| 1. |
|
|
| 2. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
|
|
| 3. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
|
|
| 4. |
- Ariyawansa, Hiran A., et al.
(författare)
-
Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
- 2015
-
Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 75, s. 27-274
-
Tidskriftsartikel (refereegranskat)abstract
- This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range. The new families, Ascocylindricaceae, Caryosporaceae and Wicklowiaceae (Ascomycota) are introduced based on their distinct lineages and unique morphology. The new Dothideomycete genera Pseudomassariosphaeria (Amniculicolaceae), Heracleicola, Neodidymella and P s e u d o m i c ros p h a e r i o p s i s ( D id y m e l l a c e a e ) , P s e u d o p i t h o m y c e s ( D i d y m o s p h a e r i a c e a e ) , Brunneoclavispora, Neolophiostoma and Sulcosporium (Halotthiaceae), Lophiohelichrysum (Lophiostomataceae), G a l l i i c o l a , Popul o c re s c e n t i a a nd Va g i c o l a (Phaeosphaeriaceae), Ascocylindrica (Ascocylindricaceae), E l o n g a t o p e d i c e l l a t a ( R o u s s o e l l a c e a e ) , Pseudoasteromassaria (Latoruaceae) and Pseudomonodictys (Macrodiplodiopsidaceae) are introduced. The newly described species of Dothideomycetes (Ascomycota) are Pseudomassariosphaeria bromicola (Amniculicolaceae), Flammeascoma lignicola (Anteagloniaceae), Ascocylindrica marina (Ascocylindricaceae) , Lembosia xyliae (Asterinaceae), Diplodia crataegicola and Diplodia galiicola ( B o t r yosphae r i a cea e ) , Caryospor a aquat i c a (Caryosporaceae), Heracleicola premilcurensis and Neodi dymell a thai landi cum (Didymellaceae) , Pseudopithomyces palmicola (Didymosphaeriaceae), Floricola viticola (Floricolaceae), Brunneoclavispora bambusae, Neolophiostoma pigmentatum and Sulcosporium thailandica (Halotthiaceae), Pseudoasteromassaria fagi (Latoruaceae), Keissleriella dactylidicola (Lentitheciaceae), Lophiohelichrysum helichrysi (Lophiostomataceae), Aquasubmersa japonica (Lophiotremataceae) , Pseudomonodictys tectonae (Macrodiplodiopsidaceae), Microthyrium buxicola and Tumidispora shoreae (Microthyriaceae), Alloleptosphaeria clematidis, Allophaeosphaer i a c y t i s i , Allophaeosphae r i a subcylindrospora, Dematiopleospora luzulae, Entodesmium artemisiae, Galiicola pseudophaeosphaeria, Loratospora(Basidiomycota) are introduced together with a new genus Neoantrodiella (Neoantrodiellaceae), here based on both morphology coupled with molecular data. In the class Agaricomycetes, Agaricus pseudolangei, Agaricus haematinus, Agaricus atrodiscus and Agaricus exilissimus (Agaricaceae) , Amanita m e l l e i a l b a , Amanita pseudosychnopyramis and Amanita subparvipantherina (Amanitaceae), Entoloma calabrum, Cora barbulata, Dictyonema gomezianum and Inocybe granulosa (Inocybaceae), Xerocomellus sarnarii (Boletaceae), Cantharellus eucalyptorum, Cantharellus nigrescens, Cantharellus tricolor and Cantharellus variabilicolor (Cantharellaceae), Cortinarius alboamarescens, Cortinarius brunneoalbus, Cortinarius ochroamarus, Cortinarius putorius and Cortinarius seidlii (Cortinariaceae), Hymenochaete micropora and Hymenochaete subporioides (Hymenochaetaceae), Xylodon ramicida (Schizoporaceae), Colospora andalasii (Polyporaceae), Russula guangxiensis and Russula hakkae (Russulaceae), Tremella dirinariae, Tremella graphidis and Tremella pyrenulae (Tremellaceae) are introduced. Four new combinations Neoantrodiella gypsea, Neoantrodiella thujae (Neoantrodiellaceae), Punctulariopsis cremeoalbida, Punctulariopsis efibulata (Punctulariaceae) are also introduced here for the division Basidiomycota. Furthermore Absidia caatinguensis, Absidia koreana and Gongronella koreana (Cunninghamellaceae), Mortierella pisiformis and Mortierella formosana (Mortierellaceae) are newly introduced in the Zygomycota, while Neocallimastix cameroonii and Piromyces irregularis (Neocallimastigaceae) ar e i n t roduced i n the Neocallimastigomycota. Reference specimens or changes in classification and notes are provided for Alternaria ethzedia, Cucurbitaria ephedricola, Austropleospora, Austropleospora archidendri, Byssosphaeria rhodomphala, Lophiostoma caulium, Pseudopithomyces maydicus, Massariosphaeria, Neomassariosphaeria and Pestalotiopsis montellica.
|
|
| 5. |
- Tang, Ting-Ting, et al.
(författare)
-
Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
-
Tidskriftsartikel (refereegranskat)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
|
|
| 6. |
- Berzunza, Gabriel, et al.
(författare)
-
The k-cut model in deterministic and random trees
- 2021
-
Ingår i: The Electronic Journal of Combinatorics. - : ELECTRONIC JOURNAL OF COMBINATORICS. - 1097-1440 .- 1077-8926. ; 28:1
-
Tidskriftsartikel (refereegranskat)abstract
- The k-cut number of rooted graphs was introduced by Cai et al. as a generalization of the classical cutting model by Meir and Moon. In this paper, we show that all moments of the k-cut number of conditioned Galton-Watson trees converge after proper rescaling, which implies convergence in distribution to the same limit law regardless of the offspring distribution of the trees. This extends the result of Janson. Using the same method, we also show that the k-cut number of various random or deterministic trees of logarithmic height converges in probability to a constant after rescaling, such as random split-trees, uniform random recursive trees, and scale-free random trees.
|
|
| 7. |
- Berzunza Ojeda, Gabriel, et al.
(författare)
-
The fluctuations of the giant cluster for percolation on random split trees
- 2022
-
Ingår i: Latin American Journal of Probability and Mathematical Statistics. - : Institute for Applied and Pure Mathematics (IMPA). - 1980-0436. ; 19:1, s. 665-700
-
Tidskriftsartikel (refereegranskat)abstract
- A split tree of cardinality n is constructed by distributing n “balls” in a subset ofvertices of an infinite tree which encompasses many types of random trees such as m-ary searchtrees, quad trees, median-of-(2k + 1) trees, fringe-balanced trees, digital search trees and randomsimplex trees. In this work, we study Bernoulli bond percolation on arbitrary split trees of large butfinite cardinality n. We show for appropriate percolation regimes that depend on the cardinalityn of the split tree that there exists a unique giant cluster, the fluctuations of the size of the giantcluster as n → ∞ are described by an infinitely divisible distribution that belongs to the class ofstable (asymmetric) Cauchy laws. This work generalizes the results for the random m-ary recursivetrees by Berzunza (2015). Our approach is based on a remarkable decomposition of the size of thegiant percolation cluster as a sum of essentially independent random variables which may be usefulfor studying percolation on other trees with logarithmic height; for instance in this work we studyalso the case of regular trees.
|
|
| 8. |
- Cai, Fanfan, et al.
(författare)
-
Characteristics and mechanisms of low-alloy high-strength steel corrosion behavior under barnacle adhesion based on a comparison experiment
- 2023
-
Ingår i: Corrosion Science. - : Elsevier BV. - 0010-938X. ; 217
-
Tidskriftsartikel (refereegranskat)abstract
- A comparative experiment was set up in a field site and laboratory to study the effect of barnacles (model organisms of macrofouling) on the corrosion behavior of a low-alloy high-strength steel. The results indicated that barnacle adhesion can slow the corrosion rate of steel in an immersion environment by hindering the diffusion of corrosive ions. It was found that barnacle adhesion had a significant promotion effect on localized corrosion. Due to steel’s high corrosion rate, the corrosion-impeding effect was improved, and the promotioneffect on localized corrosion was weakened. The study proposed a corrosion mechanism model influenced by barnacles.
|
|
| 9. |
- Cai, Xing Shi, et al.
(författare)
-
A note on the asymptotic expansion of the Lerch's transcendent
- 2019
-
Ingår i: Integral transforms and special functions. - : TAYLOR & FRANCIS LTD. - 1065-2469 .- 1476-8291. ; 30:10, s. 844-855
-
Tidskriftsartikel (refereegranskat)abstract
- In Ferreira and Lopez [Asymptotic expansions of the Hurwitz-Lerch zeta function. J Math Anal Appl. 2004;298(1):210-224], the authors derived an asymptotic expansion of the Lerch's transcendent Phi(z, s, a) for large vertical bar a vertical bar, valid for Ra > 0, Rs > 0 and z is an element of C \ [1, infinity). In this paper, we study the special case z >= 1 not covered in Ferreira and Lopez [Asymptotic expansions of the Hurwitz-Lerch zeta function. J Math Anal Appl. 2004; 298(1): 210-224], deriving a complete asymptotic expansion of the Lerch's transcendent Phi(z, s, a) for z > 1 and Rs > 0 as Ra goes to infinity. We also show that when a is a positive integer, this expansion is convergent for Rz >= 1. As a corollary, we get a full asymptotic expansion for the sum Sigma(m)(n=1) z(n)/n(s) for fixed z > 1 as m -> infinity. Some numerical results show the accuracy of the approximation.
|
|
| 10. |
- Cai, Xing Shi, et al.
(författare)
-
Cutting resilient networks - complete binary trees
- 2019
-
Ingår i: The Electronic Journal of Combinatorics. - : ELECTRONIC JOURNAL OF COMBINATORICS. - 1097-1440 .- 1077-8926. ; 26:4
-
Tidskriftsartikel (refereegranskat)abstract
- In our previous work [2, 3], we introduced the random k-cut number for rooted graphs. In this paper, we show that the distribution of the k-cut number in complete binary trees of size n, after rescaling, is asymptotically a periodic function of lg n - lg lg n. Thus there are different limit distributions for different subsequences, where these limits are similar to weakly 1-stable distributions. This generalizes the result for the case k = 1, i.e., the traditional cutting model, by Janson [12].
|
|
