Biology subjects

Knox, R.

Publications and source records attributed to Knox, R..

7 recordsLinked to original sources

bioRxiv2025

Positive selection on hotspot and reinforcing regulatory alleles contributed to hexaploid bread wheat improvement.

BackgroundGenetic variation of regulatory alleles plays a key role in evolution and breeding. In polyploids, regulatory differences may preferentially affect genes on homoeologous chromosomes or sub-genomes. Selection in plant breeding may act upon total transcript dosage across homoeologous genes and on alleles that have strong effects on the transcriptome. ResultsTo investigate these questions, we identified regulatory polymorphisms between an old and a recent hexaploid bread wheat cultivar (Triticum aestivum, 2n=6x=42, AABBDD). The recent cultivar was the product of decades of selection for grain yield and quality. Regulatory allele polymorphisms preferentially affected genes on homoeologous chromosomes but rarely affected genes on specific sub-genomes. The chromosomal distributions of regulatory alleles indicated that past selection had acted upon them, and the effect of selection differed between alleles targeting environmental response genes and genes involved in other processes. Modern cultivar alleles that affected many genes transcripts corresponded to known selection targets and improved field crop performance. Modern cultivar alleles also had significant effects on homoeologous genes, and these alleles also improved crop performance. ConclusionsPolyploid breeding across many species has been and will continue to be the key factor in plant improvement. By enhancing the favorability of strong regulatory alleles and by expanding the range of gene transcript abundances, genome duplications enable breeding progress.

genomics↗

bioRxiv2023

Paradoxical dominant negative activity of an immunodeficiency-associated activating PIK3R1 variant

PIK3R1 encodes three regulatory subunits of class IA phosphoinositide 3-kinase (PI3K), each associating with any of three catalytic subunits, namely p110, p110{beta} or p110{delta}. Constitutional PIK3R1 mutations cause diseases with a genotype-phenotype relationship not yet fully explained: heterozygous loss-of-function mutations cause SHORT syndrome, featuring insulin resistance and short stature attributed to reduced p110 function, while heterozygous activating mutations cause immunodeficiency, attributed to p110{delta} activation and known as APDS2. Surprisingly, APDS2 patients do not show features of p110 hyperactivation, but do commonly have SHORT syndrome-like features, suggesting p110 hypofunction. We sought to investigate this. In dermal fibroblasts from an APDS2 patient, we found no increased PI3K signalling, with p110{delta} expression markedly reduced. In preadipocytes, the APDS2 variant was potently dominant negative, associating with Irs1 and Irs2 but failing to heterodimerise with p110. This attenuation of p110 signalling by a p110{delta}-activating PIK3R1 variant potentially explains co-incidence of gain-of-function and loss-of-function PIK3R1 phenotypes.

biochemistry↗

bioRxiv2019

Dissociating proprioceptive deficits in Autism Spectrum Disorders: Intact acuity but impaired sensory integration in postural control.

We investigated the presence of proprioceptive deficits in adults with Autism Spectrum Disorder (ASD), by assessing peripheral proprioceptive information (or proprioceptive acuity) as well as integration of proprioceptive information in the context of postural control. We hypothesized that proprioceptive acuity would be intact but that integration during a postural control task would be impaired. Sixteen adults with ASD and sixteen Neurotypical (NT) adults were screened using an IQ test and the adolescent-adult sensory profile. Proprioceptive acuity was assessed using an ankle Joint Position Sense (JPS) task and integration of proprioceptive information was assessed using a postural adaptation task. This task comprised standing upright, without vision in three phases: standing on a fixed surface for 2 minutes (baseline), followed by standing on a surface tilting in proportion to participants body sway, or support-surface sway reference for 3 minutes (adaptation) and finally standing on the restored fixed surface for 3 minutes (reintegration). Results showed no group differences in proprioceptive acuity and in the baseline phase, but greater postural sway during adaptation in individuals with ASD compared with NT controls. Specifically, group differences were not present in the first 30s of adaptation, but emerged after the second window suggesting a deficit in sensory integration of proprioception in adults with ASD. Our results suggest that peripheral proprioceptive information is intact in ASD but neural sensory integration of proprioception is impaired in this group.

neuroscience↗

bioRxiv2018

Oncogenic PIK3CA promotes cellular stemness in an allele dose-dependent manner

The PIK3CA gene, which encodes the p110 catalytic subunit of PI3-kinase (PI3K), is mutationally activated in cancer and in overgrowth disorders known as PIK3CA-related overgrowth spectrum (PROS). To determine the consequences of genetic PIK3CA activation in a developmental context of relevance to both PROS and cancer, we engineered isogenic human induced pluripotent stem cells (iPSCs) with heterozygous or homozygous knock-in of PIK3CAH1047R. While heterozygous iPSCs remained largely similar to wild-type cells, homozygosity for PIK3CAH1047R caused widespread, cancer-like transcriptional remodeling, partial loss of epithelial morphology, upregulation of stemness markers and impaired differentiation to all three germ layers in vitro and in vivo. Genetic analysis of PIK3CA-associated cancers revealed that 64 % had multiple oncogenic PIK3CA copies (39 %) or additional PI3K signaling pathway-activating \"hits\" (25 %). This contrasts with the prevailing view that PIK3CA mutations occur heterozygously in cancer. Our findings suggest that a PI3K activity threshold determines pathological consequences of oncogenic PIK3CA activation and provide the first insight into the specific role of this pathway in human pluripotent stem cells.

