Secondary Transport Research Articles

Conservation of knotted and slipknotted topology in transmembrane transporters

The existence of nontrivial topology is well accepted in globular proteins but not in membrane proteins. Our comprehensive topological analysis of the Protein Data Bank structures reveals 18 families of transmembrane proteins with nontrivial topology, showing that they constitute a significant number of membrane proteins. Moreover, we found that they comprise one of the largest groups of secondary active transporters. We classified them based on their knotted fingerprint into four groups: three slipknotted and one knotted. Unexpectedly, we found that the same protein can possess two distinct slipknot motifs that correspond to its outward- and inward-open conformational state. Based on the analysis of structures and knotted fingerprints, we show that slipknot topology is directly involved in the conformational transition and substrate transfer. Therefore, entanglement can be used to classify proteins and to find their structure-function relationship. Furthermore, based on the topological analysis of the transmembrane protein structures predicted by AlphaFold, we identified new potentially slipknotted protein families.

Integrating Pre-Trained protein language model and multiple window scanning deep learning networks for accurate identification of secondary active transporters in membrane proteins

Secondary active transporters play pivotal roles in regulating ion and molecule transport across cell membranes, with implications in diseases like cancer. However, studying transporters via biochemical experiments poses challenges. We propose an effective computational approach to identify secondary active transporters from membrane protein sequences using pre-trained language models and deep learning neural networks.Our dataset comprised 290 secondary active transporters and 5,420 other membrane proteins from UniProt. Three types of features were extracted - one-hot encodings, position-specific scoring matrix profiles, and contextual embeddings from the ProtTrans language model. A multi-window convolutional neural network architecture scanned the ProtTrans embeddings using varying window sizes to capture multi-scale sequence patterns.The proposed model combining ProtTrans embeddings and multi-window convolutional neural networks achieved 86% sensitivity, 99% specificity and 98% overall accuracy in identifying secondary active transporters, outperforming conventional machine learning approaches.This work demonstrates the promise of integrating pre-trained language models like ProtTrans with multi-scale deep neural networks to effectively interpret transporter sequences for functional analysis. Our approach enables more accurate computational identification of secondary active transporters, advancing membrane protein research.

Molecular evolution and interaction of 14-3-3 proteins with H+-ATPases in plant abiotic stresses.

Environmental stresses severely affect plant growth and crop productivity. Regulated by 14-3-3 proteins (14-3-3s), H+-ATPases (AHAs) are important proton pumps that can induce diverse secondary transport via channels and co-transporters for the abiotic stress response of plants. Many studies demonstrated the roles of 14-3-3s and AHAs in coordinating the processes of plant growth, phytohormone signaling, and stress responses. However, the molecular evolution of 14-3-3s and AHAs has not been summarized in parallel with evolutionary insights across multiple plant species. Here, we comprehensively review the roles of 14-3-3s and AHAs in cell signaling to enhance plant responses to diverse environmental stresses. We analyzed the molecular evolution of key proteins and functional domains that are associated with 14-3-3s and AHAs in plant growth and hormone signaling. The results revealed evolution, duplication, contraction, and expansion of 14-3-3s and AHAs in green plants. We also discussed the stress-specific expression of those 14-3-3and AHA genes in a eudicotyledon (Arabidopsis thaliana), a monocotyledon (Hordeum vulgare), and a moss (Physcomitrium patens) under abiotic stresses. We propose that 14-3-3s and AHAs respond to abiotic stresses through many important targets and signaling components of phytohormones, which could be promising to improve plant tolerance to single or multiple environmental stresses.

Functional Roles of the Conserved Amino Acid Sequence Motif C, the Antiporter Motif, in Membrane Transporters of the Major Facilitator Superfamily.

