This paper aims to establish lighting as a key facilitator in the placemaking processes for World Heritage Sites. Placemaking is a process of designing, managing, planning and programming the development of shared public spaces within the urban fabric. Research methods inspired from ethnography such as interviews, observations and questionnaires are used to gather data from three main groups of people related to the lighting of World Heritage Sites namely: heritage experts, lighting designers, and locals and visitors. Two UNESCO designated World Heritage Sites are investigated as case studies: Saint-Avit-Sénieur in Dordogne, France and Naghshe-Jahan-Square in Isfahan, Iran. Thematic analysis of the data collected from these investigations reveal key lighting characteristics and lighting design considerations that can facilitate the placemaking process for World Heritage Sites. The lighting characteristics include: avoiding over-lighting, overly theatrical lighting and homogeneous lighting; balancing floodlighting; preventing glare; providing flexible and harmonious lighting. The lighting design considerations include: accounting meanings and values; amplifying narratives; balancing genders; building attraction and excitement; creating layers; enhancing atmospheres; ensuring safety; improving functionality; offering interpretations; and supporting activities.

In the context of growing global political tension and introduction of world trade barriers, the urgent task is to develop new tools for assessing their consequences. In the paper we present the agent-based model of trade wars, considering organizations, states and residents generated using initial statistical data. Simulation determines changes in output and supplies of organizations under trade restrictions. Results of calculations on the developed model and comparison of various model complexes forecasts with real consequences of trade wars between the USA and China in 2018 and Western countries against Russia in 2022 are presented. Within calculations four scenarios were considered: (1) baseline, (2) new restrictions between China and the USA, (3) more serious sanctions against China and Russia by the USA and the EU, (4) a global trade war. In the second scenario deviation GDP of the USA and China from the baseline scenario does not exceed 0.5%. In the third scenario, the range of countries involved is expanding, and the fall in GDP in them is expected at the level of 0.7-1%. In the fourth scenario, the entire world economy experiences a serious slowdown, and the EU are facing the most severe consequences, going into recession.

We provide quantitative results from GIS-based modelling of urban emission functions for a range of representative low- and mid-rise locations, ranging from individual streets to residential communities within cities as well as entire towns and city regions with the aim of whether lantern photometry or built environment has the dominant effect on light pollution. We demonstrate the scalability of our work by providing results for the largest urban area modelled to date, comprising the central 117 km2 area of Dublin City and containing nearly 42,000 public lights. Our results show a general similarity in the shape of the azimuthally-averaged emission function for all areas examined, with differences in total light output distribution depending primarily on the nature of the lighting and, to a smaller extent, on the obscuring environment including seasonal foliage effects. A comparison with global satellite observations shows that they are consistent with the deduced angular emission function for other low-rise areas worldwide. We further validate our approach by comparing results for a range of urban locations by the close agreement observed in a detailed comparison of with calibrated imagery from the International Space Station. To our knowledge, this is the first such detailed quantitative verification of light loss calculations.

This article aims to create the nexus between sustainable development and the quality of the political regime. The current social and political context is characterized by a series of crises generated by COVID-19 pandemic, economic imbalances and regional conflicts. In this context, sustainable development is affected by the economic dynamics and the “democratic recession”. The study aims to respond to the following research questions: “how could influence the quality of the democracy the dynamics of the Sustainable Development Goals (SDGs 17)?” and “what are the premises for sustainable development in the new political context, characterized by democratic recession?” The purpose of the study is to underline the fact that democratic regimes are inclined to create both participative and deliberative frames for achieving the SDGs in accordance with UN 2030 Agenda. The research methodology used in this study is based on descriptive and inferential statistics. The research data are collected from secondary sources in the years between 2015 and 2021, from 193 countries covering all the geographical areas. The empirical results suggest two models of development: the Asian model of sustainable development characterized by economic growth and the Western democratic model based on democratic institutions, fair justice and mechanisms for preserving peace. We noticed that the key-variables for explaining the dynamics of sustainability in correlation with democratic index are represented by the functioning of the governments and the political participation. Through civic engagement and political ac-countability, democracy could be seen as a pre-requisite for achieving an optimal level of the SDGs. All these empirical results could prove valuable for the scholars interested in the relation between democracy and sustainability and for the political decision makers involved in shaping strategies for social, economic and environmental development.

The aim of this paper is to attempt to understand why the popular academic and policy field of promoting, studying and evangelising “entrepreneurship” should have been associated with great success but, in the past twenty years or more in many advanced economies, so much failure. From the US to lesser and developing countries, emerging economies and the European Union, entrepreneurship, especially in regard to start-ups and particularly high-tech start-ups have been in constant more or less recent decline. This is seldom registered in the mainstream literature where a positive and benign profile is generally presented. The paper examines this phenomenon, ties it partly with the “productivity paradox” and seeks tentative hypotheses in relation to the apparent illusions if not delusions regarding “entrepreneurship”.

