Activity

Results We found that metabolic networks of bacteria that are significantly enriched in CRC metagenomic samples either depend on metabolites that are more abundant in CRC samples or specifically benefit from these metabolites for biomass production. This suggests that metabolic alterations in the cancer environment are a major component shaping the CRC microbiome. Conclusion Here, we show with in sillico models that supplementing the intestinal environment with CRC metabolites specifically predicts the outgrowth of CRC-associated bacteria. We thus mechanistically explain why a range of CRC passenger bacteria are associated with CRC, enhancing our understanding of this disease. Our methods are applicable to other microbial communities, since it allows the systematic investigation of how shifts in the microbiome can be explained from changes in the metabolome. © The Author(s). 2020.The zygotic embryos of angiosperms develop buried deep within seeds and surrounded by two main extra-embryonic tissues the maternally derived seed coat tissues and the zygotic endosperm. Generally, these tissues are considered to play an important role in nurturing the developing embryo by acting as conduits for maternally derived nutrients. They are also critical for key seed traits (dormancy establishment and control, longevity, and physical resistance) and thus for seed and seedling survival. However, recent studies have highlighted the fact that extra-embryonic tissues in the seed also physically and metabolically limit embryonic development and that unique mechanisms may have evolved to overcome specific developmental and genetic constraints associated with the seed habit in angiosperms. The aim of this review is to illustrate how these studies have begun to reveal the highly complex physical and physiological relationship between extra-embryonic tissues and the developing embryo. Where possible I focus on Arabidopsis because of space constraints, but other systems will be cited where relevant. Copyright © 2020 Ingram GC.P-glycoprotein, ABCG2, and MRP1 are members of the ATP-binding cassette (ABC) transporter superfamily that utilize energy from ATP-binding and hydrolysis to efflux a broad range of chemically dissimilar substrates including anticancer drugs. As a consequence, they play an important role in the pharmacokinetics and bioavailability of many drugs; in particular, their role in multidrug resistance in cancer cells as well as at the blood-brain barrier has been the subject of studies for decades. However, the atomic structures of these transporters in the presence of substrates or modulators and at different stages of the ATP-hydrolysis cycle have only recently been resolved by using cryo-electron microscopy. In addition, new animal models have shed new light on our understanding of the role of these transporters at the blood-brain barrier. This new information should open doors for the design of novel chemotherapeutics and treatments to bypass recognition by ABC drug pumps to overcome clinical drug resistance. In this review, we discuss the most recent advances in our understanding of ligand interactions and mechanistic aspects of drug transport based on atomic structures of these transporters as well as the development of new in vivo models to study their role in clinical drug resistance in cancer. Copyright © 2020 Lusvarghi S et al.Background Since 2013, there has been a dramatic increase in the number of preprint servers available online. To date, little is known about the position of researchers, funders, research performing organisations and other stakeholders with respect to this fast-paced landscape. In this article, we explore the benefits and challenges of preprint posting, along with issues such as infrastructure and financial sustainability. this website We also discuss the definition of a ‘preprint’ in different communities, and the impact this has on further uptake. Methods This study is based on 38 detailed semi-structured interviews of key stakeholders based on a purposive heterogeneous sampling approach. Interviews were undertaken between October 2018 and January 2019. These were recorded, transcribed and subjected to thematic analysis to identify trends. Interview questions were designed based on Innovation Diffusion Theory, which is also used to interpret the results of this study. Results Our study is the first using empirical data iarelli A et al.Background The search for putative enzymes that can facilitate gene editing has recently focused its attention on Argonaute proteins from prokaryotes (pAgos). Though they are structural homologues of human Argonaute protein, which uses RNA guides to interfere with RNA targets, pAgos use ssDNA guides to identify and, in many cases, cut a complementary DNA target. Thermophilic pAgos from Thermus thermophilus, Pyrococcus furiosus and Methanocaldococcus jasmanii have been identified and thoroughly studied, but their thermoactivity makes them of little use in mesophilic systems such as mammalian cells. Methods Here we search for and identify CbcAgo, a prokaryotic Argonaute protein from a mesophilic bacterium, and characterize in vitro its DNA interference activity. Results CbcAgo efficiently uses 5’P-ssDNA guides as small as 11-mers to cut ssDNA targets, requires divalent cations (preferentially, Mn 2+) and has a maximum activity between 37 and 42 °C, remaining active up to 55 °C. Nicking activity on supercoiled dsDNA was shown. However, no efficient double-strand breaking activity could be demonstrated. Conclusions CbcAgo can use gDNA guides as small as 11 nucleotides long to cut complementary ssDNA targets at 37ºC, making it a promising starting point for the development of new gene editing tools  for mammalian cells. Copyright © 2019 García-Quintans N et al.Background Durian peel is a type of biomass waste that contains cellulose, hemicelluloses, and lignin. The pyrolysis of these compounds results in production of liquid smoke which can be used as a natural preservative to replace current synthetic preservatives. This research assessed the ability of liquid smoke produced during pyrolysis of durian peel to preserve fish. Methods Dry durian peel waste underwent batch reactor pyrolysis at 340°C and 380°C, resulting in production of liquid smoke (grade 3), charcoal, and tar. This liquid smoke was then distilled at 190°C to produce grade 1 liquid smoke, which was used to preserve mackerel. The preservation process was conducted by soaking the mackerel samples in liquid smoke at 0.5, 1, 2, and 3% concentration levels followed by observations every 6 hours. Tests to determine the total volatile base (TVB) content, antibacterial quality of the liquid smoke and organoleptic quality of the fish were conducted in order to assess the preservation properties of the liquid smoke.