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Yeo, D.

Publications and source records attributed to Yeo, D..

11 recordsLinked to original sources
bioRxiv2025

The extracellular matrix in selective decussation of retinal ganglion cell axons: β2 laminins regulate the ipsilateral projection

AbstractIn binocular animals, retinal ganglion cell (RGC) axons selectively decussate at the optic chiasm. Selective decussation is directed by radial glia and midline neurons in the optic chiasm. Radial glia attach to the underlying pial basement membrane (PBM) that is rich in {beta}2 laminins. Here, we asked whether {beta}2 laminins in the PBM control the selective decussation of RGC axons. Genetic deletion of the {beta}2 subunit increased the proportion of non-decussating RGC axons in the ipsilateral tract. {beta}2 laminins are expressed in the PBM during the peak and late phases of RGC axon growth, and their deletion results in fragmentation of the PBM and dysmorphic radial glia. Consistent with the increase in the proportion of ipsilateral axons, we found persistent expression of the ipsilateral guidance cue EphrinB2 in radial glia during the late phase of axonal decussation, thus extending the developmental window for the development of the ipsilateral projection. Surprisingly, this increase in EphrinB2 was accompanied by an increase in the number of ipsilateral RGCs in the ventrotemporal retina. These results suggest that {beta}2 laminins regulate the size of the ipsilateral projection by providing cues that control the generation of ipsilateral RGCs and the expression of the ipsilateral cue EphrinB2 in the optic chiasm. Together, these findings position {beta}2 laminins as a novel regulator of the ipsilateral projection.

developmental biology↗
bioRxiv2024

Tissue Tension and Strain as Indicators of Suction-mediated Cutaneous DNA Transfection: A Parametric Study

Cutaneous suction-based transfection is a recently developed technique that is painless and simple-to-use for the delivery of DNA for nucleic-acid-based vaccines. The technique promises high efficiency for both antigen expression and immunogenicity as demonstrated in both animal studies and human clinical trials. To realize this promise, a parametric study and systematic evaluation on the efficacy of cutaneous suction as a transfection method was performed. Using Green Fluorescent Protein (GFP) plasmid expression as a transfection reporter in a rat model, the expression level as a function of both suction nozzle size and suction pressure was quantified. A numerical model was employed to compute skin deformation in terms of strain, which was used to correlate with GFP expression. Based on these results, two quantities, total integrated strain and tissue tension, are proposed as indicators of expression level that can be used to guide protocol development and optimization. These indicators are also discussed in relation to possible cellular uptake mechanisms.

bioengineering↗
bioRxiv2023

An integrative taxonomic treatment of the Mycetophilidae (Diptera: Bibionomorpha) from Singapore reveals 115 new species on 730km2

