary phases and supplemented with synthetic L-Trp to provide 105, 119, 133, 147, 162, 176, and 190 mg digestible Trp on a daily basis over the experimental period. To adapt the hens to experimental diets, pullets were fed complete diets that contained increasing amounts of corn gluten meal. Hens received a controlled amount of feed daily based on feed intake expected under commercial conditions. Linear and quadratic broken-line, and quadratic polynomial models were used to estimate digestible Trp requirements based on hen-housed egg production (HHEP), egg mass (EM), and feed efficiency (FE). FE was calculated using EM and feed intake. Digestible Trp requirements were estimated to be 137, 183, and 192 mg/d for HHEP; 133, 180, and 183 for EM and 133, 177, and 173 for FE using linear broken-line, quadratic broken-line, and quadratic polynomial analysis, respectively. The quadratic broken line model in this experiment resulted in the best fit (R²) for all parameters measured. Linear broken line estimates resulted in lower estimates that the other models, and HHEP resulted in higher estimated digestible Trp requirement than EM and FE.

Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation

Although Polycomb repressive complex 2 (PRC2) is now recognized as an RNA-binding complex, the full range of binding motifs and why PRC2-RNA complexes often associate with active genes have not been elucidated. Here we identify high-affinity RNA motifs whose mutations weaken PRC2 binding and attenuate its repressive function in mouse embryonic stem cells. Interactions occur at promoter-proximal regions and frequently coincide with pausing of RNA Polymerase II (POL-II). Surprisingly, while PRC2-associated nascent transcripts are highly expressed, ablating PRC2 further upregulates expression via loss of pausing and enhanced transcription elongation. Thus, PRC2-nascent RNA complexes operate as rheostats to fine-tune transcription by regulating transitions between pausing and elongation, explaining why PRC2-RNA complexes frequently occur within active genes. Nascent RNA also targets PRC2 in cis and downregulates neighboring genes. We propose a unifying model in which RNA specifically recruits PRC2 to repress genes through POL-II pausing and, more classically, H3K27-trimethylation.

Determining the 4th limiting amino acid in low crude protein diets for male and female Cobb MV × 500 broilers

1. Four experiments were conducted to determine the 4th limiting amino acid (AA) in maize-soybean meal-based diets. 2. Deletion assay methodology was used to quantify performance and carcase trait responses to potential deficiencies in essential and conditionally essential AA caused by reductions in dietary crude protein of maize-soybean meal-based diets from 202.9 to 186.5 g/kg. 3. The deletion of Val, Phe and Gly + Pro resulted in negative effects on live performance and carcase traits for male broilers, whereas AA deletion only affected wing weights for females with no response on live performance. 4. Further experimentation could not duplicate a response to Phe or Pro in male broilers. 5. Valine was identified as the potential 4th limiting AA in maize-soybean meal-based diets and was not found to be co-limiting with Ile.

Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover

How allelic asymmetry is generated remains a major unsolved problem in epigenetics. Here we model the problem using X-chromosome inactivation by developing "BioRBP", an enzymatic RNA-proteomic method that enables probing of low-abundance interactions and an allelic RNA-depletion and -tagging system. We identify messenger RNA-decapping enzyme 1A (DCP1A) as a key regulator of Tsix, a noncoding RNA implicated in allelic choice through X-chromosome pairing. DCP1A controls Tsix half-life and transcription elongation. Depleting DCP1A causes accumulation of X-X pairs and perturbs the transition to monoallelic Tsix expression required for Xist upregulation. While ablating DCP1A causes hyperpairing, forcing Tsix degradation resolves pairing and enables Xist upregulation. We link pairing to allelic partitioning of CCCTC-binding factor (CTCF) and show that tethering DCP1A to one Tsix allele is sufficient to drive monoallelic Xist expression. Thus, DCP1A flips a bistable switch for the mutually exclusive determination of active and inactive Xs.

