Biology subjects

Adams, M.

Publications and source records attributed to Adams, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Structural Insights into The Role of MAGEA4 in RAD18 Regulation: Implications for Ubiquitin Ligase-Binding across the MAGE Protein Family

Melanoma associated antigen 4 (MAGEA4) is a cancer-testis antigen (CTA) that is primarily expressed in the testes of healthy adults but is aberrantly overexpressed and also a poor prognostic marker in several human cancers. In its cancer-specific role, MAGEA4 interacts with RAD18 and activates trans-lesion DNA synthesis (TLS), potentially favouring tumour evolution. However, the precise mode of interaction between RAD18 and MAGEA4 and its implications on the ubiquitination activity of RAD18 are unknown. Here, we employed NMR and AlphaFold2 (AF) to reveal that the ubiquitin-conjugating enzyme RAD6-binding domain (R6BD) of RAD18 interacts with a groove in the C-terminal winged-helix subdomain (WH) of MAGEA4. Using cross-linking mass spectrometry (XL-MS), we found that MAGEA4 displaces RAD6 from the R6BD of RAD18 and inhibits degradative autoubiquitination of RAD18, which could be countered by a competing short peptide of the RAD18 R6B region. AF and XL-MS also revealed an evolutionary invariant intramolecular interaction within RAD18 between the catalytic RING and the DNA-binding SAP domains that is essential for the ubiquitination of PCNA. Using interaction proteomics, we revealed that another Type-I MAGE, MAGE-C2, interacts with the RING ubiquitin ligase TRIM28 in a similar fashion as the MAGEA4/RAD18 complex. We propose that the peptide-binding groove identified in the C-terminal WH of MAGEA4 exists in other type-I MAGE proteins and serves as a ligase-binding cleft. Our data reveal crucial insights into RAD18-mediated ubiquitination of PCNA and its regulation by MAGE-A4.

biochemistry↗

bioRxiv2023

Undergraduates' reactions to errors mediates the association between growth mindset and study strategies

BackgroundStudents employ a variety of study strategies to learn and master content in their courses. Strategies vary widely in their effectiveness for promoting deep, long-term learning, yet most students use ineffective strategies frequently. Efforts to educate students about effective study strategies have revealed that knowledge about effective strategies is by itself insufficient for encouraging widespread and lasting changes. An important next step is to uncover factors that influence the decisions students make about study strategy use. We explored the association between beliefs about intelligence (mindset, universality, and brilliance) and study strategies. The most effective study strategies are error-prone, and beliefs about intelligence carry implications for whether errors are a normal and even beneficial part of the learning process (e.g., growth mindset) or signs of insufficient intelligence (e.g., fixed mindset). Therefore, we hypothesized that beliefs about and reactions to errors would mediate a relationship between beliefs about intelligence and study strategies. We tested this hypothesis by surveying 345 undergraduates enrolled in an introductory biology class at a public, research-active university in northwestern United States. ResultsConfirmatory factor analysis indicated that the internal structure of all measures functioned as expected in our sample. We fit a structural equation model to evaluate our hypothesized model. We found that mindset, but not universality nor brilliance, predicts variance in both beliefs about errors and reactions to errors. In turn, adaptive reactions to errors (but not beliefs about errors) are associated with the use of highly effective study strategies and spacing study sessions. There was a significant indirect relationship between growth mindset and spacing of study sessions. ConclusionsOur results provide evidence for a mechanism explaining the association between students mindset beliefs and academic outcomes: believing that intelligence is improvable is associated with more adaptive reactions to making errors, which correlates with choosing more error-prone and therefore more effective study strategies. Future interventions aimed at improving students study strategies may be more effective if they simultaneously target reacting adaptively to errors and emphasize that intelligence is improvable.

scientific communication and education↗

bioRxiv2023

A monocarboxylate transporter rescues frontotemporal dementia and Alzheimer's disease models