Abstract"Open ended" or "dark taxa" are species-rich clades that are so abundant and diverse that conventional taxonomic methods tend to struggle with the onslaught of specimens and species. New approaches based on presorting specimens to putative species with low-cost DNA barcodes may make tackling these taxa manageable. However, this will still require limiting the geographic scope of taxonomic revisions, given that most countries and biogeographic regions will have too many specimens and species for comprehensive coverage. We demonstrate the power of this approach by carrying out a revision of the Mycetophilidae fungus gnats (Diptera) of Singapore. The material revised here was obtained from 496 samples collected with 71 Malaise traps placed at 107 sites in different habitats in Singapore: mangroves, swamp forests, freshwater swamps, primary rainforests, and different types of secondary forests (old, maturing, young, urban). Based on molecular and morphological data for 1,454 specimens, we delimit 120 species of 23 genera. Of these, only five were species previously described. The remaining 115 species are new to science and described here. We name, however, only 98 of these species since 14 species are currently only known from females and we cannot prepare a fully satisfying morphological diagnosis (Manota spp. A-G and Neoempheria spp. A-G), and three species lack molecular data (Epicypta sp. A, Epicypta sp. B, and Neoempheria sp. H). To assess congruence between species delimited with DNA barcodes (3% clusters) and morphology, we determined a match ratio and found it to be overall high (95%) with even higher match ratios (99%) observed for MOTUs clustered at 5% with Objective Clustering and MOTUs obtained with ABGD set to (P=0.060). Overall, the ratio of undescribed to described is an astonishing 20:1. Only revising the Singapore fauna increases the number of described species of Oriental Mycetophilidae by about 25%, highlighting the size of the taxonomic impediment for fungus gnats. Most of the Singapore Mycetophilidae diversity belongs to three genera--Neoempheria Osten-Sacken (31 species), Epicypta Winnertz (29 species) and Manota Williston (14 species), but we also describe a new genus-- Integricypta, gen. n., which is the putative sistergroup of Aspidionia Colless--belonging to the Mycetophilinae Mycetophilini based on three species. The species sequenced, illustrated, and named are: Leptomorphus rafflesi, sp. n.; Monoclona simhapura, sp. n.; Azana demeijeri, sp. n.; Azana leekongchiani, sp. n. (Sciophilinae); Tetragoneura crawfurdi, sp. n.; Tetragoneura chola, sp. n.; Tetragoneura dayuan, sp. n.; Tetragoneura farquhari, sp. n.; Ectrepesthoneura johor, sp. n. (Tetragoneurinae); Mohelia zubirsaidi, sp. n.; Allactoneura tumasik, sp. n.; Allactoneura limbosengi, sp. n.; Manota banzu, sp. n.; Manota tantocksengi, sp. n.; Manota bukittimah, sp. n.; Manota chiamassie, sp. n.; Manota danmaxi, sp. n.; Manota mahuan, sp. n.; Manota temenggong, sp. n.; Clastobasis sritribuana, sp. n.; Clastobasis bugis, sp. n.; Clastobasis oranglaut, sp. n. (Leiinae); Parempheriella mait, sp. n.; Parempheriella longyamen, sp. n.; Parempheriella peranakan, sp. n.; Mycomya sachmatich, sp. n.; Neoempheria merlio, sp. n.; Neoempheria sabana, sp. n.; Neoempheria sangabo, sp. n.; Neoempheria shicheng, sp. n.; Neoempheria ujong, sp. n.; Neoempheria subaraji, sp. n.; Neoempheria kokoiyeeae, sp. n.; Neoempheria mandai, sp. n.; Neoempheria malacca, sp. n.; Neoempheria sinkapho, sp. n.; Neoempheria singapura, sp. n.; Neoempheria xinjiapo, sp. n.; Neoempheria puluochung, sp. n.; Neoempheria merdeka, sp. n.; Neoempheria neesoon, sp. n.; Neoempheria pulau, sp. n.; Neoempheria cinkappur, sp. n.; Neoempheria temasek, sp. n.; Neoempheria polunini, sp. n.; Neoempheria fajar, sp. n.; Neoempheria riatanae, sp. n. (Mycomyinae); Brachycampta glorialimae, sp. n.; Brachycampta murphyi, sp. n.; Brachycampta limtzepengi, sp. n.; Rymosia teopohlengi, sp. n.; Exechia tanswiehiani, sp. n.; Exechia alinewongae, sp. n.; Mycetophila chngseoktinae, sp. n.; Mycetophila georgettechenae, sp. n.; Mycetophila aishae, sp. n.; Platyprosthiogyne phanwaithongae, sp. n.; Platyprosthiogyne gohsookhimae, sp. n.; Platyprosthiogyne rahimahae, sp. n.; Platyprosthiogyne lynetteseahae, sp. n.; Platyprosthiogyne neilaae, sp. n.; Platyprosthiogyne