Biology subjects

Brewster, R.

Publications and source records attributed to Brewster, R..

8 recordsLinked to original sources

bioRxiv2023

Reference genome of the endangered eastern quoll (Dasyurus viverrinus)

The eastern quoll (Dasyurus viverrinus) is an endangered marsupial mesopredator native to Australia. Since the extirpation of the last mainland Australian populations in the late 20th century, wild populations of this species have been restricted to two islands at the far southern end of its historical range. Eastern quolls are the subject of captive breeding programs and attempts have recently been made to re-establish a population in mainland Australia through translocations. However, few resources currently exist to guide the genetic management of this species. Here, we generated a chromosome-scale reference genome for the eastern quoll, along with gene annotations supported by multi-tissue transcriptomes. Through comparisons with related species, we find that our reference genome is among the most complete marsupial assemblies currently available. Using this assembly, we infer the species demographic history and identify potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely drives differences in pelage color between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii). The genomic resources we present are valuable new tools for evolutionary and conservation genomic studies.

genomics↗

bioRxiv2021

N-myc Downstream Regulated Gene 1 (NDRG1) functions as a molecular switch for cellular adaptation to hypoxia

Lack of oxygen (hypoxia and anoxia) is detrimental to cell function and survival and underlies many disease conditions. Hence, metazoans have evolved mechanisms to adapt to low oxygen. One such mechanism, metabolic suppression, decreases the cellular demand for oxygen by downregulating ATP-demanding processes. However, the molecular mechanisms underlying this adaptation are poorly understood. Here, we report on the role of ndrg1a in hypoxia adaptation of the anoxia-tolerant zebrafish embryo. ndrg1a is expressed in the kidney and ionocytes, cell types that use large amounts of ATP to maintain ion homeostasis. ndrg1a mutants are viable and develop normally when raised under normal oxygen. However, their survival and kidney function is reduced relative to WT embryos following exposure to prolonged anoxia. We further demonstrate that Ndrg1a binds to the energy-demanding sodium-potassium ATPase (NKA) pump under anoxia and is required for its degradation, which may preserve ATP in the kidney and ionocytes and contribute to energy homeostasis. Lastly, we show that sodium azide treatment, which increased lactate levels, was sufficient to trigger NKA degradation in an Ndrg1a-dependent manner. These findings support a model whereby Ndrg1a is essential for hypoxia adaptation and functions downstream of lactate signaling to induce NKA degradation, a process known to conserve cellular energy.

developmental biology↗

bioRxiv2020

Hypoxia Regulation of ndrgs

Many organisms rely on oxygen to generate energy in the form of adenosine triphosphate (ATP). During severe hypoxia, the production of ATP decreases due to diminished activity of the electron transport chain, leading to cell damage or death. Conversely, excessive oxygen causes oxidative stress that is equally damaging to cells. To mitigate pathological outcomes, organisms have evolved mechanisms to adapt to fluctuations in oxygen levels. Zebrafish embryos are remarkably hypoxia-tolerant, surviving anoxia (zero oxygen) for hours in a hypometabolic, energy-conserving state. To begin to unravel underlying mechanisms, we analyze here the distribution and hypoxia-dependent regulation of members of the N-myc Downstream Regulated Gene (Ndrg) family, Ndrg 1-4. These genes have primarily been studied in cancer cells, and hence little is understood about their normal function. We show here using in situ hybridization that, under normoxic conditions, ndrgs are expressed in metabolically-demanding organs of the zebrafish embryo, such as the brain, kidney, and heart. Following exposure of embryos to different severity and durations of hypoxia, we observed that ndrgs are differentially regulated and that ndrg1a is the most responsive member of this family, with nine-fold upregulation following prolonged anoxia. We further show that this treatment resulted in de novo expression of ndrg1a in tissues where it is not observed under normoxia, such as head vasculature, the inner ear, and somites. These findings provide an entry point into understanding the role of this conserved gene family in hypoxia adaptation of normal cells.

developmental biology↗

bioRxiv2020

Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa

Human gut microbiome research focuses on populations living in high-income countries or on the other end of the spectrum, namely non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the worlds population. We present the first study evaluating gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyzed stool samples from adult females (age 40 - 72) living in rural Bushbuckridge municipality (n=118) or urban Soweto (n=51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterization of microbiomes of individuals living outside high-income countries, resulting in artificially low species-level beta diversity measurements. To improve reference databases, we generated complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas species. Our results suggest that the gut microbiome in South African populations do not exist along a simple "western-nonwestern" axis and that these populations contain microbial diversity that remains to be described.

