University at Buffalo

About: University at Buffalo is a education organization based out in Buffalo, New York, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 33773 authors who have published 63840 publications receiving 2278954 citations. The organization is also known as: UB & State University of New York at Buffalo.

Chromatin accessibility: a window into the genome

Abstract: Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.

Nontypable Haemophilus influenzae: A Review of Clinical Aspects, Surface Antigens, and the Human Immune Response to Infection

Abstract: Nontypable Haemophilus influenzae has now become well established as an important pathogen in both adults and children. Recent work has identified clear distinctions between nontypable and type b strains of H. influenzae. These organisms affect different patient populations, cause different infections, present different surface antigens to the host, and are genetically different. The commonest clinical manifestation of infection due to nontypable H. influenzae in adults is lower respiratory tract infection, particularly in the elderly and in those with chronic bronchitis. The bacterium is a frequent cause of acute otitis media in children. The surface of nontypable H. influenzae is composed of outer-membrane proteins and lipooligosaccharide, and both of these demonstrate substantial antigenic heterogeneity, which can be used to serotype isolates. Some respiratory tract isolates are fimbriated, but the role of fimbriae in pathogenesis is unclear. Antibodies to outer-membrane proteins and lipooligosaccharide are present in human serum. Investigation of human immunity to infection is focusing on identification of those antigens to which protective antibody is directed.

Removal of the mechanoprotective influence of the cytoskeleton reveals PIEZO1 is gated by bilayer tension

Abstract: Mechanosensitive ion channels are force-transducing enzymes that couple mechanical stimuli to ion flux. Understanding the gating mechanism of mechanosensitive channels is challenging because the stimulus seen by the channel reflects forces shared between the membrane, cytoskeleton and extracellular matrix. Here we examine whether the mechanosensitive channel PIEZO1 is activated by force-transmission through the bilayer. To achieve this, we generate HEK293 cell membrane blebs largely free of cytoskeleton. Using the bacterial channel MscL, we calibrate the bilayer tension demonstrating that activation of MscL in blebs is identical to that in reconstituted bilayers. Utilizing a novel PIEZO1–GFP fusion, we then show PIEZO1 is activated by bilayer tension in bleb membranes, gating at lower pressures indicative of removal of the cortical cytoskeleton and the mechanoprotection it provides. Thus, PIEZO1 channels must sense force directly transmitted through the bilayer.

Risk factors for and management of cognitive dysfunction in multiple sclerosis

Abstract: Cognitive impairment is common in multiple sclerosis (MS), especially when assessed by neuropsychological tests that emphasize mental processing speed, episodic memory, and some aspects of executive function. In this Review, we question why some MS patients develop severe impairment in cognitive abilities, while cognitive ability remains intact in others. We find that the heterogeneity in neuropsychological presentation among patients with MS reflects the influence of many factors, including genetics, sex, intelligence, disease course, comorbid neuropsychiatric illness, and health behaviors. Neuropsychological deficits are also robustly correlated with brain MRI metrics. Male patients with early evidence of cerebral gray matter atrophy are most prone to impairment, whereas high premorbid intelligence improves the neuropsychological prognosis. Routine evaluation of cognition is useful for helping patients to navigate problems related to activities of daily living and work disability and, if reliable methods are employed, cognitive decline can be detected and included among the many clinical signs of disease progression or treatment failure. Pharmacological treatments for neuropsychological impairment are on the horizon, although presently no firm medical indications exist for the condition.

Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach

Abstract: An energy decomposition scheme based on the block-localized wave function (BLW) method is proposed. The key of this scheme is the definition and the full optimization of the diabatic state wave function, where the charge transfer among interacting molecules is deactivated. The present energy decomposition (ED), BLW-ED, method is similar to the Morokuma decomposition scheme in definition of the energy terms, but differs in implementation and the computational algorithm. In addition, in the BLW-ED approach, the basis set superposition error is fully taken into account. The application of this scheme to the water dimer and the lithium cation–water clusters reveals that there is minimal charge transfer effect in hydrogen-bonded complexes. At the HF/aug-cc-PVTZ level, the electrostatic, polarization, and charge-transfer effects contribute 65%, 24%, and 11%, respectively, to the total bonding energy (−3.84 kcal/mol) in the water dimer. On the other hand, charge transfer effects are shown to be significant in Lewis acid–base complexes such as H3NSO3 and H3NBH3. In this work, the effect of basis sets used on the energy decomposition analysis is addressed and the results manifest that the present energy decomposition scheme is stable with a modest size of basis functions.