Biology subjects

Miller, A.

Publications and source records attributed to Miller, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

The genetic basis of tail-loss evolution in humans and apes

The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans and to the "anthropomorphous apes"1,2. This morphological reprogramming in the ancestral hominoids has been long considered to have accommodated a characteristic style of locomotion and contributed to the evolution of bipedalism in humans3-5. Yet, the precise genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. Primate genome sequencing projects have made possible the identification of causal links between genotypic and phenotypic changes6-8, and enable the search for hominoid-specific genetic elements controlling tail development9. Here, we present evidence that tail-loss evolution was mediated by the insertion of an individual Alu element into the genome of the hominoid ancestor. We demonstrate that this Alu element - inserted into an intron of the TBXT gene (also called T or Brachyury10-12) - pairs with a neighboring ancestral Alu element encoded in the reverse genomic orientation and leads to a hominoid-specific alternative splicing event. To study the effect of this splicing event, we generated a mouse model that mimics the expression of human TBXT products by expressing both full-length and exon-skipped isoforms of the mouse TBXT ortholog. We found that mice with this genotype exhibit the complete absence of a tail or a shortened tail, supporting the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype, albeit with incomplete penetrance. We further noted that mice homozygous for the exon-skipped isoforms exhibited embryonic spinal cord malformations, resembling a neural tube defect condition, which affects [~]1/1000 human neonates13. We propose that selection for the loss of the tail along the hominoid lineage was associated with an adaptive cost of potential neural tube defects and that this ancient evolutionary trade-off may thus continue to affect human health today.

evolutionary biology↗

bioRxiv2021

PRC1 Sustains the Memory of Neuronal Fate Independent of PRC2 Function

Polycomb repressive complexes (PRCs) 1 and 2 maintain stable cellular memories of early fate decisions by establishing heritable patterns of gene repression. PRCs repress transcription through histone modifications and chromatin compaction, but their roles in neuronal subtype diversification are poorly defined. We unexpectedly found that PRC2 is dispensable to preserve the morphogen-induced positional fates of spinal motor neurons (MNs), while PRC1 is essential for the specification of segmentally-restricted subtypes. Mutation of the core PRC1 component Ring1 in mice leads to increased chromatin accessibility and ectopic expression of a broad variety of fates determinants, including Hox transcription factors, while neuronal class-specific features are maintained. Loss of MN subtype identities in Ring1 mutants is due to the suppression of Hox networks by derepressed caudal Hox genes. These results indicate that PRC1 can function independently of de novo PRC2-dependent histone methylation to maintain chromatin topology and transcriptional memory at the time of neuronal differentiation.

neuroscience↗

bioRxiv2021

Inhibition of cancer cells in culture. The effects of treatment with ketone bodies and/or rapamycin treatment

BackgroundThe potential for ketogenic diets or administration of exogenous ketone bodies to treat or prevent to cancer remains encouraging. Of particular interest is the possibility that, whatever the effect of a nutritional intervention alone, the diet might enhance the effect of existing cancer drugs, thereby requiring lower doses and a reduction in toxicity and side effects. MethodsSW480, a human cell line derived from colon, was treated with ketone bodies (sodium 3-hydroxy butyrate (common name, {square}-hydroxy butyrate) or with sodium acetoacetate in the presence or absence of rapamycin. Cells were incubated for 96 hours in DMEM with 10 mM glucose medium. HSF2617, a human epithelial fibroblast line served as control and cells were subjected to similar treatment as the SW480 cells. Cell proliferation and glucose consumption were determined with standard reagents. ResultsThe ketone bodies inhibited proliferation of SW480 cells in culture. Rapamycin also inhibited proliferation and its action was enhanced by the ketone bodies although there was little synergistic effect under these conditions. Human fibroblast controls were not inhibited by the ketone bodies. Both SW480 and control lines showed consumption of glucose during a 96 hour incubation period, suggesting that normal controls can switch to ketogenic metabolism while the cancer cells, which proliferate poorly, cannot. Results are consistent with recent reports of a mouse model showing the synergy of rapamycin and a ketogenic diet (Zou Y, et al. (2020) PLoS ONE 15 (5)) as well as earlier publications describing additive or synergistic effects of ketogenic diets with other modalities of cancer treatment. ConclusionsThe results show that the growth of a cancer cell line in culture can be inhibited by the addition of ketone bodies or rapamycin to the growth medium. The combination of treatments was found to be additive, consistent with results from a previously published mouse model. The data demonstrate the potential for a strategy whereby doses of anti-cancer agents that have detrimental or toxic side-effects can be reduced if coupled to an appropriate source of ketone bodies.

