Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.

Mouse (Mus musculus) models have been heavily utilized in developmental biology research to understand mammalian embryonic development, as mice share many genetic, physiological, and developmental characteristics with humans. New explorations into the integration of temporal (stage-specific) and transcriptional (tissue-specific) data have expanded our knowledge of mouse embryo tissue-specific gene functions. To better understand the substantial impact of synonymous mutational variations in the cell-state-specific transcriptome on a tissue's codon and codon pair usage landscape, we have established a novel resource-Mouse Embryo Codon and Codon Pair Usage Tables (Mouse Embryo CoCoPUTs).

Tuning Mechanical Properties, Swelling, and Enzymatic Degradation of Chitosan Cryogels Using Diglycidyl Ethers of Glycols with Different Chain Length as Cross-Linkers.

Cross-linking chitosan at room and subzero temperature using a series of diglycidyl ethers of glycols (DEs)-ethylene glycol (EGDE), 1,4-butanediol (BDDE), and poly(ethylene glycol) (PEGDE) has been investigated to demonstrate that DEs can be a more powerful alternative to glutaraldehyde (GA) for fabrication of biocompatible chitosan cryogels with tunable properties. Gelation of chitosan with DEs was significantly slower than with GA, allowing formation of cryogels with larger pores and higher permeability, more suitable for flow-through applications and cell culturing. Increased hydration of the cross-links with increased DE chain length weakened intermolecular hydrogen bonding in chitosan and improved cryogel elasticity.

Insights on long-term ecosystem changes from stable isotopes in historical squid beaks.

Background: Assessing the historical dynamics of key food web components is crucial to understand how climate change impacts the structure of Arctic marine ecosystems. Most retrospective stable isotopic studies to date assessed potential ecosystem shifts in the Arctic using vertebrate top predators and filter-feeding invertebrates as proxies. However, due to long life histories and specific ecologies, ecosystem shifts are not always detectable when using these taxa.

A review of the genus Muusoctopus (Cephalopoda: Octopoda) from Arctic waters.

We report two Arctic species of incirrate octopods new to science. One is formally described here as Muusoctopus aegir Golikov, Gudmundsson & Sabirov sp. nov.

Hybrid Silicon Nitride Photonic Integrated Circuits Covered by Single-Walled Carbon Nanotube Films.

The integration of low-dimensional materials with optical waveguides presents promising opportunities for enhancing light manipulation in passive photonic circuits. In this study, we investigate the potential of aerosol-synthesized single-walled carbon nanotube (SWCNT) films for silicon nitride photonic circuits as a basis for developing integrated optics devices. Specifically, by measuring the optical response of SWCNT-covered waveguides, we retrieve the main SWCNT film parameters, such as absorption, nonlinear refractive, and thermo-optic coefficients, and we demonstrate the enhancement of all-optical wavelength conversion and the photoresponse with a 1.

Extended Rate Constants Distribution (RCD) Model for Sorption in Heterogeneous Systems: 4. Kinetics of Metal Ions Sorption in the Presence of Complexing Agents-Application to Cu(II) Sorption on Polyethyleneimine Cryogel from Acetate and Tartrate Solutions.

Here, we report a new version of the extended Rate Constants Distribution (RCD) model for metal ion sorption, which includes complex-formation equilibria. With the RCD-complex model, one can predict sorbent performance in the presence of complexing agents using data on metal ion sorption from ligand-free solutions and a set of coefficients for sorption rate constants of different ionic species. The RCD-complex model was applied to breakthrough curves of Cu(II) sorption from acetate and tartrate solutions on polyethyleneimine (PEI) monolith cryogel at different flow rates and ionic speciation.

Miles down for lunch: deep-sea observations of Arctic finned octopods suggest pelagic-benthic feeding migration.

Deep-sea cephalopods are diverse, abundant, and poorly understood. The Cirrata are gelatinous finned octopods and among the deepest-living cephalopods ever recorded. Their natural feeding behaviour remains undocumented.

Corrigendum: The significance of cephalopod beaks as a research tool: An update.

[This corrects the article DOI: 10.3389/fphys.2022.

Ultrasensitive Nanophotonic Random Spectrometer with Microfluidic Channels as a Sensor for Biological Applications.

Spectrometers are widely used tools in chemical and biological sensing, material analysis, and light source characterization. However, an important characteristic of traditional spectrometers for biomedical applications is stable operation. It can be achieved due to high fabrication control during the development and stabilization of temperature and polarization of optical radiation during measurements.