Aberrant mitochondrial function in patient-derived neural cells from CDKL5 deficiency disorder and Rett syndrome

The X-linked neurodevelopmental diseases CDKL5 deficiency disorder (CDD) and Rett syndrome (RTT) are associated with intellectual disability, infantile spasms and seizures. Although mitochondrial dysfunction has been suggested in RTT, less is understood about mitochondrial function in CDD. A comparison of bioenergetics and mitochondrial function between isogenic wild-type and mutant neural progenitor cell (NPC) lines revealed increased oxygen consumption in CDD mutant lines, which is associated with altered mitochondrial function and structure. Transcriptomic analysis revealed differential expression of genes related to mitochondrial and REDOX function in NPCs expressing the mutant CDKL5. Furthermore, a similar increase in oxygen consumption specific to RTT patient-derived isogenic mutant NPCs was observed, though the pattern of mitochondrial functional alterations was distinct from CDKL5 mutant-expressing NPCs. We propose that aberrant neural bioenergetics is a common feature between CDD and RTT disorders. The observed changes in oxidative stress and mitochondrial function may facilitate the development of therapeutic agents for CDD and related disorders.

Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding

Nucleoporin proteins (Nups) have been proposed to mediate spatial and temporal chromatin organization during gene regulation. Nevertheless, the molecular mechanisms in mammalian cells are not well understood. Here, we report that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. NUP153 depletion results in altered CTCF and cohesin binding and differential gene expression - specifically at the bivalent developmental genes. To investigate the molecular mechanism, we utilize epidermal growth factor (EGF)-inducible immediate early genes (IEGs). We find that NUP153 controls CTCF and cohesin binding at the cis-regulatory elements and POL II pausing during the basal state. Furthermore, efficient IEG transcription relies on NUP153. We propose that NUP153 links the nuclear pore complex (NPC) to chromatin architecture allowing genes that are poised to respond rapidly to developmental cues to be properly modulated.

Two- and three-color STORM analysis reveals higher-order assembly of leukotriene synthetic complexes on the nuclear envelope of murine neutrophils

Over the last several years it has become clear that higher order assemblies on membranes, exemplified by signalosomes, are a paradigm for the regulation of many membrane signaling processes. We have recently combined two-color direct stochastic optical reconstruction microscopy (dSTORM) with the (Clus-DoC) algorithm that combines cluster detection and colocalization analysis to observe the organization of 5-lipoxygenase (5-LO) and 5-lipoxygenase-activating protein (FLAP) into higher order assemblies on the nuclear envelope of mast cells; these assemblies were linked to leukotriene (LT) C4 production. In this study we investigated whether higher order assemblies of 5-LO and FLAP included cytosolic phospholipase A2 (cPLA2) and were linked to LTB4 production in murine neutrophils. Using two- and three-color dSTORM supported by fluorescence lifetime imaging microscopy we identified higher order assemblies containing 40 molecules (median) (IQR: 23, 87) of 5-LO, and 53 molecules (62, 156) of FLAP monomer. 98 (18, 154) molecules of cPLA2 were clustered with 5-LO, and 77 (33, 114) molecules of cPLA2 were associated with FLAP. These assemblies were tightly linked to LTB4 formation. The activation-dependent close associations of cPLA2, FLAP, and 5-LO in higher order assemblies on the nuclear envelope support a model in which arachidonic acid is generated by cPLA2 in apposition to FLAP, facilitating its transfer to 5-LO to initiate LT synthesis.

Administration of dietary prebiotics improves growth performance and reduces pathogen colonization in broiler chickens

Dietary prebiotics are thought to be potentially important alternatives to antibiotic growth promoters in poultry production because of their beneficial performance and health effects. The administration of dietary prebiotics has been demonstrated to improve animal health, growth performance, and microbial food safety in poultry production. In this study, we evaluated the effects of Saccharomyces- derived prebiotic refined functional carbohydrates (RFC) with yeast culture on growth performance and gastrointestinal and environmental microbiota when administered in-feed and through drinking water to broiler chickens. Broilers were administered 2 doses of prebiotic in-feed through 42 d of production and prebiotic-treated water in the final 72 h. Administration of prebiotic RFC improved ADG and decreased cecal Campylobacter counts, while the high dose also increased final BW. Additionally, significant main effects of prebiotic RFC dose were observed with the high dose improving ADG and ADFI over the finisher phase and final BW. Although the effects were not significant, the prevalence of Campylobacter in the cecum after feed withdrawal was 17% lower when broilers were administered the high prebiotic dose, and recovery of Campylobacter from litter was up to 50% lower when broilers were administered prebiotic RFC. Our results suggest that co-administration of RFC with yeast culture as a prebiotic can be used to improve growth performance and reduce human foodborne pathogens in poultry.

