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Article ; Online: Dendritic Integration Dysfunction in Neurodevelopmental Disorders.

Nelson, Andrew D / Bender, Kevin J

2021 Volume 43, Issue 3-4, Page(s) 201–221

Abstract: Neurodevelopmental disorders (NDDs) that affect cognition, social interaction, and learning, including autism spectrum disorder (ASD) and intellectual disability (ID), have a strong genetic component. Our current understanding of risk genes highlights ... ...

Abstract	Neurodevelopmental disorders (NDDs) that affect cognition, social interaction, and learning, including autism spectrum disorder (ASD) and intellectual disability (ID), have a strong genetic component. Our current understanding of risk genes highlights two main groups of dysfunction: those in genes that act as chromatin modifiers and those in genes that encode for proteins localized at or near synapses. Understanding how dysfunction in these genes contributes to phenotypes observed in ASD and ID remains a major question in neuroscience. In this review, we highlight emerging evidence suggesting that dysfunction in dendrites - regions of neurons that receive synaptic input - may be key to understanding features of neuronal processing affected in these disorders. Dendritic integration plays a fundamental role in sensory processing, cognition, and conscious perception, processes hypothesized to be impaired in NDDs. Many high-confidence ASD genes function within dendrites where they control synaptic integration and dendritic excitability. Further, increasing evidence demonstrates that several ASD/ID genes, including chromatin modifiers and transcription factors, regulate the expression or scaffolding of dendritic ion channels, receptors, and synaptic proteins. Therefore, we discuss how dysfunction of subsets of NDD-associated genes in dendrites leads to defects in dendritic integration and excitability and may be one core phenotype in ASD and ID.
MeSH term(s)	Autism Spectrum Disorder/genetics ; Humans ; Intellectual Disability/genetics ; Neurodevelopmental Disorders/genetics ; Neurons ; Synapses
Language	English
Publishing date	2021-06-17
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	556887-0
ISSN	1421-9859 ; 0378-5866
ISSN (online)	1421-9859
ISSN	0378-5866
DOI	10.1159/000516657
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Article ; Online: High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms.

Nelson Dittrich, Anna C / Nelson, Andrew D L

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2512, Page(s) 45–60

Abstract: Comparative genomic and transcriptomic analyses can help prioritize and facilitate the functional analysis of long noncoding RNAs (lncRNAs). Evolinc-II is a bioinformatic pipeline that automates comparative analyses, searching for sequence and structural ...

Abstract	Comparative genomic and transcriptomic analyses can help prioritize and facilitate the functional analysis of long noncoding RNAs (lncRNAs). Evolinc-II is a bioinformatic pipeline that automates comparative analyses, searching for sequence and structural conservation for thousands of lncRNAs at once. In addition, Evolinc-II takes a phylogenetic approach to infer key evolutionary events that may have occurred during the emergence of each query lncRNA. Here, we describe how to use command line or GUI (CyVerse's Discovery Environment) versions of Evolinc-II to identify lncRNA homologs and prioritize them for functional analysis.
MeSH term(s)	Computational Biology ; Evolution, Molecular ; Genomics ; Phylogeny ; RNA, Long Noncoding/genetics
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2429-6_3
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Article: Effects of chronic lithium treatment on neuronal excitability and GABAergic transmission in an

Caballero-Florán, René N / Nelson, Andrew D / Min, Lia / Jenkins, Paul M

bioRxiv : the preprint server for biology

2023

Abstract: Bipolar disorder (BD) is a common psychiatric disease that can lead to psychosocial disability, decreased quality of life, and high risk for suicide. Genome-wide association studies have shown that ... ...

Abstract	Bipolar disorder (BD) is a common psychiatric disease that can lead to psychosocial disability, decreased quality of life, and high risk for suicide. Genome-wide association studies have shown that the
Language	English
Publishing date	2023-10-30
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.26.564203
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Article ; Online: Interdecadal variation in sediment yield from a forested mountain basin: The role of hydroclimatic variability, anthropogenic disturbances, and geomorphic connectivity.