cancer biology↗

bioRxiv2018

Crop Information Engine and Research Assistant (CIERA) for managing genealogy, phenotypic and genotypic data for breeding programs

BackgroundWith the advent of next-generation marker platforms and phenomics in crop breeding programs, the volume of both the genotypic and phenotypic data produced has increased exponentially. Often the data remain underutilized if not properly collated, managed and accessed. Effective management of the data is paramount to making sound and timely decision on cross planning in order to accelerate genetic gain ({Delta}G) in crops for disease resistance, agronomic and end-use quality traits.\n\nResultsTo address the challenges in managing and efficient utilization of the sheer volume of data generated in a crop breeding program, we developed an electronic information system called the Crop Information Engine and Research Assistant (CIERA). The CIERA, written in Visual Basic, runs on the Microsoft Windows operating system and requires the .Net Framework 4.7 as well as the MySQL Community Server 5.7. The highly intuitive graphical user interface of CIERA includes user-friendly query tools to facilitate the collation of data across relevant phenotypic environments from its phenotypic data management database and can combine that information with the genealogy and genetic data from its genealogy management and genetic data management databases, respectively.\n\nConclusionsUsing CIERA, breeders can build a comprehensive profile of germplasm, within a few minutes, to assist them in planning crosses for enhancing genetic gain by selecting superior lines for crosses.

bioinformatics↗

bioRxiv2017

C-terminal truncation of Pik3r1 in mice models human lipodystrophic insulin resistance uncoupled from dyslipidemia

Heterodimeric class IA phosphatidylinositol-3-kinases (PI3K) transduce signals from many receptor tyrosine kinases including the insulin receptor. PI3K recruitment to phosphotyrosines is mediated by Pik3r1 gene products including the most intensely studied PI3K regulatory subunit, p85, which also binds and regulates the PIP3 phosphatase Pten, and the lipogenic transcription factor Xbp1. Mutations in human PIK3R1 cause SHORT syndrome, featuring lipodystrophy and severe insulin resistance which, uniquely, are uncoupled from fatty liver and dyslipidemia. We describe a novel mouse model of SHORT syndrome made by knock in of the Pik3r1 Y657X mutation. Homozygous embryos die at E11.5, while heterozygous mice exhibit pre-and postnatal growth impairment with diminished placental vascularity. Adipose tissue accretion on high fat feeding was reduced, however adipocyte size was unchanged and preadipocyte differentiation ex vivo unimpaired. Despite severe insulin resistance, heterozygous mice were hypolipidemic, and plasma adiponectin, liver weight, cholesterol, glycogen and triglyceride content were unchanged. Mild downregulation of lipogenic Srebp1, Srebp2 and Chrebp transcriptional activity but no suppression of Xbp1 target genes was seen after fasting. These findings give new insights into the developmental role of Pik3r1, and establish a model of lipodystrophic insulin resistance dissociated from dyslipidemia as seen in SHORT syndrome.

biochemistry↗

bioRxiv2017

Quantification of autism recurrence risk by direct assessment of paternal sperm mosaicism

De novo genetic mutations represent a major contributor to pediatric disease, including autism spectrum disorders (ASD), congenital heart disease, and muscular dystrophies1,2, but there are currently no methods to prevent or predict them. These mutations are classically thought to occur either at low levels in progenitor cells or at the time of fertilization1,3 and are often assigned a low risk of recurrence in siblings4,5. Here, we directly assess the presence of de novo mutations in paternal sperm and discover abundant, germline-restricted mosaicism. From a cohort of ASD cases, employing single molecule genotyping, we found that four out of 14 fathers were germline mosaic for a putatively causative mutation transmitted to the affected child. Three of these were enriched or exclusively present in sperm at high allelic fractions (AF; 7-15%); and one was recurrently transmitted to two additional affected children, representing clinically actionable information. Germline mosaicism was further assessed by deep (>90x) whole genome sequencing of four paternal sperm samples, which detected 12/355 transmitted de novo single nucleotide variants that were mosaic above 2% AF, and more than two dozen additional, non-transmitted mosaic variants in paternal sperm. Our results demonstrate that germline mosaicism is an underestimated phenomenon, which has important implications for clinical practice and in understanding the basis of human disease. Genetic analysis of sperm can assess individualized recurrence risk following the birth of a child with a de novo disease, as well as the risk in any male planning to have children.

genetics↗