snehalethaae, sp. n.; Platurocypta adeleneweeae, sp. n.; Platurocypta tanhoweliangi, sp. n.; Epicypta constancesingamae, sp. n.; Epicypta jennylauae, sp. n.; Epicypta limchiumeiae, sp. n.; Epicypta janetyeeae, sp. n.; Epicypta kohkhenglianae, sp. n.; Epicypta daintoni, sp. n.; Epicypta holltumi, sp.n.; Epicypta ridleyi, sp. n.; Epicypta chezaharaae, sp. n.; Epicypta tanjiakkimi, sp. n.; Epicypta gehminae, sp. n.; Epicypta jackieyingae, sp. n.; Epicypta khatijunae, sp. n.; Epicypta purchoni, sp. n.; Epicypta foomaoshengi, sp. n.; Epicypta ganengsengi, sp. n.; Epicypta nanyangu, sp. n.; Epicypta nus, sp. n.; Epicypta peterngi, sp. n.; Epicypta maggielimae, sp. n.; Epicypta yupeigaoae, sp. n.; Epicypta annwee, sp. n.; Epicypta wallacei, sp. n.; Epicypta lamtoongjini, sp. n.; Epicypta catherinelimae, sp. n.; Epicypta grootaerti, sp. n.; Epicypta joaquimae, sp. n.; Aspidionia cheesweeleeae, sp. n.; Aspidionia janetjesudasonae, sp. n.; Aspidionia fatimahae, sp. n.; Integricypta fergusondavie, sp. n.; Integricypta teosoonkimae, sp. n.; Integricypta shirinae, sp. n.; Integricypta hoyuenhoeae, sp. n. (Mycetophilinae). The previously described species are Metanepsia malaysiana Kallweit, Eumanota racola Soli, Parempheriella defectiva (Edwards), Neoempheria dizonalis (Edwards) (all known from Sumatra and/or the Malaysian peninsula), and Chalastonepsia hokkaidensis Kallweit a species spread in east Asia. The mycomyine genus Vecella Wu & Yang is here proposed as a new synonym to Parempheriella, with P. guadunana (Wu & Yang), n. comb. corresponding to an additional Palearctic species of Parempheriella. Barcodes for a second set of 1,493 Singapore mycetophilid specimens suggest the presence of an additional 18 MOTUs. We thus estimate that approximately 85% of all the Singapore species that routinely enter Malaise traps are identified or described here. The revision concludes with a discussion of the biogeography and generic composition of the mycetophilid fauna at the southern end of the Malay Peninsula. Zusammenfassung"Open-ended" oder "Dark Taxa" sind artenreiche Klade, die so abundant und arteinreich sind, dass die herkommlichen taxonomischen Methoden angesichts der gro{beta}en Anzahl von Exemplaren und Arten nicht gut funktionieren. Neue Ansatze, die auf das Vorsortierung von Exemplaren mit DNA Barcodes bis zum Artniveau basieren, erlauben es jetzt aber solche Taxa zu revidieren. Allerdings kann auch mit DNA Barcodes, nur die Fauna eines vergleichsweise kleinen Gebietes bearbeiten werden, weil fur die meisten Lander und biogeografischen Regionen zu viele Exemplare und Arten abgedeckt werden mussten. Wir demonstrieren hier wie eine solche Revision durchgefuhrt werden kann. Wir revidieren hier die Pilzmucken (Diptera: Mycetophilidae) von Singapur, die mit Malaisefallen gefangen werden konnen. Das hier uberarbeitete Material stammt aus 496 Malaise-Fallenproben, die mit 71 Malaise-Fallen an 107 Sammelstellen in verschiedenen Habitaten gefangen wurden: Mangroven, Sumpfwalder, Su{beta}wassersumpfe, Primarregenwalder und Sekundarwalder. Basierend auf molekularen und morphologischen Daten fur mehr als 1454 Tiere grenzen wir 120 Arten mit molekularen und morphologischen Daten ab, wobei nur 5 dieser Arten bereits beschrieben sind. Die verbleibenden 115 werden hier beschrieben. Allerdings benennen wir nur 98 Arten, da fur zwei Arten molekulare Daten fehlen und fur 14 weitere Arten derzeit nur Weibchen bekannt sind. Daher konnen wir derzeit keine zufriedenstellende morphologische Diagnose erstellen. Daruber hinaus fehlen molekulare Daten fur drei Arten (Epicypta sp. A, Epicypta sp. B und Neoempheria sp. H). Was die Artgrenzen betrifft, so stimmen die molekularen und morphologischen Daten in den meisten Fallen uberein (match ratio: 95% fur 3% MOTUs). Eine noch hohere "match ratio" von 99% wird fur 5% und ABGD MOTUs (P=0,060) beobachtet. Insgesamt ist das Verhaltnis zwischen unbeschrieben und beschrieben erstaunlich hoch (20:1), und die Uberarbeitung der singapurer Fauna erhoht die Anzahl der beschriebenen Arten in der Orientalischen Region um uber 25%. Dies unterstreicht den Ausma{beta} des "taxonomic impediments" fur Pilzmucken. Die meisten der Mycetophilidenarten in Singapur gehoren zu drei von 22 Gattungen - Neoempheria Osten-Sacken (31 Arten), Epicypta Winnertz (29 Arten) und Manota Williston (14 Arten), aber