Pressure and transit in the small intestine. The concept of propulsion and peripheral resistance in the alimentary canal

Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains

Chromosomal organization, scaling from the 147-base pair (bp) nucleosome to megabase-ranging domains encompassing multiple transcriptional units, including heritability loci for psychiatric traits, remains largely unexplored in the human brain. In this study, we constructed promoter- and enhancer-enriched nucleosomal histone modification landscapes for adult prefrontal cortex from H3-lysine 27 acetylation and H3-lysine 4 trimethylation profiles, generated from 388 controls and 351 individuals diagnosed with schizophrenia (SCZ) or bipolar disorder (BD) (n = 739). We mapped thousands of cis-regulatory domains (CRDs), revealing fine-grained, 104-106-bp chromosomal organization, firmly integrated into Hi-C topologically associating domain stratification by open/repressive chromosomal environments and nuclear topography. Large clusters of hyper-acetylated CRDs were enriched for SCZ heritability, with prominent representation of regulatory sequences governing fetal development and glutamatergic neuron signaling. Therefore, SCZ and BD brains show coordinated dysregulation of risk-associated regulatory sequences assembled into kilobase- to megabase-scaling chromosomal domains.

BRD4 orchestrates genome folding to promote neural crest differentiation

Higher-order chromatin structure regulates gene expression, and mutations in proteins mediating genome folding underlie developmental disorders known as cohesinopathies. However, the relationship between three-dimensional genome organization and embryonic development remains unclear. Here we define a role for bromodomain-containing protein 4 (BRD4) in genome folding, and leverage it to understand the importance of genome folding in neural crest progenitor differentiation. Brd4 deletion in neural crest results in cohesinopathy-like phenotypes. BRD4 interacts with NIPBL, a cohesin agonist, and BRD4 depletion or loss of the BRD4-NIPBL interaction reduces NIPBL occupancy, suggesting that BRD4 stabilizes NIPBL on chromatin. Chromatin interaction mapping and imaging experiments demonstrate that BRD4 depletion results in compromised genome folding and loop extrusion. Finally, mutation of individual BRD4 amino acids that mediate an interaction with NIPBL impedes neural crest differentiation into smooth muscle. Remarkably, loss of WAPL, a cohesin antagonist, rescues attenuated smooth muscle differentiation resulting from BRD4 loss. Collectively, our data reveal that BRD4 choreographs genome folding and illustrates the relevance of balancing cohesin activity for progenitor differentiation.

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

In contrast to single-cell approaches for measuring gene expression and DNA accessibility, single-cell methods for analyzing histone modifications are limited by low sensitivity and throughput. Here, we combine the CUT&Tag technology, developed to measure bulk histone modifications, with droplet-based single-cell library preparation to produce high-quality single-cell data on chromatin modifications. We apply single-cell CUT&Tag (scCUT&Tag) to tens of thousands of cells of the mouse central nervous system and probe histone modifications characteristic of active promoters, enhancers and gene bodies (H3K4me3, H3K27ac and H3K36me3) and inactive regions (H3K27me3). These scCUT&Tag profiles were sufficient to determine cell identity and deconvolute regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter-enhancer connectivity. We also used scCUT&Tag to investigate the single-cell chromatin occupancy of transcription factor OLIG2 and the cohesin complex component RAD21. Our results indicate that analysis of histone modifications and transcription factor occupancy at single-cell resolution provides unique insights into epigenomic landscapes in the central nervous system.

DeepC: predicting 3D genome folding using megabase-scale transfer learning

Predicting the impact of noncoding genetic variation requires interpreting it in the context of three-dimensional genome architecture. We have developed deepC, a transfer-learning-based deep neural network that accurately predicts genome folding from megabase-scale DNA sequence. DeepC predicts domain boundaries at high resolution, learns the sequence determinants of genome folding and predicts the impact of both large-scale structural and single base-pair variations.

Neurally mediated propagating discrete clustered contractions superimposed on myogenic ripples in ex vivo segments of human ileum

Narrow muscle strips have been extensively used to study intestinal contractility. Larger specimens from laboratory animals have provided detailed understanding of mechanisms that underlie patterned intestinal motility. Despite progress in animal tissue, investigations of motor patterns in large, intact specimens of human gut ex vivo have been sparse. In this study, we tested whether neurally dependent motor patterns could be detected in isolated specimens of intact human ileum. Specimens (n = 14; 7-30 cm long) of terminal ileum were obtained with prior informed consent from patients undergoing colonic surgery for removal of carcinomas. Preparations were set up in an organ bath with an array of force transducers, a fiberoptic manometry catheter, and a video camera. Spontaneous and distension-evoked motor activity was recorded, and the effects of lidocaine, which inhibits neural activity, were studied. Myogenic contractions (ripples) occurred in all preparations (6.17 ± 0.36/min). They were of low amplitude and formed complex patterns by colliding and propagating in both directions along the specimen at anterograde velocities of 4.1 ± 0.3 mm/s and retrogradely at 4.9 ± 0.6 mm/s. In five specimens, larger amplitude clusters of contractions were seen (discrete clustered contractions), which propagated aborally at 1.05 ± 0.13 mm/s and orally at 1.07 ± 0.09 mm/s. These consisted of two to eight phasic contractions that aligned with ripples. These motor patterns were abolished by addition of lidocaine (0.3 mM). The ripples continued unchanged in the presence of this neural blocking agent. These results demonstrate that both myogenic and neurogenic motor patterns can be studied in isolated specimens of human small intestine.

