The most widespread intracellular bacteria in the animal kingdom are maternally-inherited endosymbionts of the genus Wolbachia. Their prevalence in arthropods and nematodes worldwide and a stunning arsenal of parasitic and mutualistic adaptations make these bacteria a biological archetype for basic studies of symbiosis and applied outcomes for curbing human and agricultural diseases. Here, we conduct a summative, centennial analysis of living in the Wolbachia world. We synthesize literature on Wolbachia’s host range, phylogenetic diversity, genomics, cell biology, and applications to filarial, arboviral, and agricultural diseases. We also review the mobilome of Wolbachia including phage WO and its essentiality to hallmark phenotypes in arthropods. Finally, the Wolbachia system is an exemplar for discovery-based science education using biodiversity, biotechnology, and bioinformatics lessons. As we approach a century of Wolbachia research, applications, and education, the interdisciplinary science and knowledge from this symbiosis stand as a model for consolidating and teaching the integrative rules of endosymbiotic life.

Many academics are critical of the current publishing system, but it is difficult to create a better alternative. This review relates to the Sciences and Social Sciences, and discusses the primary purpose of academic journals as providing a seal of approval for perceived quality, impact, significance, and importance. The key issues considered include the role of anonymous refereeing, continuous rather than discrete frequency of publications, avoidance of time wasting, and seeking adventure. Here we give recommendations about the organization of journal articles, the roles of associate editors and referees, measuring the time frame for refereeing submitted articles in days and weeks rather than months and years, encouraging open access internet publishing, emphasizing the continuity of publishing online, academic publishing as a continuous dynamic process, and how to improve research after publication. Citations and functions thereof, such as the journal impact factor and h-index, are the benchmark for evaluating the importance and impact of academic journals and published articles. Even in the very top journals, a high proportion of published articles are never cited, not even by the authors themselves. Top journal publications do not guarantee that published articles will make significant contributions, or that they will ever be highly cited. The COVID-19 world should encourage academics worldwide not only to rethink academic teaching, but also to re-evaluate key issues associated with academic journal publishing in the future.

Introduction: A large number of COVID-19 publications has created a need to collect all research-related material in practical and reliable centralized databases. The aim of this study was to evaluate the functionality and quality of the compiled World Health Organisation COVID-19 database and compare it to Pubmed and Scopus. Methods: Article metadata for COVID-19 articles and articles on 8 specific topics related to COVID-19 was exported from the WHO global research database, Scopus and Pubmed. The analysis was conducted in R to investigate the number and overlapping of the articles between the databases and the missingness of values in the metadata. Results: The WHO database contains the largest number of COVID-19 related articles overall but retrieved the same number of articles on 8 specific topics as Scopus and Pubmed. Despite having the smallest number of exclusive articles overall, the highest number of exclusive articles on specific COVID-19 related topics was retrieved from the Scopus database. Further investigation revealed that PubMed and Scopus have more comprehensive structure than the WHO database, and less missing values in the categories searched by the information retrieval systems. Discussion: This study suggests that the WHO COVID-19 database, even though it is compiled from multiple databases, has a very simple and limited structure, and significant problems with data quality. As a consequence, relying on this database as a source of articles for systematic reviews or bibliometric analyses is undesirable.

Limnologists often adhere to a discretized view of waterbodies—they classify them, divide them into zones, promote discrete management targets, and use research tools, experimental designs, and statistical analyses focused on discretization. This approach to limnology has profoundly benefited the way we understand, manage, and communicate about waterbodies. But the research questions and the research tools in limnology are changing rapidly with consequences for the relevance of our current discretization schemes. Here, I examine how and why we discretize and argue that selectively rethinking the extent to which we must discretize gives us an exceptional chance to advance limnology in new ways.

Nanotechnology is a multidisciplinary science covering matters involving nanoscale level that is being developed for a great variety of applications. Nanomedicine is one of these attractive and challenging uses focused on the employment of nanomaterials in medical applications such as drug delivery. However, the uses of these nanometric systems requires specific parameters to establish the possible advantages and disadvantages in specific applications. This review presents the fundamental factors of nanoparticles and it´s microenvironment that must be considered to make an appropriate design for medical applications: (i) Interactions between nanoparticles and their biological environment, (ii) the interaction mechanisms, (iii) and the physicochemical properties of nanoparticles. On the other hand, the repercussions of the control, alteration and modification of these parameters in the final applications. Additionally, we here briefly report the implications of nanoparticles in nanomedicine and provide perspectives for some particular applications which still are challenged

The outbreak of COVID-19, the disease caused by SARS-CoV-2, continues to affect millions of people around the world. The absence of a globally distributed effective treatment makes the exploration of new mechanisms of action a key step to address this situation. Stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS-CoV has been reported as a valid strategy to inhibit viral replication. In this study, the applicability of this unexplored mechanism of action against SARS-CoV-2 is analyzed. During our research, we were able to find three inducible interfaces of SARS-CoV-2 N protein NTD, compare them to the previously reported MERS-CoV stabilized dimers, and identify those residues that are responsible for their formation. A drug discovery protocol implemented consisting of docking, molecular dynamics and MM-GBSA enabled us to find several compounds that might be able to exploit this mechanism of action. In addition, a common catechin skeleton was found among many of these molecules, which might be useful for further drug design. We consider that our findings could motivate future research in the fields of drug discovery and design towards the exploitation of this previously unexplored mechanism of action against COVID-19.

This study assessed bio-equivalence of high-quality, plant-based protein blends versus Whey Protein Isolate (WPI) in healthy, resistance-trained men. The primary endpoint was incremental area under the curve (iAUC) of blood essential Amino Acids (eAAs) 4 hours after consumption of each product. Cmax and Tmax of blood leucine were secondary outcomes. Subjects (n=18) consumed three plant-based protein blends and WPI (control). Analysis of Variance model was used to assess for bio-equivalence of total sum of blood eAA concentrations. The total blood eAA iAUC ratios of the three blends were: [90% CI]: #1: 0.66 [0.58-0.76]; #2: 0.71 [0.62-0.82]; #3: 0.60 [0.52-0.69], not completely within the pre-defined equivalence range [0.80-1.25], indicative of 30-40% lower iAUC versus WPI. Leucine Cmax of the three blends was not equivalent to WPI, #1: 0.70 [0.67-0.73]; #2: 0.72 [0.68-0.75]; #3: 0.65 [0.62 – 0.68], indicative of a 28-35% lower response. Leucine Tmax for two blends were similar to WPI (#1: 0.94 [0.73-1.18]; #2: 1.56 [1.28-1.92]; #3: 1.19 [0.95-1.48]). The plant-based protein blends were not bio-equivalent. However, blood leucine kinetic data across the blends approximately doubled from fasting concentrations whereas blood Tmax data across two blends was similar to WPI. This suggests evidence of rapid hyperleucinemia, which correlates with a protein’s anabolic potential.

In this article, we present solutions for one of the oldest mathematical problems, the Collatz Conjecture, and provide a proof for the Riemann Hypothesis, utilizing a new number theory based on newly discovered number properties, which will also be presented in this paper. This is made possible through the Sophy-Peter mathematical framework, built upon this new number theory. The Collatz Conjecture will be disproven, but as an alternative, the Oscillating Theorem will be introduced, with its correctness proven within this article. Furthermore, we present the general version of the Riemann zeta function, developed based on the new number theory. The correctness of this function is verified by comparing it with existing results of the zeta function. Using this approach and the Sophy-Peter framework, we have successfully proven the Riemann Hypothesis, long considered a millennium problem. Moreover, since the general zeta function is proven, this implies the correctness of the new number theory and the Sophy-Peter framework.

Predicting and evaluating the vitality level of public spaces of urban design is crucial before new construction and renewal, especially for developing countries, to avoid failures like "ghost neighborhood" and reduce resource waste. However, existing assessment methods for the urban vitality are either static and ignore changes in the time dimension, or rely on historical big data and are unable to predict unbuilt projects. This study combines previous methods and crowds’ characteristics observation in public space, puts forward the crowd-frequency hypothesis and constructs an algorithm, and establishes a time-dimensional urban vitality dynamic prediction model. Taking the Rundle Mall neighborhood in Adelaide, Australia, as an example, the effec-tiveness of the prediction model was proved through on-site observation sampling comparative verification method. In addition, the decision tree model was used to conduct machine learning on the case data, and a set of algorithm programs were obtained that can directly input some basic information to obtain the urban vitality level (high-medium-low) in a certain period. It can be used as a tool to support the design and decision-making processes of urban planners and government officials, providing a low-cost way to achieve sustainable urban vitality construction of late-developing cities directly.

Given the accelerating scientific, clinical and consumer interest in highly-prevalent functional gastrointestinal disorders, appropriate therapeutic strategies are needed to address the many aspects of digestive dysfunction. Accumulating evidence for the crucifer-derived bioactive molecule, sulforaphane in upstream cellular defence mechanisms highlights its potential as a therapeutic candidate in targeting functional gastrointestinal conditions together with systemic disorders. This article catalogues the evolution of and rationale for a hypothesis that utilises multifunctional sulforaphane as the initial step in restoring the ecology of the gut ecosystem; it does this primarily by targeting the functions of intestinal epithelial cells. A growing body of work has identified the colonocyte as the driver of dysbiosis, so that targeting gut epithelial function could provide an alternative to targeting the microbes themselves for remediation of microbial dysbiosis. The hypothesis discussed herein has evolved over several years and is supported by case studies showing the application of sulforaphane in gastrointestinal disorders, related food intolerance and several systemic conditions. To our knowledge, this is the first time the effects of sulforaphane have been reported in a clinical environment where several of its key properties within the gut ecosystem appear to be related to its nutrigenomic effects on gene expression.

We present a plausible solution to the now forty seven year old paleoclimatology riddle of the so-called Faint Young Sun Paradox via the combined hypothesis of the conservation of the state of radiation balance between the Earth and Sun and that of an expanding Earth, where, in the face of a changing (increasing) Solar luminosity, the Earth would maintain steady temperatures by re-adjusting the height of its atmosphere. That is to say, depending on whether or not the radius of the solid Earth is changing, this re-adjustment of the height of the Earth’s atmosphere would mean two things — i.e.: (1) either the height increases — in which event the Earth accretes matter from its immediate surroundings (i.e., the obvious pool formed by the Solar wind) thereby increasing the mass of the Earth’s atmosphere, or: (2) the height decreases — in which event the Earth naturally expels matter from its atmosphere, thereby decreasing the effective mass of the Earth. We demonstrate that if –- as the current state of the art ITRF observations seem to indicate, namely that — the Earth’s landmass is steadily expanding globally at a paltry rate of ∼+0.45±0.05mm·yr−1, and, that the Earth’s atmosphere is to have a present radial vertical height of about one third of the Earth’s radius (∼2860km) from the Earth’s surface, then, one can (might) with relative ease, explain not only the presence of liquid water on the Earth’s surface some ∼3.20±0.70Gyr ago during the Archaean eon when the Sun was about 75% of its current luminosity, but also the present radial expansion rate of the Earth. When all is said and done, the Earth system is herein cast as an auto-self-regulating incubator where the auto-self-regulating mechanism is as a result of the Earth’s atmosphere responding by automatically re-adjusting its height.

No single evolutionary event has been identified as the cause for the final emergence of our species. I propose that a mutation on CD155 receptor gene occurred to establish a symbiosis with poliovirus, which exerted its beneficial impact via RNA dependent non-genetic transgenerational inheritance, which caused a qualitative enhancement of cognitive functions. I posit that this mutation occurred in what we call, Anatomically Modern Humans, our immediate ancestor species and that the disruption of this symbiosis causes autism spectrum disorder. Positive selection of CD155 to the extent of becoming a species defining characteristic, the chronology of autism spectrum disorder prevalence increase and continued increase, the multigenerational nature of RNA inheritance, the universal infection of humans by poliovirus and a very low associated mortality rate, and several other factors support this hypothesis. Specific genetic, epidemiological and sperm miRNA content studies are suggested to test this hypothesis.

The sheer number of gene variants and the extent of the observed clinical and molecular heterogeneity recorded in neuropsychiatric disorders (NPDs), could be due to the magnified downstream effects initiated by a smaller group of genomic higher order alterations in response to endogenous or environmental stress. Chromosomal common fragile sites (CFS) are functionally linked with microRNA’s, gene copy number variants (CNVs), sub-microscopic deletions and duplications of DNA, rare single-nucleotide variants (SNVs/SNPs) and small insertions/deletions (indels), as well as chromosomal translocations, gene duplications, altered methylation, microRNA and L1 transposon activity and 3-D chromosomal topology characteristics. These genomic structural features have been linked with various NPDs in mostly isolated reports, and have usually only been viewed as areas harboring potential candidate genes of interest. The suggestion to use a higher level entry point, (the ‘fragilome’ and associated features), activated by a central mechanism (‘stress’) for studying NPD genetics, has the potential to unify the existing vast number of different observations in this field. This approach may explain the continuum of gene findings distributed between affected and unaffected individuals, the clustering of NPD phenotypes and overlapping comorbidities, the extensive clinical and molecular heterogeneity and the association with certain other medical disorders.

