The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, ...sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and validated through PATRICK and TYGS. A FastTree 2 phylogenetic tree was constructed using several type strain sequences from relevant species. Bacteriocin and ribosomally synthesized polypeptide (RiPP) genes were discovered, and a safety check was performed to test for toxins, antibiotic resistance, and genetic drift genes. Except for two products with unclaimed species, the labeling was taxonomically correct. In three product formulations,
Lactobacillus acidophilus, Limosilactobacillus reuteri, Lacticaseibacillus paracasei
, and
Bifidobacterium animalis
exhibited two to three genomic alterations, while
Streptococcus equinus
was found in one. TYGS and GDTB discovered
E. faecium
and
L. paracasei
in distinctly different ways. All the bacteria tested had the genetic repertoire to tolerate GIT transit, although some exhibited antibiotic resistance, and one strain had two virulence genes. Except for
Bifidobacterium
strains, the others revealed a variety of bacteriocins and ribosomally synthesized polypeptides (RiPP), 92% of which were unique and non-homologous to known ones. Plasmids and mobile genetic elements are present in strains of
L. reuteri
(NPLps01.et_L.r and NPLps02.uf_L.r),
Lactobacillus delbrueckii
(NPLps01.et_L.d),
Streptococcus thermophilus
(NPLps06.ab_S.t),
and E. faecium
(NPLps07.nf_E.f). Our findings support the use of metagenomics to build better and efficient production and post-production practices for probiotic quality and safety assessment.
An urgent need exists to better understand the transition from short-term opioid use to unintended prolonged opioid use (UPOU). The purpose of this work is to propose a conceptual framework for ...understanding UPOU that posits the influence of 3 principal domains that include the characteristics of (1) individual patients, (2) the practice environment, and (3) opioid prescribers. Although no standardized method exists for developing a conceptual framework, the process often involves identifying corroborative evidence, leveraging expert opinion to identify factors for inclusion in the framework, and developing a graphic depiction of the relationships between the various factors and the clinical problem of interest. Key patient characteristics potentially associated with UPOU include (1) medical and mental health conditions; (2) pain etiology; (3) individual affective, behavioral, and neurophysiologic reactions to pain and opioids; and (4) sociodemographic factors. Also, UPOU could be influenced by structural and health care policy factors: (1) the practice environment, including the roles of prescribing clinicians, adoption of relevant practice guidelines, and clinician incentives or disincentives, and (2) the regulatory environment. Finally, characteristics inherent to clinicians that could influence prescribing practices include (1) training in pain management and opioid use; (2) personal attitudes, knowledge, and beliefs regarding the risks and benefits of opioids; and (3) professionalism. As the gatekeeper to opioid access, the behavior of prescribing clinicians directly mediates UPOU, with the 3 domains interacting to determine this behavior. This proposed conceptual framework could guide future research on the topic and allow plausible hypothesis-based interventions to reduce UPOU.
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, ...whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the
Tara
Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.
Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These ‘marine plankton’ are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called
Tara
has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence.
To understand the hidden geography of plankton communities in Earth’s oceans, Richter et al. pored over DNA from the
Tara
Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities.
Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography.
The second phase of the Fifth International Ice Nucleation Workshop (FIN-02) involved the gathering of a large number of researchers at the Karlsruhe Institute of Technology's Aerosol Interactions ...and Dynamics of the Atmosphere (AIDA) facility to promote characterization and understanding of ice nucleation measurements made by a variety of methods used worldwide. Compared to the previous workshop in 2007, participation was doubled, reflecting a vibrant research area. Experimental methods involved sampling of aerosol particles by direct processing ice nucleation measuring systems from the same volume of air in separate experiments using different ice nucleating particle (INP) types, and collections of aerosol particle samples onto filters or into liquid for sharing amongst measurement techniques that post-process these samples. In this manner, any errors introduced by differences in generation methods when samples are shared across laboratories were mitigated. Furthermore, as much as possible, aerosol particle size distribution was controlled so that the size limitations of different methods were minimized. The results presented here use data from the workshop to assess the comparability of immersion freezing measurement methods activating INPs in bulk suspensions, methods that activate INPs in condensation and/or immersion freezing modes as single particles on a substrate, continuous flow diffusion chambers (CFDCs) directly sampling and processing particles well above water saturation to maximize immersion and subsequent freezing of aerosol particles, and expansion cloud chamber simulations in which liquid cloud droplets were first activated on aerosol particles prior to freezing. The AIDA expansion chamber measurements are expected to be the closest representation to INP activation in atmospheric cloud parcels in these comparisons, due to exposing particles freely to adiabatic cooling.