Brains are highly metabolically active organs, consuming 20% of an organisms energy at resting state. A decline in glucose metabolism is a common feature across a number of neurodegenerative diseases. Another common feature is the progressive accumulation of insoluble protein deposits, its unclear if the two are linked. Glucose metabolism in the brain is highly coupled between neurons and glia, with glucose taken up by glia and metabolised to lactate, which is then shuttled via transporters to neurons, where it is converted back to pyruvate and fed into the TCA cycle for ATP production. Monocarboxylates are also involved in signalling, and play broad ranging roles in brain homeostasis and metabolic reprogramming. However, the role of monocarboxylates in dementia has not been tested. Here, we find that increasing pyruvate import in Drosophila neurons by over-expression of the transporter bumpel, leads to a rescue of lifespan and behavioural phenotypes in fly models of both frontotemporal dementia and Alzheimers disease. The rescue is linked to a clearance of late stage autolysosomes, leading to degradation of toxic peptides associated with disease. We propose upregulation of pyruvate import into neurons as potentially a broad-scope therapeutic approach to increase neuronal autophagy, which could be beneficial for multiple dementias.

neuroscience↗

bioRxiv2023

Spatial transcriptomics reveals molecular dysfunction associated with Lewy pathology

Lewy pathology composed of -synuclein is the key pathological hallmark of Parkinsons disease (PD), found both in dopaminergic neurons that control motor function, and throughout cortical regions that control cognitive function. Recent work has investigated which dopaminergic neurons are most susceptible to death, but little is known about which neurons are vulnerable to developing Lewy pathology and what molecular changes an aggregate induces. In the current study, we use spatial transcriptomics to selectively capture whole transcriptome signatures from cortical neurons with Lewy pathology compared to those without pathology in the same brains. We find, both in PD and in a mouse model of PD, that there are specific classes of excitatory neurons that are vulnerable to developing Lewy pathology in the cortex. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. This gene signature indicates that neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. However, beyond DNA repair gene upregulation, we find that neurons also activate apoptotic pathways, suggesting that if DNA repair fails, neurons undergo programmed cell death. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and identify a conserved signature of molecular dysfunction in both mice and humans.

neuroscience↗

bioRxiv2023

Long-term climatic stability drives accumulation and maintenance of divergent lineages in a temperate biodiversity hotspot

Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic in the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.

evolutionary biology↗

bioRxiv2023

p53 modulates kinase inhibitor resistance and lineage plasticity in NF1-related MPNSTs

Malignant peripheral nerve sheath tumors (MPNSTs) are chemotherapy resistant sarcomas that are a leading cause of death in neurofibromatosis type 1 (NF1). Although NF1-related MPNSTs derive from neural crest cell origin, they also exhibit intratumoral heterogeneity. TP53 mutations are associated with significantly decreased survival in MPNSTs, however the mechanisms underlying TP53-mediated therapy responses are unclear in the context of NF1-deficiency. We evaluated the role of two commonly altered genes, MET and TP53, in kinome reprograming and cellular differentiation in preclinical MPNST mouse models. We previously showed that MET amplification occurs early in human MPNST progression and that Trp53 loss abrogated MET-addiction resulting in MET inhibitor resistance. Here we demonstrate a novel mechanism of therapy resistance whereby p53 alters MET stability, localization, and downstream signaling leading to kinome reprogramming and lineage plasticity. Trp53 loss also resulted in a shift from RAS/ERK to AKT signaling and enhanced sensitivity to MEK and mTOR inhibition. In response to MET, MEK and mTOR inhibition, we observed broad and heterogeneous activation of key differentiation genes in Trp53-deficient lines suggesting Trp53 loss also impacts lineage plasticity in MPNSTs. These results demonstrate the mechanisms by which p53 loss alters MET dependency and therapy resistance in MPNSTS through kinome reprogramming and phenotypic flexibility.

cancer biology↗

bioRxiv2022

Combined single-sample metabolomics and RNAseq reveals a hepatic pyrimidine metabolic response to acute viral infection