wir beschreiben hier auch eine neue Gattung, Integricypta, gen. n. basierend auf drei Arten. Die Gattung gehort zu den Mycetophilinae Mycetophilini und ist die mutma{beta}liche Schwestergruppe von Aspidionia Colless. Die sequenzierten, illustrierten und benannten Arten sind: Leptomorphus rafflesi, sp. n.; Monoclona simhapura, sp. n.; Azana demeijeri, sp. n.; Azana leekongchiani, sp. n. (Sciophilinae); Tetragoneura crawfurdi, sp. n.; Tetragoneura chola, sp. n.; Tetragoneura dayuan, sp. n.; Tetragoneura farquhari, sp. n.; Ectrepesthoneura johor, sp. n. (Tetragoneurinae); Mohelia zubirsaidi, sp. n.; Allactoneura tumasik, sp. n.; Allactoneura limbosengi, sp. n.; Manota banzu, sp. n.; Manota tantocksengi, sp. n.; Manota bukittimah, sp. n.; Manota chiamassie, sp. n.; Manota danmaxi, sp. n.; Manota mahuan, sp. n.; Manota temenggong, sp. n.; Clastobasis sritribuana, sp. n.; Clastobasis bugis, sp. n.; Clastobasis oranglaut, sp. n. (Leiinae); Parempheriella mait, sp. n.; Parempheriella longyamen, sp. n.; Parempheriella peranakan, sp. n.; Mycomya sachmatich, sp. n.; Neoempheria merlio, sp. n.; Neoempheria sabana, sp. n.; Neoempheria sangabo, sp. n.; Neoempheria shicheng, sp. n.; Neoempheria ujong, sp. n.; Neoempheria subaraji, sp. n.; Neoempheria kokoiyeeae, sp. n.; Neoempheria mandai, sp. n.; Neoempheria malacca, sp. n.; Neoempheria sinkapho, sp. n.; Neoempheria singapura, sp. n.; Neoempheria xinjiapo, sp. n.; Neoempheria puluochung, sp. n.; Neoempheria merdeka, sp. n.; Neoempheria neesoon, sp. n.; Neoempheria pulau, sp. n.; Neoempheria cinkappur, sp. n.; Neoempheria temasek, sp. n.; Neoempheria polunini, sp. n.; Neoempheria fajar, sp. n.; Neoempheria riatanae, sp. n. (Mycomyinae); Brachycampta glorialimae, sp. n.; Brachycampta murphyi, sp. n.; Brachycampta limtzepengi, sp. n.; Rymosia teopohlengi, sp. n.; Exechia tanswiehiani, sp. n.; Exechia alinewongae, sp. n.; Mycetophila chngseoktinae, sp. n.; Mycetophila georgettechenae, sp. n.; Mycetophila aishae, sp. n.; Platyprosthiogyne phanwaithongae, sp. n.; Platyprosthiogyne gohsookhimae, sp. n.; Platyprosthiogyne rahimahae, sp. n.; Platyprosthiogyne lynetteseahae, sp. n.; Platyprosthiogyne neilaae, sp. n.; Platyprosthiogyne snehalethaae, sp. n.; Platurocypta adeleneweeae, sp. n.; Platurocypta tanhoweliangi, sp. n.; Epicypta constancesingamae, sp. n.; Epicypta jennylauae, sp. n.; Epicypta limchiumeiae, sp. n.; Epicypta janetyeeae, sp. n.; Epicypta kohkhenglianae, sp. n.; Epicypta daintoni, sp. n.; Epicypta holltumi, sp.n.; Epicypta ridleyi, sp. n.; Epicypta chezaharaae, sp. n.; Epicypta tanjiakkimi, sp. n.; Epicypta gehminae, sp. n.; Epicypta jackieyingae, sp. n.; Epicypta khatijunae, sp. n.; Epicypta purchoni, sp. n.; Epicypta foomaoshengi, sp. n.; Epicypta ganengsengi, sp. n.; Epicypta nanyangu, sp. n.; Epicypta nus, sp. n.; Epicypta peterngi, sp. n.; Epicypta maggielimae, sp. n.; Epicypta yupeigaoae, sp. n.; Epicypta annwee, sp. n.; Epicypta wallacei, sp. n.; Epicypta lamtoongjini, sp. n.; Epicypta catherinelimae, sp. n.; Epicypta grootaerti, sp. n.; Epicypta joaquimae, sp. n.; Aspidionia cheesweeleeae, sp. n.; Aspidionia janetjesudasonae, sp. n.; Aspidionia fatimahae, sp. n.; Integricypta fergusondavie, sp. n.; Integricypta teosoonkimae, sp. n.; Integricypta shirinae, sp. n.; Integricypta hoyuenhoeae, sp. n. (Mycetophilinae). Die Tiere, die zu den bereits beschriebenen Arten gehoren, gehoren zu den folgenden Arten: Metanepsia malaysiana Kallweit, Eumanota racola Soli, Parempheriella defectiva (Edwards), Neoempheria dizonalis (Edwards) (alle Arten sind derzeit aus Sumatra und/oder der malaysischen Halbinsel bekannt), und Chalastonepsia hokkaidensis Kallweit, eine in Ostasien verbreitete Art. Die Gattung Vecella Wu & Yang wird hier als neues Synonym fur Parempheriella vorgeschlagen, wobei P. guadunana (Wu & Yang), n. comb., wobei die Gattung damit eine zusatzlichen palaarktischen Art erhalt. Die DNA Barcodes fur eine zweite Stichprobe mit 1.493 Pilzmucken deuten darauf hin, dass in Singapur 18 zusatzliche Arten mit Malaisefallen gefangen werden konnen. Es sieht aber dennoch so aus, als wurden wir bereits hier circa 85% aller Arten beschreiben, die regelma{beta}ig in Malaise-Fallen geraten. Die Revision endet mit einer Diskussion der Biogeographie und taxonomische Zusammensetzung der Mycetophilidenfauna im sudlichen Teil der Malaiischen Halbinsel.

