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Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced GōMartini model, which combines a virtual-site implementation of Gō models with Martini 3. The implementation has been extensively tested by the community since the release of the new version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with Gō models.
Using a microscopic transport model together with a coalescence after-burner, we study the formation of deuterons in Au + Au central collisions at s = 200 AGeV . It is found that the deuteron transverse momentum distributions are strongly a ected by the nucleon space-momentum correlations, at the moment of freeze-out, which are mostly determined by the number of rescatterings. This feature is useful for studying collision dynamics at ultrarelativistic energies.
Serial quantification of BCR–ABL1 mRNA is an important therapeutic indicator in chronic myeloid leukaemia, but there is a substantial variation in results reported by different laboratories. To improve comparability, an internationally accepted plasmid certified reference material (CRM) was developed according to ISO Guide 34:2009. Fragments of BCR–ABL1 (e14a2 mRNA fusion), BCR and GUSB transcripts were amplified and cloned into pUC18 to yield plasmid pIRMM0099. Six different linearised plasmid solutions were produced with the following copy number concentrations, assigned by digital PCR, and expanded uncertainties: 1.08±0.13 × 106, 1.08±0.11 × 105, 1.03±0.10 × 104, 1.02±0.09 × 103, 1.04±0.10 × 102 and 10.0±1.5 copies/μl. The certification of the material for the number of specific DNA fragments per plasmid, copy number concentration of the plasmid solutions and the assessment of inter-unit heterogeneity and stability were performed according to ISO Guide 35:2006. Two suitability studies performed by 63 BCR–ABL1 testing laboratories demonstrated that this set of 6 plasmid CRMs can help to standardise a number of measured transcripts of e14a2 BCR–ABL1 and three control genes (ABL1, BCR and GUSB). The set of six plasmid CRMs is distributed worldwide by the Institute for Reference Materials and Measurements (Belgium) and its authorised distributors (https://ec.europa.eu/jrc/en/reference-materials/catalogue/; CRM code ERM-AD623a-f).
The actual prevalence and diversity of the elusive Asian ant genus Rhopalomastix Forel, 1900 in Southeast Asia are largely unknown; only two named species were previously known from Thailand. Following substantial newly-collected museum material made available, we used a combined approach based on morphology and complementary DNA evidence to revise the genus in Thailand. Specimens were sorted to putative species by objective clustering of short fragment (313 bp) COI barcodes, after which specimens of each molecular cluster were morphologically examined. With morphology and supporting genetic evidence, we recognize five species of Rhopalomastix in Thailand, including three species new to science: R. impithuksai Wang & Jaitrong sp. nov., R. parva Wang & Jaitrong sp. nov., and R. robusta Wang & Jaitrong sp. nov. Different castes and sexes are described for most species where available. Descriptions of the two extant described species – R. javana Wheeler, 1929 and R. johorensis Wheeler, 1929 – are also revised, taking into account observations from the additional material. A key to Thai species based on the worker caste, with the three new species included, is further provided.
The present corrigendum corrects errors that occurred in: Wang W.Y., Yong G.W.J. & Jaitrong W. 2021. Revision of the elusive ant genus Rhopalomastix (Hymenoptera, Formicidae, Myrmicinae) in Thailand based on morphology and DNA barcodes, with descriptions of three new species. European Journal of Taxonomy 739: 117–157. https://doi.org/10.5852/ejt.2021.739.1271