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

Two-Dimensional Titanium and Molybdenum Carbide MXenes as Electrocatalysts for CO2 Reduction

Electrocatalytic CO2 reduction reaction (CO2RR) is an attractive way to produce renewable fuel and chemical feedstock, especially when coupled with efficient CO2 capture and clean energy sources. On the fundamental side, research on improving CO2RR activity still revolves around late transition metal-based catalysts, which are limited by unfavorable scaling relations despite intense investigation. Here, we report a combined experimental and theoretical investigation into electrocatalytic CO2RR on Ti- and Mo-based MXene catalysts. Formic acid is found as the main product on Ti2CTx and Mo2CTx MXenes, with peak Faradaic efficiency of over 56% on Ti2CTx and partial current density of up to −2.5 mA cm−2 on Mo2CTx. Furthermore, simulations reveal the critical role of the Tx group: a smaller overpotential is found to occur at lower amounts of –F termination. This work represents an important step toward experimental demonstration of MXenes for more complex electrocatalytic reactions in the future

Genome Editing of Pik3cd Impedes Abnormal Retinal Angiogenesis

Abnormal angiogenesis is associated with myriad human diseases including proliferative diabetic retinopathy. Signaling transduction via phosphoinositide 3-kinases (PI3Ks) plays a critical role in angiogenesis. Herein, we showed that p110δ, the catalytic subunit of PI3Kδ, was highly expressed in pathological retinal vascular endothelial cells (ECs) in a mouse model of oxygen-induced retinopathy (OIR) and in fibrovascular membranes from patients with proliferative diabetic retinopathy. To explore novel intervention with PI3Kδ expression, we developed a recombinant dual adeno-associated viral (rAAV) system for delivering CRISPR/Cas9 in which Streptococcus pyogenes (Sp) Cas9 expression was driven by an endothelial specific promoter of intercellular adhesion molecule 2 (pICAM2) to edit genomic Pik3cd, the gene encoding p110δ. We then demonstrated that infection of cultured mouse vascular endothelial cells with the dual rAAV1s of rAAV1-pICAM2-SpCas9 and rAAV1-SpGuide targeting genomic Pik3cd resulted in 80% DNA insertion/deletion in the locus of genomic Pik3cd and 70% depletion of p110δ expression. Furthermore, we showed that in the mouse model of OIR editing retinal Pik3cd with the dual rAAV1s resulted in not only a significant decrease in p110δ expression, and Akt activation, but also a dramatic reduction in pathological retinal angiogenesis. These findings reveal that Pik3cd editing is a novel approach to treating abnormal retinal angiogenesis

Correction to: Genome Editing of Pik3cd Impedes Abnormal Retinal Angiogenesis, by Wu et al. Hum Gene Ther 2023;34(1-2):30-41; doi: 10.1089/hum.2022.079

In the January 2023 issue of Human Gene Therapy (vol. 34, no. 1-2; 30–41), the article titled Genome Editing of Pik3cd Impedes Abnormal Retinal Angiogenesis, by Wu et al. requires correction. The author byline originally appeared with the 13th author's name incorrectly published as GuomingZhao Wenyi Wu,1,2,3 Gaoen Ma,4 Hui Qi,5 Lijun Dong,5 Fang Chen,6 Yun Wang,5 Xingxing Mao,5 Xiaoqing Guo,2,3 Jing Cui,7 Joanne Aiko Matsubara,7 Bart Vanhaesebroeck,8 Xiaohe Yan,5Guoming Zhao,5 Shaochong Zhang,5,* and Hetian Lei 5,* The correct spelling of the author's name is GuomingZhang The online version of the article has been corrected to reflect this. The authors apologize for the error

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-

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

Using existing buildings as material banks in the UK

Although the practice of Building As Material Banks (BAMB) is gaining momentum, it remains in its nascent stages compared to recycling or retrofitting. Existing knowledge either pertains to broader circular economy topics or lacks focus on the UK-built environment. Given the dynamic nature of the subject, with new guidelines emerging rapidly, it is crucial to comprehend the lack of actions in BAMB even with its economic and social benefits. This paper presents insights obtained through interviews with nine UK circular economy experts from diverse stakeholder roles, including architects, clients, stockists etc. Utilising both quantitative and qualitative analysis methods, the research sheds light on both the hierarchy of urgency for barriers and suggestions as well as the current practice for reuse. Despite cost barriers being identified as a primary obstacle, most participants exhibited a positive outlook towards the current progress, indicating a growing interest in reuse. The study emphasises the need for effective legislation and inter-stakeholder collaboration in promoting BAMB adoption. Furthermore, the interviewer’s sentiments underscore the significance of swift action in overcoming psychological barriers such as risk and unfamiliarity with BAMB practices

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

Moisture content-affected electrokinetic remediation of Cr(VI)-contaminated clay by a hydrocalumite barrier

An electrokinetic–permeable reaction barrier (EKPRB) system was introduced in this study with hydrocalumite as the barrier material. The combined system effectively remediated the Cr(VI)-contaminated clay after a 72-h treatment, and the Cr(VI) removal efficiency increased with the initial soil moisture content. Further evidence was found that the changing soil pH value and current density were highly associated with the initial moisture content, showing its important roles in the Cr(VI) removal process. Additionally, the total Cr removal efficiency was much lower than that of Cr(VI) owing to the partial conversion of Cr(VI) to Cr(III) in the electrokinetic remediation process. Under high soil moisture conditions (40 %), the removal efficiency of Cr(VI) and total Cr was 96.6 and 67.3 %, respectively. Further analysis also revealed the new mineral phase, chromate hydrocalumite, for Cr fixation in the hydrocalumite barrier, which was significantly affected by the initial soil moisture content. Our results showed that the EK-PRB system with a hydrocalumite barrier is highly promising with great potential for the effective remediation of Cr(VI)-contaminated clay and engineering implementation