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Article ; Online: Involvement of superior colliculus in complex figure detection of mice.

Cazemier, J Leonie / Haak, Robin / Tran, T K Loan / Hsu, Ann T Y / Husic, Medina / Peri, Brandon D / Kirchberger, Lisa / Self, Matthew W / Roelfsema, Pieter / Heimel, J Alexander

eLife

2024 Volume 13

Abstract: Object detection is an essential function of the visual system. Although the visual cortex plays an important role in object detection, the superior colliculus can support detection when the visual cortex is ablated or silenced. Moreover, it has been ... ...

Abstract	Object detection is an essential function of the visual system. Although the visual cortex plays an important role in object detection, the superior colliculus can support detection when the visual cortex is ablated or silenced. Moreover, it has been shown that superficial layers of mouse SC (sSC) encode visual features of complex objects, and that this code is not inherited from the primary visual cortex. This suggests that mouse sSC may provide a significant contribution to complex object vision. Here, we use optogenetics to show that mouse sSC is involved in figure detection based on differences in figure contrast, orientation, and phase. Additionally, our neural recordings show that in mouse sSC, image elements that belong to a figure elicit stronger activity than those same elements when they are part of the background. The discriminability of this neural code is higher for correct trials than for incorrect trials. Our results provide new insight into the behavioral relevance of the visual processing that takes place in sSC.
MeSH term(s)	Animals ; Mice ; Superior Colliculi ; Optogenetics ; Visual Cortex ; Visual Perception
Language	English
Publishing date	2024-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.83708
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A parameter-free statistical test for neuronal responsiveness.

Montijn, Jorrit S / Seignette, Koen / Howlett, Marcus H / Cazemier, J Leonie / Kamermans, Maarten / Levelt, Christiaan N / Heimel, J Alexander

eLife

2021 Volume 10

Abstract: Neurophysiological studies depend on a reliable quantification of whether and when a neuron responds to stimulation. Simple methods to determine responsiveness require arbitrary parameter choices, such as binning size, while more advanced model-based ... ...

Abstract	Neurophysiological studies depend on a reliable quantification of whether and when a neuron responds to stimulation. Simple methods to determine responsiveness require arbitrary parameter choices, such as binning size, while more advanced model-based methods require fitting and hyperparameter tuning. These parameter choices can change the results, which invites bad statistical practice and reduces the replicability. New recording techniques that yield increasingly large numbers of cells would benefit from a test for cell-inclusion that requires no manual curation. Here, we present the parameter-free ZETA-test, which outperforms t-tests, ANOVAs, and renewal-process-based methods by including more cells at a similar false-positive rate. We show that our procedure works across brain regions and recording techniques, including calcium imaging and Neuropixels data. Furthermore, in illustration of the method, we show in mouse visual cortex that (1) visuomotor-mismatch and spatial location are encoded by different neuronal subpopulations and (2) optogenetic stimulation of VIP cells leads to early inhibition and subsequent disinhibition.
MeSH term(s)	Animals ; Male ; Mice ; Neural Inhibition/physiology ; Neurons/physiology ; Optogenetics ; Visual Cortex/physiology
Language	English
Publishing date	2021-09-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.71969
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Article: Connectomic Analysis of Brain Networks: Novel Techniques and Future Directions.

Cazemier, J Leonie / Clascá, Francisco / Tiesinga, Paul H E

Frontiers in neuroanatomy

2016 Volume 10, Page(s) 110

Abstract: Brain networks, localized or brain-wide, exist only at the cellular level, i.e., between specific pre- and post-synaptic neurons, which are connected through functionally diverse synapses located at specific points of their cell membranes. "Connectomics" ...

Abstract	Brain networks, localized or brain-wide, exist only at the cellular level, i.e., between specific pre- and post-synaptic neurons, which are connected through functionally diverse synapses located at specific points of their cell membranes. "Connectomics" is the emerging subfield of neuroanatomy explicitly aimed at elucidating the wiring of brain networks with cellular resolution and a quantified accuracy. Such data are indispensable for realistic modeling of brain circuitry and function. A connectomic analysis, therefore, needs to identify and measure the soma, dendrites, axonal path, and branching patterns together with the synapses and gap junctions of the neurons involved in any given brain circuit or network. However, because of the submicron caliber, 3D complexity, and high packing density of most such structures, as well as the fact that axons frequently extend over long distances to make synapses in remote brain regions, creating connectomic maps is technically challenging and requires multi-scale approaches, Such approaches involve the combination of the most sensitive cell labeling and analysis methods available, as well as the development of new ones able to resolve individual cells and synapses with increasing high-throughput. In this review, we provide an overview of recently introduced high-resolution methods, which researchers wanting to enter the field of connectomics may consider. It includes several molecular labeling tools, some of which specifically label synapses, and covers a number of novel imaging tools such as brain clearing protocols and microscopy approaches. Apart from describing the tools, we also provide an assessment of their qualities. The criteria we use assess the qualities that tools need in order to contribute to deciphering the key levels of circuit organization. We conclude with a brief future outlook for neuroanatomic research, computational methods, and network modeling, where we also point out several outstanding issues like structure-function relations and the complexity of neural models.
Language	English
Publishing date	2016-11-09
Publishing country	Switzerland
Document type	Review ; Journal Article
ZDB-ID	2452969-2
ISSN	1662-5129
ISSN	1662-5129
DOI	10.3389/fnana.2016.00110
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Article ; Online: A parameter-free statistical test for neuronal responsiveness

Jorrit S Montijn / Koen Seignette / Marcus H Howlett / J Leonie Cazemier / Maarten Kamermans / Christiaan N Levelt / J Alexander Heimel

eLife, Vol

2021 Volume 10

Abstract	Neurophysiological studies depend on a reliable quantification of whether and when a neuron responds to stimulation. Simple methods to determine responsiveness require arbitrary parameter choices, such as binning size, while more advanced model-based methods require fitting and hyperparameter tuning. These parameter choices can change the results, which invites bad statistical practice and reduces the replicability. New recording techniques that yield increasingly large numbers of cells would benefit from a test for cell-inclusion that requires no manual curation. Here, we present the parameter-free ZETA-test, which outperforms t-tests, ANOVAs, and renewal-process-based methods by including more cells at a similar false-positive rate. We show that our procedure works across brain regions and recording techniques, including calcium imaging and Neuropixels data. Furthermore, in illustration of the method, we show in mouse visual cortex that (1) visuomotor-mismatch and spatial location are encoded by different neuronal subpopulations and (2) optogenetic stimulation of VIP cells leads to early inhibition and subsequent disinhibition.
Keywords	neural data analysis ; statistics ; responsiveness ; response latency ; visual cortex ; VIP disinhibition ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of 2020-21 and 2021-22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands.

Caliendo, Valentina / Kleyheeg, Erik / Beerens, Nancy / Camphuysen, Kees C J / Cazemier, Rommert / Elbers, Armin R W / Fouchier, Ron A M / Kelder, Leon / Kuiken, Thijs / Leopold, Mardik / Slaterus, Roy / Spierenburg, Marcel A H / van der Jeugd, Henk / Verdaat, Hans / Rijks, Jolianne M

Emerging infectious diseases

2023 Volume 30, Issue 1, Page(s) 50–57

Abstract: The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020-September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during ... ...

Abstract	The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020-September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during those epidemics, we collected and recorded mortality data of wild birds in the Netherlands. HPAI virus infection was reported in 51 bird species. The species with the highest numbers of reported dead and infected birds varied per epidemic year; in 2020-21, they were within the Anatidae family, in particular barnacle geese (Branta leucopsis) and in 2021-22, they were within the sea bird group, particularly Sandwich terns (Thalasseus sandvicensis) and northern gannet (Morus bassanus). Because of the difficulty of anticipating and modeling the future trends of HPAI among wild birds, we recommend monitoring live and dead wild birds as a tool for surveillance of the changing dynamics of HPAI.
MeSH term(s)	Animals ; Influenza in Birds/epidemiology ; Netherlands/epidemiology ; Influenza A Virus, H5N1 Subtype ; Animals, Wild ; Birds ; Ducks ; Charadriiformes
Language	English
Publishing date	2023-12-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid3001.230970
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Article ; Online: Effect of 2020–21 and 2021–22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands

Valentina Caliendo / Erik Kleyheeg / Nancy Beerens / Kees C.J. Camphuysen / Rommert Cazemier / Armin R.W. Elbers / Ron A.M. Fouchier / Leon Kelder / Thijs Kuiken / Mardik Leopold / Roy Slaterus / Marcel A.H. Spierenburg / Henk van der Jeugd / Hans Verdaat / Jolianne M. Rijks

Emerging Infectious Diseases, Vol 30, Iss 1, Pp 50-

2024 Volume 57

Abstract: The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020–September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during ... ...

Abstract	The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020–September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during those epidemics, we collected and recorded mortality data of wild birds in the Netherlands. HPAI virus infection was reported in 51 bird species. The species with the highest numbers of reported dead and infected birds varied per epidemic year; in 2020–21, they were within the Anatidae family, in particular barnacle geese (Branta leucopsis) and in 2021–22, they were within the sea bird group, particularly Sandwich terns (Thalasseus sandvicensis) and northern gannet (Morus bassanus). Because of the difficulty of anticipating and modeling the future trends of HPAI among wild birds, we recommend monitoring live and dead wild birds as a tool for surveillance of the changing dynamics of HPAI.
Keywords	influenza ; avian influenza ; HPAI ; wild birds ; H5N1 ; barnacle goose ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Subject code	590
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of 2020–21 and 2021–22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands

Caliendo, Valentina / Kleyheeg, Erik / Beerens, Nancy / Camphuysen, Kees C.J. / Cazemier, Rommert / Elbers, Armin R.W. / Fouchier, Ron A.M. / Kelder, Leon / Kuiken, Thijs / Leopold, Mardik / Slaterus, Roy / Spierenburg, Marcel A.H. / van der Jeugd, Henk / Verdaat, Hans / Rijks, Jolianne

Emerging Infectious Diseases

2024 Volume 30, Issue 1

Abstract	The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020–September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during those epidemics, we collected and recorded mortality data of wild birds in the Netherlands. HPAI virus infection was reported in 51 bird species. The species with the highest numbers of reported dead and infected birds varied per epidemic year; in 2020–21, they were within the Anatidae family, in particular barnacle geese (Branta leucopsis) and in 2021–22, they were within the sea bird group, particularly Sandwich terns (Thalasseus sandvicensis) and northern gannet (Morus bassanus). Because of the difficulty of anticipating and modeling the future trends of HPAI among wild birds, we recommend monitoring live and dead wild birds as a tool for surveillance of the changing dynamics of HPAI.
Keywords	Life Science
Subject code	590
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	1380686-5
ISSN	1080-6040
ISSN	1080-6040
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Advies voor het rapporteren en opruimen van wilde vogelkarkassen in boerenland tijdens de hoog-pathogene vogelgriepuitbraak H5NX, 2020-2021

Werkgroep AImpact2021, 27 november 2020

2022

Keywords	Life Science
Language	Dutch
Publishing country	nl
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration.

Schaffer, Ashleigh E / Eggens, Veerle R C / Caglayan, Ahmet Okay / Reuter, Miriam S / Scott, Eric / Coufal, Nicole G / Silhavy, Jennifer L / Xue, Yuanchao / Kayserili, Hulya / Yasuno, Katsuhito / Rosti, Rasim Ozgur / Abdellateef, Mostafa / Caglar, Caner / Kasher, Paul R / Cazemier, J Leonie / Weterman, Marian A / Cantagrel, Vincent / Cai, Na / Zweier, Christiane /

Altunoglu, Umut / Satkin, N Bilge / Aktar, Fesih / Tuysuz, Beyhan / Yalcinkaya, Cengiz / Caksen, Huseyin / Bilguvar, Kaya / Fu, Xiang-Dong / Trotta, Christopher R / Gabriel, Stacey / Reis, André / Gunel, Murat / Baas, Frank / Gleeson, Joseph G

Cell

2014 Volume 157, Issue 3, Page(s) 651–663

Abstract: Neurodegenerative diseases can occur so early as to affect neurodevelopment. From a cohort of more than 2,000 consanguineous families with childhood neurological disease, we identified a founder mutation in four independent pedigrees in cleavage and ... ...

Abstract	Neurodegenerative diseases can occur so early as to affect neurodevelopment. From a cohort of more than 2,000 consanguineous families with childhood neurological disease, we identified a founder mutation in four independent pedigrees in cleavage and polyadenylation factor I subunit 1 (CLP1). CLP1 is a multifunctional kinase implicated in tRNA, mRNA, and siRNA maturation. Kinase activity of the CLP1 mutant protein was defective, and the tRNA endonuclease complex (TSEN) was destabilized, resulting in impaired pre-tRNA cleavage. Germline clp1 null zebrafish showed cerebellar neurodegeneration that was rescued by wild-type, but not mutant, human CLP1 expression. Patient-derived induced neurons displayed both depletion of mature tRNAs and accumulation of unspliced pre-tRNAs. Transfection of partially processed tRNA fragments into patient cells exacerbated an oxidative stress-induced reduction in cell survival. Our data link tRNA maturation to neuronal development and neurodegeneration through defective CLP1 function in humans.
MeSH term(s)	Animals ; Brain/metabolism ; Brain/pathology ; Cerebellum/growth & development ; Cerebellum/pathology ; Cleavage And Polyadenylation Specificity Factor/genetics ; Cleavage And Polyadenylation Specificity Factor/metabolism ; Female ; Humans ; Male ; Mice ; Models, Molecular ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/pathology ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Pedigree ; Phosphotransferases/genetics ; Phosphotransferases/metabolism ; RNA Splicing ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Saccharomyces cerevisiae/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Zebrafish ; Zebrafish Proteins/genetics ; Zebrafish Proteins/metabolism
Chemical Substances	Cleavage And Polyadenylation Specificity Factor ; Nuclear Proteins ; Transcription Factors ; Zebrafish Proteins ; RNA, Transfer (9014-25-9) ; CLP1 protein, human (EC 2.7.-) ; CLP1 protein, zebrafish (EC 2.7.-) ; Phosphotransferases (EC 2.7.-)
Language	English
Publishing date	2014-04-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2014.03.049
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Article: CLP1 Founder Mutation Links tRNA Splicing and Maturation to Cerebellar Development and Neurodegeneration

Schaffer, AshleighÂ E / VeerleÂ R.C. Eggens / AhmetÂ Okay Caglayan / MiriamÂ S. Reuter / Eric Scott / NicoleÂ G. Coufal / JenniferÂ L. Silhavy / Yuanchao Xue / Hulya Kayserili / Katsuhito Yasuno / RasimÂ Ozgur Rosti / Mostafa Abdellateef / Caner Caglar / PaulÂ R. Kasher / J.Â Leonie Cazemier / MarianÂ A. Weterman / Vincent Cantagrel / Na Cai / Christiane Zweier /

Umut Altunoglu / N.Â Bilge Satkin / Fesih Aktar / Beyhan Tuysuz / Cengiz Yalcinkaya / Huseyin Caksen / Kaya Bilguvar / Xiang-Dong Fu / Christopher R. Trotta / Stacey Gabriel / AndrÃ© Reis / Murat Gunel / Frank Baas / JosephÂ G. Gleeson

Cell. 2014 Apr. 24, v. 157

2014

Abstract	Neurodegenerative diseases can occur so early as to affect neurodevelopment. From a cohort of more than 2,000 consanguineous families with childhood neurological disease, we identified a founder mutation in four independent pedigrees in cleavage and polyadenylation factor I subunit 1 (CLP1). CLP1 is a multifunctional kinase implicated in tRNA, mRNA, and siRNA maturation. Kinase activity of the CLP1 mutant protein was defective, and the tRNA endonuclease complex (TSEN) was destabilized, resulting in impaired pre-tRNA cleavage. Germline clp1 null zebrafish showed cerebellar neurodegeneration that was rescued by wild-type, but not mutant, human CLP1 expression. Patient-derived induced neurons displayed both depletion of mature tRNAs and accumulation of unspliced pre-tRNAs. Transfection of partially processed tRNA fragments into patient cells exacerbated an oxidative stress-induced reduction in cell survival. Our data link tRNA maturation toÂ neuronal development and neurodegeneration through defective CLP1 function in humans.
Keywords	Danio rerio ; cell viability ; cerebellum ; childhood ; germ cells ; humans ; messenger RNA ; mutants ; mutation ; neurodegenerative diseases ; neurodevelopment ; neurons ; patients ; pedigree ; small interfering RNA ; transfection ; transfer RNA
Language	English
Dates of publication	2014-0424
Size	p. 651-663.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2014.03.049
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