Biolaitos November 2021

biolaitos@lists.oulu.fi

17 participants
41 discussions

Reminder: Biology Thu seminar today at 16:30 Dr. James Thorson on statistical models for whole-ecosystem understanding
by Heikki Helanterä 25 Nov '21

25 Nov '21

Dear colleagues, please remember today's seminar, and note the unusual time 16:30 (due to time zone differences): The seminar will be hosted by Sami Kivelä. Heikki Biology Thursday seminar 25th Nov at 16:30 (note unusual hour!) on zoom (link below): Dr. James Thorson, the Program lead at the Habitat and Ecologial Processes Research Program / Alaska Fisheries Science Center / National Marine Fisheries Service in Seattle, WA. His title: Statistical models for whole-of-ecosystem understanding, and what they say about changes in the Pacific gateway to the Arctic Topics: * Tweedie stomachs * Pacific cod movement * Whole-of-ecosystem Bering Sea synthesis Abstract: The central Arctic and adjacent oceans are rapidly changing due to loss of sea ice resulting from the climate crisis. Changes are apparent in planktonic advection and phenology, shifting habitat preferences for mobile consumers, as well as consumer diet and bioenergetics. However, there are few methods to synthesize spatial patterns in numerical abundance, diet, and physiological condition for multiple trophic levels, as well as how these change among seasons and years. To address this, I present three new statistical methods to facilitate whole-of-ecosystem spatio-temporal synthesis. First, I discuss a simple approach to analyze food-habits data (stomach contents, etc.) using a Tweedie generalized linear model (GLM). This GLM approximates a thinned and double-marked Poisson point process representing foraging processes, and shows multidecadal shifts in prey for a central-place forager (Middleton Island tufted puffins). Second, I introduce a "diffusion-taxis" movement model, which I fit to data from multi-decadal surveys, fishery catch-and-effort, tagging data, and output from global climate models. This model demonstrates the rapid northward movement for Pacific cod into the northern Bering Sea. Finally, I introduce a whole-of-ecosystem "empirical orthogonal function" (EOF) model for the eastern Bering Sea. This EOF demonstrates the outsize importance of cold near-bottom waters created by spring ice formation, where warm ice-free years result in detrimental conditions for Alaska pollock. Throughout, I emphasize that whole-of-ecosystem synthesis is feasible using off-the-shelf statistical software, and that the Pacific Arctic in particular is experiencing rapid changes due to climate. Also, don't forget that prof. Virpi Lummaa is giving a talk in the Biodiverse Anthropocenes monthly series on Friday 26th Nov at 12-2pm at Tellus Stage (including snacks and refreshments and time to mingle! So see you online on Thursday, and on site in Tellus on Friday, Heikki Heikki Helanterä is inviting you to a scheduled Zoom meeting. Topic: Biology Thursday seminar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://oulu.zoom.us/j/62917763539?pwd=WENZRy9Bb3NlSzlyeVlVamJ4RHR5Zz09 Meeting ID: 629 1776 3539 Passcode: 166151 Join by SIP 62917763539(a)109.105.112.236<mailto:62917763539@109.105.112.236> 62917763539(a)109.105.112.235<mailto:62917763539@109.105.112.235> Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 629 1776 3539 Passcode: 166151 =============================================== Heikki Helanterä Associate Professor (tenure track) Ekologian ja genetiikan tutkimusyksikkö / Ecology and Genetics Research Unit Oulun Yliopisto / University of Oulu / Finland heikki.helantera(a)oulu.fi<mailto:heikki.helantera@oulu.fi> +358-40-7507 334

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updated instructions for grading master's theses
by Juhani Hopkins 24 Nov '21

24 Nov '21

Hi, some small updates have been made to the master's thesis grading instructions. If you have copies of the previous versions, please replace them with these. You can also find the latest version on the master's seminar moodle pages or the teaching teams group. Juhani Hopkins Degree program in Biology University of Oulu +358 (0)294 481 330

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Biology Thursday seminar 25th Nov at 16:30 James Thorson
by Heikki Helanterä 22 Nov '21

22 Nov '21

Dear colleagues, Biology Thursday seminar continues on the 25th Nov at 16:30 (note unusual hour!) on zoom (link below). Our speaker is Dr. James Thorson who is the Program lead at the Habitat and Ecologial Processes Research Program / Alaska Fisheries Science Center / National Marine Fisheries Service in Seattle, WA. His title: Statistical models for whole-of-ecosystem understanding, and what they say about changes in the Pacific gateway to the Arctic Topics: . Tweedie stomachs . Pacific cod movement . Whole-of-ecosystem Bering Sea synthesis Abstract: The central Arctic and adjacent oceans are rapidly changing due to loss of sea ice resulting from the climate crisis. Changes are apparent in planktonic advection and phenology, shifting habitat preferences for mobile consumers, as well as consumer diet and bioenergetics. However, there are few methods to synthesize spatial patterns in numerical abundance, diet, and physiological condition for multiple trophic levels, as well as how these change among seasons and years. To address this, I present three new statistical methods to facilitate whole-of-ecosystem spatio-temporal synthesis. First, I discuss a simple approach to analyze food-habits data (stomach contents, etc.) using a Tweedie generalized linear model (GLM). This GLM approximates a thinned and double-marked Poisson point process representing foraging processes, and shows multidecadal shifts in prey for a central-place forager (Middleton Island tufted puffins). Second, I introduce a "diffusion-taxis" movement model, which I fit to data from multi-decadal surveys, fishery catch-and-effort, tagging data, and output from global climate models. This model demonstrates the rapid northward movement for Pacific cod into the northern Bering Sea. Finally, I introduce a whole-of-ecosystem "empirical orthogonal function" (EOF) model for the eastern Bering Sea. This EOF demonstrates the outsize importance of cold near-bottom waters created by spring ice formation, where warm ice-free years result in detrimental conditions for Alaska pollock. Throughout, I emphasize that whole-of-ecosystem synthesis is feasible using off-the-shelf statistical software, and that the Pacific Arctic in particular is experiencing rapid changes due to climate. Also, don't forget that prof. Virpi Lummaa is giving a talk in the Biodiverse Anthropocenes monthly series on Friday 26th Nov at 12-2pm at Tellus Stage (including snacks and refreshments and time to mingle! So see you online on Thursday, and on site in Tellus on Friday, Heikki Heikki Helanterä is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://oulu.zoom.us/j/62917763539?pwd=WENZRy9Bb3NlSzlyeVlVamJ4RHR5Zz09 Meeting ID: 629 1776 3539 Passcode: 166151 Join by SIP 62917763539(a)109.105.112.236 62917763539(a)109.105.112.235 Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 629 1776 3539 Passcode: 166151

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Biology Thu seminar 25th Nov at 16:30 Dr. James Thorson on statistical models for whole-ecosystem understanding
by Heikki Helanterä 22 Nov '21

22 Nov '21

Dear colleagues, Biology Thursday seminar continues on the 25th Nov at 16:30 (note unusual hour!) on zoom (link below). Our speaker is Dr. James Thorson who is the Program lead at the Habitat and Ecologial Processes Research Program / Alaska Fisheries Science Center / National Marine Fisheries Service in Seattle, WA. His title: Statistical models for whole-of-ecosystem understanding, and what they say about changes in the Pacific gateway to the Arctic Topics: * Tweedie stomachs * Pacific cod movement * Whole-of-ecosystem Bering Sea synthesis Abstract: The central Arctic and adjacent oceans are rapidly changing due to loss of sea ice resulting from the climate crisis. Changes are apparent in planktonic advection and phenology, shifting habitat preferences for mobile consumers, as well as consumer diet and bioenergetics. However, there are few methods to synthesize spatial patterns in numerical abundance, diet, and physiological condition for multiple trophic levels, as well as how these change among seasons and years. To address this, I present three new statistical methods to facilitate whole-of-ecosystem spatio-temporal synthesis. First, I discuss a simple approach to analyze food-habits data (stomach contents, etc.) using a Tweedie generalized linear model (GLM). This GLM approximates a thinned and double-marked Poisson point process representing foraging processes, and shows multidecadal shifts in prey for a central-place forager (Middleton Island tufted puffins). Second, I introduce a "diffusion-taxis" movement model, which I fit to data from multi-decadal surveys, fishery catch-and-effort, tagging data, and output from global climate models. This model demonstrates the rapid northward movement for Pacific cod into the northern Bering Sea. Finally, I introduce a whole-of-ecosystem "empirical orthogonal function" (EOF) model for the eastern Bering Sea. This EOF demonstrates the outsize importance of cold near-bottom waters created by spring ice formation, where warm ice-free years result in detrimental conditions for Alaska pollock. Throughout, I emphasize that whole-of-ecosystem synthesis is feasible using off-the-shelf statistical software, and that the Pacific Arctic in particular is experiencing rapid changes due to climate. Also, don't forget that prof. Virpi Lummaa is giving a talk in the Biodiverse Anthropocenes monthly series on Friday 26th Nov at 12-2pm at Tellus Stage (including snacks and refreshments and time to mingle! So see you online on Thursday, and on site in Tellus on Friday, Heikki Heikki Helanterä is inviting you to a scheduled Zoom meeting. Topic: Biology Thursday seminar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://oulu.zoom.us/j/62917763539?pwd=WENZRy9Bb3NlSzlyeVlVamJ4RHR5Zz09 Meeting ID: 629 1776 3539 Passcode: 166151 Join by SIP 62917763539(a)109.105.112.236<mailto:62917763539@109.105.112.236> 62917763539(a)109.105.112.235<mailto:62917763539@109.105.112.235> Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 629 1776 3539 Passcode: 166151 =============================================== Heikki Helanterä Associate Professor (tenure track) Ekologian ja genetiikan tutkimusyksikkö / Ecology and Genetics Research Unit Oulun Yliopisto / University of Oulu / Finland heikki.helantera(a)oulu.fi<mailto:heikki.helantera@oulu.fi> +358-40-7507 334

