Comparative studies of the role of hormone-sensitive lipase and adipose triglyceride lipase in human fat cell lipolysis

Hormone-sensitive lipase (HSL) and adipose triglyceride lipase (ATGL) regulate adipocyte lipolysis in rodents. The purpose of this study was to compare the roles of these lipases for lipolysis in human adipocytes. Subcutaneous adipose tissue was investigated. HSL and ATGL protein expression were related to lipolysis in isolated mature fat cells. ATGL or HSL were knocked down by RNA interference (RNAi) or selectively inhibited, and effects on lipolysis were studied in differentiated preadipocytes or adipocytes derived from human mesenchymal stem cells (hMSC). Subjects were all women. There were 12 lean controls, 8 lean with polycystic ovary syndrome (PCOS), and 27 otherwise healthy obese subjects. We found that norepinephrine-induced lipolysis was positively correlated with HSL protein levels (P < 0.0001) but not with ATGL protein. Women with PCOS or obesity had significantly decreased norepinephrine-induced lipolysis and HSL protein expression but no change in ATGL protein expression. HSL knock down by RNAi reduced basal and catecholamine-induced lipolysis. Knock down of ATGL decreased basal lipolysis but did not change catecholamine-stimulated lipolysis. Treatment of hMSC with a selective HSL inhibitor during and/or after differentiation in adipocytes reduced basal lipolysis by 50%, but stimulated lipolysis was inhibited completely. In contrast to findings in rodents, ATGL is of less importance than HSL in regulating catecholamine-induced lipolysis and cannot replace HSL when this enzyme is continuously inhibited. However, both lipases regulate basal lipolysis in human adipocytes. ATGL expression, unlike HSL, is not influenced by obesity or PCOS.     

Thermococcus waiotapuensis sp. nov., an extremely thermophilic archaeon isolated from a freshwater hot spring

An extremely thermophilic, sulfur-dependent archaeon, strain WT1, was isolated from a freshwater hot spring in the Lake Taupo area of North Island, New Zealand. The cells are flagellated, strictly anaerobic cocci that grow optimally at 85 °C and 5.4 g NaCl l^–1. The strain grows heterotrophically on complex proteinaceous substrates or on appropriate salts plus amino acid mixtures and is also able to utilize maltose, starch, and pyruvate. Elemental sulfur could be replaced by cystine or thioglycollate. The range of temperatures allowing growth is from 60 to 90 °C; the pH supporting growth ranges from 5 to 8 (optimum, pH 7). Strain WT1 grew in a defined medium containing amino acids as the sole carbon and energy sources. The required amino acids were: Arg, His, Ile, Leu, Phe, Ser, Thr, Trp, Tyr, and Val. Strain WT1 showed sensitivity to rifampicin. DNA G+C content was 50.4 mol%. Phylogenetic analysis of the sequence encoding the 16S rRNA gene indicated that this isolate is a member of the Thermococcales. DNA/DNA hybridization studies revealed no similarity to several species of Thermococcus and Pyrococcus, with the exception of Thermococcus zilligii. Based on the reported results, we propose strain WT1 as a new species to be named Thermococcus waiotapuensis sp. nov. Received: 5 January 1999 / Accepted: 19 May 1999     

Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data

Background

The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. Technologies like mass spectrometry are commonly being used in proteomic research. Mass spectrometry signals show the proteomic profiles of the individuals under study at a given time. These profiles correspond to the recording of a large number of proteins, much larger than the number of individuals. These variables come in addition to or to complete classical clinical variables. The objective of this study is to evaluate and compare the predictive ability of new and existing models combining mass spectrometry data and classical clinical variables. This study was conducted in the context of binary prediction.

Results

To achieve this goal, simulated data as well as a real dataset dedicated to the selection of proteomic markers of steatosis were used to evaluate the methods. The proposed methods meet the challenge of high-dimensional data and the selection of predictive markers by using penalization methods (Ridge, Lasso) and dimension reduction techniques (PLS), as well as a combination of both strategies through sparse PLS in the context of a binary class prediction. The methods were compared in terms of mean classification rate and their ability to select the true predictive values. These comparisons were done on clinical-only models, mass-spectrometry-only models and combined models.

Conclusions

It was shown that models which combine both types of data can be more efficient than models that use only clinical or mass spectrometry data when the sample size of the dataset is large enough.     

Surface properties of bacteria sensitive and resistant to the class IIa carnobacteriocin Cbn BM1

Aims: Class IIa bacteriocins are small antimicrobial peptides synthesized by lactic acid bacteria. The proposed mechanisms of action for class IIa bacteriocins suggest that the physicochemical properties of the target bacterial surface govern the bacteriocin antimicrobial activity. The aim of this study is to decipher the relationship between both sensitivity and resistance to a class IIa bacteriocin, carnobacteriocin BM1 and physicochemical surface properties of bacteria. Methods and Results: The study was performed on 18 strains by a microbial adhesion to solvents process and with electrophoretic mobility measurements considering bacteria as soft particles. A large variation in bacterial surface properties is observed among the bacterial populations. Electro‐hydrodynamic parameters values appear to be more homogeneous for sensitive strains than for the resistant ones, which can exhibit more extreme values. Conclusions: Physicochemical surface properties of 18 strains determined show large variations between the strains. However, no direct link between these surface properties and the resistant/sensitive phenotypes of the strains can be stated. Significance and Impact of the Study: The surface physicochemical properties tested have a low predictive power to discriminate sensitive or resistant strains when determined at the bacterial population scale.     

Chromatin techniques for plant cells

A large number of recent studies have demonstrated that many important aspects of plant development are regulated by heritable changes in gene expression that do not involve changes in DNA sequence. Rather, these regulatory mechanisms involve modifications of chromatin structure that affect the accessibility of target genes to regulatory factors that can control their expression. The central component of chromatin is the nucleosome, containing the highly conserved histone proteins that are known to be subject to a wide range of post-translational modifications, which act as recognition codes for the binding of chromatin-associated factors. In addition to these histone modifications, DNA methylation can also have a dramatic influence on gene expression. To accommodate the burgeoning interest of the plant science community in the epigenetic control of plant development, a series of methods used routinely in our laboratories have been compiled that can facilitate the characterization of putative chromatin-binding factors at the biochemical, molecular and cellular levels.     

Mapping global cropland and field size

A new 1 km global IIASA‐IFPRI cropland percentage map for the baseline year 2005 has been developed which integrates a number of individual cropland maps at global to regional to national scales. The individual map products include existing global land cover maps such as GlobCover 2005 and MODIS v.5, regional maps such as AFRICOVER and national maps from mapping agencies and other organizations. The different products are ranked at the national level using crowdsourced data from Geo‐Wiki to create a map that reflects the likelihood of cropland. Calibration with national and subnational crop statistics was then undertaken to distribute the cropland within each country and subnational unit. The new IIASA‐IFPRI cropland product has been validated using very high‐resolution satellite imagery via Geo‐Wiki and has an overall accuracy of 82.4%. It has also been compared with the EarthStat cropland product and shows a lower root mean square error on an independent data set collected from Geo‐Wiki. The first ever global field size map was produced at the same resolution as the IIASA‐IFPRI cropland map based on interpolation of field size data collected via a Geo‐Wiki crowdsourcing campaign. A validation exercise of the global field size map revealed satisfactory agreement with control data, particularly given the relatively modest size of the field size data set used to create the map. Both are critical inputs to global agricultural monitoring in the frame of GEOGLAM and will serve the global land modelling and integrated assessment community, in particular for improving land use models that require baseline cropland information. These products are freely available for downloading from the http://cropland.geo-wiki.org website.     

Enteric bacterial catalysts for fuel ethanol production.

