Jekyll2021-01-31T13:14:19+00:00https://mikheyevlab.github.io/EcoEvoUnit/feed.xmlMikheyev LabsLab web siteThrowback: Agneesh pushes forward our understanding of snake venom evolution2020-06-22T00:00:00+00:002020-06-22T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Agneesh-Snake-venom-evolution-paper<p>Our team is incredibly proud to see that Agneesh’s passion for evolution has pushed forward the frontiers of knowledge on Snake venom evolutionary rates. His tenacious investigation into the gene expression data from 52 venomous snake species is available since late April 2020 in <a href="https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.0613?af=R#d9166490e1">Proceedings of the Royal Society B</a> with stunning graphics.</p>
<figure>
<a href="Agneesh_2ndpaper"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/Agneesh_2ndpaper.jpg" alt="Agneesh_2ndpaper" width="800" /></a>
<figcaption>Agneesh explaining his new results to Nurit in OIST EcoEvo lab</figcaption>
</figure>
<p>If you haven’t got the chance to read his work, we invite you to read the very nice summary on <a href="http://blog.pnas.org/2020/05/snake-venom-evolved-in-fits-and-spurts/">PNAS blog post</a> written by Amy McDermott. Also for the more curious, Agneesh is part of the lab initiative to make science more reproducible and always include <a href="https://agneeshbarua.github.io/venom-phenotype-evolution/">interactive codes</a>, so check it out here!</p>
<p>We surely will looking out for what Agneesh will craft next from his venom extracts data!</p>
<figure>
<a href="venomextract"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/venomextract.jpg" alt="venomextract" align="center" width="100" /></a>
</figure>Maevamaeva.techer@oist.jpOur team is incredibly proud to see that Agneesh’s passion for evolution has pushed forward the frontiers of knowledge on Snake venom evolutionary rates. His tenacious investigation into the gene expression data from 52 venomous snake species is available since late April 2020 in Proceedings of the Royal Society B with stunning graphics.Varroa mite evolution review out in Current Opinion in Insect Science2020-02-26T00:00:00+00:002020-02-26T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Varroa-mite-evolution-review-out<p>Nurit and Sasha review about <a href="https://www.sciencedirect.com/science/article/abs/pii/S2214574520300067">“Varroa mite evolution: a neglected aspect of worldwide bee collapses?”</a> is finally out in Current Opinion in Insect Science.</p>Maevamaeva.techer@oist.jpNurit and Sasha review about “Varroa mite evolution: a neglected aspect of worldwide bee collapses?” is finally out in Current Opinion in Insect Science.How honey bee could help to protect Okinawan coral reefs2019-09-11T00:00:00+00:002019-09-11T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Honeybees-to-save-coral%20copy<p>We are highly excited to start a new research project in collaboration with Onna Village Office (where OIST is located). This collaboration is part of the Red Soil project from Onna Village and our own honeybee/microbiome/parasite research in the Mikheyev Unit. The connection may sound surprising at a first view: “bees save coral”, but the intelligent idea of Onna Village office is to promote beekeeping in farmlands to grow diverse flowers, which would ultimately help to reduce red soil erosion in the sea threatening corals.</p>
<figure>
<a href="Bee team"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/banner-bee-collab.jpg" alt="1st bees cerana" width="1000" /></a>
<figcaption>Our first A. cerana colonies</figcaption>
</figure>
<p>You can read more on <a href="https://www.oist.jp/news-center/news/2019/9/6/honeybees-help-save-okinawan-coral">this OIST article</a> nicely covered by Christopher Richarson.</p>
<figure>
<a href="Chris"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/Chris-media.jpg" alt="Chris-media" width="200" /></a>
<figcaption>Christopher helped us a lot in promoting this project in English and Japanese </figcaption>
</figure>
