Significant variation in the assessment and management of screen-detected colorectal polyp cancers.

Purpose: Endoscopic resection is appropriate for selected colorectal polyp cancers, but significant variation exists in treatment. This study aims to investigate variation in management of screen-detected polyp cancers (T1), factors predicting primary endoscopic polypectomy and threshold for subsequent surgical resection.

Method: Patients with polyp cancers (T1) diagnosed by the bowel cancer screening programme (BCSP) were investigated at two screening centres (5 individual sites and 4 MDTs, 2012-2022).

A matrix-centered view of mass spectrometry platform innovation for volatilome research.

Volatile organic compounds (VOCs) are carbon-containing molecules with high vapor pressure and low water solubility that are released from biotic and abiotic matrices. Because they are in the gaseous phase, these compounds tend to remain undetected when using conventional metabolomic profiling methods. Despite this omission, efforts to profile VOCs can provide useful information related to metabolic status and identify potential signaling pathways or toxicological impacts in natural or engineered environments.

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.

Background: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.

Microfluidics as a Powerful Tool to Investigate Microvascular Dysfunction in Trauma Conditions: A Review of the State-of-the-Art.

Skeletal muscle trauma such as fracture or crush injury can result in a life-threatening condition called acute compartment syndrome (ACS), which involves elevated compartmental pressure within a closed osteo-fascial compartment, leading to collapse of the microvasculature and resulting in necrosis of the tissue due to ischemia. Diagnosis of ACS is complex and controversial due to the lack of standardized objective methods, which results in high rates of misdiagnosis/late diagnosis, leading to permanent neuro-muscular damage. ACS pathophysiology is poorly understood at a cellular level due to the lack of physiologically relevant models.

Disrupted H synthesis combined with methyl viologen treatment inhibits photosynthetic electron flow to synergistically enhance glycogen accumulation in the cyanobacterium Synechocystis sp. PCC 6803.

Under nitrogen deprivation (-N), cyanobacterium Synechocystis sp. PCC 6803 exhibits growth arrest, reduced protein content, and remarkably increased glycogen accumulation. However, producing glycogen under this condition requires a two-step process with cell transfer from normal to -N medium.

3D Bioprinting of Food Grade Hydrogel Infused with Living Mycelium in Non-sterile Conditions.

Mycelium is the root-like network of fungi. Mycelium biocomposites prepared by template replication (molding) can function as environmentally friendly alternatives to conventional polystyrene foams, which are energy- and carbon-intensive to manufacture. Recently, several studies have shown that 3D bioprinting technologies can be used to produce high value functional mycelium products with intricate geometries that are otherwise difficult or impossible to achieve via template replication.

Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease.

Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD.

Constraining the oxygen requirements for modern microbial eukaryote diversity.

Eukaryotes originated prior to the establishment of modern marine oxygen (O) levels. According to the body fossil and lipid biomarker records, modern (crown) microbial eukaryote lineages began diversifying in the ocean no later than ~800 Ma. While it has long been predicted that increasing atmospheric O levels facilitated the early diversification of microbial eukaryotes, the O levels needed to permit this diversification remain unconstrained.

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater.

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant.

Methionine-producing tumor micro(be) environment fuels growth of solid tumors.

Background: Recent studies have uncovered the near-ubiquitous presence of microbes in solid tumors of diverse origins. Previous literature has shown the impact of specific bacterial species on the progression of cancer. We propose that local microbial dysbiosis enables certain cancer phenotypes through provisioning of essential metabolites directly to tumor cells.

A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters.

Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption.

Corrigendum: The survivor strain: Isolation and characterization of AB48, a filamentous phototactic cyanobacterium with biotechnological potential.

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

A Guide to Gene-Centric Analysis Using TreeSAPP.

Gene-centric analysis is commonly used to chart the structure, function, and activity of microbial communities in natural and engineered environments. A common approach is to create custom ad hoc reference marker gene sets, but these come with the typical disadvantages of inaccuracy and limited utility beyond assigning query sequences taxonomic labels. The Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software package standardizes analysis of phylogenetic and functional marker genes and improves predictive performance using a classification algorithm that leverages information-rich reference packages consisting of a multiple sequence alignment, a profile hidden Markov model, taxonomic lineage information, and a phylogenetic tree.

Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment.

We report the genome of Phormidium yuhuli AB48, which includes a circular chromosome and a circular plasmid (4,747,469 bp and 51,599 bp, respectively). This is currently the only closed reference genome of an isolate of the genus, based on the Genome Taxonomy Database (GTDB), providing a potential model system for sustainable biotechnology innovation.

Metagenome-Assembled Genomes for " Phormidium sp. Strain AB48" and Co-occurring Microorganisms from an Industrial Photobioreactor Environment.

Here, we report metagenome-assembled genomes for " Phormidium sp. strain AB48" and three cooccurring microorganisms from a biofilm-forming industrial photobioreactor environment, using the PacBio sequencing platform. Several mobile genetic elements, including a double-stranded DNA phage and plasmids, were also recovered, with the potential to mediate gene transfer within the biofilm community.

Emerging enzyme surface display systems for waste resource recovery.

The current century marks an inflection point for human progress, as the developed world increasingly comes to recognize that the ecological and socioeconomic impacts of resource extraction must be balanced with more sustainable modes of growth that are less reliant on non-renewable sources of energy and materials. This has opened a window of opportunity for cross-sector development of biotechnologies that harness the metabolic problem-solving power of microbial communities. In this context, recovery has emerged as an organizing principal to create value from industrial and municipal waste streams, and the search is on for new enzymes and platforms that can be used for waste resource recovery at scale.

Development of a data science CURE in microbiology using publicly available microbiome datasets.

Scientific and technological advances within the life sciences have enabled the generation of very large datasets that must be processed, stored, and managed computationally. Researchers increasingly require data science skills to work with these datasets at scale in order to convert information into actionable insights, and undergraduate educators have started to adapt pedagogies to fulfill this need. Course-based undergraduate research experiences (CUREs) have emerged as a leading model for providing large numbers of students with authentic research experiences including data science.

The survivor strain: isolation and characterization of AB48, a filamentous phototactic cyanobacterium with biotechnological potential.

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments.

Molecular characterization of colorectal cancer related peritoneal metastatic disease.

A significant proportion of colorectal cancer (CRC) patients develop peritoneal metastases (PM) in the course of their disease. PMs are associated with a poor quality of life, significant morbidity and dismal disease outcome. To improve care for this patient group, a better understanding of the molecular characteristics of CRC-PM is required.

Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis.

Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation.

The nature of gas production patterns associated with methanol degradation in natural aquifer sediments: A microcosm study.

With growing global use of methanol as a fuel additive and extensive use in other industrial processes, there is the potential for unintended release and spills into soils and aquifers. In these subsurface systems it is likely that methanol will be readily biodegraded; however, degradation may lead to the production of by-products, most importantly methane possibly resulting in explosion hazards and volatile fatty acids (VFAs) causing aesthetic issues for groundwater. In this study, the formation of these potentially harmful by-products due to methanol biodegradation was investigated in natural sand and silt sediments using microcosms inoculated with neat methanol (100%) ranging in concentration from 100 to 100,000 ppm.

The Bacteroidetes sp. and Produce Promiscuous Esterases With PET-Hydrolyzing Activity.

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae.

Application of diffusion-weighted whole-body MRI for response monitoring in multiple myeloma after chemotherapy: a systematic review and meta-analysis.

Objective: Myeloma Response Assessment and Diagnosis System recently published provides a framework for the standardised interpretation of DW-WBMRI in response assessment of multiple myeloma (MM) based on expert opinion. However, there is a lack of meta-analysis providing higher-level evidence to support the recommendations. In addition, some disagreement exists in the literature regarding the effect of timing and lesion subtypes on apparent diffusion coefficient (ADC) value changes post-treatment.

Using government documents in open pedagogy: A method for engagement and building skills.

This method utilizes a template for an open pedagogy lesson plan using US government documents that can be applied to academic levels ranging from elementary to post-secondary. This method addresses concerns about OER quality, exposes students to the wealth of information in U.S.