Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering.

Development of medicines using gene editing has been hampered by enzymological and immunological impediments. We described previously the discovery and characterization of improved, novel gene-editing systems from metagenomic data. In this study, we substantially advance this work with three such gene-editing systems, demonstrating their utility for cell therapy development.

Endoplasmic Reticulum Stress-Regulated Chaperones as a Serum Biomarker Panel for Parkinson's Disease.

Examination of post-mortem brain tissues has previously revealed a strong association between Parkinson's disease (PD) pathophysiology and endoplasmic reticulum (ER) stress. Evidence in the literature regarding the circulation of ER stress-regulated factors released from neurons provides a rationale for investigating ER stress biomarkers in the blood to aid diagnosis of PD. The levels of ER stress-regulated proteins in serum collected from 29 PD patients and 24 non-PD controls were measured using enzyme-linked immunosorbent assays.

Antibiotic resistance genes are differentially mobilized according to resistance mechanism.

Background: Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualization of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids, which may contribute to high expression of accessory genes.

A protease-mediated switch regulates the growth of magnetosome organelles in .

Magnetosomes are lipid-bound organelles that direct the biomineralization of magnetic nanoparticles in magnetotactic bacteria. Magnetosome membranes are not uniform in size and can grow in a biomineralization-dependent manner. However, the underlying mechanisms of magnetosome membrane growth regulation remain unclear.

Engraftment of strictly anaerobic oxygen-sensitive bacteria in irritable bowel syndrome patients following fecal microbiota transplantation does not improve symptoms.

Dysbiosis of the gut microbiome has been correlated with irritable bowel syndrome (IBS). Fecal microbiota transplantation (FMT) is being explored as a therapeutic option. Little is known of the mechanisms of engraftment of microbes following FMT and whether the engraftment of certain microbes correlate with clinical improvement in IBS.

The effect of faecal microbiota transplantation on abdominal pain, stool frequency, and stool form in patients with moderate-to-severe irritable bowel syndrome: results from a randomised, double-blind, placebo-controlled study.

Background: Irritable bowel syndrome (IBS) is associated with intestinal dysbiosis. Therefore, faecal microbiota transplantation (FMT) has been hypothesised to have a positive effect in patients with IBS. In this study, we analysed previously unexamined data from our randomised, double-blind, placebo-controlled study (trial registration number NCT02788071).

An improved direct metamobilome approach increases the detection of larger-sized circular elements across kingdoms.

Mobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate genetic diversity. MGEs serve as a vast communal gene pool and include DNA elements such as plasmids and bacteriophages (phages) among others. These mobile DNA elements represent a human health risk as they can introduce new traits, such as antibiotic resistance or virulence, to a bacterial strain.

Applicability and tolerability of electrical stimulation applied to the upper and lower leg skin surface for cueing applications in Parkinson's disease.

Due to possible sensory impairments in people with Parkinson's disease, several methodological aspects of electrical stimulation as a potential cueing method remain to be explored. This study aimed to investigate the applicability and tolerability of sensory and motor electrical stimulation in 10 people with Parkinson's disease. The study focused on assessing the electrical stimulation voltages and visual analogue scale discomfort scores at the electrical sensory, motor, discomfort, and pain thresholds.

Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina.

Soil microbiomes, as a primary reservoir for plant colonizing fungi and bacteria, play a major role in determining plant productivity and preventing invasion by pathogenic microorganisms. The use of 16S rRNA and ITS high-throughput amplicon sequencing for analysis of complex microbial communities have increased dramatically in recent years, establishing links between wine specificity and, environmental and viticultural factors, which are framed into the elusive terroir concept. Given the diverse and complex role these factors play on microbial soil structuring of agricultural crops, the main aim of this study is to evaluate how external factors, such as vintage, vineyard location, cultivar and soil characteristics, may affect the diversity of the microbial communities present.

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms.

