Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity

BACKGROUND: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship. METHODS: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity. RESULTS: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy. CONCLUSIONS: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as "OGDHL-related disorders"

Curation of viral genomes: challenges, applications and the way forward

BACKGROUND: Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targeted efforts towards understanding principles of evolution with an application envisaged to improve human health. These efforts culminated in the development of dedicated resources. Whereas a large number of viral genomes have been sequenced by groups or individuals with an interest to study antigenic variation amongst strains and species. These independent efforts enabled viruses to attain the status of 'best-represented taxa' with the highest number of genomes. However, due to lack of concerted efforts, viral genomic sequences merely remained as entries in the public repositories until recently. RESULTS: VirGen is a curated resource of viral genomes and their analyses. Since its first release, it has grown both in terms of coverage of viral families and development of new modules for annotation and analysis. The current release (2.0) includes data for twenty-five families with broad host range as against eight in the first release. The taxonomic description of viruses in VirGen is in accordance with the ICTV nomenclature. A well-characterised strain is identified as a 'representative entry' for every viral species. This non-redundant dataset is used for subsequent annotation and analyses using sequenced-based Bioinformatics approaches. VirGen archives precomputed data on genome and proteome comparisons. A new data module that provides structures of viral proteins available in PDB has been incorporated recently. One of the unique features of VirGen is predicted conformational and sequential epitopes of known antigenic proteins using in-house developed algorithms, a step towards reverse vaccinology. CONCLUSION: Structured organization of genomic data facilitates use of data mining tools, which provides opportunities for knowledge discovery. One of the approaches to achieve this goal is to carry out functional annotations using comparative genomics. VirGen, a comprehensive viral genome resource that serves as an annotation and analysis pipeline has been developed for the curation of public domain viral genome data . Various steps in the curation and annotation of the genomic data and applications of the value-added derived data are substantiated with case studies

Can Technology Empower? The Impact of Technology Access On Women\u27s Decision-Making Power in India

Technology access has the power to transform women’s empowerment and increase economic development across the world. This thesis analyzes the impact of state-level technology access on women’s empowerment in India. I assess whether increased state technology levels, measured by mobile phone access, increase urban women’s education levels, household income levels and women’s decision-making power. My data is sourced from two rounds of the Indian Human Development Survey (IHDS) conducted in 2004-05 and 2011-12 as well as The Telecom Statistics of India, that measures telecom subscriber rates in each state. I use a linear regression model to measure education and income levels and a probit regression model to assess women’s decision-making power, measured through their purchase power, if they have a bank account, and if their name is on home ownership or rental papers. This model controls for women’s age, caste, religion, and household size, and my results show that state-level technology access has a limited impact on women’s empowerment. Technology access has the largest positive impact on women having a bank account. These findings are essential to better understand how generalized and universal technology access do not affect women significantly, and that targeted, gender-based technology provisions should be employed instead

Design and Analysis of Multi-Level Active Queue Management Mechanisms for Emergency Traffic

Active Queue Management (AQM) is proposed as a solution for providing available and dependable service to traffic from emergency users after disasters. MAMT is a simple but effective approach that can be applied at strategic network locations where heavy congestion is anticipated. It can provide low loss to emergency packets while dropping non-emergency packets only as much as necessary. Fluid flow analysis and simulation is conducted to provide guidelines for proper MAMT design, especially regarding the queue size and averaging parameters that are most important. This work considers non-responsive traffic exclusively, since non-responsive traffic types are currently getting the most attention from emergency management organizations. Plus, very little work has been performed regarding AQM and non-responsive traffic. It demonstrates queue oscillation problems that previously may have been attributed to the interactions between TCP and AQM, but which are actually inherent to AQM and can be greatly reduced with proper parameter settings. MAMT is shown to perform well over a range of loads and can effectively protect emergency traffic from surges in non-emergency traffic. Keywords—System design, simulations, active queue management, emergency services, quality of service. I

Removal of the Noise Source Inherent to AQM

implementations drop packets randomly as a function of the average queue fill. Over a short window of time, all packets are dropped with virtually equal probability. This causes the actual number of dropped packets to vary according to a binomial distribution, and can result in a significant difference between the actual numbers of dropped packets and the expected. As a result, this introduces unnecessary noise to the system which substantially affects variations in queue fill. A new approach to calculating dropping probabilities is proposed here that adapts the dropping probability over a window of packets and ensures that the number of packets that are actually dropped is virtually equal to the number that are expected to be dropped. It is shown here that this substantially reduces unnecessary variance in queue fill. Index Terms—Active queue management, random early dropping. I

Characterization of the ligand binding site of β₂AR variants.

<p>(A) Top-view of the β₂AR represented as ribbons. The residues (113, 203, 289 and 312) that define the topology of the binding site are represented as licorice and the distances between them are indicated by lines. (B) Average distance between residues 289 and 203 for the Arg (red) and Gly (green) variants. (C) Average distance between residues 312 and 203 for the Arg (red) and Gly (green) variants. Docking of carazolol to (D) the 2RH1 structure, (E) Arg variant and (F) Gly variant. The crystal structure pose of carazolol is colored yellow, and the docked pose is colored purple.</p

Vestibules of ligand entry in β₂AR variants.

<p>Grids representing vestibule openings for (A) vestibule1 and (B) vestibule 2 of β₂AR are shown in yellow. Residues defining the vestibules are shown in surface representation while the rest of the receptor is rendered as ribbons and colored blue. Panel C and D represent volumes (in ų) of the non-occluded grid of vestibule 1 for the Arg and Gly variants, respectively. Panel E and F represent volumes (in ų) of the non-occluded grid of vestibule 2 for the Arg and Gly variants, respectively. For each plot, the blue line indicates the first simulation, the red indicates the second and the green line indicates the third simulation.</p

Contact maps of Arg and Gly variants of β₂AR.

<p>Contacts between the N-terminal region of (A) Arg and (B) Gly variants and the rest of the receptor were computed from the average distance over simulation time. Average distances that were less than or equal to 1 nm were plotted. A color bar is indicated in which white indicates no-contacts and black indicates a close contact.</p