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1. Energy Sources of the Depth-Generalist Mixotrophic Coral Stylophora pistillata

   https://doi.org/10.3389/fmars.2020.566663  

   Martinez, Stephane; Kolodny, Yuval; Shemesh, Eli; Scucchia, Federica; Nevo, Reinat; Levin-Zaidman, Smadar; Paltiel, Yossi; Keren, Nir; Tchernov, Dan; Mass, Tali (November 2020, Frontiers in Marine Science)

   null (Ed.)

   Energy sources of corals, ultimately sunlight and plankton availability, change dramatically from shallow to mesophotic (30–150 m) reefs. Depth-generalist corals, those that occupy both of these two distinct ecosystems, are adapted to cope with such extremely diverse conditions. In this study, we investigated the trophic strategy of the depth-generalist hermatypic coral Stylophora pistillata and the ability of mesophotic colonies to adapt to shallow reefs. We compared symbiont genera composition, photosynthetic traits and the holobiont trophic position and carbon sources, calculated from amino acids compound-specific stable isotope analysis (AA-CSIA), of shallow, mesophotic and translocated corals. This species harbors different Symbiodiniaceae genera at the two depths: Cladocopium goreaui (dominant in mesophotic colonies) and Symbiodinium microadriaticum (dominant in shallow colonies) with a limited change after transplantation. This allowed us to determine which traits stem from hosting different symbiont species compositions across the depth gradient. Calculation of holobiont trophic position based on amino acid δ 15 N revealed that heterotrophy represents the same portion of the total energy budget in both depths, in contrast to the dogma that predation is higher in corals growing in low light conditions. Photosynthesis is the major carbon source to corals growing at both depths, but the photosynthetic rate is higher in the shallow reef corals, implicating both higher energy consumption and higher predation rate in the shallow habitat. In the corals transplanted from deep to shallow reef, we observed extensive photo-acclimation by the Symbiodiniaceae cells, including substantial cellular morphological modifications, increased cellular chlorophyll a , lower antennae to photosystems ratios and carbon signature similar to the local shallow colonies. In contrast, non-photochemical quenching remains low and does not increase to cope with the high light regime of the shallow reef. Furthermore, host acclimation is much slower in these deep-to-shallow transplanted corals as evident from the lower trophic position and tissue density compared to the shallow-water corals, even after long-term transplantation (18 months). Our results suggest that while mesophotic reefs could serve as a potential refuge for shallow corals, the transition is complex, as even after a year and a half the acclimation is only partial. 

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2. NOVEL STAIN SEPARATION METHOD FOR AUTOMATIC STEREOLOGY OF IMMUNOSTAINED TISSUE SECTIONS

   https://doi.org/10.1093/geroni/igz038.958  

   Dave, Palak; Goldgof, Dmitry; Hall, Lawrence O; Alahmari, Saeed; Mouton, Peter R (November 2019, Innovation in Aging)

   Abstract Many studies of brain aging and neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases require rapid counts of high signal: noise (S:N) stained brain cells such as neurons and neuroglial (microglia cells) on tissue sections. To increase throughput efficiency of this work, we have combined deep learned (DL) neural networks and computerized stereology (DL-stereology) for automatic cell counts with low error (<10%) compared to time-intensive manual counts. To date, however, this approach has been limited to sections with a single high S:N immunostain for neurons (NeuN) or microglial cells (Iba-1). The present study expands this approach to protocols that combine immunostains with counterstains, e.g., cresyl violet (CV). In our method, a stain separation technique called Sparse Non-negative Matrix Factorization (SNMF) converts a dual-stained color image to a single gray image showing only the principal immunostain. Validation testing was done using semi- and automatic stereology-based counts of sections immunostained for neurons or microglia with CV counterstaining from the neocortex of a transgenic mouse model of tauopathy (Tg4510 mouse) and controls. Cell count results with principal stain gray images show an average error rate of 16.78% and 28.47% for the semi-automatic approach and 8.51% and 9.36% for the fully-automatic DL-stereology approach for neurons and microglia, respectively, as compared to manual cell counts (ground truth). This work indicates that stain separation by SNMF can support high throughput, fully automatic DL-stereology based counts of neurons and microglia on counterstained tissue sections. 

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3. Target of Rapamycin in Control of Autophagy: Puppet Master and Signal Integrator

   https://doi.org/10.3390/ijms21218259  

   Mugume, Yosia; Kazibwe, Zakayo; Bassham, Diane C. (November 2020, International Journal of Molecular Sciences)

   null (Ed.)

   The target of rapamycin (TOR) is an evolutionarily-conserved serine/threonine kinase that senses and integrates signals from the environment to coordinate developmental and metabolic processes. TOR senses nutrients, hormones, metabolites, and stress signals to promote cell and organ growth when conditions are favorable. However, TOR is inhibited when conditions are unfavorable, promoting catabolic processes such as autophagy. Autophagy is a macromolecular degradation pathway by which cells degrade and recycle cytoplasmic materials. TOR negatively regulates autophagy through phosphorylation of ATG13, preventing activation of the autophagy-initiating ATG1-ATG13 kinase complex. Here we review TOR complex composition and function in photosynthetic and non-photosynthetic organisms. We also review recent developments in the identification of upstream TOR activators and downstream effectors of TOR. Finally, we discuss recent developments in our understanding of the regulation of autophagy by TOR in photosynthetic organisms. 

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4. netNMF-sc: Leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis

   Elyanow, Rebecca; Dumitrascu, Bianca; Engelhardt, Barbara E; Raphael, Benjamin J. (January 2019, Research in Computational Biology (RECOMB))

   Single-cell RNA-sequencing (scRNA-seq) enables high throughput measurement of RNA expression in individual cells. Due to technical limitations, scRNA-seq data often contain zero counts for many transcripts in individual cells. These zero counts, or dropout events, complicate the analysis of scRNA-seq data using standard analysis methods developed for bulk RNA-seq data. Current scRNA-seq analysis methods typically overcome dropout by combining information across cells, leveraging the observation that cells generally occupy a small number of RNA expression states. We introduce netNMF-sc, an algorithm for scRNA-seq analysis that leverages information across both cells and genes. netNMF-sc combines network-regularized non-negative matrix factorization with a procedure for handling zero inflation in transcript count matrices. The matrix factorization results in a low-dimensional representation of the transcript count matrix, which imputes gene abundance for both zero and non-zero entries and can be used to cluster cells. The network regularization leverages prior knowledge of gene-gene interactions, encouraging pairs of genes with known interactions to be close in the low-dimensional representation. We show that netNMF-sc outperforms existing methods on simulated and real scRNA-seq data, with increasing advantage at higher dropout rates (e.g. above 60%). Furthermore, we show that the results from netNMF-sc -- including estimation of gene-gene covariance -- are robust to choice of network, with more representative networks leading to greater performance gains. 

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5. Photosynthetic modulation during the diurnal cycle in a unicellular diazotrophic cyanobacterium grown under nitrogen-replete and nitrogen-fixing conditions

   https://doi.org/10.1038/s41598-022-21829-6  

   Liberton, Michelle; Biswas, Sandeep; Pakrasi, Himadri B. (November 2022, Scientific Reports)

   Abstract Cyanobacteria are the only oxygenic photosynthetic organisms that can fix nitrogen. In diazotrophic cyanobacteria, the regulation of photosynthesis during the diurnal cycle is hypothesized to be linked with nitrogen fixation and involve the D1 protein isoform PsbA4. The amount of bioavailable nitrogen has a major impact on productivity in aqueous environments. In contrast to low- or nitrogen-fixing (−N) conditions, little data on photosynthetic regulation under nitrogen-replete (+ N) conditions are available. We compared the regulation of photosynthesis under −N and + N conditions during the diurnal cycle in wild type and apsbA4deletion strain of the unicellular diazotrophic cyanobacteriumCyanothecesp. ATCC 51142. We observed common changes to light harvesting and photosynthetic electron transport during the dark in + N and −N conditions and found that these modifications occur in both diazotrophic and non-diazotrophic cyanobacteria. Nitrogen availability increased PSII titer when cells transitioned from dark to light and promoted growth. Under −N conditions, deletion of PsbA4 modified charge recombination in dark and regulation of PSII titer during dark to light transition. We conclude that darkness impacts the acceptor-side modifications to PSII and photosynthetic electron transport in cyanobacteria independently of the nitrogen-fixing status and the presence of PsbA4. 

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