The technology is available to produce fuel ethanol from renewable lignocellulosic biomass. The current challenge is to assemble the various process options into a commercial venture and begin the task of incremental improvement. Current process designs for lignocellulose are far more complex than grain to ethanol processes. This complexity results in part from the complexity of the substrate and the biological limitations of the catalyst. Our work at the University of Florida has focused primarily on the genetic engineering of Enteric bacteria using genes encoding Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase. These two genes have been assembled into a portable ethanol production cassette, the PET operon, and integrated into the chromosome of Escherichia coli B for use with hemicellulose-derived syrups. The resulting strain, KO11, produces ethanol efficiently from all hexose and pentose sugars present in the polymers of hemicellulose. By using the same approach, we integrated the PET operon into the chromosome of Klebsiella oxytoca to produce strain P2 for use in the simultaneous saccharification and fermentation (SSF) process for cellulose. Strain P2 has the native ability to ferment cellobiose and cellotriose, eliminating the need for one class of cellulase enzymes. Recently, the ability to produce and secrete high levels of endoglucanase has also been added to strain P2, further reducing the requirement for fungal cellulase. The general approach for the genetic engineering of new biocatalysts using the PET operon has been most successful with Enteric bacteria but was also extended to Gram positive bacteria, which have other useful traits for lignocellulose conversion. Many opportunities remain for further improvements in these biocatalysts as we proceed toward the development of single organisms that can be used for the efficient fermentation of both hemicellulosic and cellulosic substrates.     

Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2

The SARS-CoV-2 pandemic is a major concern all over the world and, as vaccines became available at the end of 2020, optimal vaccination strategies were subjected to intense investigation. Considering their critical role in reducing disease burden, the increasing demand outpacing production, and that most currently approved vaccines follow a two-dose regimen, the cost-effectiveness of delaying the second dose to increment the coverage of the population receiving the first dose is often debated. Finding the best solution is complex due to the trade-off between vaccinating more people with lower level of protection and guaranteeing higher protection to a fewer number of individuals. Here we present a novel extended age-structured SEIR mathematical model that includes a two-dose vaccination schedule with a between-doses delay modelled through delay differential equations and linear optimization of vaccination rates. By maintaining the minimum stock of vaccines under a given production rate, we evaluate the dose interval that minimizes the number of deaths. We found that the best strategy depends on an interplay between the vaccine production rate and the relative efficacy of the first dose. In the scenario of low first-dose efficacy, it is always better to vaccinate the second dose as soon as possible, while for high first-dose efficacy, the best strategy of time window depends on the production rate and also on second-dose efficacy provided by each type of vaccine. We also found that the rate of spread of the infection does not affect significantly the thresholds of the best window, but is an important factor in the absolute number of total deaths. These conclusions point to the need to carefully take into account both vaccine characteristics and roll-out speed to optimize the outcome of vaccination strategies.     

Influence of compressed fluids treatment on the activity of Yarrowia lipolytica lipase

This work investigated the influence of temperature, pressure, exposure times and depressurization rate on the activity of a non-commercial immobilized lipase from Yarrowia lipolytica (YLL) submitted to compressed carbon dioxide, propane and n-butane. A high-pressure cell was employed in the experiments, in the pressure range of 10–280 bar, varying the temperature from 35 to 75 °C, exposure times from 1 to 6 h, and adopting distinct decompression rates. Results showed that significant activity losses were obtained when the treatment was conducted in carbon dioxide, while negligible losses were observed in both propane and n-butane. For the treatment with carbon dioxide, within the range studied, the decompression rate affected positively enzyme activity, while the exposure time and temperature presented an opposite effect on the non-commercial immobilized lipase from Y. lipolytica (YLL). Additionally, the performance of two commercial immobilized lipases (Lipozyme IM and Novozym 435) and the immobilized YLL in the three solvents was compared. Immobilized YLL has shown to be more suitable than Lipozyme IM for enzyme-catalyzed reactions using compressed propane and n-butane as solvents, but with inferior performance compared to Novozym 435 treated in these solvents.