bioRxiv Science⌕ Search

Biology subjects

Richards, M.

Publications and source records attributed to Richards, M..

At least 19 recordsLinked to original sources

Prostate cancer associated fibroblasts have distinct morphomechanical features that are associated with patient outcome

Tumour development and progression reshape the physical properties of the surrounding tumour microenvironment (TME) including its biomechanical traits. This is driven by a prominent cell type in the TME, cancer associated fibroblasts (CAFs), which increases tissue stiffness via extracellular matrix deposition and remodelling. Currently, it is unclear whether there are also physical changes to CAFs at the cellular level and, if so, how they relate to patient outcome. Here we show that CAFs have distinct morphological and biomechanical features from normal fibroblasts. We examined matched, patient-derived CAFs and non-malignant prostate fibroblasts (NPFs) from 35 patients with primary prostate cancer. Morphologically, CAFs had more aligned stress fibres, and larger and more elongated nuclei, based on quantitative image analysis of confocal microscopy images. In addition, single-cell mechanical measurements using real-time deformability cytometry showed that CAFs are larger and stiffer than NPFs. These changes were consistent across patients and validated with atomic force microscopy. A combined morphomechanical score encompassing these features was significantly associated with patient outcome. In transcriptomic analyses, the score was correlated with microtubule dynamics and a myofibroblast phenotype. Importantly, we also demonstrated that morphomechanical features of prostate fibroblasts are modified by approved treatments for prostate cancer, such as docetaxel, and other small molecular inhibitors, such as axitinib. In summary, changes in cellular morphomechanical properties are a consistent feature of CAFs and associated with patient outcome. Moreover, cellular morphomechanical properties can be therapeutically targeted, potentially providing a new strategy for manipulating the TME to control cancer progression.

cancer biology↗

Do the shuffle: Expanding the synthetic biology toolkit for shufflon-like recombination systems

Naturally occurring DNA inversion systems play an important role in the generation of genetic variation and adaptation in prokaryotes. Shufflon invertase (SI) Rci from plasmid R64, recognizing asymmetric sfx sites, has been adopted as a tool for synthetic biology. However, the availability of a single enzyme with moderate rates of recombination has hampered the more widespread use of SIs. We identified 14 previously untested SI genes and their sfx sites in public databases. We established an assay based on single-molecule sequencing that allows the quantification of the inversion rates of these enzymes and determined cross-recognition to identify orthogonal SI/sfx pairs. We describe SI enzymes with substantially improved shuffling rates when expressed in an inducible manner in E. coli. Our findings will facilitate the use of SIs in engineering biology where synthetic shufflons enable the generation of millions of sequence variants in vivo for applications such as barcoding or experimental selection.

synthetic biology↗

Neuropilin-1 controls vascular permeability through juxtacrine regulation of endothelial adherens junctions

Neuropilin-1 (NRP1) regulates endothelial cell (EC) biology through modulation of vascular endothelial growth factor receptor 2 (VEGFR2) signalling by presenting VEGFA to VEGFR2. How NRP1 impacts VEGFA-mediated vascular hyperpermeability has however remained unresolved, described as exerting either a positive or a passive function. Using EC-specific Nrp1 knock-out mice, we discover that EC-expressed NRP1 exerts an organotypic role. In the ear skin, VEGFA/VEGFR2-mediated vascular leakage was increased following loss of EC NRP1, implicating NRP1 in negative regulation of VEGFR2 signalling. In contrast, in the back skin and trachea, loss of EC NRP1 decreased vascular leakage. In accordance, phosphorylation of vascular endothelial (VE)-cadherin was increased in the ear skin but suppressed in the back skin of Nrp1 iECKO mice. NRP1 expressed on perivascular cells has been shown to impact VEGF-mediated VEGFR2 signalling. Importantly, expression of NRP1 on perivascular cells was more abundant in the ear skin than in the back skin. Global loss of NRP1 resulted in suppressed VEGFA-induced vascular leakage in the ear skin, implicating perivascular NRP1 as a juxtacrine co-receptor of VEGFA in this compartment. Altogether, we demonstrate that perivascular NRP1 is an active participant in EC VEGFA/VEGFR2 signalling and acts as an organotypic modifier of EC biology.

