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Rational design and optimization of synthetic gene switches for controlling cell-fate decisions in pluripotent stem cells
<p>Data underlying the figures in the publication “Rational Design and Optimization of Synthetic Gene Switches for Controlling Cell-fate Decisions in Pluripotent Stem Cells”, published in <em>Metabolic Engineering</em>, <strong>2021</strong>, 65, 99-110. <a href="https://doi.org/10.1016/j.ymben.2021.03.009">https://doi.org/10.1016/j.ymben.2021.03.009</a></p> <p>Table of contents:</p> <p><strong>1. Dataset 1</strong>; Excel file with the curated data underlying the figures.</p> <p><strong>Figure 1. </strong>Comparative analysis of synthetic gene switches in HEK-293T and hiPSCs. (A) Erythromycin-responsive synthetic gene switch consisting of a constitutively expressed erythromycin-responsive transactivator (pVH620; PmPGK1-E-VP16-pA) and an inducible Nluc expression vector controlled by an operator containing two erythromycin transcription response (ETR) sites (pVH619; OETR2-PCMVmin-2-Nluc-pA), assessed in terms of production of secreted Nluc 24 h after transfection. EM indicates addition of erythromycin (2.0 µg/mL) to the culture medium. (B) Phloretin-responsive synthetic gene switch consisting of a constitutively expressed phloretin-responsive transactivator (pVH655; PmPGK1-TtgR-VP16-pA) and an inducible Nluc expression vector controlled by an operator containing two TtgR binding sites (pVH654; OTtgO2-PCMVmin-2-Nluc-pA), assessed in terms of production of secreted Nluc 24 h after transfection. Phlo indicates addition of phloretin (50 µM) to the culture medium. (C) Vanillic acid-responsive synthetic gene switch consisting of a constitutively expressed vanillic acid-responsive transactivator (pVH238-1; PmPGK1-VanR-VP16-pA) and an inducible Nluc expression vector controlled by an operator containing two VanR binding sites (pVH294-1.3; OVanO2-PCMVmin-2-Nluc-pA), assessed in terms of production of secreted Nluc 24 h after transfection. VA indicates addition of vanillic acid (500 µM) to the culture medium.</p> <p><strong>Figure 2.</strong> Rational design and assembly of a vanillic acid-controlled synthetic gene switch in hiPSCs. (B) Combinatorial analysis of constitutive promoters in hiPSCs for the expression of the VanR-VP16 trans-activator (pVH238-1; PmPGK1-VanR-VP16-pA, pVH238-2; PhEF1a-VanR-VP16-pA) and inducible expression cassette minimal promoters (pVH294-1.1; OVanO2-Pmin-Nluc-pA, pVH294-1.3; OVanO2-PCMVmin-2-Nluc-pA, pVH294-1.2; OVanO2-PCMVmin-1-Nluc-pA), assessed in terms of the production of secreted Nluc 24 h after transfection. (C) Tuning the induction level of the inducible expression cassette in hiPSCs by increasing the number of VanR binding sites within the operator (pVH294-1.1; OVanO2-Pmin-Nluc-pA, pVH294-2.1; OVanO4-Pmin-Nluc-pA, pVH294-3.1; OVanO6-Pmin-Nluc-pA), assessed in terms of the production of secreted Nluc 24 h after co-transfection with PmPGK1-driven VanR-VP16 (pVH238-1; PmPGK1-VanR-VP16-pA). (D) Assessment of the structural assembly of the VanR-VP16 transactivator in hiPSCs, comparing direct fusion of VanR and VP16 (pVH238-1; PmPGK1-VanR-VP16-pA), fusion with a short flexible (pVH261; PmPGK1-VanR-FL1-VP16-pA, FL1; GGGGS) or rigid (pVH263; PmPGK1-VanR-RL1-VP16-pA, RL1; EAAAK) linker, and fusion with a longer flexible (pVH262; PmPGK1-VanR-FL2-VP16-pA, FL2; GGGGSGGGGS) or rigid (pVH264; PmPGK1-VanR-RL2-VP16-pA, RL2; EAAAKEAAAK) linker, assessed in terms of the production of secreted Nluc 24 h after co-transfection with a Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-2.1; OVanO4-Pmin-Nluc-pA). (E) Tuning the induction level of the VA-controlled synthetic gene switch in hiPSCs by promoting active nuclear translocation of VanR-VP16 (pVH238-1; PmPGK1-VanR-VP16-pA) with importin-alpha (pVH250; PmPGK1-NLSSV40-VanR-VP16-pA) or importin-beta (pVH252; PmPGK1-NLSG46-VanR-VP16-pA)-recognized NLS peptide, assessed in terms of the production of secreted Nluc 24 h after