29 Works

NGS Data from: Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage

Stephan Riesenberg, Nelly Helmbrecht, Philipp Kanis, Tomislav Maricic & Svante Pääbo
We engineered gRNAs with highly stable hairpins in their constant parts and further enhanced their stability by chemical modifications. The ‘Genome-editing Optimized Locked Design’ (GOLD)-gRNA increases genome editing efficiency up to around 1000-fold (from 0.08% to 80.5%) with a mean increase across different other targets of 7.4-fold. The related NGS data is deposited here.

Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA

Elena Zavala, Ayinuer Aximu-Petri, Julia Richter, Birgit Nickel, Benjamin Vernot & Matthias Meyer
The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains (Mathieson et al., 2015; Narasimhan et al., 2019) or sediments (Vernot et al., 2021; Wang et al., 2021; Zavala et al., 2021) in single studies. Yet demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents,...

Supplementary material from \"Association patterns of female gorillas\"

Christopher Young & Martha M. Robbins
Social interactions ultimately impact health and fitness in gregarious mammals. However, research focusing on the strength of affiliative interactions has primarily been conducted on female philopatric species. Gorillas provide an interesting counterpoint to previous research as females emigrate multiple times throughout their lives. We compare female–female association strength, duration and consistency in wild mountain (Gorilla beringei beringei) and western gorillas (Gorilla gorilla gorilla). Additionally, we examine if the alpha male influences female association strength and...

Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Abstract Increasing evidence suggests synaptic dysfunction is a central and possibly triggering factor in Amyotrophic Lateral Sclerosis (ALS). Despite this, we still know very little about the molecular profile of an ALS synapse. To address this gap, we designed a synaptic proteomics experiment to perform an unbiased assessment of the synaptic proteome in the ALS brain. We isolated synaptoneurosomes from fresh-frozen post-mortem human cortex (11 controls and 18 ALS) and stratified the ALS group based...

Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease

Alexandra Pokhilko, Gaia Brezzo, Lahiru Handunnetthi, Raphael Heilig, Rachel Lennon, Colin Smith, Stuart M Allan, Alessandra Granata, Sanjay Sinha, Tao Wang, Hugh S Markus, Alexandra Naba, Roman Fischer, Tom Van Agtmael, Karen Horsburgh & M Zameel Cader
The extracellular matrix (ECM) is a key interface between the cerebrovasculature and adjacent brain tissues. Deregulation of the ECM contributes to a broad range of neurological disorders. However, despite this importance, our understanding of the ECM composition remains very limited mainly due to difficulties in its isolation. To address this, we developed an approach to extract the cerebrovascular ECM from mouse and human post-mortem normal brain tissues. We then used mass spectrometry with off-line high-pH...

Gorilla data code from Association patterns of female gorillas

Christopher Young & Martha M. Robbins
R notebook with code required for the analysis

Supplementary material from \"Association patterns of female gorillas\"

Christopher Young & Martha M. Robbins
Social interactions ultimately impact health and fitness in gregarious mammals. However, research focusing on the strength of affiliative interactions has primarily been conducted on female philopatric species. Gorillas provide an interesting counterpoint to previous research as females emigrate multiple times throughout their lives. We compare female–female association strength, duration and consistency in wild mountain (Gorilla beringei beringei) and western gorillas (Gorilla gorilla gorilla). Additionally, we examine if the alpha male influences female association strength and...

Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease

Alexandra Pokhilko, Gaia Brezzo, Lahiru Handunnetthi, Raphael Heilig, Rachel Lennon, Colin Smith, Stuart M Allan, Alessandra Granata, Sanjay Sinha, Tao Wang, Hugh S Markus, Alexandra Naba, Roman Fischer, Tom Van Agtmael, Karen Horsburgh & M Zameel Cader
The extracellular matrix (ECM) is a key interface between the cerebrovasculature and adjacent brain tissues. Deregulation of the ECM contributes to a broad range of neurological disorders. However, despite this importance, our understanding of the ECM composition remains very limited mainly due to difficulties in its isolation. To address this, we developed an approach to extract the cerebrovascular ECM from mouse and human post-mortem normal brain tissues. We then used mass spectrometry with off-line high-pH...

Additional file 1 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 1. Complete analysis ready dataset containing all protein identifications associated with the manuscript.

Additional file 4 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 4. Supplementary Table 2, primary antibody information.

Supplement 1 from Association patterns of female gorillas

Christopher Young & Martha M. Robbins
Results tables of additional analysis

Gorilla data code from Association patterns of female gorillas

Christopher Young & Martha M. Robbins
R notebook with code required for the analysis

Supplement 1 from Association patterns of female gorillas

Christopher Young & Martha M. Robbins
Results tables of additional analysis

Gorilla data data from Association patterns of female gorillas

Christopher Young & Martha M. Robbins
Excel file containing data for the analysis

Gorilla data data from Association patterns of female gorillas

Christopher Young & Martha M. Robbins
Excel file containing data for the analysis

Girls in early childhood increase food returns of nursing women during subsistence activities of the BaYaka in the Republic of Congo

Haneul Jang, Karline R. L. Janmaat, Vidrige Kandza & Adam Boyette
Nursing mothers face an energetic trade-off between infant care and work. Under pooled energy budgets, this trade-off can be reduced by assistance in food acquisition and infant care tasks from non-maternal caregivers. Across cultures, children also often provide infant care. Yet the question of who helps nursing mothers during foraging has been understudied, especially the role of children. Using focal follow data from 140 subsistence expeditions by BaYaka women in the Republic of Congo, we...

Additional file 2 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 2. All Supplementary Figures and legends.

Additional file 2 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 2. All Supplementary Figures and legends.

Additional file 3 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 3. Supplementary Table 1, extended patient cohort information.

Additional file 5 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 5. Appendix 1, example images from whole western blots used in this manuscript

Additional file 3 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 3. Supplementary Table 1, extended patient cohort information.

NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations

Martin Lackner, Nelly Helmbrecht, Svante Pääbo & Stephan Riesenberg
We developed a method to detect copy number variation and loss of heterozygosity in genome-edited cell lines by only sequencing the edited site. We introduced different substitutions on both chromosomes of diploid H9 human embryonic stem cells using CRISPR/Cas9 and a mixture of homology-directed repair donor DNAs carrying different substitutions. Here, we deposit the associated sequencing data (BAM-files) generated by extracting genomic DNA from genome-edited H9 cells, PCR amplifying the region of interest and sequencing...

How community forest management performs when REDD+ payments fail

Amy Collins, Mark Grote, Tim Caro, Aniruddha Ghosh, James Thorne, Jonathan Salerno & Monique Borgerhoff Mulder
The reduced emissions in deforestation and degradation (REDD+) initiative uses payments for ecosystem services as incentives for developing countries to manage and protect their forests. REDD+ initiatives also prioritize social (and environmental) co-benefits aimed at improving the livelihoods of communities that are dependent on forests. Despite the incorporation of co-benefits into REDD+ goals, carbon sequestration remains the primary metric for which countries can receive payments from REDD+, but after more than 10 years of REDD+,...

Coevolution of relative brain size and life expectancy in parrots

Simeon Q. Smeele, Dalia A. Conde, Annette Baudisch, Simon Bruslund, Andrew Iwaniuk, Johanna Staerk, Timothy F. Wright, Anna M. Young, Mary Brooke McElreath & Lucy Aplin
Previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa. Little research has been devoted to understanding this link in parrots; yet parrots are well-known for both their exceptionally long lives and cognitive complexity. We employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on longevity in parrots. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the Cognitive Buffer Hypothesis,...

Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Abstract Increasing evidence suggests synaptic dysfunction is a central and possibly triggering factor in Amyotrophic Lateral Sclerosis (ALS). Despite this, we still know very little about the molecular profile of an ALS synapse. To address this gap, we designed a synaptic proteomics experiment to perform an unbiased assessment of the synaptic proteome in the ALS brain. We isolated synaptoneurosomes from fresh-frozen post-mortem human cortex (11 controls and 18 ALS) and stratified the ALS group based...

Registration Year

  • 2022
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Affiliations

  • Max Planck Institute for Evolutionary Anthropology
    29
  • La Trobe University
    14
  • University of Burgos
    14
  • University of Edinburgh
    12
  • University of Dundee
    11
  • West China Second University Hospital of Sichuan University
    2
  • West China Hospital of Sichuan University
    2
  • Institute of Hydrobiology
    2
  • Huazhong University of Science and Technology
    2
  • Anhui University of Science and Technology
    2