Design of a Semi-Powered Stance-Control Swing-Assist Transfemoral Prosthesis

This paper describes the design of a new type of knee prosthesis called a stance-control, swing-assist (SCSA) knee prosthesis. The device is motivated by the recognition that energetically-passive stance-controlled microprocessor-controlled knees (SCMPKs) offer many desirable characteristics, such as quiet operation, low weight, high-impedance stance support, and an inertially-driven swing-phase motion. Due to the latter, however, SCMPKs are also highly susceptible to swing-phase perturbations, which can increase the likelihood of falling. The SCSA prosthesis supplements the behavior of an SCMPK with a small motor that maintains the low output impedance of the SCMPK swing state, while adding a supplemental closed-loop controller around it. This paper elaborates upon the motivation for the SCSA prosthesis, describes the design of a prosthesis prototype, and provides human-subject testing data that demonstrates potential device benefits relative to an SCMPK during both non-perturbed and perturbed walking.

Research Note: Evaluation of manganese hydroxychloride in 45-wk-old white leghorn layers using yolk and shell manganese content

The objective of the current study was to evaluate increasing levels of manganese hydroxychloride (MHC) in 45-wk-old white leghorn laying hens, using yolk and shell manganese (Mn) content as a potential marker for Mn concentration. A total of 80, 45-wk-old white leghorns were assigned to 6 dietary treatments, each consisting of 14 individually caged laying hens, with the exception of the reference diet containing 10 individually caged laying hens. The experiment consisted of a reference diet that contained 70 ppm of supplemental inorganic Mn in the form of Mn oxide and 5 experimental treatments each containing 0, 15, 30, 60, and 90 ppm supplemental MHC. Experimental birds were subjected to a 21 D depletion phase in which no supplemental Mn was included in the diet; however, during this time reference fed birds were fed the control diet (70 ppm Mn). After the 21 D depletion phase, the depleted birds were fed experimental diets for a 35 D evaluation period. Yolk and shell Mn content were analyzed at the end of the depletion phase and during the experimental phase on day 5, 10, 15, 25, and 35. During the experimental phase, Mn was replenished in the yolk and shell in all experimental treatments containing supplemental Mn; however, dose and time impacted the rate of replenishment. The yolk tended to be more sensitive to variations in Mn level as increases in Mn inclusion significantly (P < 0.05) increased concentration. These data demonstrate the ability to deplete and replenish Mn, and the use of egg yolk Mn concentration as measurement for determining changes in dietary Mn. At the conclusion of the experiment at 35 D, 60 ppm of Mn hydroxychloride seemed to be adequate in replenishing Mn to the level of the reference.

Long Noncoding RNA Functionality Beyond Sequence: The Jpx Model: Commentary on "Functional Conservation of lncRNA JPX Despite Sequence and Structural Divergence" by Karner et al. (2019)

The mouse lncRNA Jpx has been shown as an essential regulator in X-chromosome inactivation (XCI). Jpx RNA activates Xist expression through its trans-acting ability to evict CTCF from Xist promoter. Karner et al. (2019) reveals the intriguing finding that human JPX and mouse Jpx are functionally conserved although they have low similarity in the primary sequence and the secondary structure. This study provides an excellent model for studying lncRNA's evolution and epigenetic function.

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis.

Targeting RNA with Small Molecules: Identification of Selective, RNA-Binding Small Molecules Occupying Drug-Like Chemical Space

Although the potential value of RNA as a target for new small molecule therapeutics is becoming increasingly credible, the physicochemical properties required for small molecules to selectively bind to RNA remain relatively unexplored. To investigate the druggability of RNAs with small molecules, we have employed affinity mass spectrometry, using the Automated Ligand Identification System (ALIS), to screen 42 RNAs from a variety of RNA classes, each against an array of chemically diverse drug-like small molecules (~50,000 compounds) and functionally annotated tool compounds (~5100 compounds). The set of RNA–small molecule interactions that was generated was compared with that for protein–small molecule interactions, and naïve Bayesian models were constructed to determine the types of specific chemical properties that bias small molecules toward binding to RNA. This set of RNA-selective chemical features was then used to build an RNA-focused set of ~3800 small molecules that demonstrated increased propensity toward binding the RNA target set. In addition, the data provide an overview of the specific physicochemical properties that help to enable binding to potential RNA targets. This work has increased the understanding of the chemical properties that are involved in small molecule binding to RNA, and the methodology used here is generally applicable to RNA-focused drug discovery efforts.