co-transfection with a Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-2.1; OVanO4-Pmin-Nluc-pA). (F) Combinatorial analysis for the final assembly of the VA-controlled synthetic gene switch in hiPSCs using a Pmin-driven reporter construct controlled by either four (pVH294-2.1; OVanO4-Pmin-Nluc-pA) or six (pVH294-3.1; OVanO4-Pmin-Nluc-pA) VanR binding sites and different combinations of selected components from previous characterization steps to assemble the transactivator (pVH238-1; PmPGK1-VanR-VP16-pA, pVH263; PmPGK1-VanR-RL1-VP16-pA, pVH262; PmPGK1-VanR-FL2-VP16-pA, pVH250; PmPGK1-NLSSV40-VanR-VP16-pA, pVH252; PmPGK1-NLSG46-VanR-VP16-pA, pVH629; PmPGK1-NLSSV40-VanR-RL1-VP16-pA, pVH628; PmPGK1-NLSSV40-VanR-FL2-VP16-pA, pVH300; PmPGK1-NLSG46-VanR-RL1-VP16-pA, pVH624; PmPGK1-NLSG46-VanR-FL2-VP16-pA), assessed in terms of the production of secreted Nluc 24 h after transfection. (G) Dose-response curves in hiPSCs of the PmPGK1-driven NLSG46-VanR-VP16 (pVH252; PmPGK1-NLSG46-VanR-VP16-pA) and the basic VanR-VP16 (pVH238-1; PmPGK1- VanR-VP16-pA) fusion constructs using the Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-1.2; OVanO4-Pmin-Nluc-pA), assessed in terms of the production of secreted Nluc 24 h after transfection. (B-F) VA indicates addition of vanillic acid (500 µM) to the culture medium.</p> <p><strong>Figure 3.</strong> Regulation of the VanA system during the generation of the three germ layers. hiPSCs transiently transfected with the complete VA-controlled expression vector (pVH438; 5’ITR-OVanO4-Pmin-Nluc-pA-PmPGK1-NLSG46-VanR-VP16-2A-NeoR-pA-3’ITR) were specified for 3 days into (A) DE or (B) ME, and for 5 days into (C) EC. The VanA system was maintained in its repressed state by the addition of VA (500 µM) and induced by the removal of VA from the differentiation medium on the last day of differentiation. Induction of the VanA system was assessed in terms of the intracellular production of non-secreted Nluc.</p> <p><strong>Figure 4. </strong>Synthetic gene-switch-guided posterior foregut lineage specification. (C) The mRNA expression levels of HHEX and TGIF2 in iHHEX/iTGIF2 hiPSCs cultured for 24 h in the presence of different combinations of VA and DOX were determined by means of qRT-PCR. VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Values were normalized to those in the VA (+)/DOX(-) condition. (G-H) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiated towards PG with FGF7 (25 ng/mL) for 3 days, and subsequently towards PFG with FGF7 (25 ng/mL), noggin (50 ng/mL), and retinoic acid (RA; 2 µM) for 1 day. During differentiation HHEX and TGIF2 was maintained uninduced/repressed (VA on D0-7, No DOX), or HHEX was induced on day 2-3 by the addition of DOX and TGIF2 was induced on day 3-7 by removal of VA from the differentiation medium (VA on D3-7, DOX on D2-3). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. (G) Quantification of PDX1-expressing PFG cells. Flow cytometry results quantification of PDX1-expressing PFG cells differentiated using growth-factor-directed (VA on D0-7, No DOX) and TGIF2/HHEX-guided (VA on D0-3, DOX on D2-3) differentiation protocols. (H) Relative mRNA expression levels for PP (PDX1), PFG (SOX9, HNF6), HP (ALB), MHG (CDX2), and AFG (OTX2) genes on day 7 in iHHEX/iTGIF2 hiPSC-derived PFG cells generated with the indicated HHEX and TGIF2 induction conditions were determined by means of qRT-PCR. Values were normalized to those in day 0 iHHEX/iTGIF2 hiPSCs.</p> <p><strong>Figure S1.</strong> Effect of constitutive promoter expression strength (pVH238-1; PmPGK1-VanR-VP16-pA, pVH238-2; PhEF1a-VanR-VP16-pA) on the basal expression levels of inducible vectors containing different minimal promoters (pVH294-1.1; OVanO2-Pmin-Nluc-pA, pVH294-1.3; OVanO2-PCMVmin-2-Nluc-pA, pVH294-1.2; OVanO2-PCMVmin-1-Nluc-pA) relative to mock transfection (pColaDuet-1) in hiPSCs, assessed in terms of the production of secreted Nluc 24 h after transfection. VA indicates addition of vanillic acid (500 µM) to the culture medium.</p> <p><strong>Figure S2.</strong> Assessment of optimal fusion configurations for NLS peptides. (A) NLSSV40 or (B) NLSG46 was fused to the N-terminus of VanR-VP16 (pVH250; PmPGK1-NLSSV40VanR-VP16-pA, pVH252; PmPGK1-NLSG46-VanR-VP16-pA), in between VanR and VP16 as a linker (pVH260; PmPGK1-VanR-NLSSV40-VP16-pA, pVH622; PmPGK1-VanR-NLSG46-VP16-pA), or to the C-terminus (pVH251; PmPGK1-VanR-VP16-NLSSV40-pA, pVH623; PmPGK1-VanR-VP16-NLSG46-pA) to identify the best conformation in hiPSCs, assessed in terms of the production of secreted Nluc 24 h after co-transfection with a Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-2.1; OVanO4-Pmin-Nluc-pA). (A-B) VA indicates addition of vanillic acid (500 µM) to the culture medium.</p> <p><strong>Figure S3.</strong> Complete expression vector design for stable integration encoding OVanO4-Pmin-driven Nluc expression cassette and PmPGK1-driven NLSG46-VanR-VP16 (pVH438; 5’ITR-OVanO4-Pmin-Nluc-pA-PmPGK1-NLSG46-VanR-VP16-2A-NeoR-pA-3’ITR). (B) Transient performance characterization in hiPSCs assessed in terms of the production of intracellular Nluc 24 h after transfection. VA indicates addition of vanillic acid (500 µM) to the culture medium.</p> <p><strong>Figure S4.</strong> Generation of the three germ layers from hiPSCs transfected with complete VA-controlled expression vector (pVH438; 5’ITR-OVanO4-Pmin-Nluc-pA-PmPGK1-NLSG46-VanR-VP16-2A-NeoR-pA-3’ITR). (A) Relative mRNA expression levels of definitive endoderm (DE) genes (EOMES, SOX17, FOXA2, CXCR4) in cells transfected with the complete VA system expression vector after 3 days of DE specification with VA. (B) Relative mRNA expression levels of mesoderm (ME) genes (T, PDGFRa, TBX6, HAND1) in cells transfected with the complete VA system expression vector after 3 days of ME specification with VA. (C) Relative mRNA expression levels of ectoderm (EC) genes (PAX6, NES, OTX2, SOX10) in cells transfected with the complete VA system expression vector after 5 days of EC specification with VA. (A-C) Values were normalized to those of day 0 hiPSCs. VA indicates the addition of vanillic acid (500 µM) to the differentiation medium.</p> <p><strong>Figure S5.</strong> Performance comparison and multiplexing of the VanA and rtTA systems in hIPSCs. (A) Comparison of selected inducible expression cassette containing four VanR response elements (pVH294-2.1; OVanO4-Pmin-Nluc-pA) in combination with PmPGK1-driven NLSG46-VanR-VP16 (pVH252; PmPGK1-NLSG46-VanR-VP16-pA) fusion construct relative to the DOX-controlled rtTA system (pVH627; OTetO7-Pmin-Nluc-pA / pVH235; PmPGK1-rtTA-pA) in hiPSCs assessed in terms of the production of secreted Nluc 24 h after transfection. (B) Assessment of multiplexing potential of the VA system (pVH425; OVanO4-Pmin-Nluc-pA / pVH252; PmPGK1-NLSG46-VanR-VP16-pA) and the DOX-controlled rtTA system (pVH424; OTetO7-Pmin-Fluc-pA / pVH235; PmPGK1-rtTA-pA) in hiPSCs assessed in terms of the production of intracellular Nluc and Fluc 48 h after transfection. (A-B) VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (1 µg/mL) to the culture medium.</p> <p><strong>Figure S6.</strong> (C) iHHEX/iTGIF2 hiPSCs were differentiated towards anterior primitive streak (APS) and DE using the standard combination of exogenous Wnt (GSK3 inhibition CHIR99021 [CHIR]; 3 µM) and TGF-β (Activin A [AA]; 100 ng/mL) induction. During differentiation, TGIF2 was maintained repressed by the addition of VA (VA on D0-3) and HHEX was maintained uninduced (No DOX). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Relative mRNA expression levels for pluripotency markers (POU5F1, NANOG, SOX2), and definitive endoderm (DE) markers (EOMES, SOX17, FOXA2, CXCR4) on day 3 in iHHEX/iTGIF2 hiPSC-derived DE cells were determined by means of qRT-PCR. Values were normalized to those of day 0 iHHEX/iTGIF2 hiPSCs. (E) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiation towards PG for 1 day with FGF7 (25 ng/mL). During PG specification, TGIF2 was induced alone (VA on D0-3, No DOX), HHEX was induced alone (VA on D0-4, No DOX), or TGIF2 and HHEX were both maintained uninduced (VA on D0-4, No DOX) on day 3-4 by removal or addition of VA and DOX as specified. VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. The expression levels for HHEX and TGIF2 on day 4 during PG differentiation of iHHEX/iTGIF2 hiPSC-derived DE cells were determined by means of qRT-PCR. Values were normalized to GAPDH and TBP expression levels in day 4 iHHEX/iTGIF2 hiPSCs.</p> <p><strong>Figure S7.</strong> (B) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiated towards PG with FGF7 (25 ng/mL) for 3 days, and subsequently towards PFG with FGF7 (25 ng/mL), noggin (50 ng/mL), and retinoic acid (RA; 2 µM) for 1 day. During differentiation TGIF2 was maintained repressed under all conditions by the addition of VA to the differentiation media on day 0-7 (VA on D0-7). HHEX was either maintained uninduced (No DOX) or induced on day 2-3, 2-4, or 2-5 by the addition of DOX to the differentiation media (DOX on D2-3, D2-4, or D2-5). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Relative mRNA expression levels for PP (PDX1), HP (ALB), and PFG (SOX9, HNF6) genes on day 7 in iTGIF2/iHHEX hiPSC-derived PFG cells generated with the indicated differentiation protocol and HHEX induction conditions were determined by means of qRT-PCR. Values were normalized to those of day 0 iHHEX/iTGIF2 hiPSCs. (D) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiated towards PG with FGF7 (25 ng/mL) for 3 days, and subsequently towards PFG with FGF7 (25 ng/mL), noggin (50 ng/mL), and retinoic acid (RA; 2 µM) for 1 day. During differentiation HHEX was maintained uninduced under all conditions (No DOX). TGIF2 was either maintained uninduced by the addition of VA (VA on D0-7) or induced on day 5-7, 4-7, or 3-7 by removal of VA from the differentiation medium (VA on D0-5, D0-4, or D0-3). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Relative mRNA expression levels for PP (PDX1), HP (ALB), and PFG (SOX9, HNF6) genes on day 7 in iHHEX/iTGIF2 hiPSC-derived PFG cells generated with the indicated differentiation protocol and TGIF2 induction conditions were determined by means of qRT-PCR. Values were normalized to those of day 0 iHHEX/iTGIF2 hiPSCs.</p>
The different fates of two Asian horseshoe crab species with different dispersal abilities
<p>Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms' evolutionary responses to past sea level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. <em>Carcinoscorpius rotundicauda</em> Latreille, a less mobile mangrove species, has finer population structure and lower genetic diversity compared to the dispersive deep-sea <em>Tachypleus gigas</em> Müller. Even though the source populations of both species during the Last Glacial Maximum exhibited comparable effective population sizes, the less dispersive <em>C. rotundicauda</em> seems to lose genetic diversity much more quickly because of population fragmentation. Contra previous studies' results, we predict that the more commonly sighted <em>C. rotundicauda</em> faces a more uncertain conservation plight, with a continuing loss in evolutionary potential and higher vulnerability to future climate change. Our study provides important genomic baseline data for the redirection of conservation measures in the face of climate change, and can be used as a blueprint for assessment and mitigation of the adverse effects of impending sea level rise in other systems.</p>
Data from: On the fate of seasonally plastic traits in a rainforest butterfly under relaxed selection
Many organisms display phenotypic plasticity as adaptation to seasonal environmental fluctuations. Often, such seasonal responses entails plasticity of a whole suite of morphological and life-history traits that together contribute to the adaptive phenotypes in the alternative environments. While phenotypic plasticity in general is a well-studied phenomenon, little is known about the evolutionary fate of plastic responses if natural selection on plasticity is relaxed. Here, we study whether the presumed ancestral seasonal plasticity of the rainforest butterfly Bicyclus sanaos (Fabricius, 1793) is still retained despite the fact that this species inhabits an environmentally stable habitat. Being exposed to an atypical range of temperatures in the laboratory revealed hidden reaction norms for several traits, including wing pattern. In contrast, reproductive body allocation has lost the plastic response. In the savannah butterfly, B. anynana (Butler, 1879), these traits show strong developmental plasticity as an adaptation to the contrasting environments of its seasonal habitat and they are coordinated via a common developmental hormonal system. Our results for B. sanaos indicate that such integration of plastic traits – as a result of past selection on expressing a coordinated environmental response – can be broken when the optimal reaction norms for those traits diverge in a new environment.
Identify key transcription factors in cell fate determination using ANANSE
<p>The example data used in ANANSE protocol.</p>
Data from: Seed fates in crop-wild hybrid sunflowers: crop allele and maternal effects
Domestication has resulted in selection upon seed traits found in wild populations, yet crop-wild hybrids retain some aspects of both parental phenotypes. Seed fates of germination, dormancy, and mortality can influence the success of crop allele introgression in crop-wild hybrid zones, especially if crop alleles or crop-imparted seed coverings result in out-of-season germination. We performed a seed burial experiment using crop, wild, and diverse hybrid sunflower (Helianthus annuus) cross types to test how a cross type's maternal parent and nuclear genetic composition might affect its fate under field conditions. We observed higher maladaptive fall germination in the crop- and F1- produced seeds than wild-produced seeds and, due to an interaction with percent crop alleles, fall germination was higher for cross types with more crop-like nuclear genetics. By spring, crop-produced cross types had the highest overwintering mortality, primarily due to higher fall germination. Early spring germination was identical across maternal types, but germination continued for F1-produced seeds. In conclusion, the more wild-like the maternal parent or the less proportion of the cross type's genome contributed by the crop, the greater likelihood a seed will remain ungerminated than die. Wild-like dormancy may facilitate introgression through future recruitment from the soil seed bank.
Figure 2 in The fate of the TARDIS offspring: no intergenerational effects of space exposure
Figure 2. Schematic description of the different generations of Milnesium tardigradum referred to in this study.
Figure 5 in The fate of the TARDIS offspring: no intergenerational effects of space exposure
Figure 5. Mean percentage (SE) of viable animals in Echiniscus testudo and Ramazzottius oberhaeuseri exposed to space vacuum and cosmic radiation within the TARDIS experiment in 2007. Figure data are based on four replicate samples in each species.
Figure 4 in The fate of the TARDIS offspring: no intergenerational effects of space exposure
Figure 4. Mean percentage (with SE) hatching success and survival until day 7 post-hatching in controls, space vacuum and UVAB treatment groups of the F1 (A) and F3 (B) generations of Milnesium tardigradum, representing descendants of the parental (P) generation that was exposed to space conditions in the TARDIS experiment (Jonsson et al., 2008). Treatment categories: Control, Earth laboratory control; SV, space vacuum and cosmic radiation; SV+UVAB, space vacuum, cosmic radiation and UVAB. Mean (SD) values: Hatching success F1: Control, 86.8% (5.3); SV, 92.5% (3.8); SV+UVAB, 91.7% (—). Hatching success F3: Control, 98.1% (0.82); SV, 95.9% (2.8); SV+UVAB, 98.0% (—). Survival 7-days post-hatch F1: Control, 92.9% (4.2); SV, 88.2% (3.8); SV+UVAB, 93.5% (—). Survival 7-days post-hatch F3: Control, 91.2% (3.3); SV, 88.3% (4.0); SV+UVAB, 91.3% (—).
Figure 3 in The fate of the TARDIS offspring: no intergenerational effects of space exposure
Figure 3. Mean fecundity (with SE) in the F1 generation (eggs produced by the P generation exposed in space) and the F3 generation (eggs produced by the F2 generation) in Milnesium tardigradum, based on the number of eggs in individual exuvia. Treatment categories: Control, Earth laboratory control; SV, space vacuum and cosmic radiation; SV+UVAB, space vacuum, cosmic radiation and UVAB. Number of replicate samples: F1, n = 4 for both controls and SV; F3: n = 4 for controls and 3 for SV. The analysis included only one sample of UV-exposed animals. Mean (SD) values F1: Control, 8.0 (1.15); SV, 7.1 (1.35); SV+UVAB, 7.0 (—). Mean (SD) values F3: Control, 9.6 (0.54); SV, 9.9 (0.058); SV+UVAB, 9.8 (—).
A single-cell atlas of Drosophila trachea reveals glycosylation-mediated Notch signaling in cell fate specification
<p>Processed data files for the following article:</p><p>Li Y, Lu T, Dong P, Chen J, Zhao Q, Wang Y, Xiao T, Wu H, Zhao Q and Huang H. A single-cell atlas of Drosophila trachea reveals glycosylation-mediated Notch signaling in cell fate specification.</p><p>Please also refer to code at https://github.com/Tianfeng-Lu/single-cell-atlas-of-fly-trachea</p>
Assessing the fate and behaviour of plant nutrients in aquaponic systems by chemical equilibrium modelling: A meta-analytical approach
<p>Cleaned dataset and Visual MINTEQ input files (without and without assumed presence of dissolved organic matter) for each record in the dataset.</p>
Morphological characteristics of pollen from triploid watermelon and its fate on stigmas in a hybrid crop production system
<p>Hybrid crop production is more reliant on pollinators compared to open-pollinated crops because they require cross-pollination between a male-fertile and a male-sterile line. Little is known about how stigma receipt of pollen from male-sterile genotypes affects reproduction in hybrids. Non-viable and non-compatible pollen cannot fertilise plant ovules, but may still interfere with pollination success. Here we used seedless watermelon (<em>Citrullus lanatus</em> (Thunb.) Matsum. & Nakai) as a model hybrid plant, to evaluate the morphology, physiology, and movement of pollen from inter-planted genotypes (diploids and triploids). We found that pollen from triploids ('Exclamation' and 'Royal Armada') and diploids ('SP-6', 'Summer Flavor 800', and 'Tiger') was visually distinguishable. Pollen in triploids had more deformities (42.4–46%), tetrads (43–44%), and abnormal growth of callose plugs in pollen tubes. The amount of pollen in triploids to germinate on stigmas was low (8 ± 3%), and few pollen grains produced pollen tubes (6.5 ± 2%). Still, contrary to previous reports our results suggest that some viable pollen grains are produced by triploid watermelons. However, whilst honey bees can collect and deposit pollen from triploids onto stigmas, its effect on hybrid watermelon reproduction is likely to be minimal due to its low germination rate.</p>
Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye
<p>Pattern formation of biological structures involves the arrangement of different types of cells in an ordered spatial configuration. In this study, we investigate the mechanism of patterning the <em>Drosophila</em> eye into a precise triangular grid of photoreceptor clusters called ommatidia. Previous studies had led to a long-standing biochemical model whereby a reaction-diffusion process is templated by recently formed ommatidia to propagate a molecular prepattern across the eye epithelium. Here, we find that the templating mechanism is instead, mechanical in origin; newly born columns of ommatidia serve as a template to spatially pattern cell flows that move the cells in the epithelium into position to form each new column of ommatidia. Cell flow is generated by a pressure gradient that is caused by a narrow zone of cell dilation precisely positioned behind the growing wavefront of ommatidia. The newly formed lattice grid of ommatidia cells are immobile, deflecting and focusing the flow of other cells. Thus, the self-organization of a regular pattern of cell fates in an epithelium is mechanically driven.</p>
Model outputs and observation data for "Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)"
<p>Model outputs and observation data for paper "Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)".</p>
Data for "Diverging fates of the Pacific Ocean oxygen minimum zone and its core in a warming world" (2022, AGU Advances)
<p>Preprocessed Plotting Data to reproduce Figures from "Diverging fates of the Pacific Ocean oxygen minimum zone and its core in a warming world" (2022, AGU Advances)</p>
Fate Bell Shelter
Seminole Canyon State Park, Texas. Source: Objaverse 1.0 / Sketchfab
CLM-FATES parameter estimation using the 'calibrate, emulate, sample' approach - experimental results
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Data from: "Eddington envelopes: The fate of stars on parabolic orbits tidally disrupted by supermassive black holes" (Price et al. 2024)
<p>The paper by Price et al. (2024; <a href="https://arxiv.org/abs/2404.09381">arXiv:2404.09381</a>) simulates the tidal disruption of a one solar mass polytropic star by a million-solar-mass supermassive black hole, using the Phantom general relativistic smoothed particle hydrodynamics code (Price et al. 2018). The code used to perform the simulations is available at:</p> <p><a href="https://github.com/danieljprice/phantom">https://github.com/danieljprice/phantom</a></p> <p>This dataset contains:</p> <ol> <li>Scripts, intermediate data products and other small files used to create each figure in the paper</li> <li>Selected snapshots and other raw data from the four main calculations shown in the paper</li> </ol> <p>The main datasets contain parameter files and snapshots from the simulations used to create figures in the paper.small data files from the simulations and post-processing scripts used to create the scientific results and figures shown in the paper. Each simulation dataset contains:</p> <p><strong>.setup file:</strong> parameter file used by phantomsetup to create the initial conditions for the star itself<br><br><strong>.in file:</strong> parameter file used by phantom to perform the calculation<br><br><strong>tde_00000, tde_00100, tde_00200 etc:</strong> binary code snapshots containing raw data (particle positions, velocities, thermal energy, etc), these can be read/visualised/converted using the free and open source codes SPLASH (Price et al. 2007):<br><br><a href="https://github.com/danieljprice/splash">https://github.com/danieljprice/splash</a></p> <p>or Sarracen:</p> <p><a href="https://github.com/ttricco/sarracen">https://github.com/ttricco/sarracen</a></p> <p>SPLASH was used to create figures in the paper. The format and ways to read these data files are described in:</p> <p><a href="https://phantomsph.readthedocs.io/en/latest/user-guide/dumpfile.html">https://phantomsph.readthedocs.io/en/latest/user-guide/dumpfile.html</a></p> <p><strong>tde01.ev, tde02.ev etc:</strong> ascii files (see header) containing global quantities like total angular momentum, total momentum, total energy etc as a function of time. Each number corresponds to a restart of the code (i.e. resubmission of the job to the queue on the cluster).</p> <p><strong>tde01.log, tde02.log: </strong>output log from the simulations themselves, this contains some useful information like the unit scalings, typical timestep and code performance, hardware information etc.</p> <p><em><strong>.defaults, .limits, .units and .filenames:</strong> parameter files used by SPLASH to create particular figures. For example, to use the files lightcurve.defaults, lightcurve.units, lightcurve.limits and lightcurve.filenames one would plot using splash -p lightcurve</em></p> <p>The relevant raw data directories are:</p> <p><strong>beta1_hres: </strong>raw data from the adiabatic, beta=1 calculation</p> <p><strong>beta5_hres:</strong> raw data from the adiabatic, beta=5 calculation</p> <p><strong>beta1_isentropic: </strong>raw data from the isentropic, beta=1 calculation with a non-spinning black hole</p> <p><strong>beta1_isentropic_kerr_a99_i60:</strong> raw data from the isentropic, beta=1 calculation with a maximally-spinning black hole with the initial stellar orbit at an incliation of 60 degrees to the black hole spin</p> <p><strong>The procedure to recreate each figure and post-processing analysis used in the paper is explained in the README.md placed in each directory unpacked from the figureX.zip file</strong></p> <p> </p>
Twin Worlds, Divergent Fates: How Obliquity has differently shaped Pluto's and Triton's landscapes and climates
<p>Netcdf files : simulations of Pluto and Triton (Fig. 3)</p> <p> </p>
The Fate of Nitrogen during Early Silicate Differentiation of Rocky Bodies Constrained by Experimental Mineral-Melt Partitioning
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