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.

Non-polymeric asymmetric binary glass-formers. II. Secondary relaxation studied by dielectric, 2H NMR, and 31P NMR spectroscopy.

We investigate the secondary (ß-) relaxations of an asymmetric binary glass former consisting of a spirobichroman derivative (SBC; Tg = 356 K) as the high-Tg component and the low-Tg component tripropyl phosphate (TPP; Tg = 134 K). The main relaxations are studied in Paper I [B. Pötzschner et al., J. Chem. Phys. 146, 164503 (2017)]. A high Tg contrast of ΔTg = 222 K is put into effect in a non-polymeric system. Component-selective studies are carried out by combining results from dielectric spectroscopy (DS) for mass concentrations cTPP ≥ 60% and those from different methods of 2H and 31P NMR spectroscopy. In the case of NMR, the full concentration range (10% ≤ cTPP ≤ 100%) is covered. The neat components exhibit a ß-relaxation (ß1 (SBC) and ß2 (TPP)). The latter is rediscovered by DS in the mixtures for all concentrations with unchanged time constants. NMR spectroscopy identifies the ß-relaxations as being alike to those in neat glasses. A spatially highly restricted motion with angular displacement below ±10° encompassing all molecules is involved. In the low temperature range, where TPP shows the typical 31P NMR echo spectra of the ß2-process, very similar spectral features are observed for the (deuterated) SBC component by 2H NMR, in addition to its "own" ß1-process observed at high temperatures. Apparently, the small TPP molecules enslave the large SBC molecules to perform a common hindered reorientation. The temperature dependence of the spin-lattice relaxation time of both components is the same and reveals an angular displacement of the SBC molecules somewhat smaller than that of TPP, though the time constants τß2 are the same. Furthermore, T1(T) of TPP in the temperature region of the ß2-process is absolutely the same as in the mixture TPP/polystyrene investigated previously. It appears that the manifestations of the ß-process introduced by one component are essentially independent of the second component. Finally, at cTPP ≤ 20% one finds indications that the ß2-process starts to disintegrate. More and more TPP molecules get immobilized upon decreasing cTPP. We conclude that the ß-process is a cooperative process.

Non-polymeric asymmetric binary glass-formers. I. Main relaxations studied by dielectric, 2H NMR, and 31P NMR spectroscopy.

In Paper I of this series of two papers we study the main relaxations of a binary glass former made of the low-Tg component tripropyl phosphate (TPP, Tg = 134 K) and of a specially synthesized (deuterated) spirobichroman derivative (SBC, Tg = 356 K) as the non-polymeric high-Tg component for the full concentration range. A large Tg contrast of the neat components is put into effect. Dielectric spectroscopy and different techniques of 2H nuclear magnetic resonance (NMR) as well as of 31P NMR spectroscopy allow to selectively probe the dynamics of the components. For all concentrations, two well separated liquid-like processes are identified. The faster α2-process associated with the low-Tg component TPP shows pronounced dynamic heterogeneities reflected by quasi-logarithmic correlation functions at low TPP concentrations. The slower α1-process involves the reorientation of the high-Tg component SBC. Its correlation function is Kohlrausch-like as in neat glass formers. The corresponding time constants and consequently their glass transition temperatures Tg1 and Tg2 differ more the lower the TPP concentration is. Plasticizer and anti-plasticizer effect, respectively, is observed. At low temperatures a situation arises that the TPP molecules isotropically reorient in an arrested SBC matrix (Tg2 < T < Tg1). At T < Tg2 the liquid-like reorientation of TPP gets arrested too. We find indications that a fraction of the TPP molecule takes part in the slower α1-process of the high-Tg component. All the features known from polymer-plasticizer systems are rediscovered in this non-polymeric highly asymmetric binary mixture. In Paper II [B. Pötzschner et al., J. Chem. Phys. 146, 164504 (2017)] we study the secondary (ß-) relaxations of the mixtures.

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.

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.

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.

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.

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.

[Delayed rupture of the spleen]. / Zweizeitige Milzruptur

From 1964 to 1974 14 patients affected with a delayed rupture of the spleen, were operated in the Surgical Clinic of the University of Mainz. 12 of these 14 patients had a polytrauma. Head-, brain- and thorax injuries were prevalent. Because of the risk of a delayed spleen rupture each blunt trauma has to be hospitalized and observed under clinical conditions. In unconscious patients and in all doubtful cases a peritoneal lavage should be done. If a spleen rupture is caused by an intraabdominal bleeding, Splenectomy is the therapy of choice as further complications can be avoided by this measure.

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.

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.

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 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%.