cell biology↗

Trapping studies reveal phenology and reproductive behaviour in two solitary sweat bees (Hymenoptera: Halictidae)

A transition from univoltine to bivoltine life histories, potentially due to the lengthening of flight seasons, is thought to have preceded the evolutionary transition from solitary to eusocial behaviour in halictid bees. Most behavioral studies which allow us to map these demographic and social transitions on phylogenies have focused on eusocial species, leaving a gap in behavioral data regarding solitary halictid bees. This lack of behavioral trait data is due to the great difficulty in locating the nests of solitary bees for study. However, long-term trapping studies are an effective method providing insights into the demography and social status of halictid bees. We used pan-trapped specimens to investigate flight phenology and solitary reproduction Lasioglossum leucozonium (Schrank) and L. zonulum (Smith), from the socially and demographically labile subgenus Leuchalictus. We found L. leucozonium to be univoltine and solitary across its range, regardless of the length of flight season. In contrast, L. zonulum is phenologically flexible, being univoltine in the shorter flight seasons of Alberta, but bivoltine in southern Ontario. In both L. leucozonium and univoltine L. zonulum, higher than expected numbers of old, worn females with declining ovarian development foraged late into the season, suggesting that an indeterminate breeding strategy represents an ancestral condition not found in eusocial species. In bivoltine L. zonulum, the large size and higher fecundity of Brood 1 offspring suggest that after evolutionary reversion from eusocial to solitary behaviour, selection for worker-sized daughters may be reversed to selection for larger body sizes. The demographic plasticity demonstrated by L. zonulum may hint that partial bivoltinism is more widespread than currently documented. Future studies aimed at clarifying the demographic and social traits of more halictids will pave the way for comparative studies and eventual confidence in tracing how behavioral traits have changed and evolved in halictid bees.

animal behavior and cognition↗

Costs and benefits of maternal nest choice: tradeoffs between brood survival and thermal stress for small carpenter bees

Nest site selection is a crucial decision for bees because where mothers construct their nests influences the developmental environment of their offspring. Small carpenter bees (Ceratina calcarata) nest in sun or shade, suggesting that maternal decisions about nest sites are influenced by thermal conditions that influence juvenile growth and survival. We investigated the costs and benefits to mothers and their offspring of warmer or cooler nest sites using a field experiment in which mothers and newly founded nests were placed in sunny or shady habitats. Maternal costs and benefits in sunny and shady treatments were quantified by comparing brood provisioning behaviour, nest size, number of brood cells, and offspring survival rates. Juvenile costs and benefits were quantified as body size, high temperature tolerance (CTmax), metabolic rate, and pupal duration. The major maternal benefit of nesting in sun was significantly lower rates of total nest failure (caused by predation, parasitism or abandonment), which led to sun mothers producing 3.2 brood on average, while shade mothers produced only 2.9. However, sun nesting entailed costs to brood, which were significantly smaller, less likely to survive to adulthood and had significantly elevated CTmax. This suggests that juvenile bees in sun nests bees experienced thermal stress during development, causing them to shunt resources from growth to thermoprotection, at the cost of smaller size and higher mortality. Pupae raised in a thermal-gradient "BeeCR" machine developed significantly faster at warmer average temperatures, which may be an additional benefit of sun nesting. Overall, our results highlight a tradeoff between maternal benefits and offspring costs when mothers choose nest sites, in which maternal fitness is enhanced by nesting in sun, despite significant physiological costs to offspring, due to the necessity for thermoprotective responses. Thinking through pandemic researchThe first lockdowns of the COVID-19 pandemic began as we prepared to enter the second field season of this study in 2020. Student research halted overnight. Lab access and travel were restricted. With limited access to field sites and no access to lab equipment, we brainstormed alternative approaches that would repeat, if not replicate, our main experiments of 2019 and fulfill degree requirements for JL de Haans MSc in a satisfying way. Our 2019 results had provided convincing evidence developmental temperature has long-term impacts on C. calcarata physiology, so we thought about which physiological measurements would be feasible outside the lab. Authors MH Richards and GJ Tattersall suggested collecting more measurements of CTmax: the Peltier plate device required running water, but a portable water pump and a bucket allowed the apparatus to be set up anywhere. No calibration of instruments was required, and the only maintenance was to change the water in the bucket after a few hours of use. Thus, a students home basement became a laboratory. To investigate how temperatures affect developmental rate, we needed to raise bees in controlled environments, but incubators were not available. Author A Skandalis suggested repurposing a gradient PCR unit as a portable insect incubator ("The BeeCR"). The idea was tested successfully at home in 20202, so a larger study was done by J Maretzki in 2021 when undergraduate lab access was permitted again. Two outcomes of our pandemic pivot produced long-term benefits for our research. The BeeCR is a flexible, inexpensive, easy-to-use incubator perfectly suited for raising small insects at multiple simultaneous sets of variable temperatures. And the ease with which "field" sites could be established in our backyards demonstrates how amenable small carpenter bees are to field manipulations, suggesting this is a model species for addressing a variety of ecological and physiological questions.