ObjectiveMetabolomics and RNA sequencing (RNAseq) each provide powerful readouts of phenotype, and integration of these data can provide information greater than the sum of their parts. The ability to conduct such analysis on a single sample has many practical advantages, especially when dealing with rare or difficult-to-obtain samples. While methods exist to isolate multiple biomolecular subclasses from the same sample, in-depth analysis of the suitability of these approaches for multi- omics readouts is lacking. MethodsMice were injected with lymphocytic choriomeningitis virus (LCMV) or vehicle (Veh) control and liver tissue was harvested 2.5-days later. RNA was isolated from aliquots of pulverized liver tissue either following metabolite extraction using 80% methanol (MetRNA) or directly from frozen tissue (RNA). RNA sequencing data was evaluated by differential expression analysis via edgeR and dispersion using Ginis mean differences. Differential metabolite abundance was assessed using LIMMA. Pathway enrichment analysis was conducted on metabolomics and RNAseq data using MetaboAnalysts joint-integration tools. ResultsPrior metabolite extraction had no deleterious effects on quality or quantity of isolated RNA. RNA and MetRNA generated from the same sample clustered together by principal component analysis, indicating that inter-individual differences were the largest source of variance. Of the 2,169 genes that were differentially expressed between LCMV and Veh, the vast majority (n=1,848) were shared between extraction method, with the remainder evenly divided between RNA (n=165) and MetRNA (n=156). These differentially expressed genes unique to extraction method were attributed to randomness around the false discovery rate (FDR) = 0.05 cutoff and stochastic changes in variance estimation. Gini analysis further revealed that extraction method had no effect on the dispersion of detected transcripts across the entire dataset. To demonstrate the power of multi-omics integration on interrogated metabolic phenotypes, we next performed integrated pathway enrichment analysis on RNAseq data and metabolomics data. Our analysis revealed pyrimidine metabolism as the most impacted pathway by LCMV infection. Plotting up- and down-regulated genes and metabolites on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pyrimidine pathway exposed a pattern enzymatic degradation of pyrimidine nucleotides to generate the nucleobase uracil. Further, uracil was among the most differentially abundant metabolite in serum of LCMV infected mice, suggesting a novel mechanism of hepatic uracil export in acute infection response. ConclusionsWe demonstrate that prior metabolite extraction does not have a deleterious effect on RNAseq quality, which enables investigators to confidently perform metabolomics and RNAseq on the same sample. Implementation of this approach revealed a novel involvement of the hepatic pyrimidine metabolism during acute viral infection.

molecular biology↗

bioRxiv2022

Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion

The Mandalorion tool, which we have continuously developed over the last 5 years, identifies and quantifies high-confidence isoforms from accurate full-length transcriptome sequencing reads produced by methods like PacBio Iso-Seq and ONT-based R2C2. In this manuscript, we introduce and benchmark Mandalorion v4 which further improves upon the already strong performance of Mandalorion v3.6 used in the LRGASP consortium challenge. By processing real and simulated accurate full-length transcriptome sequencing data sets, we show three main features of Mandalorion: First, Mandalorion-based isoform identification has very high Precision and maintains high Recall even when used in the absence of any genome annotation. Second, isoform read counts as quantified by Mandalorion show high correlation with simulated read counts. Third, isoforms identified by Mandalorion closely reflect the full-length transcriptome sequencing data sets they are based on.

bioinformatics↗

bioRxiv2022

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary leading to the diversification of this genus over the last 20 million years. Here, we report the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

evolutionary biology↗

bioRxiv2022

DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

We have developed a mouse Infinium DNA methylation array that contains 297,415 probes to capture the diversity of mouse DNA methylation biology. We present a mouse DNA methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, age, sex, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This MM285 mouse array is widely accessible to the research community, and will accelerate future high sample-throughput studies in this important model organism.

genomics↗

bioRxiv2022

STORM-seq Reveals Differentiation Trajectories of Primary Human Fallopian Tube Epithelium

Despite significant advances, current single-cell RNA sequencing (scRNA-seq) technologies often struggle with accurately detecting non-coding transcripts, achieving full-length RNA coverage, and/or resolving transcript-level complexity. Many are also difficult to implement or inaccessible without specialized liquid handlers, further limiting their utility. We present Single-cell TOtal RNA-seq Miniaturized (STORM-seq), a random- hexamer primed, ribo-reduced single-cell total RNA sequencing (sc-total-RNA-seq) protocol using standard laboratory equipment. Adapted as a kit, STORM-seq constructs sequence-ready libraries in one working day, producing the highest complexity scRNA- seq libraries to-date, robustly measuring transcript isoforms and clinically relevant gene fusions in single cells. STORM-seq faithfully reconstructs expression profiles of locus- level transposable elements (TEs), and provides high-resolution profiling of transient, low- abundance enhancer RNAs (eRNAs), offering a powerful tool to dissect single-cell gene regulatory networks in unprecedented detail. Applied to human fallopian tube epithelium, the improved transcriptional resolution reveals a putative progenitor-like population and intermediate cell states, shaped by TEs and non-coding RNAs.

molecular biology↗

bioRxiv2022

ARID1A maintains transcriptionally repressive H3.3 associated with CHD4-ZMYND8 chromatin interactions