Low nasal nitric oxide (nNO) is a typical feature in Primary Ciliary Dyskinesia (PCD). nNO is part of the PCD diagnostic algorithm due to its discriminative power against other lung diseases such cystic fibrosis (CF). However, the underlying pathomechanisms are elusive. To better understand NO dysregulation in PCD, the L-arginine/NO (Arg/NO) pathway in patients with PCD (pwPCD) and CF (pwCF) and in healthy control (HC) subjects was investigated. In a prospective, controlled study, we measured in 24 pwPCD, 25 age-matched pwCF, and 14 HC the concentrations of the NO precursors Arg and homoarginine (hArg), the arginase metabolite ornithine (Orn), the NO inhibitor asymmetric dimethylarginine (ADMA), and the major NO metabolites (nitrate, nitrite) in sputum, plasma and urine by validated methods. In comparison to HC, the sputum contents (in µmol/mg) of L-Arg (PCD 18.43 vs. CF 329.46 vs. HC 9.86, p < 0.001) and of ADMA (PCD 0.055 vs. CF 0.015 vs. HC 0.010, p < 0.001) were higher. In contrast, the sputum contents (in µmol/mg) of nitrate and nitrite were lower in PCD compared to HC (nitrite 4.54 vs. 9.26, p = 0.023; nitrate 12.86 vs. 40.33, p = 0.008), but higher in CF (nitrite 16.28, p <0.001; nitrate 56.83, p = 0.002). The metabolite concentrations in urine and plasma were similar in all groups. The results of our study indicate that PCD, unlike CF, is associated with impaired NO synthesis in the lung, presumably due to mechano-chemical uncoupling.

How important are institutions for the development of nations? Are there any existing measures which quantify the behavior of institutions? Is there any theoretical justification for measuring their behavior? This paper introduces a framework influenced by Plato’s needs theory to provide justification for measuring the behavior of institutions. This involves introducing the humanization hypothesis which states that the behavior of institutions can be measured as they, similar to human beings, are living entities with similar hierarchical needs which are essential for their survival. The paper employs an explanatory and descriptive research design which is highly theoretical in nature.

In the current era of ‘big data’, scientists are able to quickly amass enormous amount of data in a limited number of experiments. The investigators then try to hypothesize about the root cause based on the observed trends for the predictors and the response variable. This involves identifying the discriminatory predictors that are most responsible for explaining variation in the response variable. In the current work, we investigated three related multivariate techniques: Principal Component Regression (PCR), Partial Least Squares or Projections to Latent Structures (PLS), and Orthogonal Partial Least Squares (OPLS). To perform a comparative analysis, we used a publicly available dataset for Parkinson’ disease patien ts. We first performed the analysis using a cross-validated number of principal components for the aforementioned techniques. Our results demonstrated that PLS and OPLS were better suited than PCR for identifying the discriminatory predictors. Since the X data did not exhibit a strong correlation, we also performed Multiple Linear Regression (MLR) on the dataset. A comparison of the top five discriminatory predictors identified by the four techniques showed a substantial overlap between the results obtained by PLS, OPLS, and MLR, and the three techniques exhibited a significant divergence from the variables identified by PCR. A further investigation of the data revealed that PCR could be used to identify the discriminatory variables successfully if the number of principal components in the regression model were increased. In summary, we recommend using PLS or OPLS for hypothesis generation and systemizing the selection process for principal components when using PCR.rewordexplain later why MLR can be used on a dataset with no correlation

World Health Organization (WHO) provides the guideline for managing the Particulate Matter (PM) level because when the PM level is higher, it threats the human health. For managing PM level, the procedure for measuring PM value is needed firstly. We use Tapered Element Oscillating Microbalance (TEOM)-based PM measuring sensors because it shows higher cost-effectiveness than Beta Attenuation Monitor (BAM)-based sensor. However, TEOM-based sensor has higher probability of malfunctioning than BAM-based sensor. In this paper, we call the overall malfunction as an anomaly, and we aim to detect anomalies for the maintenance of PM measuring sensors. We propose a novel architecture for solving the above aim that named as Hypothesis Pruning Generative Adversarial Network (HP-GAN). We experimentally compare the several anomaly detection architectures to certify ours performing better.

The article addresses the function of (post)colonial nostalgia in a context of multidirectional memory (Rothberg 2009) in contemporary Europe. How can different cultural memories of the Second Word War be put into respectful dialogue with each other? The text is based on a contrapuntal reading (Said 1994) of British and Egyptian popular narratives, using a qualitative content analysis of 10 British tv documentary films about the North Africa Campaign, and data from qualitative interviews collected during ethnographic fieldwork in Alexandria and Cairo, Egypt, during visits 2013--2015. The study highlights considerable differences between the British and Egyptian narratives, but also significant similarities regarding the use and function of nostalgia. In addition, the Egyptian narrative expresses a profound cosmopolitan nostalgia and a longing for what is regarded as Egypt’s lost, modern Golden Age, identified as the decades before the nation’s fundamental change from western-oriented monarchy to Nasser’s Arab nationalist military state. The common elements between the two national narratives indicate a possibly fruitful way to open up for a shared popular memory culture about the war years, including postcolonial aspects.

Heat Shock Proteins play a crucial role in maintaining cellular integrity during thermal stress conditions, acting as chaperones and participating in the regulation of cellular responses. The focus was to contribute valuable insights into the potential role of hypericin in modulating these heat shock proteins and its implications for anti-tumoral properties. This study employs computational methods, specifically molecular docking, to investigate the potential biological interactions between the chaperone proteins HSP90 and HSC70 and Hypericin, a natural compound recognized for its anti-tumor properties. Despite the limited existing studies in this domain, this research aims to uncover structural insights into the binding mechanisms between Hypericin and these heat shock proteins. In the docking assessments, hypericin demonstrated notable binding energy results, exhibiting a binding energy of -10.5 kcal/mol with Heat Shock Cognate 71 kDa protein and -11.2 kcal/mol with Heat Shock Protein HSP90-alpha.

The aim of this study was to investigate the biochemical properties and gel-forming capacity of duck myofibrillar proteins under the effects of 2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH)-mediated oxidation. Duck myofibrillar proteins were extracted and treated with different concentrations of AAPH solutions (0, 1, 3, 5, 10 mmol/L) and then analysed for carbonyl content, dynamic rheology, protein profiles and gel-forming properties (colour, water holding capacity, hardness, protein profile, microstructure). The results showed that with increasing AAPH concentration, the carbonyl content of protein showed an increasing trend (p < 0.05); SDS-PAGE pattern results indicated that moderate oxidation (3 mmol/L AAPH) induced myosin aggregation via covalent bonds including disulfide, enhanced protein-protein, and thus improved protein-water interactions and gel strength of DMPs heat-induced gels. However, high oxidation (5 and 10 mmol/L AAPH) led to partial degradation of myosin heavy chain (MHC), as evidenced by lower storage modulus and irregular microstructure, which significantly reduced gelation ability. These results suggest that the internal relationship between alkanoperoxy radical-induced oxidation should be taken into account in the processing of duck meat, as mild protein oxidation is conducive to improving gel quality.

The expanding global population has increased the demand for sustainable protein sources, and microbial protein (MP) has emerged as a promising alternative. However, conventional carbon (glucose) and nitrogen (ammonia, urea) sources needed for MP production pose environmental and economic issues. This study aims to produce protein using lignocellulosic biomass (LCB) as a carbon source and the nitrogen fixation ability of Klebsiella oxytoca M5A1 as a nitrogen source. The study investigates the pretreatment of LCB (switchgrass), enzymatic hydrolysis, protein quantification, and high-performance liquid chromatography system (HPLC) analysis to track glucose utilization and organic acid production. K. oxytoca M5A1 harnessed free nitrogen from the atmosphere through nitrogen fixation and used abundant, cheap glucose from LCB to produce MP and organic acids as by-products. Protein production occurred in two phases: first within the initial 8 hours and secondly, within the last 16 hours. The highest protein concentration was at 40 hours, with approximately 68.3% protein content. HPLC analysis revealed a dynamic profile of glucose utilization and organic acids (Lactic acid, Propionic acid, Acetic acid, and Succinic acid). K. oxytoca M5A1 exhibited an early high rate of glucose consumption, and conversion to organic acids that were later used for second-phase protein production. The acids profile revealed intra-conversion from one acid to another via metabolic pathways (glycolysis and tricarboxylic acid cycle). Overall, leveraging LCB and the nitrogen-fixing ability of K. oxytoca M5A1 for MP production offers an eco-friendly and cost-effective alternative to traditional protein sources, contributing to a sustainable circular economy.

Industrialization, intensive farming, rapid population growth and urbanization are the source of a large number of pollutants entering the environment. The current concentration of xenobiotics released into the environment exceeds its natural ability to decompose them. Enzymatic degradation of pollutants seems to be an environmentally friendly process. Due to the wide spectrum of substrate specificity, from inorganic compounds to high molecular weight organic compounds such as PAH or dyes, as well as favorable biochemical properties, laccase has been used in the biological removal of xenobiotics from the environment. It is important to understand the degradation mechanisms of pollutants and to evaluate the final products in terms of their toxicity. The laccase oxidizes the substrates with the simultaneous reduction of molecular oxygen to water, which is the purest reaction co-substrate. That is why it is called a green biocatalyst. The trend is an increase in the production of enzymes related to the intensive development of industry, bioremediation or synthetic chemistry. This leads to the search for laccases with greater activity and stability under extreme conditions. The potential of laccases to degrade xenobiotics can be promoted by improving enzymatic catalytic characterization using protein engineering and other genetic engineering methods.

The Rho guanine nucleotide exchange factor (RGNEF) protein encoded by the ARHGEF28 gene has been implicated in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Biochemical and pathological studies have shown that RGNEF is a component of the hallmark neuronal cytoplasmic inclusions in ALS-affected neurons. Additionally, a heterozygous mutation in ARHGEF28 has been identified in a number of familial ALS (fALS) cases that may give rise to one of two truncated variants of the protein. Little is known about the normal biological function of RGNEF or how it contributes to ALS pathogenesis. To further explore RGNEF biology we have established and characterized a yeast model and characterized RGNEF expression in several mammalian cell lines. We demonstrate that RGNEF is toxic when overexpressed and forms inclusions. We also found that the fALS-associated mutation in ARGHEF28 gives rise to an inclusion-forming and toxic protein. Additionally, through unbiased screening using the split-ubiquitin system, we have identified RGNEF interacting proteins, including two ALS-associated proteins. Functional characterization of other RGNEF interactors identified in our screen suggest that RGNEF functions as a microtubule regulator. Our findings indicate that RGNEF misfolding and toxicity may cause impairment of the microtubule network and contribute to ALS pathogenesis.

The exploration and identification of targets and pathways for Atopic dermatitis (AD) treatment and diagnosis are critical for AD control. The conventional target exploration approach such as the literature review is not satisfying in terms of efficiency and accuracy. Recently, the bioinformatic approach is drawing attention for its unique advantage of high-volume data analysis for target and pathway exploration; Open Targets Platform is the targets source for this study to extract top 200 high-rank proteins from 3122 AD associated proteins. STRING, Cytoscape, CytoHubba, ClueGo, and CluePedia function had been applied for data analysis. The KEGG Mapper search & colour pathway was the pathway map resource for identified pathways; 23 key hub genes (VDR, KIT, BCL2L11, NFKBIA, KRAS, IL13, JAK2, STAT3, IL21, IL4R, REL, PDGFRB, FOXP3, RARA, RELB, EGFR, IL21R, MYC, CREBBP, NR3C1, IL2, JAK1, and KITLG). Additionally, 8 correlated pathways and the biological process had been identified; Through this study, a viable approach for target and pathway exploration had been presented. The identified AD targets and pathways will be tested for upcoming research for traditional Chinese medicinal herb interactions

Proteins having a variety of functions play many essential roles in maintaining various life activities in organisms. Various methods, by which new protein functions can be artificially produced, have progressed rapidly upon development in recombinant DNA technology and effective screening techniques. However, the obtainable scope of the new functions has been restricted in a narrow range, because only functions of presently existing proteins can be used. On the other hand, it has been considered that it would be impossible to create an entirely new protein, which does not show any meaningful homology with any other amino acid sequences of previously existing proteins. The reason is because one amino acid sequence for a protein cannot be selected out from an extraordinary large amino acid sequence diversity as ~10130. As a matter of course, it is impossible to design an amino acid sequence of a protein in advance and a gene encoding the protein cannot be also formed through random process. Nevertheless, extant organisms have generated a variety of entirely new proteins in some way to make full use of them. This means that extant organisms have equipped a mechanism with which entirely new proteins can be produced under the present core life system composed of protein, tRNA (genetic code) and gene. In this article, first I introduce the mechanism, with which entirely new proteins are created in extant organisms, and further propose a novel strategy for application of the mechanism to protein engineering through creation of entirely new proteins, which could contribute to development of various industries.

We describe real-world use of mavacamten in 50 patients with oHCM. Consistent with EXPLORER-HCM and VALOR-HCM, we report significant improvement in wall thickness, mitral regurgitation, left ventricular outflow tract obstruction and NYHA class. Moreover, in our center’s experience, neither arrhythmia burden, nor contractility have worsened in the vast majority of patients: We note a clinically insignificant mean decrease in left ventricular ejection fraction (LVEF), with only two patients requiring temporary mavacamten discontinuance for LVEF < 50%. Adverse events were rare, unrelated to mavacamten itself, and seen solely in patients with disease too advanced to have been represented in clinical trials. Our multidisciplinary pathway enabled us to provide a large number of patients with a novel closely-monitored therapeutic within just a few months of commercial availability. These data lead us to conclude that mavacamten, as a first-in-class cardiac myosin inhibitor, is safe and efficacious in real-world settings.

