Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

Cost effective technologies and renewable substrates for biosurfactants’ production

Diverse types of microbial surface-active amphiphilic molecules are produced by a range of microbial communities. The extraordinary properties of biosurfactant / bioemulsifier (BS/BE) as surface active products allows them to have key roles in various field of applications such as bioremediation, biodegradation, enhanced oil recovery, pharmaceutics, food processing among many others. This leads to a vast number of potential applications of these BS/BE in different industrial sectors. Despite the huge number of reports and patents describing BS and BE applications and advantages, commercialization of these compounds remain difficult, costly and to a large extent irregular. This is mainly due to the usage of chemically synthesized media for growing producing microorganism and in turn the production of preferred quality products. It is important to note that although a number of developments have taken place in the field of biosurfactant industries, large scale production remains economically challenging for many types of these products. This is mainly due to the huge monetary difference between the investment and achievable productivity from the commercial point of view. This review discusses low cost, renewable raw substrates and fermentation technology in BS/BE production processes and their role in reducing the production cost

The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020

Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology

The study of atmospheric ice-nucleating particles via microfluidically generated droplets

Ice-nucleating particles (INPs) play a significant role in the climate and hydrological cycle by triggering ice formation in supercooled clouds, thereby causing precipitation and affecting cloud lifetimes and their radiative properties. However, despite their importance, INP often comprise only 1 in 10³–10⁶ ambient particles, making it difficult to ascertain and predict their type, source, and concentration. The typical techniques for quantifying INP concentrations tend to be highly labour-intensive, suffer from poor time resolution, or are limited in sensitivity to low concentrations. Here, we present the application of microfluidic devices to the study of atmospheric INPs via the simple and rapid production of monodisperse droplets and their subsequent freezing on a cold stage. This device offers the potential for the testing of INP concentrations in aqueous samples with high sensitivity and high counting statistics. Various INPs were tested for validation of the platform, including mineral dust and biological species, with results compared to literature values. We also describe a methodology for sampling atmospheric aerosol in a manner that minimises sampling biases and which is compatible with the microfluidic device. We present results for INP concentrations in air sampled during two field campaigns: (1) from a rural location in the UK and (2) during the UK’s annual Bonfire Night festival. These initial results will provide a route for deployment of the microfluidic platform for the study and quantification of INPs in upcoming field campaigns around the globe, while providing a benchmark for future lab-on-a-chip-based INP studies

Visualization of Events for Detection of Relevant Patterns

As devices no longer function in isolation, opportunities will emerge for synergies to be created between disparate information pieces. However the user can and will quickly be overwhelmed with the amount and clutter of the available information. We envision a tool in which a user could define the information pattern/event and action (s) to be taken in some exploratory fashion in order to efficiently create relevant and personalized events. A number of visualization tools for communication patterns [1, 2] exist, but these tend to be non-trivial implementations typically not intended for the end user. Implementation of an event visualization tool is a significant challenge, in this paper we will highlight some initial exploratory work performed and some future possibilities in this area

Production of sophorolipids from whey II. Product composition, surface active properties, cytotoxicity and stability against hydrolases by enzymatic treatment

WOS: 000083529900006PubMed ID: 10570796Sophorolipids. obtained by a two-stage process starting from deproteinized whey concentrate using Cryptococcus curvatus ATCC 20509 and Candida bombicola ATCC 22214, were compared to products from one-stage processes, using different lipidic compounds as substrates. Results showed that above all carbon source and not cultivation conditions had a distinct influence on the composition of the crude product mixture and therefore on the physicochemical and biological properties of the sophorolipids, such as, for example, surface activity, cytotoxicity and stability against hydrolases. The results were completed by corresponding data for purified mono- and diacetylated (17-hydroxyoctadecenoic)-1',4 "-lactonized sophorolipids. Crude sophorolipid mixtures showed moderate to good surface active properties (SFTmin 39 mN m(-1), CMC 130 mg l(-1)), water solubilities (2-3 g l(-1)) and low cytotoxicities (LC50 300-700 mg l(-1)). In contrast, purified sophorolipids were more surface active (SFTmin 36 mN m(-1), CMC 10 mg l(-1)), less water soluble (max. 70 mg l(-1)) and showed stronger cytotoxic effects (LC50 15 mg l(-1)). Incubation of crude sophorolipid mixtures with different hydrolases demonstrated that treatment with commercially available lipases such as from Candida rugosa and Mucor miehei distinctly reduced the surface active properties of the sophorolipids, while treatment with porcine liver esterase and glycosidases had no effect

Production of sophorolipids from whey: II. Product composition, surface active properties, cytotoxicity and stability against hydrolases by enzymatic treatment

PubMed ID: 10570796Sophorolipids, obtained by a two-stage process starting from deproteinized whey concentrate using Cryptococcus curvatus ATCC 20509 and Candida bombicola ATCC 22214, were compared to products from one-stage processes, using different lipidic compounds as substrates. Results showed that above all carbon source and not cultivation conditions had a distinct influence on the composition of the crude product mixture and therefore on the physicochemical and biological properties of the sophorolipids, such as, for example, surface activity, cytotoxicity and stability against hydrolases. The results were completed by corresponding data for purified mono- and diacetylated (17-hydroxyoctadecenoic)-1',4'-lactonized sophorolipids. Crude sophorolipid mixtures showed moderate to good surface active properties (SFT(min) 39 mN m-1, CMC 130 mg l-1), water solubilities (2-3 g l-1) and low cytotoxicities (LC50 300-700 mg l-1). In contrast, purified sophorolipids were more surface active (SFT(min) 36 mN m-1, CMC 10 mg l- 1), less water soluble (max. 70 mg l-1) and showed stronger cytotoxic effects (LC50 15 mg l-1). Incubation of crude sophorolipid mixtures with different hydrolases demonstrated that treatment with commercially available lipases such as from Candida rugosa and Mucor miehei distinctly reduced the surface active properties of the sophorolipids, while treatment with porcine liver esterase and glycosidases had no effect.Verband der Chemischen IndustrieAcknowledgements Ralf T. Otto was supported by a grant from the Fonds der Chemischen Industrie (Frankfurt, Germany) and Hans-Joachim Daniel by the Arbeitsgemeinschaft industrieller Forschungsvereinigungen (AiF) ``Otto von Guericke'' 10771 N/I. Whey was kindly provided by Milei GmbH, Leutkirch-Adrazhofen, Germany. We declare that the experiments described in this paper comply with the current laws of the Federal Republic of Germany. -