eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells.

Background: Bioinformatics capability to analyze spatio-temporal dynamics of gene expression is essential in understanding animal development. Animal cells are spatially organized as functional tissues where cellular gene expression data contain information that governs morphogenesis during the developmental process. Although several computational tissue reconstruction methods using transcriptomics data have been proposed, those methods have been ineffective in arranging cells in their correct positions in tissues or organs unless spatial information is explicitly provided.

The role of the endolithic alga Ostreobium spp. during coral bleaching recovery.

In this study, we explore how the Caribbean coral Orbicella faveolata recovers after bleaching, using fragments from 13 coral colonies exposed to heat stress (32 °C) for ten days. Biological parameters and coral optical properties were monitored during and after the stress. Increases in both, the excitation pressure over photosystem II (Qm) and pigment specific absorption (a*) were observed in the stressed corals, associated with reductions in light absorption at the chlorophyll a red peak (D) and symbiont population density.

Effect of short- and long-term melatonin treatments on the reproductive activity of the tropical damselfish Chrysiptera cyanea.

Photoperiod plays a role in controlling the initiation and termination of reproduction in fish. Melatonin is an internal transducer of environmental photoperiod and is involved in regulating reproduction. The present study aimed to examine how melatonin impacts the transcript levels of kisspeptin (kiss1 and kiss2), gonadotropin-releasing hormones (gnrh1), and the β-subunit of gonadotropins (fshβ and lhβ) in the brain of the sapphire devil, a tropical damselfish with long photoperiod preference.

Programmable Macroscopic Self-Assembly of DNA-Decorated Hydrogels.

The precise and predictable formation of double-helical structures from complementary DNA sequences has made DNA an extremely versatile tool for programming self-assembled structures from the nanometer to micrometer scale. While a number of supramolecular interactions have been shown to drive self-assembly of macroscopic building blocks of the millimeter scale, DNA-driven self-assembly of macroscopic objects has not been well-established. In this work, we developed a postpolymerization coupling strategy to conjugate short DNA sequences to polyacrylamide-based hydrogel blocks.

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources.

Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer.

Horizontal gene transfer (HGT) is the movement of genetic material between different species. Although HGT is less frequent in eukaryotes than in bacteria, several instances of HGT have apparently shaped animal evolution. One well-known example is the tunicate cellulose synthase gene, , in which a gene, probably transferred from bacteria, greatly impacted tunicate evolution.

The mRNA expression patterns of kisspeptins, GnRHs, and gonadotropins in the brain and pituitary gland of a tropical damselfish, Chrysiptera cyanea, during the reproductive cycle.

The sapphire devil (Chrysiptera cyanea) is a tropical damselfish that undergoes active reproduction under long-day conditions. To elucidate the physiological regulation of the brain-pituitary-gonadal axis in female sapphire devil, we cloned and characterized the genes of two kisspeptins (kiss1 and kiss2), three gonadotropin-releasing hormones (gnrh1, gnrh2, gnrh3), and the β-subunit of two gonadotropins (fshβ and lhβ) and investigated the gene expression changes during ovarian development. Quantitative polymerase chain reaction analyses in various brain parts revealed high expression levels of kiss1, kiss2, and gnrh2 in the diencephalon; gnrh2 and gnrh3 in the telencephalon; and fshβ and lhβ in the pituitary.

Involvement of melatonin in transducing moon-related signals into the reproductive network of the female honeycomb grouper Epinephelus merra.

Most groupers (genus Epinephelus) inhabiting tropical and subtropical waters exhibit lunar-related reproductive cycles. Their gametes develop synchronously toward and are released around the species-selected moon phase. Periodical changes in cues from the moon are likely used as zeitgeber, and the hypothalamic-pituitary-gonadal (HPG) axis may be activated after cues are perceived by the sensory organ and transduced as internal signals.

Daily expression of a clock gene in the brain and pituitary of the Malabar grouper (Epinephelus malabaricus).

Recent studies have revealed that, in addition to regulating the circadian system, clock genes such as cryptochrome (Cry) genes are involved in seasonal and lunar rhythmicity in fish. This study clarified the transcriptional characteristics of a Cry subtype (mgCry2) in the brain of the Malabar grouper, Epinephelus malabaricus, which is an important aquaculture species that spawns around the new moon. The cDNA sequence of mgCry2 showed high identity (97-99%) with fish Cry2 and had an open reading frame encoding a protein with 170 amino acids.

Total Capture, Convection-Limited Nanofluidic Immunoassays Exhibiting Nanoconfinement Effects.

Understanding nanoconfinement phenomena is necessary to develop nanofluidic technology platforms. One example of nanoconfinement phenomena is shifts in reaction equilibria toward reaction products in nanoconfined systems, which have been predicted theoretically and observed experimentally in DNA hybridization. Here we demonstrate a convection-limited nanofluidic immunoassay that achieves total capture of a target analyte and an apparent shift in the antibody-antigen reaction equilibrium due to nanoconfinement.

Regulating Higher-Order Organization through the Synergy of Two Self-Sorted Assemblies.

The extracellular matrix (ECM) is the natural fibrous scaffold that regulates cell behavior in a hierarchical manner. By mimicking the dynamic and reciprocal interactions between ECM and cells, higher-order molecular self-assembly (SA), mediated through the dynamic growth of scaffold-like nanostructures assembled by different molecular components, was developed. Designed and synthesized were two self-sorted coumarin-based gelators, a peptide molecule and a benzoate molecule, which self-assemble into nanofibers and nanobelts, respectively, with different dynamic profiles.

Plasma-Assisted Large-Scale Nanoassembly of Metal-Insulator Bioplasmonic Mushrooms.

Large-scale plasmonic substrates consisting of metal-insulator nanostructures coated with a biorecognition layer can be exploited for enhanced label-free sensing by utilizing the principle of localized surface plasmon resonance (LSPR). Most often, the uniformity and thickness of the biorecognition layer determine the sensitivity of plasmonic resonances as the inherent LSPR sensitivity of nanomaterials is limited to 10-20 nm from the surface. However, because of time-consuming nanofabrication processes, there is limited work on both the development of large-scale plasmonic materials and the subsequent surface functionalizing with biorecognition layers.

Low-dose electron energy-loss spectroscopy using electron counting direct detectors.

Since the development of parallel electron energy loss spectroscopy (EELS), charge-coupled devices (CCDs) have been the default detectors for EELS. With the recent development of electron-counting direct-detection cameras, micrographs can be acquired under very low electron doses at significantly improved signal-to-noise ratio. In spectroscopy, in particular in combination with a monochromator, the signal can be extremely weak and the detection limit is principally defined by noise introduced by the detector.

Microfluidic device flow field characterization around tumor spheroids with tunable necrosis produced in an optimized off-chip process.

Tumor spheroids are a 3-D tumor model that holds promise for testing cancer therapies in vitro using microfluidic devices. Tailoring the properties of a tumor spheroid is critical for evaluating therapies over a broad range of possible indications. Using human colon cancer cells (HCT-116), we demonstrate controlled tumor spheroid growth rates by varying the number of cells initially seeded into microwell chambers.

Glucose restriction induces transient G2 cell cycle arrest extending cellular chronological lifespan.

While glucose is the fundamental source of energy in most eukaryotes, it is not always abundantly available in natural environments, including within the human body. Eukaryotic cells are therefore thought to possess adaptive mechanisms to survive glucose-limited conditions, which remain unclear. Here, we report a novel mechanism regulating cell cycle progression in response to abrupt changes in extracellular glucose concentration.