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Development of compact transcriptional effectors using high-throughput measurements in diverse contexts

HT-recruit and CRISPR HT-recruit processed datasets  Abstract: Transcriptional effectors are protein domains known to activate or repress gene expression, however, a systematic understanding of which effector domains regulate transcription robustly across genomic, cell-type, and DNA-binding domain (DBD) contexts is lacking. Here, we develop dCas9-mediated high-throughput recruitment (HT-recruit), a pooled screening method for quantifying effector function at endogenous target genes, and test effector function for a library containing 5,092 nuclear protein Pfam domains across varied contexts. We also map context dependencies of effectors drawn from unannotated protein regions using a larger library containing 114,288 sequences tiling chromatin regulators and transcription factors. We find that many effectors depend on target and DBD contexts, such as HLH domains that can act as either activators or repressors. To enable efficient perturbations, we select context-robust domains, including ZNF705 KRAB, that improve CRISPRi tools to silence promoters and enhancers. We engineer a compact human activator NFZ by combining several domains, which enables efficient CRISPRa with better viral delivery, and inducible control of CAR T-cells. Together, this effector-by-context functional map reveals context-dependence across human effectors and guides effector selection for manipulating transcription.

The code and data for paper: "Observing Fine-Grained Changes in Jupyter Notebooks During Development Time"

<div> This package represents supplementary materials for the paper "Observing Fine-Grained Changes in Jupyter Notebooks During Development Time". Please refer to README in the archive for details. </div>

Data from the article titled: Transforming into community. Development process of the Algarabía Occupational Center as an expanded community of practice Transforming into community. Development process of the Algarabía Occupational Center as an expanded community of practice

Project PID2020-117020GB-I00 , funded by : Ministerio de Ciencia e Innovación de España/ AEI/10.13039/501100011033 and by the predoctoral contracts grant for the training of PhD implemented by the [grant number PRE2021-098075]

Figure 11 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 11. The egg tooth of Lacerta agilis at developmental stage 36. A, labiolingual histological section through the egg tooth and higher magnification of the area from the smaller box (inset), stained with H&E. B, labiolingual histological section through the egg tooth and dentin under higher magnification (inset) from the egg tooth tip, stained with AZAN trichrome. C, higher magnification of the area from the larger box in A showing a reversal line (arrows). D, transverse histological section through the anterior snout showing the cellular attachment tissue connecting the egg tooth to pleura, stained with H&E. E, sagittal cutaway of the snout (left), microtomographic sagittal (middle) and labiolingual (right) sections of the egg tooth. F, 3D reconstruction of the premaxilla and premaxillary teeth with exclusion of the egg tooth, ventral view. G, 3D reconstruction of the premaxilla and all premaxillary teeth, ventral view. H, 3D reconstruction of the premaxilla and the egg tooth (semi-transparent), right posterolateral view. Asterisks in E and F show the forming successor of the egg tooth. Scale bars: 100 μm.

Figure 4 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 4. The egg tooth of Lacerta agilis at developmental stage 31. A, transverse histological section through the snout at the level of the egg tooth and forming premaxilla (asterisks), stained with H&E. B, 3D reconstruction of the palate. C, transverse histological section posterior to A, stained with H&E. D, transverse histological section posterior to C, stained with H&E. E, 3D reconstruction of the snout showing the egg tooth and forming premaxilla (asterisks), anterior semi-transparent view. F, microtomographic frontal section through the anterior snout. G, microtomographic frontal section through the anterior snout, ventral to F. Scale bars: 50 μm for histological sections; 500 μm for microtomographic sections.

Figure 7 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 7. The premaxillary teeth of Lacerta agilis at developmental stage 34. A, labiolingual histological section through the egg tooth, stained with H&E. B, labiolingual histological section through the egg tooth, stained with AZAN trichrome. C, 3D reconstruction of the anterior snout, right lateral semi-transparent view. D, sagittal cutaway of the anterior snout. E, labiolingual histological section through the regular premaxillary tooth, stained with AZAN trichrome. F, labiolingual histological section through the regular premaxillary tooth, stained with H&E. Scale bars: 50 μm for histological sections; 200 μm for 3D reconstructions.

Figure 3 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 3. The egg tooth of Lacerta agilis at developmental stage 29. A, transverse histological section through the snout at the level of the epithelial thickening of the forming egg tooth, stained with H&E. B, 3D reconstruction of the snout, lateroventral view. C, transverse histological section through the snout posterior to A, showing epithelial thickening of the forming regular premaxillary tooth (arrow). D, sagittal cutaway of the snout, stage 29, but slightly older than in A–C. E, 3D reconstruction of the snout, lateroventral semi-transparent view, stage 29, but slightly older than in A–C. F, transverse histological section through the snout at the level of the egg tooth bud (dotted line) stained with AZAN trichrome, stage 29, but slightly older than in D and E. G, transverse histological section through the snout at the level of the premaxillary dental lamina, stained with AZAN trichrome, posterior to F. Scale bars: 50 μm for histological sections; 500 μm for 3D reconstructions.

Figure 10 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 10. The egg tooth of Lacerta agilis at developmental stage 36. A, stereomicroscope photomicrograph of the anterior snout, left ventrolateral view (mirrored). B, stereomicroscope photomicrograph of the anterior palate. C, 3D reconstruction of the snout, anterior view. D, scanning electron micrograph of the egg tooth showing a disruption of the enamel organ (arrow), ventral view. E, scanning electron micrograph of the lateral border of the egg tooth showing small bulges (arrowhead). F, scanning electron micrograph of the periderm cells covering the egg tooth. G, scanning electron micrograph of the microridges on the egg tooth periderm cells. Scale bars: 200 μm in A–D; 1 μm in E–G.

Figure 6 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 6. The egg tooth of Lacerta agilis at developmental stage 34. A, stereomicroscope photomicrograph of the anterior palate. B, 3D reconstruction of the snout, anterior semi-transparent view. C, 3D reconstruction of the palate, anteroventral view. D, scanning electron micrograph of the anterior palate and the egg tooth surface (inset). Scale bars: 100 μm; 1 μm for inset in D.

Figure 2 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 2. Transverse histological section through the snout of a Lacerta agilis embryo, stained with AZAN trichrome; developmental stage 28. A, section at the level of the facial prominence fusion (arrows). B, section at the level of the nasal plug, anterior to A. Scale bars: 50 μm.

Figure 5 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 5. Transverse histological section through the snout of Lacerta agilis at developmental stage 32, stained with H&E. A, middle part of the developing egg tooth. B, anterior part of the developing egg tooth. C, posterior part of the developing egg tooth. D, premaxillary regular teeth at bud stage, section posterior to C. Scale bars: 50 μm; 25 μm for inset in B.

Figure 9 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 9. The premaxillary teeth of Lacerta agilis at developmental stage 35. A, labiolingual histological section through the egg tooth showing the forming attachment tissue (asterisks), stained with AZAN trichrome. B, labiolingual histological section through the egg tooth showing the forming attachment tissue (asterisks), stained with H&E. C, 3D reconstruction of the palate, non-transparent (left) and semitransparent (right) view. D, sagittal cutaway of the anterior snout. E, labiolingual histological section through the regular premaxillary tooth and forming the subsequent premaxillary teeth (arrow), stained with AZAN trichrome. F, labiolingual histological section through the regular premaxillary teeth and primordium of the egg tooth successor (arrowhead), stained with H&E. Scale bars: 50 μm for histological sections; 100 μm for 3D reconstructions.

Figure 1 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 1. Distribution of the egg tooth (teeth) and caruncle in amniotes. The snout drawings, except for Unidentata (based on this study), are based on the literature: Gekkota (Hermyt et al. 2020b), Sphenodon, turtle (Fioroni 1962), bird (Wang et al. 2017), crocodilian (García 2007), and monotreme (Fenelon et al. 2023). Silhouettes are from http://phylopic.org/. Note that this simplified phylogenetic tree assumes the existence of the molecular clades Unidentata (Burbrink et al. 2020) and Archelosauria (Crawford et al. 2015).

Figure 13 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 13. The developmental sequences of the egg tooth, the most advanced regular premaxillary teeth, and the most advanced maxillary teeth.

Figure 12 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 12. The premaxillary teeth of Lacerta agilis at developmental stage 36. A, 3D reconstruction of the anterior palate including semitransparent view (right). B, labiolingual histological section through the largest regular premaxillary tooth and higher magnification of the collagen fibres of the forming attachment tissue (asterisks in the inset), stained with AZAN trichrome. C, labiolingual histological section through the regular premaxillary teeth showing a reversal line (arrows) between the alveolar bone and premaxilla, stained with H&E. D, labiolingual histological section through the successor of the egg tooth, stained with AZAN trichrome. E, labiolingual histological section through the successor of the egg tooth, stained with H&E. F, transverse histological section through the snout at the level of maxillary and premaxillary dental laminae apposition, stained with H&E. Scale bars: 200 μm in A; 50 μm in B–F.

Figure 8 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth

Figure 8. The egg tooth of Lacerta agilis at developmental stage 35. A, stereomicroscope photomicrograph of the anterior snout, left lateral view (mirrored), early developmental stage 35. B, stereomicroscope photomicrograph of the anterior snout, left lateral view (mirrored), at late developmental stage 35. C, stereomicroscope photomicrograph of the anterior palate, early developmental stage 35. D, stereomicroscope photomicrograph of the anterior palate, late developmental stage 35. E, scanning electron micrograph of the anterior palate, late developmental stage 35. F, magnification of the area from the box in E showing the egg tooth. G, magnification of the area from the box in F showing the small bulges (arrowheads) on the lateral border of the egg tooth. Scale bars: 200 μm in A–D; 50 μm in E, F; 5 μm in G.

Bulgarian dataset SafeFood4EU Feedback on Project and Course Developed

These are the Bulgarian language results from the feedback of the SafeFood4EU project and course.

openSep 2024View details →

hmc development testing repo

This is NOT the Human Microbiome Compendium dataset. This is a repository used for development testing to make sure our systems are interacting politely with Zenodo. The data isn't up to date. Don't use this. <a href="https://doi.org/10.5281/zenodo.8186993">You want the real one</a>

Scale invariance in early embryonic development

Data and analysis accompanying the paper: "Scale invariance in early embryonic development"  Milos Nikolic, Victoria Antonetti, Feng Liu, Gentian Muhaxheri, Mariela D. Petkova, Martin Scheeler, Eric M. Smith, William Bialek and Thomas Gregor.  arxiv.org/abs/2312.17684

Development of Indoor Vegetable Plant Rack Design Based on IOTs to Prevent Stunts

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