Patients with more comorbidities have better detection but poorer management of chronic diseases

Background

The burden of non-communicable diseases (NCDs) is rising rapidly in middle-income countries (MICs), where NCDs are often undiagnosed, untreated and uncontrolled. How comorbidity impacts diagnosis, treatment, and control of NCDs is an emerging area of research inquiry and have significant clinical implications as highlighted in the recent National Institute for Care Excellence (NICE) guidelines for treating patients suffering from multiple NCDs. This is the first study to examine the association between increasing numbers of comorbidities with being undiagnosed, intreated, and uncontrolled for NCDs, in six large MICs.

Methods

Cross-sectional analysis of WHO SAGE Wave 1 (2007-10), which consisted of adults aged ≥18 years from six populous MICs including, China, Ghana, India, Mexico, Russia and South Africa (overall n = 41, 557).

Results

Higher number of comorbidities was associated with better detection of hypertension, angina and arthritis, and better odds of having treatment for hypertension and angina. However, increasing comorbidity had the opposite effect on being uncontrolled, and was associated with increased odds of uncontrolled hypertension, angina, arthritis, and asthma. Comorbidity with concordant conditions was associated with improved diagnosis and treatment of hypertension and angina. Comorbidity with concordant conditions was not associated with decreased nor increased odds of being uncontrolled for all NCDs.

Conclusions

Patients with more comorbidities have better diagnosis of chronic conditions, but this does not translate into better management and control of these conditions. Improving continuity of care and monitoring treatment are priorities for health systems with ageing populations.

Key messages

Patients with more comorbidities have better diagnosis of chronic conditions. but this does not translate into better management and control of these conditions.

Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans

Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex-specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromosomes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. Ablating Smchd1 results in aberrant expression of these genes, coinciding with altered chromatin states and three-dimensional (3D) topological organization. In a subset of FSHD2 and arhinia patients, we also found dysregulation of clustered PCDH, but not HOX genes. Overall, our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters.

Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3' UTRs to Regulate mRNA Expression

Interaction networks between chromatin complexes and long noncoding RNAs have become a recurrent theme in epigenetic regulation. However, technical limitations have precluded identification of RNA binding motifs for chromatin-associated proteins. Here, we add a denaturation step to UV-crosslink RNA immunoprecipitation (dCLIP) and apply dCLIP to mouse and human chromobox homolog 7 (CBX7), an RNA binding subunit of Polycomb repressive complex 1 (PRC1). In both species, CBX7 predominantly binds 3' UTRs of messenger RNAs. CBX7 binds with a median RNA "footprint" of 171-183 nucleotides, the small size of which facilitates motif identification by bioinformatics. We find four families of consensus RNA motifs in mouse, and independent analysis of human CBX7 dCLIP data identifies similar motifs. Their mutation abolishes CBX7 binding in vitro. Pharmacological intervention with antisense oligonucleotides paradoxically increases CBX7 binding and enhances gene expression. These data support the utility of dCLIP and reveal an unexpected functional interaction between CBX7 and the 3' UTRs of mRNA.

PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments

X-chromosome inactivation triggers fusion of A/B compartments to inactive X (Xi)-specific structures known as S1 and S2 compartments. SMCHD1 then merges S1/S2s to form the Xi super-structure. Here, we ask how S1/S2 compartments form and reveal that Xist RNA drives their formation via recruitment of Polycomb repressive complex 1 (PRC1). Ablating Smchd1 in post-XCI cells unveils S1/S2 structures. Loss of SMCHD1 leads to trapping Xist in the S1 compartment, impairing RNA spreading into S2. On the other hand, depleting Xist, PRC1, or HNRNPK precludes re-emergence of S1/S2 structures, and loss of S1/S2 compartments paradoxically strengthens the partition between Xi megadomains. Finally, Xi-reactivation in post-XCI cells can be enhanced by depleting both SMCHD1 and DNA methylation. We conclude that Xist, PRC1, and SMCHD1 collaborate in an obligatory, sequential manner to partition, fuse, and direct self-association of Xi compartments required for proper spreading of Xist RNA.

The inactive X (Xi)-specific S1/S2 chromosome compartments are merged by SMCHD1, but how the S1/S2 structure is constructed is unclear. The authors find that PRC1 drives the formation of S1/S2s and that the stepwise folding process of the Xi facilitates Xist RNA spreading between Xi compartments.