Cienciala, Piotr / Melendez Bernardo, Mishel / Nelson, Andrew D / Haas, Andrew D

The Science of the total environment

2022 Volume 826, Page(s) 153876

Abstract: Variation in sediment yield may reflect a signal of disturbances in the upstream landscape, modified by sediment routing. This study, conducted in a forested drainage basin in the inland Pacific Northwest, USA, sought to generate a better insight into ... ...

Abstract	Variation in sediment yield may reflect a signal of disturbances in the upstream landscape, modified by sediment routing. This study, conducted in a forested drainage basin in the inland Pacific Northwest, USA, sought to generate a better insight into the interdecadal variability of sediment yield in mountain landscapes in response to environmental change during the last century. To this end, we examined: (1) sediment yield fluctuations; and (2) their association with streamflow and land use changes; as well as (3) streamflow links to climate variability modes; and (4) the influence of sediment delivery from hillslope sources to streams (lateral connectivity) and its downstream routing through the stream network (longitudinal connectivity) on land use signal at the basin's outlet. Sediment yield between 1910 and 2017, estimated based on reconstructed fluvial delta growth, displayed an order of magnitude variability, which indicates a substantial geomorphic sensitivity. The interpretation of temporal patterns and an exploratory statistical analysis pointed to land use-related sediment supply changes as the primary driver of these fluctuations, dominating system behavior before changes in environmental regulations and practices in the mid-1970s. Hydroclimatically controlled streamflow variability appeared to be more prominent in the subsequent period. Our connectivity analysis suggested that a considerable portion of coarse sediment mobilized by harvest and road construction may still reside within the channel network. In light of previous research in this landscape system, we speculate that, despite limited anthropogenic pressures in the recent decades, its characteristics and behavior continue to be conditioned by land use legacies. Overall, this study contributes to the growing understanding of profound anthropogenic transformation of the earth surface. Specifically, it demonstrates that historical resource extraction may have left a lasting imprint even in relatively remote mountain landscapes. Given the ongoing rapid environmental change, such understanding is crucial for watershed management, conservation, and restoration.
MeSH term(s)	Anthropogenic Effects ; Environmental Monitoring ; Forests ; Geologic Sediments/analysis ; Northwestern United States
Language	English
Publishing date	2022-02-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.153876
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Article ; Online: Composition and function of stress granules and P-bodies in plants.

Kearly, Alyssa / Nelson, Andrew D L / Skirycz, Aleksandra / Chodasiewicz, Monika

Seminars in cell & developmental biology

2022 Volume 156, Page(s) 167–175

Abstract: Stress Granules (SGs) and Processing-bodies (P-bodies) are biomolecular condensates formed in the cell with the highly conserved purpose of maintaining balance between storage, translation, and degradation of mRNA. This balance is particularly important ... ...

Abstract	Stress Granules (SGs) and Processing-bodies (P-bodies) are biomolecular condensates formed in the cell with the highly conserved purpose of maintaining balance between storage, translation, and degradation of mRNA. This balance is particularly important when cells are exposed to different environmental conditions and adjustments have to be made in order for plants to respond to and tolerate stressful conditions. While P-bodies are constitutively present in the cell, SG formation is a stress-induced event. Typically thought of as protein-RNA aggregates, SGs and P-bodies are formed by a process called liquid-liquid phase separation (LLPS), and both their function and composition are very dynamic. Both foci are known to contain proteins involved in translation, protein folding, and ATPase activity, alluding to their roles in regulating mRNA and protein expression levels. From an RNA perspective, SGs and P-bodies primarily consist of mRNAs, though long non-coding RNAs (lncRNAs) have also been observed, and more focus is now being placed on the specific RNAs associated with these aggregates. Recently, metabolites such as nucleotides and amino acids have been reported in purified plant SGs with implications for the energetic dynamics of these condensates. Thus, even though the field of plant SGs and P-bodies is relatively nascent, significant progress has been made in understanding their composition and biological role in stress responses. In this review, we discuss the most recent discoveries centered around SG and P-body function and composition in plants.
MeSH term(s)	Processing Bodies ; Stress Granules ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Cytoplasmic Granules ; Stress, Physiological
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2022-12-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2022.11.008
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Article ; Online: Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.

Palos, Kyle / Yu, Li'ang / Railey, Caylyn E / Nelson Dittrich, Anna C / Nelson, Andrew D L

The Plant cell

2023 Volume 35, Issue 6, Page(s) 1762–1786

Abstract: Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to ... ...

Abstract	Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
MeSH term(s)	RNA, Long Noncoding/genetics ; RNA, Plant/genetics ; Transcriptome ; Plants/genetics
Chemical Substances	RNA, Long Noncoding ; RNA, Plant
Language	English
Publishing date	2023-02-06
Publishing country	England
Document type	Review ; Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1093/plcell/koad027
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Article ; Online: Multiscaling behavior of braided channel networks: An alternative formulation of Taylor's law variate transformations.

Rizzello, Stefano / Scaraggi, Michele / Nelson, Andrew D / Primavera, Leonardo / Napoli, Gaetano / Stecca, Guglielmo / Vitolo, Raffaele / De Bartolo, Samuele

Physical review. E

2024 Volume 109, Issue 3-1, Page(s) 34306

Abstract: Braided channel networks exhibit a complex interplay between spatial and temporal dynamics. Their behavior is characterized by both simple and multiscaling patterns, and the mechanisms underlying the stochastic processes associated with this dynamics ... ...

Abstract	Braided channel networks exhibit a complex interplay between spatial and temporal dynamics. Their behavior is characterized by both simple and multiscaling patterns, and the mechanisms underlying the stochastic processes associated with this dynamics remain incompletely understood. Leveraging Taylor's pioneering work [Nature (London) 189, 732 (1961)NATUAS0028-083610.1038/189732a0], which unveiled scaling relations in a plethora of natural phenomena through what is now known as the Taylor power law (TPL), we propose a physical interpretation of braided channel systems. This interpretation utilizes a specific class of transformation functions applied to the mean of fluvial geomorphic variables measured along cross sections, namely, the number of wet channels, the average width of wet channels, and the entropic braiding index. By analyzing remotely sensed data of the Brahmaputra-Jamuna River in Bangladesh we obtain valuable insight into the spatiotemporal scaling of these geomorphological variables and gather a deeper understanding of the complexity of braided channel systems. Finally, through a direct analysis employing the TPL in conjunction with a fixed-mass multifractal algorithm, we prove that braided channel networks exhibit a multiscaling behavior.
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.109.034306
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Article ; Online: Development of a mobile, high-throughput, and low-cost image-based plant growth phenotyping system.

Yu, Li'ang / Sussman, Hayley / Khmelnitsky, Olga / Rahmati Ishka, Maryam / Srinivasan, Aparna / Nelson, Andrew D L / Julkowska, Magdalena M

Plant physiology

2024

Abstract: Nondestructive plant phenotyping forms a key technique for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-throughput phenotyping facilities can further our understanding of plant ... ...

Abstract	Nondestructive plant phenotyping forms a key technique for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-throughput phenotyping facilities can further our understanding of plant development and stress responses, their high costs greatly hinder scientific progress. To democratize high-throughput plant phenotyping, we developed sets of low-cost image- and weight-based devices to monitor plant shoot growth and evapotranspiration. We paired these devices to a suite of computational pipelines for integrated and straightforward data analysis. The developed tools were validated for their suitability for large genetic screens by evaluating a cowpea (Vigna unguiculata) diversity panel for responses to drought stress. The observed natural variation was used as an input for a genome-wide association study, from which we identified nine genetic loci that might contribute to cowpea drought resilience during early vegetative development. The homologs of the candidate genes were identified in Arabidopsis (Arabidopsis thaliana) and subsequently evaluated for their involvement in drought stress by using available T-DNA insertion mutant lines. These results demonstrate the varied applicability of this low-cost phenotyping system. In the future, we foresee these setups facilitating the identification of genetic components of growth, plant architecture, and stress tolerance across a wide variety of plant species.
Language	English
Publishing date	2024-05-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiae237
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Article ; Online: Impaired cerebellar plasticity hypersensitizes sensory reflexes in SCN2A-associated ASD.

