A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses.

Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology

The dinoflagellate cyst genera Achomosphaera Evitt 1963 and Spiniferites Mantell 1850 in Pliocene to modern sediments: a summary of round table discussions

Source at https://doi.org/10.1080/01916122.2018.1465739. We present a summary of two round-table discussions held during two subsequent workshops in Montreal (Canada) on 16 April 2014 and Ostend (Belgium) on 8 July 2015. Five species of the genus Achomosphaera Evitt 1963 and 33 of the genus Spiniferites Mantell 1850 emend. Sarjeant 1970 occuring in Pliocene to modern sediments are listed and briefly described along with remarks made by workshop participants. In addition, several holotypes and topotypes are reillustrated. Three species previously assigned to Spiniferites are here considered/accepted as belonging to other genera: Impagidinium inaequalis (Wall and Dale in Wall et al.1973) Londeix et al. 2009, Spiniferites? rubinus (Rossignol 1962 ex Rossignol 1964) Sarjeant 1970, and Thalassiphora balcanica Baltes ̧ 1971. This summary forms the basis for a set of papers that follows, where points raised during the workshops are explored in greater detail

Drying banana seeds for ex situ conservation

The ability of seeds to withstand drying is fundamental to ex situ seed conservation but drying responses are not well known for most wild species including crop wild relatives. We look at drying responses of seeds of Musa acuminata and Musa balbisiana, the two primary wild relatives of bananas and plantains, using the following four experimental approaches: (i)We equilibrated seeds to a range of relative humidity (RH) levels using non-saturated lithium chloride solutions and subsequently measured moisture content (MC) and viability. At each humidity levelwe tested viability using embryo rescue (ER), tetrazolium chloride staining and germination in an incubator.We found that seed viabilitywas not reduced when seedswere dried to 4% equilibrium relative humidity (eRH; equating to 2.5% MC). (ii)We assessed viability ofmature and less mature seeds using ER and germination in the soil and tested responses to drying. Findings showed that seeds must be fully mature to germinate and immature seeds had negligible viability. (iii) We dried seeds extracted from ripe/unripe fruit to 35–40% eRH at different rates and tested viability with germination tests in the soil. Seeds from unripe fruit lost viability when dried and especially when dried faster; seeds from ripe fruit only lost viability when fast dried. (iv) Finally, we dried and re-imbibed mature and less mature seeds and measured embryo shrinkage and volume change using X-ray computer tomography. Embryos of less mature seeds shrank significantly when dried to 15% eRH from 0.468 to 0.262 mm3, but embryos of mature seeds did not. Based on our results, mature seeds from ripe fruit are desiccation tolerant to moisture levels required for seed genebanking but embryos from immature seeds are mechanistically less able to withstand desiccation, especially when water potential gradients are high

HUGO Gene Nomenclature Committee (HGNC) recommendations for the designation of gene fusions.

Gene fusions have been discussed in the scientific literature since they were first detected in cancer cells in the early 1980s. There is currently no standardized way to denote the genes involved in fusions, but in the majority of publications the gene symbols in question are listed either separated by a hyphen (-) or by a forward slash (/). Both types of designation suffer from important shortcomings. HGNC has worked with the scientific community to determine a new, instantly recognizable and unique separator-a double colon (::)-to be used in the description of fusion genes, and advocates its usage in all databases and articles describing gene fusions

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

Determining the absolute abundance of dinoflagellate cysts in recent marine sediments, II: further tests of the Lycopodiummarker-grain method

Lycopodium clavatum tablets are commonly added as a spike to determine dinoflagellate cyst concentrations in sediments. In this study we investigate the effects of different processing techniques on dinoflagellate cyst concentrations using well-mixed sediment samples from Saanich Inlet, British Columbia, Canada. At the onset of any dinoflagellate cyst investigation, we suggest following the recommendations of Maher (1981) to experimentally adjust the sample size to obtain a ratio close to ~ 2 of dinoflagellate cysts counted to Lycopodium spores counted, in order to obtain reproducible concentrations. Results further show that both oven-drying at ~ 45 °C and freeze-drying are viable, non-destructive techniques yielding reproducible results. Use of warm HCl (40–60 °C) for a short time (30 min) is harmless, whereas treatment with warm HF (40–60 °C) affects the reproducibility of the concentrations. Pre-sieving can result in loss of cysts and/or spike but this can be easily monitored by checking the residue. Perforated metal sieves show more consistent results than the Nitex nylon meshes. The use of 30 second sonication does not affect the reproducibility, and is advised to remove amorphous organic matter. Adding the Lycopodium spike at the end of preparation yields consistently lower concentrations, which were usually not reproducible, suggesting noticeable losses of Lycopodium spores during processing if the Lycopodium spores are added at the beginning. This method can be considered a viable alternative, but the discrepancy should be taken into account