Towards high-throughput 3D insect capture for species discovery and diagnostics

Digitisation of natural history collections not only preserves precious information about biological diversity, it also enables us to share, analyse, annotate and compare specimens to gain new insights. High-resolution, full-colour 3D capture of biological specimens yields color and geometry information complementary to other techniques (e.g., 2D capture, electron scanning and micro computed tomography). However 3D colour capture of small specimens is slow for reasons including specimen handling, the narrow depth of field of high magnification optics, and the large number of images required to resolve complex shapes of specimens. In this paper, we outline techniques to accelerate 3D image capture, including using a desktop robotic arm to automate the insect handling process; using a calibrated pan-tilt rig to avoid attaching calibration targets to specimens; using light field cameras to capture images at an extended depth of field in one shot; and using 3D Web and mixed reality tools to facilitate the annotation, distribution and visualisation of 3D digital models.Comment: 2 pages, 1 figure, for BigDig workshop at 2017 eScience conferenc

An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging

Digitization of natural history collections is a major challenge in archiving biodiversity. In recent years, several approaches have emerged, allowing either automated digitization, extended depth of field (EDOF) or multi-view imaging of insects. Here, we present DISC3D: a new digitization device for pinned insects and other small objects that combines all these aspects. A PC and a microcontroller board control the device. It features a sample holder on a motorized two-axis gimbal, allowing the specimens to be imaged from virtually any view. Ambient, mostly reflection-free illumination is ascertained by two LED-stripes circularly installed in two hemispherical white-coated domes (front-light and back-light). The device is equipped with an industrial camera and a compact macro lens, mounted on a motorized macro rail. EDOF images are calculated from an image stack using a novel calibrated scaling algorithm that meets the requirements of the pinhole camera model (a unique central perspective). The images can be used to generate a calibrated and real color texturized 3Dmodel by ‘structure from motion’ with a visibility consistent mesh generation. Such models are ideal for obtaining morphometric measurement data in 1D, 2D and 3D, thereby opening new opportunities for trait-based research in taxonomy, phylogeny, eco-physiology, and functional ecology

Centipede venoms as a source of drug leads

peerreview_statement: The publishing and review policy for this title is described in its Aims & Scope. aims_and_scope_url: http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=iedc20© 2016 Taylor and Francis. The attached document is the authors' final submitted version of the journal article. You are advised to consult the publisher's version if you wish to cite from it

2011 Strategic roadmap for Australian research infrastructure

The 2011 Roadmap articulates the priority research infrastructure areas of a national scale (capability areas) to further develop Australia’s research capacity and improve innovation and research outcomes over the next five to ten years. The capability areas have been identified through considered analysis of input provided by stakeholders, in conjunction with specialist advice from Expert Working Groups   It is intended the Strategic Framework will provide a high-level policy framework, which will include principles to guide the development of policy advice and the design of programs related to the funding of research infrastructure by the Australian Government. Roadmapping has been identified in the Strategic Framework Discussion Paper as the most appropriate prioritisation mechanism for national, collaborative research infrastructure. The strategic identification of Capability areas through a consultative roadmapping process was also validated in the report of the 2010 NCRIS Evaluation. The 2011 Roadmap is primarily concerned with medium to large-scale research infrastructure. However, any landmark infrastructure (typically involving an investment in excess of $100 million over five years from the Australian Government) requirements identified in this process will be noted. NRIC has also developed a ‘Process to identify and prioritise Australian Government landmark research infrastructure investments’ which is currently under consideration by the government as part of broader deliberations relating to research infrastructure. NRIC will have strategic oversight of the development of the 2011 Roadmap as part of its overall policy view of research infrastructure

Modern venomics – Current insights, novel methods and future perspectives in biological and applied animal venom research

Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit

Development of Microsphere-based Molecular and Serodiagnostics and Their Clinical Utility

