Set-Codes with Small Intersections and Small Discrepancies

We are concerned with the problem of designing large families of subsets over a common labeled ground set that have small pairwise intersections and the property that the maximum discrepancy of the label values within each of the sets is less than or equal to one. Our results, based on transversal designs, factorizations of packings and Latin rectangles, show that by jointly constructing the sets and labeling scheme, one can achieve optimal family sizes for many parameter choices. Probabilistic arguments akin to those used for pseudorandom generators lead to significantly suboptimal results when compared to the proposed combinatorial methods. The design problem considered is motivated by applications in molecular data storage and theoretical computer science

Bestrophin 1 is indispensable for volume regulation in human retinal pigment epithelium cells

In response to cell swelling, volume-regulated anion channels (VRACs) participate in a process known as regulatory volume decrease (RVD). Only recently, first insight into the molecular identity of mammalian VRACs was obtained by the discovery of the leucine-rich repeats containing 8A (LRRC8A) gene. Here, we show that bestrophin 1 (BEST1) but not LRRC8A is crucial for volume regulation in human retinal pigment epithelium (RPE) cells. Whole-cell patch-clamp recordings in RPE derived from human-induced pluripotent stem cells (hiPSC) exhibit an outwardly rectifying chloride current with characteristic functional properties of VRACs. This current is severely reduced in hiPSC-RPE cells derived from macular dystrophy patients with pathologic BEST1 mutations. Disruption of the orthologous mouse gene (Best1−/−) does not result in obvious retinal pathology but leads to a severe subfertility phenotype in agreement with minor endogenous expression of Best1 in murine RPE but highly abundant expression in mouse testis. Sperm from Best1−/− mice showed reduced motility and abnormal sperm morphology, indicating an inability in RVD. Together, our data suggest that the molecular identity of VRACs is more complex—that is, instead of a single ubiquitous channel, VRACs could be formed by cell type- or tissue-specific subunit composition. Our findings provide the basis to further examine VRAC diversity in normal and diseased cell physiology, which is key to exploring novel therapeutic approaches in VRAC-associated pathologies

Covariation Among Vowel Height Effects on Acoustic Measures

Covariation among vowel height effects on vowel intrinsic fundamental frequency (IF0), voice onset time (VOT), and voiceless interval duration (VID) is analyzed to assess the plausibility of a common physiological mechanism underlying variation in these measures. Phrases spoken by 20 young adults, containing words composed of initial voiceless stops or /s/ and high or low vowels, were produced in habitual and voluntarily increased F0 conditions. High vowels were associated with increased IF0 and longer VIDs. VOT and VID exhibited significant covariation with IF0 only for males at habitua

Bestrophin1: A Gene that Causes Many Diseases

Bestrophinopathies are a group of clinically distinct inherited retinal dystrophies that lead to the gradual loss of vision in and around the macular area. There are no treatments for patients suffering from bestrophinopathies, and no measures can be taken to prevent visual deterioration in those who have inherited disease-causing mutations. Bestrophinopathies are caused by mutations in the Bestrophin1 gene (BEST1), a protein found exclusively in the retinal pigment epithelial (RPE) cells of the eye. Mutations in BEST1 affect the function of the RPE leading to the death of overlying retinal cells and subsequent vision loss. The pathogenic mechanisms arising from BEST1 mutations are still not fully understood, and it is not clear how mutations in BEST1 lead to diseases with distinct clinical features. This chapter discusses BEST1, the use of model systems to investigate the effects of mutations and the potential to investigate individual bestrophinopathies using induced pluripotent stem cells

Pitch strength of normal and dysphonic voices

Two sounds with the same pitch may vary from each other based on saliency of their pitch sensation. This perceptual attribute is called “pitch strength.” The study of voice pitch strength may be important in quantifying of normal and pathological qualities. The present study investigated how pitch strength varies across normal and dysphonic voices. A set of voices (vowel /a/) selected from the Kay Elemetrics Disordered Voice Database served as the stimuli. These stimuli demonstrated a wide range of voice quality. Ten listeners judged the pitch strength of these stimuli in an anchored magnitude estimation task. On a given trial, listeners heard three different stimuli. The first stimulus represented very low pitch strength (wide-band noise), the second stimulus consisted of the target voice and the third stimulus represented very high pitch strength (pure tone). Listeners estimated pitch strength of the target voice by positioning a continuous slider labeled with values between 0 and 1, reflecting the two anchor stimuli. Results revealed that listeners can judge pitch strength reliably in dysphonic voices. Moderate to high correlations with perceptual judgments of voice quality suggest that pitch strength may contribute to voice quality judgments

Preserved respiratory chain capacity and physiology in mice with profoundly reduced levels of mitochondrial respirasomes