Iron is an essential element for nearly all organisms, and under anoxic and/or reducing conditions, Fe2+ is the dominant form of iron available to bacteria. The ferrous iron transport (Feo) system is ...the primary prokaryotic Fe2+ import machinery, and two constituent proteins (FeoA and FeoB) are conserved across most bacterial species. However, how FeoA and FeoB function relative to one another remains enigmatic. In this work, we explored the distribution of feoAB operons encoding a fusion of FeoA tethered to the N-terminal, G-protein domain of FeoB via a connecting linker region. We hypothesized that this fusion poises FeoA to interact with FeoB to affect function. To test this hypothesis, we characterized the soluble NFeoAB fusion protein from Bacteroides fragilis, a commensal organism implicated in drug-resistant infections. Using X-ray crystallography, we determined the 1.50-Å resolution structure of BfFeoA, which adopts an SH3-like fold implicated in protein–protein interactions. Using a combination of structural modeling, small-angle X-ray scattering, and hydrogen–deuterium exchange mass spectrometry, we show that FeoA and NFeoB interact in a nucleotide-dependent manner, and we mapped the protein–protein interaction interface. Finally, using guanosine triphosphate (GTP) hydrolysis assays, we demonstrate that BfNFeoAB exhibits one of the slowest known rates of Feo-mediated GTP hydrolysis that is not potassium-stimulated. Importantly, truncation of FeoA from this fusion demonstrates that FeoA–NFeoB interactions function to stabilize the GTP-bound form of FeoB. Taken together, our work reveals a role for FeoA function in the fused FeoAB system and suggests a function for FeoA among prokaryotes.
Sonoran Desert habitat in southern Arizona is increasingly altered by urban development near metropolitan areas. Understanding how reptiles respond in these impacted habitats is critical to ...conservation efforts to retain intact biotic communities, especially those with a high diversity of reptile species. We surveyed snakes at one impacted site on the northern edge of the Phoenix metropolitan area in desert/urban interface, and at another site in a desert/rural interface near Florence, Arizona. The site near Phoenix was lower in species richness (15 spp.), and evenness: two snake species accounted for 75 % of all snakes encountered (total = 420). The site near Florence was higher in species richness (19 spp.), and a more even community: no species accounted for more than 20 % of snakes encountered (total = 594). Sampling methodology had a strong influence on species richness and abundance of snakes at the respective sites: road riding, coverboards, and traps each provided evidence of unique species missed by other methods. These results were compared with inventories at three other sites in the central Sonoran Desert of Arizona, and are consistent with the view that the impacted site near Phoenix is uneven, potentially as a result of a single species reacting to shifts in prey availability.
Idiopathic Scoliosis Newton, Peter O; Samdani, Amer F; Shufflebarger, Harry L
2021
eBook
The definitive practical reference on managing idiopathic scoliosis from world-renowned experts Idiopathic Scoliosis: The Harms Study Group Treatment Guide, Second Edition, edited by Peter O. Newton, ...Amer F. Samdani, Harry L. Shufflebarger, Randal R. Betz, and Jürgen Harms and written by an impressive group of experts reflects treatment advances made in the last decade. Greater understanding of the etiology and improved 3D anatomy has resulted in significant strides in clinical management of scoliosis. This richly illustrated book presents all facets of evaluation and treatment of abnormal curvature of the spine, supported by a solid foundation of evidence-based data culled from the prestigious Harms Study Group. Divided into four sections and 31 chapters, this one-stop reference encompasses the full spectrum of surgical and nonoperative interventions--from early treatments to modern novel growth modulation techniques. In this second edition, each chapter has been updated and several new ones have been added, reflecting current literature, practice, and expert perspective. Throughout the book, masters share clinical pearls and firsthand knowledge on managing diverse types of adolescent idiopathic spinal deformity, with the common goal of improved patient outcomes. Key Highlights Innovative topics include teamwork and safety in spine surgery, halo traction for large curves, anterior growth modulation, intraoperative neuromonitoring, and kyphosis restoration in scoliosis surgery Surgical chapters follow a consistent layout, encompassing rationales, techniques, and outcomes Postoperative chapters feature discussion of long-term clinical and radiographic outcomes, infections, complications, and rapid post-op recovery A wealth of illustrations enhance the reader's knowledge of specific techniques This comprehensive textbook is essential
reading for orthopaedic and neurosurgical residents, fellows, and researchers. Young spine surgeons embarking on their careers and senior surgeons who wish to remain up-to-date on new techniques for treating adolescent idiopathic scoliosis will also benefit from this illuminating resource.