Microbial infections share many symptoms in common, rendering diagnosis difficult solely on clinical grounds. Thus, rapid, cost-effective and reliable tests are necessary for the diagnosis of infectious diseases. While the traditional diagnosis is mostly confined to detection of one pathogen at a time, a multiplex array could be a feasible alternative to improve the efficiency in the detection of infections. The Luminex xMAP-based high-throughput platform can provide simultaneous analysis of multiple analytes from the same sample by utilising differentially dyed microspheres. In this thesis, I developed xMAP-based Suspension Immuno Assays (SIAs) for the determination of IgG antibodies, IgM antibodies, as well as the avidity of IgG against the human cytomegalovirus (HCMV), Toxoplasma gondii (T. gondii) or human parvovirus B19 (B19V). Moreover, I also developed xMAP-based multiplex DNA assays for 13 human polyomaviruses (HPyVs). Primary infections by HCMV, T. gondii and B19V during pregnancy can result in severe consequences to the foetus. The serological status of the mother is critically important in counselling and recognition of infections. Hereby, I developed and evaluated SIAs for IgG, IgM and IgG-avidity against these three important pathogens. Diagnostic performances of the new assays were assessed with more than 1000 well-characterised serum samples. All the newly developed assays exhibited excellent performance compared to corresponding high-quality reference methods. The positive and negative percent agreements of the antibody-SIAs in comparison with high-standard reference assays were 92-100% and 95-100%, respectively. Kappa efficiencies between SIAs and corresponding reference assays were 0.94-1. Intra-assay and inter-assay coefficients of variations ranged between 2-12% and 1-19%, respectively. Among clinical samples from individuals with primary infection, the IgM- and IgG-SIAs served as highly sensitive screening means for detection of acute infections and immune status; and IgG-avidity-SIAs as a highly specific confirmatory approach for separation of primary infections from long-term B-cell immunity. On the other hand, during the past 12 years, a dozen viruses have joined the known family members of HPyVs. Serological studies have shown that HPyV infections occur at young age and most of the viruses circulate widely in the general population. Although HPyV infections are generally asymptomatic, severe complications can arise due to virus reactivations in immunocompromised or elderly individuals. HPyVs can persist lifelong after primary infection; however, their tissue specificities, persistence sites and transmission routes are still unclear. Also, the clinical manifestations of HPyVs with regard to immune suppression are largely unidentified. To this end, I developed xMAP-based multiplex DNA assays for all 13 HPyVs known before 2017, by using primer pairs and probes targeting the respective HPyV major capsid protein VP1 genes. The xMAP-based multiplex assays allowed for simultaneous detection of all the HPyVs with detection limits of 1-100 copies/µl. At high copies (105 copies/µl) each of the 13 target sequences were identified correctly with no cross-reactions. With this novel and specific assay, the extent to which the lymphoid system plays a role in the HPyV infection and persistence was assessed. The frequency of occurrence of HPyV viral genomes was explored in 78 lymphoid tissues from children and