Biology subjects

Lai, A.

Publications and source records attributed to Lai, A..

26 records · Page 2Linked to original sources

bioRxiv2020

Visual Perception in the Periphery: The Role of Covert Attention Vectors in the Extraction of Semantic Information

Under covert attention, our visual perception deteriorates dramatically as eccentricity increases. This reduction of peripheral visual acuity (PVA) is partially due to the coarse sampling of the retinal ganglion cells towards the periphery, but this property cannot be solely responsible. Other factors, such as character crowding, have been studied, yet the origin of the poor PVA is not entirely understood. This gap motivated us to investigate the PVA by varying the crowding conditions systematically. Under completely crowded conditions (i.e. resembling a full page of text), PVA was observed to be eight times worse than the PVA under uncrowded conditions. By partially crowding the periphery, we obtained PVA values between the fully crowded and uncrowded conditions. On the other hand, crowding the fovea center while leaving the periphery uncrowded improved PVA relative to the uncrowded case. These results support a model for a top-down "covert attention vector" that assists the resulting PVA in a manner analogous to saccadic eye movement for overt attention. We speculate that the attention vector instructs the dorsal pathway to transform the peripheral character to the foveal center. Then, the scale-invariant log-polar retinotopy of the ventral pathway can scale the centered visual input to match the prior memory of the specific character shape.

neuroscience↗

bioRxiv2019

Leptin signaling and the intervertebral disc: Sex dependent effects of leptin receptor deficiency and Western diet on the spine in a type 2 diabetes mouse model

Type 2 diabetes and obesity are associated with back pain in juveniles and adults and are implicated in intervertebral disc (IVD) degeneration. Hypercaloric Western diets are associated with both obesity and type 2 diabetes. The objective of this study was to determine if obesity and type 2 diabetes result in spinal pathology in a sex-specific manner using in vivo diabetic and dietary mouse models. Leptin is an appetite-regulating hormone, and its deficiency leads to polyphagia, resulting in obesity and diabetes. Leptin is also associated with IVD degeneration, and increased expression of its receptor was identified in degenerated IVDs. We used young, leptin receptor deficient (Db/Db) mice to mimic the effect of diet and diabetes on adolescents. Db/Db and Control mice were fed either Western or Control diets, and were sacrificed at 3 months of age. Db/Db mice were obese, while only female mice developed diabetes. Female Db/Db mice displayed altered IVD morphology, with increased intradiscal notochordal band area, suggesting delayed IVD cell proliferation and differentiation, rather than IVD degeneration. Motion segments from Db/Db mice exhibited increased failure risk with decreased torsional failure strength. Db/Db mice also had inferior bone quality, which was most prominent in females. We conclude that obesity and diabetes due to impaired leptin signaling contribute to pathological changes in vertebrae, as well as an immature IVD phenotype, particularly of females, suggesting a sex-dependent role of leptin in the spine.

physiology↗

bioRxiv2019

μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells

Genome regulation depends on carefully programmed protein-DNA interactions that maintain or alter gene expression states, often by influencing chromatin organization. Most studies of these interactions to date have relied on bulk methods, which in many systems cannot capture the dynamic single-cell nature of these interactions as they modulate cell states. One method allowing for sensitive single-cell mapping of protein-DNA interactions is DNA adenine methyltransferase identification (DamID), which records a proteins DNA-binding history by methylating adenine bases in its vicinity, then selectively amplifies and sequences these methylated regions. These interaction sites can also be visualized using fluorescent proteins that bind to methyladenines. Here we combine these imaging and sequencing technologies in an integrated microfluidic platform (DamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We apply this system to generate paired single-cell imaging and sequencing data from a human cell line, in which we map and validate interactions between DNA and nuclear lamina proteins, providing a measure of 3D chromatin organization and broad gene regulation patterns. DamID provides the unique ability to compare paired imaging and sequencing data for each cell and between cells, enabling the joint analysis of the nuclear localization, sequence identity, and variability of protein-DNA interactions.

bioengineering↗

bioRxiv2019

Metabolism of fatty acids and ketone bodies for glioblastoma growth: Implications for Ketogenic Diet Therapy

Glioblastoma (GBM) metabolism has traditionally been characterized by a primary dependence on aerobic glycolysis, prompting the use of the ketogenic diet (KD) as a potential therapy. In this study we evaluated the effectiveness of the KD in GBM and assessed the role of fatty acid oxidation (FAO) in promoting GBM propagation. In vitro assays revealed FA utilization throughout the GBM metabolome, and growth inhibition in nearly every cell line in a broad spectrum of patient-derived glioma cells treated with FAO inhibitors. In vivo assessments revealed that knockdown of carnitine palmitoyltransferase 1A (CPT1A), the rate limiting enzyme for FAO, reduced the rate of tumor growth and increased survival. However, the unrestricted ketogenic diet did not reduce tumor growth, and for some models significantly reduced survival. Altogether, these data highlight important roles for FA and ketone body metabolism that could serve to improve targeted therapies in GBM.

