Tree-based ensembles unveil the microhabitat suitability for the invasive bleak (Alburnus alburnus L.) and pumpkinseed (Lepomis gibbosus L.): Introducing XGBoost to eco-informatics

Random Forests (RFs) and Gradient Boosting Machines (GBMs) are popular approaches for habitat suitability modelling in environmental flow assessment. However, both present some limitations theoretically solved by alternative tree-based ensemble techniques (e.g. conditional RFs or oblique RFs). Among them, eXtreme Gradient Boosting machines (XGBoost) has proven to be another promising technique that mixes subroutines developed for RFs and GBMs. To inspect the capabilities of these alternative techniques, RFs and GBMs were compared with: conditional RFs, oblique RFs and XGBoost by modelling, at the micro-scale, the habitat suitability for the invasive bleak (Alburnus alburnus L.) and pumpkinseed (Lepomis gibbosus L.). XGBoost outperformed the other approaches, particularly conditional and oblique RFs, although there were no statistical differences with standard RFs and GBMs. The partial dependence plots highlighted the lacustrine origins of pumpkinseed and the preference for lentic habitats of bleak. However, the latter depicted a larger tolerance for rapid microhabitats found in run-type river segments, which is likely to hinder the management of flow regimes to control its invasion. The difference in the computational burden and, especially, the characteristics of datasets on microhabitat use (low data prevalence and high overlapping between categories) led us to conclude that, in the short term, XGBoost is not destined to replace properly optimised RFs and GBMs in the process of habitat suitability modelling at the micro-scale.     

Evaluating a thesaurus for discovery of ecological data

The increasing availability of data has driven a need for improved capabilities to discover data. Use of keywords drawn from a thesaurus is one way to enable browse-based discovery and to enhance searching. To assess the effect of using a thesaurus on the discoverability of ecological data, use of 81,415 keywords derived from 6132 data packages drawn from 28 ecological research projects in the U.S. Long-term Ecological Research Network were examined. The vast majority (95%) of data packages included at least one keyword drawn from the thesaurus, thus enabling their discovery using a hierarchical browse interface. For searching, keywords derived from the thesaurus would reveal 17 times more data packages than ad hoc keywords not in the thesaurus. Additionally, searches using keywords derived from the thesaurus returned data from a median of four different projects, whereas ad hoc search terms would typically yield data from only a single project. Of the search terms that yielded more than five data packages across two or more projects, 78% were found in the thesaurus. Use of keywords drawn from the thesaurus increased when compared to their use prior to establishment of the thesaurus, indicating that terms from the thesaurus are being actively added to metadata. A questionnaire assessed the process by which keywords were selected and indicated that information management personnel played an important role in assigning keywords drawn from the thesaurus. These results support the idea that adoption of a thesaurus can be an effective way to enhance the discoverability of ecological data, and that keywording practices play an important role in supporting that enhancement.     

Development and application of photoautotrophic micropropagation plant system

Research has revealed that most chlorophyllous explants/plants in vitro have the ability to grow photoautotrophically (without sugar in the culture medium), and that the low or negative net photosynthetic rate of plants in vitro is not due to poor photosynthetic ability, but to the low CO₂ concentration in the air-tight culture vessel during the photoperiod. Moreover, numerous studies have been conducted on improving the in vitro environment and investigating its effects on growth and development of cultures/plantlets on nearly 50 species since the concept of photoautotrophic micropropagation was developed more than two decades ago. These studies indicate that the photoautotrophic growth in vitro of many plant species can be significantly promoted by increasing the CO₂ concentration and light intensity in the vessel, by decreasing the relative humidity in the vessel, and by using a fibrous or porous supporting material with high air porosity instead of gelling agents such as agar. This paper reviews the development and characteristics of photoautotrophic micropropagation systems and the effects of environmental conditions on the growth and development of the plantlets. The commercial applications and the perspective of photoautotrophic micropropagation systems are discussed.     

Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates

The pathogens Vibrio cholerae and Haemophilus influenzae use tripartite ATP-independent periplasmic transporters (TRAPs) to scavenge sialic acid from host tissues. They use it as a nutrient or to evade the innate immune system by sialylating surface lipopolysaccharides. An essential component of TRAP transporters is a periplasmic substrate binding protein (SBP). Without substrate, the SBP has been proposed to rest in an open-state, which is not recognised by the transporter. Substrate binding induces a conformational change of the SBP and it is thought that this closed state is recognised by the transporter, triggering substrate translocation. Here we use real time single molecule FRET experiments and crystallography to investigate the open- to closed-state transition of VcSiaP, the SBP of the sialic acid TRAP transporter from V. cholerae. We show that the conformational switching of VcSiaP is strictly substrate induced, confirming an important aspect of the proposed transport mechanism. Two new crystal structures of VcSiaP provide insights into the closing mechanism. While the first structure contains the natural ligand, sialic acid, the second structure contains an artificial peptide in the sialic acid binding site. Together, the two structures suggest that the ligand itself stabilises the closed state and that SBP closure is triggered by physically bridging the gap between the two lobes of the SBP. Finally, we demonstrate that the affinity for the artificial peptide substrate can be substantially increased by varying its amino acid sequence and by this, serve as a starting point for the development of peptide-based inhibitors of TRAP transporters.     

RssB-mediated σS Activation is Regulated by a Two-Tier Mechanism via Phosphorylation and Adaptor Protein – IraD

Regulation of bacterial stress responding σ^S is a sophisticated process and mediated by multiple interacting partners. Controlled proteolysis of σ^S is regulated by RssB which maintains minimal level of σ^S during exponential growth but then elevates σ^S level while facing stresses. Bacteria developed different strategies to regulate activity of RssB, including phosphorylation of itself and production of anti-adaptors. However, the function of phosphorylation is controversial and the mechanism of anti-adaptors preventing RssB-σ^S interaction remains elusive. Here, we demonstrated the impact of phosphorylation on the activity of RssB and built the RssB-σ^S complex model. Importantly, we showed that the phosphorylation site - D58 is at the interface of RssB-σ^S complex. Hence, mutation or phosphorylation of D58 would weaken the interaction of RssB with σ^S. We found that the anti-adaptor protein IraD has higher affinity than σ^S to RssB and its binding interface on RssB overlaps with that for σ^S. And IraD-RssB complex is preferred over RssB-σ^S in solution, regardless of the phosphorylation state of RssB. Our study suggests that RssB possesses a two-tier mechanism for regulating σ^S. First, phosphorylation of RssB provides a moderate and reversible tempering of its activity, followed by a specific and robust inhibition via the anti-adaptor interaction.     

Chimeric contribution of human extended pluripotent stem cells to monkey embryos ex vivo

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Coupling of N7-methyltransferase and 3′-5′ exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading

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Structure Basis for Shaping the Nse4 Protein by the Nse1 and Nse3 Dimer within the Smc5/6 Complex

The Smc5/6 complex facilitates chromosome replication and DNA break repair. Within this complex, a subcomplex composed of Nse1, Nse3 and Nse4 is thought to play multiple roles through DNA binding and regulating ATP-dependent activities of the complex. However, how the Nse1-Nse3-Nse4 subcomplex carries out these multiple functions remain unclear. To address this question, we determine the crystal structure of the Xenopus laevis Nse1-Nse3-Nse4 subcomplex at 1.7 Å resolution and examine how it interacts with DNA. Our structural analyses show that the Nse1-Nse3 dimer adopts a closed conformation and forms three interfaces with a segment of Nse4, forcing it into a Z-shaped conformation. The Nse1-Nse3-Nse4 structure provides an explanation for how the lung disease immunodeficiency and chromosome breakage syndrome-causing mutations could dislodge Nse4 from Nse1-Nse3. Our DNA binding and mutational analyses reveal that the N-terminal and the middle region of Nse4 contribute to DNA interaction and cell viability. Integrating our data with previous crosslink mass spectrometry data, we propose potential roles of the Nse1-Nse3-Nse4 complex in binding DNA within the Smc5/6 complex.     

Negative regulation of AMPK signaling by high glucose via E3 ubiquitin ligase MG53

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