Hemicellulose is a complex heteropolysaccharide with branched structure and consisting of different monosacchride building blocks. For its hydrolysis an array of enzymes (hemicellulasen) with different specificity is needed. In the discovery, initial screening and characterization of enzymes active on lignocellulose, a limited amount of substrates is used (chromogenic substrates, commercially available oligosaccharides or xylan model substrates). These give little information on the substrate specificity of the enzymes. Recently, a different class of enzymes is discovered that boost lignocellulose degradation. These enzymes were originally classified in glycoside hydrolase family 61 (GH61), but use a O2- and metal-dependent oxidative mechanism using unknown molecules in the lignocellulose matrix. One of the bottlenecks in this research is the detection and quantification of the oligosaccharide products formed. In this project, a fast and sensitive assay for the high-throughput screening of biomass active enzymes is presented that is based on a library of biomass-derived oligosaccharides. The assay will be optimized and validated with hemicellulases produced by the model organisms Aspergillus niger and Trichoderma reesei (Hypocrea jecorina). We will build further on the assembly of an oligosaccharide library derived from lignocellulosic biomass. The sugars are analysed in parallel with DSA-FACE en HPAEC-PAD and yield a 2D-plot where the spots are clearly separated (Multiplexed Analytical Glycomics Technologie). This database will contribute to the identification of unknown oligosacchride products. It is also demonstrated that the developed 2D technologie is of added-value in the detection/qauntification of oxidized cellodextins in the degradation of lignocellulose by GH family 61 enzymes. A case study with arabinofuranosidases will show that the DSA-FACE technology is perfetly suited for enzyme kinetics on real substrates. Also we will show that the methodology –due to its high resolution- is suited to determine the substrate specificity of arabinofuranosidases. All expertise will at the end result in a technology allowing a high through-put functional annotation of hemicellulases and other related enzymes.
"},{"end_date":"2022-01-31","abstract":"Bioethanol constitutes an important alternative for the petroleum-based industry. Instead of food crops (corn, sugar cane), the focus shifted to lignocellulosic biomass side streams as sustainable source for sugars for bioethanol production. This research proposal implements an in house developed enzyme engineering method to customize the enzymatic step in an efficient way for any lignocellulosic source.
","title":"Designer cellulosomics for customized solutions towards sustainable bioethanol production","iweto_id":"01N02416","_id":"01N02416","start_date":"2016-02-01","gismo_id":"0e24f71e-4a3a-447d-85bc-a04dad92afea","publication_count":1},{"publication_count":1,"gismo_id":"2ed76399-1970-11e9-9296-432664c4991f","start_date":"2018-01-01","end_date":"2021-12-31","_id":"01D08617","iweto_id":"01D08617","title":"Designer cellulosomics for a customized conversion of lignocellulosic biomass to bioethanol","abstract":"Bioethanol is an alternative biofuel that can substitute for the diminishing fossil fuel stocks. This PhD project focuses on the development of yeast cell populations equipped with highly diverse multi-enzyme complexes, called designer cellulosomes. With the aid of these designer cellulosomes, the yeast cell populations will be able to efficiently convert lignocellulose-rich plant
material and waste streams into bioethanol.
Microorganisms drive the global carbon and nutrient cycles that underlie essential ecosystem functioning. Yet, our understanding of microbial speciation, evolutionary history and biogeography remains elusive. Especially terrestrial protists are heavily understudied. Given the rapid and irreversible environmental changes affecting the Polar Regions today, this knowledge-gap is critical for the Arctic and Antarctic, where terrestrial microalgae dominate biodiversity. Here, I will combine large-scale phylogenetic and population genetic studies of the terrestrial diatom species complex Pinnularia borealis, with a strong focus on the Polar Regions. Specifically, I will (i) create a phylogenomic framework of the P. borealis complex to study levels of ancient introgression and patterns of positive selection related to the colonization of polar environments, (ii) investigate population structure, gene flow, and mode of speciation in a bipolar P. borealis species, and (iii) study ancient DNA to investigate Late-Pleistocene and Holocene dynamics in Antarctic P. borealis species and populations, and the impact of glacial/interglacial cycles thereon. This project will provide novel insights into the drivers of species- and population-level diversity of a diatom species complex, and how this is affected by past environmental change. As such, the results will serve as a model for understanding the evolutionary history of both terrestrial microalgae and polar terrestrial diversity.
