- Jun 2024
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www.biorxiv.org www.biorxiv.org
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Photo-activation of a diffraction-limited spot in a CAD cell expressing PaGFPactin shows asymmetricmovement toward the front of the cell.
This text appears to be the same as that describing panel a. Is this intended? I assume C is an image of a blebbistatin experiment?
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The EGFP-actin network of NG108 cells was rapidly bleached between 0.3 and 1.3s. At3.9s, bleached actin monomer from the network has been transported (recycled) to the front ofthe cell, repolymerized at the leading edge, and traveled rearward (thin dark line indicated byarrow).
Out of curiosity (and ignorance) why is the line containing the repolymerized bleached monomer so thin? The volume of bleached monomer appears to be large. Is the width of the repolymerized line impacted by the relative position of the bleaching?
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- Feb 2024
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www.biorxiv.org www.biorxiv.org
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We measured Raman spectra of single cells
It would be nice to have a more expansive description of how Raman spectra (optical layout of apparatus, single cell capture, etc...) were collected.
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Here we show that proteome profiles
This is an extremely compelling result and you provide significant evidence that Raman spectra and proteomes can be related. Such a result has extremely compelling implications for the possible uses of Raman spectroscopy for predicting proteome profiles. Here you work with proteomic data from another group and collect raman spectra from single bacterial cells grown in conditions that are as close as possible to the original conditions. It would be even more compelling if you could do this analysis, capture the Raman spectra, then validate (for at least some growth conditions) the proteomic profile matches that which was previously published.
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- Dec 2023
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www.biorxiv.org www.biorxiv.org
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l of 15,000 images were generated for each condition. Each image was assigned a unique random seed,
It seems likely this approach will require more data than a similar approach using pre-registered images. Do you have a sense of how much more data would be required for similar accuracy?
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15,000 images
Have you determined how much data is required for reasonable accuracy? If we were designing an experiment, how many images would be necessary for reasonable accuracy?
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trainsfer
typo: transferred
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clases
Typo: Classes
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www.biorxiv.org www.biorxiv.org
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Humans have adapted to a much longer lifespan compared with other primate species, which have a median lifespan of 20-30 years, suggesting that increased selection on TERT may have occurred as part of human adaption towards extended longevity
Is it clear what the relative telomere lengths are in these species and whether they are correlated with selection on TERT?
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The remaining 19 variants appear to be truly pathogenic in human, and are presumably tolerated in primate because of primate-human differences, such as interactions with changes in the neighboring sequence context (45, 46).
Have you considered the possibility that these deleterious influences in humans might be modified by differences between humans and primates that act at a larger range. For example, a change in a specific transcription factor binding site might have a compensatory shift in the transcription factor. These types of interactions could act at long range and may underlie some of these species-species differences in deleterious effect.
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However, deleterious variants were incompletely removed in humans, consistent with the shorter amount of time they were exposed to natural selection.
It would be great to hear alternative explanations for the presence of 'deleterious' variants in humans. For example, it might be true that the deleterious effect of a variant may be different across species.
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- Oct 2023
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www.biorxiv.org www.biorxiv.org
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Live cell imaging of the fission yeast Schizosaccharomyces pombe at 3, 11, 22, 27, 30, and 34 mins in (a-f) (See Visualization I). This strain expresses the nuclear pore protein nup211 fused with the green fluorescent protein (nup211-GFP), marking the position of the nucleus. Arrowheads point to the septum, where cytokinesis occurs. Scale bar: 5µm.
It would be great to have a comparison to a standard DIC image here. It would help to answer questions like, is the image of the cleavage furrow substantially clearer in the PDIC image.
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The phase images for the stained and unstained serial cuts are overall similar. However, slight elevation of the phase is noticeable for the H&E stained section, especially in the areas surrounding some stromal regions.
The ability to image structural components of unstained material is very impressive. You have shown two examples of biological samples that are very thin. Have you looked at thicker samples? is there a limit to the thickness of samples that can be imaged?
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- Sep 2023
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www.biorxiv.org www.biorxiv.org
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the recombination block
Did you estimate a recombination rate? would be interesting to compare to genetic maps from other fish.
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Extended Data Fig. 7 sh
Maybe this should be extended figure 5? Extended figure 7 is something else.
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he square in the top1164right-hand corner is created by samples 550-648, which have distinct genotypes to the rest of1165the samples due to their having been bred from different F1 parents
How did you account for different parental lines in your analysis?
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we excluded766the 22 samples that showed poor coverage across the genome
What constitutes poor coverage?
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In short, 1.25681uL of each sample was taken into a tagmentation reaction containing 1.25 uL of682Dimethylformamide, 1.25 uL of tagmentation buffer (40 mM Tris-HCl pH 7.5,68340 mM MgCl2) and 1.25 uL of an in-house generated and purified Tn556 an
This is an extremely clever way of reducing the overall cost of marker typing in the F2 generation, but there are alternatives. Have you considered something like RADseq or other reduced representation libraries? It might enable analysis of cohorts larger than 600 animals.
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- Aug 2023
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www.biorxiv.org www.biorxiv.org
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herefore, we hypothesize that the association of Dop2R with variation in female productivity in the DGRP may at least partially arise from naturally occurring variation in expression of Dop2R in DGRP females, which then causes variation in the amount of DA that regulates fertility via changes in JH and 20E titers. Dop2R expression is genetically variable in the DGRP, with a broad sense heritability in females ∼ 0.70 [16]. We found a strong correlation between Dop2R expression in females with productivity (r = 0.34, P = 9.81e-7, Figure 4b) but a relatively weak effect of the Dop2R SNP on expression (P = 0.09). Mediation analysis revealed that approximately 19% (P = 0.09) of the effect of the Dop2R SNP on productivity was mediated by the effect of Dop2R expression.
I believe there is a Dop2R mutant available. Have you looked at these animals? they might prove useful in testing some mechanistic hypotheses.
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The most significant SNP (P = 3.42 × 10−7) is 1,612 bp downstream of the gene encoding the dopamine 2-like receptor (Dop2R), and explained approximately 47% of the genetic variance of productivity in females.
Wow! This is an amazing result!
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Therefore, we adjusted productivity for the Wolbachia infection status of parents before further analyses.
Did you examine whether there was an interaction between Wolbachia infection and any of the alleles you mapped?
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- Apr 2023
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www.biorxiv.org www.biorxiv.org
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The resulting top terms after this trimming define the latent space.
What is the expected distribution of weights in the latent space? Would a discriminator network to impose different distributions be useful here?
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o verify the validity of these predictions, we performed a gene-set enrichment analysis (GSEA) using as a ground truth the differentially expressed genes in a recently published dataset of bulk RNA-seq carried out on muscle samples from LGMD patients (n=16) and healthy individuals (n=15)25, where we had determined the genes that were significantly up- (LGMD_up) or downregulated (LGMD_dn) in patients compared to age-matched controls (Supplementary Table 3).
The significance of the difference in gene expression will be related to the size of the effect on the expression, but many genes that influence a phenotype may only show small changes in expression level. How well does this model deal with genes that show small changes in expression? Would this miss genes that show small changes in expression but are nevertheless important?
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- Feb 2023
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arxiv.org arxiv.org
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expressive
It would be great to have a clear definition of 'expressive' here. It can be inferred from the results, but, given 'expressiveness' is one of the differentiating features of the IAE, it would be nice to have a statement here as to what is intended.
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- Dec 2022
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www.biorxiv.org www.biorxiv.org
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o verify the validity of these predictions, we performed a gene-set enrichment analysis (GSEA) using as a ground truth the differentially expressed genes in a recently published dataset of bulk RNA-seq carried out on muscle samples from LGMD patients (n=16) and healthy individuals (n=15)25, where we had determined the genes that were significantly up- (LGMD_up) or downregulated (LGMD_dn) in patients compared to age-matched controls (Supplementary Table 3).
The significance of the difference in gene expression will be related to the size of the effect on the expression, but many genes that influence a phenotype may only show small changes in expression level. How well does this model deal with genes that show small changes in expression? Would this miss genes that show small changes in expression but are nevertheless important?
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The resulting top terms after this trimming define the latent space.
What is the expected distribution of weights in the latent space? Would a discriminator network to impose different distributions be useful here?
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The resulting top terms after this trimming define the latent space.
What is the expectation for the distribution of weights in the latent space? would it be useful to use a discriminator network to structure the weight distribution in this layer?
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