genomics↗

bioRxiv2020

Flexibility and constraint in preimplantation gene regulation in mouse

Although many features of embryonic development exhibit remarkable stability in the face of environmental perturbations, it is also clear that some aspects of early embryogenesis can be modulated by non-genetic influences during and after fertilization. Among potential perturbations experienced during reproduction, understanding the consequences of differing ex vivo fertilization methods at a molecular level is imperative for comprehending both the basic biology of early development and the potential consequences of assisted reproduction. Here, we set out to explore stable and flexible aspects of preimplantation gene expression using single-embryo RNA-sequencing of mouse embryos fertilized by natural mating, in vitro fertilization, or intracytoplasmic sperm injection, as well as oocytes parthenogenetically activated to develop (parthenotes). This dataset comprises a resource of over eight hundred individual embryos, which we use for three primary analyses. First, we characterize the effects of each fertilization method on early embryonic gene regulation, most notably finding decreased expression of trophectoderm markers at later stages of preimplantation development in ICSI embryos. Second, we find massive gene misregulation in parthenotes beyond the expected defects in imprinted gene expression, and show that many of these changes can be suppressed by sperm total RNA. Finally, we make use of the single-embryo resolution of our dataset to identify both stably-expressed genes and highly-variable genes in the early mouse embryo. Together, our data provide a detailed survey of the molecular consequences of different fertilization methods, establish parthenotes as a "tabula rasa" for understanding the role for sperm RNAs in preimplantation gene regulation, and identify subtypes of preimplantation embryos based on their expression of epivariable gene modules.

developmental biology↗

bioRxiv2020

Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition

BackgroundComparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most African adults. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To better characterize the microbiome of African adults living in more mainstream lifestyle settings and to investigate associations between the microbiome and obesity, we conducted a pilot study in two South African cohorts that are representative of urban and rural populations. The study was designed collaboratively with community leaders. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. ResultsWe found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, our results show a relatively higher than expected abundance of Western gut-associated taxa such as Barnesiella and the presence of Bifidobacteria and Bacteroides together with the more traditionally non-Western gut-associated Prevotella, Treponema and Succinivibrio. Interestingly, we observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in the rural cohort. We also found Prevotella, despite its generally high prevalence relative to all taxa present in the cohort, to be associated with obesity. ConclusionsAltogether, this work identifies putative microbial features associated with host health in a historically understudied community. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research in this regard.

microbiology↗

bioRxiv2019

Hingepoints and neural folds reveal conserved features of primary neurulation in the zebrafish forebrain

ABSTRACTPrimary neurulation is the process by which the neural tube, the central nervous system precursor, is formed from the neural plate. Incomplete neural tube closure occurs frequently, yet underlying causes remain poorly understood. Developmental studies in amniotes and amphibians have identified hingepoint and neural fold formation as key morphogenetic events and hallmarks of primary neurulation, the disruption of which causes neural tube defects. In contrast, the mode of neurulation in teleosts such as zebrafish has remained highly debated. Teleosts are thought to have evolved a unique pattern of neurulation, whereby the neural plate infolds in absence of hingepoints and neural folds (NFs), at least in the hindbrain/trunk where it has been studied. We report here on zebrafish forebrain morphogenesis where we identify these morphological landmarks. Our findings reveal a deeper level of conservation of neurulation than previously recognized and establish the zebrafish as a model to understand human neural tube development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2019

Probing mechanisms of transcription elongation through cell-to-cell variability of RNA polymerase

The process of transcription initiation and elongation are primary points of control in the regulation of gene expression. While biochemical studies have uncovered the mechanisms involved in controlling transcription at each step, how these mechanisms manifest in vivo at the level of individual genes is still unclear. Recent experimental advances have enabled single-cell measurements of RNAP molecules engaged in the process of transcribing a gene of interest. In this manuscript, we use Gillespie simulations to show that measurements of cell-to-cell variability of RNAP numbers and inter-polymerase distances can reveal the prevailing mode of regulation of a given gene. Mechanisms of regulation at each step, from initiation to elongation dynamics, produce qualitatively distinct signatures which can further be used to discern between them. Intriguingly, depending on the initiation kinetics, stochastic elongation can either enhance or suppress cell-to-cell variability at the RNAP level. To demonstrate the value of this framework, we analyze RNAP number distribution data for ribosomal genes in S. cerevisiae from three previously published studies and show that this approach provides crucial mechanistic insights into the transcriptional regulation of these genes.\n\nAuthor SummaryThe process of transcription comprises many distinct steps and understanding the regulation of each of these steps provides insight into how the levels of gene expression are controlled in the cell. In this manuscript, we use stochastic simulations to explore how regulation at the level of elongation and initiation together influences the distribution of actively transcribing RNAP on a gene. We find that each of these steps of regulation leaves a distinct imprint on the gene-to-gene variability of number of actively transcribing RNAP on the gene and their inter-RNAP distances. Using these results, we analyze recent experimental data of transcribing RNAP distributions and find that the perturbations in these studies primarily impact the transcription initiation dynamics of the genes.

cell biology↗