Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions

Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties

Conducting polymer-based multilayer films for instructive biomaterial coatings

Aim: To demonstrate the design, fabrication and testing of conformable conducting biomaterials that encourage cell alignment. Materials & methods: Thin conducting composite biomaterials based on multilayer films of poly (3,4-ethylenedioxythiophene) derivatives, chitosan and gelatin were prepared in a layer-by-layer fashion. Fibroblasts were observed with fluorescence microscopy and their alignment (relative to the dipping direction and direction of electrical current passed through the films) was determined using ImageJ. Results: Fibroblasts adhered to and proliferated on the films. Fibroblasts aligned with the dipping direction used during film preparation and this was enhanced by a DC current. Conclusion: We report the preparation of conducting polymer-based films that enhance the alignment of fibroblasts on their surface which is an important feature of a variety of tissues. Lay abstract: Cells inhabit environments known as the extracellular matrix (ECM) which consists of a mixture of different biomolecules, and the precise composition and topographical properties are different in different tissues (e.g., bone, brain, muscle, skin). Cells interact intimately with the ECM, not only constructing the biomolecules, but assist its organization in 3D space, and its degradation (which is important for tissue remodeling); reciprocally, cells respond to the ECM (e.g., by modifying their size, shape, etc). Cellular alignment is observed in organs and tissues such as bones, muscles and skin, and this alignment is important for the healthy functioning of the organ/tissue. Here, we present a novel method of aligning cells on biomaterials, simply by applying an electrical current through the biomaterial

Multiferroic Magnon Spin-Torque Based Reconfigurable Logic-In-Memory

Magnons, bosonic quasiparticles carrying angular momentum, can flow through insulators for information transmission with minimal power dissipation. However, it remains challenging to develop a magnon-based logic due to the lack of efficient electrical manipulation of magnon transport. Here we present a magnon logic-in-memory device in a spin-source/multiferroic/ferromagnet structure, where multiferroic magnon modes can be electrically excited and controlled. In this device, magnon information is encoded to ferromagnetic bits by the magnon-mediated spin torque. We show that the ferroelectric polarization can electrically modulate the magnon spin-torque by controlling the non-collinear antiferromagnetic structure in multiferroic bismuth ferrite thin films with coupled antiferromagnetic and ferroelectric orders. By manipulating the two coupled non-volatile state variables (ferroelectric polarization and magnetization), we further demonstrate reconfigurable logic-in-memory operations in a single device. Our findings highlight the potential of multiferroics for controlling magnon information transport and offer a pathway towards room-temperature voltage-controlled, low-power, scalable magnonics for in-memory computing

Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

Ketosis is a common metabolic disease during the transition period in dairy cattle, resulting in long-term economic loss to the dairy industry worldwide. While genetic selection of resistance to ketosis has been adopted by many countries, the genetic and biological basis underlying ketosis is poorly understood. We collected a total of 24 blood samples from 12 Holstein cows, including 4 healthy and 8 ketosis-diagnosed ones, before (2 weeks) and after (5 days) calving, respectively. We then generated RNA-Sequencing (RNA-Seq) data and seven blood biochemical indicators (bio-indicators) from leukocytes and plasma in each of these samples, respectively. By employing a weighted gene co-expression network analysis (WGCNA), we detected that 4 out of 16 gene-modules, which were significantly engaged in lipid metabolism and immune responses, were transcriptionally (FDR < 0.05) correlated with postpartum ketosis and several bio-indicators (e.g., high-density lipoprotein and low-density lipoprotein). By conducting genome-wide association signal (GWAS) enrichment analysis among six common health traits (ketosis, mastitis, displaced abomasum, metritis, hypocalcemia and livability), we found that 4 out of 16 modules were genetically (FDR < 0.05) associated with ketosis, among which three were correlated with postpartum ketosis based on WGCNA. We further identified five candidate genes for ketosis, including GRINA, MAF1, MAFA, C14H8orf82 and RECQL4. Our phenome-wide association analysis (Phe-WAS) demonstrated that human orthologues of these candidate genes were also significantly associated with many metabolic, endocrine, and immune traits in humans. For instance, MAFA, which is involved in insulin secretion, glucose response, and transcriptional regulation, showed a significantly higher association with metabolic and endocrine traits compared to other types of traits in humans. In summary, our study provides novel insights into the molecular mechanism underlying ketosis in cattle, and highlights that an integrative analysis of omics data and cross-species mapping are promising for illustrating the genetic architecture underpinning complex traits.https://doi.org/10.1186/s12864-020-06909-