The biological membrane surrounding all living cells forms a hydrophobic barrier to the passage of biologically important molecules. Integral membrane proteins called transporters circumvent the cellular barrier and transport molecules across the cell membrane. These molecular transporters enable the uptake and exit of molecules for cell growth and homeostasis. One important collection of related transporters is the major facilitator superfamily (MFS). This large group of proteins harbors passive and secondary active transporters. The transporters of the MFS consist of uniporters, symporters, and antiporters, which share similarities in structures, predicted mechanism of transport, and highly conserved amino acid sequence motifs. In particular, the antiporter motif, called motif C, is found primarily in antiporters of the MFS. The antiporter motif's molecular elements mediate conformational changes and other molecular physiological roles during substrate transport across the membrane. This review article traces the history of the antiporter motif. It summarizes the physiological evidence reported that supports these biological roles.

Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.

Acid tolerance of lactate-utilizing bacteria of the order Bacteroidales contributes to prevention of ruminal acidosis in goats adapted to a high-concentrate diet.

The rapid accumulation of organic acids, particularly lactate, has been suggested as the main cause of ruminal acidosis (RA) for ruminants fed high-concentrate diets. Previous research has shown that a gradual shift from low-to high-concentrate diets within 4 to 5 weeks effectively reduces the risk for RA. However, the mechanisms remain unknown. In this study, 20 goats were randomly allocated into four groups (n=5) and fed with a diet containing a weekly increasing concentrate portion of 20%, 40%, 60%, and 80% over 28d. At d 7, 14, 21, and 28, one group (named C20, C40, C60, and C80 according to the last concentrate level that they received) was killed and the ruminal microbiome was collected. Ruminal acidosis was not detected in any of the goats during the experiment. Nonetheless, ruminal pH dropped sharply from 6.2 to 5.7 (P<0.05) when dietary concentrate increased from 40% to 60%. A combined metagenome and metatranscriptome sequencing approach identified that this was linked to a sharp decrease in the abundance and expression of genes encoding nicotinamide adenine dinucleotide (NAD)-dependent lactate dehydrogenase (nLDH), catalyzing the enzymatic conversion of pyruvate to lactate (P<0.01), whereas the expression of two genes encoding NAD-independent lactate dehydrogenase (iLDH), catalyzing lactate oxidation to pyruvate, showed no significant concomitant change. Abundance and expression alterations for nLDH- and iLDH-encoding genes were attributable to bacteria from Clostridiales and Bacteroidales, respectively. By analyzing the gene profiles of 9 metagenome bins (MAG) with nLDH-encoding genes and 5 MAG with iLDH-encoding genes, we identified primary and secondary active transporters as being the major types of sugar transporter for lactate-producing bacteria (LPB) and lactate-utilizing bacteria (LUB), respectively. Furthermore, more adenosine triphosphate was required for the phosphorylation of sugars to initiate their catabolic pathways in LPB compared to LUB. Thus, the low dependence of sugar transport systems and catabolic pathways on primary energy sources supports the acid tolerance of LUB from Bacteroidales. It favors ruminal lactate utilization during the adaptation of goats to a high-concentrate diet. This finding has valuable implications for the development of measures to prevent RA.

ClpP protease modulates bacterial growth, stress response, and bacterial virulence in Brucella abortus

The process of intracellular proteolysis through ATP-dependent proteases is a biologically conserved phenomenon. The stress responses and bacterial virulence of various pathogenic bacteria are associated with the ATP-dependent Clp protease. In this study, a Brucella abortus 2308 strain, ΔclpP, was constructed to characterize the function of ClpP peptidase. The growth of the ΔclpP mutant strain was significantly impaired in the TSB medium. The results showed that the ΔclpP mutant was sensitive to acidic pH stress, oxidative stress, high temperature, detergents, high osmotic environment, and iron deficient environment. Additionally, the deletion of clpP significantly affected Brucella virulence in macrophage and mouse infection models. Integrated transcriptomic and proteomic analyses of the ΔclpP strain showed that 1965 genes were significantly affected at the mRNA and/or protein levels. The RNA-seq analysis indicated that the ΔclpP strain exhibited distinct gene expression patterns related to energy production and conversion, cell wall/membrane/envelope biogenesis, carbohydrate transport, and metabolism. The iTRAQ analysis revealed that the differentially expressed proteins primarily participated in amino acid transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis, transport and catabolism. This study provided insights into the preliminary molecular mechanism between Clp protease to bacterial growth, stress response, and bacterial virulence in Brucella strains.

