Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders

Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.

Faraday tilting of water-immersed granular beds

Under low-frequency vertical vibration, a system of fine grains within a fluid is observed to tilt or to form piles, an effect studied by Faraday for grains in air. Here, we investigate the physical mechanisms behind Faraday tilting in a bed of vertically vibrated bronze spheres fully immersed in water. Experimental observations of surface tilting and bulk convection are compared with the results of molecular dynamics simulations in which the water is treated as an incompressible fluid. Our simulations reproduce the main features observed experimentally. Most tilt construction is shown to be due to horizontal fluid flow within the bed, principally occurring when the gap between the bed and the supporting platform is close to a maximum. Tilt destruction occurs by granular surface flow and in the bulk of the bed at times during each vibratory cycle close to and just later than bed impact. Destruction becomes more important for higher values of frequency and vibration amplitude, leading to lower tilt angles, partial tilting, or the symmetric domed geometry of Muchowski flow.

Generalized lattice Boltzmann algorithm for the flow of a nematic liquid crystal with variable order parameter

A lattice Boltzmann (LB) scheme is described, which recovers the equations developed by Qian-Sheng for the hydrodynamics of a nematic liquid crystal with a tensor order parameter. The standard mesoscopic LB scalar density is generalized to a tensor quantity and the macroscopic momentum, density, and tensor order parameter are recovered from appropriate moments of this mesoscopic density. A single lattice Boltzmann equation is used with a direction dependent Bhatnagar, Gross, and Krook (BGK) collision term, with additional forcing terms to recover the antisymmetric terms in the stress tensor. A Chapman-Enskog analysis is presented, which demonstrates that the Qian-Sheng scheme is recovered, provided a lattice with sixth-order isotropy is used. The method is validated against analytical results for a number of cases including flow alignment of the order tensor and the Miesowicz viscosities in the presence of an aligning magnetic field. The algorithm accurately recovers the predicted changes in the order parameter in the presence of aligning flow, and magnetic, fields. Preliminary results are given for an extension of the method to model the interface between isotropic and nematic fluids.

Lattice Boltzmann equation hydrodynamics

By inserting position and time dependent "source" or "forcing" terms into the microscopic evolution equation of a lattice Boltzmann fluid and treating the generalized scheme within the usual Chapman-Enskog methodology, we show that the emergent dynamics of the lattice fluid may be usefully transformed. Our method of adjustment is demonstrated by implementing the cylindrical polar coordinate form of the continuity and momentum equations on a rectangular lattice and generating results for pipe flow. With straightforward systematic adjustment of the simulation, our approach produces results in excellent agreement with theory.

Olfactory deficits in schizophrenia are not a function of task complexity

The purpose of the current study was to determine if olfactory identification deficits in patients with schizophrenia were related to task complexity. Given that we had previously reported that male patients with schizophrenia are the most impaired on olfactory identification tests (the University of Pennsylvania Smell Identification Test, UPSIT), we wished to determine whether a similar deficit would exist for this group on a task of similar format and complexity, the Colour Identification Test (CIT). Sixty-five neuroleptically medicated patients with a DSM-III-R diagnosis of schizophrenia and 30 normal control subjects participated. The dependent measures were scores on the UPSIT and CIT. Overall, patients with schizophrenia had significantly lower USPIT scores than did the normal control subjects whereas no mean difference was observed for colour identification. Male patients with schizophrenia had olfactory identification deficits but performed comparably to all other groups on the CIT. Furthermore, microsmic patients with schizophrenia had CIT scores that did not differ from normal control subjects. Finally, CIT and UPSIT scores were not significantly correlated for the study sample as a whole. The results of this study suggest that the olfactory identification deficits observed in patients with schizophrenia likely reflect abnormalities of brain areas involved in olfactory pathways and are not a function of task complexity.

Olfactory identification ability in anorexia nervosa

OBJECTIVE

The hypothesis tested was that patients with severe eating disorders would demonstrate olfactory identification deficits as a result of zinc deficiency or malnutrition.

METHOD

The University of Pennsylvania Smell Identification Test (UPSIT) was administered to 27 hospitalized female patients with anorexia nervosa and 50 normal control female subjects. For a subgroup of patients, serum zinc levels and body mass indices were obtained at pre- and post-nutritional repletion phases.

RESULTS

UPSIT scores for patients with eating disorders were equivalent to normal control subjects in spite of the fact that the patients were nutritionally compromised as determined by body mass index. Serum zinc levels were not significantly different at pre- and post-nutritional repletion.

CONCLUSIONS

In contrast to patients with schizophrenia, patients with severe eating disorders have intact olfactory function. This finding suggests that transient metabolic or nutritional disturbances alone cannot account for previously reported olfactory deficits.

Olfactory identification ability in pre- and postmenopausal women with schizophrenia

Previously we reported olfactory deficits in young male but not female patients with schizophrenia. In the present report, olfactory identification ability in pre- and postmenopausal women with schizophrenia and normal control subjects was assessed using the University of Pennsylvania Smell Identification Test (UPSIT). Additionally, serum estradiol levels were measured on the same 2 days as smell testing was completed. Olfactory deficits were observed in pre- and postmenopausal women with schizophrenia but were more pronounced in the postmenopausal patients. Regarding estradiol levels, women with schizophrenia had lower estradiol levels than did normal control subjects. The findings of this study indicate that olfactory deficits do exist in women with schizophrenia and may be accentuated by estrogen depletion.

Expression and activity of gamma-glutamyl transpeptidase in the rat epididymis

Following Northern analysis, GGT mRNA was found predominantly within the caput epididymides and kidney. The size of mRNAs for kidney, caput, corpus, and ductus deferens were 2.2, 2.3, 2.2, and 2.3 kb, respectively, whereas cauda showed a doublet of 2.2 and 2.3 kb. GGT transpeptidation and hydrolytic activity within epididymal luminal fluids collected by micropuncture showed caput = corpus greater than cauda and corpus greater than caput greater than cauda, respectively. Caput luminal GGT transpeptidation activity was significantly inhibited by serine-borate and was optimal at pH 8.0. The calculated Km and Vmax values for hydrolysis of GSH by caput luminal GGT were 0.06 microM and 2.19 nmoles/min/microliters luminal fluid at pH 8.5 compared to 0.49 microM and 0.49 nmoles/min/microliters luminal fluid, respectively, at the physiological pH 6.5 of caput fluid. These studies would suggest that the epididymis can control the activity of luminal GGT by pH. Lower Km (0.12 microM) and higher Vmax (1.13 nmoles/min/microliters luminal fluid) values were also calculated when GSSG was used compared to GSH. Results from Triton X-114 partitioning experiments suggest that luminal GGT probably exists in both membrane bound and nonmembrane bound forms. Western blot analysis of proteins within epididymal luminal fluids revealed both subunits of GGT in all epididymal regions studied. However, two lower molecular bands, approximately 22 kDa and 21 kDa, were also observed in cauda fluid. It is suggested that as GGT is transported along the epididymal duct it undergoes degradation, which accounts for its loss of activity in the distal epididymal regions.(ABSTRACT TRUNCATED AT 250 WORDS)