Wang, Chenyu / Derderian, Kimberly D / Hamada, Elizabeth / Zhou, Xujia / Nelson, Andrew D / Kyoung, Henry / Ahituv, Nadav / Bouvier, Guy / Bender, Kevin J

Neuron

2024 Volume 112, Issue 9, Page(s) 1444–1455.e5

Abstract: Children diagnosed with autism spectrum disorder (ASD) commonly present with sensory hypersensitivity or abnormally strong reactions to sensory stimuli. Such hypersensitivity can be overwhelming, causing high levels of distress that contribute markedly ... ...

Abstract	Children diagnosed with autism spectrum disorder (ASD) commonly present with sensory hypersensitivity or abnormally strong reactions to sensory stimuli. Such hypersensitivity can be overwhelming, causing high levels of distress that contribute markedly to the negative aspects of the disorder. Here, we identify a mechanism that underlies hypersensitivity in a sensorimotor reflex found to be altered in humans and in mice with loss of function in the ASD risk-factor gene SCN2A. The cerebellum-dependent vestibulo-ocular reflex (VOR), which helps maintain one's gaze during movement, was hypersensitized due to deficits in cerebellar synaptic plasticity. Heterozygous loss of SCN2A-encoded Na
MeSH term(s)	Animals ; NAV1.2 Voltage-Gated Sodium Channel/genetics ; NAV1.2 Voltage-Gated Sodium Channel/metabolism ; Mice ; Neuronal Plasticity/physiology ; Cerebellum/metabolism ; Autism Spectrum Disorder/genetics ; Autism Spectrum Disorder/physiopathology ; Humans ; Reflex, Vestibulo-Ocular/physiology ; Male ; Purkinje Cells/metabolism ; Mice, Inbred C57BL
Chemical Substances	NAV1.2 Voltage-Gated Sodium Channel ; Scn2a protein, mouse ; SCN2A protein, human
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	808167-0
ISSN	1097-4199 ; 0896-6273
ISSN (online)	1097-4199
ISSN	0896-6273
DOI	10.1016/j.neuron.2024.01.029
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Zs.A 2496: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Interdecadal variation in sediment yield from a forested mountain basin: The role of hydroclimatic variability, anthropogenic disturbances, and geomorphic connectivity

Cienciala, Piotr / Melendez Bernardo, Mishel / Nelson, Andrew D. / Haas, Andrew D.

Science of the total environment. 2022 June 20, v. 826

2022

Abstract	Variation in sediment yield may reflect a signal of disturbances in the upstream landscape, modified by sediment routing. This study, conducted in a forested drainage basin in the inland Pacific Northwest, USA, sought to generate a better insight into the interdecadal variability of sediment yield in mountain landscapes in response to environmental change during the last century. To this end, we examined: (1) sediment yield fluctuations; and (2) their association with streamflow and land use changes; as well as (3) streamflow links to climate variability modes; and (4) the influence of sediment delivery from hillslope sources to streams (lateral connectivity) and its downstream routing through the stream network (longitudinal connectivity) on land use signal at the basin's outlet. Sediment yield between 1910 and 2017, estimated based on reconstructed fluvial delta growth, displayed an order of magnitude variability, which indicates a substantial geomorphic sensitivity. The interpretation of temporal patterns and an exploratory statistical analysis pointed to land use-related sediment supply changes as the primary driver of these fluctuations, dominating system behavior before changes in environmental regulations and practices in the mid-1970s. Hydroclimatically controlled streamflow variability appeared to be more prominent in the subsequent period. Our connectivity analysis suggested that a considerable portion of coarse sediment mobilized by harvest and road construction may still reside within the channel network. In light of previous research in this landscape system, we speculate that, despite limited anthropogenic pressures in the recent decades, its characteristics and behavior continue to be conditioned by land use legacies. Overall, this study contributes to the growing understanding of profound anthropogenic transformation of the earth surface. Specifically, it demonstrates that historical resource extraction may have left a lasting imprint even in relatively remote mountain landscapes. Given the ongoing rapid environmental change, such understanding is crucial for watershed management, conservation, and restoration.
Keywords	basins ; climate ; environment ; landscapes ; road construction ; sediment yield ; sediments ; statistical analysis ; stream flow ; streams ; topographic slope ; watershed management ; watersheds
Language	English
Dates of publication	2022-0620
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.153876
Database	NAL-Catalogue (AGRICOLA)

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