Fast response measurements of particle size distributions, bulk submicron particle composition, and single particle composition were made aboard the NOAA WP‐3D research aircraft in the free ...troposphere over the eastern Pacific Ocean and the western coast of North America. Measurements of gas‐phase compounds and meteorological analysis show evidence of long‐range transport of layers of aerosol particles from anthropogenic and biomass‐burning sources in eastern Asia. Layers of crustal particles with no evident sources were also encountered. Measurements of substantially enhanced particulate sulfate mass and gas‐phase H2SO4 encountered during one transport event were interpreted with the aid of a numerical model of particle formation and growth and trajectory analysis. The observed particle size distributions and sulfate mass concentration were consistent with the simulation, indicating that the particles were formed over the mid‐Pacific from gas‐to‐particle conversion following long‐range transport of SO2 through a midlatitude cyclonic system. Such cloud systems appear to effectively scavenge most pre‐existing particle mass, but can allow transport of gas‐phase precursors which substantially alter downstream particle microphysical and chemical properties.
Abundant wind‐related features occur along Spirit's traverse into the Columbia Hills over the basaltic plains of Gusev Crater. Most of the windblown sands are probably derived from weathering of ...rocks within the crater, and possibly from deposits associated with Ma'adim Vallis. Windblown particles act as agents of abrasion, forming ventifacts, and are organized in places into various bed forms. Wind‐related features seen from orbit, results from atmospheric models, and considerations of topography suggest that the general wind patterns and transport pathways involve: (1) winter nighttime winds that carry sediments from the mouth of Ma'adim Vallis into the landing site area of Spirit, where they are mixed with locally derived sediments, and (2) winter daytime winds that transport the sediments from the landing site southeast toward Husband Hill; similar patterns occur in the summer but with weaker winds. Reversals of daytime flow out of Gusev Crater and nighttime wind flow into the crater can account for the symmetry of the bed forms and bimodal orientations of some ventifacts.
Purpose We used MAPP data to identify participants with urological chronic pelvic pain syndromes only or a chronic functional nonurological associated somatic syndrome in addition to urological ...chronic pelvic pain syndromes. We characterized these 2 subgroups and explored them using 3 criteria, including 1) MAPP eligibility criteria, 2) self-reported medical history or 3) RICE criteria. Materials and Methods Self-reported cross-sectional data were collected on men and women with urological chronic pelvic pain syndromes, including predominant symptoms, symptom duration and severity, nonurological associated somatic syndrome symptoms and psychosocial factors. Results Of 424 participants with urological chronic pelvic pain syndromes 162 (38%) had a nonurological associated somatic syndrome, including irritable bowel syndrome in 93 (22%), fibromyalgia in 15 (4%), chronic fatigue syndrome in 13 (3%) and multiple syndromes in 41 (10%). Of 233 females 103 (44%) had a nonurological associated somatic syndrome compared to 59 of 191 males (31%) (p = 0.006). Participants with a nonurological associated somatic syndrome had more severe urological symptoms and more frequent depression and anxiety. Of 424 participants 228 (54%) met RICE criteria. Of 228 RICE positive participants 108 (47%) had a nonurological associated somatic syndrome compared to 54 of 203 RICE negative patients (28%) with a nonurological associated somatic syndrome (p <0.001). Conclusions Nonurological associated somatic syndromes represent important clinical characteristics of urological chronic pelvic pain syndromes. Participants with a nonurological associated somatic syndrome have more severe symptoms, longer duration and higher rates of depression and anxiety. RICE positive patients are more likely to have a nonurological associated somatic syndrome and more severe symptoms. Because nonurological associated somatic syndromes are more common in women, future studies must account for this potential confounding factor in urological chronic pelvic pain syndromes.
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