zoology↗
bioRxiv2023

"Dark taxonomy": a new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment

We are entering the 6th mass extinction with little data for "dark taxa" although they comprise most species. Much of the neglect is due to the fact that conventional taxonomic methods struggle with handling thousands of specimens belonging to hundreds of species. We thus here propose a new strategy that we call "dark taxonomy." It addresses (1) taxonomic impediments, (2) lack of biodiversity baselines, (3) and low impact of revisionary research. Taxonomic impediments are reduced by carrying out revisions at small geographic scales to keep the number of specimens low. The risk of taxonomic error is kept low by delimiting species based on two types of data. We then show that dark taxonomy can yield important biodiversity baseline data because it uses samples obtained with biomonitoring traps. Lastly, we argue that the impact of research can be improved by publishing two manuscripts addressing different readerships. The principles of dark taxonomy are illustrated by our taxonomic treatment of Singapores fungus gnats (Mycetophilidae) based only on Malaise trap samples. We show that a first batch of specimens (N=1,454) contains 120 species, of which 115 are new to science thus reducing taxonomic impediments by increasing the number of described Oriental species by 25%. Species delimitation started with using DNA barcodes to estimate the number of MOTUs before "LIT" (Large-scale Integrative Taxonomy) was used to obtain the species boundaries for the 120 species by integrating morphological and molecular data. To test the taxonomic completeness of the revision, we then analyzed a second batch of 1,493 specimens and found that >97% belonged to the 120 species described based on the first batch. Indeed, the second batch only contained 18 new and rare MOTUs; i.e. our study suggests that a single revision can simultaneously yield the names for all important species and relevant biodiversity baseline data. Overall, we believe that "dark taxonomy" can quickly ready a large unknown taxon for biomonitoring.

