Autism spectrum disorder trios from consanguineous populations are enriched for rare biallelic variants, identifying 32 new candidate genes

Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder that affects about 1 in 55 children worldwide and imposes enormous economic and socioemotional burden on families and communities. Genetic studies of ASD have identified de novo copy number variants (CNVs) and point mutations that contribute significantly to the genetic architecture of ASD, but the majority of these studies were conducted in outbred populations, which are not ideal for detecting autosomal recessive (AR) inheritance. However, several studies have investigated ASD genetics in consanguineous populations and point towards AR as an under-appreciated source of ASD variants. Here, we used trio whole exome sequencing (WES) to look for rare variants for ASD in 115 proband-mother-father trios from populations with high rates of consanguinity, namely Pakistan, Iran, and Saudi Arabia. In total, we report 87 candidate sequence variants, with 57% biallelic, 21% autosomal dominant/de novo, and the rest X-linked. 52% of the variants were loss of function (LoF) or putative LoF (splice site, stop loss) and 47% non-synonymous. Our analysis indicates an enrichment of previously identified and candidate AR genes. These include variants in genes previously reported for AR ASD and/or intellectual disability (ID), such as AGA, ASL, ASPA, BTN3A2, CC2D1A, DEAF1, HTRA2, KIF16B, LINS1, MADD, MED25, MTHFR, RSRC1, TECPR2, VPS13B, ZNF335, and 32 previously unreported candidates, including 15 LoF or splice variants, in genes such as DAGLA, EFCAB8, ENPP6, FAXDC2, ILDR2, PKD1L1, SCN10A, and SLC36A1. We also identified candidate biallelic exonic loss CNVs a number of trios, implicating genes including DNAH7, and DHRS4/DHRS4L2.

Transcriptome-wide analysis of microRNA-mRNA correlations in unperturbed tissue transcriptomes identifies microRNA targeting determinants.

MicroRNAs are small RNAs that regulate gene expression through complementary base pairing with their target mRNAs. Given the small size of the pairing region and the large number of mRNAs that each microRNA can control, the identification of biologically relevant targets is difficult. Since current knowledge of target recognition and repression has mainly relied on in vitro studies, we sought to determine if the interrogation of gene expression data of unperturbed tissues could yield new insight into these processes. The transcriptome-wide repression at the microRNA-mRNA canonical interaction sites (seed and 3'-supplementary region, identified by sole base complementarity) was calculated as a normalized Spearman correlation (Z-score) between the abundance of the transcripts in the PRAD-TCGA tissues (RNA-seq and small RNA-seq data of 546 samples). Using the repression values obtained we confirmed established properties or microRNA targeting efficacy, such as the preference for gene regions (3'UTR>CDS>5'UTR), the proportionality between repression and seed length (6mer<7mer<8mer) and the contribution to the repression exerted by the supplementary pairing at 13-16nt of the microRNA. Our results suggest that the 7mer-m8 seed could be more repressive than the 7mer-A1, while they have similar efficacy when they interact using the 3'-supplementary pairing. Strikingly, the 6mer+suppl sites yielded normalized Z-score of repression similar to the sole 7mer-m8 or 7mer-A1 seeds, which raise awareness of its potential biological relevance. We then used the approach to further characterize the 3'-supplementary pairing, using 39 microRNAs that hold repressive 3'-supplementary interactions. The analysis of the bridge between seed and 3'-supplementary pairing site confirmed the optimum +1 offset previously evidenced, but higher offsets appear to hold similar repressive strength. In addition, they show a low GC content at position 13-16, and base preferences that allow the selection of a candidate sequence motif. Overall, our study demonstrates that transcriptome-wide analysis of microRNA-mRNA correlations in large, matched RNA-seq and small-RNA-seq data has the power to uncover hints of microRNA targeting determinants operating in the in vivo unperturbed set. Finally, we made available a bioinformatic tool to analyze microRNA-target mRNA interactions using our approach.