adults with tonsillar diseases. HPyV-DNA was found in 17.9% (14/78) of tonsils: JC polyomavirus (JCPyV, n=1), WU polyomavirus (WUPyV, n=3), Merkel cell polyomavirus (MCPyV, n=1), human polyomavirus 6 (HPyV6, n=6), trichodysplasia spinulosa polyomavirus (TSPyV, n=3). The observed frequent occurrence of HPyVs in human tonsils suggests the lymphoid tissue plays an important role as a potential transmission route and a location of persistence for these viruses. However, whether or not the undetected HPyVs share the same infection route requires more investigation with different sample types. Furthermore, to determine the occurrences in skin and clinical associations of HPyVs, I studied their genoprevalences in biopsies of premalignant [squamous cell carcinoma in situ (SCCis) or actinic keratosis (AK)] lesional vs. benign skin from 126 liver transplant recipients (LiTRs); as well as in healthy skin of 80 immunocompetent adults. Multiplex screening was followed by singleplex qPCRs of positive samples, for reference and quantification of the viral DNAs. In total, five dermal HPyVs – MCPyV, HPyV6, human polyomavirus 7, TSPyV, and Lyon IARC polyomavirus (LIPyV) – were found in 26.2% (58/221) skin biopsies. The prevalences and quantities of MCPyV in premalignant vs. benign skin of LiTRs were similar to those in healthy skin of controls. TSPyV was found in a single skin lesion at very low copies. The other three HPyVs occurred exclusively in benign skin. Overall, in 10 out of 12 SCCis/AK patients the viral DNA findings in skin were alike. Thereby, the occurrences of HPyVs in the skin of LiTRs and controls speak against a role for any of HPyVs in SCC development. The work presented in this thesis shows that the xMAP-based serological approaches exhibit excellent diagnostic performances compared to corresponding conventional methods. Moreover, the developed xMAP-based multiplex PCR for 13 HPyVs could be applied successfully in a variety of clinical materials. Altogether, the newly developed systems provide a powerful tool for medical diagnosis and research.Tartuntatautien nimeäminen pelkästään kliinisen kuvan perusteella on haasteellista ja usein jopa mahdotonta. Tarvitaan luotettavia, nopeita ja kustannushyödyllisiä laboratoriomenetelmiä. Siinä missä perinteiset menetelmät ovat taudinaiheuttajakohtaisia, monikanavaisten ns. multiplex-menetelmien etuna on ylivoimainen tehokkuus ja kustannushyödyllisyys. Luminex xMAP -testialustalla voidaan kustakin potilasnäytteestä tehdä suuri joukko samanaikaisia määrityksiä perustuen erivärisiin mikrohelmiin. Väitöstyössä suunniteltiin ja pystytettiin xMAP -perustaisia ns. suspensio-immunomenetelmiä (SIA) mikrobikohtaisiin IgG-, IgM- ja IgG-aviditeetti (AVI) -määrityksiin, kahdelle virukselle ja yhdelle alkueläimelle: sytomegalovirus (HCMV), parvorokkovirus (B19V) ja toksoplasma (T. gondii). Niin ikään pystytettiin xMAP-perustainen multiplex-menetelmä 13:n ihmis-polyoomaviruksen (HPYV) nukleiinihappo (DNA) -diagnostiikkaan. Raskaudenaikaiset HCMV-, B19V ja T. gondii- ensitartunnat voivat vahingoittaa sikiötä. Koska odottavan äidin vasta-ainetulokset ovat hyvin tärkeitä kyseisten infektioiden ja niihin kohdistuvan immuniteetin määrityksessä, kehitimme ja evaluoimme IgG-, IgM- ja AVI-SIA-menetelmät näille kolmelle tärkeälle patogeenille. Uusien menetelmien suorituskyky selvitettiin >1000:n hyvinkarakterisoidun seeruminäytteen avulla. Menetelmien suorituskyky osoittautui erinomaiseksi korkeatasoisten vertailumenetelmien suhteen: Positiiviset ja negatiiviset yhtäpitävyysprosentit olivat 92-100% ja 95-100% (vast). Kappa-vakiot olivat 0.94-1. Testien sisäiset ja testien väliset variaatiokertoimet olivat 2-12% ja 1-19% (vast). IgM- ja IgG-SIA:t toimivat erittäin sensitiivisinä seulontamenetelminä akuutin infektion ja immuniteetin tunnistuksessa; ja AVI-SIA:t erittäin spesifisinä varmistusmenetelminä, erotettaessa k.o. ensitartuntoja vanhasta B-soluimmuniteetista. Toisaalta, viimeisten 12 vuoden aikana on löydetty 12 aiemmin tuntematonta ihmis-polyoomavirusta (HPyV). Polyoomavirusheimon jäsenille on tunnusomaista tartuntojen ajoittuminen nuoreen ikään ja virusten yleisyys väestössä. Vaikka infektiot useimmiten ovat oireettomia, näiden virusten uudelleen-aktivaatiolla immuunipuutteisissa tai iäkkäissä yksilöissä voi olla vakavia seurauksia. HPyV:t pesiytyvät elimistöön piilevässä muodossa koko eliniäksi; tämän persistenssin kudos- ja solutyypit ovat kuitenkin epäselvät, samoin kuin tartuntareitit. Puutteellisesti tunnettuja ovat myöskin HBoV:ien kliiniset ilmentymät immuunipuutoksien yhteydessä. Tämänlaisia tarkoitusperiä varten pystytimme xMAP-perustaiset multiplex-DNA-monistusmenetelmät kaikille 13:lle HPyV:lle (jotka tunnettiin 2017). Alukeparit ja koettimet suuntautuivat kussakin tapauksessa pääasiallisen kapsidiproteiinin VP1 geenialueelle. Aikaansaaduilla multiplex-menetelmillä kyettiin löytämään jokainen HPyV, detektiorajoilla 1-100 kopiota/ml. Korkeammissa pitoisuuksissa (105 geenikopiota/µl) identifioitui kukin 13:sta kohteesta ilman ristireaktioita. Tällä spesifisellä, uudella menetelmällä ryhdyimme ensialkuun selvittämään imukudoksen merkitystä HPyV-infektiossa ja -persistenssissä. Määritimme HPyV-genomien esiintyvyyden 78 (lasten, aikuisten) nielurisakudosnäytteessä. Kaikkinensa HPyV-DNA:ta löytyi 17,9% (14/78) tonsilloista, seuraavin lukumäärin: JCPyV (1), WUPyV (3), MCPyV (1), HPyV6 (6) TSPyV (3). Monilukuisuus ihmistonsilloissa viittaa imukudoksen oleelliseen rooliin kyseisten virusten tartunnoissa ja/tai persistenssissä. Löytymättä jääneiden HPyV:ien johtopäätökset riippuvat lisätutkimuksista. Seuraavaksi selvitimme HPyV:ien esiintyvyyttä ja kliinistä merkitystä ihokudoksessa. Tutkimuskohteina olivat koepalat ihon okasolusyövän esiasteista (ca in situ [SCCis] sekä aktiininen keratoosi [AK]). Näytteinä oli sekä sairaita että terveitä ihoalueita 126:n maksansiirtopotilaan seurannasta; ja vertailukohtana 80:n perusterveen henkilön tavanomainen iho. Multiplex-DNA-seulontatuloksia verrattiin viruskohtaisiiin (singleplex-formaatin) kvantitatiivisiin PCR-tuloksiin. Kaiken kaikkiaan, 221:stä ihobiopsiasta 58:sta (26,2%) löytyi viiden eri HPyV:n DNA:ta: MCPyV, HPyV6, HPyV7, TSPyV, LIPyV. Tulokset maksansiirtopotilaiden ihosyöpä-esiasteissa ja terveessä ihossa olivat samankaltaiset sekä keskenänsä että verrattuna terveeseen normaaliväestöön. Tuloksemme puhuvat voimakkaasti polyoomavirusten etiologista osuutta vastaan ihon okasolusyövän synnyssä. Tässä väitöstyössä todistetaan pystyttämämme xMAP-pohjaisen ”täsmäserologian” erinomainen suorituskyky verrattuna totunnaisiin diagnoosimenetelmiin. Toisaalta, uutta xMAP-multiplex-PCR-menetelmäämme käytetään menestyksellisesti 13:n ihmis-polyoomaviruksen DNA:n osoitukseen erityyppisissä potilasnäyteaineistoissa. Kaikkinensa, aikaansaatujen uusien tutkimusmenetelmiemme osoitetaan soveltuvan oivallisesti sekä lääketieteelliseen taudinmääritykseen että tieteentekoon

The Boston University Photonics Center annual report 2015-2016

This repository item contains an annual report that summarizes activities of the Boston University Photonics Center in the 2015-2016 academic year. The report provides quantitative and descriptive information regarding photonics programs in education, interdisciplinary research, business innovation, and technology development. The Boston University Photonics Center (BUPC) is an interdisciplinary hub for education, research, scholarship, innovation, and technology development associated with practical uses of light.This has been a good year for the Photonics Center. In the following pages, you will see that this year the Center’s faculty received prodigious honors and awards, generated more than 100 notable scholarly publications in the leading journals in our field, and attracted $18.9M in new research grants/contracts. Faculty and staff also expanded their efforts in education and training, and cooperated in supporting National Science Foundation sponsored Sites for Research Experiences for Undergraduates and for Research Experiences for Teachers. As a community, we emphasized the theme of “Frontiers in Plasmonics as Enabling Science in Photonics and Beyond” at our annual symposium, hosted by Bjoern Reinhard. We continued to support the National Photonics Initiative, and contributed as a cooperating site in the American Institute for Manufacturing Integrated Photonics (AIM Photonics) which began this year as a new photonics-themed node in the National Network of Manufacturing Institutes. Highlights of our research achievements for the year include an ambitious new DoD-sponsored grant for Development of Less Toxic Treatment Strategies for Metastatic and Drug Resistant Breast Cancer Using Noninvasive Optical Monitoring led by Professor Darren Roblyer, continued support of our NIH-sponsored, Center for Innovation in Point of Care Technologies for the Future of Cancer Care led by Professor Cathy Klapperich, and an exciting confluence of new grant awards in the area of Neurophotonics led by Professors Christopher Gabel, Timothy Gardner, Xue Han, Jerome Mertz, Siddharth Ramachandran, Jason Ritt, and John White. Neurophotonics is fast becoming a leading area of strength of the Photonics Center. The Industry/University Collaborative Research Center, which has become the centerpiece of our translational biophotonics program, continues to focus onadvancing the health care and medical device industries, and has entered its sixth year of operation with a strong record of achievement and with the support of an enthusiastic industrial membership base

Modern venomics--Current insights, novel methods, and future perspectives in biological and applied animal venom research

Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.This work is funded by the European Cooperation in Science and Technology (COST, www.cost.eu) and based upon work from the COST Action CA19144 – European Venom Network (EUVEN, see https://euven-network.eu/). This review is an outcome of EUVEN Working Group 2 (“Best practices and innovative tools in venomics”) led by B.M.v.R. As coordinator of the group Animal Venomics until end 2021 at the Institute for Insectbiotechnology, JLU Giessen, B.M.v.R. acknowledges the Centre for Translational Biodiversity Genomics (LOEWE-TBG) in the programme “LOEWE – Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse's Ministry of Higher Education, Research, and the Arts. B.M.v.R. and I.K. further acknowledge funding on venom research by the German Science Foundation to B.M.v.R. (DFG RE3454/6-1). A.C., A.V., and G.Z. were supported by the European Union's Horizon 2020 Research and Innovation program through Marie Sklodowska-Curie Individual Fellowships (grant agreements No. A.C.: 896849, A.V.: 841576, and G.Z.: 845674). M.P.I. is supported by the TALENTO Program by the Regional Madrid Government (2018-T1/BIO-11262). T.H.'s venom research is funded by the DFG projects 271522021 and 413120531. L.E. was supported by grant No. 7017-00288 from the Danish Council for Independent Research (Technology and Production Sciences). N.I. acknowledges funding on venom research by the Research Fund of Nevsehir Haci Bektas Veli University (project Nos. ABAP20F28, BAP18F26). M.I.K. and A.P. acknowledge support from GSRT National Research Infrastructure structural funding project INSPIRED (MIS 5002550). G.A. acknowledges support from the Slovenian Research Agency grants P1-0391, J4-8225, and J4-2547. G.G. acknowledges support from the Institute for Medical Research and Occupational Health, Zagreb, Croatia. E.A.B.U. is supported by a Norwegian Research Council FRIPRO-YRT Fellowship No. 287462

Novel approaches in chromatographic purification process development for low concentrated proteins in complex mixtures

Analytical separations, based on pH, salt gradient ion exchange chromatography, were laid out and combined with modern protein analytical technologies for the characterization of protein mixtures. Methods were used to obtain parameters necessary for purification process development / simulation. The applicability of the obtained parameters was further experimentally proven. Additionally, a method for high resolution separation and identification of protein PEGylation isoforms is demonstrated