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Book ; Online ; Thesis: Eine Überprüfung des Job Demands-Resources-Modells bei Nachwuchslehrenden an deutschen Universitäten im sequentiell qualitativ-quantitativen Mixed-Method-Design

Schulze, Katharina [Verfasser]

2023

Author's details	Katharina Schulze
Keywords	Psychologie ; Psychology
Subject code	sg150
Language	German
Publisher	Universitätsbibliothek der Johannes Gutenberg-Universität Mainz
Publishing place	Mainz
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article: A first-generation genome-wide map of correlated DNA methylation demonstrates highly coordinated and tissue-independent clustering across regulatory regions.

Jajoo, Aarti / Hirschi, Owen / Schulze, Katharina / Guan, Yongtao / Hanchard, Neil A

Research square

2023

Abstract: Genome-wide DNA methylation studies have typically focused on quantitative assessments of CpG methylation at individual loci. Although methylation states at nearby CpG sites are known to be highly correlated, suggestive of an underlying coordinated ... ...

Abstract	Genome-wide DNA methylation studies have typically focused on quantitative assessments of CpG methylation at individual loci. Although methylation states at nearby CpG sites are known to be highly correlated, suggestive of an underlying coordinated regulatory network, the extent and consistency of inter-CpG methylation correlation across the genome, including variation between individuals, disease states, and tissues, remains unknown. Here, we leverage image conversion of correlation matrices to identify correlated methylation units (CMUs) across the genome, describe their variation across tissues, and annotate their regulatory potential using 35 public Illumina BeadChip datasets spanning more than 12,000 individuals and 26 different tissues. We identified a median of 18,125 CMUs genome-wide, occurring on all chromosomes and spanning a median of ~1 kb. Notably, 50% of CMUs had evidence of long-range correlation with other proximal CMUs. Although the size and number of CMUs varied across datasets, we observed strong intra-tissue consistency among CMUs, with those in testis encompassing those seen in most other tissues. Approximately 20% of CMUs were highly conserved across normal tissues (i.e. tissue independent), with 73 loci demonstrating strong correlation with non-adjacent CMUs on the same chromosome. These loci were enriched for CTCF and transcription factor binding sites, always found within putative TADs, and associated with the B compartment of chromosome folding. Finally, we observed significantly different, but highly consistent, patterns of CMU correlation between diseased and non-diseased states. Our first-generation, genome-wide, DNA methylation map suggests a highly coordinated CMU regulatory network that is sensitive to disruptions in its architecture.
Language	English
Publishing date	2023-05-15
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-2852818/v1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: How will land degradation neutrality change future land system patterns? A scenario simulation study

Schulze, Katharina / Malek, Žiga / Verburg, Peter H.

Environmental science & policy. 2021 Oct., v. 124

2021

Abstract: Land degradation is a major global issue and achieving a land degradation-neutral world is one of the Sustainable Development Goals. However, striving for land degradation neutrality (LDN) is challenged by increasing claims on land resources and could ... ...

Abstract	Land degradation is a major global issue and achieving a land degradation-neutral world is one of the Sustainable Development Goals. However, striving for land degradation neutrality (LDN) is challenged by increasing claims on land resources and could result in major land use conflicts. The aim of this study is to demonstrate how LDN can be implemented in land system modelling and how achieving LDN alongside sufficient supplies of food, timber and shelter could affect future land system patterns, using the Republic of Turkey as a case study. We developed a LDN scenario with full implementation of the guidelines and a business-as-usual scenario without pursuing LDN, and compared the resulting differences in land system changes. Additionally, the influence of different elements of the LDN framework on the land use projections was tested. Our results show that although it is possible to achieve LDN in the context of increasing demands for resources and housing, it might require a considerable re-organization of the land systems. Intensification of annual cropland systems was the main driver of new land degradation, which was in the LDN scenario primarily counterbalanced by large areas of afforestation, while other land improvement options only played a minor role. To achieve a no-net-loss, about 20% of Turkey’s territory was afforested in our scenario, mainly claiming extensively used annual cropland (∼70%) and grassland (∼30%). All individual LDN principles had a substantial impact on the final land system patterns meaning that the final outcome is not the result of just one of the principles, it is affected by all. Our findings suggest that pursuing LDN under growing demands for land-based products could stimulate a land sparing approach which might have trade-offs with other sustainability dimensions. This highlights the need for local support and new solutions for rural areas, thereby avoiding poverty, migration and illegal use of restoration areas.
Keywords	Turkey (country) ; afforestation ; case studies ; cropland ; grasslands ; issues and policy ; land degradation ; land improvement ; land use ; poverty ; sustainable development
Language	English
Dates of publication	2021-10
Size	p. 254-266.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1454687-5
ISSN	1462-9011
ISSN	1462-9011
DOI	10.1016/j.envsci.2021.06.024
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Biases in arginine codon usage correlate with genetic disease risk.

Schulze, Katharina V / Hanchard, Neil A / Wangler, Michael F

Genetics in medicine : official journal of the American College of Medical Genetics

2020 Volume 22, Issue 8, Page(s) 1407–1412

Abstract: Purpose: The persistence of hypermutable CGN (CGG, CGA, CGC, CGU) arginine codons at high frequency suggests the possibility of negative selective pressure at these sites and that arginine codon usage could be a predictive indicator of human disease ... ...

Abstract	Purpose: The persistence of hypermutable CGN (CGG, CGA, CGC, CGU) arginine codons at high frequency suggests the possibility of negative selective pressure at these sites and that arginine codon usage could be a predictive indicator of human disease genes. Methods: We analyzed arginine codons (CGN, AGG, AGA) from all canonical Ensembl protein coding gene transcripts before comparing the frequency of CGN codons between genes with and without human disease associations and with gnomAD constraint metrics. Results: The frequency of CGN codons among a gene's total arginine codon count was higher in genes linked to syndromic autism spectrum disorder (ASD) compared with genes not associated with ASD. A comparison of genes annotated as dominant or recessive with control genes not matching either classification revealed a progressive increase in CGN codon frequency. Moreover, CGN frequency was positively correlated with a gene's probability of loss-of-function intolerance (pLI) score and negatively correlated with observed-over-expected ratios for both loss-of-function and missense variants. Conclusion: Our findings indicate that genes utilizing CGN arginine codons rather than AGG or AGA are more likely to underlie single-gene disorders, particularly for dominant phenotypes, and thus constitute candidate genes for the study of human genetic disease.
MeSH term(s)	Arginine/genetics ; Autism Spectrum Disorder/genetics ; Bias ; Codon Usage ; Escherichia coli/genetics ; Humans
Chemical Substances	Arginine (94ZLA3W45F)
Language	English
Publishing date	2020-05-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	1455352-1
ISSN	1530-0366 ; 1098-3600
ISSN (online)	1530-0366
ISSN	1098-3600
DOI	10.1038/s41436-020-0813-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Impact of Accounting for Future Wood Production in Global Vertebrate Biodiversity Assessments.

Schulze, Katharina / Malek, Žiga / Verburg, Peter H

Environmental management

2020 Volume 66, Issue 3, Page(s) 460–475

Abstract: Forests are among the most species rich habitats and the way they are managed influences their capacity to protect biodiversity. To fulfill increasing wood demands in the future, planted and non-planted wood production will need to expand. While ... ...

Abstract	Forests are among the most species rich habitats and the way they are managed influences their capacity to protect biodiversity. To fulfill increasing wood demands in the future, planted and non-planted wood production will need to expand. While biodiversity assessments usually focus on the impacts of deforestation, the effects of wood harvest are mostly not considered, especially not in a spatially explicit manner. We present here a global approach to refine the representation of forest management through allocating future wood production to planted and non-planted forests. Wood production, following wood consumption projections of three Shared Socioeconomic Pathways, was allocated using likelihood maps for planted and production forests. On a global scale, plantations for wood production were projected to increase by 45-65% and harvested area in non-planted forests by 1-17%. The biodiversity impacts of changes in wood production patterns were estimated by applying two commonly used indicators: (1) changes in species richness and (2) changes in habitat-suitable ranges of single species. The impact was analyzed using forest cover changes as reference. Our results show that, although forest cover changes have the largest impact on biodiversity, changes in wood production also have a significant effect. The magnitude of impacts caused by changes of wood production substantially differs by region and taxa. Given the importance of forest production changes in net negative emission pathways, more focus should be put on assessing the effects of future changes in wood production patterns as part of overall land use change impacts.
MeSH term(s)	Animals ; Biodiversity ; Conservation of Natural Resources ; Forests ; Vertebrates ; Wood
Language	English
Publishing date	2020-07-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1478932-2
ISSN	1432-1009 ; 0364-152X
ISSN (online)	1432-1009
ISSN	0364-152X
DOI	10.1007/s00267-020-01322-4
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Article: The Impact of Accounting for Future Wood Production in Global Vertebrate Biodiversity Assessments