Bio-electrosequence interpretation of late cretaceous sediments of the Southern Bornu Basin, Nigeria

Integrated analysis that involves physical sedimentological, standard palynological and electrofacies analyses on ditch cuttings and suite of wireline logs from Gaibu–1 Well, southern Bornu were examined to identify critical sequence elements and construct a bio-sequence stratigraphical framework. Four (4) palynozones consisting of Triorites africaensis, Cretacaeiporites scabratus - Odontochitina costata, Droseridites senonicus and Syncolporites/Milfordia spp Assemblage Zones construed to be Late Cretaceous – younger successions. Nine (9) depositional sequences each with candidate maximum flooding surfaces (375, 900, 1875, 2250, 2600, 3050, 3400, 3800, 4300 m) marked by marker shales with high abundance and diversity of palynomorphs. Thus, equate with the local lithostratigraphy and global large-scale depositional cycles with candidate sequence boundaries (50, 725, 1625, 2175, 2490, 2850, 3300, 3610, 3960, 4470 m) ranging about 96.28 to 70.07 Ma. The delineated transgressive surfaces along the built sequences mark the subjected onset of marine flooding characterised with interchange of progradational to retrogradational facies. Delineated sequence elements generally show up-hole from progradational to retrogradational and aggradational that represents Lowstand Systems Tracts (LSTs), Transgressive Systems Tracts (TSTs) and Highstand Systems Tracts (HSTs) respectively. The LSTs are seen in form of prograding complex and slope fans, suggestive of good reservoirs. The TSTs consist of channel sand units and shales that depict retrogradational marine units, which could serve as both seals and source rocks for the sand units. The HSTs are made up of interplay of aggradational to progradational sediment packages that could serve as a potential source rock. The palaeoenvironmental indices depict the successions are deposited within continental to open marine settings.

Sequence Stratigraphic Interpretation of FX-1 and FX-2 wells, Onshore Western Niger Delta, Nigeria

The area of study is a portion of the Greater Ughelli Depobelt in Niger Delta Basin. The main aim of the paper is to interpret the sequence stratigraphy of FX-1 and FX-2 wells by employing data sets from biostratigraphic data and well logs. Standard laboratory techniques were used for data treatment while computer software such as Petrel and StrataBugs were used for data simulation, processing, integration and interpretation. Sedimentology, interpreted gamma ray and resistivity well logs integrated with biostratigraphic data were utilized to define the candidate maximum flooding surfaces and sequence boundaries. The wells have the following distributions of sequences: FX-1 well have five depositional sequences with eight candidate maximum flooding surfaces at depths 10011 ft., 9509 ft., 9437 ft., 6362 ft., 5752 ft., 5507 ft., 5161 ft. and 4816 ft. dated 34.0 Ma, 33.0 Ma, 31.3 Ma, 28.1 Ma, 26.2 Ma, 24.3 Ma, 23.2 Ma and 22.0 Ma and seven candidate sequence boundaries at 9616 ft., 6656 ft., 6116 ft., 5639 ft., 5424 ft., 4859 ft. and 4581 ft. dated 33.3 Ma, 29.3 Ma, 27.3 Ma, 24.9 Ma, 23.7 Ma, 22.2 Ma and 21.8 Ma, respectively. FX-2 well have four depositional sequences, five candidate MFSs were identified at 7764 ft., 7196 ft., 6721 ft., 5862 ft. and 5571 ft. dated 34.0 Ma, 33.0 Ma, 31.3 Ma, 28.1 Ma and 24.3 Ma and five candidate SBs at 6941 ft., 6029 ft., 5688 ft., 5653 ft. and 5542 ft. dated 32.4 Ma, 29.3 Ma, 27.3 Ma, 24.9 Ma and 23.7 Ma respectively. The correlation of the two wells and sequence stratigraphic interpretation is a supplementary understanding of the subsurface geology of the Onshore, western Niger Delta area of Nigeria. Keywords: Bio-stratigraphic data, Well logs, Sequence stratigraphy, Well correlation.

OPPORTUNITIES AND CHALLENGES OF WOMEN LEGISLATIVE CANDIDATES ON ELECTIONS IN BANDA ACEH

Purpose: This research is focused on the public space in the field of politics that explains how women candidates legislative from political parties and local political parties national participate in contestation with the men in the legislative election in 2019 the level of the city Banda Aceh. Methodology: This paper uses qualitative research methods with an ethnographic approach contemporary feminist and collection of data through observation, documentation and semi-structured interviews were conducted with fifteen legislative women candidates of local political parties and national political parties from the electoral districts of Banda Aceh were scattered on 9 districts in Banda Aceh. Main Findings: The findings of this study indicate that there are three forces of elected women candidate to continue to increase each election period: (1) The full support of the family, (2) Grassroots women's community (Balee Inong), (3) The presence of government support through Musrena and Musrenbang forum which became the strength of women's bargaining position in planning and budgeting. Although on the other hand patriarchy culture is still a separate constraint for women working in the public arena. Implications/Applications: The results showed that the dominance of men who are members of local and national political parties in Aceh making space for women in the general election is getting narrower, plus a serial number of women in a legislative candidate sequence that is in the last number makes women, not the candidates featured in his political party. But the election of women in the legislature is much better than the previous period. Novelty: The political arena became a force for women of Banda Aceh in scraping patriarchy culture that has been very inherent to Acehnese people wrapped in a religious culture or the habit of Acehnese people who put women into numbers two in development.

Heterologous Expression of Human Norovirus GII.4 VP1 Leads to Assembly of T=4 Virus-Like Particles

ABSTRACTHuman noroviruses are a leading cause of acute gastroenteritis, yet there are still no vaccines or antivirals available. Expression of the norovirus capsid protein (VP1) in insect cells typically results in the formation of virus-like particles (VLPs) that are morphologically and antigenically comparable to native virions. Previous structural analysis of norovirus VLPs showed that the capsid has a T=3 icosahedral symmetry and is composed of 180 copies of VP1 that are folded into three quasi-equivalent subunits (A, B, and C). In this study, we determined the cryo-EM VLP structures of two GII.4 variants, termed CHDC-1974 and NSW-2012. Surprisingly, we found that greater than 95% of these GII.4 VLPs were larger than virions and 3D reconstruction showed that these VLPs exhibited T=4 icosahedral symmetry. We found that the T=4 VLPs showed several structural differences to the T=3 VLPs. The T=4 particles assemble from 240 copies of VP1 that adopt four quasi-equivalent conformations (A, B, C, and D) that form two distinct dimers, A/B and C/D. The T=4 protruding domains were elevated ∼21-Å off the capsid shell, which was ∼7-Å more than the previously studied GII.10 T=3 VLPs. A small cavity and flap-like structure at the icosahedral twofold axis disrupted the contiguous T=4 shell, a consequence of the D-subunit S-domains having smaller contact interfaces with neighboring dimers. Overall, our findings that old and new GII.4 VP1 sequences assemble T=4 VLPs might have implications for the design of potential future vaccines.IMPORTANCEThe discovery that the GII.4 VLPs have a T=4 symmetry is of significance, since this represents the first known T=4 calicivirus structure. Interestingly, the GII.4 2012 variant shares 96% amino acid identity with a current GII.4 VLP vaccine candidate sequence, which suggests that this vaccine might also have a T=4 symmetry. Our previous results with these GII.4 VLPs showed functional binding properties to antibodies and Nanobodies that were raised against T=3 (GII.10) VLPs. This suggests that the T=4 VLPs were antigenically comparable to T=3 particles, despite the obvious structural and size differences. On the other hand, these larger T=4 VLPs with novel structural features and possibly new epitopes might elicit antibodies that do not recognize equivalent epitopes on the T=3 VLPs. Further structural and binding studies using a library of GII.4-specific Nanobodies are planned in order to precisely investigate whether new epitopes are formed.

SEDIMENTOLOGY AND SEQUENCE STRATIGRAPHY OF SHALLOW MARINE SEDIMENTS IN A SYN-RIFT SETTING: HUGIN FORMATION, SOUTH VIKING GRABEN

Fault growth and linkage within rift basins generates localised uplift and subsidence, which may exert significant control over syn-rift sedimentation. The shallow-marine Hugin Formation within the South Viking Graben, a salt-influenced rift basin, is studied as an example of such sedimentation. The principal aims of this thesis are to: (1) characterise the sedimentology and sequence stratigraphy of the succession, (2) investigate structural development within the graben by analysis of the hangingwall dipslope, and (3) establish the impact of syn-depositional structural development on shallow marine sedimentation. Sedimentological analysis of the Hugin Formation has recognised fifteen facies that are grouped into six facies associations: bay-fill, shoreface, fluvio-tidal channel fill, mouth bar, coastal plain and offshore open marine. Combining the results of this analysis with biostratigraphy, the studied succession is subdivided into a series of units delineated by regionally correlatable maximum flooding surfaces. Within the stratigraphic framework delineated by these surfaces each of the main facies associations are developed coevally in distinct and different geographical locations. Higher order flooding surfaces, transgressive surfaces and candidate sequence boundaries can also be interpreted within this framework which are geographically localised. Structural analysis of the hangingwall dipslope identified a series of distinct structural features that were evolving contemporaneous with Hugin Formation deposition. To the north, the gravity-driven Gudrun-Brynhild fault array initiated as a series of distinct segments which subsequently propagated and linked. Further south, the salt-cored highs at Dagny and Alpha Central were also developing. Palaeogeographical localisation of facies associations is interpreted to reflect deposition within these different structural locations along with proximity to the axial fluvial feeder system to the south of the basin. Sediment supply via wave-driven longshore drift from the north of the basin and local re-working of structurally controlled palaeohighs was also important.

Linked-Read sequencing resolves complex structural variants

SummaryLarge genomic structural variants (>50bp) are important contributors to disease, yet they remain one of the most difficult types of variation to accurately ascertain, in part because they tend to cluster in duplicated and repetitive regions, but also because the various signals for these events can be challenging to detect with short reads. Clinically, aCGH and karyotype remain the most commonly used assays for genome-wide structural variant (SV) detection, though there is clear potential benefit to an NGS-based assay that accurately detects both SVs and single nucleotide variants. Linked-Read sequencing is a relatively simple, fast, and cost-effective method that is applicable to both genome and targeted assays. Linked-Reads are generated by performing haplotype-level dilution of long input DNA molecules into >1 million barcoded partitions, generating barcoded short reads within those partitions, and then performing short read sequencing in bulk. We performed 30x Linked-Read genome sequencing on a set of 23 samples with known balanced or unbalanced SVs. Twenty-seven of the 29 known events were detected and another event was called as a candidate. Sequence downsampling was performed on a subset to determine the lowest sequence depth required to detect variations. Copy-number variants can be called with as little as 1-2x sequencing depth (5-10Gb) while balanced events require on the order of 10x coverage for variant calls to be made, although specific signal is clearly present at 1-2x sequencing depth. In addition to detecting a full spectrum of variant types with a single test, Linked-Read sequencing provides base-level resolution of breakpoints, enabling complete resolution of even the most complex chromosomal rearrangements.

Identification of genetic causes of congenital neurodevelopmental disorders using genome wide molecular technologies

Background. Intellectual disability affects about 1–2% of the general population worldwide, and this is the leading socio-economic problem of health care. The evaluation of the genetic causes of intellectual disability is challenging because these conditions are genetically heterogeneous with many different genetic alterations resulting in clinically indistinguishable phenotypes. Genome wide molecular technologies are effective in a research setting for establishing the new genetic basis of a disease. We describe the first Lithuanian experience in genome-wide CNV detection and whole exome sequencing, presenting the results obtained in the research project UNIGENE.Materials and methods. The patients with developmental delay/intellectual disability have been investigated (n = 66). Diagnostic screening was performed using array-CGH technology. FISH and real time-PCR were used for the confirmation of gene-dose imbalances and investigation of parental samples. Whole exome sequencing using the next generation high throughput NGS technique was used to sequence the samples of 12 selected families.Results. 14 out of 66 patients had pathogenic copy number variants, and one patient had novel likely pathogenic aberration (microdeletion at 4p15.2). Twelve families have been processed for whole exome sequencing. Two identified sequence variants could be classified as pathogenic (in MECP2, CREBBP genes). The other families had several candidate intellectual disability gene variants that are of unclear clinical significance and must be further investigated for possible effect on the molecular pathways of intellectual disability.Conclusions. The genetic heterogeneity of intellectual disability requires genome wide approaches, including detection of chromosomal aberrations by chromosomal microarrays and whole exome sequencing capable of uncovering single gene mutations. This study demonstrates the benefits and challenges that accompany the use of genome wide molecular technologies and provides genotype-phenotype information on 32 patients with chromosomal imbalances and ID candidate sequence variants.