zoology↗
bioRxiv2022

Global convergence of dominance and neglect in flying insect diversity

Most of arthropod biodiversity is unknown to science. For this reason, it has been unclear whether insect communities around the world are dominated by the same or different taxa. This question can be answered through standardized sampling of biodiversity followed by estimation of species diversity and community composition with DNA sequences. This approach is here applied to flying insects sampled by 39 Malaise traps placed in five biogeographic regions, eight countries, and numerous habitats (>220,000 specimens belonging to >25,000 species in 463 families). Unexpectedly, we find that 20 insect families account for >50% of local species diversity regardless of continent, climatic region, and habitat type. These consistent differences in family-level dominance explain two-thirds of variation in community composition despite massive levels of species turnover, with most species (>97%) in the top 20 families encountered at a single site only. Alarmingly, the same families that dominate global insect diversity also suffer from extreme taxonomic neglect with little signs of increasing activities in recent years. Tackling the biodiversity of these "dark taxa" thereby emerges as an urgent priority because the arthropod groups comprising most of the global flying insect diversity are particularly poorly known.

ecology↗
bioRxiv2021

A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science

Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") while another is caused by the large number of superficial species descriptions which can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) are converted into species by assigning binominal names (e.g., BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (usually consisting only of a consensus barcode). We here show that many of Sharkey et al.s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.s approach of using consensus barcodes as diagnoses is not functional because it cannot be consistently applied. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species and voice concerns over Sharkey et al.s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers, and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.

evolutionary biology↗
bioRxiv2021

MinION barcodes: biodiversity discovery and identification by everyone, for everyone

BackgroundDNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to <10 cents, and allows fast turnaround from specimen to sequence by using the portable, real-time sequencer MinION. ResultsWe describe cost-effective and rapid procedures for barcoding individual specimens with MinION sequencing. We illustrate how tagged amplicons can be obtained and sequenced with the portable, real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for >10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (>99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. ConclusionsWe propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.

ecology↗
bioRxiv2021

Tandem-Cleavage Linkers Improve the In Vivo Stability and Tolerability of Antibody-Drug Conjugates

Although peptide motifs represent the majority of cleavable linkers used in clinical-stage antibody-drug conjugates (ADCs), the sequences are often sensitive to cleavage by extracellular enzymes, such as elastase, leading to systemic release of the cytotoxic payload. This action reduces the therapeutic index by causing off-target toxicities that can be dose-limiting. For example, a common side-effect of ADCs made using peptide-cleavable linkers is myelosuppression, including neutropenia. Only a few reports describe methods for optimizing peptide linkers to maintain efficient and potent tumor payload delivery while enhancing circulating stability. Herein, we address these critical limitations through the development of a tandem-cleavage linker strategy, where two sequential enzymatic cleavage events mediate payload release. We prepared dipeptides that are protected from degradation in the circulation by a sterically-encumbering glucuronide moiety. Upon ADC internalization and lysosomal degradation, the monosaccharide is removed and the exposed dipeptide is degraded, liberating the attached payload inside the target cell. We used CD79b-targeted monomethyl auristatin E (MMAE) conjugates as our model system, and compared the stability, efficacy, and tolerability of ADCs made with tandem-cleavage linkers to ADCs made using standard technology with the vedotin linker. The results--where rat studies showed dramatically improved tolerability in the hematopoietic compartment--highlight the role that linker stability plays in efficacy and tolerability, and offer a means of improving an ADCs therapeutic index for improved patient outcomes.