cancer biology↗

bioRxiv2018

On-ratio PDMS bonding for multilayer microfluidic device fabrication

Integrated elastomeric valves, also referred to as Quake valves, enable precise control and manipulation of fluid within microfluidic devices. Fabrication of such valves requires bonding of multiple layers of the silicone polymer polydimethylsiloxane (PDMS). The conventional method for PDMS-PDMS bonding is to use varied base to crosslinking agent ratios between layers, typically 20:1 and 5:1. This bonding technique, known as \"off-ratio bonding,\" provides strong, effective PDMS-PDMS bonding for multi-layer soft-lithography, but it can yield adverse PDMS material properties and can be wasteful of PDMS. Here we demonstrate the effectiveness of on-ratio PDMS bonding for multilayer soft lithography. We show the efficacy of this technique among common variants of PDMS: Sylgard 184, RTV 615, and Sylgard 182.

bioengineering↗

bioRxiv2017

The Abrogation Of Condensin Function Provides Independent Evidence For Defining The Self-Renewing Population Of Pluripotent Stem Cells

Heterogeneity of planarian neoblast stem cells has been categorised on the basis of single cell expression analyses and subsequent experiments to demonstrate lineage relationships. Some data suggest that despite gene expression heterogeneity amongst cells in the cell cycle, in fact only one sub-population, known as sigma neoblasts, can self-renew. Without the tools to perform live in vivo lineage analysis, we instead took an alternative approach to provide independent evidence for defining the self-renewing stem cell population. We exploited the role of highly conserved condensin proteins to functionally assay neoblast self-renewal properties. Condensins are involved in forming properly condensed chromosomes to allow cell division to proceed during mitosis, and their abrogation inhibits mitosis and can lead to repeated endoreplication of the genome in cells that make repeated attempts to divide. We find that planarians possess only the condensin I complex, and that this is required for normal stem cell function. Abrogation of condensin function led to rapid stem cell depletion accompanied by the appearance of giant cells with increased DNA content. Using previously discovered markers of heterogeneity we show that enlarged cells are always from the sigma-class of the neoblast population and we never observe evidence for endoreplication for the other neoblast subclasses. Overall, our data establish that condensins are essential for stem cell maintenance and provide independent evidence that only sigma-neoblasts are capable of multiple rounds of cell division and hence self-renewal.

developmental biology↗

bioRxiv2017

MLL3/4 Prevents Stem Cell Hyperplasia And Controls Differentiation Programs In A Planarian Cancer Stem Cell Model

Currently, little is known about the evolution of epigenetic regulation in animal stem cells. Using the planarian stem cell system to investigate the role of the COMPASS family of MLL3/4 histone methyltransferases, we demonstrate that their role as tumour suppressors in stem cells is conserved over a large evolutionary distance in animals. This also suggested the potential conservation of a genome wide epigenetic regulation program in animal stem cells, so we assessed the regulatory effects of Mll3/4 loss of function by performing RNA-seq and ChIP-seq on the G2/M planarian stem cell population, part of which contributes to the formation of outgrowths. We find many oncogenes and tumour suppressors among the affected genes that are therefore likely candidates for mediating MLL3/4 tumour suppression function in mammals, where little is known about in vivo regulatory targets. Our work demonstrates conservation of an important epigenetic regulatory program in animals and highlights the utility of the planarian model system for studying epigenetic regulation.

developmental biology↗

bioRxiv2017

Epigenetic analyses of the planarian genome reveals conservation of bivalent promoters in animal stem cells.

Planarian flatworms have an indefinite capacity to regenerate missing or damaged body parts owing to a population of pluripotent adult stems cells called neoblasts (NBs). Currently, little is known about the importance of the epigenetic status of NBs and how histone modifications regulate homeostasis and cellular differentiation. We have developed an improved and optimized ChIP-seq protocol for NBs in Schmidtea mediterranea and have generated genome-wide profiles for the active marks H3K4me3 and H3K36me3, and suppressive marks H3K4me1 and H3K27me3. The genome-wide profiles of these marks were found to correlate well with NB gene expression profiles. We found that genes with little transcriptional activity in the NB compartment but which switch on in post-mitotic progeny during differentiation are bivalent, being marked by both H3K4me3 and H3K27me3 at promoter regions. In further support of this hypothesis bivalent genes also have a high level of paused RNA Polymerase II at the promoter-proximal region. Overall, this study confirms that epigenetic control is important for the maintenance of a NB transcriptional program and makes a case for bivalent promoters as a conserved feature of animal stem cells and not a vertebrate specific innovation. By establishing a robust ChIP-seq protocol and analysis methodology, we further promote planarians as a promising model system to investigate histone modification mediated regulation of stem cell function and differentiation.

developmental biology↗