cancer biology↗

bioRxiv2021

Host poly(A) polymerases PAPD5 and PAPD7 provide two layers of protection that ensure the integrity and stability of hepatitis B virus RNA

Noncanonical poly(A) polymerases PAPD5 and PAPD7 (PAPD5/7) stabilize HBV RNA via the interaction with the viral post-transcriptional regulatory element (PRE), representing new antiviral targets to control HBV RNA metabolism, HBsAg production and viral replication. Inhibitors targeting these proteins are being developed as antiviral therapies, therefore it is important to understand how PAPD5/7 coordinate to stabilize HBV RNA. Here, we utilized a potent small-molecule AB-452 as a chemical probe, along with genetic analyses to dissect the individual roles of PAPD5/7 in HBV RNA stability. AB-452 inhibits PAPD5/7 enzymatic activities and reduces HBsAg both in vitro (EC50 ranged from 1.4 to 6.8 nM) and in vivo by 0.93 log10. Our genetic studies demonstrate that the stem-loop alpha sequence within PRE is essential for both maintaining HBV poly(A) tail integrity and determining sensitivity towards the inhibitory effect of AB-452. Although neither single knock-out (KO) of PAPD5 nor PAPD7 reduces HBsAg RNA and protein production, PAPD5 KO does impair poly(A) tail integrity and confers partial resistance to AB-452. In contrast, PAPD7 KO could not result in any measurable phenotypic changes, but displays a similar antiviral effect as AB-452 treatment when PAPD5 is depleted simultaneously. PAPD5/7 double KO confers complete resistance to AB-452 treatment. Our results thus indicate that PAPD5 plays a dominant role in stabilizing viral RNA by protecting the integrity of its poly(A) tail, while PAPD7 serves as a second line of protection. These findings inform PAPD5 targeted therapeutic strategies and open avenues for further investigating PAPD5/7 in HBV replication. ImportanceChronic hepatitis B affects more than 250 million patients and is a major public health concern worldwide. HBsAg plays a central role in maintaining HBV persistence and as such, therapies reducing HBsAg have been extensively investigated. PAPD5/7 targeting inhibitors, with oral bioavailability, represent an opportunity to reduce both HBV RNA and HBsAg. Here we uncover that the SL sequence is required for HBV poly(A) tail integrity and RNA stability, and that the antiviral activity of AB-452 mimics the SL mutants. Although PAPD5 and PAPD7 regulate HBV RNA stability, it remains unclear how they coordinate in stabilizing HBV RNA. Based on our studies, PAPD5 plays a dominant role to stabilize viral RNA by protecting the integrity of its poly(A) tail, while PAPD7 serves as a backup protection mechanism. Our studies may point out a direction towards developing PAPD5-selective inhibitors that could be used effectively to treat chronic hepatitis B.

microbiology↗

bioRxiv2020

A Genetic Screen for Temperature-sensitive Morphogenesis-defective Caenorhabditis elegans Mutants

Morphogenesis involves coordinated cell migrations and cell shape changes that generate tissues and organs, and organize the body plan. Cell adhesion and the cytoskeleton are important for executing morphogenesis, but their regulation remains poorly understood. As genes required for embryonic morphogenesis may have earlier roles in development, temperature-sensitive embryonic-lethal mutations are useful tools for investigating this process. From a collection of [~]200 such Caenorhabditis elegans mutants, we have identified 17 that have highly penetrant embryonic morphogenesis defects after upshifts from the permissive to the restrictive temperature, just prior to the cell shape changes that mediate elongation of the ovoid embryo into a vermiform larva. Using whole genome sequencing, we identified the causal mutations in seven affected genes. These include three genes that have roles in producing the extracellular matrix, which is known to affect the morphogenesis of epithelial tissues in multicellular organisms. The rib-1 and rib-2 genes encode glycosyltransferases, and the emb-9 gene encodes a collagen subunit. We also used live imaging to characterize epidermal cell shape dynamics in one mutant, or1219ts, and observed cell elongation defects during dorsal intercalation and ventral enclosure that may be responsible for the body elongation defects. These results indicate that our screen has identified factors that influence morphogenesis and provides a platform for advancing our understanding of this fundamental biological process. SUMMARYWe performed a systematic, forward genetics screen for temperature-sensitive embryonic-lethal (TS-EL) Caenorhabditis elegans mutants that are specifically defective in embryonic morphogenesis. By taking advantage of temperature-upshifts, we identified several essential genes influencing morphogenesis. We also demonstrated that one mutant has defects in epidermal cell shape changes that likely account for the failure in morphogenesis. The TS-EL mutants we identified will be useful tools for advancing our understanding of the gene networks controlling cell shape changes and movements during morphogenesis.

genetics↗

bioRxiv2020

Extracellular Matrix Remodeling Associated With Bleomycin-Induced Lung Injury Supports Pericyte-To-Myofibroblast Transition

Of the many origins of pulmonary myofibroblasts, microvascular pericytes are a known source. Prior literature has established the ability of pericytes to transition into myofibroblasts, but provide limited insight into molecular cues that drive this process during lung injury repair and fibrosis. Fibronectin and RGD-binding integrins have long been considered pro-fibrotic factors in myofibroblast biology, and here we test the hypothesis that these known myofibroblast cues coordinate pericyte-to-myofibroblast transitions. Specifically, we hypothesized that v{beta}3 integrin engagement on fibronectin induces pericyte transition into myofibroblastic phenotypes in the murine bleomycin lung injury model. Myosin Heavy Chain 11 (Myh11)-CreERT2 lineage tracing in transgenic mice allows identification of cells of pericyte origin and provides a robust tool for isolating pericytes from tissues for further evaluation. We used this murine model to track and characterize pericyte behaviors during tissue repair. The majority of Myh11 lineage-positive cells are positive for the pericyte surface markers, PDGFR{beta} (55%) and CD146 (69%), and display typical pericyte morphology with spatial apposition to microvascular networks. After intratracheal bleomycin treatment of mice, Myh11 lineage-positive cells showed significantly increased contractile and secretory markers, as well as v integrin expression. According to RNASeq measurements, many disease and tissue-remodeling genesets were upregulated in Myh11 lineage-positive cells in response to bleomycin-induced lung injury. In vitro, blocking v{beta}3 binding through cyclo-RGDfK prevented expression of the myofibroblastic marker SMA relative to controls. In response to RGD-containing provisional matrix proteins present in lung injury, pericytes may alter their integrin profile. This altered matrix-integrin axis contributes to pericyte-to-myofibroblastic transition and represents a possible therapeutic target for limiting the myofibroblastic burden in lung fibrosis. HighlightsO_LIPericyte lineage model enables study of transdifferentiating pericytes C_LIO_LIHigh dimensional flow cytometry used to characterize pulmonary stromal cells C_LIO_LIPulmonary pericytes express matrix-remodeling genes and proteins in lung injury C_LIO_LIMyofibroblasts derived from pericytes have active v{beta}3 integrin C_LIO_LIIn vitro assay reveals necessity of RGD for pericyte transdifferentiation C_LI

cell biology↗

bioRxiv2020

Combined assessment of MHC binding and antigen expression improves T cell epitope predictions

MHC class I antigen processing consists of multiple steps that result in the presentation of MHC bound peptides that can be recognized as T cell epitopes. Many of the pathway steps can be predicted using computational methods, but one is often neglected: mRNA expression of the epitope source proteins. In this study, we improve epitope prediction by taking into account both peptide-MHC binding affinities and expression levels of the peptides source protein. Specifically, we utilized biophysical principles and existing MHC binding prediction tools in concert with RNA expression to derive a function that estimates the likelihood of a peptide being presented on a given MHC class I molecule. Our combined model of Antigen eXpression based Epitope Likelihood-Function (AXEL-F) outperformed predictions based only on binding or based only on antigen expression for discriminating eluted ligands from random background peptides as well as in predicting neoantigens that are recognized by T cells. We also showed that in cases where cancer patient-specific RNA-Seq data is not available, cancer-type matched expression data from TCGA can be used to accurately estimate patient-specific gene expression. Using AXEL-F together with TGCA expression data we were able to more accurately predict neoantigens that are recognized by T cells. The method is available in the IEDB Analysis Resource and free to use for the academic community. Significance statementEpitope prediction tools have been used to call epitopes in viruses and other pathogens for almost 30 years, and more recently, to call cancer neoantigens. Several such tools have been developed, however most of them ignore the mRNA expression of the epitope source proteins. In the present study, we have, to our knowledge for the first time, developed a biophysically motivated model to combine peptide-MHC binding and abundance of the peptides source protein to improve epitope predictions. Our novel tool AXEL-F is freely available on the IEDB and presents a clear opportunity for predicting and selecting epitopes more efficiently.

bioinformatics↗

bioRxiv2020

Effects of sheared chromatin length on ChIP-seq quality and sensitivity

Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for identifying, on a genome-wide scale, the segments of DNA bound by specific transcription factors (TFs) or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets vary over a wide range, with a substantial fraction being of intermediate to poor quality. Such experimental variability can lead to many false positives or false negatives, impairing the ability to interpret the data. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focus on the sonication step to produce sheared chromatin, a variable controllable by the user and applicable to all ChIP-seq protocols. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measured the distribution of resultant fragment lengths using the Agilent Bioanalzyer 2100, and then immunoprecipitated these batches of chromatin using highly specific antibodies against either TAL1 or CTCF. We found that the level of sonication, which was affected by both the number of sonication cycles, as well as the starting cell number, had a pronounced impact on the quality of resulting ChIP-seq signals. Specifically, over-sonication led to degradation of quality (e.g. increased background and reduction in signal), while the impact of under-sonication of chromatin differed between the two transcription factors, leading to the loss of sites occupied by TAL1 but not those bound by CTCF. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in primary hematopoietic progenitor cells, including several rare cell types. Together, these results suggest that the amount of sonication is a key variable in success of ChIP-seq experiments, and that carefully monitoring the level of chromatin sonication is one way to improve ChIP-seq quality and reproducibility, which in turn facilitates low input ChIP-seq in rare cell types.

genomics↗

bioRxiv2020

Rapid Development of Improved Data-dependent Acquisition Strategies.

Tandem mass spectrometry (LC-MS/MS) is widely used to identify unknown ions in untargeted metabolomics. Data Dependent Acquisition (DDA) chooses which ions to fragment based upon intensity observed in MS1 survey scans and typically only fragment a small subset of the ions present. Despite this inefficiency, relatively little work has addressed the development of new DDA methods, partly due to the high overhead associated with running the many extracts necessary to optimise approaches in busy MS facilities. In this work, we firstly provide theoretical results that show how much improvement is possible over current DDA strategies. We then describe an in silico framework for fast and cost efficient development of new DDA acquisition strategies using a previously developed Virtual Metabolomics Mass Spectrometer (ViMMS). Additional functionality is added to ViMMS to allow methods to be used both in simulation and on real samples via an instrument application programming interface (API). We demonstrate this framework through the development and optimisation of two new DDA methods which introduce new advanced ion prioritisation strategies. Upon application of the here developed methods to two complex metabolite mixtures, our results show that they are able to fragment more unique ions than standard DDA acquisition strategies.

