Diversity of Transcriptional Regulatory Adaptation in E. coli.

The transcriptional regulatory network (TRN) in bacteria is thought to rapidly evolve in response to selection pressures, modulating transcription factor (TF) activities and interactions. In order to probe the limits and mechanisms surrounding the short-term adaptability of the TRN, we generated, evolved, and characterized knockout (KO) strains in Escherichia coli for 11 regulators selected based on measured growth impact on glucose minimal media. All but one knockout strain (Δlrp) were able to recover growth and did so requiring few convergent mutations.

iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.

Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory network function. Here, we introduce a five-step computational pipeline, called iModulonMiner, to compile, process, curate, analyze, and characterize the totality of RNA-seq data for a given organism or cell type. This workflow is centered around the data-driven computation of co-regulated gene sets using Independent Component Analysis, called iModulons, which have been shown to have broad applications.

Enhanced Rock Weathering as a Source of Metals to Promote Methanogenesis and Counteract CO Sequestration.

Enhanced weathering of (ultra)mafic rocks has been proposed as a promising approach to sequester atmospheric CO and mitigate climate change. However, these silicate rocks contain varying amounts of trace metals, which are essential cofactors of metallaenzymes in methanogens. We found that weathering of crushed peridotite and basalt significantly promoted the growth and methanogenesis of a model methanogen─ C2A under the condition of excess substrate.

Edge and dense attention U-net for atrial scar segmentation in LGE-MRI.

The segmentation of atrial scars in LGE-MRI images has huge potential value for clinical diagnosis and subsequent treatment. In clinical practice, atrial scars are usually manually calibrated by experienced experts, which is time-consuming and prone to errors. However, automatic segmentation also faces difficulties due to myocardial scars' small size and variable shape.

MXene-based composite aerogels with bifunctional ferrous ions for the efficient degradation of phenol from wastewater.

Herein, MXene-based composite aerogel (MXene-Fe aerogel) are constructed by a one-step freeze-drying method, using TiCT MXene layers as substrate material and ferrous ion (Fe) as crosslinking agent. With the aid of the Fe induced Fenton reaction, the synthesized aerogels are used as the particle electrodes to remove phenol from wastewater with three-dimensional electrode technology. Combined with the dual roles of Fe and the highly conductive MXene, the obtained particle electrode possesses extremely effective phenol degradation.

Bio-based P-N flame retardant with ZIF-67 in-situ growth on flexible polyurethane foam with excellent fire safety performance.

The wide application of flexible polyurethane foam (FPUF) poses a giant challenge to human society in terms of fire prevention and environmental pollution. To solve this problem, the lignocellulose-based P-N flame retardant (LFPN) has been developed using mechanochemical methods. It was found that FPUF treated using LFPN exhibited good flame retardancy, but suffered from high smoke generation and toxicity.

Monolithic thin-film lithium niobate broadband spectrometer with one nanometre resolution.

Miniaturised optical spectrometers are attractive due to their small footprint, low weight, robustness and stability even in harsh environments such as space or industrial facilities. We report on a stationary-wave integrated Fourier-transform spectrometer featuring a measured optical bandwidth of 325 nm and a theoretical spectral resolution of 1.2 nm.

Reconstructing the transcriptional regulatory network of probiotic is enabled by transcriptomics and machine learning.

Unlabelled: , a probiotic microbe instrumental to human health and sustainable food production, adapts to diverse environmental shifts via dynamic gene expression. We applied the independent component analysis (ICA) to 117 RNA-seq data sets to decode its transcriptional regulatory network (TRN), identifying 35 distinct signals that modulate specific gene sets. Our findings indicate that the ICA provides a qualitative advancement and captures nuanced relationships within gene clusters that other methods may miss.

Splicing Factor PQBP1 Curtails BAX Expression to Promote Ovarian Cancer Progression.

Splicing factor polyglutamine binding protein-1 (PQBP1) is abundantly expressed in the central nervous system during development, and mutations in the gene cause intellectual disability. However, the roles of PQBP1 in cancer progression remain largely unknown. Here, it is shown that PQBP1 overexpression promotes tumor progression and indicates worse prognosis in ovarian cancer.

HSPA12A was identified as a key driver in colorectal cancer GWAS loci 10q26.12 and modulated by an enhancer-promoter interaction.

Although genome-wide association studies (GWASs) have identified over 100 colorectal cancer (CRC) risk loci, an understanding of causal genes or risk variants and their biological functions in these loci remain unclear. Recently, genomic loci 10q26.12 with lead SNP rs1665650 was identified as an essential CRC risk loci of Asian populations.