The Covid-19 crisis has been one of the most relevant economic shocks in the history of the modern economy, mainly due to the restrictions on travel and social interaction taken by the authorities (quarantines, closure of schools, artistic activities, bars, and restaurants, capacity in stores), to reduce the transmission of the virus (Sars-Cov2), having consequences on the national productions of all countries (about 7% for the loss of GDP worldwide). In our study, we analyze, through clustering methods, the effects of the level of contagion, economic projections, and economic mitigation measures taken by governments for managing the pandemic. According to the analyses, it can be concluded that a low infection rate implies a lower loss of product and economic savings when applying economic mitigation measures, taking relevance in the management of sanitary measures to reduce the transmission of the virus (and the temporality of these).

The connectivity level of last-generation vehicles is constantly on the rise. The combined use of Vehicle-To-Everything (V2X) connectivity and autonomous driving can provide remarkable benefits through the optimization of the route and speed trajectory. In this framework, this paper focuses on vehicle eco-driving optimization in a connected environment. The virtual test rig of a premium segment passenger car was used for generating the simulation scenarios. The benefits, in terms of energy and time savings, that the introduction of V2X communication, integrated with cloud computing, can have in a real-world scenario were assessed. The Reference Scenario is a pre-defined Real Driving Emissions (RDE) compliant route, while the simulation scenarios were generated by assuming two different penetration levels of V2X technologies. The associated energy minimization problem is formulated and solved by means of a global optimization algorithm, i.e., Dynamic Programming (DP). The optimization framework includes information coming from the surrounding environment, e.g., traffic lights state, speed limits, distance to travel, etc. The simulations show that introducing a smart infrastructure along with optimizing the vehicle speed in a real-world route can potentially reduce the required energy by 54% while shortening the travel time by 38%. Finally, a sensitivity analysis is performed on the bi-objective optimization cost function to find a set of Pareto optimal solutions, between energy and travel time minimization.

Fashion industry is the second most polluting industry in the world representing a 2 trillion dollars and growing valuation (Pal, 2017). This dual context makes its challenges hard to address. From one side, fashion design education and practice systems have been perpetuating an industrial-focused approach which relies mostly in the economic improvement through fast cycles of product development (Pal, 2017). On the other side, fashion industry has also been closed to either multidisciplinary and transdisciplinary initiatives outside the scope of the artistic disciplines. Therefore, innovative approaches are needed to solve fashion industrial challenges. One of the most promising fields to tackle fashion current environment and technological problems is microbiology (Mazzoto et al., 2021). During the past 50 years, microbiology has played a vital role in solving human grand challenges in health, agriculture, food, and waste management sectors, and it also represents an opportunity for fashion industry as well. Microbiology biotechnological potential for the fashion industry relies mostly on the improvement of toxic waste bioremediation and the development of novel biomaterials and biomolecules. Moreover, the emergent field of synthetic biology is expanding the tools and approaches available, and they can already be seen in the development of engineered living materials that have functional properties (Mazzoto et al., 2021). Despite the urgent need for change, there is still a long way until a more sustainable fashion industry is achieved. Therefore, microbiological research and innovation need maturation to be able to scale-up and reach a global impact for tackling fashion industrial problems.

Brucella abortus is a facultative intracellular Gram-negative bacterium that causes chronic persistent infections in humans and livestock. In this study, conventional bio-typing, multiple-locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing-single-nucleotide polymorphism (WGS-SNP) were used to investigate the molecular epidemiology characteristics of Brucella abortus strains in China and their relationships to world lineages. A total of 100 strains were collected from 1953 to 2013, suggesting that B. abortus circulated in China in the past five decades. Moreover, most strains were mainly distributed in the northwest area. During this period, seven biovars were found, indicating that B. abortus displayed a high diversity of biovars and that the main epidemic areas are in the northern provinces. Strains have high genetic diversity, and bruce07 is the most helpful locus for genotyping of this population. Moreover, 17 MLVA-11 genotypes were found; 13 of them are of known genotypes and four are unassigned genotypes, indicating that B. abortus in this study had several geographic origins. Still, strains from unassigned genotypes may originate from China. Many shared MLVA-16 genotypes were observed in strains from the same provinces in Northern China, which confirmed a brucellosis outbreak within northern regions. WGS-SNP analysis showed that eight Chinese strains formed a ladder-like phylogram (C. Ⅶ) with strains from nine countries, including Uganda, Iraq, Russia, Georgia, Spain, Italy, Egypt, Mongolia, and China; strains were introduced to these countries from a single source. Notably, Chinese strains were closely related to strains from Russia and Mongolia; frequent animal (cattle) trade and exchanges may promote this process. We will provide new and insightful information for strength surveillance and control of B. abortus brucellosis in China.

Corn silage (Zea mays L.) is the most widely used energy resource in the diets of dairy cattle around the world; it stands out for its higher biomass yields, good palatability, homogeneous quality at harvest and ease of silage due to its higher soluble sugar content. It was carried out a search of studies related to dry matter yield (ton ha-1), population density (plant density ha-1), dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), non-fibrous carbohydrates (NFC), organic matter (OM), DM digestibility (DMD) and neutral detergent fiber digestibility (NDFD) and milk production per hectare (kg of milk ha-1) that was determined using MILK2006®. It was carried out a cluster analysis (CL, PROC CLUSTER) obtaining six groups of corn silage: CL1: "Starch", which included DMD, DFDN, TDN1xDM, Mega calories per kg of DM and kg of milk/ton/DM; CL2: "Fats" which included TDN1xMS, Mcal/kg/DM and kg of milk/ton/DM; CL3: "Dry Matter", conformed only by DFDN; CL4: "Plant Density" including Yield of DM ha-1 and Milk Production ha-1; CL5: "Neutral Detergent Fiber" and CL6: "Raw Protein". It is concluded that CL1 was characterized by a higher DMD, DFND, CNF and starch that allow a higher TNDx1DM and an energy concentration (Mcal/kg/DM) that shows a higher milk production (kg of milk/ton/DM ha-1). The characteristics of CL2 with higher EE, allow a higher TNDx1DM and an energy concentration (Mcal/kg/DM) with a higher milk production (kg of milk/ton/DM ha-1).

Cell therapy has used mesenchymal stem cells (MSCs) which in cell culture are multipotent progenitors, capable of producing a variety of cells limited to the mesoderm layer. There are two types of MSCs sources: 1) adult MSCs, which are obtained from the bone marrow, adipose tissue, peripheral blood, and dental pulp; and 2) neonatal tissue-derived MSCs, obtained from extra-embryonic tissues such as the placenta, amnion, and umbilical cord. Until April 2023, there are 1,120 registered clinical trials using MSCs therapies worldwide, but there are only 12 MSCs therapies that have been approved by regulatory agencies for commercialization. Nine of the twelve approved MSCs products are from Asia, with South Korea being the country with the most approved therapies. In the future, MSCs will play an important role in the treatment of many diseases. However, there are many issues to deal with before their application and usage in medical practice. Some strategies have been proposed to face these problems with the hope of reaching the objective of applying these MSCs therapies at optimal therapeutic levels.

(1) Background: New sensor technologies in wearables and other consumer health devices open up promising opportunities to collect real-world data. As cardiovascular diseases remain reason number one for disease and mortality worldwide, cardiology offers potent monitoring use-cases with patients in their out-of-hospital daily routine. Therefore, the aim of this systematic review is to investigate the status quo of studies monitoring patients with cardiovascular risks and patients suffering from cardiovascular diseases in a telemedical setting using not only a smartphone-based app, but also consumer health devices such as wearables and other sensor-based devices. (2) Methods: A literature search was conducted across five databases and the results were examined according to the study protocols, technical approaches and qualitative and quantitative parameters measured. (3) Results: Out of 166 articles, 8 studies were included in this systematic review. These cover interventional and observational monitoring approaches in the area of cardiovascular diseases, heart failure and atrial fibrillation using various app, wearable and health device combination. (4) Conclusions: Depending on the researcher’s motivation a fusion of apps, patient reported outcome measures and non-invasive sensors can be orchestrated in a meaningful way adding major contributions to monitoring concepts for both, individual patients and larger cohorts.

Most traditional theories of intelligence have little to do with the question of whether people with high intelligence can successfully address real world problems. A high IQ is correlated with many important outcomes (e.g., academic prominence, reduced crime), but it does not protect against cognitive biases, partisan thinking, reactance, confirmation bias, and even falling for discredited beliefs such as alchemy, cold fusion, and astrology. There are several newer theories that directly address the question about solving real-world problems. Prominent among them is Sternberg’s adaptive intelligence with “adaptation to the environment” as the central premise, a construct that does not exist on standardized IQ tests (e.g., Sternberg, 2019). Similarly, Stanovich and West (2014) argue that standardized tests of intelligence are not measures of rational thought—the sort of skill/ability that would be needed to address complex real-world problems. Halpern and Butler (2020) advocate for critical thinking as a better model of intelligence for addressing real-world problems than those that are based on psychometric properties of general intelligence. Yes, intelligence (i.e., critical thinking) can be enhanced and used for solving a real-world problem like Covid-19, which we use as an example of contemporary problems that need a new approach. Critical thinking may be an antidote for the chaos of the modern world.

In this paper, we propose two novel methods for robot-world/hand-eye calibration and provide a comparative analysis against six state-of-the-art methods. We examine the calibration problem from two alternative geometrical interpretations, called hand-eye and robot-world-hand-eye, respectively. The study analyses the effects of specifying the objective function as pose error or reprojection error minimization problem. We provide three real and three simulated datasets with rendered images as part of the study. In addition, we propose a robotic arm error modeling approach to be used along with the simulated datasets for generating a realistic response. The tests on simulated data are performed in both ideal cases and with pseudo-realistic robotic arm pose and visual noise. Our methods show significant improvement and robustness on many metrics in various scenarios compared to state-of-the-art methods.

Causal relationships lie at the very core of our scientific description of biophysical phenomena. Nevertheless, observable facts such as chaotic dynamics, symmetry breaks, long-range collisionless neural interactions, zero-value energy singularities, particle/wave duality, ecological approaches to visual perception elude cause effect inductive explanations. We illustrate how simple topological claims, seemingly useless and far away from scientific inquiry (e.g., “given at least some wind on Earth, there must at all times be a cyclone or anticyclone somewhere”; “if one stirs to dissolve a lump of sugar in a cup of coffee, it appears there is always a point without motion”; “at any moment, there is always a pair of antipodal points on the Earth’s surface with equal temperatures and barometric pressures”) describe a real world, made of projections and mappings unsupplied with causality. Unavoidable, necessary, passive, spontaneous changes in systems’ shapes, dimensions and symmetries incarnate biophysical quantifiable counterparts of abstract mathematical concepts. Real features arising from topological mechanisms do not require causal powers to be produced, because are independent of exerted physical forces, energetic fields’ actions and thermodynamic constraints. Providing examples that shed novel interpretative light on phenomena such as double slit experiments, cellular mechanisms and brain function, we conclude as follows: countless scientific matters can be accessed through methodological weapons which not just break causality, replace temporal correlations and probabilistic a priori knowledge of previous cases, but also permit augments in available information devoid of entropy increases and energy losses.

Formally specifying hedonic well-being is difficult, but relevant to utilitarian theories of morality. In this paper we describe a starting point based on attitudinal hedonism, which posits that hedonic well-being is determined by the extent to which a moral patient believes her preferences to be fulfilled. While this assumption probably does not capture the sought-out notion of well-being fully, our formalization seems to be relevant first step towards more satisfactory definition of hedonic well-being.

Purpose: The study investigates soil pores' impact on carbon dynamics and sequestration processes, examining their physical and chemical characteristics and their mechanisms for carbon sequestration.Research Method: Existing literature and research on soil pores, carbon dynamics, and carbon sequestration are analyzed. The interrelationships between soil pore structure, water movement, microbial activity, root penetration, carbon input, soil aggregation, and gas exchange are examined. Traditional techniques and advanced imaging methods are used to quantify and characterize soil pores.Findings: Soil pores play a critical role in facilitating carbon sequestration through various mechanisms. They affect water movement, microbial activity, root penetration, carbon input, soil aggregation, and gas exchange. Understanding these relationships is crucial for sustainable soil management.Research Limitations: This study relies on existing literature and research, which may have limitations and uncertainties. Further research is needed to address these gaps and enhance understanding.Originality Value: This research enhances the existing knowledge by comprehensively examining the significance of soil pores in carbon dynamics and sequestration. It incorporates both traditional and advanced methods, providing insights for soil management and contributing to climate change mitigation efforts.