Rabies is a neurological disease that causes between 40,000 and 70,000 deaths every year. Once a rabies patient has become symptomatic, there is no effective treatment for the illness, and in unvaccinated individuals, the case-fatality rate of rabies is close to 100%. French scientists Louis Pasteur and Émile Roux developed the first vaccine for rabies in 1885. If administered before the virus reaches the brain, the modern rabies vaccine imparts long-lasting immunity to the virus and saves more than 250,000 people every year. However, the rabies virus can suppress the host’s immune response once it has entered the cells of the brain, making death likely. This study aims to make use of disorder-based proteomics and bioinformatics to determine the impact that intrinsically disordered protein regions (IDPRs) in the proteome of the rabies virus have on the infectivity and lethality of the disease. This study uses the proteome of Rabies Lyssavirus (RABV) strain Pasteur Vaccins (PV), one of the best understood strains due to its use in the first rabies vaccine, as a model. The study suggests that the high levels of intrinsic disorder in the phosphoprotein (P-protein) and nucleoprotein (N-protein) allow them to participate in creation of the Negri bodies and help this virus suppress the antiviral immune response in the host cells. Additionally, the study suggests that there is a link between disorder in the matrix (M) protein and the modulation of viral transcription. The disordered regions in the M protein have a possible role in initiating viral budding within the cell. Furthermore, we checked the prevalence of functional disorder in a set of 37 host proteins directly involved in the interaction with the RABV proteins. The hope is that these new insights will aid in the development of treatments for rabies that are effective after infection.

Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain makes it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.

Variable and sometimes contrasting effects of using artificial rhizobium inocula to increase grain legume performance have been reported. The objectives of this systematic review and meta-analysis were therefore to (i) estimate the overall effect of rhizobium inocula on grain yield and protein content and (ii) identify potential confounding factors that explain the observed variation. A web of Science database literature search was carried out in 2016. Data from all field experiments, greenhouse and pot experiments that compared grain yields and protein contents in Rhizobium/Bradyrhizobium-inoculated with non-inoculated control crops were extracted and analyzed using previously described unweighted and weighted meta-analysis protocols. GRADE assessments of the strength of evidence of results from the weighted meta-analyses were carried which included an assessment of the risk of publication bias. Results: For unweighted meta-analyses we identified eligible data in 236 and 36 studies for grain yield and protein content respectively. For weighted meta-analyses we identified eligible data in 92 and 8 studies for grain yield and protein content respectively. Rhizobium inoculation was found to (i) significantly increase grain yield in both the unweighted (mean percent difference: 41%, 95%CI 36,46, p<0.0001) and weighted meta-analysis (Standardized mean difference: 1.56, 95%CI 1.26,1.87, p<0.0001) and (ii) significantly increase protein content in the unweighted meta-analysis (mean percent difference: 11%, 95%CI 5,18, p<0.0001), but not the weighed meta-analyses which only detected a trend (0.1>p>0.05) towards higher protein content in inoculated grain legume crops. Multi-level model-based weighted meta-analyses suggest that the (i) type of experiment, (ii) type of fertilizer used in experiments, (iii) grain legume type/species and (iv) the country in which experiments were carried out, were confounding factors. The main limitation of the evidence is that a large number of publications did not report measures of variation and could therefore not be included in the more scientifically sound weighted meta-analyses. However based on the large evidence-base available for grain yield it can be concluded that overall Bradyrhizobium/Rhizobium seed inoculation results can increase grain yield by ~40% compared with non-inoculated grain legume crops.

The Zika virus (ZIKV) is a mosquito-borne Flavivirus and can be transmitted through an infected mosquito bite or through human-to-human interaction by sexual activity, blood transfusion, breastfeeding or perinatal exposure. After the 2015-2016 outbreak in Brazil, a strong link between ZIKV infection and microcephaly emerged. ZIKV specifically targets human neural progenitor cells, suggesting that proteins encoded by ZIKV bind and inactivate host cell proteins leading to microcephaly. Here, we present a systematic annotation of interactions between human proteins and the seven non-structural ZIKV proteins corresponding to a Brazilian isolate. The interaction network was generated by combining tandem-affinity purification followed by mass spectrometry with yeast two-hybrid screens. We identified 150 human proteins, involved in distinct biological processes, as interactors to ZIKV non-structural proteins. Our interacting network is composed of proteins that have been previously associated with microcephaly in human genetic disorders and/or animal models. This study builds on previously published interacting networks of ZIKV and genes related to autosomal recessive primary microcephaly to generate a catalog of human cellular targets of ZIKV proteins implicated in processes related to microcephaly in humans. Collectively, this data can be used as a resource for future characterization of ZIKV infection biology and help create a basis for the discovery of drugs which may disrupt the interaction and reduce the health damage to the fetus.