bioinformatics↗

bioRxiv2020

Rethinking GPS Navigation: Creating Cognitive Maps Through Auditory Clues

GPS navigation is commonplace in everyday life. While it has the capacity to make our lives easier, it is often used to automate functions that were once exclusively performed by our brain. Staying mentally active is key to healthy brain aging. Therefore, is GPS navigation causing more harm than good? Here we demonstrate that traditional turn-by-turn navigation promotes passive spatial navigation and ultimately, poor spatial learning of the surrounding environment. We propose an alternative form of GPS navigation based on sensory augmentation, that has the potential to fundamentally alter the way we navigate with GPS. By implementing a 3D spatial audio system similar to an auditory compass, users are directed towards their destination without explicit directions. Rather than being led passively through verbal directions, users are encouraged to take an active role in their own spatial navigation, leading to more accurate cognitive maps of space. Technology will always play a significant role in everyday life; however, it is important that we actively engage with the world around us. By simply rethinking the way we interact with GPS navigation, we can engage users in their own spatial navigation, leading to a better spatial understanding of the explored environment.

neuroscience↗

bioRxiv2020

Diminished adherence of snail hemocytes to schistosome sporocysts of Schistosoma mansoni following programmed knockout of the allograft inflammatory factor of Biomphalaria glabrata

BackgroundLarval development in an intermediate host gastropod snail of the genus Biomphalaria is an obligatory component of the life cycle of Schistosoma mansoni. Understanding of the mechanism(s) of host defense may hasten the development of tools that block transmission of schistosomiasis. The allograft inflammatory factor 1, AIF, which is evolutionarily conserved and expressed in phagocytes, is a marker of macrophage activation in both mammals and invertebrates. AIF enhances cell proliferation and migration. The embryonic cell line, termed Bge, from Biomphalaria glabrata is a versatile resource for investigation of the snail-schistosome relationship since Bge exhibits a hemocyte-like phenotype. Hemocytes perform central roles in innate and cellular immunity in gastropods and in some cases can kill the parasite. However, the Bge cells do not kill the parasite in vitro. MethodsBge cells were transfected by electroporation with plasmid pCas-BgAIFx4, encoding the Cas9 nuclease and a guide RNA specific for exon 4 of the B. glabrata AIF (BgAIF) gene. Transcript levels for Cas9 and for BgAIF were monitored by quantitative reverse-transcription-PCR and, in parallel, adhesion of gene-edited Bge cells during co-culture with of schistosome sporocysts was assessed. ResultsGene knockout manipulation induced gene-disrupting indels, frequently 1-2 bp insertions and/or 8-30 bp deletions, at the programmed target site; a range from 9 to 17% of the copies of the BgAIF gene in the Bge population of cells were mutated. Transcript levels for BgAIF were reduced by up to 73% (49.5{+/-}20.2% S.D, P [≤] 0.05, n =12). Adherence by BgAIF gene-edited ({Delta}BgAIF) Bge to sporocysts diminished in comparison to wild type cells, although cell morphology did not change. Specifically, as scored by a semi-quantitative cell adherence index (CAI), fewer {Delta}BgAIF than control wild type cells adhered to sporocysts; control CAI, 2.66{+/-}0.10, {Delta}BgAIF, 2.30{+/-}0.22 (P [≤] 0.01). ConclusionThe findings supported the hypothesis that BgAIF plays a role in the adherence of B. glabrata hemocytes to sporocysts during schistosome infection in vitro. This demonstration of the activity of programmed gene editing will enable functional genomics approaches using CRISPR/Cas9 to investigate additional components of the snail-schistosome host-parasite relationship.

molecular biology↗

bioRxiv2020

Orally Bioavailable Endochin-like Quinolone Carbonate Ester Prodrug Reduces Toxoplasma gondii Brain Cysts

Toxoplasmosis is a potentially fatal infection for immunocompromised people and the developing fetus. Current medicines for toxoplasmosis have high rates of adverse effects that interfere with therapeutic and prophylactic regimens. Endochin-like quinolones (ELQs) are potent inhibitors of Toxoplasma gondii proliferation in vitro and in animal models of acute and latent infection. ELQ-316, in particular, was found to be effective orally against acute toxoplasmosis in mice and highly selective for the T. gondii cytochrome b over the human cytochrome b. Despite oral efficacy, the high crystallinity of ELQ-316 limits oral absorption, plasma concentrations and therapeutic potential. A carbonate ester prodrug of ELQ-316, ELQ-334, was created to decrease crystallinity and increase oral bioavailability, which resulted in a six-fold increase in both Cmax (maximum plasma concentration) and AUC (area under the curve) of ELQ-316. The increased bioavailability of ELQ-316, when administered as ELQ-334, resulted in greater efficacy than the equivalent dose of ELQ-316 against acute toxoplasmosis and had similar efficacy against latent toxoplasmosis compared to intraperitoneal administration of ELQ-316. Carbonate ester prodrugs are a successful strategy to overcome the limited oral bioavailability of ELQs for the treatment of toxoplasmosis.