<p>Our research Unit offered to use ~15 of our Western honey bee colonies (<em>Apis mellifera</em> 西洋ミツバチ) to promote the Onna Village project and to foster closer interactions between OIST and Onna Village. More excitingly, our bee team and Onna village office want in joint effort establish the Japanese honey bee (<em>Apis cerana japonica</em> 日本のミツバチ) here in Okinawa for research purposes and beekeeping.</p>
<figure>
<a href="Bee team meeting"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/meeting.jpg" alt="meeting bee" width="600" /></a>
<figcaption>Meeting between OIST bee team and Onna village bee team </figcaption>
</figure>
<p>With the great help of Onna Village we already received two Japanese bee colonies, which are the only ones on Okinawa so far. The Onna Village beekeepers are taking care of the Japanese honey bees, and once the bees adapted to Okinawa, they can start producing rare honey. The profit from selling the honey will benefit the Red Soil project. Also, educational tours to the honey bees showing e.g., the differences between the two species would be possible in the future.</p>
<p>Japanese bees are exceptional as they are the original host of the devastating parasite <em>Varroa destructor</em> (ミツバチヘギイタダニ) but in contrast to Western bees, can defend themselves very well. They also show other extraordinary abilities such as heat-balling against hornets (スズメバチ.) Thanks to the Onna Village’s extensive work and effort in taking care of the colonies, we will also be able to tackle diverse important research questions regarding differences between Western and Japanese honey bee regarding microbiome and parasite adaptation.</p>Viennavienna.kowallik@oist.jpWe are highly excited to start a new research project in collaboration with Onna Village Office (where OIST is located). This collaboration is part of the Red Soil project from Onna Village and our own honeybee/microbiome/parasite research in the Mikheyev Unit. The connection may sound surprising at a first view: “bees save coral”, but the intelligent idea of Onna Village office is to promote beekeeping in farmlands to grow diverse flowers, which would ultimately help to reduce red soil erosion in the sea threatening corals.Prof. R. Manjunatha Kini invited to talk about venom2019-09-11T00:00:00+00:002019-09-11T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Prof.%20R.%20Manjunatha%20Kini%20invited%20to%20talk%20about%20venom<p>We are extremely pleased to host Prof. R. Manjunatha Kini from the Department of Biological Sciences, Faculty of Science, National University of Singapore for his talk on <strong>“Venom and Toxin Research: Biochemist’s Bliss and Pharmacologist’s Paradise”</strong> on Tuesday, November 12, 2019 at 15:30 in B503.</p>
<figure>
<a href="ProfKini"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/ProfKini.jpg" alt="ProfKini" width="800" /></a>
</figure>
<p>Find his abstract below:<br />
Venoms form the armory of several animals in prey capture and/or predator deterrence. They have evolved as cocktails of several toxins and induce various pharmacological effects in key systems. These toxins are thought as villains as they cause death and debilitation. In reality, they have contributed more to improving our lives than cause death. Toxins have played crucial roles in the discovery and development of therapeutic and diagnostic agents for human diseases. They have also contributed as important research tools and helped us to understand molecular mechanisms of normal physiological processes such as neurotransmission, blood coagulation and platelet aggregation. Our lab in NUS has been studying structure-function relationships and mechanism of actions of novel toxins from various sources. Our research has contributed to both basic and applied sciences. Based on the functional sites of the toxins, we have developed several therapeutic agents for various human diseases. This talk will provide an overview of toxin research and the distinct dimension of both basic and applied research in the field.</p>Maevamaeva.techer@oist.jpWe are extremely pleased to host Prof. R. Manjunatha Kini from the Department of Biological Sciences, Faculty of Science, National University of Singapore for his talk on “Venom and Toxin Research: Biochemist’s Bliss and Pharmacologist’s Paradise” on Tuesday, November 12, 2019 at 15:30 in B503.The return of Darko: a spider’s tale2019-09-06T00:00:00+00:002019-09-06T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Darko-Cotoras-visit-ecoevo<p>It is our pleasure to welcome again in our unit, Dr. Darko Cotoras, a <a href="https://www.calacademy.org/staff/ibss/entomology/darko-d-cotoras">research associate at the California Academy of Sciences</a>, from September 4th to October 6th, 2019.</p>
<figure>
<a href="Darko"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/cotoras-molokai.jpg" alt="Darko" width="1200" /></a>
</figure>
<p>If you do not know about spiders or island biogeography principles and look for a passionate researcher to share with you about it, get ready if you meet Darko! If you happened to be in Okinawa, just come to lab 2 level C at OIST. Aside from being a Japanese karaoke enthusiast and enjoying the beautiful summer in Okinawa, Darko is with us to sequence and analyze some <em>Wendilgarda</em> spiders collected from his recent field trip in Costa Rica. He is aiming at better understanding the evolutionary history of the genus of spiders by performing a molecular phylogenetic reconstruction of this group.</p>
<p>We look forward to learning more about his results in his talk on the <strong>Friday 27th September 2019 at 14:00</strong>, entitled <a href="https://groups.oist.jp/evolution/event/seminar-adaptive-radiation-or-exceptional-behavioural-plasticity-genetic">“Adaptive radiation or exceptional behavioural plasticity? Genetic consequences of niche partition in Wendilgarda galapagensis (Araneae, Theridiosomatidae) from Isla del Coco, Costa Rica”.</a></p>
<p>Also <em>congratulations on his Humboldt Research Fellowship</em>, which will lead him to the Senckenberg Museum in Germany in a few months. Here he will study spiders evolution in temperate rain forests of southern South America.</p>Maevamaeva.techer@oist.jpIt is our pleasure to welcome again in our unit, Dr. Darko Cotoras, a research associate at the California Academy of Sciences, from September 4th to October 6th, 2019.Agneesh’s first experience at ESEB20192019-08-23T00:00:00+00:002019-08-23T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Agneesh-talk-ESEB2019<p>Agneesh, our PhD student in evolutionary genetics, worked hard to understand how complex traits evolve through millions of years and how snakes perfected their venom recipes. He was selected to give a talk at the European Society for Evolutionary Biology (ESEB2019) in Turku, Finland.</p>
<figure>
<a href="Agneesh profile"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/Agneesh-TED.jpg" alt="Agneesh" width="500" /></a>
</figure>
<p>If you missed his <a href="https://twitter.com/LaPepena/status/1164867951331336192">talk</a> and want to hear more about his research, you can find all about it in his recently published paper in MBE <a href="https://academic.oup.com/mbe/article/36/9/1964/5492084"><em>“Many Options, Few Solutions: Over 60 My Snakes Converged on a Few Optimal Venom Formulations”</em></a>.</p>
<p>We invite you to read a summary of this study with the associated <a href="https://www.oist.jp/news-center/news/2019/6/14/snakes-best-bartenders-animal-kingdom">OIST media news</a>.</p>
<p>Congratulations, we will keep following the rest of your science adventures.</p>Maevamaeva.techer@oist.jpAgneesh, our PhD student in evolutionary genetics, worked hard to understand how complex traits evolve through millions of years and how snakes perfected their venom recipes. He was selected to give a talk at the European Society for Evolutionary Biology (ESEB2019) in Turku, Finland.Samuel Ramsey’s (aka Dr. Buggs) visit and talk at OIST2019-08-16T00:00:00+00:002019-08-16T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Samuel-Ramsey-(aka-Dr.-Buggs)_visit<p>Dr. Samuel Ramsey (also know as Dr. Buggs), a postdoctoral researcher at the USDA Maryland is a honey bee mite expert and parasitologist and visited our unit from August 11 to 16, 2019.</p>
<figure>
<a href="Samuel"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/Sammy.jpg" alt="Varroa-sammy" width="1200" /></a>
<figcaption>Dr. Samuel Ramsey gave a talk about honey bee mites at OIST on 13/08/2019</figcaption>
</figure>
<p>We were lucky to host and hear his fantastic talk <strong>“Despicable Mites: Recent Findings in the Study of Two Honey Bee Parasites”</strong> with a focus on his recently published work on how and where Varroa destructor feeds on its honey host (<a href="https://www.pnas.org/content/116/5/1792">spoiler alert: it feeds on fat body and not hemolymph as it was though for decades!</a>). Samuel also shared about his ongoing project in Thailand to better understand the biology of another terrible mite <em>Tropilaelaps mercedesae</em> and its behavioral interactions with its honey bee host in the native range. Learning from past mistakes with <em>V. destructor</em> global invasion, Samuel plans to learn from this already terrible parasite and help preventing its spread out of Asia.</p>
<p>We look forward to hearing more about his research and fieldwork in Asia, and keep collaborating with him on the world biogeography Varroa mites project.</p>Maevamaeva.techer@oist.jpDr. Samuel Ramsey (also know as Dr. Buggs), a postdoctoral researcher at the USDA Maryland is a honey bee mite expert and parasitologist and visited our unit from August 11 to 16, 2019.Tis’ the season of visitors!2019-04-08T00:00:00+00:002019-04-08T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Young-researchers-visiting-EcoEvo<p>April is here, and in Okinawa this means the start of rainy season and temperature rising up… In our lab, this is also the time of the year we welcome the most visitors!</p>
<p>Claire Morandin, EMBO long-term fellow, is one of our favorite and frequent visitor who has been working with Vienna this year on a honey bee experiment.</p>
<p>We also welcome a long term visitor (January-July 2019), Chao Dong, postdoctoral researcher from the Linksvayer lab at the University of Pennsylvania. Chao is here to prepare and sequence many ants and spiders for his collaborative work between Sasha and the Linkvasyer group.</p>
<figure>
<a href="visitors"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/team-visitors-April2019.jpg" alt="visitors" width="800" /></a>
</figure>
<p>Manasee Weerathunga joined us as a research intern from Sri Lanka (February-April 2019), and has been analyzing with an undefeatable determination, to better understand the leaf-cutting ant foraging using a dataset from Sasha’s graduate expereinece in 2003.</p>
<p>Elroy Kwan-Au joined us as a honour student from ANU, and will prepare libraries and sequence museum samples of the beautiful variegated fairywren <em>Malurus lamberti</em> and related species for three months. He will return to Canberra and will analyze these data for his honour “Population genomics of climate change in the purple-backed fairy wren”.</p>
<figure>
<a href="ManaseeElroy"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/maanasee-elroy.jpg" alt="ManaseeElroy" width="500" /></a>
</figure>Maevamaeva.techer@oist.jpApril is here, and in Okinawa this means the start of rainy season and temperature rising up… In our lab, this is also the time of the year we welcome the most visitors!Varroa mite genomes resource and preprint2019-01-09T00:00:00+00:002019-01-09T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/Varroa-genomes-preprint<p>Over the past decades, the ectoparasitic <em>Varroa</em> mite has been the key driver of honey bee population declines worldwide. Surprisingly, no modern genome reference existed for the global beekeeping pest <em>V. destructor</em>, nor any other Varroidae. We developed new reference genomes for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_002443255.1/"><em>V. destructor</em></a> and its sister species <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_002532875.1/"><em>V. jacobsoni</em></a> which also jumped last decade, from the eastern honey bee <em>Apis cerana</em> to the western honey bee <em>A. mellifera</em>. Using a combination of HiSeq, PacBio, and Hi-C sequencing, we obtained a genome at a chromosomal-level for <em>V. destructor</em> with the <a href="http://i5k.github.io/arthropod_genomes_at_ncbi">best N50 scaffold for any arachnid</a> to date.</p>