En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements

The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and its functional motifs remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, 11 smaller XIST segments, including repeats A, D and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted in K562 cells using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and RNA fluorescence in situ hybridization experiments. Clones containing en bloc and promoter deletions that consistently displayed no XIST RNAs and a global up-regulation of X-linked genes confirmed that the deletion of XIST reactivates the inactive X chromosome. Systematic analyses of segmental deletions delineated that exon 5 harboring the non-repeat element is important for X-inactivation maintenance, whereas exons 2, 3 and 4 as well as the other repeats in exon 1 are less important, a different situation from that of mouse Xist. This Cas9-assisted dissection of XIST allowed us to understand the unique functional domains within the human XIST RNA.

Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

During X-inactivation, Xist RNA spreads along an entire chromosome to establish silencing. However, the mechanism and functional RNA elements involved in spreading remain undefined. By performing a comprehensive endogenous Xist deletion screen, we identify Repeat B as crucial for spreading Xist and maintaining Polycomb repressive complexes 1 and 2 (PRC1/PRC2) along the inactive X (Xi). Unexpectedly, spreading of these three factors is inextricably linked. Deleting Repeat B or its direct binding partner, HNRNPK, compromises recruitment of PRC1 and PRC2. In turn, ablating PRC1 or PRC2 impairs Xist spreading. Therefore, Xist and Polycomb complexes require each other to propagate along the Xi, suggesting a positive feedback mechanism between RNA initiator and protein effectors. Perturbing Xist/Polycomb spreading causes failure of de novo Xi silencing, with partial compensatory downregulation of the active X, and also disrupts topological Xi reconfiguration. Thus, Repeat B is a multifunctional element that integrates interdependent Xist/Polycomb spreading, silencing, and changes in chromosome architecture.

Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition

The zinc finger CCCTC-binding protein (CTCF) carries out many functions in the cell. Although previous studies sought to explain CTCF multivalency based on sequence composition of binding sites, few examined how CTCF post-translational modification (PTM) could contribute to function. Here, we performed CTCF mass spectrometry, identified a novel phosphorylation site at Serine 224 (Ser224-P), and demonstrate that phosphorylation is carried out by Polo-like kinase 1 (PLK1). CTCF Ser224-P is chromatin-associated, mapping to at least a subset of known CTCF sites. CTCF Ser224-P accumulates during the G2/M transition of the cell cycle and is enriched at pericentric regions. The phospho-obviation mutant, S224A, appeared normal. However, the phospho-mimic mutant, S224E, is detrimental to mouse embryonic stem cell colonies. While ploidy and chromatin architecture appear unaffected, S224E mutants differentially express hundreds of genes, including p53 and p21. We have thus identified a new CTCF PTM and provided evidence of biological function.

Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome

The noncoding RNA Xist recruits silencing factors to the inactive X chromosome (Xi) and facilitates re-organization of Xi structure. Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion triggers a gain of accessibility of selective chromatin regions that is regulated by BRG1, an ATPase subunit of the SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits nucleosome remodeling and ATPase activities of BRG1, while in cell culture Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, starting from pre-existing BRG1 sites that are free of Xist. BRG1 re-association correlates with cohesin binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi “superloops.” Thus, Xist binding inhibits BRG1’s nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi.

Multiple Histone Methyl-Lysine Readers Ensure Robust Development and Germline Immortality in Caenorhabditis elegans

Chromatin modifications, including methylation of histone H3 at lysine 27 (H3K27me) by the Polycomb group proteins, play a broadly conserved role in the maintenance of cell fate. Diverse chromatin organization modifier (chromo) domain proteins act as "readers" of histone methylation states. However, understanding the functional relationships among chromo domains and their roles in the inheritance of gene expression patterns remains challenging. Here, we identify two chromo-domain proteins, CEC-1 and CEC-6, as potential readers of H3K27me in Caenorhabditis elegans, where they have divergent expression patterns and contribute to distinct phenotypes. Both cec-1 and cec-6 genetically interact with another chromo-domain gene, cec-3, a reader of H3K9 methylation. Combined loss of cec-1 and cec-3 leads to developmental defects in the adult that result in decreased fitness. Furthermore, loss of cec-6 and cec-3 surprisingly leads to a progressive loss of fertility across generations, a "mortal germline" phenotype. Our results provide evidence of functional compensation between H3K27me and H3K9me heterochromatin pathways, and show that histone methylation readers contribute to both somatic development and transgenerational fitness.

