Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli

Background Bioconversion of levoglucosan, a promising sugar derived from the pyrolysis of lignocellulose, into biofuels and chemicals can reduce our dependence on fossil-based raw materials. However, this bioconversion process in microbial strains is challenging due to the lack of catalytic enzyme relevant to levoglucosan metabolism, narrow production ranges of the native strains, poor cellular transport rate of levoglucosan, and inhibition of levoglucosan metabolism by other sugars co-existing in the lignocellulose pyrolysate. The heterologous expression of eukaryotic levoglucosan kinase gene in suitable microbial hosts like Escherichia coli could overcome the first two challenges to some extent; however, no research has been dedicated to resolving the last two issues till now. Results Aiming to resolve the two unsolved problems, we revealed that seven ABC transporters (XylF, MalE, UgpB, UgpC, YtfQ, YphF, and MglA), three MFS transporters (KgtP, GntT, and ActP), and seven regulatory proteins (GalS, MhpR, YkgD, Rsd, Ybl162, MalM, and IraP) in the previously engineered levoglucosan-utilizing and ethanol-producing E. coli LGE2 were induced upon exposure to levoglucosan using comparative proteomics technique, indicating these transporters and regulators were involved in the transport and metabolic regulation of levoglucosan. The proteomics results were further verified by transcriptional analysis of 16 randomly selected genes. Subsequent gene knockout and complementation tests revealed that ABC transporter XylF was likely to be a levoglucosan transporter. Molecular docking showed that levoglucosan can bind to the active pocket of XylF by seven H-bonds with relatively strong strength. Conclusion This study focusing on the omics discrepancies between the utilization of levoglucosan and non-levoglucosan sugar, could provide better understanding of levoglucosan transport and metabolism mechanisms by identifying the transporters and regulators related to the uptake and regulation of levoglucosan metabolism. The protein database generated from this study could be used for further screening and characterization of the transporter(s) and regulator(s) for downstream enzymatic/genetic engineering work, thereby facilitating more efficient microbial utilization of levoglucosan for biofuels and chemicals production in future.

Mathematical models of neuronal growth

The establishment of a functioning neuronal network is a crucial step in neural development. During this process, neurons extend neurites—axons and dendrites—to meet other neurons and interconnect. Therefore, these neurites need to migrate, grow, branch and find the correct path to their target by processing sensory cues from their environment. These processes rely on many coupled biophysical effects including elasticity, viscosity, growth, active forces, chemical signaling, adhesion and cellular transport. Mathematical models offer a direct way to test hypotheses and understand the underlying mechanisms responsible for neuron development. Here, we critically review the main models of neurite growth and morphogenesis from a mathematical viewpoint. We present different models for growth, guidance and morphogenesis, with a particular emphasis on mechanics and mechanisms, and on simple mathematical models that can be partially treated analytically.

Tell me what type of extracellular vesicles you secrete, and I will tell you who you are: yeast or hypha

The transition between yeast and hyphal morphologies plays a crucial role in the pathogenicity of Candida albicans. Recent studies have pointed out the great relevance of extracellular vesicles (EVs) secreted by microorganisms in a wide variety of biological processes including interaction with the host. Therefore, the main objective of this work was to compare the EVs secreted by yeast and hyphal forms to shed light on C. albicans-host interaction. EVs were obtained by ultracentrifugation of the culture medium supernatant and analysed by mass spectrometry. They were characterized by transmission electronic microscopy (TEM) and dynamic light scattering (DLS). DLS and TEM analysis showed that yeast EVs were significantly bigger than hyphal EVs, being most of them in the range between 400 to 500nm while hyphal EVs were ranged mostly around 100-200nm. Proteomic analysis showed greater protein diversity in hyphal EVs when compared to yeast EVs (up to 1700 different proteins identified versus 300), although less amount of total protein was obtained. Gene Ontology (GO) analysis showed that yeast EVs were enriched in surface proteins while hyphal EVs, although containing also most of these surface proteins, were also significantly and exclusively enriched in proteins involved in protein metabolism (ribosomal proteins, many aminoacid-pathway enzymes and proteasome) and cellular transport. The differences between YEVs and HEVs also prompted a different immune host response, as tested with macrophage cell cultures and human sera from patients with invasive candidiasis. All these differences point out a possible different biogenesis and roles of EVs secreted by both morphologies.

A Comparative Transcriptomic Meta-Analysis Revealed Conserved Key Genes and Regulatory Networks Involved in Drought Tolerance in Cereal Crops

Drought affects plant growth and development, causing severe yield losses, especially in cereal crops. The identification of genes involved in drought tolerance is crucial for the development of drought-tolerant crops. The aim of this study was to identify genes that are conserved key players for conferring drought tolerance in cereals. By comparing the transcriptomic changes between tolerant and susceptible genotypes in four Gramineae species, we identified 69 conserved drought tolerant-related (CDT) genes that are potentially involved in the drought tolerance of all of the analysed species. The CDT genes are principally involved in stress response, photosynthesis, chlorophyll biogenesis, secondary metabolism, jasmonic acid signalling, and cellular transport. Twenty CDT genes are not yet characterized and can be novel candidates for drought tolerance. The k-means clustering analysis of expression data highlighted the prominent roles of photosynthesis and leaf senescence-related mechanisms in differentiating the drought response between tolerant and sensitive genotypes. In addition, we identified specific transcription factors that could regulate the expression of photosynthesis and leaf senescence-related genes. Our analysis suggests that the balance between the induction of leaf senescence and maintenance of photosynthesis during drought plays a major role in tolerance. Fine-tuning of CDT gene expression modulation by specific transcription factors can be the key to improving drought tolerance in cereals.