ARID1A is a signature subunit of the mammalian SWI/SNF (BAF) chromatin remodeling complex and is mutated at a high rate in malignancies and benign diseases originating from the uterine endometrium. Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements. ARID1A loss leads to H3.3 depletion at ARID1A bound active regulatory elements and a concomitant redistribution of H3.3 towards genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3-containing chromatin regulation. ZMYND8, the CHD4-interacting acetyl-histone H4 reader, specifies ARID1A-CHD4-H3.3 target regulatory activity towards histone H4 lysine 16 acetylation (H4K16ac) to repress super-enhancers. ARID1A, H3.3, CHD4, and ZMYND8 co-repress the expression of genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas. Altogether, these studies demonstrate that cooperation among a histone reader and different types of chromatin remodelers safeguards the endometrium through transcriptionally repressive H3.3.

genetics↗

bioRxiv2021

Illumina But With Nanopore: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2

High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays exist today to take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities, and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the R2C2 method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, as well as regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.

genomics↗

bioRxiv2021

A Budding Yeast Model and Screen to Define the Functional Consequences of Oncogenic Histone Missense Mutations

Somatic missense mutations in histone genes turn these essential proteins into oncohistones, which can drive oncogenesis. Understanding how missense mutations alter histone function is challenging in mammals as mutations occur in a single histone gene. For example, described oncohistone mutations predominantly occur in the histone H3.3 gene, despite the human genome encoding 15 H3 genes. To understand how oncogenic histone missense mutations alter histone function, we leveraged the budding yeast model, which contains only two H3 genes, to explore the functional consequences of oncohistones H3K36M, H3G34W, H3G34L, H3G34R, and H3G34V. Analysis of cells that express each of these variants as the sole copy of H3 reveals that H3K36 mutants show different drug sensitivities compared to H3G34 mutants. This finding suggests that changes to proximal amino acids in the H3 N-terminal tail alter distinct biological pathways. We exploited the caffeine sensitive growth of H3K36 mutant cells to perform a high copy suppressor screen. This screen identified genes linked to histone function and transcriptional regulation, including Esa1, a histone H4/H2A acetyltransferase; Tos4, a forkhead-associated domain-containing gene expression regulator; Pho92, an N6-methyladenosine RNA binding protein and Sgv1/Bur1, a cyclin-dependent kinase. We show that the Esa1 lysine acetyltransferase activity is critical for suppression of the caffeine sensitive growth of H3K36R mutant cells while the previously characterized binding interactions of Tos4 and Pho92 are not required for suppression. This screen identifies pathways that could be altered by oncohistone mutations and highlights the value of yeast genetics to identify pathways altered by such mutations.

genetics↗

bioRxiv2021

Combined PI3K and MLL inhibition synergizes in models of HR+ breast cancer

The high frequency of aberrant PI3K pathway activation in hormone receptor-positive (HR+) breast cancer has led to the development, clinical testing, and approval of the p110-selective PI3K inhibitor alpelisib. The limited clinical efficacy of alpelisib and other PI3K inhibitors is partially attributed to the functional antagonism between PI3K and estrogen receptor (ER) signaling, which is mitigated via combined PI3K inhibition and endocrine therapy. We and others have previously demonstrated a chromatin-associated mechanism by which PI3K supports cancer development and antagonizes ER signaling through the modulation of H3K4 methylation. Here we show that inhibition of the H3K4 histone methyltransferase MLL1 in combination with PI3K inhibition impairs HR+ breast cancer clonogenicity and cell proliferation. While combined PI3K/MLL1 inhibition reduces AKT effector signaling and H3K4 methylation, MLL1 inhibition increases PI3K effector signaling and upregulates the expression of receptor tyrosine kinase signaling cascades upstream of and including AKT. These data reveal a feedback loop between MLL1 and AKT in which MLL1 inhibition reactivates AKT. We additionally show that combined PI3K and MLL1 inhibition synergizes to cause cell death in in vitro and in vivo models of HR+ breast cancer, which is enhanced by the additional genetic ablation of the H3K4 methyltransferase and AKT target MLL4. Together, our data provide evidence of a feedback mechanism connecting histone methylation with AKT and may support the preclinical development and testing of pan-MLL inhibitors. Significance StatementPharmacological inhibition of PI3K provides limited efficacy in PIK3CA-mutated, HR+ breast cancers. Here the authors leverage PI3K/AKT-driven chromatin modification to identify MLL histone methyltransferases as a therapeutic target. Dual PI3K and MLL inhibition synergize to reduce clonogenicity and cell proliferation while enhancing apoptosis in in vitro models, and induces tumor regression in xenograft models of PI3K-activated, HR+ breast cancer. Furthermore, MLL1 inhibition reveals a feedback loop leading to AKT hyperactivation, which is relieved with combined PI3K/MLL inhibition. These findings demonstrate the utility of MLL inhibitors for the treatment of some solid cancers, as patients with HR+ breast cancer characterized by PIK3CA mutation may derive clinical benefit from combined PI3K/MLL inhibition.

cancer biology↗

bioRxiv2021

Structural basis for protein glutamylation by the Legionella pseudokinase SidJ

Legionella pneumophila (LP) avoids phagocytosis by secreting nearly 300 effector proteins into the host cytosol. SidE family of effectors (SdeA, SdeB, SdeC and SidE) employ phosphoribosyl serine ubiquitination to target an array of host Rab GTPases and innate immune factors. To suppress the deleterious toxicity of SidE enzymes in a timely manner, LP employs a metaeffector named SidJ. Upon activation by host Calmodulin (CaM), SidJ executes an ATP-dependent glutamylation to modify the catalytic residue Glu860 in the mono-ADP-ribosyl transferase (mART) domain of SdeA. SidJ is a unique glutamylase that adopts a kinase-like fold but contains two nucleotide-binding pockets. There is a lack of consensus about the substrate recognition and catalytic mechanism of SidJ. Here, we determined the cryo-EM structure of SidJ in complex with its substrate SdeA in two different states of catalysis. Our structures reveal that both phosphodiesterase (PDE) and mART domains of SdeA make extensive contacts with SidJ. In the pre-glutamylation state structure of the SidJ-SdeA complex, adenylylated E860 of SdeA is inserted into the non-canonical (migrated) nucleotide-binding pocket of SidJ. Structure-based mutational analysis indicates that SidJ employs its migrated pocket for the glutamylation of SdeA. Finally, using mass spectrometry, we identified several transient autoAMPylation sites close to both the catalytic pockets of SidJ. Our data provide unique insights into the substrate recognition and the mechanism of protein glutamylation by the pseudokinase SidJ.

biochemistry↗

bioRxiv2021

Neuron-type specificity of dorsal raphe projections to ventral tegmental area

The midbrain dorsal raphe (DR) and ventral tegmental area (VTA) contain two of the brains main ascending neuromodulatory transmitters: serotonin and dopamine. We studied the pathway from DR to VTA using single-cell RNA sequencing, anatomical tracing, and electrophysiology and behavior in mice. Single-cell sequencing confirmed a differential distribution of dopamine cell types between medial and lateral aspects of the VTA. This molecular diversity included differential expression of a subset of glutamatergic and serotonergic receptors. Anatomical data showed that distinct serotonergic and glutamatergic populations of DR neurons project to distinct medial-lateral locations in VTA. Physiological data showed that serotonergic neurons are positioned to excite putative dopaminergic neurons in lateral VTA on short timescales (within trial), and inhibit them on long timescales (on the next trial). Our results reveal precise anatomical specificity of DR projections to VTA, and suggest a functional role for serotonergic modulation of dopaminergic function across multiple timescales.

neuroscience↗

bioRxiv2019

Chromosome-scale genome assembly of a single outbred Drosophila melanogaster

A high quality genome assembly is a vital first step for the study of an organism. Recent advances in technology have made the creation of high quality chromosome scale assemblies feasible and low cost. However, the amount of input DNA needed for an assembly project can be a limiting factor for small organisms or precious samples. Here we demonstrate the feasibility of creating a chromosome scale assembly using a hybrid method for a low input sample, a single outbred Drosophila melanogaster. Our approach combines an Illumina shotgun library, Oxford nanopore long reads, and chromosome conformation capture for long range scaffolding. This single fly genome assembly has a N50 of 26 Mb, a length that encompasses entire chromosome arms, contains 95% of expected single copy orthologs, and a nearly complete assembly of this individuals Wolbachia endosymbiont. The methods described here enable the accurate and complete assembly of genomes from small, field collected organisms as well as precious clinical samples.

genomics↗