","end_date":"2027-03-31"}],"biblio_id":"01KM2X885SJPCZKAQTSFK43ZRG","copyright_statement":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","publication_status_sort":1,"classification":"A1","doi":["10.1080/09670262.2026.2626682"],"type":"journalArticle","language":["eng"],"affiliation":[{"name":"Department of Biology","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE11"}],"ugent_id":"WE11"}],"date_created":"2026-03-19 11:21:21","jcr":{},"created_by":{"ugent_id":["802001900226","979709823268"],"affiliation":[{"ugent_id":"WE11","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE11"}]}],"last_name":"Pinseel","name":"Eveline Pinseel","first_name":"Eveline","orcid_id":"0000-0002-1801-2187","_id":"00B703D0-2565-11E3-BB7C-F0BB10BDE39D","biblio_id":"00B703D0-2565-11E3-BB7C-F0BB10BDE39D","name_last_first":"Pinseel, Eveline"},"page":{"first":"1","last":"25"},"issn":["0967-0262","1469-4433"],"title":"A polyphasic taxonomy of the pseudocryptic diatom species complex Pinnularia acidicola, including description of new species","author":[{"name_last_first":"Kollár, Jan","name":"Jan Kollár","last_name":"Kollár","first_name":"Jan"},{"name":"Bart Van de Vijver","name_last_first":"Van de Vijver, Bart","first_name":"Bart","last_name":"Van de Vijver"},{"last_name":"Kulichová","first_name":"Jana","name":"Jana Kulichová","name_last_first":"Kulichová, Jana"},{"first_name":"Eva","last_name":"Hejduková","name":"Eva Hejduková","name_last_first":"Hejduková, Eva"},{"first_name":"Raquel","last_name":"Viso","name_last_first":"Viso, Raquel","name":"Raquel Viso"},{"last_name":"Kohler","first_name":"Tyler J.","name_last_first":"Kohler, Tyler J.","name":"Tyler J. Kohler"},{"name_last_first":"Kahlert, Maria","name":"Maria Kahlert","first_name":"Maria","last_name":"Kahlert"},{"name":"Eveline Pinseel","ugent_id":["802001900226","979709823268"],"last_name":"Pinseel","affiliation":[{"ugent_id":"WE11","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE11"}]}],"orcid_id":"0000-0002-1801-2187","_id":"00B703D0-2565-11E3-BB7C-F0BB10BDE39D","biblio_id":"00B703D0-2565-11E3-BB7C-F0BB10BDE39D","name_last_first":"Pinseel, Eveline","first_name":"Eveline"},{"first_name":"Aloisie","last_name":"Poulíčková","name":"Aloisie Poulíčková","name_last_first":"Poulíčková, Aloisie"},{"name_last_first":"Zimmermann, Jonas","name":"Jonas Zimmermann","last_name":"Zimmermann","first_name":"Jonas"},{"first_name":"Jiří","last_name":"Neustupa","name_last_first":"Neustupa, Jiří","name":"Jiří Neustupa"},{"last_name":"Vyverman","affiliation":[{"ugent_id":"WE11","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE11"}]}],"ugent_id":["801000629345","978025521837"],"name":"Wim Vyverman","first_name":"Wim","_id":"F43B244E-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Vyverman, Wim","biblio_id":"F43B244E-F0ED-11E1-A9DE-61C894A0A6B4","orcid_id":"0000-0003-0850-2569"},{"first_name":"Kateřina","last_name":"Kopalová","name":"Kateřina Kopalová","name_last_first":"Kopalová, Kateřina"}],"status":"public","related_dataset":[{"_id":"01KM2XXV9HVJXXAKDM2PT8VBV9"}],"keyword":["Bacillariophyceae","cryptic species diversity","environmental DNA (eDNA)","integrative taxonomy","island biogeography","sub-Antarctica","CALIBRATED MULTIGENE PHYLOGENY","GENUS PINNULARIA","EPIPHYTIC DIATOMS","DIVERSITY","BACILLARIOPHYTA","DELIMITATION","EVOLUTION","ISLAND","RBCL","IDENTIFICATION"],"abstract":["Diatoms are one of the most species-rich and environmentally significant protist groups on Earth, playing important roles in the biogeochemical cycles and food webs of many (semi)aquatic ecosystems. However, much of their species-level diversity lies beyond the resolution of traditional microscopy-based methods that are routinely, and sometimes exclusively, utilized in diatom taxonomy. One such cryptic species complex is Pinnularia acidicola, which was recently shown to consist of at least three different species-level lineages inhabiting remote southern hemisphere islands. Here, we (1) compare the P. acidicola complex to its closest relatives from P. subcapitata and P. sinistra using both published and newly established strains, (2) integrate all currently available evidence – including from light and scanning electron microscopy, conventional and geometric morphometrics, molecular phylogenetics, eDNA-based biogeography and ecology – and (3) formally resolve the three species. The P. acidicola name is reserved for the type population found on Ile de la Possession and Marion Island, while the population found on Réunion is described as P. acidireunionensis. The population sampled on Ile Amsterdam is newly recognized as the already described P. vixconspicua, and epitypes including DNA sequences are designated. The three species are genetically distinct, exhibit non-overlapping geographic distributions and are morphologically differentiated by subtle, yet significant morphometric differences in valve dimensions, fascia and striation. Despite this, all three species appear to share an ecological preference for acidic soils, ponds or streams. Altogether, our comprehensive analysis of the P. acidicola species complex highlights the importance of combining both morphological and genetic approaches in uncovering diatom species diversity."],"publication_status":"inpress","handle":"http://hdl.handle.net/1854/LU-01KM2X885SJPCZKAQTSFK43ZRG","parent":{"short_title":"Eur. J. Phycol.","title":"EUROPEAN JOURNAL OF PHYCOLOGY"},"_id":"01KM2X885SJPCZKAQTSFK43ZRG","cite":{"bof":"Edible insects are one of the solutions for Europe’s growing dependency on imported protein. Because of their ability to convert organic lowgrade residual streams into a nutritional rich product they can be used as a sustainable and locally produced high quality protein source.
\nDespite the legal approval, the use of edible insects is almost nonexistent in food for dogs and cats. The implementations of edible insects are fairly new in Europe, hence there are still some fundamental questions before the widespread application will kick off. The focus of Petsect is gathering knowledge about the fundamental baselines of the use of insects as ingredients for pet food and novel health applications, such as processing techniques, nutritional value, digestibility and especially the effect on immune system. More research is necessary to develop a palatable insect-based pet food with a high nutritional value. Petsect will focus on the use of yellow mealworms (YMW) and black soldier fly larvae (BSFL) as these production processes are currently the furthest developed which has a direct impact on the mass availability and the price.
\nThe overall goal of Petsect is to create a nutritional balanced food, with an extra benefit for gastrointestinal health, for both cats and dogs with insect larvae (fractions) as main protein source or functional (chitin, lipid or protein based) ingredient. The leveled ingredient approach for selecting promising feed ingredients comprises 1) nutritional analyses 2) in vitro digestibility & bioactivity evaluation. 3) in vivo digestibility and palatability with 4) monitoring of gastrointestinal health effects by means of microbiome and metabolome analyses. Additionally, the sustainability of the whole process from farming the insects up to the development of the pet food will be assessed to ensure a sustainable end product.
\n"},{"end_date":"2026-09-30","title":"DNA adductomics to study exposomic drivers of disease","abstract":"
DNA adducts provide information on the exposure and biological effects of chemical hazards. Hence, the birth of DNA adductomics has not gone unnoticed in the era of exposomics, in which the aim is to study the whole of environmental exposures and biological consequences thereof. This project will apply DNA adductomics in large-scale exposomics for the very first time, to further unravel the determinants of food allergy and esophageal cancer. Firstly, this project aims to lay the foundation for DNA adductomics data preprocessing. The second and third aim are to study differences in DNA adduct formation in food allergy and esophageal cancer cases versus controls. Observed shifts in the DNA adductome will be linked to exposure to environmental pollutants, as assessed in children with food allergy in the ENVIRONAGE cohort in Flanders (n > 400), and to (multiple) mycotoxin exposure(s) in adults with esophageal cancer in an IARC/WHO sub-Saharan esophageal cancer cohort (n > 300) using state-of-the-art multivariate and machine-learning based modelling. Results will be explored mechanistically using in vitro digestions and/or in vivo rodent or zebrafish experiments, to increase knowledge on the molecular underpinnings of environmental exposures in relation to food allergy and esophageal cancer and infer causality to proposed determinants. Furthermore, this project will pave the way towards scientific independence and the very first dedicated DNA adductomics research line in Europe.
","iweto_id":"1297623N","_id":"1297623N","start_date":"2022-10-01","publication_count":12,"gismo_id":"83850213-3012-11ed-8665-03ed376344a5"}],"date_updated":"2026-03-31 05:34:13","issn":["2352-4588"],"year":"2026","external":0,"article_type":"review"},{"copyright_statement":"No license (in copyright)","volume":"23","type":"journalArticle","classification":"A2","doi":["10.1108/jamr-11-2024-0412"],"publication_status_sort":2,"issue":"2","esci_id":"001461239700001","affiliation":[{"ugent_id":"EB24","path":[{"ugent_id":"UGent"},{"ugent_id":"EB"},{"ugent_id":"EB24"}],"name":"Department of Business Informatics and Operations Management"}],"language":["eng"],"jcr":{},"date_created":"2025-11-14 10:58:49","subject":["Business and Economics","Technology and Engineering"],"abstract_full":[{"lang":"eng","text":"Purpose. The digital era requires organizations to realign their work practices, culture, and structure. This study investigates the complex dynamics of organizational adaptation to rapid technological advancements by examining the interplay between technological resources and institutional factors over time.\nDesign/methodology/approach. An in-depth long-term case study of a public sector organization forms the basis of this research. The study employs the resource-based view (RBV) and institutional theory as theoretical frameworks to analyze the organization's digital transformation journey, integrating qualitative and quantitative data collection methods.\nFindings. The findings reveal a gradual evolution in the organization's digital maturity, transitioning from a focus on IT infrastructure to a comprehensive integration of technological resources with organizational processes and human capital. The study underscores the critical synergy between institutional factors and technological adaptation, with key milestones marking the organization's progress toward a digitally integrated and employee-centric state. External factors, such as the COVID-19 pandemic, are shown to accelerate digital transformation.\nPractical implications. The study outlines a tailored roadmap for public sector organizations to align institutional culture and structure with technological resources, facilitating successful digital transformation.\nOriginality/value. This study provides a novel long-term perspective on digital transformation, emphasizing the importance of balancing resource optimization with institutional alignment. It offers strategic guidance for organizations embarking on digital transformation journeys, highlighting the role of institutional culture, employee engagement, and external catalysts in achieving sustainable digital integration."}],"file":[{"publication_version":"publishedVersion","_id":"01KN4987R0GAMB5B6DYWE0M0M9","size":"3142680","url":"https://biblio.ugent.be/publication/01KA10953JHH42JWEMQQ8VDB80/file/01KN4987R0GAMB5B6DYWE0M0M9.pdf","name":"publisher_version.pdf","content_type":"application/pdf","kind":"fullText","sha256":"9333657da7bbfab2aae5ee2d982fdf00bc4378e2fd786d9993f3729adf016122","access":"restricted"}],"year":"2026","external":0,"article_type":"original","biblio_id":"01KA10953JHH42JWEMQQ8VDB80","project":[{"gismo_id":"be8beafd-a79f-11e9-bcd2-c58490666d27","publication_count":8,"start_date":"2019-10-01","title":"The DNA of digital business processes .","abstract":"The project’s main objective is to offer best practices for Business Process Management (BPM) in a digital economy. The focus is on how to evaluate the potential impact and value of new IT for business processes, rather than explaining how disruptive technologies work. This project helps gain insights into the future of jobs with grounding in various organization management theories.
","iweto_id":"01N14219","_id":"01N14219","end_date":"2024-07-31"}],"date_updated":"2026-04-01 10:26:21","abstract":["Purpose. The digital era requires organizations to realign their work practices, culture, and structure. This study investigates the complex dynamics of organizational adaptation to rapid technological advancements by examining the interplay between technological resources and institutional factors over time.\nDesign/methodology/approach. An in-depth long-term case study of a public sector organization forms the basis of this research. The study employs the resource-based view (RBV) and institutional theory as theoretical frameworks to analyze the organization's digital transformation journey, integrating qualitative and quantitative data collection methods.\nFindings. The findings reveal a gradual evolution in the organization's digital maturity, transitioning from a focus on IT infrastructure to a comprehensive integration of technological resources with organizational processes and human capital. The study underscores the critical synergy between institutional factors and technological adaptation, with key milestones marking the organization's progress toward a digitally integrated and employee-centric state. External factors, such as the COVID-19 pandemic, are shown to accelerate digital transformation.\nPractical implications. The study outlines a tailored roadmap for public sector organizations to align institutional culture and structure with technological resources, facilitating successful digital transformation.\nOriginality/value. This study provides a novel long-term perspective on digital transformation, emphasizing the importance of balancing resource optimization with institutional alignment. It offers strategic guidance for organizations embarking on digital transformation journeys, highlighting the role of institutional culture, employee engagement, and external catalysts in achieving sustainable digital integration."],"keyword":["Long-term case study","Resource-based view","Institutional logic","Digital transformation","Digital work","Public sector","Organizational adaptation","Technological evolution","Maturation","TRANSFORMATION","FIRM","ORGANIZATIONS","CHALLENGES","FUTURE","PERSPECTIVE","MANAGEMENT","INNOVATION","MODEL"],"status":"public","publication_status":"published","parent":{"title":"JOURNAL OF ADVANCES IN MANAGEMENT RESEARCH","short_title":"J. Adv. Manag. Res."},"_id":"01KA10953JHH42JWEMQQ8VDB80","cite":{"chicago-author-date":"Europe's environment is in an alarming state, with climate change effects aggravating. To secure economic prosperity, human wellbeing and social peace, systemic transformative change of our society is imperative. Ecosystem restoration using nature-based solutions (NbS) is key to this change, in which freshwaters hold a pivotal role. MERLIN will demonstrate freshwater restoration bestpractice; implement innovative NbS at landscape-scale; upscale systemic restoration seizing green growth and private investment opportunities; mainstream restoration by co-development with local communities and economic sectors; multiply solutions for transformative restoration to key players of systemic change. MERLIN will capitalise on successful freshwater restoration projects across Europe. Success factors of 17 flagship projects will be scrutinized, generating a blueprint for proficient NbS implementation.
With investments of 10 mio Euro in hands-on upscaling measures along scalability plans, MERLIN will transform these projects into beacons of innovation for systemic change. Upscaling to the European level, MERLIN will identify landscapes with high potential for transformative restoration and will analyse cost-benefits of restoration scenarios. Economic analyses of European regions will seize green growth opportunities arising from restoration. MERLIN will delineate models for private investment into restoration alongside public funding. MERLIN's initiatives will co-design win-win solutions with economic sectors (agriculture, water supply, insurance, navigation) and local communities, spearheading systemic economic, social and environmental change. The MERLIN Academy and virtual marketplace will multiply innovations to the community of practice, investors and policy makers across Europe and beyond. \n MERLIN is committed to a sustainable, climate-neutral and -resilient, inclusive and transformative path, mainstreaming restoration as a cornerstone for systemic change. \n","end_date":"2026-03-31","eu_framework_programme":"H2020","eu_id":"101036337","start_date":"2021-10-01","gismo_id":"e468e475-d54d-457b-b1a2-0f8a9b172eca"},{"title":"Protecting urban aquatic ecosystems to promote One Health","abstract":"Aquatic ecosystems provide diverse habitats and support biodiversity and ecosystem services that are essential to life on Earth. However, aquatic urban ecosystems often become polluted by garbage and noise, and more. Their space decreases and their ecosystems are threatened, leading to deteriorating health conditions for humans, animals and plants. In this context, the EU-funded OneAquaHealth project will showcase the importance of these ecosystems for human mental and physical health while also providing a novel AI-based environmental surveillance system to monitor and protect these places.
","_id":"41V09123","iweto_id":"41V09123","end_date":"2026-12-31","gismo_id":"781a1edb-1c8a-415d-826e-117e1acc5c18","publication_count":1,"start_date":"2023-01-01","eu_id":"101086521"}],"author":[{"first_name":"Thi Kim Dung","orcid_id":"0000-0003-3300-1985","_id":"10217CAC-1740-11E3-846B-F97910BDE39D","biblio_id":"10217CAC-1740-11E3-846B-F97910BDE39D","name_last_first":"Pham, Thi Kim Dung","ugent_id":["000121111570","802003645923","976785402297"],"last_name":"Pham","affiliation":[{"ugent_id":"LA22","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA22"}]}],"name":"Thi Kim Dung Pham"}],"title":"An integrated environmental–epigenetic study of the mangrove crab Ucides occidentalis in the Guayas Estuary in Ecuador","biblio_id":"01KGJ3GNYEVD05K79CREJP2PFY","publisher":{"name":"Ghent University. Faculty of Bioscience Engineering","location":"Ghent, Belgium"},"isbn":["9789463579599"],"subject":["Biology and Life Sciences"],"abstract_full":[{"text":"Het begrijpen van hoe organismen omgaan met omgevingsstress in dynamische estuaria-systemen vraagt om een integratie van natuurlijke en menselijke invloeden. Traditionele milieurisicobeoordelingen bekijken deze factoren vaak apart, terwijl onderzoek steeds duidelijker maakt dat saliniteit (zoutgehalte) een sleutelrol speelt in zowel het gedrag van verontreinigingen als de biologische reacties daarop.\r\nDit doctoraat onderzocht hoe saliniteit het lot van verontreinigingen en moleculaire stressreacties beïnvloedt in tropische estuaria. De rode mangrovekrab Ucides occidentalis diende als modelspecies in het Guayas-estuarium (Ecuador). Twee vragen stonden centraal: hoe beïnvloedt saliniteit de opname van pesticiden en metalen (vooral arseen) en hoe hangen omgevingscondities samen met epigenetische en metabole processen zoals DNA-methylatie en aminozuurstofwisseling?\r\nEen geïntegreerde milieuscheikundige en moleculaire aanpak werd toegepast in twee contrasterende gebieden: Churute (lage saliniteit, landbouwinvloed) en Salado (hoge saliniteit, stedelijke invloed). Analyses van sedimenten en krabweefsels toonden aan dat landbouwgebieden vooral herbiciden en fungiciden bevatten, soms boven richtwaarden, maar met beperkte opname in krabben. In stedelijke zones vonden we daarentegen meer en diverse pesticiden in de krabben, ondanks lage sedimentconcentraties, wat een aanwijzing kan zijn van meerdere blootstellingsroutes.\r\nHoewel sedimenten in het lage-saliniteitgebied meer metalen bevatten, accumuleerden krabben uit zoutere gebieden meer arseen, cadmium en kwik. De biologisch beschikbare fracties bleken betere voorspellers van weefselconcentraties dan totale sedimentgehalten, wat mogelijk kan geassocieerd worden aan de saliniteit. Bovendien was saliniteit ook de sterkste voorspeller van DNA-methylatie, met tot tienmaal hogere niveaus in zoute gebieden — onafhankelijk van verontreiniging. Dit wijst op een directe invloed van saliniteit op epigenetische regulatie.\r\nDe gecombineerde analyse van arseen, aminozuren en DNA-methylatie suggereert een gedeelde biochemische route, waarbij arseendetoxificatie en DNA-methylatie concurreren om dezelfde methyldonor.\r\nDe studie toont aan dat totale sedimentconcentraties geen betrouwbare voorspellers zijn van ecologisch risico in estuaria met sterke zoutgradiënten. Natuurlijke factoren zoals saliniteit kunnen evenveel of meer invloed hebben op biologische processen dan verontreinigingen zelf. Saliniteit blijkt zo een sleutelfactor in zowel contaminantengedrag als moleculaire aanpassing — cruciaal voor het begrijpen van ecosysteemgezondheid en effect van verontreiniging in estuaria.","lang":"dut"}],"created_by":{"first_name":"Thi Kim Dung","_id":"10217CAC-1740-11E3-846B-F97910BDE39D","name_last_first":"Pham, Thi Kim Dung","biblio_id":"10217CAC-1740-11E3-846B-F97910BDE39D","orcid_id":"0000-0003-3300-1985","last_name":"Pham","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA22"}],"ugent_id":"LA22"}],"ugent_id":["000121111570","802003645923","976785402297"],"name":"Thi Kim Dung Pham"},"file":[{"url":"https://biblio.ugent.be/publication/01KGJ3GNYEVD05K79CREJP2PFY/file/01KF21QED8AEAGH47X7AQRXYPF.pdf","change":{"to":"open","on":"2029-01-30"},"kind":"fullText","thumbnail_url":"https://biblio.ugent.be/publication/01KGJ3GNYEVD05K79CREJP2PFY/file/01KF21QED8AEAGH47X7AQRXYPF/thumbnail.png","publication_version":"publishedVersion","access":"restricted","sha256":"696338d3d6ffa70ea74f6589cbe92a8065baab77529a6e4cf11337303ff348c5","name":"9656.pdf","content_type":"application/pdf","_id":"01KF21QED8AEAGH47X7AQRXYPF","size":"13235761"}],"page":{"count":"XXXVI, 313"}},{"article_type":"original","external":0,"pubmed_id":"42203494","year":"2026","issn":["1040-4651","1532-298X"],"author":[{"name":"Qian-Qian Li","last_name":"Li","affiliation":[{"ugent_id":"UGent","path":[{"ugent_id":"UGent"}],"name":"Ghent University"}],"ugent_id":["977664180467"],"biblio_id":"420b379d-b207-11ec-a5c1-c7e5bac3054c","name_last_first":"Li, Qian-Qian","_id":"420b379d-b207-11ec-a5c1-c7e5bac3054c","orcid_id":"0000-0002-4221-8134","first_name":"Qian-Qian"},{"first_name":"Huiying","biblio_id":"cd11a727-5a5c-11ee-a643-f3dc81f106a5","name_last_first":"Li, Huiying","_id":"cd11a727-5a5c-11ee-a643-f3dc81f106a5","last_name":"Li","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}],"ugent_id":"WE09"}],"ugent_id":["000231154737","802004463652"],"name":"Huiying Li"},{"first_name":"Jolien","orcid_id":"0009-0003-2763-1339","_id":"4A8BB4B6-BD4D-11E9-9789-FFA75607D3EF","name_last_first":"De Moor, Jolien","biblio_id":"4A8BB4B6-BD4D-11E9-9789-FFA75607D3EF","ugent_id":["000190513050","802004763140"],"affiliation":[{"ugent_id":"WE09","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}]}],"last_name":"De Moor","name":"Jolien De Moor"},{"first_name":"Irene","last_name":"Sbrocca","name_last_first":"Sbrocca, Irene","name":"Irene Sbrocca"},{"first_name":"Yanli","orcid_id":"0000-0002-0954-857X","biblio_id":"8c763487-1e28-11eb-a765-99eddc39dfbc","name_last_first":"Xiang, Yanli","_id":"8c763487-1e28-11eb-a765-99eddc39dfbc","ugent_id":["974500452113"],"affiliation":[{"path":[{"ugent_id":"UGent"}],"name":"Ghent University","ugent_id":"UGent"}],"last_name":"Xiang","name":"Yanli Xiang"},{"affiliation":[{"ugent_id":"WE09","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}]}],"last_name":"Yang","ugent_id":["000211711893","802003960767"],"name":"Shao-Li Yang","first_name":"Shao-Li","biblio_id":"2afcda76-8933-11ec-827b-805b35985514","name_last_first":"Yang, Shao-Li","_id":"2afcda76-8933-11ec-827b-805b35985514","orcid_id":"0000-0003-0989-5448"},{"first_name":"Zhi-Yi","last_name":"Jiang","name":"Zhi-Yi Jiang","name_last_first":"Jiang, Zhi-Yi"},{"name":"Lin He","name_last_first":"He, Lin","last_name":"He","first_name":"Lin"},{"name_last_first":"Wang, Jia-Yang","name":"Jia-Yang Wang","first_name":"Jia-Yang","last_name":"Wang"},{"orcid_id":"0000-0002-6253-4927","biblio_id":"5dcad9ae-c99a-11ec-a040-df20a9ed1dd9","name_last_first":"Herbst, Josephine","_id":"5dcad9ae-c99a-11ec-a040-df20a9ed1dd9","first_name":"Josephine","name":"Josephine Herbst","ugent_id":["973379969848"],"last_name":"Herbst","affiliation":[{"ugent_id":"UGent","name":"Ghent University","path":[{"ugent_id":"UGent"}]}]},{"first_name":"Brigitte","biblio_id":"F4D96AD2-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Van De Cotte, Brigitte","_id":"F4D96AD2-F0ED-11E1-A9DE-61C894A0A6B4","orcid_id":"0000-0001-7236-9243","last_name":"Van De Cotte","affiliation":[{"name":"Ghent University","path":[{"ugent_id":"UGent"}],"ugent_id":"UGent"}],"ugent_id":["971904778488"],"name":"Brigitte Van De Cotte"},{"orcid_id":"0000-0003-4607-8893","biblio_id":"2427C36A-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"De Smet, Ive","_id":"2427C36A-F0EE-11E1-A9DE-61C894A0A6B4","first_name":"Ive","name":"Ive De Smet","ugent_id":["801001606116"],"last_name":"De Smet","affiliation":[{"ugent_id":"WE09","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}]}]},{"name_last_first":"Cimini, Sara","name":"Sara Cimini","first_name":"Sara","last_name":"Cimini"},{"orcid_id":"0000-0003-1150-4426","_id":"F4C04C64-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"De Veylder, Lieven","biblio_id":"F4C04C64-F0ED-11E1-A9DE-61C894A0A6B4","first_name":"Lieven","name":"Lieven De Veylder","ugent_id":["801000929338"],"last_name":"De Veylder","affiliation":[{"ugent_id":"WE09","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}]}]}],"title":"Ancestral and divergent roles of the Marchantia polymorpha ATR kinase in maintaining genome integrity and clonal fitness","project":[{"abstract":"\nAluminum (Al) toxicity represents an important limitation to worldwide crop production, occurring in upwards of 50 % of the world’ arable land The most evident symptom and important consequence of Al toxicity is root growth inhibition Additionally, Al influences phosphorus (Pi) availability, eventually resulting in nutritional deficiency in shoots and leaves Recently, we have identified through a chemical genomics screen in Arabidopsis thaliana a compound (nominated C43) that confers Al resistance, being a potential Casein Kinase 2 (CK2) inhibitor Our preliminary data indicate that CK2 grants Al toxicity resistance through phosphorylation of the SOG1 transcription factor, being an essential regulator arresting cell cycle progression in response to DNA damage Strikingly, C43 also grants growth under low Pi conditions, suggesting that Pi-deficiency and Al-toxicity converge via the CK2-SOG1 pathway Within this project, we aim to test this hypothesis through a detailed structural-functional analysis in combination with physiological experiments In particular, the interactions between C43, CK2 and SOG1 will be studies at the biochemical, biophysical and structural level Additionally, the obtained structural data will be correlated with growth experiments under conditions of Al toxicity and Pi depletion\n\n
","title":"Functional-structural analysis of Casein Kinase 2 and SOG1 in response to Al-induced DNA damage and phosphate starvation","_id":"3G036020","iweto_id":"3G036020","end_date":"2023-12-31","publication_count":12,"gismo_id":"4896f6d6-225c-11ea-9b15-d7676230cb7f","start_date":"2020-01-01"},{"end_date":"2027-12-31","_id":"G0A6J24N","iweto_id":"G0A6J24N","abstract":"Due to their immobility, plants cannot escape unfavorable conditions. Probably because of this, they have evolved intrinsic molecular mechanisms that allow fine-tuning of cell division with developmental programs and environmental conditions. Research in Arabidopsis thaliana has implicated a role for the SIAMESE/SIAMESE-RELATED (SIM/SMR) gene family in these processes, encoding for plant-specific cell cycle inhibitors acting on cyclin-dependent kinase activity. However, currently any fundament knowledge on SIM/SMR genes in crop species is lacking, undoubtedly in part due to gene redundancy. Here, we aim to overcome this redundancy in maize by using BREEDIT technology that makes use of multiplex CRISPR/Cas9 technology in combination with classical breeding to combine traits. Using this technology, we will generate on basis of co-expression data a collection of 100 maize genotypes randomly differing in SIM/SMR knockout combinations. Subsequently, these lines will be phenotypically screened under mild drought and DNA damage-inducing conditions. Additionally, being a pivotal part for feed and human diet, kernels will be quantitatively and qualitatively characterized. Combined, the data obtained should not only represent a pioneering phenotypic characterization of the SIM/SMR gene family in a crop species but might as well address the question of whether SIM/SMR genes represent attractive targets for engineering of climate-resilient plants.
","title":"A systematic phenotypic analysis of SIM/SMR cyclin-dependent kinase inhibitors in maize","start_date":"2024-01-01","publication_count":2,"gismo_id":"8e8c76c4-abe3-11ee-93fb-0db84e20c636"}],"date_updated":"2026-06-02 10:30:05","biblio_id":"01KSSNMX5G9EA8K8B5G7ZZ85MV","subject":["Biology and Life Sciences"],"created_by":{"name":"Annick Bleys","ugent_id":["801001668457"],"last_name":"Bleys","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}],"ugent_id":"WE09"}],"orcid_id":"0000-0002-1977-4263","biblio_id":"F68A8C76-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Bleys, Annick","_id":"F68A8C76-F0ED-11E1-A9DE-61C894A0A6B4","first_name":"Annick"},"file":[{"thumbnail_url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KSSNT2TVYR87F3T2THDWEDWG/thumbnail.png","publication_version":"acceptedVersion","size":"2973373","_id":"01KSSNT2TVYR87F3T2THDWEDWG","sha256":"a3f40f8d8f3c0d1fc952a9421b788f7ef8a78a6b202cda14f34eab1d53a1503f","access":"private","kind":"fullText"},{"size":"4861090","_id":"01KSSP01AQ5K5XFZ0PHA0GPTW6","thumbnail_url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KSSP01AQ5K5XFZ0PHA0GPTW6/thumbnail.png","content_type":"application/pdf","kind":"dataset","name":"Supplementary Figures.pdf","access":"open","sha256":"cfec28022e9cc46c5b682dcf6bac26343989dedd52e427f9e4351182381fcda7","url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KSSP01AQ5K5XFZ0PHA0GPTW6.pdf"},{"name":"Supplemental Data Set S1.xlsx","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","kind":"dataset","access":"open","sha256":"094c905a201bbbdb80d9c7ad4beeb839676c9abae6107c67c2ff544dc8b3d438","url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KSSP0F8VQKY0Z9BND45C8AZZ.xlsx","_id":"01KSSP0F8VQKY0Z9BND45C8AZZ","size":"574680"},{"access":"open","sha256":"bc5a9bb33f320c0ed575a0469774ec5f1a433e658294ad659331dbf56a76a72f","name":"Supplemental Table S1.xlsx","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","kind":"dataset","url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KSSP0TE13AG83CN72WNC15C6.xlsx","_id":"01KSSP0TE13AG83CN72WNC15C6","size":"134132"},{"url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KSSP1VBKQP7F1QCJ00YM4JGD.xlsx","name":"Supplemental Table S2.xlsx","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","kind":"dataset","access":"open","sha256":"cf53e8c99d45269464a0ddd546d0c8aec294ce8984a9bd10bf75e2571aaa9e35","_id":"01KSSP1VBKQP7F1QCJ00YM4JGD","size":"16030342"},{"name":"Supplemental Table S3.xlsx","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","kind":"dataset","access":"open","sha256":"041912f2066d8409ff2c0b5a60a7282db47f9eda4d810d0cce1e63d82fd61ce5","url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KSSP24D3212P4ZG2QN8X627Y.xlsx","_id":"01KSSP24D3212P4ZG2QN8X627Y","size":"11479"},{"publication_version":"acceptedVersion","size":"3115014","_id":"01KT3Y1R4S1VMBWHTRDR4M2EJH","url":"https://biblio.ugent.be/publication/01KSSNMX5G9EA8K8B5G7ZZ85MV/file/01KT3Y1R4S1VMBWHTRDR4M2EJH.pdf","change":{"to":"open","on":"2026-11-27"},"content_type":"application/pdf","kind":"fullText","name":"accepted_manuscript.pdf","access":"restricted","sha256":"54e56f73f1687df3189a0f4e05dc77f449c3b3dd7dfd177c65d35e55e38a5843"}],"abstract_full":[{"text":"The eukaryotic ATAXIA-TELANGIECTASIA AND RAD3-RELATED (ATR) kinase is essential for ensuring genomic integrity under conditions that cause replication defects. It triggers a transient cell cycle arrest and DNA repair by activating the DNA damage response (DDR) pathway. While ATR kinases appear to be functionally conserved, species-specific phenotypes can be observed across the plant kingdom. To investigate the ancestral roles of the plant ATR, we identified its homolog in the model liverwort Marchantia polymorpha, which we named MpATR. Similar to other plant species, MpATR preserves meristematic cells during replication stress, whereas it mediates the response to double-strand breaks redundantly with ATAXIA-TELANGIECTASIA MUTATED (MpATM). However, unlike its counterpart in vascular plants, MpATR activity in liverwort is also essential for repressing the proliferation of differentiated cells. Furthermore, M. polymorpha does not rely on MpATR-controlled stem cell death to eliminate malignant cells. Moreover, even under control growth conditions, Mpatr mutants exhibit increasingly severe growth defects across successive vegetative clonal generations, which are aggravated in the Mpatm/atr double mutant, underscoring the critical role of MpATR in sustaining normal growth over successive generations. Overall, our study sheds light on the differential dependency on ATR in liverwort versus vascular plants, emphasizing its evolutionary adaptation across plant species.","lang":"eng"}],"language":["eng"],"affiliation":[{"ugent_id":"WE09","name":"Department of Plant Biotechnology and Bioinformatics","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}]},{"ugent_id":"VIB","name":"VIB","path":[{"ugent_id":"ResearchCenter"},{"ugent_id":"VIB"}]}],"publication_status":"inpress","handle":"http://hdl.handle.net/1854/LU-01KSSNMX5G9EA8K8B5G7ZZ85MV","article_number":"koag151","date_created":"2026-05-29 10:49:28","jcr":{},"cite":{"mla":"The global population growth and the westernization of cultures causes an increase in animal-based protein demand. Current agriculture will not be adequate to meet this demand in a sustainable manner. A more efficient protein production is needed utilizing less resources like fertilizers, water and energy. This can be achieved by a microbial protein production approach. Through the use of microorganisms, feed or food can be decoupled from land use, minimizing water use whilst increasing nutrient uptake. However, a feedstock still needs to be supplied. Nevertheless, due the versatility of microorganisms, a broad spectrum of feedstocks can be used, even industrial side streams can be exploited. One of these streams is cheese whey containing high value compounds such as lactose, minerals and vitamins. However, one vital component is missing to improve the protein production specifically nitrogen. This limiting factor can be provided by the agriculture side streams producing biogas and nitrogen rich digestate. To that end, we will study three possible protein production approaches valorizing both side streams. In a first part we will screen different microorganisms and their ability to grow in the salt concentrated whey environment. Secondly, the three protein production routes will be optimized and evaluated in regards of environmental impact and economic feasibility. Finally, the proposed route will be validated on lab-scale in regard to side stream valorization.
","end_date":"2024-10-31"},{"start_date":"2024-01-01","publication_count":8,"gismo_id":"08152184-70ec-11ef-9cdc-4fa7d5228e91","end_date":"2025-12-31","title":"Novel Bioprocesses for a Sustainable Society","abstract":"Our society is currently transitioning from a linear to a circular economic model, and biotechnology can play a key role in enabling this sustainable transformation. By providing a means of upcycling waste and by-products, biotechnology can offer innovative solutions for reducing environmental impact. However, this transition is not straightforward, given the inherent complexity and heterogeneity of residues and the challenge of economically competing with petrochemical production.
\nThis project aims to explore the use of microorganisms in novel bioprocesses for bioproduction from residues, contributing to a more sustainable society. We will investigate the eco-physiology of non-model microorganisms in both pure and mixed microbial cultures and their potential for bioconversions. Our approach will combine bottom-up and top-down bioprocess engineering techniques to optimize these processes.
","iweto_id":"bof/baf/4y/2024/01/700","_id":"bof/baf/4y/2024/01/700"},{"_id":"01P02324","iweto_id":"01P02324","abstract":"To meet the increasing demand for meat without further compromising the environment efforts are directed at alternatives of plant origin. However, plants cannot replace all meat properties. A promising alternative is microbial biomass, which has more protein and is more resource efficient compared to animal and plant proteins, but its CO2 footprint should be improved. The most successful commercial example has a considerable CO2 footprint mostly ascribed to the use of sugars as growth substrate and the often-required addition of ingredients with high footprint. The footprint of microbial foods can be substantially improved using CO2- and renewable electricity-generated substrates like methanol and the minimization of external ingredients during food formulation. To enable this, we can harness the properties of near-extremophilic methylotrophic microbes, for which food-related properties and the environmental footprint of their production and processing to food ingredients are hardly studied. In MIC1RO-FOOD we will develop processes for microbial biomass production from methanol, with appropriate techno-functional properties for meat alternatives, while minimizing the need for external resource-intensive ingredients. We will explore novel avenues in microbial food production by integrating microbiology, bioprocess engineering, food process engineering and environmental sustainability assessment to improve food properties towards attractive, sustainable meat alternatives.
","title":"MIC1RO-FOOD: Towards production of more sustainable meat alternatives from microbial biomass grown using renewable methanol","end_date":"2028-03-31","start_date":"2025-04-01","publication_count":6,"gismo_id":"68f64270-1e79-11ef-8443-dd06ab27f40e"}],"biblio_id":"01KM2FH9R9GJSQDJYY1MDQ6B7X","article_type":"original","external":0,"year":"2026","publication_status_sort":2,"classification":"A2","doi":["10.1016/j.biteb.2026.102696"],"type":"journalArticle","volume":"34","copyright_statement":"No license (in copyright)","date_created":"2026-03-19 07:21:37","jcr":{},"language":["eng"],"affiliation":[{"ugent_id":"LA25","name":"Department of Biotechnology","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA25"}]}],"esci_id":"001722519300001"},{"handle":"http://hdl.handle.net/1854/LU-01KAEEM1M9BX3DFN2TGX56KFZX","wos_type":"Article","_id":"01KAEEM1M9BX3DFN2TGX56KFZX","parent":{"short_title":"Equine Vet. J.","title":"EQUINE VETERINARY JOURNAL"},"cite":{"fwo":"