Asc-Seurat: analytical single-cell Seurat-based web application

BACKGROUND

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat's capabilities by analyzing a peripheral blood mononuclear cell dataset.

CONCLUSIONS

Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

Synthesen mit Nitrilen, LXV [1]. Pyrazolo [3,4-b] pyridine und Polymethine aus Benzoylacetonitril-hydrazonen und Tetracyanethylen / Syntheses with Nitriles, LXV [1]. Pyrazolo[3,4-b]pyridines and Polymethines from Benzoylacetonitrile-hydrazones and Tetracyanoethylene

Condensation of benzoylacetonitrile (1a) and benziminoacetonitriles (1b, c), resp., with tho hydrazines 2a-f leads to benzoylacetonitrile-hydrazones (3a-i), which react with tetracyanoethylene to give pyrazolo[3,4-b]pyridines (6a-d) and polymethines (7a, b, 8), resp.

Semiempirische SCF-LCAO-MO-Rechnungen als Zuordnungshilfe für 13C-chemische Verschiebungen / Semiempirical SCF-LCAO-MO-calculations as an Aid for the 13C-shift Determination

It has been shown that charge density- and bondorder values in different linear relationships can build up a basis for the calculation of 13C-chemical shifts. This could be an aid for the assignement of different 13C signals

Melatonin increases anagen hair rate in women with androgenetic alopecia or diffuse alopecia: results of a pilot randomized controlled trial

BACKGROUND

In addition to the well-known hormonal influences of testosterone and dihydrotestosterone on the hair cycle, melatonin has been reported to have a beneficial effect on hair growth in animals. The effect of melatonin on hair growth in humans has not been investigated so far.

OBJECTIVES

To examine whether topically applied melatonin influences anagen and telogen hair rate in women with androgenetic or diffuse hair loss.

METHODS

A double-blind, randomized, placebo-controlled study was conducted in 40 women suffering from diffuse alopecia or androgenetic alopecia. A 0.1% melatonin or a placebo solution was applied on the scalp once daily for 6 months and trichograms were performed to assess anagen and telogen hair rate. To monitor effects of treatment on physiological melatonin levels, blood samples were taken over the whole study period.

RESULTS

Melatonin led to a significantly increased anagen hair rate in occipital hair in women with androgenetic hair loss compared with placebo (n=12; P=0.012). For frontal hair, melatonin gave a significant increase in the group with diffuse alopecia (n=28; P=0.046). The occipital hair samples of patients with diffuse alopecia and the frontal hair counts of those with androgenetic alopecia also showed an increase of anagen hair, but differences were not significant. Plasma melatonin levels increased under treatment with melatonin, but did not exceed the physiological night peak.

CONCLUSIONS

To the authors' knowledge, this pilot study is the first to show that topically applied melatonin might influence hair growth in humans in vivo. The mode of action is not known, but the effect might result from an induction of anagen phase.

Synthesis of novel cationic poly(ethylene glycol) containing lipids

In this paper, the synthesis of novel divalent cationic lipids with poly(ethylene glycol) segments is described. The lipids consist of an unsaturated double-chain hydrophobic moiety based on 3, 4-dihydroxy benzoic acid, attached to a hydrophilic poly(ethylene glycol) spacer which contains a divalent cationic end group. As poly(ethylene glycol) spacers monodisperse triethylene glycol and telechelic poly(ethylene glycol)s with an average degree of polymerization of 9, 23, and 45 were used. The divalent cationic end group was attached by coupling a protected dibasic amino acid to the PEG spacer and following cleavage of the protecting groups. These novel class of cationic lipids is of particular interest for nonviral gene delivery applications.

Synthesis of 4-methoxy-2,3,5-trimethylpyridine: a specific building block for compounds with gastric-acid inhibiting activity

A new synthesis of 4-methoxy-2,3,5-trimethylpyridine (2), an important building block for the preparation of gastric-acid inhibiting compounds, is described. Condensation of ethyl 3-amino-2-methyl-2-butenoate (3) and diethyl 2-methylmalonate (4) gives 4-hydroxy-3,5,6-trimethyl-2(1H)-pyridone 5. Reaction of 5 with phosphoryl chloride affords 2,4-dichloro-3,5,6-trimethylpyridine (9a), which, upon hydrogenolysis with palladium on charcoal, gives 2,3,5-trimethylpyridine (10). However, selective hydrogenolysis in acidic solution yields 4-chloro-2-3-5-trimethylpyridine (11). Substitution of the chlorine in 11 with methoxide ion gives 4-methoxy-2,3,5-trimethylpyridine (2), which can be oxidized to the corresponding N-oxide (13). This constitutes a new and efficient route to compound 2 in an overall yield of 43%.

Water permeability of periderm membranes isolated enzymatically from potato tubers (Solanum tuberosum L.)

The fine structure and water permeability of potato tuber periderm have been studied. Periderm membranes (PM) were isolated enzymatically using pectinase and cellulase. They were composed of, about six layers of phellem cells arranged in radial rows. The walls of phellem cells consist of cellulosic primary and tertiary walls and suberized secondary walls which are lamellated. Middle lamellae and primary walls contain lignin. Since the PM did not disintegrate during enzymatic isolation it appears that lignin also extends into the secondary suberized walls. The water permeability of PM was low, ranging from 1-3·10(-10) m s(-1). This low water permeability developed only during storage of tubers in air. Periderm membranes from freshly harvested tubers had a relatively high permeability. The low permeability of PM from stored tubers is attributed to soluble lipids associated with suberin since: (1) extraction of soluble lipids from PM increased permeability by more than 100-fold, (2) a phase transition of soluble lipids was observed between 46 and 51° C, and (3) only the permeability of PM decreased during storage while the permeability of extracted PM remained unchanged. Evidence is presented that two pathways for water movement exist in parallel. Pathway 1 is represented by middle lamellae and primary walls extending in radial direction across the membranes. This pathway has a relatively high specific permeability. Pathway 2 is represented by a polylaminated structure made up of tangential walls of phellem cells which are orientated normal to the direction of water flow. This pathway has a low specific permeability because of the properties of secondary walls incrusted with soluble lipids. It is calculated that about 10% of the water flows across pathway 1 and 90% across pathway 2 which has a volume fraction of 0.995.