Life History of the Arctic Squid (Cephalopoda: Oegopsida) Reconstructed by Analysis of Individual Ontogenetic Stable Isotopic Trajectories.

Cephalopods are important in Arctic marine ecosystems as predators and prey, but knowledge of their life cycles is poor. Consequently, they are under-represented in the Arctic ecosystems assessment models. One important parameter is the change in ecological role (habitat and diet) associated with individual ontogenies.

The significance of cephalopod beaks as a research tool: An update.

The use of cephalopod beaks in ecological and population dynamics studies has allowed major advances of our knowledge on the role of cephalopods in marine ecosystems in the last 60 years. Since the 1960's, with the pioneering research by Malcolm Clarke and colleagues, cephalopod beaks (also named jaws or mandibles) have been described to species level and their measurements have been shown to be related to cephalopod body size and mass, which permitted important information to be obtained on numerous biological and ecological aspects of cephalopods in marine ecosystems. In the last decade, a range of new techniques has been applied to cephalopod beaks, permitting new kinds of insight into cephalopod biology and ecology.

In Situ Monitoring of Layer-by-Layer Assembly Surface Modification of Nanophotonic-Microfluidic Sensor.

An elaboration of the photonic based sensors is the most promising direction in modern analytical chemistry from the point of view of real clinical applications. The highest sensitivity is demonstrated by sensors based on photonic integrated circuits (PICs). This type of sensor has been recently successfully combined with microfluidics, which decreased the analyte volume for analysis down to microliter units.

Hybrid nanophotonic-microfluidic sensor for highly sensitive liquid and gas analyses.

Today, a lab-on-a-chip is one of the most promising ways to create sensor devices for gas and liquid analysis for environmental monitoring, early diagnosis, and treatment effectiveness assessment. On the one hand, this requires a large number of measurements and, on the other hand, involves minimum consumption of the test analytes. Combination of highly sensitive photonic integrated circuits (PICs) with microfluidic channels (MFCs) is necessary to solve this problem.

New Data on Distribution of Nereilinum murmanicum (Annelida, Siboglinidae) in the Barents Sea.

The article presents a report on the findings of representatives of frenulate pogonophorans Nereilinum murmanicum in the northern and central parts of the Barents Sea, which significantly expands the range of this species and provides guidance on its distribution in this basin. Here we present the coordinates of new finds with an indication of the depth. Find points were associated with data on known and potential hydrocarbon deposits.

Hydrothermal oxidation of pre-dissolved resorcinol-formaldehyde resins as a new approach to safe processing of spent cesium-selective organic ion-exchangers.

Here we report a new approach to predisposal processing of spent resorcinol-formaldehyde resins (RFR) selective to cesium radionuclides via dissolution and hydrothermal oxidation (HTO) with the mineralization efficiency above 85%. Using a combination of potentiometric and colloid titration, we have shown that dissolution of RFR by consecutive treatment with nitric acid and sodium hydroxide solutions at optimal concentrations of 3-5 mol/L and 1 mol/L, respectively, yields colloid solutions of partially depolymerized and oxidized RFR. The efficiency of HTO of resorcinol and RFR solutions with hydrogen peroxide was investigated in a flow-type stainless steel reactor in the temperature range 165-250 °С and at linear flow rates of 1-3 cm/min.

Composite Zn(II) Ferrocyanide/Polyethylenimine Cryogels for Point-of-Use Selective Removal of Cs-137 Radionuclides.

The feasibility of several approaches to the fabrication of monolith composite cryogels containing transition-metal ferrocyanides for Cs ion uptake has been evaluated. Although in the series of investigated metal ion precursors (Cu(II), Zn(II), Ni(II), and Co(II)), in situ formation of the sorption active phase in polyethyleneimine (PEI) cryogel was feasible only in the case of Zn(II) ferrocyanide, this approach has shown significant advantages over the immobilization of ex situ synthesized ferrocyanide nanoparticles. Nanoparticles of the mixed ferrocyanide ZnK[Fe(CN)] formed in situ had an average size of 516 ± 146 nm and were homogeneously distributed in the monolith located at the polymer surface rather than embedded in the matrix.

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.

Background: Gene expression is highly variable across tissues of multi-cellular organisms, influencing the codon usage of the tissue-specific transcriptome. Cancer disrupts the gene expression pattern of healthy tissue resulting in altered codon usage preferences. The topic of codon usage changes as they relate to codon demand, and tRNA supply in cancer is of growing interest.

Bioinformatics tools developed to support BioCompute Objects.