Background: Metagenomic sequencing is a well-established tool in the modern biosciences. While it promises unparalleled insights into the genetic content of the biological samples studied, conclusions drawn are at risk from biases inherent to the DNA sequencing methods, including inaccurate abundance estimates as a function of genomic guanine-cytosine (GC) contents.

Results: We explored such GC biases across many commonly used platforms in experiments sequencing multiple genomes (with mean GC contents ranging from 28.

The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.

Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation.

The Whole Genome Sequence and mRNA Transcriptome of the Tropical Cyclopoid Copepod .

Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc.

The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution.

Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only six copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content, and small animal size.

A Technological Review of Wearable Cueing Devices Addressing Freezing of Gait in Parkinson's Disease.

Freezing of gait is one of the most debilitating symptoms of Parkinson's disease and is an important contributor to falls, leading to it being a major cause of hospitalization and nursing home admissions. When the management of freezing episodes cannot be achieved through medication or surgery, non-pharmacological methods such as cueing have received attention in recent years. Novel cueing systems were developed over the last decade and have been evaluated predominantly in laboratory settings.

Drastic Change in Zinc Speciation during Anaerobic Digestion and Composting: Instability of Nanosized Zinc Sulfide.

Zinc (Zn) is a potentially toxic trace element that is present in large amounts in organic wastes (OWs) spread on agricultural lands as fertilizer. Zn speciation in OW is a crucial parameter to understand its fate in soil after spreading and to assess the risk associated with agricultural recycling of OW. Here, we investigated changes in Zn speciation from raw OWs up to digestates and/or composts for a large series of organic wastes sampled in full-scale plants.

Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study.

Objective: IBS is associated with an intestinal dysbiosis and faecal microbiota transplantation (FMT) has been hypothesised to have a positive effect in patients with IBS. We performed a randomised, double-blind placebo-controlled trial to investigate if FMT resulted in an altered gut microbiota and improvement in clinical outcome in patients with IBS.

Design: We performed this study in 52 adult patients with moderate-to-severe IBS.

Corrigendum: Analysis of Correlation between an Accelerometer-Based Algorithm for Detecting Parkinsonian Gait and UPDRS Subscales.

[This corrects the article on p. 431 in vol. 8, PMID: 28919877.

The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages.

This study describes the first molecular characterization of a bacteriophage infecting a member of the environmentally important Sphingomonadaceae family. Both bacteriophage Lacusarx and its host Sphingobium sp. IP1 were isolated from activated sludge from a wastewater treatment plant.

A "HOLTER" for Parkinson's disease: Validation of the ability to detect on-off states using the REMPARK system.

Unlabelled: The treatment of Parkinson's disease (PD) with levodopa is very effective. However, over time, motor complications (MCs) appear, restricting the patient from leading a normal life. One of the most disabling MCs is ON-OFF fluctuations.

Atmospheric contribution to boron enrichment in aboveground wheat tissues.

Boron is an essential trace element for all organisms and has both beneficial and harmful biological functions. A particular amount of boron is discharged into the environment every year because of industrial activities; however, the effects of environmental boron emissions on boron accumulation in cereals has not yet been estimated. The present study characterized the accumulation of boron in wheat under different ecological conditions in the Yangtze River Delta (YRD) area.

Home detection of freezing of gait using support vector machines through a single waist-worn triaxial accelerometer.

Among Parkinson's disease (PD) symptoms, freezing of gait (FoG) is one of the most debilitating. To assess FoG, current clinical practice mostly employs repeated evaluations over weeks and months based on questionnaires, which may not accurately map the severity of this symptom. The use of a non-invasive system to monitor the activities of daily living (ADL) and the PD symptoms experienced by patients throughout the day could provide a more accurate and objective evaluation of FoG in order to better understand the evolution of the disease and allow for a more informed decision-making process in making adjustments to the patient's treatment plan.

Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments.

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H-CO utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats.