A review on nirS-type and nirK-type denitrifiers via a scientometric approach coupled with case studies

The denitrification process plays an important role in improving water quality and is a source/sink of nitrous oxide to the atmosphere. The second important rate-limiting step of denitrification process is...

A 13CO2 Enrichment Experiment to Study the Synthesis Pathways of Polyunsaturated Fatty Acids of the Haptophyte Tisochrysis lutea

The production of polyunsaturated fatty acids (PUFA) in Tisochrysis lutea was studied using the gradual incorporation of a 13C-enriched isotopic marker, 13CO2, for 24 h during the exponential growth of the algae. The 13C enrichment of eleven fatty acids was followed to understand the synthetic pathways the most likely to form the essential polyunsaturated fatty acids 20:5n-3 (EPA) and 22:6n-3 (DHA) in T. lutea. The fatty acids 16:0, 18:1n-9 + 18:3n-3, 18:2n-6, and 22:5n-6 were the most enriched in 13C. On the contrary, 18:4n-3 and 18:5n-3 were the least enriched in 13C after long chain polyunsaturated fatty acids such as 20:5n-3 or 22:5n-3. The algae appeared to use different routes in parallel to form its polyunsaturated fatty acids. The use of the PKS pathway was hypothesized for polyunsaturated fatty acids with n-6 configuration (such as 22:5n-6) but might also exist for n-3 PUFA (especially 20:5n-3). With regard to the conventional n-3 PUFA pathway, Δ6 desaturation of 18:3n-3 appeared to be the most limiting step for T. lutea, “stopping” at the synthesis of 18:4n-3 and 18:5n-3. These two fatty acids were hypothesized to not undergo any further reaction of elongation and desaturation after being formed and were therefore considered “end-products”. To circumvent this limiting synthetic route, Tisochrysis lutea seemed to have developed an alternative route via Δ8 desaturation to produce longer chain fatty acids such as 20:5n-3 and 22:5n-3. 22:6n-3 presented a lower enrichment and appeared to be produced by a combination of different pathways: the conventional n-3 PUFA pathway by desaturation of 22:5n-3, the alternative route of ω-3 desaturase using 22:5n-6 as precursor, and possibly the PKS pathway. In this study, PKS synthesis looked particularly effective for producing long chain polyunsaturated fatty acids. The rate of enrichment of these compounds hypothetically synthesized by PKS is remarkably fast, making undetectable the 13C incorporation into their precursors. Finally, we identified a protein cluster gathering PKS sequences of proteins that are hypothesized allowing n-3 PUFA synthesis.

Capillary Endothelial Insulin Transport: The Rate Limiting Step for Insulin-stimulated Glucose Uptake

The rate limiting step for skeletal muscle glucose uptake is transport from microcirculation to muscle interstitium. Capillary endothelium poses a barrier that delays the onset of muscle insulin action. Defining physiological barriers that control insulin access to interstitial space is difficult due to technical challenges that confront study of microscopic events in an integrated physiological system. Two physiological variables determine muscle insulin access. These are the number of perfused capillaries and the permeability of capillary walls to insulin. Disease states associated with capillary rarefaction are closely linked to insulin resistance. Insulin permeability through high resistant capillary walls of muscle poses a significant barrier to insulin access. Insulin may traverse the endothelium through narrow intercellular junctions or vesicular trafficking across the endothelial cell. Insulin is large compared to intercellular junctions making this an unlikely route. Transport by endothelial vesicular trafficking is likely the primary route of transit. Studies in vivo show movement of insulin is not insulin receptor-dependent. This aligns with single cell transcriptomics that show the insulin receptor is not expressed in muscle capillaries. Work in cultured endothelial cell lines suggest that insulin receptor activation is necessary for endothelial insulin transit. Controversies remain in the understanding of trans-endothelial insulin transit to muscle. These controversies closely align with experimental approaches. Control of circulating insulin accessibility to skeletal muscle is an area that remains ripe for discovery. Factors that impede insulin access to muscle may contribute to disease and factors that accelerate access may be of therapeutic value for insulin resistance.

Revealing a hidden intermediate of rotatory catalysis with X-ray crystallography and Molecular simulations

The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remain an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multi-step rotation process. Here, using Vacuolar or V1-type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using X-ray crystallography a new intermediate or 'dwell' is identified, which enables the release of an inorganic phosphate (or Pi) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transfor-mations, and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the sidechain level interactions transcend into larger scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. Inspection of all known rates encompassing the 4-step rotation mechanism implicates overcoming of the ADP interactions with V1-ATPase to be the rate-limiting step of motor action.

Using pH dependence to understand mechanisms in electrochemical CO reduction

Electrochemical conversion of CO(2) into hydrocarbons and oxygenates is envisioned as a promising path towards closing the carbon cycle in modern technology. To this day, however, the reaction mechanisms towards the plethora of products are disputed, complicating the search for novel catalyst materials. In order to conclusively identify the rate-limiting steps in CO reduction on Cu, we analyzed the mechanisms on the basis of constant potential DFT kinetics and experiments at a wide range of pH values (3 - 13). We find that *CO dimerization is energetically favoured as the rate limiting step towards multi-carbon products. This finding is consistent with our experiments, where the reaction rate is nearly unchanged on an SHE potential scale, even under acidic conditions. For methane, both theory and experiments indicate a change in the rate-limiting step with electrolyte pH from the first protonation step in acidic/neutral conditions to a later one in alkaline conditions. We also show, through a detailed analysis of the microkinetics, that a surface combination of *CO and *H is inconsistent with the measured current densities and Tafel slopes. Finally, we discuss the implications of our understanding for future mechanistic studies and catalyst design.