Saturated fatty acid intake, genetic risk and colorectal cancer incidence: A large-scale prospective cohort study.

Previous investigations mainly focused on the associations of dietary fatty acids with colorectal cancer (CRC) risk, which ignored gene-environment interaction and mechanisms interpretation. We conducted a case-control study (751 cases and 3058 controls) and a prospective cohort study (125 021 participants) to explore the associations between dietary fatty acids, genetic risks, and CRC. Results showed that high intake of saturated fatty acid (SFA) was associated with a higher risk of CRC than low SFA intake (HR =1.

A critical review of mineral-microbe interaction and co-evolution: mechanisms and applications.

Mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation and precipitation of minerals through their activity, resulting in either genetically controlled or metabolism-induced biomineralization.

sp. ., a New Petroleum-Degrading Bacteria Isolated from Oily Soils.

The microbial remediation technology had great potential and attracted attention to total petroleum hydrocarbon pollution (TPH) remediation, but its efficiency is limited by its application in the field. In this study, a new TPH-degrading strain, TDYN1, was isolated from contaminated oil soil in Dagang Oilfield in Tianjin, China, and identified as sp. by 16S rRNA sequence analysis.

Cr(VI) Reduction by Siderophore Alone and in Combination with Reduced Clay Minerals.

Siderophores and iron-containing clays are known to influence the transformation of chromium in the environment. The role of clays in hexavalent chromium [Cr(VI)] reduction has been reported extensively. However, the mechanisms of Cr(VI) reduction by siderophores and their combination with iron-bearing clays are poorly known.

Fungi and Archaea Control Soil NO Production Potential in Chinese Grasslands Rather Than Bacteria.

Nitrous oxide (NO) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of NO but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial NO production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe.

Oxidative degradation of commingled trichloroethylene and 1,4-dioxane by hydroxyl radicals produced upon oxygenation of a reduced clay mineral.

Improper disposal of chlorinated solvents such as trichloroethylene (TCE) and its stabilizer 1,4-dioxane has resulted in extensive contamination in soils and groundwater. Oxidative degradation of these contaminants by strong oxidants has been proposed recently as a remediation strategy, but specific mechanisms and degradation efficiencies are still poorly understood, especially in commingled systems. In this study, a reduced iron-bearing clay (RIC), nontronite (rNAu-2), was oxygenated to produce hydroxyl radicals (•OH) for degradation of TCE and 1,4-dioxane under circumneutral and dark conditions.

[Advances in bioremediation of hydrocarbon-contaminated soil].

With continuous improvement of people's living standards, great efforts have been paid to environmental protection. Among those environmental issues, soil contamination by petroleum hydrocarbons has received widespread concerns due to the persistence and the degradation difficulty of the pollutants. Among the various remediation technologies, in-situ microbial remediation enhancement technologies have become the current hotspot because of its low cost, environmental friendliness, and in-situ availability.

Distribution of MITE family Monkey King in rapeseed (Brassica napus L) and its influence on gene expression.

Miniature inverted-repeat transposable elements (MITEs) are a group of class II transposable elements. The MITE Monkey King (MK) was first discovered upstream of BnFLC.A10.

An Extreme Energy-Saving Carbohydrazide Oxidization Reaction Directly Driven by Commercial Graphite Paper in Alkali and Near-Neutral Seawater Electrolytes.

The energy-saving anode with low oxidization potential has been an intriguing pursue for earth-abundant seawater electrolysis. In this paper, we first introduced a superior energy-saving carbohydrazide oxidization reaction catalysis system in the anode section, which can be driven by commercial graphite paper with good durability. Combining this catalysis reaction and common graphite paper, the lowest anodic potentials 0.

High-Q titanium dioxide micro-ring resonators for integrated nonlinear photonics.

We report on the nonlinear characterizations of the titanium dioxide micro-ring resonators (TiO MRRs). By utilizing optimized fabrication processes, high quality factors (Q∼1.4 × 10) doubling that of the previous work are achieved here for TiO MRRs with high-confinement TiO waveguides.

TiO microring resonators with high Q and compact footprint fabricated by a bottom-up method.

Titanium dioxide () microring resonators (MRRs) with high quality factors (Qs) are demonstrated by using a new, to the best of our knowledge, bottom-up fabrication method. Pattern platforms with a T-shaped cross section are first defined by etching a thin top layer of silicon nitride and a thick bottom layer of silica and partially undercutting the silica. Then, is deposited on the platforms to form the waveguides and devices.