The conventional phytopathogen Pseudomonas syringae has been identified several significant virulence determinants against Caenorhabditis elegans, but their mechanisms of action remain elusive. Here, we report the nematicidal activity and action receptor of a methyl-accepting chemotaxis protein (MCP03) of a wild-type P. syringae MB03 against C. elegans. Purified MCP03 exhibited significant nematicidal toxicity against C. elegans, with a half-lethal concentration of 124.4 μg mL1, and detrimental effects on the growth and brood size of C. elegans. Additionally, MCP03-treated worms showed severe pathological destruction of the intestine and ovary, and depressed wrinkles of the cuticle. Through yeast two-hybrid assays, we identified a subunit of a COP9 signalosome, namely CSN-5, functionated as an action receptor of MCP03. In vitro pull-down and in vivo co-localization assays verified the binding interaction between MCP03 and CSN-5. RNA interference assays confirmed that MCP03 acts on CSN-5 to adversely affect the brood size, growth, and cuticle integrity of C. elegans. Following MCP03 infection, the expression of several genes relative to reproduction, growth, and cuticle formation, such as kgb-1, unc-98, and col-117, were significantly downregulated, which implicated the pathological changes of MCP03-treated nematodes. Thus, this study demonstrates that MCP03 acted on the receptor protein CSN-5 causing lethality and detrimental effects on the fertility, growth, and morphogenesis of C. elegans, which will provide new insights into the signaling pathways and mechanism underlying the nematicidal action of MCP03 towards C. elegans.

One of the most important unresolved mysteries in mathematics is the Riemann Hypothesis, which suggests a fundamental connection between the non-trivial zeros of the Riemann zeta function and the distribution of prime numbers. Here, we explore the fascinating union of trigonometric functions, prime numbers, and the Riemann zeta function through an examination of the zeros in the statement ln(sec(π·n log(n))). We demonstrate a strong mathematical connection between these components, providing information on the mysterious properties of prime numbers and their complex relationships to basic mathematical operations. Our thorough investigation adds to the current discussion of the Riemann Hypothesis by offering possible solutions and deepening our comprehension of the intricate relationship between number theory and analytic functions.

3,4-dihydroxyphenylacetaldehyde (DOPAL) is the focus of the catecholaldehyde hypothesis for the pathogenesis of Parkinson disease and other Lewy body diseases. The catecholaldehyde is produced via oxidative deamination catalyzed by monoamine oxidase (MAO) acting on cytoplasmic dopamine. DOPAL is autotoxic, in that it can harm the same cells in which it is produced. Normally DOPAL is detoxified by aldehyde dehydrogenase (ALDH)-mediated conversion to 3,4-dihydroxyphenylacetic acid (DOPAC), which rapidly exits the neurons. Genetic, environmental, or drug-induced manipulations of ALDH that build up DOPAL promote catecholaminergic neurodegeneration. A concept derived from the catecholaldehyde hypothesis imputes deleterious interactions between DOPAL and the protein alpha-synuclein (S), a major component of Lewy bodies. DOPAL potently oligomerizes S, and S oligomers impede vesicular and mitochondrial functions, shifting the fate of cytoplasmic dopamine toward MAO-catalyzed formation of DOPAL—destabilizing vicious cycles. Direct and indirect effects of DOPAL and of DOPAL-induced misfolded proteins could “freeze” intra-neuronal reactions, plasticity of which is required for neuronal homeostasis. The extent to which DOPAL toxicity is mediated by interactions with S, and vice versa, are poorly understood. Because of numerous secondary effects such as augmented spontaneous oxidation of dopamine by MAO inhibition, there has been insufficient testing of the catecholaldehyde hypothesis in animal models. The clinical pathophysiological significance of genetics, emotional stress, environmental agents, and interactions with numerous proteins relevant to the catecholaldehyde hypothesis are matters for future research. The imposing complexity of intra-neuronal catecholamine metabolism seems to require a computational modeling approach to elucidate clinical pathogenetic mechanisms and devise pathophysiology-based, individualized treatments.

Cerebrospinal fluid (CSF)-contacting neurons (CSF-N) located in the surface of both brain ventricles and the central canal (cc) in the spinal cord. The cc and CSF maintain a proliferative niche for neural progenitor cells and play a vital role in development of the brain. The CSF circulates in the ventricles and the subarachnoid spaces with the CSF rhythmic flow: cardiac pulsation and respiratory fluctuation. A new concept of CSF motion may be contrary to the classical one that the direction of CSF motion may vary in direction and may be dynamic in its location. The CSF pressure may also depend on the body position. Moderate music-making has been considered a potential approach for rehabilitative and restorative therapy of brain dysfunctions. Recently, we find that the CSF-Ns are present in both the interior CFS in the cc and also exterior CSF around the surface of the spinal cord. We hypothesize that CSF-N as mechanical sensors in the spinal cord could sense motion of the spinal cord. The myodural bridge is a ligament connecting a pair of deep, upper-neck muscles to the dura mater, which envelops the arachnoid mater and contains the CSF surrounding the brain and the spinal cord. We figure out the term “CSF-static compartment” and classify CSF storage location as rostral pool and caudal pool to demonstrate our hypothesis. We presume that the somatic body movement with music-making and rehabilitation-based interventions would orchestrate the CSF motion with head movement, myodural bridge stretching and puling as well as spinal bending.

In tropical Africa, forests and savannas are the two most widespread biomes and potentially represent alternative stable states with divergent species composition. A classic, but untested, hypothesis posited by White (1983) suggests that the transition zones between forests and savannas contain a floristically impoverished assemblage with few representatives from each biome. Further, the evolutionary dimension of diversity has received limited attention, despite its importance for understanding the biogeographic history of biomes. Here, we quantify species richness and several measures of evolutionary diversity in 1° grid cells, using c. 300K occurrence records of trees and shrubs combined with biome affiliation data for 3,125 species. We find that assemblages in transition zones hold fewer woody species than assemblages in forest and savanna zones, as posited by White. However, transition zones hold more phylogenetic diversity than expected given their species richness, whether one considers forest and savanna assemblages separately or together. We also show that the Congo basin forest has low levels of phylogenetic diversity given the number of species and highlight south-eastern African savannas as a centre of savanna woody species richness and phylogenetic diversity. Regions with high phylogenetic diversity given the number of both forest and savanna species were centred around the Dahomey Gap and Cameroon, mainly in transition zones. Overall, our study shows that even if floristically impoverished, transition zones lead to unexpectedly high evolutionary diversity, suggesting they are important centres of evolutionary innovation and diversification.

Suicidal behaviour is a public health problem whose magnitude is both substantial and increasing. Since many individuals seek medical treatment following a suicide attempt, strategies aimed at reducing further attempts in this population are a valid and feasible secondary prevention approach. An evaluation of the available evidence suggests that existing treatment approaches have limited efficacy in this setting, highlighting the need for innovative approaches to suicide prevention. Existing research on the neurobiology of social pain has highlighted the importance of this phenomenon as a risk factor for suicide, and has also yielded several attractive targets for pharmacological preventive strategies. In this paper, the available evidence related to these targets is synthesized and critically evaluated. The way in which social pain is related to the “anti-suicidal” properties of recently approved treatments, such as ketamine and psilocybin, is also examined. Such strategies may be effective for the short-term reduction of suicidal ideation and behaviour in individuals who have made a suicide attempt suicide prevention, particularly in cases where social pain is identified as a contributory factor. These pharmacological approaches may be effective regardless of the presence or absence of a specific psychiatric diagnosis.

Alzheimer’s disease (AD) is a genetically complex senile neurodegeneration with unknown etiology. The first gene discovered to be mutated in early-onset AD, the amyloid precursor protein (APP), has been widely assumed as a causal factor in the disease cascade due to its generation of Aβ species. APP has an evolutionarily conserved biological role and activates a signaling program with notable similarities to integrin—a cell adhesion receptor with a wide array of functions. Intriguingly, several AD genome-wide association study (GWAS) candidate genes, including the SHARPIN locus recently reported by us and others, influence signaling of the integrin pathway. Integrins are focal adhesion regulators and serve in nervous system development, synaptic plasticity, and Tau phosphorylation. These observations suggest that the function of APP probably goes beyond Aβ generation in AD. Aging—the strongest risk factor for AD—is associated with various clock-like events in cells. For instance, neurons are continuously impacted by stochastic ‘hits’ to their genomes in aging, in the forms of DNA damage, insertion-deletions, copy-number variations (CNVs) and other types of somatic mutations. DNA damage and somatic mutations can result in neoplastic changes and cancer in mitotically active cells. However, their consequences in post-mitotic cells such as aging neurons are less defined. The current hypothesis holds that the stochastic loss of DNA sequence data at random loci in aging affects longer genes by chance more frequently. As a result, the biological processes coordinated by long genes may be more vulnerable to such random aging effects. Curiously, as shown by us and others, long genes are strongly enriched for synapse- and cell adhesion-related ontologies, more than any other biological process or cellular compartment. In addition, among various cell types, neurons possess the highest levels of long gene expression and are therefore more vulnerable to such harmful effects. The long gene vulnerability hypothesis provides a simple link between aging and the genetic landscape of AD and warrants new strategies for disease modification.

Transcription factors (TFs) regulate gene expression by recognizing specific target enhancers in the genome. The DNA-binding and regulatory activity of TFs depend on the presence of additional protein partners, leading to the formation of versatile and dynamic multimeric protein complexes. Visualizing these protein-protein interactions (PPIs) in the nucleus is key for decrypting the molecular cues underlying TF specificity in vivo. Over the last years, Bimolecular Fluorescence Complementation (BiFC) has been developed in several model systems and applied for the analysis of different types of PPIs. In particular, BiFC has been applied for analyzing PPIs with hundreds of TFs in the nucleus of live Drosophila embryos. However, the visualization of PPIs at the level of specific target enhancers or genomic regions of interest awaits the advent of DNA-labelling methods that could be coupled with BiFC. Here, we present a novel experimental strategy that we called BiFOR and that is based on the coupling of BiFC with the bacterial ANCHOR DNA-labelling system. We demonstrate that BiFOR enables to precisely quantify the enrichment of specific dimeric protein complexes on target enhancers in Drosophila salivary gland nuclei. Given its versatility and sensitivity, BiFOR could be applied more largely in other tissues during Drosophila development. Our work set up the experimental basis for these future applications.

The number of applications for nanobodies is steadily expanding, positioning these molecules as fast-growing biologic products in the biotechnology market. Several of their applications require protein engineering, which in turn would greatly benefit from having a reliable structural model of the nanobody of interest. However, as with antibodies, structural modeling of nanobodies is still a challenge. With the rise of artificial intelligence (AI), several methods have been developed in recent years that attempt to solve the problem of protein modeling. In this study, we have compared the performance in nanobody modeling of several state-of-the-art AI-based programs, either designed for general protein modeling, such as AlphaFold2, OmegaFold, ESMFold and Yang-Server, or specifically designed for antibody modeling, such as IgFold, and Nanonet. While all these programs performed rather well in constructing the nanobody framework and CDRs 1 and 2, modeling of CDR3 sill represents a big challenge. Interestingly, tailoring an AI method for antibody modeling does not necessarily translate into better results for nanobodies.

Silybum Marianum, is a plant belonging to the family Asteraceae. For many centuries it has been used a natural remedy for many diseases like Liver and Biliary tract diseases. It is effective as an anti-oxidant and is used in a variety of diseases. This study was conducted to check the effects of Silybum Marianum on PARP protein (4UND protein).The Molecular Docking techniques was chosen to check the effects of different chemical constituents of Silybum marianum on DNA damaging protein. For this purpose, different PARP inhibitor drugs were taken as standard. The Molecular Docking of the chemical constituents of Silybum marianum was performed using 4UND protein with the help of PyRx software along with BIOVIA Drug Discovery studio software. The result of molecular docking showed that some of the chemical constituent have higher binding affinity than standard PARP inhibitor drugs.

Inteins are prevalent among extremophiles. Mini-inteins with robust splicing properties are of particular interest for biotechnological applications due to their small size. However, biochemical and structural characterization has still been limited to a small number of inteins, and only a few inteins serve as widely used tools in protein engineering approaches. We determined the crystal structure of a naturally-occurring Pol-II mini-intein from Pyrococcus horikoshii and compared it with two other natural mini-inteins from Pyrococcus horikoshii. Despite the similar sizes, the comparison revealed distinct differences in insertions and deletions, implying specific evolutionary pathways from distinct ancestral origins. Our studies suggest that sporadically distributed mini-inteins might be more promising for further protein engineering applications than the highly conserved mini-inteins. Structural investigations of more inteins could guide the shortest path to finding novel robust mini-inteins suitable for protein engineering purposes.

We summarize how to obtain protein crystals from which better diffraction images can be obtained. In particular, we describe in detail the quality evaluation of the protein sample, the crystallization methods and crystallization conditions, the flash-cooling protection of the crystal, and the crystallization under a microgravity environment.

We study a conformation of an albumin protein in the temperature range of 300K-315K, i.e. in the physiological range of temperature. Using simulations we calculate values of two backbone angles, that carry most of information about positioning of the protein chain in a conformational space. Given these, we calculate energy components of such protein. Further, using the Flory theory we determine the temperature in which investigated albumin chain model is closest to the free joined chain model. Near the Flory temperature, we study energy components and the conformational entropy, both derived from two angles that reflect most of the chain dynamics in a conformational space. We show that the conformational entropy is an oscillating function of time in considered range of temperature. Our finding is that, the only regular oscillation pattern appears near the Flory temperature.

The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling disordered protein interactions and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein-peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein-peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution and studies of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.

The quality prediction of quaternary structure models of a protein complex, in the absence of its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for ranking predicted protein complex structures and using them appropriately in biomedical research, such as protein-protein interaction studies, protein design, and drug discovery. With the advent of more accurate protein complex (multimer) prediction tools, such as AlphaFold2-Multimer and ESMFold, the estimation of the accuracy of protein complex structures has attracted increasing attention. Many deep learning methods have been developed to tackle this problem; however, there is a noticeable absence of a comprehensive overview of these methods to facilitate future development. Addressing this gap, we present a review of deep learning EMA methods for protein complex structures developed in the past several years, analyzing their methodologies and impacts. We also provide a prospective summary of some potential new developments for further improving the accuracy of the EMA methods.

Mutations, especially those at the protein-protein interaction (PPI) interface, have been associated with various diseases. Meanwhile, though de novo mutations (DNMs) have been proven important in neuropsychiatric disorders, such as developmental delay (DD), the relationship between PPI interface DMNs and DD has not been well studied. Here we curated developmental delay DNM datasets from the PsyMuKB database and showed that DD patients showed a higher rate and deleteriousness in DNM missense on the PPI interface than sibling control. Next, we identified 302 DD-related PsychiPPIs, defined as PPI harboring a statistically significant number of DNM missenses at their interface, and 42 DD candidate genes from PsychiPPI. We then observed that PsychiPPIs preferentially affected hub proteins in the human protein interactome network. When analyzing DD candidate genes using gene ontology and gene spatio-expression, we found that PsychiPPI genes carrying PPI interface mutations, such as FGFR3 and ALOX5, were enriched in development-related pathways and the development of the neocortex, and cerebellar cortex, suggesting their potential involvement in the etiology of DD. Our results demonstrated that DD patients carried an excess burden of PPI-truncating DNM, which could be used to efficiently search for disease-related genes and mutations in large-scale sequencing studies. In conclusion, our comprehensive study indicated the significant role of PPI interface DNMs in developmental delay pathogenicity.

Three finger toxins (3FTX) are a group of peptides that affect multiple receptor types. One group of proteins affected by 3FTX are nicotinic acetylcholine receptors (nAChR). Structural information on how neurotoxins interact with nAChR is limited and are confined to a small group of neurotoxins. Therefore, in silico methods are valuable in understanding the interactions between 3FTX and different nAChR subtypes, but there are no established protocols to model 3FTX – nAChR interactions. We developed a homology modeling and protein docking protocol to address this issue and tested its success on three different systems. First, neurotoxin peptides co-crystallized with acetylcholine binding protein (AChBP) were re-docked to assess whether Rosetta protein – protein docking can reproduce the native poses. Second, experimental data on peptide binding to AChBP was used to test whether the docking protocol can qualitatively distinguish AChBP-binders from non-binders. Finally, we docked eight peptides with known α7 and muscle-type nAChR binding properties to test whether the protocol can explain the differential activities of the peptides at the two receptor subtypes. Overall, our docking protocol succeeded in predicting both qualitative and specific aspects of 3FTX binding to nAChR and shed light on some unknown aspects of 3FTX binding to different receptor subtypes.

Various peptides or non-structural amino acids are recognized by their specific target proteins and perform biological role in various pathways in vivo. Understanding the interactions between target protein and peptides (or non-structural amino acids) provides key information on the molecular interactions, which can be potentially translated to the development of novel drugs. However, it is experimentally challenging to determine the crystal structure of protein-peptide complexes. To obtain structural information on substrate recognition of peptide-recognizing enzyme, X-ray crystallographic studies were performed using triglycine (Gly-Gly-Gly) as main-chain of peptide. The crystal structure of Parengyodontium album Proteinase K in complex with triglcyine was determined at 1.4 Å resolution. Two different bound conformations of triglycine were observed at the substrate recognition site. The triglycine backbone forms stable interactions with β5-α4 and α5-β6 loops of main-chain. One of the triglycine-binding conformations was identical with the binding mode of a peptide-based inhibitor from a previously reported crystal structure of Proteinase K. Triglycine has potential application X-ray crystallography to identify substrate recognition sites in peptide binding enzymes.

Peptides of hydrolysates of food proteins are an easily digestible source of amino acids necessary for the body to adapt to physical stress. Commercially significant hydrolysates include whey protein, casein, and other animal proteins. Hydrolysates of plant proteins are gaining popularity, but they are less common, then animal ones. Soy protein isolate is promising for obtaining the hydrolysates due to its affordable price and balanced amino acid profile. However, there are no direct studies showing an improvement in the result of physical activity when eating soy protein isolate hydrolysate (SPIH). In this work, for the first time, the study was conducted on the safety and efficacy of SPIH during physical load on model animals (rats). It was shown that the hydrolysate did not lead to pathological changes in the viscera, food intake, and weight of animals did not differ from the control group (animals consumed whey protein). Under physical load rats enteral fed SPIH showed a tendency to adapt more quickly to physical stress than the control group and the group of animals that was fed by free amino acids. The metabolites of animal blood serum were studied by NMR spectroscopy. It was shown that by the 95th minute after feeding in the group of rats receiving SPIH, the difference of proteinogenic amino acids concentrations in blood between individuals was significantly less than in the groups receiving whey protein or a mixture of amino acids. In other words, individual biochemical and physiological characteristics of individuals did not affect the assimilation of amino acids of hydrolysate.

This study was conducted to investigate the effect of supplementing different types of methionine (L and D-type) and its precursor (HMBi) on milk protein synthesis using immortalized bovine mammary epithelial cell line (MAC-T Cell); D-methionine (D-Met), L-methionine (L-met) and 2-hydroxy-4-methylthiobutanoic acid I (HMBi), an isopropyl ester of the hydroxy analogue precursor of methionine. The underlying mechanism of milk protein synthesis by adding D- and L-type amino acid as well as HMBi was elucidated through omics analysis to verify the metabolism pathway. Results showed that HMBi group showed the highest beta casein mRNA expression levels compared to D- and L-Met groups and highest medium protein although not different with the L-Met treatment. The observed upregulated (>2 protein expression vs. control) and downregulated (<0.5 protein expression vs. control) proteins in L-Met, D-Met and HMBi treated groups were: 39, 77; 46, 68; and 40, 78, respectively. Interestingly, based on protein pathway analysis, L-Met treated group stimulated the ATP synthesis, PI3 kinase and pyruvate metabolism. On the other hand, the D-Met group stimulated fructose-galactose metabolism, glycolysis pathway, PI3 kinase and pyruvate metabolism. And lastly HMBi-treated group stimulated pentose phosphate pathway and glycolysis pathway. Metabolite analysis revealed that L-Met treated group resulted in the increase in 11 metabolites. On the other hand, D-Met treated group showed increase in 7 metabolites and decreased of uridine monophosphate (UMP). HMBi supplementation caused increases of 3 metabolites and decreased of UMP and N-acetyl-L-glutamate Addition of different isoforms of Met stimulated the production of intermediate metabolites for energy production. Addition of L-Met stimulated the production of energy metabolites such as pyruvate, malate, and fumarate, well-known as intermediates of Krebs cycle. On the other hand, HMBi supplementation resulted in increases of energy metabolite glucose 1-phosphate and 6-phosphogluconate. Results showed that HMBi-treated group exhibited highest expression of β-casein mRNA expression by stimulating proteins and metabolites as well as protein and metabolic pathways involved in protein and energy synthesis. As a result, HMBi-treated group resulted in highest protein concentration but not significantly different with L-Met. Both the D- and L-isoforms has considerably the same medium protein concentration and β-casein mRNA expression higher than the control. So, D- and L-Met isoforms can be used alternatively without any significant change in protein synthesis efficiency in bovine mammary epithelial cells.

Specialized classes of proteins, working together in a tightly orchestrated manner, induce and maintain highly curved cellular and organelles membrane morphology. Due to the various ex- perimental constraints, including the resolution limits of imaging techniques, it is non-trivial to accurately elucidate interactions among the various components involved in membrane deformation. The spatial and temporal scales of the systems also make it formidable to investigate them using simulations with molecular details. Interestingly, mechanics-based mesoscopic models have been used with great success in recapitulating the membrane defor- mations observed in experiments. In this review, we collate together and discuss the various mechanics based mesoscopic models for protein-mediated membrane deformation studies. In particular, we provide an elaborate description of a mesoscopic model where the membrane is modeled as a triangulated sheet and proteins are represented as either nematics or fila- ments. This representation allows us to explore the various aspects of protein-protein and protein-membrane interactions as well as examine the underlying mechanistic pathways for emergent behavior such as curvature-mediated protein localization and membrane deforma- tion. We also put forward current efforts in the field towards back-mapping these mesoscopic models to finer-grained particle based models - a framework that could be used to explore how molecular interactions propagate to physical scales and vice-versa. We end the review with an integrative-modeling based road map where experimental imaging micrograph and biochemical data are combined with mesoscopic and molecular simulations methods in a theoretically consistent manner to faithfully recapitulate the multiple length and time scales in the membrane remodeling processes.

Intrinsically disordered proteins mediate crucial biological functions through their interactions with other proteins. Mutual synergistic folding (MSF) occurs when all interacting proteins are disordered, folding into a stable structure in the course of the complex formation. In these cases, the folding and binding processes occur in parallel, lending the resulting structures uniquely heterogeneous features. Currently there are no dedicated classification approaches that would take into account the particular biological and biophysical properties of MSF complexes. Here we present a scalable clustering-based classification scheme, built on redundancy-filtered features that describe the sequence and structure properties of the complexes, and the role of the interaction, which is directly responsible for structure formation. Using this approach, we define six major types of MSF complexes, corresponding to biologically meaningful groups. Hence, the presented method also shows that differences in binding strength, subcellular localization, and regulation are encoded in the sequence and structural properties of proteins. While current structure classification methods can also handle complex structures, we show that the developed scheme is fundamentally different, and since it takes into account defining features of MSF complexes, it serves as a better representation of structures arising through this specific interaction mode.

The emergence of pathogenic fungi is a major and rapidly growing problem (7% increase) that affects human and animal health, ecosystems, food security and the economy worldwide. The Dermocystida group in particular has emerged relatively recently and includes species that affect both humans and animals. Within this group, one species in particular, Sphareothecum destruens, also known as the Rosette agent, represents a major risk to global aquatic biodiversity and aquaculture and has caused severe declines in wild fish populations in Europe and large losses in salmon farms in the USA. It is a species that has been associated with a healthy carrier for millions of years but the host has managed in recent decades to invade parts of Southeast Asia, Central Asia, Europe and North Africa. In order to better understand the emergence of this new disease, we have for the first time synthesised current knowledge on the distribution, detection, prevalence of S. destruens as well as the associated mortality curves, and the potential economic impact in countries where the healthy carrier has been introduced. Finally, we propose solutions and perspectives to manage and mitigate the emergence of this fungus in countries where it has been introduced.

Surface water availability is a fundamental environmental variable to implement effective climate adaptation and mitigation plans, as expressed by scientific, financial and political stakeholders. Recently published requirements urge the need for homogenised access to long historical records at a global scale, together with the standardised characterisation of the accuracy of observations. While satellite altimeters offer world coverage measurements, existing initiatives and online platforms provide derived water level data. However, these are sparse, particularly in complex topographies. This study introduces a new methodology in two steps 1) teroVIR, a virtual station extractor for a more comprehensive global and automatic monitoring of water bodies, and 2) teroWAT, a multi-mission, interoperable water level processor, for handling all terrain types. L2 and L1 altimetry products are used, with state-of-the-art retracker algorithms in the methodology. The work presents a benchmark between teroVIR and current platforms in West Africa, Kazakhastan and the Arctic: teroVIR shows an unprecedented increase from 55% to 99% in spatial coverage.A large-scale validation of teroWAT results in an average of unbiased root mean square error ubRMSE of 0.638 m on average for 36 locations in West Africa. Traditional metrics (ubRMSE, median, absolute deviation, Pearson coefficient) disclose significantly better values for teroWAT when compared with existing platforms, of the order of 8 cm and 5% improved respectively in error and correlation. teroWAT shows unprecedented excellent results in the Arctic, using a L1 products based algorithm instead of L2 one, reducing the error of almost 4 m on average. To further compare teroWAT with existing methods, a new scoring option, teroSCO, is presented, measuring the quality of the validation of time series transversally and objectively across different strategies. Finally, teroVIR and teroWAT are implemented as platform-agnostic modules and used by flood forecasting and river discharge methods as relevant examples. A review of various applications for miscellaneous end-users is given, tackling the educational challenge raised by the community.

Sexual Issues played a significant role in Judaism’s engagement with its Greco-Roman world. This paper will examine that engagement in the Hellenistic Greco-Roman era to the end of the first century CE. In part sexual issues were a key element of demarcation between Jews and the wider community, alongside such matters as circumcision, food laws, sabbath keeping and idolatry. Jewish writers, such as Philo of Alexandria, make much of the alleged sexual profligacy of their Gentile contemporaries, not least in association with wild drunken parties, same-sex relations and pederasty. Jews, including the emerging Christian movement, claimed the moral high ground. In part, however, matters of sexuality were also areas where intercultural influence is evident, such as in the shift in Jewish tradition from polygyny to monogyny, but also in the way Jewish and Christian writers adapted the suspicion and sometimes rejection of passions characteristic of some popular philosophies of their day, seeing them as allies in their moral crusade.

Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and are able to form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in formation of the ribosome functional sites such as the mRNA binding site, tRNA binding sites, the peptidyl- transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many of r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. Extraribosomal activities of r-proteins have been intensively studied over decades (reviewed in [1]). The past decade brought significant advancement in our knowledge of r-protein functions due to expanding studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis, but also in previously little-explored bacterial species from various phyla. This review is aimed to update the information on multiple functions of r-proteins in bacteria.

Live cell imaging is a powerful technique to study the dynamics and mechanics of various biological molecules like proteins, organelles, DNA, and RNA. With the rapid evolution of optical microscopy, our understanding of how these molecules is implicated in the cells’ most critical physiological roles deepens. Here in this review, we focus on how spatiotemporal nanoscale live cell imaging on a single molecule level allows for profound contributions towards new discoveries in life science. This review will start by summarizing how single molecule tracking has been used to analyze membrane dynamics, receptor ligand interactions, protein-protein interactions, inner- and extracellular transport, gene expression/transcription, and whole organelle tracking. We then move on to how current authors are trying to improve single molecule tracking and overcome current limitations by offering new ways in labeling protein of interests, multi-channel/color detection, improvements in time laps imaging, and new methods and programs to analyze colocalization and movement of targets. We later discuss how single molecule tracking can be a beneficial tool used for medical diagnosis. Finally wrapping up with limitation and future perspective of single molecule tracking and total internal refection microscopy.

Classic mitochondrial DNA phylogenetic and phylogeographic studies on the aboriginal, historical, and extant human populations of the Canary Islands have contributed to reconstructing the origin and settlement on the islands of the pre-European colonizers. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples has greatly improved these molecular results, but it has also revealed significant contamination in the islands' previous aboriginal genetic pool. Following a thorough review of these cases, new phylogeographic analysis revealed the existence of a heterogeneous aboriginal population, asymmetrically distributed across the various islands, and most likely descended from a unique main settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple on the Canary Islands.

Climate change has become a major concern for developing countries given the risk that it posses on energy and food independence, and on general productivity. Despite having an energy system with low carbon intensity when compared to other Latin American countries, Colombia is already facing climate change impacts and requires urgent efforts to mitigate them. As a developing country, the challenge is bigger as policies for economic growth should be in line with the global commitment of reducing greenhouse gas emissions. With the aim of contributing to the design of climate policies, this study assesses the impact of economic development on the environment by examining the validity of the Environmental Kuznets Curve hypothesis for Colombia. Statistically validated and stable autoregressive distributed lag models are estimated for three different environmental indicators: carbon dioxide emissions, methane emissions, and ecological footprint. Moreover, the effects of other variables such as urbanization, foreign direct investment, value added of agricultural and industrial sectors, and energy use are analyzed with dynamic simulations. Empirical evidence supports a long-run equilibrium relationship among investigated variables and the existence of an inverted U-shaped EKC relationship between Gross Domestic Product (GDP) and methane emissions, and GDP and ecological footprint. Shifting to renewable energy sources and leveraging the use of cleaner technologies in agricultural and industrial sectors are found to be key for economic growth without harming the environment.

Dear Ladies and Gentlemen, I thank you for suggesting to submit the manuscript with the title “Insulin resistance develops due to an imbalance in the synthesis of cyclic AMP and the natural cyclic AMP antagonist prostaglandylinositol cyclic phosphate (cyclic PIP)” to the Editorial Board of the MDPI journal Stresses, and I ask for consideration to publish it in the journal Stresses. It was previously submitted to the MDPI journal Int. J. Mol. Sci. (IJMS-195 6513), but it was found that 1) it would not fit within the scope of this special edition and 2) it would primarily deal with cyclic PIP and would have not enough literature citation on the topic insulin resistance. The present version of the manuscript is improved, but the content is the same. The goal of this review is not to write again a summary on nearly all reports on insulin resistance as this was done by Dr. Petersen and Dr. Shulman, whose review has 961 literature citations. The present manuscript compiles what is known on cyclic PIP in relation to insulin resistance and the reason of writing this manuscript was that the discovered facts on cyclic PIP synthesis allow to suggest how insulin resistance most likely starts. Hitherto, reports on insulin resistance did not come close to this question. I am convinced that the manuscript makes an essential contribution to the question what causes the development of insulin resistance, and I have to say that stress overload is one of the reasons. Unfortunately, I have to mention a topic, about which I do not like to talk. Years ago, research groups postulated with rigor that the mediator of insulin action would be a peptide and then they suggested various, extracellularly synthesized glycans as mediators. They caused confusions and a high degree of disbelief in the matter of mediators of insulin action. In my review on cyclic PIP in IUBMB Life from 2020, I wrote in the introduction that cyclic PIP should not be confused with these mediators. But I cannot write this in the introduction of every report. I am keeping fingers crossed so that the editor in charge will find fair and openminded reviewers. Last not least I confirm that neither the manuscript nor any part of its content is currently under consideration or published in another journal. Kind regards, Henrich Wasner, PhD, BioReg Biopharm, TiLab; University of Illinois at Chicago; 2242 West Harrison St., Ste. 201, Chicago, Il 60612; USA

Weight thresholding (WT) is a method intended to decrease the number of links within weighted networks that may otherwise be excessively dense for network science applications. WT aims to remove links to simplify the networks by holding most of the features of the original network. Here, we test the robustness and the efficacy of the node attack strategies on real-world networks subjected to WT that remove links of higher weight (strong links). We measure the network robustness along node removal with the largest connected component (LCC). We find that the real-world networks under study are generally stable in terms of robustness when subjected to WT. Nonetheless, WT by strong link removal changes the efficacy of the attack strategies and the rank of node centralities. Also, WT by strong link removal may trigger a greater change in node centrality rank than WT by removing weak links. Network science research finding important/influential nodes in the network has to consider that simplifying the network with WT methodologies may change the node centrality.

This work is the first part of a series of papers on a comprehensive analysis of the processes of prebiotic self-organization and protophotosynthesis on the surface of semiconductor minerals and in systems of natural dispersed semiconductors. Comprehensive analysis within the framework of the "semiconductor world" concept allows integrating a variety of models on a single physical basis - from ZnS world and FeS world (based on inorganic semiconductors) to the PAH world and aromatic world (including organic semiconductors). Thus, we do not put forward a new alternative hypothesis of chemical evolution - a new "chemical world", but only integrate the evolutionary and geochemical criteria of different "chemical worlds" into a single "physical world", which gives one the opportunity to reconstruct and predict the directions of chemical evolution according to the uniform principles of physical chemistry. In the first part of this series we consider photoinduced self-organization and "photo-controlled" evolution of the early protobiological systems performing solar energy conversion on the surface of dispersed semiconductor minerals capable of (photo)catalyzing and photosensitizing prebiological processes. The latter include a transition from the elementary cycles of photocatalytic reactions on the surface of semiconductors to protophotometabolic cycles and protophotosynthesis, from photophysical processes on the surface of mineral semiconductors to photoinduced membrane potentials, from photocontrolled sorption on the surface of such minerals to the formation of photosensitive protomembranes and selection of photosynthetic structures. The evolutionary approach to the analysis of protobiological mechanisms and protobioenergetics within the framework of the "semiconductor world" concept provides a new approach to the study of the last common point of divergence of protobiological systems, where the emergence principles of different energy supply schemes (like the energy source-specific photoautotrophy and substrate-specific chemoautotrophy) merge at the physicochemical level. The proposed integrating scheme is consistent with most biological, geological, and physicochemical concepts, which ensures its complete cross-checking and internal consistency.

Purpose: Therapeutic targeting of RAF1 is promising, but it requires further investigation for the relation between clinical features and RAF1 aberrations regarding the MAPK signaling pathway in various solid tumors to realize the precision medicine. Methods: Between October 2019 and June 2023, Samsung Medical Center, 3,895 patients with metastatic cancer patients received a next-generation sequencing (NGS) using TruSight Oncology 500 (TSO500) assay as a routine clinical practice. We surveyed the incidence of RAF1 aberration including mutation (single-nucleotide variant [SNV]), amplification (copy-number variation), and fusion. Results: In 3,895 metastatic cancer patients, 77 (2.0%) had RAF1 aberrations in their tumor specimen. Of 77 patients, 44 (1.1%) had RAF1 mutations (SNV), 25 (0.6%) had RAF1 amplification and 10 (0.3%) had RAF1 fusions. Among 10 patients with RAF1 fusion, concurrent RAF1 amplification and RAF1 mutation were detected in one patient each. The most common tumor types were bladder cancer (11.5%), followed by ampulla of Vater (AoV) cancer (5.3%), melanoma (3.0%), gallbladder (GB) cancer (2.6%), and gastric cancer (2.3%). Microsatellite instability high (MSI-H) tumors were found in 5 out of 76 patients (6.6%) with RAF1 aberration, while MSI-H tumors were found only in 2.1% of patients with wild-type RAF1 cancer (p < 0.0001). Conclusion: We showed that when patients with metastatic solid cancer receive NGS test, approximately 2.0% have RAF1 aberrations in their tumor specimen.

Fire-related cues could alter vegetation community composition by promoting or excluding different types of plants. Smoke-derived compounds have been a hot topic in plant and crop physiology. There are some fire-prone areas in Australia, both Americas, some Mediterranean countries and regions with extensive prescribed or illegal burning like central European, which are subjected to a direct impact of fire (heat, minerals accumulation from the burning matter) and/or the indirect one (smoke) and undergo compositional and structural changes. This review first updates information about the effect of the compounds on plants' kingdoms and focuses on the research advances in the field of smoke compounds and attempts to gather and summarize the recent state of research and opinions on the role of smoke-derived compounds in plants' lives. We finish our review by discussing major research gaps, which include: Why plants respond to smoke chemicals? Is the response of seeds to smoke and smoke compounds an evolutionary-driven trait allowing plants to adapt to local environment?

We analyze the question of GDP Growth-GDPG rate in the context of Environmental, Social and Governance-ESG framework. We use World Bank data for 193 countries in the period 2011-2020 using different econometric techniques i.e., Panel Data with Fixed Effects, Panel Data with Random Effects, Pooled Ordinary Least Squares-OLS. We found that GDPG rate is positively associated, among others, to “Government Effectiveness” and “Prevalence of Undernourishment” and negatively associated among others to “Unemployment” and “Research and Development Expenditure”. Furthermore, we have applied the k-Means algorithm optimized with the Elbow method and we found the presence of four clusters in the sense of GDPG rate. Finally, we confront eight machine learning algorithms to predict the value of GDPG rate and we found that the Polynomial Regression is the best predictor. The Polynomial Regression predicts an increase of GDPG rate equal to 2.88% on average for the analysed countries.

A foundational model has been developed based on trends built from empirical data of space exploration and computing power through the first six plus decades of the Space Age which projects earliest possible launch dates for human-crewed missions from cis-lunar space to selected Solar System and interstellar destinations. The model uses computational power, expressed as transistors per microprocessor, as a key broadly limiting factor for deep space missions’ reach and complexity. The goal of this analysis is to provide a projected timeframe for humanity to become a multi-world species through off-world colonization, and in so doing all but guarantees the long-term survival of the human race from natural and human-caused calamities that could befall life on Earth. Be-ginning with the development and deployment of the first nuclear weapons near the end of World War II, humanity entered a ‘Window of Peril’ which will not be safely closed until robust off-world colonies become a reality. Our findings suggest the first human-crewed missions to land on Mars, selected Asteroid Belt objects, and selected moons of Jupiter and Saturn can occur before the end of the 21^st century. Launches of human-crewed interstellar missions to exoplanet destinations within roughly 40 lightyears of the Solar System are seen as possible during the 23^rd century and launch of intragalactic missions by the end of the 24^th century. An aggressive and sustained space exploration program, which includes colonization, is thus seen as critical to the long-term survival of the human race.

Abstract Background The number of immune-related endocrine dysfunctions (irEDs) has concurrently increased with the widespread use of immunotherapy in clinical practice and further expansion of the approved indications for immune checkpoint inhibitor (ICI) combinations using different modalities of anti-cancer treatment. Method A retrospective analysis was conducted on consecutive patients >18 years of age with advanced solid malignancies who had received at least one dose of anti-programmed cell death protein 1 (anti-PD-1) and/or anti-CTLA4 antibodies between January 2014 and December 2019 at a Hong Kong university hospital. Patients were reviewed for up to two months after the last administration of an ICI. The types, onset times and grades of irEDs, including hypothyroidism, hyperthyroidism, adrenal insufficiency and immune-related diabetes mellitus, were recorded. Factors associated with irEDs were identified using multivariate analysis. Result A total of 953 patients (male: 603, 64.0%; median age: 62.0 years) received ICIs during the study period. Of these, 580 patients (60.9%) used ICI-alone, 132 (13.9%) used dual-ICI, 187 (19.6%) used an ICI combined with chemotherapy (chemo+ICI), and 54 (5.70%) used immunotherapy with a targeted agent (targeted+ICI). A significantly higher proportion of patients using targeted+ICI had irEDs and hypothyroidism; in contrast, a higher proportion of patients using dual-ICI had adrenal insufficiency. There was no significant difference in the incidence of irED between the younger (<65 years) and older (>65 years) patients. Using logistic regression, only treatment type was significantly associated with irEDs. Notably, older patients had a higher risk of having immune-related diabetes mellitus. Conclusions This large, real-world cohort demonstrates that combining ICI with targeted therapy has a higher risk of overall irED and hypothyroidism. Immunotherapy is safe and well-tolerated regardless of age, but close monitoring of fasting glucose is needed in older populations.

Fruits play an important role in human diet and to maintain better health. Globally, India ranks second in fruits production after China. Grapes, mangoes, bananas and oranges were the selected fruit crops for study purpose. The study period is from 1990 to 2018. The present study analyzed the growth rates, instability and elasticity of export quantity, prices of selected fruit crops from major producing countries in the world and also dealt with the major export destinations of Indian fruits. The results showed that an exporting countries should export grapes to Peru, Spain and Chile; bananas to the Panama, Philippines and Ecuador; mangoes to Italy, Egypt and Australia; and, oranges to Thailand, Philippines and Mexico for generating higher revenue because in global market those countries were associated with highest export price with the stability. Globally, the export price elasticity was inelastic in all countries of grapes, oranges and bananas except Italy in oranges and panama in bananas. The study found that export price elasticity of mangoes was marginally higher in the Spain and the Netherlands. The study showed that the major destinations for Indian fruits are; USA, Germany and Netherlands for grapes; USA, Belgium and Germany for bananas; USA, the Netherlands and Viet Nam for mangoes; and, Germany, France and Netherlands for oranges. Globally, the current study gave useful data to comprehend competition of prices for fruits to importing countries. This study may assist in preparing major price strategies and policies on fruits and also assisted in foreign earnings for all nations.

Following an updated outlook of global energy production and utilization, we show through selected examples from both developing and developed countries how distributed generation from renewable energy sources, and from solar energy in particular, is the key solution to ending energy poverty across the world. Guidelines aimed at policy makers suggest a systems view of energy that will be instrumental in guiding the transition from fossil fuels to combustion-free renewable energy for all energy end uses.

It is time that universities reexamine what is meant by globalization. Contemporary researchers in science and the humanities (Critchley, Chomsky, Mumford, Ostrom, Eisenstein, Ferry, Orr, Shiva, Klein, Margulis, Meadows, Capra and Tolba, just to name a few) have aptly redefined the concept of « world » as a biological and cultural ecosystem. This paper seeks ways to integrate the theory and practice of eco-citizenship into various cross-disciplinary aspects of higher education, with a focus on curricular adjustments that may be steered by World Languages and Cultures programs. While "global citizenship" is still often understood today as a form of supranational citizenship that may find its actualization through the valuable, yet often arrested efforts of the United Nations, or as the individualistic result of a neoliberal economic emancipation of markets and capital throughout the world, this notion must rather be embedded within a radically cultural, natural and ethical bedrock from which a more potent world citizenry will stem. Departments of World Languages and Cultures and cultures are ideally positioned in the academic landscape to foster the development of a greater eco-civic and biospheric awareness that can permeate new curricular orientations of universities in the US and abroad.

The emergence of the coronavirus 19 (COVID-19) has posed a major challenge to healthcare systems worldwide, especially as COVID-19 mutations complicate the development of vaccines and antiviral drugs. Therefore, the search for natural products with broad anti-COVID-19 capabilities is an important option for the prevention and treatment of infectious diseases. Lectins, which are widely recognized as antiviral agents, could contribute to the development of anti-COVID-19 drugs. In this study, we evaluated the binding ability of a total of six lectins, including MVL from Microcystis viridis NIES-102, to the spike protein RBD of the original (wild) COVID-19 and it’s three mutants: alpha, delta, and omicron. As a result, two lectins, MVL from Microcystis viridis NIES-102 and jacalin from Artocarpus altilis, showed distinct binding ability to the RBDs of the four COVID-19 strains. The other lectins (DB1, ConA, PHA-M and CSL3) did not show any binding ability. Although the glycan specificities of the two lectins, MVL and Jacalin, were different, they showed the same affinity for the RBDs of the four COVID-19 strains, i.e., alpha &gt; delta &gt; original &gt; omicron. The verification of glycan-specific inhibition revealed that jacalin binds to RBDs by glycan-specific recognition, whereas MVL binds to RBDs by protein-protein interactions in addition to glycan-specific recognition.

Living systems are intricate repositories of biomolecules, where the interactions between these molecules play an important role in maintaining homeostasis. Interruptions in these interactions can lead to diseases, underscoring the significance of biomolecular interactions and their molecular basis. HUGENICS (Human Genetic Database) is a comprehensive biological database that focuses on molecular interactions between human and microbial proteins, particularly emphasizing protein-protein interactions (PPIs). This database offers insights into disease pathways by elucidating the interplay between microbial surface/secretory proteins and human disease-related proteins. This white paper highlights the significance, scope, and potential applications of HUGENICS in advancing biomedical research and improving human health.

The recent setbacks in the withdrawal and approval delays of antibody treatments of neurodegenerative disorders (NDs) can be attributed to their poor entry across the blood-brain barrier (BBB). While several invasive and noninvasive approaches can be used to make the BBB more permeable, their inconsistency makes them a poor choice; however, if an antibody is chemically modified to attach a transferrin molecule that enhances its permeation across the BBB, this could be the most practical and useful modification that can transform the science of ND treatment. Antibodies can be conjugated with transferrin in vitro, but preferably through mRNA, as we propose to convert current treatments to bring faster treatment options. The mRNA technology yields products at a meager cost, which is a consideration for the affordability of these drugs globally. This paper provides complete details with templates to convert the current medicines and those under development into mRNA delivery systems to ensure clinical success, avoiding the current failures in their efficacy, more specifically the products that have demonstrated efficacy but are being removed from the market.

Circular dichroism (CD) spectroscopy is a valuable tool in the pharmaceutical industry for determining the secondary and tertiary structure, folding, stability, and interactions of proteins in biosimilars. However, protein aggregation due to its interaction with surfactants can introduce variations in CD spectra, leading to false interpretations. To investigate this effect, we prepared aqueous solutions of α-chymotrypsin with the same amount of surfactant but at different solution preparation steps. Interestingly, the CD spectra of these solutions showed slight differences despite having the same surfactant concentration. This suggests that the order of surfactant addition can influence protein conformation. To address this issue, we propose a method for preparing aqueous protein solutions that yields reproducible CD spectra. This method is expected to benefit the pharmaceutical industry by improving the accuracy of CD spectroscopy for protein structural analysis and evaluation of protein functionality.

Arrestin-1, or visual arrestin, exhibits an exquisite selectivity for light-activated phosphorylated rhodopsin (P-Rh*) over its other functional forms. That selectivity is believed to be mediated by two well-established structural elements in the arrestin-1 molecule, the activation sensor detecting the active conformation of rhodopsin and the phosphorylation sensor responsive to the rhodopsin phosphorylation, which only active phosphorylated rhodopsin can engage simultaneously. However, in the crystal structure of the arrestin-1-rhodopsin complex there are arrestin-1 residues located close to rhodopsin, which do not belong to either sensor. Here we tested by site-directed mutagenesis the functional role of these residues in wild type arrestin-1 using direct binding assay to P-Rh* and light-activated unphosphorylated rhodopsin (Rh*). We found that many mutations either enhanced the binding only to Rh* or increased the binding to Rh* much more than to P-Rh*. The data suggest that the native residues in these positions act as binding suppressors, specifically inhibiting the arrestin-1 binding to Rh* and thereby increasing arrestin-1 selectivity for P-Rh*. This calls for the modification of a widely accepted model of the arrestin-receptor interactions.

Zika virus (ZIKV) is a mosquito-borne flavivirus and causes an infection that is associated with neurological manifestations, including microcephaly and Guillain-Barre syndrome. The mechanism of ZIKV-mediated neuropathogenesis is not well understood. In this study, we discovered that ZIKV induces the degradation of the Numb protein, which plays a crucial role in neurogenesis by allowing asymmetric cell division during embryonic development. Our data show that ZIKV reduced the Numb protein level in a time- and dose-dependent manner. However, ZIKV infection appears to have minimal effect on the Numb transcript. Treatment of ZIKV-infected cells with a proteasome inhibitor restores the Numb protein level, which suggests the involvement of the ubiquitin-proteasome pathway. In addition, ZIKV infection shortens the half-life of the Numb protein. Among the ZIKV proteins, the capsid protein significantly reduces the Numb protein level. Immunoprecipitation of the Numb protein co-precipitates the capsid protein, indicating the interaction between these two proteins. These results provide insights into the ZIKV-cell interaction that might contribute to its impact on neurogenesis.

Dysfunction of the WW domain-containing adaptor with coiled-coil, WAC, gene underlies a rare autosomal dominant disorder, DeSanto-Shinawi syndrome (DESSH). DESSH is associated with facial dysmorphia, hypotonia, and cognitive alterations, including attention deficit hyperactivity disorder and autism. How the WAC protein localizes and functions in neural cells is critical to understanding its role during development. To understand the genotype-phenotype role of WAC, we developed a knowledgebase of WAC expression, evolution, human genomics, and structural/motif analysis combined with human protein domain deletions to assess how conserved domains guide cellular distribution. Then assessed in a cell type implicated in DESSH, cortical GABAergic neurons. WAC contains conserved charged amino acids, phosphorylation signals, and enriched nuclear motifs, suggesting a role in cellular signaling and gene transcription. Human DESSH variants are found within these regions. We also discovered and tested a nuclear localaization domain that impacts the cellular distribution of the protein. These data provide new insights into the potential roles of this critical developmental gene, establishing a platform to assess further translational studies, including the screening of missense genetic variants in WAC. Moreover, these studies are essential for understanding the role of human WAC variants in more diverse neurological phenotypes, including autism spectrum disorder.

Most non-infectious diseases are associated with dysfunction of proteins or protein complexes. Аssociation between sequence and structure is analyzed since a long time, and analysis of sequence organization in domains and motifs is actual research area. A mathematical method is proposed here to identify the hierarchical organization of protein sequences. The method is based on pentapeptide as a unit of protein sequences. This method was applied on a non-homologous dataset of protein sequences. The analysis revealed 11 hierarchical levels of protein sequence organization, showing the relationship of these multiple fragments of sequences. Using different examples, we illustrated how the fragments of the spatial structure of protein correspond to the elements of the hierarchical structure of the protein sequence. A hierarchical structure is observed in the protein sequence. This methodology is an interesting basis for mathematically based classification of elements of spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used for biotechnological and medical problems.

Prime numbers are the atoms of mathematics and mathematics is needed to make sense of the real world. Finding the Prime number structure and eventually being able to crack their code is the ultimate goal in what is called Number Theory. From the evolution of species to cryptography, Nature finds help in Prime numbers. One of the most important advances in the study of Prime numbers was the paper by Bernhard Riemann in November 1859 called “Ueber die Anzahl der Primzahlen unter einer gegebenen Grösse” (On the number of primes less than a given quantity). In that paper, Riemann gave a formula for the number of primes less than x in terms the integral of 1/log(x) and the roots (zeros) of the zeta function defined by: Where ζ(z) is a function of a complex variable z that analytically continues the Dirichlet series. Riemann also formulated a conjecture about the location of the zeros of RZF, which fall into two classes: the "trivial zeros" -2, -4, -6, etc., and those whose real part lies between 0 and 1. Riemann's conjecture Riemann hypothesis [RH] was formulated as this: [RH] The real part of every nontrivial zero z* of the RZF is 1/2. Proving the RH is, as of today, one of the most important problems in mathematics. In this paper we will provide a proof of the RH. The proof of the RH will be built following these five parts: PART 1: Description of the RZF PART 2: The C-transformation PART 3: Application of the C-transformation to in Re(z) 0 to obtain ζ(z)=X(z)-Y(z) PART 4: Analysis of the values of z such that X(z)=Y(z), and |X(z)|=|Y(z)|, that equates to ζ(z)=0 Proof that |X(z)|=|Y(z)| only if Re(z)=1/2 Conclude that ζ(z)=0 only if Re(z)=1/2 for Re(z) 0 PART 5: We will also prove that all non-trivial zeros of ζ(z) in the critical line of the form are not distributed randomly. There is a relationship between the values of those zeros and the Harmonic function that leads to an algebraic relationship between any two zeros.

Spontaneity and its connections to mental health and wellbeing are a central issue in both theory and practice of psychodrama, and the specialized literature sometimes even associates the presence of pathology to a lack of spontaneity. This paper describes spontaneity in Moreno's theory, its assessment, its association with other measures and concepts, and scientific advances in the field. Specifically, we present results obtained with the English and Portuguese-language versions concerning its assessment. The main purpose of this work was to study the spontaneity measure (SAI-R) in a 3 first-order factors version for a Portuguese sample of 719 subjects, divided into two independent samples. The participants were aged 18 to 69. The mean age of participants was 28.5 years (SD = 7.51), and ages ranged between 18 and 69 years. Data was collected through an online platform of a Portuguese market research company. The results revealed that the 3-factor model has acceptable validity when items 1 (“Creative”) and 7 (“Euphoric”), confirming the composite reliability, the convergent validity, but not the discriminant validity. Through multigroup analysis, the model showed to be stable. Notwithstanding the need for complementary studies, including clinical samples, the SAI-R is a short and valid instrument in clinical and non-clinical contexts when evaluating spontaneity.

