A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series

The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data.

Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes

The rapid emergence of SARS-CoV-2 variants is fueling the recent waves of the COVID-19 pandemic. Here, we assessed ACE2 binding and antigenicity of Mu (B.1.621) and A.2.5 Spikes. Both these variants carry some mutations shared by other emerging variants. Some of the pivotal mutations such as N501Y and E484K in the receptor-binding domain (RBD) detected in B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) are now present within the Mu variant. Similarly, the L452R mutation of B.1.617.2 (Delta) variant is present in A.2.5. In this study, we observed that these Spike variants bound better to the ACE2 receptor in a temperature-dependent manner. Pseudoviral particles bearing the Spike of Mu were similarly neutralized by plasma from vaccinated individuals than those carrying the Beta (B.1.351) and Delta (B.1.617.2) Spikes. Altogether, our results indicate the importance of measuring critical parameters such as ACE2 interaction, plasma recognition and neutralization ability of each emerging variant.

Review on Methylene Blue: Its Properties, Uses, Toxicity and Photodegradation

The unavailability of clean drinking water is one of the significant health issues in modern times. Industrial dyes are one of the dominant chemicals that make water unfit for drinking. Among these dyes, methylene blue (MB) is toxic, carcinogenic, and non-biodegradable and can cause a severe threat to human health and environmental safety. It is usually released in natural water sources, which becomes a health threat to human beings and living organisms. Hence, there is a need to develop an environmentally friendly, efficient technology for removing MB from wastewater. Photodegradation is an advanced oxidation process widely used for MB removal. It has the advantages of complete mineralization of dye into simple and nontoxic species with the potential to decrease the processing cost. This review provides a tutorial basis for the readers working in the dye degradation research area. We not only covered the basic principles of the process but also provided a wide range of previously published work on advanced photocatalytic systems (single-component and multi-component photocatalysts). Our study has focused on critical parameters that can affect the photodegradation rate of MB, such as photocatalyst type and loading, irradiation reaction time, pH of reaction media, initial concentration of dye, radical scavengers and oxidising agents. The photodegradation mechanism, reaction pathways, intermediate products, and final products of MB are also summarized. An overview of the future perspectives to utilize MB at an industrial scale is also provided. This paper identifies strategies for the development of effective MB photodegradation systems.

State of the Art of Genetic Engineering in Potato: From the First Report to Its Future Potential

Potato (Solanum tuberosum L.) is a crop of world importance that produces tubers of high nutritional quality. It is considered one of the promising crops to overcome the challenges of poverty and hunger worldwide. However, it is exposed to different biotic and abiotic stresses that can cause significant losses in production. Thus, potato is a candidate of special relevance for improvements through conventional breeding and biotechnology. Since conventional breeding is time-consuming and challenging, genetic engineering provides the opportunity to introduce/switch-off genes of interest without altering the allelic combination that characterize successful commercial cultivars or to induce targeted sequence modifications by New Breeding Techniques. There is a variety of methods for potato improvement via genetic transformation. Most of them incorporate genes of interest into the nuclear genome; nevertheless, the development of plastid transformation protocols broadened the available approaches for potato breeding. Although all methods have their advantages and disadvantages, Agrobacterium-mediated transformation is the most used approach. Alternative methods such as particle bombardment, protoplast transfection with polyethylene glycol and microinjection are also effective. Independently of the DNA delivery approach, critical steps for a successful transformation are a rapid and efficient regeneration protocol and a selection system. Several critical factors affect the transformation efficiency: vector type, insert size, Agrobacterium strain, explant type, composition of the subculture media, selective agent, among others. Moreover, transient or stable transformation, constitutive or inducible promoters, antibiotic/herbicide resistance or marker-free strategies can be considered. Although great efforts have been made to optimize all the parameters, potato transformation protocols are highly genotype-dependent. Genome editing technologies provide promising tools in genetic engineering allowing precise modification of targeted sequences. Interestingly, transient expression of genome editing components in potato protoplasts was reported to generate edited plants without the integration of any foreign DNA, which is a valuable aspect from both a scientific and a regulatory perspective. In this review, current challenges and opportunities concerning potato genetic engineering strategies developed to date are discussed. We describe their critical parameters and constrains, and the potential application of the available tools for functional analyses or biotechnological purposes. Public concerns and safety issues are also addressed.