The mammalian respiratory chain complexes I, III 2, and IV (CI, CIII 2, and CIV) are critical for cellular bioenergetics and form a stable assembly, the respirasome (CI-CIII 2-CIV), that is biochemically and structurally well documented. The role of the respirasome in bioenergetics and the regulation of metabolism is subject to intense debate and is difficult to study because the individual respiratory chain complexes coexist together with high levels of respirasomes. To critically investigate the in vivo role of the respirasome, we generated homozygous knockin mice that have normal levels of respiratory chain complexes but profoundly decreased levels of respirasomes. Surprisingly, the mutant mice are healthy, with preserved respiratory chain capacity and normal exercise performance. Our findings show that high levels of respirasomes are dispensable for maintaining bioenergetics and physiology in mice but raise questions about their alternate functions, such as those relating to the regulation of protein stability and prevention of age-associated protein aggregation

Addressing the inter-individual variation in response to consumption of plant food bioactives : Towards a better understanding of their role in healthy aging and cardiometabolic risk reduction

Bioactive compounds in plant-based foods have health properties that contribute to the prevention of age-related chronic diseases, particularly cardiometabolic disorders. Conclusive proof and understanding of these benefits in humans is essential in order to provide effective dietary recommendations but, so far, the evidence obtained from human intervention trials is limited and contradictory. This is partly due to differences between individuals in the absorption, distribution, metabolism and excretion of bioactive compounds, as well as to heterogeneity in their biological response regarding cardiometabolic health outcomes. Identifying the main factors underlying inter-individual differences, as well as developing new and innovative methodologies to account for such variability constitute an overarching goal to ultimately optimize the beneficial health effects of plant food bioactives for each and every one of us. In this respect, this position paper from the COST Action FA1403-POSITIVe examines the main factors likely to affect the individual responses to consumption of plant food bioactives and presents perspectives for assessment and consideration of inter-individual variability.Peer reviewe

Global Network Alignment Using Multiscale Spectral Signatures

Motivation: Protein interaction networks provide an important system-level view of biological processes. One of the fundamental problems in biological network analysis is the global alignment of a pair of networks, which puts the proteins of one network into correspondence with the proteins of another network in a manner that conserves their interactions while respecting other evidence of their homology. By providing a mapping between the networks of different species, alignments can be used to inform hypotheses about the functions of unannotated proteins, the existence of unobserved interactions, the evolutionary divergence between the two species and the evolution of complexes and pathways. Results: We introduce GHOST, a global pairwise network aligner that uses a novel spectral signature to measure topological similarity across disparate networks. It exhibits state-of-the-art performance on several network alignment tasks. We show that the spectral signature used by GHOST is highly discriminative, while the alignments it produces are also robust to experimental noise. When compared with other recent approaches, we find that GHOST is able to recover larger and biologically-significant, shared subnetworks between species. Availability: An efficient and parallelized implementation of GHOST, released under the Apache 2.0 license, is available at http:// cbcb.umd.edu/kingsford-group/ghostFunding: This work was supported by the National Science Foundation [CCF-1053918, EF-0849899, and IIS-0812111]; the National Institutes of Health [1R21AI085376]; and a University of Maryland Institute for Advanced Studies New Frontiers Award

Mislocalisation of BEST1 in iPSC-derived retinal pigment epithelial cells from a family with autosomal dominant vitreoretinochoroidopathy (ADVIRC)

Autosomal dominant vitreoretinochoroidopathy (ADVIRC) is a rare, early-onset retinal dystrophy characterised by distinct bands of circumferential pigmentary degeneration in the peripheral retina and developmental eye defects. ADVIRC is caused by mutations in the Bestrophin1 (BEST1) gene, which encodes a transmembrane protein thought to function as an ion channel in the basolateral membrane of retinal pigment epithelial (RPE) cells. Previous studies suggest that the distinct ADVIRC phenotype results from alternative splicing of BEST1 pre-mRNA. Here, we have used induced pluripotent stem cell (iPSC) technology to investigate the effects of an ADVIRC associated BEST1 mutation (c.704T > C, p.V235A) in patient-derived iPSC-RPE. We found no evidence of alternate splicing of the BEST1 transcript in ADVIRC iPSC-RPE, however in patient-derived iPSC-RPE, BEST1 was expressed at the basolateral membrane and the apical membrane. During human eye development we show that BEST1 is expressed more abundantly in peripheral RPE compared to central RPE and is also expressed in cells of the developing retina. These results suggest that higher levels of mislocalised BEST1 expression in the periphery, from an early developmental stage, could provide a mechanism that leads to the distinct clinical phenotype observed in ADVIRC patients