Turbine Vane Passage Cooling Experiments With a Close-Coupled Combustor–Turbine Interface Geometry Part II: Describing the Coolant Coverage

Abstract The first-stage gas turbine vane surfaces and endwalls require aggressive cooling. This two-part paper introduces a modified design of the combustor–turbine (C–T) interface, the “close-coupled interface,” that is expected to increase cooling performance of vane passage surfaces. While Part I of the paper describes secondary flows and coolant transport in the passage, this part discusses the effects of the new C–T interface geometry on adiabatic cooling effectiveness of the endwall and vane surfaces. Compared to the traditional C–T interface, the coolant requirement is reduced for the same level of cooling effectiveness on all three surfaces for the new C–T interface design, confirming that it is an improvement over the previous design. The endwall crossflow is reduced by combustor coolant injection with the new interface leading to more pitchwise-uniform cooling of the endwall. For the pressure surface, increasing combustor coolant flowrate directly increases phantom cooling effectiveness and spreading of coolant away from the endwall. With the traditional passage vortex seen in the literature replaced by the impingement vortex of the present design, the suction surface receives less phantom cooling than does the pressure surface. However, cooling performance is still improved over that of the previous C–T interface design.

Turbine Vane Passage Cooling Experiments With a Close-Coupled Combustor-Turbine Interface Geometry—Part I: Describing the Flow

Abstract Due to the proximity of the first-stage gas turbine vanes to the combustor, coolant introduced to the combustor walls interacts with the endwall film coolant and changes the vane passage flow physics. Recent results show that combustor coolant contributes significantly to cooling the endwall and vane surfaces. In this paper, the traditional combustor-turbine interface was modified to improve overall cooling performance. The performance of this new injection cooling scheme on passage fluid dynamics and surface cooling is assessed. The first of this two-part paper reports detailed experimental tests that document secondary flows and coolant transport throughout the vane passage for four combustor coolant flowrates. The experimental facility imitates combustor coolant injection and engine-level turbulence and has a modified transition duct design, called the “close-coupled combustor-turbine interface.” The “impingement vortex” seen in previous studies with combustor cooling appears as the dominant secondary flow. It is observed in the present study over a wide range of flowrates, confirming its tie to the combustor coolant flowrate and not the combustor-turbine interface geometry. It was found, however, that the location and size of the impingement vortex are affected by coolant flowrate. Part II of this paper discusses the impact of the observed secondary flows on cooling vane passage surfaces.

Identification of vaccine candidates against rhodococcus equi by combining pangenome analysis with a reverse vaccinology approach

Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant R. equi and the fact that there is no currently licensed effective vaccine against R. equi warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen’s entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of R. equi. We then used the RV approach to examine the subcellular localization, host and gut flora homology, antigenicity, transmembrane helices, physicochemical properties, and immunogenicity of the core proteins to select potential vaccine candidates. The vaccine candidates were then subjected to epitope mapping to predict the exposed antigenic epitopes that possess the ability to bind with major histocompatibility complex I/II (MHC I/II) molecules. These vaccine candidates and epitopes will form a library of elements for the development of a polyvalent or universal vaccine against R. equi. Sixteen R. equi complete proteomes were found to contain 6,238 protein families, and the core proteins consisted of 3,969 protein families (∼63.63% of the pangenome), reflecting a low degree of intraspecies genomic variability. From the pool of core proteins, 483 nonhost homologous membrane and extracellular proteins were screened, and 12 vaccine candidates were finally identified according to their antigenicity, physicochemical properties and other factors. These included four cell wall/membrane/envelope biogenesis proteins; four amino acid transport and metabolism proteins; one cell cycle control, cell division and chromosome partitioning protein; one carbohydrate transport and metabolism protein; one secondary metabolite biosynthesis, transport and catabolism protein; and one defense mechanism protein. All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. Thus, we utilized an analytical strategy that combines pangenome analysis and RV to generate a peptide antigen library that simplifies the development of multivalent or universal vaccines against R. equi and can be applied to the development of other vaccines.

A root-knot nematode effector manipulates the rhizosphere microbiome for establishing parasitism relationship with hosts.

Root-knot nematode (RKN; Meloidogyne spp.) is one of the most infamous soilborne plant diseases, causing severe crop losses every year. Effector proteins secreted by RKNs play crucial roles during plant-nematode interaction. However, less is known about whether RKN effector proteins can impact the rhizosphere microbial environment. In this study, we investigated the rhizosphere microbiome community of MiMIF-2 (a plant immunity-modulating effector) transgenic Arabidopsis thaliana with or without nematode infection using the Illumina high-throughput sequencing analysis. The results showed that the bacterial species richness index increased, while the fungi species richness index decreased in M. incognita-infected MiMIF-2 transgenic A. thaliana plants. The relative abundance of genera such as Clitopilus, Komagataeibacter, Lactobacillus, Prevotella, Moritella, Vibrio, Escherichia-Shigella, and Pseudomonas was reduced in MiMIF-2 transgenic A. thaliana plants compared to wild type, but was significantly increased after inoculation with M. incognita. The Cluster of Orthologous Genes (COG) function classification analysis revealed a decrease in the relative abundance of defense mechanisms, secondary metabolite biosynthesis, transport, and nematode infection catabolism-related functions in MiMIF-2 lines compared to the wild type. These differences may be the reason for the increased susceptibility of MiMIF-2 transgenic A. thaliana to nematode infection. Our results provide a new insight into RKN effector proteins and their association with the microbial community, host, and plant pathogens, which will lead to the exploration of new innovative ideas for future biological control of RKNs.

Intravenous Thrombolysis Is Associated With Better Outcomes in Large‐Vessel Occlusion Requiring Endovascular Therapy

Background Intravenous thrombolysis (IVT) and endovascular therapy (EVT) are both important treatments for large‐vessel occlusion stroke. However, it is still unclear how the timing of IVT, EVT, and the need for transfer of a patient to an endovascular stroke center for EVT affect outcomes. In this investigation, we study the interaction between IVT, rapidity to EVT, and need for transfer among patients with large‐vessel occlusion stroke. Methods This investigation is an analysis of the OPUS‐REACH (Optimizing the Use Prehospital Stroke Systems of Care–Reacting to Changing Paradigms) registry of patients with large‐vessel occlusion stroke from 9 endovascular centers in the United States. Using the database, we extracted baseline characteristics of patients, whether the patient received IVT, and time intervals in the patients’ care. Patient demographics and characteristics were compared between 2 groups using the χ 2 test for categorical variables and 2‐sample t ‐tests or Wilcoxon rank‐sum tests for continuous variables. Multivariable logistic regression was performed to determine the adjusted associations of the variables with 90‐day dichotomized modified Rankin Scale outcome. Results A total of 1171 patients were included in the final analysis, and 38.9% had good functional outcome at 90 days. Male sex and lower initial National Institutes of Health Stroke Scale score were nonmodifiable factors associated with good clinical outcomes. We saw no differences in outcome whether a patient underwent primary or secondary transport. On multiple variable analysis, the receipt of IVT was the only modifiable factor associated with good outcomes. We found no overall effect of time from last known well to EVT on 90‐day outcomes unless the patient received IVT. Conclusions In this investigation, receipt of IVT was independently associated with improved outcomes at 90 days with an odds ratio of 1.51. Neither shorter time from last known well to EVT nor direct transport to an endovascular stroke center versus transfer to an endovascular stroke center was associated with improved outcomes. We therefore conclude that prehospital algorithms must account for the timely administration of IVT over time to EVT.

Corrigendum for Lee CE, volume 36, 2021, p. 335–349

CorrigendumPublished Online:24 May 2023https://doi.org/10.1152/physiol.0009.2021_COROriginal articleMoreSectionsPDF (191 KB)Download PDF ToolsExport citationAdd to favoritesTrack citations Lee CE. Ion transporter gene families as physiological targets of natural selection during salinity transitions in a copepod. Physiology (Bethesda) 36: 335–349, 2021. doi: 10.1152/physiol.00009.2021.In FIGURE 5, the arrows for NHA point in the wrong direction. In FIGURE 5A, NHA (white) should have Na+ going into the cell and H+ going out. Corrected figure is shown below, and the article (HTML and PDF) has been updated online.FIGURE 5.Hypothetical models of ion uptake from fresh water by ionocytes in Eurytemora affinis complex populations Shown are primary transporters for energizing ion transport [V-type H+-ATPase (VHA) and NKA] and hypothetical secondary transporters for sodium uptake (NHA, Na+ channel [Nach], or NHE). A: model 1 (Wieczorek’s Model): VHA (blue) pumps H+ out of the cell and creates a proton gradient, through which Na+ is transported into the cell through an electrogenic NHA or Na+ channel. The stoichiometry of ion transport for NHA is not fully known, even for Drosophila. B: model 2: ammonia is transported out of the cell by an ammonia transporter (Rh), which then drives electroneutral NHE to export H+, and consequently import Na+. In both models, Na+ is transported to the hemolymph via NKA. Carbonic anhydrase (CA) supplies protons to VHA or NHE and HCO3− to anion exchanger (AE). The Na+/K+/2Cl– cotransporter (NKCC) might also play a role in ion uptake, but the localization of NKCC paralogs is unknown for E. affinis complex. In response to salinity change, certain paralogs of these ion transporters show evolutionary changes in gene expression and signatures of natural selection (see FIGURE 4). Alternative models have also been proposed, and not all potentially relevant ion transporters are shown. Adapted from Stern and Lee (35).Download figureDownload PowerPointThis article has no references to display. Download PDF Previous Back to Top FiguresReferencesRelatedInformation Related ArticlesIon Transporter Gene Families as Physiological Targets of Natural Selection During Salinity Transitions in a Copepod 27 Oct 2021Physiology More from this issue > Volume 38Issue 4July 2023Pages 000-000 Crossmark Copyright & PermissionsCopyright © 2023 Int. Union Physiol. Sci./Am. Physiol. Soc.https://doi.org/10.1152/physiol.0009.2021_CORPubMed37222465History Published online 24 May 2023 Published in print 1 July 2023 Metrics

Collective Domain Motion Facilitates Water Transport in SGLT1.

The human sodium-glucose cotransporter protein (SGLT1) is an important representative of the sodium solute symporters belonging to the secondary active transporters that are critical to the homeostasis of sugar, sodium, and water in the cell. The underlying transport mechanism of SGLT1 is based on switching between inward- and outward-facing conformations, known as the alternating access model, which is crucial for substrate transport, and has also been postulated for water permeation. However, the nature of water transport remains unclear and is disputed along the passive and active transport, with the latter postulating the presence of the pumping effect. To better examine the water transport in SGLT1, we performed a series of equilibrium all-atom molecular dynamics simulations, totaling over 6 μs of sample representative conformational states of SGLT1 and its complexes, with the natural substrates, ions, and inhibitors. In addition to elucidating the basic physical factors influencing water permeation, such as channel openings and energetics, we focus on dynamic flexibility and its relationship with domain motion. Our results clearly demonstrate a dependence of instantaneous water flux on the channel opening and local water diffusion in the channel, strongly supporting the existence of a passive water transport in SGLT1. In addition, a strong correlation found between the local water diffusion and protein domain motion, resembling the "rocking-bundle" motion, reveals its facilitating role in the water transport.

A new method for the quantification of ambient particulate-matter emission fluxes

Abstract. An inversion method has been developed in order to quantify the emission fluxes of certain aerosol pollution sources across a wide region in the Northern Hemisphere, mainly in Europe and western Asia. The data employed are the aerosol contribution factors deducted by positive matrix factorization (PMF) on a PM2.5 chemical composition dataset from 16 European and Asian cities for the period 2014 to 2016. The spatial resolution of the method corresponds to the geographic grid cell size of the Lagrangian particle dispersion model (Flexible Particle Dispersion Model, FLEXPART, 1∘ × 1∘) which was utilized for the air mass backward simulations. The area covered is also related to the location of the 16 cities under study. Species with an aerodynamic geometric mean diameter of 400 nm and 3.1 µm and a geometric standard deviation of 1.6 and 2.25, respectively, were used to model the secondary sulfate and dust aerosol transport. Potential source contribution function (PSCF) analysis and generalized Tikhonov regularization were applied so as to acquire potential source areas and quantify their emission fluxes. A significant source area for secondary sulfate on the east of the Caspian Sea is indicated, when data from all stations are used. The maximum emission flux in that area is as high as 10 × 10−12 kg m−2 s−1. When Vilnius, Dushanbe, and Kurchatov data were excluded, the areas with the highest emission fluxes were the western and central Balkans and southern Poland. The results display many similarities to the SO2 emission maps provided by the OMI-HTAP (Ozone Monitoring Instrument-Hemispheric Transport Air Pollution) and ECLIPSE (Evaluating the Climate and Air Quality Impacts of Short-Lived Pollutants) databases. For dust aerosol, measurements from Athens, Belgrade, Debrecen, Lisbon, Tirana, and Zagreb are utilized. The west Sahara region is indicated as the most important source area, and its contribution is quantified, with a maximum of 17.6 × 10−12 kg m−2 s−1. When we apply the emission fluxes from every geographic grid cell (1∘ × 1∘) for secondary sulfate aerosol deducted with the new method to air masses originating from Vilnius, a useful approximation to the measured values is achieved.

Benchmarking of Proton- and Neutron-Induced Nuclear Data with MCNP6.2 Using SINBAD Experiments

The effects of both proton and neutron nuclear data libraries on the neutron field produced in light targets and transported through shielding material were assessed. The general-purpose nuclear data libraries JENDL-4.0/HE, TENDL-2017, ENDF/B-VII.0, ENDF/B-VII.1, ENDF/B-VIII.0, JEFF-3.1.2, and JEFF-3.3 were benchmarked using the MCNP6.2 Monte Carlo transport code. Three experiments from the SINBAD database, namely, 52-MeV protons hitting a carbon target and 43- and 68-MeV protons hitting a 7Li target, were selected for benchmarking. This selection was made according to their relevance for the MYRRHA accelerator-driven system to support the design of beam dumps and shielding of the 100-MeV section of the MYRRHA accelerator. It is demonstrated that the prevailing factor determining the transmitted neutron spectrum shape is the proton library from which the secondary neutrons are sampled. The choice of neutron library applied for the secondary neutron transport in the carbon and lithium targets, concrete and iron shielding, is of second-order significance.

Transcriptomic and Metabolomic Analyses Reveal the Roles of Flavonoids and Auxin on Peanut Nodulation.

Rhizobia form symbiotic relationships with legumes, fixing atmospheric nitrogen into a plant-accessible form within their root nodules. Nitrogen fixation is vital for sustainable soil improvements in agriculture. Peanut (Arachis hypogaea) is a leguminous crop whose nodulation mechanism requires further elucidation. In this study, comprehensive transcriptomic and metabolomic analyses were conducted to assess the differences between a non-nodulating peanut variety and a nodulating peanut variety. Total RNA was extracted from peanut roots, then first-strand and second-strand cDNA were synthesized and purified. After sequencing adaptors were added to the fragments, the cDNA libraries were sequenced. Our transcriptomic analysis identified 3362 differentially expressed genes (DEGs) between the two varieties. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that the DEGs were mainly involved in metabolic pathways, hormone signal transduction, secondary metabolic biosynthesis, phenylpropanoid biosynthesis, or ABC transport. Further analyses indicated that the biosynthesis of flavonoids, such as isoflavones, flavonols, and flavonoids, was important for peanut nodulation. A lack of flavonoid transport into the rhizosphere (soil) could prevent rhizobial chemotaxis and the activation of their nodulation genes. The downregulation of AUXIN-RESPONSE FACTOR (ARF) genes and lower auxin content could reduce rhizobia's invasion of peanut roots, ultimately reducing nodule formation. Auxin is the major hormone that influences the cell-cycle initiation and progression required for nodule initiation and accumulates during different stages of nodule development. These findings lay the foundation for subsequent research into the nitrogen-fixation efficiency of peanut nodules.

Update tele-emergency medicine : Status quo and perspectives

Increasing numbers of rescue missions in recent years have led to agrowing staff shortage of paramedics as well as physicians in the emergency medical system (EMS) with an urgent need for optimized usage of resources. One option is the implementation of atele-EMS physician system, which has been established in the EMS of the City of Aachen since 2014. In addition to pilot projects, political decisions lead to the introduction of tele-emergency medicine. The expansion is currently progressing in various federal states, and acomprehensive introduction has been decided for North Rhine-Westphalia and Bavaria. The adaptation of the EMS physician catalog of indications is essential for the integration of atele-EMS physician. The tele-EMS physician offers the possibility of along-term and comprehensive EMS physician expertise in the EMS regardless of location and, therefore, to partially compensate for alack of EMS physicians. Tele-EMS physicians can also support the dispatch center in an advisory capacity and, for example, clarify secondary transport. Auniform qualification curriculum for tele-EMS physicians was introduced by the North Rhine and Westphalia-Lippe Medical Associations. In addition to consultations from emergency missions, tele-emergency medicine can also be used for innovative educational applications, for example, in the supervision of young physicians or recertification of EMS staff. Alack of ambulances could be compensated for by acommunity emergency paramedic, who could also be connected to the tele-EMS physician.

Secondary Structure-Dependent Charge Transport in iLOV Protein Junctions.

The composition and structure of proteins are crucial for charge migration in the solid-state charge transport (CTp). Despite much progress, it is still challenging to explore the relationship between conformational change and CTp in the complex protein system. Herein, we design three improved light-oxygen-voltage (iLOV) domains, and efficiently regulate the CTp of the iLOV self-assembled monolayers (SAMs) by pH induced conformation variation. The current density can be controlled in the range of one order of magnitude. Interestingly, the CTp of iLOV displays negative linear relations with the β-sheet contents. Single-level Landauer fitting and transition voltage spectroscopy analysis suggest that β-sheet-dependent CTp would be related to the coupling between iLOV and electrodes. This work proposes a new strategy to explore the CTp in complex molecular system. Our findings deepen the understanding on protein structure-CTp relationship, and provide predictive mode of protein CTp responses for the design of functional bioelectronics.

The pangenome structure of human pathogen Mycobacterium kansasii

The non-tuberculous Mycobacterium kansasii, is the causative agent of destructive pulmonary and extrapulmonary infections in immunocompromised persons. Incessant use of multiple antibiotics and lack of effective vaccines did little to combat M. kansasii mediated infections. Here, a bioinformatic analysis has been carried out using PanExplorer, to analyze the pangenome aimed at functional characterization of the bacterium, understanding it’s pathogenic lifestyle and recognize the factors shaping evolution and variations amongst strains. M. kansasii had a large core genome (60.2%), a small (11.9%) dispensable genome and 27.9% strain-specific genes. The core genome of M. kansasii had a high concentration of COGs (Cluster of orthologous genes) linked to energy production and conversion, amino acid transport and metabolism, nucleotide transport and metabolism, coenzyme transport and metabolism, and secondary me-tabolite biosynthesis, transport and metabolism. Interestingly, numerous genes within the core and dispensable genome were associated with pathogenesis and virulence. Noteworthy among them were type VII secretion, ESX, PP and PPE family proteins. Although, M. kansasii genomes revealed overall relatedness and conservation, genomic rearrangements caused variability within the strains. The information from this analysis could assist future microbial genomics research on M. kansasii, and further studies, e.g., concerning distinctive gene clusters, and evolution.