Evaluation on the responses of succinate dehydrogenase, isocitrate dehydrogenase, malate dehydrogenase and glucose-6-phosphate dehydrogenase to acid shock generated acid tolerance in Escherichia coli

Background:

Escherichia coli have an optimum pH range of 6-7 for growth and survival that's why, called neutrophiles. The ΔpH across the cytoplasmic membrane is linked to cellular bioenergetics and metabolism of the body which is the major supplier of the proton motive force, so homeostasis of cellular pH is essential. When challenged by low pH, protons enter the cytoplasm; as a result, mechanisms are required to alleviate the effects of lowered cytoplasmic pH.

Materials and Methods:

The activities of Succinate dehydrogenase, isocitrate dehydrogenase, malate dehydrogenase and glucose-6-phosphate dehydrogenase in acid shocked cells of E. coli DH5 α and E. coli W3110 subjected to pH 3, 4, and 5 by two types of acidification, like external (using 0.1 N HCl), external along with the monensin (1 μM) and cytoplasmic acidification using the sodium benzoate as an acid permeant (20 mM) which is coupled to the electron transport chain by the reducing power, as yet another system possessed by E. coli as an armor against harsh acidic environments.

Result:

Results showed that an exposure to acidic environment (pH 3, 4 and 5) for a short period of time increased the activities of these dehydrogenases in all types of acidification except cytoplasmic acidification, which shows that higher recycling of reducing power results in pumping out of protons from the cytoplasm through the electron transport chain complexes, thereby restoring the cytoplasmic pH of the bacteria in the range of 7.4-7.8.

Conclusion:

Study indicates that acid shocked E. coli for a period of 2 h can survive for a sustained period.

Preliminary mechanical characterization of the small bowel for in vivo robotic mobility

In this work we present test methods, devices, and preliminary results for the mechanical characterization of the small bowel for intra luminal robotic mobility. Both active and passive forces that affect mobility are investigated. Four investigative devices and testing methods to characterize the active and passive forces are presented in this work: (1) a novel manometer and a force sensor array that measure force per cm of axial length generated by the migrating motor complex, (2) a biaxial test apparatus and method for characterizing the biomechanical properties of the duodenum, jejunum, and ileum, (3) a novel in vitro device and protocol designed to measure the energy required to overcome the self-adhesivity of the mucosa, and (4) a novel tribometer that measures the in vivo coefficient of friction between the mucus membrane and the robot surface. The four devices are tested on a single porcine model to validate the approach and protocols. Mean force readings per cm of axial length of intestine that occurred over a 15 min interval in vivo were 1.34 ± 0.14 and 1.18 ± 0.22 N cm(-1) in the middle and distal regions, respectively. Based on the biaxial stress/stretch tests, the tissue behaves anisotropically with the circumferential direction being more compliant than the axial direction. The mean work per unit area for mucoseparation of the small bowel is 0.08 ± 0.03 mJ cm(-2). The total energy to overcome mucoadhesion over the entire length of the porcine small bowel is approximately 0.55 J. The mean in vivo coefficient of friction (COF) of a curved 6.97 cm(2) polycarbonate sled on live mucosa traveling at 1 mm s(-1) is 0.016 ± 0.002. This is slightly lower than the COF on excised tissue, given the same input parameters. We have initiated a comprehensive program and suite of test devices and protocols for mechanically characterizing the small bowel for in vivo mobility. Results show that each of the four protocols and associated test devices has successfully gathered preliminary data to confirm the validity of our test approach.

Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli

The decameric inducible lysine decarboxylase (LdcI) from Escherichia coli has been crystallized in space groups C2 and C222(1); the Ta6Br12(2+) cluster was used to derivatize the C2 crystals. The method of single isomorphous replacement with anomalous scattering (SIRAS) as implemented in SHELXD was used to solve the Ta6Br12(2+)-derivatized structure to 5 A resolution. Many of the Ta6Br12(2+)-binding sites had twofold and fivefold noncrystallographic symmetry. Taking advantage of this feature, phase modification was performed in DM. The electron-density map of LdcI displays many features in agreement with the low-resolution negative-stain electron-density map [Snider et al. (2006), J. Biol. Chem. 281, 1532-1546].

Sodium regulates Escherichia coli acid resistance, and influences GadX- and GadW-dependent activation of gadE

Enteric bacteria must survive the extreme acid of the stomach (pH 2 or less) before entering the intestine where they can colonize and cause disease. Escherichia coli is superior to most other Enterobacteriaceae in surviving pH 2 acid stress because it has four known acid-resistance systems, the most studied of which depends on glutamic acid. Glutamate-dependent acid resistance requires glutamate decarboxylase isozymes GadA and GadB, as well as a glutamate/gamma-aminobutyric acid antiporter encoded by gadC. The regulatory protein GadE is the essential activator of the gadA and gadBC genes. The transcription of gadE, however, is controlled by numerous proteins. Two of these proteins, GadX and GadW, are AraC-family regulators whose sensory input signals are not known. Since Na(+) and K(+) play important roles in pH homeostasis, the contribution of these ions toward the regulation of this acid-resistance system was examined. The results indicated that a decrease in Na(+), but not K(+), concentration coincided with diminished acid resistance, and decreased expression of the gadE, gadA and gadBC genes. However, Na(+)-dependent regulation of these genes dissipated in the absence of GadX and GadW. Since Na(+) levels did not regulate gadX or gadW transcription, it is proposed that GadX and GadW sense intracellular Na(+) concentration or some consequence of altered Na(+) levels.