pharmacology and toxicology↗

bioRxiv2020

Single Chlamydomonas reinhardi (C. reinhardtii) cell separation from bacterial cells and auto-fluorescence tracking with a nano-sieve device

A planar, transparent, and adaptable nano-sieve device is developed for efficient microalgae/bacteria separation. In our strategy, a sacrificial layer is applied in the dual photolithography patterning to achieve a one-dimensional channel with a very low aspect ratio (1:10,000). Microalgae/bacteria mixture is then introduced into the deformable polydimethylsiloxane (PDMS) nano-channel. The hydrodynamic deformation of the nano-channel is regulated to allow the bacteria cells to pass through while leaving the microalgae cells trapped in the device. At a flow rate of 4 l/min, ~100% of the microalgae cells are trapped in the device. Additionally, this device is capable of immobilizing single cells in a transparent channel for auto-fluorescence tracking. These microalgae cells demonstrate minimal photo-bleaching over 250 s laser exposure and can be used to monitor hazardous compounds in the sample with a continuous flow fashion. Our method will be valuable to purify microalgae samples containing contaminations and study single cell heterogeneity.

bioengineering↗

bioRxiv2019

Comparative therapeutic potential of ALX-0171 and palivizumab against RSV clinical isolate infection of well-differentiated primary pediatric bronchial epithelial cell cultures

Respiratory syncytial virus (RSV) causes severe lower respiratory tract infections in young infants. There are no RSV-specific treatments available. Ablynx has been developing an anti-RSV F-specific Nanobody(R), ALX-0171. To characterise the therapeutic potential of ALX-0171 we exploited our well-differentiated primary pediatric bronchial epithelial cell (WD-PBEC)/RSV infection model, which replicates several hallmarks of RSV disease in vivo. Using 2 clinical isolates (BT2a; Memphis 37), we compared the therapeutic potential of ALX-0171 with palivizumab, which is currently prescribed for RSV prophylaxis in high-risk infants. ALX-0171 treatment (900 mM) at 24 h post-infection reduced apically released RSV titers to near or below the limit of detection within 24 h for both strains. Progressively lower doses resulted in concomitantly diminished RSV neutralisation. ALX-0171 was approximately 3 fold more potent in this therapeutic RSV/WD-PBEC model than palivizumab (mean IC50 = 346.9-363.6 nM and 1048-1090 nM for ALX-0171 and palivizumab, respectively), irrespective of the clinical isolate. When viral genomic copies (GC) were measured by RT-qPCR, the therapeutic effect was considerably less and GCs were only moderately reduced (0.62 - 1.28 Log10 copies/mL) by ALX-0171 treatment at 300 and 900 nM. Similar findings were evident for palivizumab. Therefore, ALX-0171 was very potent at neutralising RSV released from apical surfaces but only had a limited impact on virus replication. The data indicate a clear disparity between viable virus neutralisation and GC viral load, the latter of which does not discriminate between viable and neutralised RSV. This study validates the RSV/WD-PBEC model for the pre-clinical evaluation of RSV antivirals.

microbiology↗

bioRxiv2019

Nanopore sequencing of the glucocerebrosidase (GBA) gene in a New Zealand Parkinsons disease cohort

