Biology subjects

Patterson, M.

Publications and source records attributed to Patterson, M..

32 records · Page 2Linked to original sources

bioRxiv2022

Felidae call type and species identification based on acoustic features

The cat family Felidae is one of the most successful carnivore lineages today. However, the study of the evolution of acoustic communication between felids remains a challenge due to the lack of fossils, the limited availability of audio recordings because of their largely solitary and secretive behavior, and the underdevelopment of computational models and methods needed to address acoustic evolutionary questions. This study is a first attempt at developing a machine learning-based approach to the classification of felid calls as well as the identification of acoustic features that distinguish felid call types and species from one another. A felid call dataset was developed by extracting audio clips from diverse sources. The audio clips were manually annotated for call type and species. Due to the limited availability of samples, this study focused on the Pantherinae subfamily. Time-frequency features were then extracted from the Pantherinae dataset. Finally, several classification algorithms were applied to the resulting data. We achieved 91% accuracy for this Pantherinae call type classification. For the species classification, we obtained 86% accuracy. We also obtained the most predictive features for each of the classifications performed. These features can inform future research into the evolutionary acoustic analysis of the felid group.

animal behavior and cognition↗

bioRxiv2022

Molecular basis of DNA recognition by the HMG-box-C1 module of Capicua

The HMG-box protein Capicua (CIC) is an evolutionarily conserved transcriptional repressor with key functions in development and disease-associated processes. CIC binds DNA using an exclusive mechanism that requires both its HMG-box and a separate domain called C1, but how these domains cooperate to recognize specific DNA sequences is not known. Here we report the crystal structure of the human CIC HMG-box and C1 domains in complex with an 18-base-pair DNA oligomer containing a consensus octameric CIC binding site. We find that both protein domains adopt independent tri-helical structures that pack against opposite sides of the DNA helix. The C1 domain in particular folds into a helix-turn-helix (HTH) structure that resembles the FF phosphoprotein binding domain. It inserts into the major groove of the DNA and plays a direct role in enhancing both the affinity and sequence specificity of CIC DNA binding. Our results reveal a unique bipartite protein module, ensuring highly specific DNA recognition by CIC, and show how this mechanism is disrupted by cancer mutations affecting either the HMG-box or C1 domains.

biochemistry↗

bioRxiv2021

Machupo virus with mutations in the transmembrane domain and glycosylation sites is attenuated and immunogenic in animal models of Bolivian Hemorrhagic Fever

Several highly pathogenic mammarenaviruses cause severe hemorrhagic and neurologic disease in humans, for which vaccines and antivirals are limited or unavailable. New World (NW) mammarenavirus Machupo virus (MACV) infection causes Bolivian hemorrhagic fever in humans. We previously reported that the disruption of specific N-linked glycan sites on the glycoprotein (GPC) partially attenuate MACV in an IFN-{beta}/{gamma} receptor knockout mouse model. However, some capability to induce neurological pathology still remained. Highly pathogenic Junin virus (JUNV) is another NW arenavirus closely related to MACV. A F427I substitution in the GPC transmembrane domain (TMD) rendered JUNV attenuated in a lethal mouse model after intracranial inoculation. In this study, we rationally designed and rescued a MACV containing mutations at two glycosylation sites and the corresponding F438I substitution in GPC TMD. The MACV mutant is fully attenuated in IFN-{beta}/{gamma} receptor knockout mice and outbred guinea pigs. Furthermore, inoculation with this mutant MACV fully protected guinea pigs from wild-type MACV lethal challenge. Lastly, we found the GPC TMD F438I substitution greatly impaired MACV growth in neuronal cell lines of mouse and human origins. Our results highlight the critical roles of the glycans and the TMD on the GPC in arenavirus virulence, which informs the rational design of potential vaccine candidates for highly pathogenic arenaviruses. ImportanceFor arenaviruses, the only vaccine available is the live-attenuated Candid#1 vaccine, a JUNV vaccine approved in Argentina. We and others have found that the glycans on GPC and the F427 residue in the GPC TMD are important for virulence of JUNV. Nevertheless, mutating either of them is not sufficient for full and stable attenuation of JUNV. Using reverse genetics, we disrupted specific glycosylation sites on MACV GPC, and also introduced the corresponding F438I substitution in the GPC TMD. This MACV mutant is fully attenuated in two animal models and protects animals from lethal infection. Thus, our studies highlight the feasibility of rational attenuation of highly pathogenic arenaviruses for vaccine development. Another important finding from this study is that the F438I substitution in GPC TMD could substantially affect MACV replication in neurons. Future studies are warranted to elucidate the underlying mechanism and the implication of this mutation in arenavirus neural tropism.