The Evolution of Preseismic Patterns Related to the Central Crete (Mw6.0) Strong Earthquake on 27 September 2021 Revealed by Multiresolution Wavelets and Natural Time Analysis

On 27 September 2021, a shallow earthquake with focal depth of 10 km and moment magnitude Mw6.0 occurred onshore in central Crete (Greece). The evolution of possible preseismic patterns in the area of central Crete before the Mw6.0 event was investigated by applying the method of multiresolution wavelet analysis (MRWA), along with that of natural time (NT). The monitoring of preseismic patterns by critical parameters defined by NT analysis, integrated with the results of MRWA as the initiation point for the NT analysis, forms a promising framework that may lead to new universal principles that describe the evolution patterns before strong earthquakes. Initially, we apply MRWA to the interevent time series of the successive regional earthquakes in order to investigate the approach of the regional seismicity towards critical stages and to define the starting point of the natural time domain. Then, using the results of MRWA, we apply the NT analysis, showing that the regional seismicity approached criticality for a prolonged period of ~40 days before the occurrence of the Mw6.0 earthquake, when the κ1 natural time parameter reached the critical value of κ1 = 0.070, as suggested by the NT method.

Light sheet based volume flow cytometry (VFC) for rapid volume reconstruction and parameter estimation on the go

Optical imaging is paramount for disease diagnosis and to access its progression over time. The proposed optical flow imaging (VFC/iLIFE) is a powerful technique that adds new capabilities (3D volume visualization, organelle-level resolution, and multi-organelle screening) to the existing system. Unlike state-of-the-art point-illumination-based biomedical imaging techniques, the sheet-based VFC technique is capable of single-shot sectional visualization, high throughput interrogation, real-time parameter estimation, and instant volume reconstruction with organelle-level resolution of live specimens. The specimen flow system was realized on a multichannel (Y-type) microfluidic chip that enables visualization of organelle distribution in several cells in-parallel at a relatively high flow-rate (2000 nl/min). The calibration of VFC system requires the study of point emitters (fluorescent beads) at physiologically relevant flow-rates (500–2000 nl/min) for determining flow-induced optical aberration in the system point spread function (PSF). Subsequently, the recorded raw images and volumes were computationally deconvolved with flow-variant PSF to reconstruct the cell volume. High throughput investigation of the mitochondrial network in HeLa cancer cell was carried out at sub-cellular resolution in real-time and critical parameters (mitochondria count and size distribution, morphology, entropy, and cell strain statistics) were determined on-the-go. These parameters determine the physiological state of cells, and the changes over-time, revealing the metastatic progression of diseases. Overall, the developed VFC system enables real-time monitoring of sub-cellular organelle organization at a high-throughput with high-content capacity.

Understanding gluten-free bread ingredients during ohmic heating: function, effect and potential application for breadmaking

Due to the absence of gluten, several challenges arise during gluten-free (GF) bread baking, affecting the mid-and-end-product quality. The main approach to overcome this issue is to combine certain functional ingredients and additives, to partially simulate wheat bread properties. In addition, the optimization of the baking process may contribute to improved product quality. A recent and very promising alternative to conventional baking is the use of ohmic heating (OH). Due to its volumetric and uniform heating principle, crumb development during baking and consequently bread volume is improved, which enhances the overall GF bread quality. Depending on the GF formulation, critical factors such as the electrical conductivity and viscosity of the batter may vary, which have a significant effect on the OH process performance. Therefore, this review attempts to provide a deeper understanding of the functionality of GF bread ingredients and how these may affect critical parameters during the OH processing.

Integrating Soft Hydrogel with Nanostructures Reinforces Stem Cell Adhesion and Differentiation

Biophysical cues can regulate stem cell behaviours and have been considered as critical parameters of synthetic biomaterials for tissue engineering. In particular, hydrogels have been utilized as promising biomimetic and biocompatible materials to emulate the microenvironment. Therefore, well-defined mechanical properties of a hydrogel are important to direct desirable phenotypes of cells. Yet, limited research pays attention to engineering soft hydrogel with improved cell adhesive property, which is crucial for stem cell differentiation. Herein, we introduce silica nanoparticles (SiO2 NPs) onto the surface of methacrylated hyaluronic (MeHA) hydrogel to manipulate the presentation of cell adhesive ligands (RGD) clusters, while remaining similar bulk mechanical properties (2.79 ± 0.31 kPa) to that of MeHA hydrogel (3.08 ± 0.68 kPa). RGD peptides are either randomly decorated in the MeHA hydrogel network or on the immobilized SiO2 NPs (forming MeHA–SiO2). Our results showed that human mesenchymal stem cells exhibited a ~1.3-fold increase in the percentage of initial cell attachment, a ~2-fold increase in cell spreading area, and enhanced expressions of early-stage osteogenic markers (RUNX2 and alkaline phosphatase) for cells undergoing osteogenic differentiation with the osteogenic medium on MeHA–SiO2 hydrogel, compared to those cultured on MeHA hydrogel. Importantly, the cells cultivated on MeHA–SiO2 expressed a ~5-fold increase in nuclear localization ratio of the yes-associated protein, which is known to be mechanosensory in stem cells, compared to the cells cultured on MeHA hydrogel, thereby promoting osteogenic differentiation of stem cells. These findings demonstrate the potential use of nanomaterials into a soft polymeric matrix for enhanced cell adhesion and provide valuable guidance for the rational design of biomaterials for implantation.