scholarly journals Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alberto Pascual-García
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Environmental Conditions ◽  
The Novel ◽  
Methodological Framework ◽  
Operational Taxonomic Units ◽  
Traditional Classification ◽  
Taxonomical Classification ◽  
Novel Concept

AbstractIn this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology.

scholarly journals Subsynaptic positioning of AMPARs by LRRTM2 controls synaptic strength

2021 ◽  
Author(s):  
A.M. Ramsey ◽  
A.H. Tang ◽  
T.A. LeGates ◽  
X.Z. Gou ◽  
B.E. Carbone ◽  
...  
Keyword(s):  
Adhesion Molecule ◽  
Ampa Receptors ◽  
Glutamate Release ◽  
Receptor Activation ◽  
Synaptic Strength ◽  
Synaptic Function ◽  
The Novel ◽  
Novel Concept ◽  
The Brain

AbstractRecent evidence suggests that nanoorganization of proteins within synapses may control the strength of communication between neurons in the brain. The unique subsynaptic distribution of glutamate receptors, which cluster in nanoalignment with presynaptic sites of glutamate release, supports this idea. However, testing it has been difficult because mechanisms controlling subsynaptic organization remain unknown. Reasoning that transcellular interactions could position AMPA receptors, we targeted a key transsynaptic adhesion molecule implicated in controlling AMPAR number, LRRTM2, using engineered, rapid proteolysis. Severing the LRRTM2 extracellular domain led quickly to nanoscale de-clustering of AMPARs away from release sites, not prompting their escape from synapses until much later. This rapid remodeling of AMPAR position produced significant deficits in evoked, but not spontaneous, postsynaptic receptor activation. These results dissociate receptor numbers from their nanopositioning in determination of synaptic function, and support the novel concept that adhesion molecules acutely position AMPA receptors to dynamically control synaptic strength.

scholarly journals Comparison of microbiome and culture techniques for determination of gastrointestinal microbial communities in ceca of chickens

2018 ◽  
Author(s):  
Kimberly Wilson ◽  
Whitney Briggs ◽  
Audrey Duff ◽  
Chasser Kaylin ◽  
Xialoun Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Illumina Miseq ◽  
Intestinal Microbiome ◽  
P Value ◽  
Culture Techniques ◽  
Operational Taxonomic Units ◽  
Colony Forming Units ◽  
Miseq Platform ◽  
Next Generation Sequencing Ngs

The use of 16S next generation sequencing (NGS) technology to identify the relative abundance of microbial communities have become the standard when studying the intestinal microbiome. The increased use is due to the ability to identify a proportion of bacteria that cannot be observed with culture-based methods. However, culture-based techniques are acceptable to identify key bacterial groups, yet may grossly underestimate the microbial community in question. Since there is limited research comparing NGS results to colony forming units (CFU), the objective of this study was to compare total Enterobacteriaceae and lactic acid bacteria (LAB) recovery with culture techniques (CFU/g ceca) to total number of reads from operational taxonomic units (OTU) categorized as Enterobacteriaceae or LAB from Illumina MiSeq platform from matched chick cecal samples at three and 10 days of age. Both CFU recovery (1.09x109 ± 2.42x108; 1.37x108 ± 5.57x107) and reads (5460 ± 1164 ; 282 ± 163) belonging to Enterobacteriaceae decreased by 10 days of age (p < 0.001). Similarly, LAB reads decreased over time (21,128 ± 2262; 6220 ± 817, respectively p < 0.0001). However, LAB CFU recovery increased by 10 days (1.18x108 ± 1.91x107; 1.62x109 ± 5.00x108, respectively p < 0.01). At three days the Pearson’s correlation was -0.082 between CFU of culturable Enterobacteriaceae to reads and culturable LAB CFU to reads at 0.097, showing no correlation (p = 0.606, 0.551; respectively). By 10 days, no correlation of reads and CFU occurred with Enterobacteriaceae (r=-0.049; p-value = 0.769) while with LAB the correlation was 0.290 (p = 0.066) at 10 days. The CFU may be appropriate to identify a few families that change due to treatment or product. Without identifying viable cells to DNA recovered from NGS, there will always be the question whether the reads within the binned OTU in the intestinal tract is accurate.

scholarly journals Subsynaptic positioning of AMPARs by LRRTM2 controls synaptic strength

2021 ◽  
Vol 7 (34) ◽  
pp. eabf3126
Author(s):  
Austin M. Ramsey ◽  
Ai-Hui Tang ◽  
Tara A. LeGates ◽  
Xu-Zhuo Gou ◽  
Beatrice E. Carbone ◽  
...  
Keyword(s):  
Adhesion Molecule ◽  
Ampa Receptors ◽  
Glutamate Release ◽  
Receptor Activation ◽  
Synaptic Strength ◽  
Synaptic Function ◽  
The Novel ◽  
Novel Concept ◽  
The Brain

Recent evidence suggests that nano-organization of proteins within synapses may control the strength of communication between neurons in the brain. The unique subsynaptic distribution of glutamate receptors, which cluster in nanoalignment with presynaptic sites of glutamate release, supports this hypothesis. However, testing it has been difficult because mechanisms controlling subsynaptic organization remain unknown. Reasoning that transcellular interactions could position AMPA receptors (AMPARs), we targeted a key transsynaptic adhesion molecule implicated in controlling AMPAR number, LRRTM2, using engineered, rapid proteolysis. Severing the LRRTM2 extracellular domain led quickly to nanoscale declustering of AMPARs away from release sites, not prompting their escape from synapses until much later. This rapid remodeling of AMPAR position produced significant deficits in evoked, but not spontaneous, postsynaptic receptor activation. These results dissociate receptor numbers from their nanopositioning in determination of synaptic function and support the novel concept that adhesion molecules acutely position receptors to dynamically control synaptic strength.

A novel method for the determination of linting propensity of paper

TAPPI Journal ◽  
2012 ◽  
Vol 11 (10) ◽  
pp. 9-17
Author(s):  
ALESSANDRA GERLI ◽  
LEENDERT C. EIGENBROOD
Keyword(s):  
Ash Content ◽  
The Novel ◽  
Offset Printing ◽  
Excellent Correlation ◽  
End Conditions ◽  
Bottom Side ◽  
Novel Method ◽  
Total Fraction

A novel method was developed for the determination of linting propensity of paper based on printing with an IGT printability tester and image analysis of the printed strips. On average, the total fraction of the surface removed as lint during printing is 0.01%-0.1%. This value is lower than those reported in most laboratory printing tests, and more representative of commercial offset printing applications. Newsprint paper produced on a roll/blade former machine was evaluated for linting propensity using the novel method and also printed on a commercial coldset offset press. Laboratory and commercial printing results matched well, showing that linting was higher for the bottom side of paper than for the top side, and that linting could be reduced on both sides by application of a dry-strength additive. In a second case study, varying wet-end conditions were used on a hybrid former machine to produce four paper reels, with the goal of matching the low linting propensity of the paper produced on a machine with gap former configuration. We found that the retention program, by improving fiber fines retention, substantially reduced the linting propensity of the paper produced on the hybrid former machine. The papers were also printed on a commercial coldset offset press. An excellent correlation was found between the total lint area removed from the bottom side of the paper samples during laboratory printing and lint collected on halftone areas of the first upper printing unit after 45000 copies. Finally, the method was applied to determine the linting propensity of highly filled supercalendered paper produced on a hybrid former machine. In this case, the linting propensity of the bottom side of paper correlated with its ash content.

scholarly journals Racism and Antiracism in the Liberal International Order

2020 ◽  
pp. 1-24
Author(s):  
Zoltán I. Búzás
Keyword(s):  
International Relations ◽  
Racial Inequality ◽  
Racial Diversity ◽  
International Order ◽  
Interdisciplinary Studies ◽  
Racial Equality ◽  
The Novel ◽  
Current Regime ◽  
Novel Concept ◽  
Comprehensive Framework

Abstract Formal racial equality is a key aspect of the current Liberal International Order (LIO). It is subject to two main challenges: resurgent racial nationalism and substantive racial inequality. Combining work in International Relations with interdisciplinary studies on race, I submit that these challenges are the latest iteration of struggles between two transnational coalitions over the LIO's central racial provisions, which I call racial diversity regimes (RDRs). The traditional coalition has historically favored RDRs based on racial inequality and racial nationalism. The transformative coalition has favored RDRs based on racial equality and nonracial nationalism. I illustrate the argument by tracing the development of the liberal order's RDR as a function of intercoalitional struggles from one based on racial nationalism and inequality in 1919 to the current regime based on nonracial nationalism and limited equality. Today, racial nationalists belong to the traditional coalition and critics of racial inequality are part of the transformative coalition. The stakes of their struggles are high because they will determine whether we will live in a more racist or a more antiracist world. This article articulates a comprehensive framework that places race at the heart of the liberal order, offers the novel concept of “embedded racism” to capture how sovereignty shields domestic racism from foreign interference, and proposes an agenda for mainstream International Relations that takes race seriously.