microbiology↗

bioRxiv2021

A Comprehensive Overview of the Physical Health of the Adolescent Brain Cognitive Development Study (ABCD) Cohort at Baseline

Physical health in childhood is crucial for neurobiological as well as overall development, and can shape long-term outcomes into adulthood. The landmark, longitudinal Adolescent Brain Cognitive Development StudySM (ABCD study(R)), was designed to investigate brain development and health in almost 12,000 youth who were recruited when they were 9-10 years old and will be followed through adolescence and early adulthood. The overall goal of this paper is to provide descriptive analyses of physical health measures in the ABCD study at baseline, including but not limited to sleep, physical activity and sports involvement, and body mass index, and how these measures vary across demographic groups. This paper outlines how the physical health of the ABCD sample corresponds with that of the US population and highlights important avenues for health disparity research. This manuscript will provide important information for ABCD users and help guide analyses investigating physical health as it pertains to adolescent and young adult development.

developmental biology↗

bioRxiv2020

Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase

Most terpene synthase reactions follow Markovnikov rules for formation of high energy carbenium ion intermediates. However, there are notable exceptions. For example, pentalenene synthase (PS) undergoes an initial anti-Markovnikov cyclization reaction followed by a 1,2-hydride shift to form an intermediate humulyl cation with positive charge on the secondary carbon C9 of the farnesyl diphosphate substrate. The mechanism by which these enzymes stabilize and guide regioselectivity of secondary carbocations has not heretofore been elucidated. In an effort to better understand these reactions, we grew crystals of apo-PS, soaked them with the non-reactive substrate analog 12,13-difluorofarnesyl diphosphate, and solved the x-ray structure of the resulting complex at 2.2 [A] resolution. The most striking feature of the active site structure is that C9 is positioned 3.5 [A] above the center of the side chain benzene ring of residue F76, perfectly poised for stabilization of the charge through a cation-{pi} interaction. In addition, the main chain carbonyl of I177 and neighboring intramolecular C6,C7-double bond are positioned to stabilize the carbocation by interaction with the face opposite that of F76. Mutagenesis experiments also support a role for residue 76 in cation-{pi} interactions. Most interesting is the F76W mutant which gives a mixture of products that likely result from stabilizing a positive charge on the adjacent secondary carbon C10 in addition to C9 as in the wild-type enzyme. The crystal structure of the F76W mutant clearly shows carbons C9 and C10 centered above the fused benzene and pyrrole rings of the indole side chain, respectively, such that a carbocation at either position could be stabilized in this complex, and two anti-Markovnikov products, pentalenene and humulene, are formed. Finally, we show that there is a rough correlation (although not absolute) of an aromatic side chain (F or Y) at position 76 in related terpene synthases from Streptomyces that catalyze similar anti-Markovnikov addition reactions.

biochemistry↗

bioRxiv2019

Changing environments reveal innovative genetic variation in children's cortisol responses

Genetic associations with biopsychosocial phenotypes are often interpreted as evidence that the genome codes for fixed end-states. Instead, a given genotype might regulate a dynamic range of phenotypes in response to environmental change. We collected hair cortisol (n = 1,104), salivary cortisol in reaction to an in-laboratory stressor (n = 537), and diurnal salivary cortisol (n = 488) from twins aged 8-15 years in the Texas Twin Project. Baseline genetic variation in both salivary and hair cortisol was not simply magnified after stressor exposure or after waking. Rather, novel genetic influences on cortisol arose over time. Thus, environmental change can reveal genetic variation that would not otherwise be observed in static cortisol levels. These findings are in line with the notion that the genome regulates individuals reactions to the environment that differ across environments.