pharmacology and toxicology↗
bioRxiv2020

Mangroves are an overlooked hotspot of insect diversity despite low plant diversity

We here compare the tropical arthropod fauna across a freshwater swamp and six different forest types (rain-, swamp, dry-coastal, urban, freshwater swamp, mangroves) based on 140,000 barcoded specimens belonging to ca. 8,500 species. Surprisingly, we find that mangroves, a globally imperiled habitat that had been expected to be species-poor for insects, are an overlooked hotspot for insect diversity despite having low plant diversity. Our study reveals a species-rich mangrove insect fauna (>3,000 species) that is distinct (>50% of species are mangrove-specific), and has high species turnover across Southeast and East Asia. For most habitats, plant diversity is a good predictor for insect diversity, but mangroves are an exception and compensate for a comparatively low number of phytophagous and fungivorous insect species by supporting an unusually rich community of predators whose larvae feed in the productive mudflats. For the remaining tropical habitats, the insect communities have diversity patterns that are largely congruent across guilds. The discovery of such a sizeable and distinct insect fauna in a globally threatened habitat underlines how little is known about global insect biodiversity.

ecology↗
bioRxiv2020

A novel HER2-targeted antibody-drug conjugate offers the possibility of clinical dosing at trastuzumab-equivalent exposure levels

Trastuzumab and the related antibody-drug conjugate (ADC), ado-trastuzumab emtansine (T-DM1), both target HER2-overexpressing cells. Together, these drugs have treatment indications in both early-stage and metastatic settings for HER2+ breast cancer. T-DM1 retains the antibody functionalities of trastuzumab and adds the potency of a cytotoxic maytansine payload. Interestingly, in the clinic, T-DM1 cannot always replace the use of trastuzumab plus chemotherapy administered together as single agents. We hypothesize that this failure may be due in part to the limited systemic exposure achieved by T-DM1 relative to trastuzumab because of toxicity-related dosing constraints on the ADC. We have developed a trastuzumab-based ADC site-specifically conjugated to maytansine through a noncleavable linker. This construct, termed CAT-01-106, has a drug-to-antibody ratio (DAR) of 1.8, approximately half the average DAR of T-DM1, which comprises a mixture of antibodies variously conjugated with DARs ranging from 0-8. The high DAR species present in T-DM1 contribute to its toxicity and limit its clinical dose. CAT-01-106 showed superior in vivo efficacy compared to T-DM1 at equal payload dosing and was equally or better tolerated compared to T-DM1 at equal payload dosing up to 120 mg/kg in Sprague-Dawley rats and 60 mg/kg in cynomolgus monkeys. CAT-01-106 also showed improved pharmacokinetics in rats relative to T-DM1, with 40% higher ADC exposure levels. Together, the data suggest that CAT-01-106 may be sufficiently tolerable to enable clinical dosing at trastuzumab-equivalent exposure levels, combining the functions of both the antibody and the payload in one drug and potentially improving patient outcomes.

pharmacology and toxicology↗
bioRxiv2019

Mini-barcodes are more suitable for large-scale species discovery in Metazoa than full-length barcodes

New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared to full-length barcodes. This is here tested based on 20 empirical datasets covering ca. 30,000 specimens and 5,500 species, as well as six clade-specific datasets from GenBank covering ca. 98,000 specimens for over 20,000 species. All specimens in these datasets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and by excising nine mini-barcodes with established primers (length: 94 - 407-bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular Operational Taxonomic Units (mOTUs) that were obtained using three different species delimitation techniques (PTP, ABGD, objective clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length (>200-bp). Only very short mini-barcodes (<200-bp) perform poorly, especially when they are located near the 5 end of the Folmer region. The mean congruence between morphospecies and mOTUs is ca. 75% for barcodes >200-bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes.

evolutionary biology↗