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master's seminar 24.11.
by Juhani Hopkins 22 Nov '21

22 Nov '21

https://oulu.zoom.us/j/66787207738 14.15 Kaarle Mäkelä 14.35 Janne Welling 14.55 Anne Asikainen 15.40 Venla Virtanen Bumblebees and cooperation in a laboratory environment Eri mykorritsatyyppien vaikutukset kasvien ravinnetalouteen isotooppitutkimuksen perusteella Lehtokasvillisuuden lajikoostumuksen muutokset pitkällä aikavälillä Pohjaeläinyhteisöt ja niiden vuosien välinen vaihtelu luonnontilaisessa jokiverkostossa Janette Arppi Matias Wolff Sanni Vesala Wille-Pekka Lepo Plan Plan Result Result Heikki Helanterä Annu Ruotsalainen Risto Virtanen Timo Muotka Olli Loukola & Cwyn Solvi Maria Väisänen & Annu Ruotsalainen Lauralotta Muurinen & Risto Virtanen Kaisa-Leena Huttunen & Timo Muotka

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Työhyvinvointikyselyn tulokset raporttina / Well being survey results reports
by Jouni Aspi 19 Nov '21

19 Nov '21

Liitttenä /Attached Jouni

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Yksikköpalaveri /Unit meeting
by Jouni Aspi 19 Nov '21

19 Nov '21

Hyvinvointikyselyn tulokset /Wellbeing survey results Jouni Aspi is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://oulu.zoom.us/j/69469144589 Meeting ID: 694 6914 4589 Join by SIP 69469144589(a)109.105.112.236 69469144589(a)109.105.112.235 Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 694 6914 4589

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Fluorescence microscope demonstrations (Leica and Olympus)
by Janne Koskimäki 18 Nov '21

18 Nov '21

Dear all, For everyone interested in light or fluorescence microscopy, there will be a demo for Leica THUNDER Tissue Imager at Ecology and Genetics RU molecular biology teaching lab B132 on next Wed 24.11 starting from 10:00. You can bring your own microscopic research samples with you for testing (on a microscope slide, mounted under coverslip). Leica THUNDER Tissue Imager https://www.leica-microsystems.com/products/thunder-imaging-systems/p/thund… Images taken with Thunder system: https://www.leica-microsystems.com/science-lab/galleries/image-gallery-thun… Then, on Thursday 25.11 9:00-12:00 there will be a demo for Olympus BX63 Automated Fluorescence Microscope (also for normal light microscopy) at Biocenter Oulu Kieppi building 4th floor Seminar room 487B. Again you can bring your own research samples for testing, if interested. In the same space there’s also testing available for the new Olympus VS200 Research slide scanner that allows multiplexed and automated high-resolution scanning of several microscope slides at one go. Olympus BX63 Automated Fluorescence Microscope https://www.olympus-lifescience.com/en/microscopes/upright/bx63/ Olympus VS200 Research Slide Scanner https://www.olympus-lifescience.com/en/solutions-based-systems/vs200/ If you need additional information, feel free to contact me. Best, Janne Janne J. Koskimäki, Ph.D. Ecology and Genetics Research Unit University of Oulu PO Box 3000 FIN-90014-Oulu Finland ---------------------------------------- Email. janne.koskimaki(a)oulu.fi<mailto:janne.koskimaki@oulu.fi> From: Petteri Valtonen <Petteri.Valtonen(a)gwb.fi> Sent: torstai 18. marraskuuta 2021 16.05 To: Janne Koskimäki <janne.koskimaki(a)oulu.fi> Subject: VS: VS200 demo [cid:image001.png@01D7DC96.06D49840] Ystävällisin terveisin / Best regards, Petteri Valtonen Tuotepäällikkö/Product Manager Mikroskopia/Microscopy Oy G.W.Berg & Co Ab Microkatu 1 , FI-70210 Kuopio, Finland Tel. +358 201 255 255 Mob. +358 40 5021420 petteri.valtonen(a)gwb.fi<mailto:petteri.valtonen@gwb.fi>

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Arctic Interactions (ArcI) Research Opportunities - Second calls of AAC and HRHR programmes (DL 30.11.2021 )
by Päivi Tomperi 18 Nov '21

18 Nov '21

Arctic Interactions (ArcI) Research Opportunities - Second calls of AAC and HRHR programmes (DL 30.11.) Arctic interactions (ArcI) is one of the research profile themes of the University of Oulu studying environmental change and human-environmental relationships in the Arctic and promoting sustainable development in the region. ArcI has now recruited a cohort of scientists in the multiple research units and is moving into the second half of the programme over the next three years. We have designed programme-based venues that have distinct goals and aims to grow UniOulu’s Arctic research profile. We now open new calls for proposals for Advanced Arctic Collaboration (AAC) and High Risk High Reward (HR2) programmes at UniOulu. * AAC programme supports the ArcI Tenure Professors through new collaborative projects between tenure professors and others (postdocs, senior research scientists, professors) within their Faculties and or across Faculties. Maximum funding per project is 60 000€ for the year 2022. The funding must be used internally at the UOulu See AAC call text and evaluation criteria.<https://patio.oulu.fi/en/media/3646/download?attachment> * HRHR programme seeks to support exceptionally high-risk research endeavours that have the potential for extraordinarily high reward focused on the Arctic. These projects need to carry out studies that are way beyond the mainstream and are transformational to Arctic Science. Maximum funding per project is 50 000€ for the year 2022 and it must be used internally at the UOulu. The funding can be applied by all researchers at different stages of their careers (postdocs, senior research scientists, professors). See HRHR call text and evaluation criteria.<https://patio.oulu.fi/en/media/3647/download?attachment> The applications must be submitted using the application form: AAC: https://webropol.com/s/ArcI-AAC2 <https://webropol.com/s/ArcI-AAC2> (deadline 30 November at 23.59) HRHR: https://webropol.com/s/ArcI-HRHR2 (deadline 30 November at 23.59) More information Professor Björn Klöve, Director of ArcI profile action, WEEE, Faculty of Technology, bjorn.klove(a)oulu.fi<mailto:bjorn.klove@oulu.fi> Research Coordinator Jouko Inkeröinen, Kvantum Institute, jouko.inkeroinen(a)oulu.fi<mailto:jouko.inkeroinen@oulu.fi> p. 040 577 6106 ArcI www: https://www.oulu.fi/en/arctic-interactions Kind regards, Päivi Päivi Tomperi Research Funding Specialist University of Oulu Research and Project Services Pentti Kaiteran katu 1 PL 8000 90014 University of Oulu Finland tel. +358 294 483972 mobile: +358 (0)40 7468503 e-mail: paivi.tomperi(a)oulu.fi<mailto:paivi.tomperi@oulu.fi>

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Reminder Thursday seminar today. Prof. Helena Freitas: The Centre for Functional Ecology – Science for People & the Planet
by Heikki Helanterä 18 Nov '21

18 Nov '21

Dear colleagues, don’t forget today’s Biology Thursday seminar at 12:15 (online, link below) with Prof. Helena Freitas from the Centre for Functional Ecology, Univ. of Coimbra, Portugal, giving an overview on their Centre and their national and international projects: The Centre for Functional Ecology – Science for People & the Planet (CFE) is a research unit hosted by the Department of Life Sciences of the University of Coimbra, in Portugal. It brings together researchers with multidisciplinary interests in ecology related subjects, seeking to produce knowledge on global ecology and on ecosystem functioning, from microorganisms, plants, and fauna biodiversity to the ecological complexity of their interactions at the community, ecosystem, and evolutionary level. Also, there is a strong commitment to knowledge transfer to the public and to the productive sector, both locally and nationally, with particular emphasis on the sustainability of the territories and its communities. Prof. Freitas is the coordinator of the Centre, and holds the UNESCO Chair in Biodiversity and Conservation for Sustainable Development at Univ. Coimbra. She has been involved in numerous large conservation programs and consortia, and held various positions of trust in international conservation and ecology organizations – this will certainly be a talk from the very center of where biologists apply their knowledge into crucial topics! The talk will be chaired by Anna-Maria Pirttilä. Have a nice seminar, Heikki Heikki Helanterä is inviting you to a scheduled Zoom meeting. Topic: Biology Thursday seminar Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://oulu.zoom.us/j/62917763539?pwd=WENZRy9Bb3NlSzlyeVlVamJ4RHR5Zz09 Meeting ID: 629 1776 3539 Passcode: 166151 Join by SIP 62917763539(a)109.105.112.236<mailto:62917763539@109.105.112.236> 62917763539(a)109.105.112.235<mailto:62917763539@109.105.112.235> Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 629 1776 3539 Passcode: 166151 =============================================== Heikki Helanterä Associate Professor (tenure track) Ekologian ja genetiikan tutkimusyksikkö / Ecology and Genetics Research Unit Oulun Yliopisto / University of Oulu / Finland heikki.helantera(a)oulu.fi<mailto:heikki.helantera@oulu.fi> +358-40-7507 334

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Biolaitos November 2021