A novel hybrid SEIQR model incorporating the effect of quarantine and lockdown regulations for COVID-19

Mitigating the devastating effect of COVID-19 is necessary to control the infectivity and mortality rates. Hence, several strategies such as quarantine of exposed and infected individuals and restricting movement through lockdown of geographical regions have been implemented in most countries. On the other hand, standard SEIR based mathematical models have been developed to understand the disease dynamics of COVID-19, and the proper inclusion of these restrictions is the rate-limiting step for the success of these models. In this work, we have developed a hybrid Susceptible-Exposed-Infected-Quarantined-Removed (SEIQR) model to explore the influence of quarantine and lockdown on disease propagation dynamics. The model is multi-compartmental, and it considers everyday variations in lockdown regulations, testing rate and quarantine individuals. Our model predicts a considerable difference in reported and actual recovered and deceased cases in qualitative agreement with recent reports.

Kinetic Probes of the Origin of Activity in MOF-Based C–H Oxidation Catalysts

The development of homogeneous catalysis is enabled by the availability of a rich toolkit of kinetics experiments, such as the Hg-drop test, that differentiate catalytic activity at ligand-supported metal complexes from potential heterogeneous catalysts derived from decomposition of molecular species. Metal-organic frameworks (MOFs) have garnered significant attention as platforms for catalysis at site-isolated, interstitial catalyst sights. Unlike homogeneous catalysis, relatively few strategies have been advanced to evaluate the origin of catalytic activity in MOF-promoted reactions. Many of the MOFs that have been examined as potential catalysts are comprised of molecular constituents that represent viable catalysts in the absence of the extended MOF lattice, and thus interfacial sites and leached homogeneous species represent potential sources of catalyst activity. Here, we demonstrate that analysis of deuterium kinetic isotope effects (KIEs) and olefin epoxidation diastereoselectivity provides direct probes of the origin of catalytic activity in MOF-promoted oxidation reactions. These analyses support direct involvement of lattice-based Fe sites in the turnover-limiting step of C–H activation with Fe-MOF-74-based materials (i.e., the MOF functions as a bona fide catalyst) and evidence that Cu2-based MOF MIL-125-Cu2O2 functions as a solid-state initiator for solution-phase oxidation chemistry and is not involved in the turnover limiting step (i.e., the MOF does not function as a catalyst). We anticipate that the simple experiments described here will provide a valuable tool for clarifying the role of MOFs in C–H oxidation reactions.

Kinetic control of nascent protein biogenesis by peptide deformylase

Synthesis of bacterial proteins on the ribosome starts with a formylated methionine. Removal of the N-terminal formyl group is essential and is carried out by peptide deformylase (PDF). Deformylation occurs co-translationally, shortly after the nascent-chain emerges from the ribosomal exit tunnel, and is necessary to allow for further N-terminal processing. Here we describe the kinetic mechanism of deformylation by PDF of ribosome-bound nascent-chains and show that PDF binding to and dissociation from ribosomes is rapid, allowing for efficient scanning of formylated substrates in the cell. The rate-limiting step in the PDF mechanism is a conformational rearrangement of the nascent-chain that takes place after cleavage of the formyl group. Under conditions of ongoing translation, the nascent-chain is deformylated rapidly as soon as it becomes accessible to PDF. Following deformylation, the enzyme is slow in releasing the deformylated nascent-chain, thereby delaying further processing and potentially acting as an early chaperone that protects short nascent chains before they reach a length sufficient to recruit other protein biogenesis factors.

Overexpression of The AtWUSCHEL Gene Promotes Somatic Embryogenesis And Lateral Branch Formation In Birch (Betula Platyphylla Suk.)

Birch (Betula platyphylla Suk.) is a deciduous tree with the value of medicinal and ornamental greening. Plant somatic embryogenesis is a limiting step in birch genetic breeding. As a transcription factor, the Arabidopsis thaliana WUSCHEL (AtWUS) gene plays an important role in maintaining and regulating stem cell characteristics. It determines whether the stem cell population is differentiated. To explore the method of inducing somatic embryogenesis in birch. We overexpressed the AtWUS gene and transferred it into birch. The expression of AtWUS increased the somatic embryogenesis rate from 101.4% to 717.1%. The expression of the AtWUS gene in calli and globular embryos led to the downregulation of the BpWUS gene. The BpLEC1, BpLEC2, BpFUS3 and BpABI3 genes were upregulated. In addition, overexpression of AtWUS increased the number of lateral branches and bud meristem in birch. Similarly, the BpWUS gene was downregulated in the bud meristem. The BpLEC1, BpLEC2, BpFUS3, BpSTM and BpCUC2 genes were upregulated. This result indicated that overexpression of the AtWUS gene promoted somatic embryogenesis (SE) by increasing the expression of SE-related genes. In conclusion, this study focused on the role of the AtWUS gene in birch SE and the molecular mechanism of promoting SE.