genetics↗

bioRxiv2019

Effective clustering for Single Cell Sequencing cancer data

Single cell sequencing (SCS) technologies provide a level of resolution that makes it indispensable for inferring from a sequenced tumor, evolutionary trees or phylogenies representing an accumulation of cancerous mutations. A drawback of SCS is elevated false negative and missing value rates, resulting in a large space of possible solutions, which in turn makes it difficult, sometimes infeasible using current approaches and tools. One possible solution is to reduce the size of an SCS instance -- usually represented as a matrix of presence, absence, and uncertainty of the mutations found in the different sequenced cells -- and to infer the tree from this reduced-size instance. In this work, we present a new clustering procedure aimed at clustering such categorical vector, or matrix data -- here representing SCS instances, called celluloid. We show that celluloid clusters mutations with high precision: never pairing too many mutations that are unrelated in the ground truth, but also obtains accurate results in terms of the phylogeny inferred downstream from the reduced instance produced by this method. We demonstrate the usefulness of a clustering step by applying the entire pipeline (clustering + inference method) to a real dataset, showing a significant reduction in the runtime, raising considerably the upper bound on the size of SCS instances which can be solved in practice. Our approach, celluloid: clustering single cell sequencing data around centroids is available at https://github.com/AlgoLab/celluloid/ under an MIT license, as well as on the Python Package Index (PyPI) at https://pypi.org/project/celluloid-clust/

cancer biology↗

bioRxiv2018

An Open-Source Plate Reader

Microplate readers are foundational instruments in experimental biology and bioengineering that enable multiplexed spectrophotometric measurements. To enhance their accessibility, we here report the design, construction, validation, and benchmarking of an open-source microplate reader. The system features full-spectrum absorbance and fluorescence emission detection, in situ optogenetic stimulation, and stand-alone touch screen programming of automated assay protocols. The total system costs <$3500, a fraction of the cost of commercial plate readers, and can detect the fluorescence of common dyes down to [~]10 nanomolar concentration. Functional capabilities were demonstrated in context of synthetic biology, optogenetics, and photosensory biology: by steady-state measurements of ligand-induced reporter gene expression in a model of bacterial quorum sensing, and by flavin photocycling kinetic measurements of a LOV (light-oxygen-voltage) domain photoreceptor used for optogenetic transcriptional activation. Fully detailed guides for assembling the device and automating it using the custom Python-based API (Application Program Interface) are provided. This work contributes a key technology to the growing community-wide infrastructure of open-source biology-focused hardware, whose creation is facilitated by rapid prototyping capabilities and low-cost electronics, optoelectronics, and microcomputers.\n\nTable of Contents Graphic\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC=\"FIGDIR/small/413781_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@c26eaborg.highwire.dtl.DTLVardef@efb695org.highwire.dtl.DTLVardef@1bc2f41org.highwire.dtl.DTLVardef@1c25c79_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2018

gpps: An ILP-based approach for inferringcancer progression with mutation losses fromsingle cell data

cancer biology↗

bioRxiv2018

High-risk human papillomaviruses down-regulate expression of the Ste20 family kinase MST1 to inhibit the Hippo pathway and promote transformation

Human papillomaviruses (HPV) are a major cause of malignancy worldwide They are the aetiological agent of almost all cervical cancers and an increasing number of head and neck carcinomas. Deregulation of the Hippo pathway component YAP1 has recently been demonstrated to play a role in HPV-mediated cervical cancer, but whether other components of this pathway are implicated in the pathogenesis of this disease remains poorly understood.\n\nThe expression level and activation status of critical Hippo pathway components were analysed across multiple cytology samples from patients with cervical disease, as well as HPV positive (HPV+) and HPV negative (HPV-) cervical cancer cell lines using real time qPCR, western blot and immunohistochemistry. In parallel, we assessed the effects of MST1 and MST2 overexpression upon cervical cancer cell proliferation, migration and invasion. Finally, we interrogated the consequences of interrupted MST1 and MST2 function using a targeted small molecule inhibitor in tandem with kinase inactive MST mutants. Our analysis found that expression of the Ste20 kinase MST1 was decreased within both HPV+ primary patient samples and cervical cancer cell lines. This effect was mediated by the virus-coded oncoproteins E6 and E7, which impair MST1 transcription. Reintroduction of MST1, or its paralogue MST2, into HPV positive cervical cancer cells re-activated the Hippo pathway, leading to a reduction in cell proliferation, migration and invasion. Finally, using a small molecule inhibitor of MST1/2 or kinase inactive mutants of either protein, we demonstrated that this effect required the kinase function of MST1/2. Our results reveal that HPV down regulates MST1 expression to inactivate the Hippo pathway and so drive cells towards transformation.