<figure>
<a href="Varroa species"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/micro-ct-varroa.jpg" alt="Varroa species" width="600" /></a>
<figcaption>Until 2000, these two cryptic species were mistakenly considered as being the same V.jacobsoni</figcaption>
</figure>
<p>Both have been on NCBI for a while now, but we finally posted our comparative genomic analysis of these two Varroa mites preprint on bioarxiv. We found out that although both <em>Varroa</em> species have the same host range and specificity, they show striking differences in genes under selection and divergent strategies of adaptation. If you want to learn more about these nasty little beasts, you can read our work here: <a href="https://www.biorxiv.org/content/early/2019/01/07/512988">Genomic analyses of sibling honey bee ectoparasitic mite species show divergent strategies of adaptation</a>, until hopefully a more formal publication soon.</p>
<p>We hope these resource will help better understanding the success of these mites and open new paths for species-specific pest control.</p>Maevamaeva.techer@oist.jpOver the past decades, the ectoparasitic Varroa mite has been the key driver of honey bee population declines worldwide. Surprisingly, no modern genome reference existed for the global beekeeping pest V. destructor, nor any other Varroidae. We developed new reference genomes for V. destructor and its sister species V. jacobsoni which also jumped last decade, from the eastern honey bee Apis cerana to the western honey bee A. mellifera. Using a combination of HiSeq, PacBio, and Hi-C sequencing, we obtained a genome at a chromosomal-level for V. destructor with the best N50 scaffold for any arachnid to date.3rd Nerd Nite Okinawa: Zombie ants!2018-11-26T00:00:00+00:002018-11-26T00:00:00+00:00https://mikheyevlab.github.io/EcoEvoUnit/3rd-Nerd-Nite-Okinawa-Zombie-ants<figure>
<a href="3rd edition Nerd Nite Okinawa"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/Rob-nerdnite.jpg" alt="Rob-nerdnite" width="600" /></a>
<figcaption>Rob and Solenopsis spp. *fire ant* (C) Robert Campbell </figcaption>
</figure>
<p>If you are in Okinawa and interested in a relaxing and fun way to hear about scientific research while drinking beer or cocktails with friends and colleagues, come to Nerd Nite Okinawa! And guess what? The 3rd edition coming next Friday 7th December will feature our own Ph.D student Rob Campbell who will talk about Zombie Ants :ant:</p>
<p>Here is a short spooky summary: “The Walking Dead meets Michael Crichton’s novel Prey – these aren’t reanimated corpses or nanotech machines but real living parasites with the power to mind-control their hosts. No insect is safe– or are they? What are these parasites and how do they take control? They already walk among us, hidden in plain sight; can we see what’s going on inside their hosts?””</p>
<p>Don’t miss out the opportunity to see this excellent talk, learn about the mysterious phorid fly and chat with Rob!</p>
<p>Thanks to Margaret Brisbin’s amazing organizating, the Nerd Nite initiative in Okinawa has been greatly appreciated by a wide audience since its 1st edition in October! You may have seen our first time participating with a talk on bees and the terrible Varroa mite, followed by curious questions and nice exchanges. Don’t hesitate to become a volunteer speaker or follow the event @nerdniteoki</p>
<figure>
<a href="1st edition Nerd Nite Okinawa"><img src="https://mikheyevlab.github.io/EcoEvoUnit/images/Maeva-nerdnite.jpg" alt="Maeva-nerdnite" width="300" /></a>
<figcaption>1st edition Nerd Nite Okinawa</figcaption>
</figure>Maevamaeva.techer@oist.jpRob and Solenopsis spp. *fire ant* (C) Robert Campbell If you are in Okinawa and interested in a relaxing and fun way to hear about scientific research while drinking beer or cocktails with friends and colleagues, come to Nerd Nite Okinawa! And guess what? The 3rd edition coming next Friday 7th December will feature our own Ph.D student Rob Campbell who will talk about Zombie Ants :ant: