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Found 36144 matches. Displaying 81-90
Tchernichovski O, Eisenberg-Edidin S, Jarvis ED
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Balanced imitation sustains song culture in zebra finches

NATURE COMMUNICATIONS 2021 MAY 7; 12(1):? Article 2562
Songbirds acquire songs by imitation, as humans do speech. Although imitation should drive convergence within a group and divergence through drift between groups, zebra finch songs sustain high diversity within a colony, but mild variation across colonies. We investigated this phenomenon by analyzing vocal learning statistics in 160 tutor-pupil pairs from a large breeding colony. Song imitation is persistently accurate in some families, but poor in others. This is not attributed to genetic differences, as fostered pupils copied their tutors' songs as accurately or poorly as biological pupils. Rather, pupils of tutors with low song diversity make more improvisations compared to pupils of tutors with high song diversity. We suggest that a frequency dependent balanced imitation prevents extinction of rare song elements and overabundance of common ones, promoting repertoire diversity within groups, while constraining drift across groups, which together prevents the collapse of vocal culture into either complete uniformity or chaos. Studying how songbirds learn songs can shed light on the development of human speech. An analysis of 160 tutor-pupil zebra finch pairs suggests that frequency dependent balanced imitation prevents the extinction of rare song elements and the overabundance of common ones, promoting song diversity within groups and species recognition across groups.
Garcia-Bermudez J, Birsoy K
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A mitochondrial gatekeeper that helps cells escape death by ferroptosis

NATURE 2021 MAY 27; 593(7860):514-515
Banho CA, Merel V, Oliveira TYK, Carareto CMA, Vieira C
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Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes

SCIENTIFIC REPORTS 2021 MAY 10; 11(1):? Article 9844
Interspecific hybridization is a stressful condition that can lead to sterility and/or inviability through improper gene regulation in Drosophila species with a high divergence time. However, the extent of these abnormalities in hybrids of recently diverging species is not well known. Some studies have shown that in Drosophila, the mechanisms of postzygotic isolation may evolve more rapidly in males than in females and that the degree of viability and sterility is associated with the genetic distance between species. Here, we used transcriptomic comparisons between two Drosophila mojavensis subspecies and D. arizonae (repleta group, Drosophila) and identified greater differential gene expression in testes than in ovaries. We tested the hypothesis that the severity of the interspecies hybrid phenotype is associated with the degree of gene misregulation. We showed limited gene misregulation in fertile females and an increase in the amount of misregulation in males with more severe sterile phenotypes (motile vs. amotile sperm). In addition, for these hybrids, we identified candidate genes that were mostly associated with spermatogenesis dysfunction.
Dunn TW, Marshall JD, Severson KS, Aldarondo DE, Hildebrand DGC, Chettih SN, Wang WL, Gellis AJ, Carlson DE, Aronov D, Freiwald WA, Wang F, Olveczky BP
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Geometric deep learning enables 3D kinematic profiling across species and environments

NATURE METHODS 2021 MAY; 18(5):564-573
Comprehensive descriptions of animal behavior require precise three-dimensional (3D) measurements of whole-body movements. Although two-dimensional approaches can track visible landmarks in restrictive environments, performance drops in freely moving animals, due to occlusions and appearance changes. Therefore, we designed DANNCE to robustly track anatomical landmarks in 3D across species and behaviors. DANNCE uses projective geometry to construct inputs to a convolutional neural network that leverages learned 3D geometric reasoning. We trained and benchmarked DANNCE using a dataset of nearly seven million frames that relates color videos and rodent 3D poses. In rats and mice, DANNCE robustly tracked dozens of landmarks on the head, trunk, and limbs of freely moving animals in naturalistic settings. We extended DANNCE to datasets from rat pups, marmosets, and chickadees, and demonstrate quantitative profiling of behavioral lineage during development.
Boisson B, Casanova JL
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TLR8 gain of function: a tall surprise

BLOOD 2021 MAY 6; 137(18):2420-2422
In this issue of Blood, Aluri et al report 6 unrelated male patients who carried gain-of-function (GOF) variants of the X-linked gene TLR8.(1) The patients had invasive bacterial and fungal infections associated with splenomegaly and lymphadenopathy. They had an excess of double-negative T cells, abnormal B-cell maturation, and neutropenia, and some patients had bone marrow failure.
Balzano E, Pelliccia F, Giunta S
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Genome (in)stability at tandem repeats

Repeat sequences account for over half of the human genome and represent a significant source of variation that underlies physiological and pathological states. Yet, their study has been hindered due to limitations in shortreads sequencing technology and difficulties in assembly. A important category of repetitive DNA in the human genome is comprised of tandem repeats (TRs), where repetitive units are arranged in a head-to-tail pattern. Compared to other regions of the genome, TRs carry between 10 and 10,000 fold higher mutation rate. There are several mutagenic mechanisms that can give rise to this propensity toward instability, but their precise contribution remains speculative. Given the high degree of homology between these sequences and their arrangement in tandem, once damaged, TRs have an intrinsic propensity to undergo aberrant recombination with non-allelic exchange and generate harmful rearrangements that may undermine the stability of the entire genome. The dynamic mutagenesis at TRs has been found to underlie individual polymorphism associated with neurodegenerative and neuromuscular disorders, as well as complex genetic diseases like cancer and diabetes. Here, we review our current understanding of the surveillance and repair mechanisms operating within these regions, and we describe how alterations in these protective processes can readily trigger mutational signatures found at TRs, ultimately resulting in the pathological correlation between TRs instability and human diseases. Finally, we provide a viewpoint to counter the detrimental effects that TRs pose in light of their selection and conservation, as important drivers of human evolution.
Kastan N, Gnedeva K, Alisch T, Petelski AA, Huggins DJ, Chiaravalli J, Aharanov A, Shakked A, Tzahor E, Nagiel A, Segil N, Hudspeth AJ
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Small-molecule inhibition of Lats kinases may promote Yap-dependent proliferation in postmitotic mammalian tissues

NATURE COMMUNICATIONS 2021 MAY 25; 12(1):? Article 3100
Hippo signaling is an evolutionarily conserved pathway that restricts growth and regeneration predominantly by suppressing the activity of the transcriptional coactivator Yap. Using a high-throughput phenotypic screen, we identified a potent and non-toxic activator of Yap. In vitro kinase assays show that the compound acts as an ATP-competitive inhibitor of Lats kinases-the core enzymes in Hippo signaling. The substance prevents Yap phosphorylation and induces proliferation of supporting cells in the murine inner ear, murine cardiomyocytes, and human Muller glia in retinal organoids. RNA sequencing indicates that the inhibitor reversibly activates the expression of transcriptional Yap targets: upon withdrawal, a subset of supporting-cell progeny exits the cell cycle and upregulates genes characteristic of sensory hair cells. Our results suggest that the pharmacological inhibition of Lats kinases may promote initial stages of the proliferative regeneration of hair cells, a process thought to be permanently suppressed in the adult mammalian inner ear. Although Hippo signaling restricts regeneration in many mammalian organs, the pharmaceutical tools available to modulate the pathway have been limited. Here, the authors report a small molecule that may inhibit a key element in the Hippo cascade and may activate regenerative responses in several mammalian tissues.
Nicolas P, Etoc F, Brivanlou AH
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The ethics of human-embryoids model: a call for consistency

In this article, we discuss the ethics of human embryoids, i.e., embryo-like structures made from pluripotent stem cells for modeling natural embryos. We argue that defining our social priorities is critical to design a consistent ethical guideline for research on those new entities. The absence of clear regulations on these emerging technologies stems from an unresolved debate surrounding natural human embryo research and one common opinion that one needs to solve the question of the moral status of the human embryo before regulating their surrogate. The recent NIH funding restrictions for research on human embryoids have made scientists even more unlikely to raise their voices. As a result, the scientific community has maintained a low profile while longing for a more favorable socio-political climate for their research. This article is a call for consistency among biomedical research on human materials, trying to position human embryoids within a spectrum of existing practice from stem cell research or IVF to research involving human subjects. We specifically note that the current practices in infertility clinics of freezing human embryos or disposing of them without any consideration for their potential benefits contradicts the assumption of special consideration for human material. Conversely, creating human embryoids for research purposes could ensure that no human material be used in vain, always serving humankind. We argue here that it is time to reconsider the full ban on embryo research (human embryos and embryoids) beyond the 14-day rule and that research on those entities should obey a sliding scale combining the completeness of the model (e.g., complete vs. partial) and the developmental stage: with more advanced completeness and developmental stage of the considered entity, being associated with more rigorous evaluation of societal benefits, statements of intention, and necessity of such research.
Bota-Rabassedas N, Banerjee P, Niu YC, Cao WJ, Luo JY, Xi YX, Tan XC, Sheng KW, Ahn YH, Lee S, Parra ER, Rodriguez-Canales J, Albritton J, Weiger M, Liu X, Guo HF, Yu J, Rodriguez BL, Firestone JJA, Mino B, Creighton CJ, Solis LM, Villalobos P, Raso MG, Sazer DW, Gibbons DL, Russell WK, Longmore GD, Wistuba II, Wang J, Chapman HA, Miller JS, Zong CH, Kurie JM
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Contextual cues from cancer cells govern cancer-associated fibroblast heterogeneity

CELL REPORTS 2021 APR 20; 35(3):? Article 109009
Cancer cells function as primary architects of the tumor microenvironment. However, the molecular features of cancer cells that govern stromal cell phenotypes remain unclear. Here, we show that cancer-associated fibroblast (CAF) heterogeneity is driven by lung adenocarcinoma (LUAD) cells at either end of the epithelial-to-mesenchymal transition (EMT) spectrum. LUAD cells that have high expression of the EMT-activating transcription factor ZEB1 reprogram CAFs through a ZEB1-dependent secretory program and direct CAFs to the tips of invasive projections through a ZEB1-driven CAF repulsion process. The EMT, in turn, sensitizes LUAD cells to pro-metastatic signals from CAFs. Thus, CAFs respond to contextual cues from LUAD cells to promote metastasis.
Islam MS, Yang XW, Euler CW, Han XQ, Liu JH, Hossen I, Zhou Y, Li JQ
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Application of a novel phage ZPAH7 for controlling multidrug-resistant Aeromonas hydrophila on lettuce and reducing biofilms

FOOD CONTROL 2021 APR; 122(?):? Article 107785
Aeromonas hydrophila is an important pathogenic bacterium that causes foodborne illness worldwide. In this study, virulent phages from the sediment of a fish farm were propagated and isolated on a multidrug-resistant strain of A. hydrophila, ZYAH75. One phage, designated as ZPAH7, featured a unique turbid halo around a clear plaque on the bacterial lawn (indicative of potential depolymerase activity), and was selected for further analysis. ZPAH7 was classified as podophage by morphological and genomic methods. Further comparisons of genome nucleotide similarity, ratios of homologous proteins and phylogenetic relatedness among the terminase large subunit and major capsid proteins of similar phage deposited in GENBANK, led us to propose a new genus, ZPAH7virus, in the Autographivirinae subfamily of Podoviridae. ZPAH7 had an adsorption rate of 79% in 5 min, an eclipse period of 15 min, a latent period of 25 min, and a burst size of 148 +/- 9 PFU/cell. Antimicrobial application experiments showed that ZPAH7 lead to significantly reduction on A. hydrophila on lettuce. Additionally, ZPAH7 was able to inhibit biofilm formation, as well as degrade and kill bacteria in established biofilms. Furthermore, lytic activity of ZPAH7 remained stable across a wide range of temperatures and pH measurements. These results suggest ZPAH7 could be used as a potential biological control agent against A. hydrophila on food and/or biofilms on food contact surfaces.