IntroductionBi-allelic mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. Gaucher disease causing GBA mutations in the heterozygous state are also high risk factors for Parkinsons disease (PD). GBA analysis is challenging due to a related pseudogene and structural variations (SVs) that can occur at this locus. We have applied and refined a recently developed nanopore DNA sequencing method to analyze GBA variants in a clinically assessed New Zealand longitudinal cohort of PD. MethodWe examined amplicons encompassing the coding region of GBA (8.9kb) from 229 PD cases and 50 healthy controls using the GridION nanopore sequencing platform, and Sanger validation. ResultsWe detected 23 variants in 21 PD cases (9.2% of patients). We detected modest PD risk variant p.N409S (rs76763715) in one case, p.E365K (rs2230288) in 12 cases, and p.T408M (rs75548401) in seven cases, one of whom also had p.E365K. We additionally detected the possible risk variants p.R78C (rs146774384) in one case, p.D179H (rs147138516) in one case which occurred on the same haplotype as p.E365K, and one novel variant c.335C>T or p.(L335=), that potentially impacts splicing of GBA transcripts. Additionally, we found a higher prevalence of dementia among patients with GBA variants. ConclusionThis work confirmed the utility of nanopore sequencing as a high-throughput method to identify known and novel GBA variants, and to assign precise haplotypes. Our observations may contribute to improved understanding of the effects of variants on disease pathogenesis, and to the development of more targeted treatments.

genetics↗

bioRxiv2019

Complex processes of cryptic speciation in mouse lemurs from a micro-endemism hotspot in Madagascar

AO_SCPLOWBSTRACTC_SCPLOWMouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic explosion has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we take an integrative approach to investigate species diversity in two pairs of sister lineages that occur in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among them. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the species-level distinction of two previously described species, M. mittermeieri and M. lehilahytsara is not supported - a result that is particularly striking when using the genealogical discordance index (gdi). Non-sister lineages occur sympatrically in two of the localities sampled for this study, despite an estimated divergence time of less than 1 Ma. This suggests rapid evolution of reproductive isolation in the focal lineages, and in the mouse lemur clade generally. The divergence time estimates reported here are based on the MSC and calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated concatenated likelihood estimates, however. We discuss the possible explanations for this discrepancy, noting that there are theoretical justifications for preferring the MSC estimates in this case.

evolutionary biology↗

bioRxiv2019

An ethnobotanical study of the genus Elymus

Grains of domesticated grasses (Poaceae) have long been a global food source and constitute the bulk of calories in the human diet. Recent efforts to establish more sustainable agricultural systems have focused in part on the development of herbaceous, perennial crops. Perennial plants have extensive root systems that stabilize soil and absorb water and nutrients at greater rates than their annual counterparts; consequently, perennial grasses are important potential candidates for grain domestication. While most contemporary grass domesticates consumed by humans are annual plants, there are over 7,000 perennial grass species that remain largely unexplored for domestication purposes. Documenting ethnobotanical uses of wild perennial grasses could aid in the evaluation of candidate species for de novo crop development. The objectives of this study are 1) to provide an ethnobotanical survey of the grass genus Elymus; and 2) to investigate floret size variation in species used by people. Elymus includes approximately 150 perennial species distributed in temperate and subtropical regions, of which at least 21 taxa have recorded nutritional, medicinal, and/or material uses. Elymus species used for food by humans warrant pre-breeding and future analyses to assess potential utility in perennial agricultural systems.

plant biology↗

bioRxiv2019

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Thousands of epigenomic datasets have been generated in the past decade, but it is difficult for researchers to effectively utilize all the data relevant to their projects. Systematic integrative analysis can help meet this need, and the VISION project was established for ValIdated Systematic IntegratiON of epigenomic data in hematopoiesis. Here, we systematically integrated extensive data recording epigenetic features and transcriptomes from many sources, including individual laboratories and consortia, to produce a comprehensive view of the regulatory landscape of differentiating hematopoietic cell types in mouse. By employing IDEAS as our Integrative and Discriminative Epigenome Annotation System, we identified and assigned epigenetic states simultaneously along chromosomes and across cell types, precisely and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of over 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and promoters. The transitions in epigenetic states of these cCREs across cell types provided insights into mechanisms of regulation, including decreases in numbers of active cCREs during differentiation of most lineages, transitions from poised to active or inactive states, and shifts in nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at cCREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website (usevision.org) to aid research in genomics and hematopoiesis.

genomics↗