microbiology↗

bioRxiv2018

Inferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations

MotivationIn recent years, the well-known Infinite Sites Assumption (ISA) has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progressions seen as an accumulation of mutations. However, recent studies (Kuipers et al., 2017) leveraging Single-cell Sequencing (SCS) techniques have shown evidence of the widespread recurrence and, especially, loss of mutations in several tumor samples. Still, established methods that can infer phylogenies with mutation losses are however lacking.\n\nResultsWe present the SASC (Simulated Annealing Single-Cell inference) tool which is a new and robust approach based on simulated annealing for the inference of cancer progression from SCS data. More precisely, we introduce a simple extension of the model of evolution where mutations are only accumulated, by allowing also a limited amount of back mutations in the evolutionary history of the tumor: the Dollo-k model. We demonstrate that SASC achieves high levels of accuracy when tested on both simulated and real data sets and in comparison with some other available methods.\n\nAvailabilityThe Simulated Annealing Single-cell inference (SASC) tool is open source and available at https://github.com/sciccolella/sasc.\n\nContacts.ciccolella@campus.unimib.it

bioinformatics↗

bioRxiv2017

HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads

BackgroundHaplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays cheaper to produce and more widely available than ever before, have been used to reduce the fragmentation of the assembled haplotypes since their ability to span several variants along the genome. These long reads are also characterized by a high error rate, an issue which may be mitigated, however, with larger sets of reads, when this error rate is uniform across genome positions. Unfortunately, current state-of-the-art dynamic programming approaches designed for long reads deal only with limited coverages.\n\nResultsHere, we propose a new method for assembling haplotypes which combines and extends the features of previous approaches to deal with long reads and higher coverages. In particular, our algorithm is able to dynamically adapt the estimated number of errors at each variant site, while minimizing the total number of error corrections necessary for finding a feasible solution. This allows our method to significantly reduce the required computational resources, allowing to consider datasets composed of higher coverages. The algorithm has been implemented in a freely available tool, HapCHAT: Haplotype Assembly Coverage Handling by Adapting Thresholds. An experimental analysis on sequencing reads with up to 60x coverage reveals improvements in accuracy and recall achieved by considering a higher coverage with lower runtimes.\n\nConclusionsOur method leverages the long-range information of sequencing reads that allows to obtain assembled haplotypes fragmented in a lower number of unphased haplotype blocks. At the same time, our method is also able to deal with higher coverages to better correct the errors in the original reads and to obtain more accurate haplotypes as a result.\n\nAvailabilityHapCHAT is available at http://hapchat.algolab.eu under the GPL license.

bioinformatics↗

bioRxiv2016

Correlated Evolution of Metabolic Functions over the Tree of Life

We are interested in the structure and evolution of metabolism in order to better understand its complexity. We study metabolic functions in 1459 species within which several hundreds of thousands of families of homologous genes have been identified [17]. Given a protein sequence, PRIAM search [5] delivers probabilities of the presence of several thousand enzymes (ECs). This allows us to infer reaction sets and to construct a metabolic network for an organism, given its set of sequences.\n\nWe then propagate these ECs to the ancestral nodes of the species tree using maximimum likelihood methods. These evolutionary scenarios are systematically compared using pairwise mutual information. We identify co-evolving enzyme sets from the graph of these relationships using community detection algorithms [1,3]. This sheds light on the structure of the metabolic networks in terms of co-evolving metabolic modules. These modules are also interpreted from a functional perspective using stoichiometric models of metabolic networks.

evolutionary biology↗

bioRxiv2016

WhatsHap: fast and accurate read-based phasing

Read-based phasing allows to reconstruct the haplotypes of a sample purely from sequencing reads. While phasing is an important step for answering questions about population genetics, compound heterozygosity, and to aid in clinical decision making, there has been a lack of accurate, usable and standards-based software.\n\nWhatsHap is a production-ready tool for highly accurate read-based phasing. It was designed from the beginning to leverage third-generation sequencing technologies, whose long reads can span many variants and are therefore ideal for phasing. WhatsHap works also well with second-generation data, is easy to use and will phase not only SNVs, but also indels and other variants. It is unique in its ability to combine read-based with pedigree-based phasing, allowing to further improve accuracy if multiple related samples are provided.

bioinformatics↗