ecology↗

Claudin5 protects the peripheral endothelial barrier in an organ and vessel type-specific manner

The pathogenesis of numerous diseases is characterised by disruption of the junctions that form the endothelial cell (EC) barrier, the composition of which may differ greatly between organs. However, the expression level variability and precise contribution of different junctional proteins is poorly understood. Here, we focus on organs with continuous endothelium to identify structural and functional in vivo characteristics of the EC barrier. Assembly of multiple single-cell RNAseq datasets into a single integrated database revealed the variability in EC barrier patterning. Across tissues Claudin5 exhibited diminishing expression along the arteriovenous axis, which correlates with EC barrier integrity. Functional analysis identified tissue-specific differences in leakage patterning and response to agonist-induced leakage. We uncover that Claudin5 loss enhances agonist-induced leakage in an organotypic, vessel type-specific and size-selective manner in an inducible, EC-specific, knock-out mouse. Mechanistically, Claudin5 loss induces no change in junction ultrastructure but alters composition, with concomitant loss of zonula occludens-1 (ZO-1) expression and upregulation of VE-Cadherin. These findings uncover the organ-specific organisation of the EC barrier and distinct importance of Claudin5 in different vascular beds and will aid our ability to modify EC barrier stability in a targeted, organ-specific manner.

cell biology↗

The novel conserved NAD+ binding micropeptide SGHRT regulates mitochondrial function and metabolism in human cardiomyocytes

AbstractsNicotinamide adenine dinucleotide (NAD) is a critical metabolite and coenzyme for multiple metabolic pathways and cellular processes (1-4). In this study, we identified Singheart, SGHRT as a nuclear genome-encoded NAD+-binding mitochondrial micropeptide. SGHRT, present in both monomeric and dimeric forms, binds directly to NAD, but not NADH or flavin adenine dinucleotide (FAD). Localized to the inner mitochondrial membrane and mitochondrial matrix, SGHRT interacts with the mitochondrial enzymes Succinate-CoA Ligase and Succinate Dehydrogenase. SGHRT deletion in human embryonic stem cell derived cardiomyocytes disrupted mitochondria morphology, decreased total NAD and ATP abundance, and resulted in defective TCA cycle metabolism, the electron transport chain and in Ox-Phos processes. These results comprise the first report of an NAD+-binding micropeptide, SGHRT, required for mitochondrial function and metabolism.

cell biology↗

Pre-determined macromolecular leakage sites with dynamic properties establish endothelial intra-vessel heterogeneity

Endothelial cells display heterogeneous properties based on location and function. How this heterogeneity influences endothelial barrier stability both between and within vessel subtypes is unexplored. We find here that endothelial cells exhibit heterogeneous barrier properties on inter-organ and intra-vessel levels. Using intravital microscopy and sequential stimulation of the ear dermis with vascular endothelial growth factor-A and/or histamine, we observe distinct, reappearing sites, common for both agonists, where leakage preferentially takes place. Further, through repetitive stimulation of the diaphragm and trachea, we find inter-organ conservation of such leakage sites. Qualitatively, pre-determined sites display distinct leakage properties and enhanced barrier breakdown compared to less susceptible regions. Mechanistically, pre-determined sites exhibit lower laminin 5 deposition, which correlates with reduced junctional vascular endothelial (VE)-Cadherin. These data thus highlight functional intra-vessel heterogeneity that defines pre-determined sites which display distinct leakage properties and which may have great impact on pathological vascular leakage and drug delivery.

cell biology↗

Phase-separation of EML4-ALK variant 3 is dependent upon an active ALK conformation

Oncogenic fusions involving tyrosine kinases are common drivers of non-small cell lung cancer (NSCLC). There are at least 15 different variants of the EML4-ALK fusion, all of which have a similar portion of ALK that includes the kinase domain, but different portions of EML4. Targeted treatment with ALK tyrosine kinase inhibitors (TKIs) has proven effective but patient outcomes are variable. Here, we focus on one common variant, EML4-ALK V3, which drives an aggressive form of the disease. EML4-ALK V3 protein forms cytoplasmic liquid droplets that contain the signalling proteins GRB2 and SOS1. The TKIs ceritinib and lorlatinib dissolve these droplets and the EML4-ALK V3 protein re-localises to microtubules, an effect recapitulated by an inactivating mutation in the ALK catalytic site. Mutations that promote a constitutively active ALK stabilise the liquid droplets even in the presence of TKIs, indicating that droplets do not depend on kinase activity per se. Uniquely, the TKI alectinib promotes droplet formation of both the wild-type and catalytically inactive EML4-ALK V3 mutant, but not in a mutant that disrupts a hallmark of the kinase activity, the Lys-Glu salt-bridge. We propose that EML4-ALK V3 liquid droplet formation occurs through transient dimerization of the ALK kinase domain in its active conformation in the context of stable EML4-ALK trimers. Our results provide insights into the relationship between ALK activity, conformational state and the sub-cellular localisation of EML4-ALK V3 protein, and reveal the different effects of structurally divergent ALK TKIs on these properties.

cell biology↗

Emergent biases in compensatory mutation can drive gene regulatory network evolution

Gene regulatory networks underlie every aspect of life; better understanding their assembly would better our understanding of evolution more generally. For example, evolutionary theory typically assumed that low-fitness intermediary pathways are not a significant factor in evolution, yet there is substantial empirical evidence of compensatory mutation. Here we revise theoretical assumptions to explore the possibility that compensatory mutation may drive rapid evolutionary recovery. Using a well-established in silico model of gene regulatory networks, we show that assuming only that deleterious mutations are not fatal, compensatory mutation is surprisingly frequent. Further, we find that it entails biases that drive the evolution of regulatory pathways. In our simulations, we find compensatory mutation to be common during periods of relaxed selection, with 8-15% of degraded networks having regulatory function restored by a single randomly-generated additional mutation. Though this process reduces average robustness, proportionally higher robustness is found in networks where compensatory mutations occur close to the deleterious mutation site, or where the compensatory mutation results in a large regulatory effect size. This location- and size-specific robustness systematically biases which networks are purged by selection for network stability, producing emergent changes to the population of regulatory networks. We show that over time, large-effect and co-located mutations accumulate, assuming only that episodes of relaxed selection occur, even very rarely. This accumulation results in an increase in regulatory complexity. Our findings help explain a process by which large-effect mutations structure complex regulatory networks, and may account for the speed and pervasiveness of observed occurrence of compensatory mutation, for example in the context of antibiotic resistance, which we discuss. If sustained by in vitro experiments, these results promise a significant breakthrough in the understanding of evolutionary and regulatory processes.

systems biology↗

An animal society based on kin competition, not kin cooperation

Animals respond to competition among kin for critical breeding resources in two ways: avoidance of direct fitness costs via dispersal of siblings to breed separately, and formation of kin-based societies in which subordinates offset direct fitness costs of breeding competition via altruism and increased indirect fitness. Here we provide the first evidence that kin competition can promote the evolution of societies based on non-kin cooperation. For eastern carpenter bees, nests are a critical breeding resource in perpetually short supply, leading to strong competition among females. Observations of individually marked and genotyped females demonstrate that sisters disperse from their natal nests to join social groups of nonrelatives. By forming social groups of non-kin, females increase their chances of successful reproduction, while avoiding the indirect fitness cost of competition among sisters. One Sentence SummaryWe describe the first known example of an animal society based on avoidance of kin competition rather than on promotion of kin cooperation.

evolutionary biology↗

Genomic interrogation of the burden and transmission of multidrug-resistant pathogens within and across hospital networks

BackgroundMultidrug-resistant organisms (MDROs) disproportionately affect hospitalized patients due to the combination of comorbidities, frequent antimicrobial use, and in-hospital MDRO transmission. Identification of MDRO transmission by hospital microbiology laboratories is difficult due to limitations of existing typing methods.\n\nMethodsWe conducted a prospective multicenter genomics implementation study (8 hospitals, 2800 beds) from 24th April to 18th June 2017 in Melbourne, Australia. Clinical and screening isolates from hospital inpatients were collected for six MDROs (vanA VRE, MRSA, ESBL E. coli [ESBL-Ec] and Klebsiella pneumoniae [ESBL-Kp], and carbapenem-resistant Pseudomonas aeruginosa [CRPa] and Acinetobacter baumannii [CRAb]), sequenced (Illumina NextSeq) and analyzed using open-source tools. MDRO transmission was assessed by genomics (core SNP phylogeny, grouped by species and ST) and compared to epidemiologic data.\n\nResults408 isolates were collected from 358 patients; 47.5% were screening isolates. ESBL-Ec was most common (52.5%), then MRSA (21.6%), vanA VRE (15.7%) and ESBL-Kp (7.6%).\n\nWe define the transmission rate for each MDRO by genomics and epidemiology; 31.6% of all study patients had potential genomic links to other study isolates; 86% of these were confirmed by epidemiologic links (probable or possible transmission). The highest transmission rates occurred with vanA VRE (88.4% of patients).\n\nConclusionsCombining genomics with high-quality epidemiologic data gives substantial insights into the burden and distribution of critical MDROs in hospitals, including in-hospital transmission. By defining transmission rates by genomics, we hope to enable comparisons over time and between sites, and introduce this as a new outcome measure to assess the efficacy of infection control interventions.

genomics↗

Metabolic Profiling of Aortic Stenosis and Hypertrophic Cardiomyopathy Identifies Mechanistic Contrasts in Substrate Utilisation

BackgroundAortic stenosis (AS) and hypertrophic cardiomyopathy (HCM) are highly distinct disorders leading to left ventricular hypertrophy (LVH), but whether cardiac metabolism substantially differs between these in humans remains to be elucidated.\n\nMethodWe undertook a detailed invasive (aortic root and coronary sinus) metabolic profiling in patients with severe AS and HCM in comparison to non-LVH controls, to investigate cardiac fuel selection and metabolic remodelling. These patients were assessed under different physiological states (at rest and during stress induced by pacing). The identified changes in the metabolome were further validated by metabolomic and orthogonal transcriptomic analysis, in separately recruited patient cohorts.\n\nResultsWe identified a highly discriminant metabolomic signature in severe AS characterised by striking accumulation of long-chain acylcarnitines, intermediates of long-chain transport and fatty acid metabolism, and validated this in a separate cohort. Mechanistically, we identify a down-regulation in the PPAR- transcriptional network, including expression of genes regulating FAO.\n\nConclusionsWe present a comprehensive analysis of changes in the metabolic pathways (transcriptome to metabolome) in severe AS, and its comparison to HCM. Our results demonstrate fundamental distinctions in substrate preference between AS and HCM, highlighting insufficient long-chain FAO, and the PPAR- signalling network as a specific metabolic therapeutic target in AS.

systems biology↗

Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy

As the general population ages and the incidence of diabetes increases epidemically, more people are affected by eye diseases, such as retinopathies. It is therefore critical to improve imaging of eye disease mouse models. Here, we demonstrate that 1) rapid, quantitative 3D and 4D (time lapse) imaging of cellular and subcellular processes in the murine eye is feasible, with and without tissue clearing, using light-sheet fluorescent microscopy (LSFM) and 2) LSFM readily reveals new features of even well studied eye disease mouse models, such as the Oxygen-Induced Retinopathy (OIR) model. Through correlative LSFM-Confocal imaging we find that flat-mounting retinas for confocal microscopy significantly distorts tissue morphology. The minimized distortion with LSFM dramatically improved analysis of pathological vascular tufts in the OIR model revealing \"knotted\" morphologies, leading to a proposed new tuft nomenclature. Furthermore, live-imaging of OIR tuft formation revealed abnormal cell motility and altered filopodia dynamics. We conclude that quantitative 3D/4D LSFM imaging and analysis has the potential to advance our understanding of pathological processes in the eye, in particular neuro-vascular degenerative processes.

developmental biology↗

EML4-ALK V3 drives cell migration through NEK9 and NEK7 kinases in non-small-cell lung cancer

EML4-ALK is an oncogenic fusion present in [~]5% lung adenocarcinomas. However, distinct EML4-ALK variants differ in the length of the EML4 microtubule-associated protein encoded within the fusion and are associated with a poorly understood variability in disease progression and therapeutic response. Here, we show that EML4-ALK variant 3, which is linked to accelerated metastatic spread and worse patient outcome, causes microtubule stabilization, formation of extended cytoplasmic protrusions, loss of cell polarity and increased cell migration. Strikingly, this is dependent upon the NEK9 kinase that interacts with the N-terminal region of EML4. Overexpression of wild-type EML4, as well as constitutive activation of NEK9, also perturbs cell morphology and accelerates cell migration in a manner that requires the downstream kinase NEK7 but not ALK activity. Moreover, elevated NEK9 is associated in patients with EML4-ALK V3 expression, as well as reduced progression-free and overall survival. Hence, we propose that EML4-ALK V3 promotes microtubule stabilization through recruitment of NEK9 and NEK7 to increase cell migration and that this represents a novel actionable pathway that drives disease progression in lung cancer.

cancer biology↗

Mitotic phosphorylation by Nek6 and Nek7 reduces microtubule affinity of EML4 to alter spindle dynamics and promote chromosome congression

EML4 is a microtubule-associated protein that promotes microtubule stability. We show here that EML4 is distributed as punctate foci along the microtubule lattice in interphase but exhibits reduced association with spindle microtubules in mitosis. Microtubule sedimentation and cryo-electron microscopy and 3D reconstruction reveal that EML4 binds via its basic N-terminal domain to the acidic C-terminal tails of - and {beta}-tubulin on the microtubule surface. The mitotic kinases Nek6 and Nek7 can phosphorylate EML4 N-terminal domain at S144 and S146 in vitro, and depletion of these kinases leads to increased EML4 binding to microtubules in mitosis. An S144A-S146A double mutant not only binds inappropriately to mitotic microtubules but also interferes with chromosome congression. Meanwhile, constitutive activation of Nek6 or Nek7 reduces EML4 association with interphase microtubules. Together, these data support a model in which Nek6 and Nek7-dependent phosphorylation promotes dissociation of EML4 from microtubules in mitosis thereby altering microtubule dynamics to enable chromosome congression.

cell biology↗

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

PREMISE OF THE STUDYAt the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high-alpine flora of the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities.\n\nMETHODSWe used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assed how maximum elevation explains phylogenetic structure. To evaluate similarities between summits we quantified phylogenetic turnover, taking into consideration micro-habitats (talus vs. meadows).\n\nKEY RESULTSWe found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely no different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: significant overdispersion degraded as elevation increased. Between summits we found high phylogenetic turnover, which was driven by greater niche heterogeneity on summits with alpine meadows.\n\nCONCLUSIONSThis study provides further evidence that stochastic processes shape the assembly of vascular plant communities in the high-alpine at regional scales. However, order-specific patterns suggest adaptations may be important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important to disentangle the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.

evolutionary biology↗

Reproducible big data science: A case study in continuous FAIRness

Big biomedical data create exciting opportunities for discovery, but make it difficult to capture analyses and outputs in forms that are findable, accessible, interoperable, and reusable (FAIR). In response, we describe tools that make it easy to capture, and assign identifiers to, data and code throughout the data lifecycle. We illustrate the use of these tools via a case study involving a multi-step analysis that creates an atlas of putative transcription factor binding sites from terabytes of ENCODE DNase I hypersensitive sites sequencing data. We show how the tools automate routine but complex tasks, capture analysis algorithms in understandable and reusable forms, and harness fast networks and powerful cloud computers to process data rapidly, all without sacrificing usability or reproducibility--thus ensuring that big data are not hard-to-(re)use data. We compare and contrast our approach with other approaches to big data analysis and reproducibility.

bioinformatics↗