Development of plant cuticles: occurrence and role of non-ester bonds in cutin of Clivia miniata Reg. leaves

The effect of BF3-methanol treatment on the mass and fine structure of isolated Clivia leaf cuticles at different stages of development has been investigated. BF3-methanol cleaves ester linkages in cutin; however, the cuticles are not completely depolymerized. With increasing age, the residue left after BF3-methanol treatment increases in mass. In very young cuticles, 10% of the total cutin resisted BF3-methanol and the fraction of nonester cutin increased up to 62% in mature leaves. Transmission electron microscopy shows that fine structure of the cuticle proper is severely distorted but not destroyed. The internal cuticular layer, which exhibits a heavy contrast when fixed with KMnO4, is completely depolymerized, while the external cuticular layer is hardly affected. The results are discussed in relation to cuticle development and to the function of cuticles as transpiration resistances.

Fine structure of isolated and non-isolated potato tuber periderm

Cell walls of the periderm of native potato tuber (Solanum tuberosum L. cv. Primura) consist of a primary wall, a suberized secondary wall and a tertiary wall. With a mixture of pectinase and cellulase intact periderm membranes can be isolated. Isolation does not affect fine structure. It is suggested that the lignin in the middle lamellae and primary walls prevents the enzymes from digesting pectinaceous materials and cellulose. In specimens fixed with OsO4, the suberized walls appear as alternating electrondense and electron-lucent lamellae. This lamellar architecture is not altered by extraction with chloroform. Therefore, the current view that the electronlucent lamellae consist of soluble lipids (waxes) can no longer be maintained. It is argued that the lamellation is a property of the suberin itself, and the suberized wall consists of alternating layers of suberins differing in polarity. A hypothesis of suberin assembly from sub-units is advanced and the subunits are shown for the first time.

Fine structure of plant cuticles in relation to water permeability: The fine structure of the cuticle of Clivia miniata reg. leaves

The fine structure of the upper cuticular membrane (CM) of Clivia miniata leaves was investigated using electron microscopy. The CM is made up of a thin (130 nm) lamellated cuticle proper (CP) and a thick (up to 7 μm over periclinal walls) cuticular layer (CL) of marbled appearance. Evidence is presented to show that the electron lucent lamellae of the CP do not simply represent layers of soluble cuticular lipids (SCL). Instead, the lamellation is probably due to layers of cutin differing in polarity. It is argued that the SCL in the Cp are the main barrier to water. Thickening of the CM during leaf development takes place by interposition of cutin between the CM and the cellin wall. The cutin of young, expanding leaves has a high affinity for KMnO4 and is therefore relatively polar. As leaves mature, the external CL underneath the CP becomes non-polar, as only little contrast can be obtained with permanganate as the post fixative.

Interaction of carbachol and isoproterenol on O2 consumption and morphology of isolated acini from rat parotid gland

Acini from rat parotid gland were isolated by digestion with collagenase. Oxygen consumption rates were measured after stimulation with carbachol and isoproterenol applied either simultaneously or subsequently to each other. The corresponding morphological effects were examined by electron microscopy. The results demonstrate that a) carbachol always induces increased O2 consumption rates with concomitant formation of vacuoles, b) isoproterenol stimulates exocytosis and higher O2 consumption rates only when added before carbachol and c) isoproterenol has no effect when given simultaneously with or subsequently to carbachol.

Water permeability of plant cuticles : Dependence of permeability coefficients of cuticular transpiration on vapor pressure saturation deficit

Using the system vapor/membrane/liquid, permeability coefficients of cuticular transpiration (P ct) were determined as functions of water activity in the vapor (a wv). Enzymatically isolated cuticular membranes (CM) of Citrus aurantium L. and nonisolated CM of onion bulb scales and eggplant fruits were investigated. P ct of Citrus and eggplant CM decreased with decreasing a wv, while permeability coefficients of CM of onion were independent of a wv. Extraction of soluble cuticular lipids (SCL) from the CM of Citrus increased permeability coefficients by a factor of approximately 500. This extraction had no effect on the dependence of P ct on a wv.Treating cuticular membranes as a resistance network consisting of SCL and the polymer matrix, it is shown that the permeability of onion CM is determined by the resistance of the SCL arranged in series with the polymer matrix. In this type of CM liquid and vapor are separated by a continuous, nonporous layer of SCL, and the driving force of transpiration is the gradient of partial pressure of water vapor across the SCL layer. In the CM of Citrus and eggplant, the SCL layer is traversed by polar pores that swell or shrink depending on a wv. However, liquid continuity is maintained across these membranes down to a wv=0.22, the lowest value used. In this type of membrane the driving force of transpiration is the water potential gradient across the membrane.

Changes in envelope permeability during chloroplast development

The permeability of the plastid envelope during the development of Avena sativa plastids was investigated by light scattering and uptake of various labelled compounds (malate, succinate, glutamate, α-ketoglutarate, citrate, glycine, sucrose). The results presented show that a primary event during greening is a change in permeability, thereby allowing an increased transport of metabolites across the membranes of very early etio-chloroplast stages. The results are discussed in view of an adaption of the plastid envelope permeability to the changing requirements of externally synthesized precursors and intermediates during development.