Physics and neuroscience share overlapping objectives, the major of which is probably the attempt to reduce the observed universe to a set of rules. The approaches are complementary, attempting to find a reduced description of the universe or of the observer, respectively. We propose here that combining the two approaches within an observer-inclusive physical scheme, bears significant advantages. In such a scheme, the same set of rules applies to the universe and its observers, and the two descriptions are entangled. We show here that analyzing special relativity in an observer-inclusive framework can resolve its contradiction with the observed non-locality of physical interactions. The contradiction is resolved by reducing the universe (including the observer) to a dynamic distribution of closed strings (“ceons”) whose vibration waves travel at c. This ceons model is consistent with general relativity, non-locality, the holographic principle and loop quantum gravity; it also eliminates Zeno’s motion paradoxes. Yet, the model entails several new empirical predictions. Finally, the ceons model suggests a fundamental physical implementation of active biological perception. Paraphrasing Torricelli, this paper suggests that we live submerged in a c of light.

Rare cardiac adverse events are reported post vaccinations. For the SARS-CoV-2 vaccines, higher numbers of these cardiac adverse events are being reported with myocarditis disproportionately occurring in younger males. The etiology of these cardiac adverse events associated with vaccines including SARS-CoV-2 is unknown. The etiology of the higher frequency of these cardiac adverse events temporally associated with SARS-CoV-2 vaccines is also unknown. This article proposes that innate immune responses to vaccines cause elevated histamine levels post vaccination; the histamine level reached may exceed the vaccinees’ histamine tolerance level for several days. This article proposes that the elevated histamine level is causative for the reported cardiac adverse events. For myocarditis reported adverse events, this article proposes that elevated histamine levels induce cardiac capillary pericyte induced vasoconstrictions followed by localized ischemia and anoxia; this is followed by the release of troponin from myocyte cells affected by anoxia. This hypothesis is supported by the temporal onset timing of adverse events reported following SARS-CoV-2 vaccinations in the United States Department of Health and Human Services Vaccine Adverse Event Reporting System (VAERS). This model applies to multiple vaccines with innate immune response histamine levels generated varying by each vaccine and incidence frequencies correlate with vaccine reactogenicity.

Splenic micronodular T-cell/histiocyte-rich large B-cell lymphoma is possibly derived from nodal T-cell/histiocyte-rich large B-cell lymphoma; however, a transition between the nodal and splenic micronodular forms has not been described to date. Of note, the only lymph nodes to be involved in association with the splenic micronodular pattern of the disease are the splenic hilar lymph nodes, and that, with partial involvement only. Kan et al, in their series of articles, have raised the possibility that corticosteroids, when prescribed prior to splenectomy, cause histopathological and functional modulations (apoptosis, necrosis, tissue shrinkage), which modify or even obscure the diagnostic morphological features. The indications for glucocorticoid therapy are either related to the suspected lymphoma, or else to other comorbidities, like asthma and autoimmune disorders. We propose that patients with the splenic, rather than nodal subset of the disease are likely to have been prescribed corticosteroids prior to histopathologic examination of the involved tissue, causing disparate morphologies in the spleen. Apoptosis, as induced by corticosteroids, is hypothesized as the major mechanism initiating the histopa-thological and functional changes in the splenic micronodular variant of our patients.

In a vacuum tube two identical and parallel Ag-O-Cs emitters A and B (work function 0.8eV) ceaselessly emit thermal electrons at room temperature. The thermal electrons are controlled by a static uniform magnetic field so that the number of electrons migrate from A to B exceeds the one from B to A (or vice versa). The net migration of thermal electrons from A to B quickly results in a charge distribution of A charged positively and B negatively, and a potential difference between A and B emerges, enabling a continuous output current and a stable power to an external load (e.g., a resistor). Thus, the tube cools down (slightly). The (slightly) cooled tube extracts heat from ambient air, and all the heat is converted into electric energy without other effect. We believe the experiment is in contradiction to the Kelvin statement of the second law.

The microspheres constituted by proteinoids synthesized from Fox’s simulation experiments. They had peptide bond structure and weak catalysis, as well as proliferated themselves. Such microspheres were believed the models for primitive life. Due to lack of metabolism and self-reproduction, the microspheres could not meet requirements of life. Thus, how microspheres could evolved into primitive life remain unsolved mysteries. The microspheres were supposed a dissipative structure and the processes of absorption and hydrolysis could be balanced to maintain their stability by consuming proteinoid. Proteinoid molecules differed in their life spans, which were mainly determined by their multi-space structures. Consequently, molecule selection and retention could occur spontaneously in microspheres and lead to a more organized and stabilized structure of the whole microsphere with time through dissipative process. More complex chain network of chemical reactions could happen in microspheres because the proteinoid with complex, ordered multi-space structure and relatively high catalytic activity would retain. In such microspheres, nucleotides could produce and further aggregate into RNA. The synthesis of real proteins could take place with RNA as the template catalyzed by proteinoids or RNA inside microspheres. When template-based protein molecules replaced the proteinoid inside the microspheres, a protein-based self-catalyzed network of chemical reactions could take place. It is plausible if Fox’s proteinoids microspheres is to dawn on a dissipative structure, then molecule selection could occur spontaneously by “dissipative” proteinoids, and the microspheres would acquire catalytic activity due to preserved the proteinoid with a large molecular weight and relatively complex and ordered multi-space structure, and relatively high catalytic activity. Thus the microspheres would spontaneously go to self-organizing, and evolve into primitive life.

VpStyA1 and VpStyA2B of Variovorax paradoxus EPS is annotated and characterized as the first representative of an E2-type styrene monooxygenase of proteobacteria. It comprises a single epoxidase (VpStyA1) and a fusion protein (VpStyA2B) which serves mainly as NADH:FAD-oxidoreductase. VpStyA2B had a Km of 33.6 ± 4.0 µM for FAD and a kcat of 22.3 ± 1.1 s-1. VpStyA2B and VpStyA1 showed monooxygenase activity on styrene of 0.14 U mg-1 and 0.46 U mg-1 as well as on benzyl methyl sulfide of 1.62 U mg-1 and of 3.11 U mg-1. A putative fusion region at position 408 (AREAV) was mutated to provide insights on VpStyA2B-function. The best mutant (408-AAAAA) obtained showed a 6.6-times higher affinity for FAD while keeping the NADH-affinity and -oxidation activity. Corresponding epoxidase activity increased (1.6-times). But, other mutants showed still NADH:FAD-oxidoreductase activity, but lost mostly their epoxidase activity indicating effects on the monooxygenase-part as well. Thus, this monooxygenase system represents an interesting candidate for biocatalyst development.

The Rosetta software suite for macromolecular modeling, docking, and design is widely used in pharmaceutical, industrial, academic, non-profit, and government laboratories. Considering its broad modeling capabilities, Rosetta consistently ranks highly when compared to other leading methods created for highly specialized protein modeling and design tasks. Developed for over two decades by a global community of scientists at more than 60 institutions, Rosetta has undergone multiple refactorings, and now comprises over three million lines of code. Here we discuss the methods developed in the last five years, involving the latest protocols for structure prediction, protein–protein and protein–small molecule docking, protein structure and interface design, loop modeling, the incorporation of various types of experimental data, and modeling of peptides, antibodies and other proteins in the immune system, nucleic acids, non-standard amino acids, carbohydrates, and membrane proteins. We briefly discuss improvements to the energy function, user interfaces, and usability of the ­­software. Rosetta is available at www.rosettacommons.org.

A model of the early RNA world is proposed. Nearly self-complementary sequences that could adopt double-stranded, smallhairpin-like (shRNA), structures would be selected for due to their greater hydrolytic stability. These would be phosphorylated attheir 5' ends. We suppose that dehydrating conditions arise (perhaps intermittently) in the early environment allowing amino acidsto condense with these RNA molecules. The resulting phosphate-amino acid anhydrides would play the role of early, charged,tRNAs. A crude genetic code could emerge owing to the greater resistance of some amino acid-shRNA pairings to hydrolysisrelative to others. Early on there is no division of labor between mRNAs and tRNAs; the same molecules perform both functions.But the first systems would have encoded little in the way of protein sequence information. Rather they would have served as catalysts for the random polymerization of amino acids. It is speculated that the selective advantage inhering in such systems lay intheir ability to supply raw materials for the formation of coacervates within which the various molecules essential to proto-lifecould be concentrated. This would greatly facilitate the necessary chemistries. The evolution of homochiral protein and RNA populations is discussed. An appealing feature of this model is its ability to explain the transition from phosphorylated amino acids to the 3' ester-linked aminoacyl-tRNAs employed by modern life.

Cells that experience high levels of oxidative stress respond with the induction of antioxidant proteins through the activation of the transcription factor Nrf2. Nrf2 is negatively regulated by Keap1 which binds to Nrf2 to facilitate its ubiquitination and ensuing proteasomal degradation under basal conditions. Here, we study protein folding and misfolding in Nrf2 and Keap1 in yeast, mammalian cells, and purified proteins under oxidative stress conditions. Both Nrf2 and Keap1 are susceptible to protein misfolding and inclusion formation upon oxidative stress. We propose that the intrinsically disordered regions within Nrf2 and the high cysteine content of Keap1 contribute to their oxidation and the ensuing misfolding. Our work reveals previously unexplored aspects of Nrf2 and Keap1 regulation and dysregulation by oxidation-induced protein misfolding.

During the coronavirus disease 2019 (COVID-19) pandemic, individuals with immune-mediated inflammatory diseases (IMIDs), such as systemic lupus erythematosus and rheumatoid arthritis, face a heightened risk of infection and severe outcomes due to immunological alterations resulting from their underlying conditions and immunosuppressive treatments. Even as the pandemic has transitioned to an endemic state, it remains crucial to recognize that these patients continue to be at risk. In this narrative review, we analyzed existing literature to explore the impact of IMIDs, clinical risk factors, and the influence of immunosuppressive therapies on COVID-19-related risks and outcomes. Notably, certain disease-modifying antirheumatic drugs (DMARDs), like rituximab, are associated with worse COVID-19 outcomes, and rituximab-treated patients show impaired immune responses to COVID-19 vaccination. Additionally, we outline the diverse effects of glucocorticoids on COVID-19 outcomes and management. To highlight real-life challenges faced by clinicians caring for patients with IMIDs, we present an illustrative scenario that underscores the importance of effective vaccination, timely boosting, and additional mitigation strategies against COVID-19. Given the clinical heterogeneity and diverse disease states within IMIDs, it is crucial to understand the ongoing implications and risks associated with COVID-19 in these patients, to guide the implementation of appropriate measures and optimize care and outcomes in the current endemic era.

A 52-day experiment was conducted to determine the crude protein (CP) requirements of juvenile matrinxã Brycon amazonicus, and to evaluate their resulting growth performance, hematological parameters and enzymatic activities. Sixty fish (29.03g ± 1.16g) were distributed in 12 tanks (310 L) with a completely randomized design, and maintained at four dietary crude protein levels (270, 320, 350, 390 g.kg-1) for 52 days. The results revealed that the fish fed diet 390 g.kg-1 CP had the best final weight, weight gain, feed conversion ratio, specific growth rate, protein efficiency ratio and lipid retention rate. The same could be stated for hematocrit, number of circulating erythrocytes, triglycerides and total proteins of the hematological profile (p&lt;0.05). In the whole body composition, dry matter content was lower in the fish fed 390 g.kg-1 CP, while lipid content was higher in the fish fed 350-390 g.kg-1 CP (p&lt;0.05). No differences were observed in CP and ash (p&gt;0.05), or in the activities of digestive enzymes (p&gt;0.05). In short, our findings suggest benefits of the 390 g.kg-1 CP feed for being the most adequate for this species’ juvenile stage.

Due to the vast conformational space proteins can adopt, accurate and efficient prediction of protein structure remains still a challenging task, coupled with the intricacies of interatomic interactions and the limitations of current computational models in effectively navigating this complex molecular landscape. Additionally, the lack of comprehensive experimental data for all protein structures further exacerbates the difficulty in reliable machine learning-based prediction of the three-dimensional conformations of the proteios building block of life. Geometrically, Cartesian coordinate system (CCS, X, Y and Z) and spherical coordinate system (SCS, ρ, θ and φ) are two interconvertible coordinate systems, and are like two sides of one coin. Since the beginning of Protein Data Bank (PDB) in 1971, CCS has been the default approach to specify atomic positions with X, Y and Z in PDB. In this manuscript, therefore, I present a novel method for the reversible spherical geometric conversion of protein backbone structure coordinate matrices to three independent vectors: ρ, θ and φ. This reversible conversion facilitates lossless extraction of essential structural features from protein backbone structural data, enabling the development of advanced novel algorithms for protein structure prediction in future. In short, this inter-atomic SCS approach offers a comprehensive yet efficient means of representing protein backbone geometry, leveraging spherical coordinates to capture spatial relationships in a compact and intuitive inter-atomic manner, and to provide a robust framework for reversible feature extraction for the ongoing efforts in advancing the field of protein structure prediction, the holy grail of computational structural biology.