Evaluation of different dietary alterations in their ability to mitigate the incidence and severity of woody breast and white striping in commercial male broilers

The following study was conducted to define how multiple nutritional strategies affect broiler performance, meat yield, and the presence and severity of white striping (WS) and woody breast (WB) in high-yielding broilers. Relative to a commercial set of reference broiler diets (Commercial reference diet; Trt 1) that were fed in a 4-phase program, the following nutritional strategies were investigated: increasing the ratio of digestible arginine: digestible lysine (dArg: dLys ranged from 113 to 126; Trt 2), supplementing Trt 1 with 94.4 mg vitamin C/kg feed (Trt 3), doubling the vitamin pack inclusion rate (Trt 4), reducing the digestible amino acid density (dAA) of only the grower phase by 15% and feeding the same Trt 1 starter, finisher, and withdraw diets (Trt 5), and combining the 4 strategies just mentioned (Trt 6). There was no difference in performance at the end of the starter phase (P = 0.066); however, at the end of the grower and finisher phases, feeding lower dAA grower diets suppressed BW (Trts 5 and 6; P < 0.001) and increased FCR. Differences in performance amongst all treatments disappeared at day 49 (P = 0.220). No differences were observed in average breast weight (P = 0.188); however, breast yield (as a % of live weight) was greatest for Trt 1 and least for Trt 6 (P = 0.041). The WB score dropped from 1.83 in Trt 1 to 1.49, 1.27, 1.74, 1.53, and 1.43 in treatments 2 to 6, respectively (P = 0.018). These changes were the result of a shift in WB score, where the WB class that contained scores of 2 and 3 shifted from 61.3% in Trt 1 to 49.3, 35.9, 60.0, 50.8, and 38.7 in treatments 2 to 6, respectively. Given the FCR, breast weight data and the fact that high WB scores result in a devaluation of breast meat, feeding a higher ratio of dArg: dLys, higher vitamin C, or lower dAA in the grower phase results in better breast meat quality and value.

Impact of a multicarbohydrase containing α-galactosidase and xylanase on ileal digestible energy, crude protein digestibility, and ileal amino acid digestibility in broiler chickens

Exogenous enzymatic supplementation of poultry feeds, including α-galactosidase and xylanase, has been shown to increase metabolically available energy, although little information has been published on the impact on amino acid digestibility. An experiment was conducted to investigate a multicarbohydrase containing α-galactosidase and xylanase on amino acid digestibility, ileal digestible energy (IDE), and CP in male broiler chicks. The experiment was a 2 × 2 (diet × enzyme) factorial arrangement with 15 replicates of 8 male broilers per replicate raised for 21 d in a battery setting. The 2 dietary treatments included a positive control (PC) and a negative control (NC) diet formulated to contain 2.5% less calculated AME and digestible amino acids. Each of these diets was fed with and without enzyme. Broilers were fed a starter diet from 0-14 d (crumble) and a grower from 14-21 d (pellet). Birds were sampled on day 21 to determine ileal amino acid digestibility, IDE, and CP digestibility. Titanium dioxide (TiO2) was used as an indigestible marker for the determination of digestibility coefficients. Total ileal amino acid digestibility was increased (P = 0.008) by 3.80% with the inclusion of enzyme. Methionine and lysine digestibility was improved (P < 0.05) with the inclusion of enzyme by 3.37% and 2.61%, respectively. Enzyme inclusion increased (P = 0.001) cysteine digestibility by 9.3%. Diet-influenced ileal amino acid digestibility with tryptophan, threonine, isoleucine, and valine digestibility being increased (P < 0.05) in the PC when compared to the NC. IDE was decreased (P = 0.037) in broilers fed the NC diet by 100 kcal/kg feed when compared to broilers fed the PC diet. Enzyme inclusion increased (P = 0.047) IDE value by 90 kcal/kg. Crude protein digestibility was not influenced by diet; however, similar improvements in CP digestibility with enzyme inclusion were observed as with energy. These data support the benefits of a multicarbohydrase containing α-galactosidase and xylanase inclusion to improve nutrient and ileal amino acid digestibility across multiple dietary nutrient profiles.

Correction to: Measuring and understanding adherence in a home-based exercise intervention during chemotherapy for early breast cancer

In the original publication, the sixth author name was published incorrectly as A. Wood. The correct author name should read as W. A. Wood.

Loss of H3K27me3 Imprinting in Somatic Cell Nuclear Transfer Embryos Disrupts Post-Implantation Development

Animal cloning can be achieved through somatic cell nuclear transfer (SCNT), although the live birth rate is relatively low. Recent studies have identified H3K9me3 in donor cells and abnormal Xist activation as epigenetic barriers that impede SCNT. Here we overcome these barriers using a combination of Xist knockout donor cells and overexpression of Kdm4 to achieve more than 20% efficiency of mouse SCNT. However, post-implantation defects and abnormal placentas were still observed, indicating that additional epigenetic barriers impede SCNT cloning. Comparative DNA methylome analysis of IVF and SCNT blastocysts identified abnormally methylated regions in SCNT embryos despite successful global reprogramming of the methylome. Strikingly, allelic transcriptomic and ChIP-seq analyses of pre-implantation SCNT embryos revealed complete loss of H3K27me3 imprinting, which may account for the postnatal developmental defects observed in SCNT embryos. Together, these results provide an efficient method for mouse cloning while paving the way for further improving SCNT efficiency.

Efficacy of β-mannanase on broiler growth performance and energy utilization in the presence of increasing dietary galactomannan

An experiment was conducted to investigate the impact of β-mannanase inclusion on growth performance, viscosity, and energy utilization in broilers fed diets varying in galactomannan (GM) concentrations. Treatments were arranged as a 3 (GM concentration) × 3 (β-mannanase inclusion) factorial randomized complete block design with 12 replicates of 29 male broilers per replicate for a 42-d experiment. Efforts were made to reduce the amount of soybean meal, and thus GM, in the basal diet with guar gum included at 0, 0.21, or 0.42% to achieve a GM supplementation of 1,500 and 3,000 ppm, respectively. Beta-mannanase was included at 0, 200, or 400 g/ton. Broilers were fed a starter (d 0 to 14), grower (d 15 to 28), and finisher diets (d 29 to 42). Growth performance was monitored and ileal contents collected on d 14, 28, and 42 to determine ileal digestible energy (IDE) and intestinal viscosity. Increasing levels of GM negatively (P < 0.05) influenced body weight (BW) following the starter and grower periods and increased (P < 0.01) mortality corrected feed conversion ratio (FCR) throughout the study. Reduced growth performance was associated with increased (P < 0.05) intestinal viscosity and decreased (P < 0.05) IDE when GM inclusion was increased. Inclusion of β-mannanase in diets containing supplemental GM on d 28, increased average BW to levels similar to diets without supplemental GM. Improvements in FCR were also observed with β-mannanase inclusion in diets containing supplemental GM. Ileal digestible energy was increased (P < 0.05) with the addition of β-mannanase on d 28 of age. Multiple interactions in growth performance, intestinal viscosity, and IDE were associated with β-mannanase administration. In conclusion, β-mannanase improved IDE, reduced intestinal viscosity, and improved growth performance; however, the observed benefit was dependent upon dietary GM concentration.

Effects of direct-fed microorganisms and enzyme blend co-administration on intestinal bacteria in broilers fed diets with or without antibiotics

Direct-fed microorganisms (DFM) and exogenous enzymes have been demonstrated to improve growth performance in poultry and are potentially important alternatives to antibiotic growth promoters (AGP). We investigated the administration of a feed additive composed of a DFM product containing spores of 3 Bacillus amyloliquefaciens strains and an enzyme blend of endo-xylanase, α-amylase, and serine-protease in diets with or without sub-therapeutic antibiotics in broiler chickens over a 42-d growth period. Evaluation of growth performance determined feed efficiency of broiler chickens which were administered the feed additive was comparable to those fed a diet containing AGPs. Characterization of the gastrointestinal microbiota using culture-dependent methods determined administration of the feed additive increased counts of total Lactic Acid Bacteria (LAB) relative to a negative control and reduced Clostridium perfringens to levels similar to antibiotic administration. Additionally, greater counts of total LAB were observed to be significantly associated with reduced feed conversion ratio, whereas greater counts of C. perfringens were observed to be significantly associated with increased feed conversion ratio. Our results suggest the co-administration of DFMs and exogenous enzymes may be an important component of antibiotic free poultry production programs and LAB and C. perfringens may be important targets in the development of alternatives to AGPs in poultry production.

Changes in immune and metabolic gut response in broilers fed β-mannanase in β-mannan-containing diets

β-galactomannans found in soy-based broiler feed are known to cause physiological effects that are hypothesized to be related to gut inflammation. Previous studies have shown that the incorporation of β-mannanase in the diet or as a supplement results in improvements to certain performance parameters related to gut health and feed conversion. Using kinome analysis, we characterized the mechanism of β-galactomannan activity and supplementation with β-mannanase on the gut of commercial broilers to understand the mode of action. Two doses of β-mannanase (200 and 400 g/ton of feed) with and without inclusion of additional β-galactomannan (3,000 ppm) were tested at 3 time points (d 14, d 28, and d 42 post hatch). Broilers were fed starter (d 0 to 14), grower (d 15 to 28), and finisher diets (d 29 to 42). Jejuna were collected from birds from each treatment condition and time point. Cluster analysis of the kinome data showed that birds clustered first by age, then predominantly by whether β-mannanase had been included in the diet. Biological pathway analysis showed that the inclusion of additional β-galactomannan into the diet resulted in increased signaling related to immune response, relative to our normal control diet (with reduced soybean meal). The addition of β-mannanase to the enhanced β-galactomannan diet eliminated the majority of this immune-related signaling, indicating that the feed-induced immune response within the jejuna had been eliminated by the addition of β-mannanase. We also saw changes in specific metabolic and gut function pathways in birds fed β-mannanase. These observed changes in β-mannanase-fed birds are likely the mechanism for the enhanced performance and feed conversion observed in birds given β-mannanase in their diets.

Measuring and understanding adherence in a home-based exercise intervention during chemotherapy for early breast cancer

PURPOSE

Ensuring and measuring adherence to prescribed exercise regimens are fundamental challenges in intervention studies to promote exercise in adults with cancer. This study reports exercise adherence in women who were asked to walk 150 min/week throughout chemotherapy treatment for early breast cancer. Participants were asked to wear a Fitbit^TM throughout their waking hours, and Fitbit steps were uploaded directly into study computers.

METHODS

Descriptive statistics are reported, and both unadjusted and multivariable linear regression models were used to assess associations between participant characteristics, breast cancer diagnosis, treatment, chemotherapy toxicities, and patient-reported symptoms with average Fitbit steps/week.

RESULTS

Of 127 women consented to the study, 100 had analyzable Fitbit data (79%); mean age was 48 and 31% were non-white. Mean walking steps were 3956 per day. Nineteen percent were fully adherent with the target of 6686 steps/day and an additional 24% were moderately adherent. In unadjusted analysis, baseline variables associated with fewer Fitbit steps were: non-white race (p = 0.012), high school education or less (p = 0.0005), higher body mass index (p = 0.0024), and never/almost never drinking alcohol (p = 0.0048). Physical activity variables associated with greater Fitbit steps were: pre-chemotherapy history of vigorous physical activity (p = 0.0091) and higher self-reported walking minutes/week (p < 0.001), and higher outcome expectations from exercise (p = 0.014). Higher baseline anxiety (p = 0.03) and higher number of chemotherapy-related symptoms rates "severe/very severe" (p = 0.012) were associated with fewer steps. In multivariable analysis, white race was associated with 12,146 greater Fitbit steps per week (p = 0.004), as was self-reported walking minutes prior to start of chemotherapy (p < 0.0001).

CONCLUSIONS

Inexpensive commercial-grade activity trackers, with data uploaded directly into research computers, enable objective monitoring of home-based exercise interventions in adults diagnosed with cancer. Analysis of the association of walking steps with participant characteristics at baseline and toxicities during chemotherapy can identify reasons for low/non-adherence with prescribed exercise regimens.

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

Master regulatory genes require stable silencing by the polycomb group (PcG) to prevent misexpression during differentiation and development. Some PcG proteins covalently modify histones, which contributes to heritable repression. The role for other effects on chromatin structure is less understood. We characterized the organization of PcG target genes in ESCs and neural progenitors using 5C and super-resolution microscopy. The genomic loci of repressed PcG targets formed discrete, small (20-140 Kb) domains of tight interaction that corresponded to locations bound by canonical polycomb repressive complex 1 (PRC1). These domains changed during differentiation as PRC1 binding changed. Their formation depended upon the Polyhomeotic component of canonical PRC1 and occurred independently of PRC1-catalyzed ubiquitylation. PRC1 domains differ from topologically associating domains in size and boundary characteristics. These domains have the potential to play a key role in transmitting epigenetic silencing of PcG targets by linking PRC1 to formation of a repressive higher-order structure.