Schulze, Katharina / Malek, Žiga / Verburg, Peter H

Environmental management. 2020 Sept., v. 66, no. 3

2020

Abstract	Forests are among the most species rich habitats and the way they are managed influences their capacity to protect biodiversity. To fulfill increasing wood demands in the future, planted and non-planted wood production will need to expand. While biodiversity assessments usually focus on the impacts of deforestation, the effects of wood harvest are mostly not considered, especially not in a spatially explicit manner. We present here a global approach to refine the representation of forest management through allocating future wood production to planted and non-planted forests. Wood production, following wood consumption projections of three Shared Socioeconomic Pathways, was allocated using likelihood maps for planted and production forests. On a global scale, plantations for wood production were projected to increase by 45–65% and harvested area in non-planted forests by 1–17%. The biodiversity impacts of changes in wood production patterns were estimated by applying two commonly used indicators: (1) changes in species richness and (2) changes in habitat-suitable ranges of single species. The impact was analyzed using forest cover changes as reference. Our results show that, although forest cover changes have the largest impact on biodiversity, changes in wood production also have a significant effect. The magnitude of impacts caused by changes of wood production substantially differs by region and taxa. Given the importance of forest production changes in net negative emission pathways, more focus should be put on assessing the effects of future changes in wood production patterns as part of overall land use change impacts.
Keywords	deforestation ; environmental management ; forests ; land use change ; species richness ; timber production ; vertebrates ; wood
Language	English
Dates of publication	2020-09
Size	p. 460-475.
Publishing place	Springer US
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1478932-2
ISSN	1432-1009 ; 0364-152X
ISSN (online)	1432-1009
ISSN	0364-152X
DOI	10.1007/s00267-020-01322-4
Database	NAL-Catalogue (AGRICOLA)

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Article: Towards better mapping of forest management patterns: A global allocation approach

Schulze, Katharina / Žiga Malek / Peter H. Verburg

Forest ecology and management. 2019 Jan. 15, v. 432

2019

Abstract: Forests provide numerous ecosystem services, such as timber yields, biodiversity protection and climate change mitigation. The type of management has an effect on the provision of these services. Often the demands for these services can lead to conflict – ...

Abstract	Forests provide numerous ecosystem services, such as timber yields, biodiversity protection and climate change mitigation. The type of management has an effect on the provision of these services. Often the demands for these services can lead to conflict – wood harvest can negatively impact biodiversity and climate change mitigation capacity. Although forest management differences are important, spatially explicit data is lacking, in particular on a global scale. We present here a first systematic approach which integrates existing data to map forest management globally through downscaling national and subnational forest data. In our forest management classification, we distinguished between two levels of forest management, with three categories each. Level 1 comprised primary, naturally regrown and planted forests. Level 2 distinguished between different forest uses. We gathered documented locations, where these forest categories were observed, from the literature and a database on ecological diversity. We then performed multinomial logit regression and estimated the effect of 21 socio-economic and bio-physical predictor variables on the occurrence of a forest category. Model results on significance and effect direction of predictor variables were in line with findings of previous studies. Soil and environmental properties, forest conditions and accessibility are important determinants of the occurrence of forest management types. Based on the model results, likelihood maps were calculated and used to spatially allocate national extents of level 1 and level 2 forest categories. When compared to previous studies, our maps showed higher agreement than random samples. Deviations between observed and predicted plantation locations were mostly below 10 km. Our map provides an estimation of global forest management patterns, enhancing previous methodologies and making the best use of data available. Next to having multiple applications, for example within global conservation planning or climate change mitigation analyses, it visualizes the currently available data on forest management on a global level.
Keywords	biodiversity ; climate change ; databases ; ecosystem services ; forest management ; forests ; models ; planning ; socioeconomics ; soil ; wood
Language	English
Dates of publication	2019-0115
Size	p. 776-785.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	751138-3
ISSN	0378-1127
ISSN	0378-1127
DOI	10.1016/j.foreco.2018.10.001
Database	NAL-Catalogue (AGRICOLA)

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Article: Genetic Variants in Carbohydrate Digestive Enzyme and Transport Genes Associated with Risk of Irritable Bowel Syndrome.

Hong, Hyejeong / Schulze, Katharina V / Copeland, Ian E / Atyam, Manasa / Kamp, Kendra / Hanchard, Neil A / Belmont, John / Ringel-Kulka, Tamar / Heitkemper, Margaret / Shulman, Robert J

medRxiv : the preprint server for health sciences

2023

Abstract: Irritable Bowel Syndrome (IBS) is characterized by abdominal pain and alterations in bowel pattern, such as constipation (IBS-C), diarrhea (IBS-D), or mixed (IBS-M). Since malabsorption of ingested carbohydrates (CHO) can cause abdominal symptoms that ... ...

Abstract	Irritable Bowel Syndrome (IBS) is characterized by abdominal pain and alterations in bowel pattern, such as constipation (IBS-C), diarrhea (IBS-D), or mixed (IBS-M). Since malabsorption of ingested carbohydrates (CHO) can cause abdominal symptoms that closely mimic those of IBS, identifying genetic mutations in CHO digestive enzymes associated with IBS symptoms is critical to ascertain IBS pathophysiology. Through candidate gene association studies, we identify several common variants in
Language	English
Publishing date	2023-09-22
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.20.23295800
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software

Koch, Timo / Gläser, Dennis / Seeland, Anett / Roy, Sarbani / Schulze, Katharina / Weishaupt, Kilian / Boehringer, David / Hermann, Sibylle / Flemisch, Bernd

2023

Abstract: Research software is an integral part of most research today and it is widely accepted that research software artifacts should be accessible and reproducible. However, the sustainable archival of research software artifacts is an ongoing effort. We ... ...

Abstract	Research software is an integral part of most research today and it is widely accepted that research software artifacts should be accessible and reproducible. However, the sustainable archival of research software artifacts is an ongoing effort. We identify research software artifacts as snapshots of the current state of research and an integral part of a sustainable cycle of software development, research, and publication. We develop requirements and recommendations to improve the archival, access, and reuse of research software artifacts based on installable, configurable, extensible research software, and sustainable public open-access infrastructure. The described goal is to enable the reuse and exploration of research software beyond published research results, in parallel with reproducibility efforts, and in line with the FAIR principles for data and software. Research software artifacts can be reused in varying scenarios. To this end, we design a multi-modal representation concept supporting multiple reuse scenarios. We identify types of research software artifacts that can be viewed as different modes of the same software-based research result, for example, installation-free configurable browser-based apps to containerized environments, descriptions in journal publications and software documentation, or source code with installation instructions. We discuss how the sustainability and reuse of research software are enhanced or enabled by a suitable archive infrastructure. Finally, at the example of a pilot project at the University of Stuttgart, Germany -- a collaborative effort between research software developers and infrastructure providers -- we outline practical challenges and experiences
Keywords	Computer Science - Software Engineering ; D.2.13 ; H.0 ; D.2.1
Subject code	020
Publishing date	2023-01-26
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

Fortin, Connor H / Schulze, Katharina V / Babbitt, Gregory A

Source code for biology and medicine

2015 Volume 10, Page(s) 10

Abstract: Background: It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, ... ...

Abstract	Background: It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. Software and implementation: We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. Results: To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software for molecular evolutionary genetics analysis to visually compare the human Forkhead box/FOX protein evolution to its binding site evolution. We also compared the DNA binding signatures of human TP53 tumor suppressor determined by two different laboratory methods (SELEX and ChIP-seq). Further analysis of the entire yeast genome, center aligned at the start codon, also revealed a distinct sequence-independent 3 bp periodic pattern in information content, present only in coding region, and perhaps indicative of the non-random organization of the genetic code. Conclusion: TRX-LOGOS is useful in any situation in which important information content in DNA can be better visualized at the positions of phosphate linkages (i.e. dinucleotides) where the dynamic properties of the DNA backbone functions to facilitate DNA-protein interaction.
Language	English
Publishing date	2015-09-25
Publishing country	England
Document type	Journal Article
ISSN	1751-0473
ISSN	1751-0473
DOI	10.1186/s13029-015-0040-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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