Comparative Study for the Assay of Plant Derived Chemicals in Pharmaceutical Formulation Using Methods Dependent on Factorized Spectra

2021 ◽  
Author(s):  
Nesma M Fahmy ◽  
Adel M Michael
Keyword(s):  
Pharmaceutical Formulations ◽  
Pharmaceutical Formulation ◽  
Ternary Mixtures ◽  
Ratio Method ◽  
The Novel ◽  
Naturally Occurring ◽  
Accuracy And Precision ◽  
Validation Parameters ◽  
Significant Difference

Abstract Background Modern built-in spectrophotometer software supporting mathematical processes provided a solution for increasing selectivity for multicomponent mixtures. Objective Simultaneous spectrophotometric determination of the three naturally occurring antioxidants—rutin(RUT), hesperidin(HES), and ascorbic acid(ASC)—in bulk forms and combined pharmaceutical formulation. Method This was achieved by factorized zero order method (FZM), factorized derivative method (FD1M), and factorized derivative ratio method (FDRM), coupled with spectrum subtraction(SS). Results Mathematical filtration techniques allowed each component to be obtained separately in either its zero, first, or derivative ratio form, allowing the resolution of spectra typical to the pure components present in Vitamin C Forte® tablets. The proposed methods were applied over a concentration range of 2–50, 2–30, and 10–100 µg/mL for RUT, HES, and ASC, respectively. Conclusions Recent methods for the analysis of binary mixtures, FZM and FD1M, were successfully applied for the analysis of ternary mixtures and compared to the novel FDRM. All were revealed to be specific and sensitive with successful application on pharmaceutical formulations. Validation parameters were evaluated in accordance with the International Conference on Harmonization guidelines. Statistical results were satisfactory, revealing no significant difference regarding accuracy and precision. Highlights Factorized methods enabled the resolution of spectra identical to those of pure drugs present in mixtures. Overlapped spectra of ternary mixtures could be resolved by spectrum subtraction coupled FDRM (SS-FDRM) or by successive application of FZM and FD1M.

scholarly journals Using green infrastructure to stimulate discourse with and for planning practice: experiences with fuzzy concepts from a pan-European, a national and a local perspective

2021 ◽  
Author(s):  
Rieke Hansen ◽  
Martina van Lierop ◽  
Werner Rolf ◽  
Damjana Gantar ◽  
Ina Šuklje Erjavec ◽  
...  
Keyword(s):  
Green Infrastructure ◽  
Regional Cooperation ◽  
Knowledge Exchange ◽  
Stakeholder Involvement ◽  
The Novel ◽  
Planning Practice ◽  
Regional Project ◽  
Development Processes ◽  
Guidance Documents ◽  
Novel Concept

AbstractConcepts such as green infrastructure, nature-based solutions, and ecosystem services gained popularity in recent discourses on urban planning. Despite their recognition as innovative concepts, all of them share a degree of ambiguity. Fuzziness can be a weakness but also an opportunity to shape novel concepts together with the stakeholders that are supposed to implement them in the planning practice. The paper traces concept development processes of green infrastructure through transdisciplinary knowledge exchange in three different projects, a European and a national research project and a local city-regional project as part of an EU regional cooperation project. In all projects, the green infrastructure concept evolved in different stages. Stakeholder involvement during these stages span from consultation to co-creation. The cases reveal two different approaches: concepts that are developed “for planning practice” might be based on a plethora of insight via consultation, while those “with planning practice” foster co-creation and might result in high acceptance among the involved stakeholders. Depending on the purpose of the novel concept, each approach can be beneficial and result in practice-related and operational products, such as guidance documents or planning strategies. However, the cases also show that in any new context an exchange about fuzzy concepts is not only needed but also a chance to stimulate cooperation and joint understanding about urban challenges and how to address them.

scholarly journals CD5 costimulation induces stable Th17 development by promoting IL-23R expression and sustained STAT3 activation

Blood ◽  
2011 ◽  
Vol 118 (23) ◽  
pp. 6107-6114 ◽  
Author(s):  
Jelle de Wit ◽  
Yuri Souwer ◽  
Astrid J. van Beelen ◽  
Rosa de Groot ◽  
Femke J. M. Muller ◽  
...  
Keyword(s):  
Th17 Cells ◽  
Transforming Growth Factor ◽  
Transforming Growth Factor Β ◽  
Orphan Receptor ◽  
The Novel ◽  
Cd28 Costimulation ◽  
Th17 Differentiation ◽  
Novel Concept ◽  
Transcription 3 ◽  
Lymphocyte Receptors

Abstract IL-17–producing CD4+ T helper (Th17) cells are important for immunity against extracellular pathogens and in autoimmune diseases. The factors that drive Th17 development in human remain a matter of debate. Here we show that, compared with classic CD28 costimulation, alternative costimulation via the CD5 or CD6 lymphocyte receptors forms a superior pathway for human Th17-priming. In the presence of the Th17-promoting cytokines IL-1β, IL-6, IL-23, and transforming growth factor-β (TGF-β), CD5 costimulation induces more Th17 cells that produce higher amounts of IL-17, which is preceded by prolonged activation of signal transducer and activator of transcription 3 (STAT3), a key regulator in Th17 differentiation, and enhanced levels of the IL-17–associated transcription factor retinoid-related orphan receptor-γt (ROR-γt). Strikingly, these Th17-promoting signals critically depend on CD5-induced elevation of IL-23 receptor (IL-23R) expression. The present data favor the novel concept that alternative costimulation via CD5, rather than classic costimulation via CD28, primes naive T cells for stable Th17 development through promoting the expression of IL-23R.

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