Developments in high-throughput sequencing (HTS) result in an exponential increase in the amount of data generated by sequencing experiments, an increase in the complexity of bioinformatics analysis reporting and an increase in the types of data generated. These increases in volume, diversity and complexity of the data generated and their analysis expose the necessity of a structured and standardized reporting template. BioCompute Objects (BCOs) provide the requisite support for communication of HTS data analysis that includes support for workflow, as well as data, curation, accessibility and reproducibility of communication.

Diet and life history reduce interspecific and intraspecific competition among three sympatric Arctic cephalopods.

Trophic niche and diet comparisons among closely sympatric marine species are important to understand complex food webs, particularly in regions most affected by climate change. Using stable isotope analyses, all ontogenetic stages of three sympatric species of Arctic cephalopods (genus Rossia) were studied to assess inter- and intraspecific competition with niche and diet overlap and partitioning in West Greenland and the Barents Sea. Seven traits related to resource and habitat utilization were identified in Rossia: no trait was shared by all three species.

Rational Design of Polyamine-Based Cryogels for Metal Ion Sorption.

Here we report the method of fabrication of supermacroporous monolith sorbents (cryogels) via covalent cross-linking of polyallylamine (PAA) with diglycidyl ether of 1,4-butandiol. Using comparative analysis of the permeability and sorption performance of the obtained PAA cryogels and earlier developed polyethyleneimine (PEI) cryogels, we have demonstrated the advantages and disadvantages of these polymers as sorbents of heavy metal ions (Cu(II), Zn(II), Cd(II), and Ni(II)) in fixed-bed applications and as supermacroporous matrices for the fabrication of composite cryogels containing copper ferrocyanide (CuFCN) for cesium ion sorption. Applying the rate constant distribution (RCD) model to the kinetic curves of Cu(II) ion sorption on PAA and PEI cryogels, we have elucidated the difference in sorption/desorption rates and affinity constants of these materials and showed that physical sorption contributed to the Cu(II) uptake by PAA, but not to that by PEI cryogels.

Extended Rate Constants Distribution (RCD) Model for Sorption in Heterogeneous Systems: 2. Importance of Diffusion Limitations for Sorption Kinetics on Cryogels in Batch.

Here we address the problem of what we can expect from investigations of sorption kinetics on cryogel beads in batch. Does macroporosity of beads indeed help eliminate diffusion limitations under static sorption conditions? Are sorption rate constants calculated using phenomenological kinetic models helpful for predicting sorption properties under dynamic conditions? Applying the rate constants distribution (RCD) model to kinetic curves of Cu(II) ions sorption on polyethyleneimine (PEI) cryogel and gel beads and fines, we have shown that diffusion limitations in highly swollen beads are very important and result in at least ten-fold underestimation of the sorption rate constants. To account for intraparticle diffusion, we have developed the RCD-diffusion model, which yields "intrinsic" kinetic parameters for the sorbents, even if diffusion limitations were important in kinetic experiments.

TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression.

Protein expression in multicellular organisms varies widely across tissues. Codon usage in the transcriptome of each tissue is derived from genomic codon usage and the relative expression level of each gene. We created a comprehensive computational resource that houses tissue-specific codon, codon-pair, and dinucleotide usage data for 51 Homo sapiens tissues (TissueCoCoPUTs: https://hive.

The first global deep-sea stable isotope assessment reveals the unique trophic ecology of Vampire Squid Vampyroteuthis infernalis (Cephalopoda).

Vampyroteuthis infernalis Chun, 1903, is a widely distributed deepwater cephalopod with unique morphology and phylogenetic position. We assessed its habitat and trophic ecology on a global scale via stable isotope analyses of a unique collection of beaks from 104 specimens from the Atlantic, Pacific and Indian Oceans. Cephalopods typically are active predators occupying a high trophic level (TL) and exhibit an ontogenetic increase in δN and TL.

Potato Pathogens in Russia's Regions: An Instrumental Survey with the Use of Real-Time PCR/RT-PCR in Matrix Format.

Viral and bacterial diseases of potato cause significant yield loss worldwide. The current data on the occurrence of these diseases in Russia do not provide comprehensive understanding of the phytosanitary situation. Diagnostic systems based on disposable stationary open qPCR micromatrices intended for the detection of eight viral and seven bacterial/oomycetal potato diseases have been used for wide-scale screening of target pathogens to estimate their occurrence in 11 regions of Russia and to assess suitability of the technology for high-throughput diagnostics under conditions of field laboratories.