Effect of sequential electrospinning and co-electrospinning on morphological and fluid mechanical wall properties of polycaprolactone and bovine gelatin scaffolds, for potential use in small diameter vascular grafts

Background Nowadays, the engineering vascular grafts with a diameter less than 6 mm by means of electrospinning, is an attracted alternative technique to create different three-dimensional microenvironments with appropriate physicochemical properties to promote the nutrient transport and to enable the bioactivity, dynamic growth and differentiation of cells. Although the performance of a well-designed porous wall is key for these functional requirements maintaining the mechanical function, yet predicting the flow rate and cellular transport are still not widely understood and many questions remain open about new configurations of wall can be used for modifying the conventional electrospun samples. The aim of the present study was to evaluate the effect of fabrication techniques on scaffolds composed of bovine gelatin and polycaprolactone (PCL) developed by sequential electrospinning and co-electrospinning, on the morphology and fluid-mechanical properties of the porous wall. Methodology For this purpose, small diameter tubular structures were manufactured and experimental tests were performed to characterize the crystallinity, morphology, wettability, permeability, degradability, and mechanical properties. Some samples were cross-linked with Glutaraldehyde (GA) to improve the stability of the gelatin fiber. In addition, it was analyzed how the characteristics of the scaffold favored the levels of cell adhesion and proliferation in an in vitro model of 3T3 fibroblasts in incubation periods of 24, 48 and 72 h. Results It was found that in terms of the morphology of tubular scaffolds, the co-electrospun samples had a better alignment with higher values of fiber diameters and apparent pore area than the sequential samples. The static permeability was more significant in the sequential scaffolds and the hydrophilic was higher in the co-electrospun samples. Therefore, the gelatin mass losses were less in the co-electrospun samples, which promote cellular functions. In terms of mechanical properties, no significant differences were observed for different types of samples. Conclusion This research concluded that the tubular scaffolds generated by sequential and co-electrospinning with modification in the microarchitecture could be used as a vascular graft, as they have better permeability and wettability, interconnected pores, and a circumferential tensile strength similar to native vessel compared to the commercial graft analyzed.

The Fly Homologue of MFSD11 Is Possibly Linked to Nutrient Homeostasis and Has a Potential Role in Locomotion: A First Characterization of the Atypical Solute Carrier CG18549 in Drosophila Melanogaster

Cellular transport and function are dependent on substrate influx and efflux of various compounds. In humans, the largest superfamily of transporters is the SoLute Carriers (SLCs). Many transporters are orphans and little to nothing is known about their expression and/or function, yet they have been assigned to a cluster called atypical SLCs. One of these atypical SLCs is MFSD11. Here we present a first in-depth characterization of the MFSD11, CG18549. By gene expression and behavior analysis on ubiquitous and brain-specific knockdown flies. CG18549 knockdown flies were found to have altered adipokinetic hormone and adipokinteic hormone receptor expression as well as reduced vesicular monoamine transporter expression; to exhibit an altered locomotor behavior, and to have an altered reaction to stress stimuli. Furthermore, the gene expression of CG18549 in the brain was visualized and abundant expression in both the larvae and adult brain was observed, a result that is coherent with the FlyAtlas Anatomy microarray. The exact mechanism behind the observed behaviors is not fully understood, but this study provides new insights into the expression and function of CG18549. Clearly, these results provide a strong example as to why it is vital to fully characterize orphan transporters and through that gain knowledge about the body during normal condition and disease.

The Role of Extended Range of Interactions in the Dynamics of Interacting Molecular Motors

Motor proteins, also known as biological molecular motors, play important roles in various intracellular processes. Experimental investigations suggest that molecular motors interact with each other during the cellular transport, but the nature of such interactions remains not well understood. Stimulated by these observations, we present a theoretical study aimed to understand the effect of the range of interactions on dynamics of interacting molecular motors. For this purpose, we develop a new version of the totally asymmetric simple exclusion processes in which nearest-neighbor as well as the next nearest-neighbor interactions are taken into account in a thermodynamically consistent way. A theoretical framework based on a cluster mean-field approximation, which partially takes correlations into account, is developed to evaluate the stationary properties of the system. It is found that fundamental current-density relations in the system strongly depend on the strength and the sign of interactions, as well as on the range of interactions. For repulsive interactions stronger than some critical value, increasing the range of interactions leads to a change from unimodal to trimodal dependence in the flux-density fundamental diagram. Theoretical calculations are tested with extensive Monte Carlo computer simulations. Although in most ranges of parameters excellent agreement between theoretical predictions and computer simulations is observed, there are situations when the cluster mean-field approach fails to describe properly the dynamics in the system. Theoretical arguments to explain these observations are presented. Our theoretical analysis clarifies the microscopic picture of how the range of interactions influences the dynamics of interacting molecular motors.