Cambogin Is Preferentially Cytotoxic to Cells Expressing PDGFR

Platelet-derived growth factor receptors (PDGFRs) have been implicated in a wide array of human malignancies, including medulloblastoma (MB), the most common brain tumor of childhood. Although significant progress in MB biology and therapeutics has been achieved during the past decades, MB remains a horrible challenge to the physicians and researchers. Therefore, novel inhibitors targeting PDGFR signaling pathway may offer great promise for the treatment of MB. In the present study, we investigated the cytotoxicity and mechanisms of cambogin in Daoy MB cells. Our results show that cambogin triggers significant S phase cell cycle arrest and apoptosis via down regulation of cyclin A and E, and activation of caspases. More importantly, further mechanistic studies demonstrated that cambogin inhibits PDGFR signaling in Daoy and genetically defined mouse embryo fibroblast (MEF) cell lines. These results suggest that cambogin is preferentially cytotoxic to cells expressing PDGFR. Our findings may provide a novel approach by targeting PDGFR signaling against MB

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Imaging of the Upper Mantle Beneath Southeast Asia: Constrained by Teleseismic P-Wave Tomography

It is of great significance to construct a three-dimensional underground velocity model for the study of geodynamics and tectonic evolution. Southeast Asia has attracted much attention due to its complex structural features. In this paper, we collected relative travel time residuals data for 394 stations distributed in Southeast Asia from 2006 to 2019, and 14,011 seismic events were obtained. Then, teleseismic tomography was applied by using relative travel time residuals data to invert the velocity where the fast marching method (FMM) and subspace method were used for every iteration. A novel 3D P-wave velocity model beneath Southeast Asia down to 720 km was obtained using this approach. The tomographic results suggest that the southeastern Tibetan Plateau, the Philippines, Sumatra, and Java, and the deep part of Borneo exhibit high velocity anomalies, while low velocity anomalies were found in the deep part of the South China Sea (SCS) basin and in the shallow part of Borneo and areas near the subduction zone. High velocity anomalies can be correlated to subduction plates and stable land masses, while low velocity anomalies can be correlated to island arcs and upwelling of mantle material caused by subduction plates. We found a southward subducting high velocity body in the Nansha Trough, which was presumed to be a remnant of the subduction of the Dangerous Grounds into Borneo. It is further inferred that the Nansha Trough and the Dangerous Grounds belong to the same tectonic unit. According to the tomographic images, a high velocity body is located in the deep underground of Indochina&ndash;Natuna Island&ndash;Borneo&ndash;Palawan, depth range from 240 km to 660 km. The location of the high velocity body is consistent with the distribution range of the ophiolite belt, so we speculate that the high velocity body is the remnant of thee Proto-South China Sea (PSCS) and Paleo-Tethys. This paper conjectures that the PSCS was the southern branch of Paleo-Tethys and the gateway between Paleo-Tethys and the Paleo-Pacific Ocean. Due to the squeeze of the Australian plate, PSCS closed from west to east in a scissor style, and was eventually extinct under Borneo

DataSheet1_Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions.docx

Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.</p

Generating a tunable narrow electron beam comb via laser-driven plasma grating

We propose a novel approach for generating a high-density, spatially periodic narrow electron beam comb (EBC) from a plasma grating induced by the interference of two intense laser pulses in subcritical-density plasma. We employ particle-in-cell (PIC) simulations to investigate the effects of cross-propagating laser pulses with specific angles overlapping in a subcritical plasma. This overlap results in the formation of a transverse standing wave, leading to a spatially periodic high-density modulation known as a plasma grating. The electron density peak within the grating can reach several times the background plasma density. The charge imbalance between electrons and ions in the electron density peaks causes mutual repulsion among the electrons, resulting in Coulomb expansion and acceleration of the electrons. As a result, some electrons expand into vacuum, forming a periodic narrow EBC with an individual beam width in the nanoscale range. To further explore the formation of the nanoscale EBC, we conduct additional PIC simulations to study the dependence on various laser parameters. Overall, our proposed method offers a promising and controlled approach to generate tunable narrow EBCs with high density