S100 is a family of over 20 structurally homologous, but functionally diverse regulatory (calcium/zinc)-binding proteins of vertebrates. The involvement of S100 proteins in numerous vital (patho)physiological processes is mediated by their interaction with various (intra/extra)cellular protein partners, including cell surface receptors. Furthermore, recent studies revealed the ability of specific S100 proteins to affect cell signaling via direct interaction with cytokines. Previously, we have revealed binding of ca. 71% of the four-helical cytokines by S100P protein due to the presence in its molecule of a cytokine-binding site, which overlaps with the binding site for S100P receptor. Here we show that another S100 protein, S100A6 (pairwise sequence identity with S100P of 35%), specifically binds numerous four-helical cytokines. We have studied affinity of recombinant forms of 35 human four-helical cytokines covering all structural families of this fold to Ca2+-loaded recombinant human S100A6, using surface plasmon resonance spectroscopy. S100A6 recognizes 26 of the cytokines from all families of this fold with the equilibrium dissociation constants ranging from 0.3 nM to 12 µM. Overall, S100A6 interacts with ca. 73% of the four-helical cytokines studied to date with selectivity equivalent to that for S100P protein, with the differences limited to binding of Interleukin-2 and Oncostatin-M. The molecular docking study evidences presence in S100A6 molecule of a cytokine-binding site, analogous to that found in S100P. The findings argue the presence in some of the promiscuous members of S100 family of a site specific to a wide range of the four-helical cytokines. This unique feature of the S100 proteins potentially allows them to serve as universal inhibitors of signaling of the four-helical cytokines, which could be of value for reduction of severity of the disorders accompanied by excessive release of the cytokines.

The main objective of this study is to compare and investigate the proximate, sensory parameters of the biscuits fortified with (1) whey protein concentrate (WPC), (2) isolated soy protein (ISP) at various proportions as a source of protein enrichment. The fortified biscuits were analysed for sensory and proximate analysis. The study evaluated and compared the effect of fortifying whey protein concentrate and isolated soy protein at various proportions T0 control (0%), T1 (5%), T2 (10%), T3 (15%), T4 (20%). The protein content in both WPC and ISP samples tends to increase, but much higher in WPC formulated biscuits. At 20% WPC the protein content peaked to 29.11%, other nutritional components such as fat, ash, fibre and moisture content of WPC samples increased significantly, whereas no such significant changes were observed and only linear increase of protein content were in ISP fortified samples. The sensory analysis of ISP fortified samples were acceptable up to 10% proportion, exceeding 10% showed unacceptable results, on comparison WPC biscuits were acceptable at all proportions, more desirable at 20% WPC. Conclusively, fortifying biscuits with either WPC or ISP might be a source of protein without any significant effect on the quality of biscuits.

Background: Night-migratory birds sense the Earth´s magnetic field by an unknown molecular mechanism. Theoretical and experimental evidence support the hypothesis that light-induced formation of a radical-pair in European robin cryptochrome 4a, ErCry4a, is the primary signalling step in the retina of the bird. In the present work, we investigated a possible route of cryptochrome signalling involving the α-subunit of the cone specific heterotrimeric G protein from European robin. Methods: Protein-protein interaction studies include surface plasmon resonance, pulldown affinity binding and Förster resonance energy transfer. Results: Surface plasmon resonance studies showed direct interaction revealing high to moderate affinity for binding of non-myristoylated and myristoylated G protein to ErCry4a, respectively. Pulldown affinity experiments confirmed this complex formation in solution. We validated these in vitro data by monitoring the interaction between ErCry4a and G protein in a transiently transfected neuroretinal cell line using Förster resonance energy transfer. Conclusions: Our results suggest that ErCry4a and the G protein also interact in vivo and might constitute the first biochemical signalling step in radical-pair-based magnetoreception.

The clinical interaction between stroke and periodontitis has been consistently studied and confirmed. Hence, forecasting potentially new protein interactions in this association using bioinformatic strategies presents potential interest. In this exploratory study, we conducted a protein-protein network interaction (PPI) search with documented encoded proteins for both stroke and periodontitis. Genes of interest were collected via GWAS database. The STRING database was used to predict the PPI networks, first in a sensitivity purpose (confidence cut-off of 0.7), and then with a highest confidence cut-off (0.9). Genes over-representation was inspected in the final network. As a result, we foresee a prospective protein network of interaction between stroke and periodontitis. Inflammation, pro-coagulant/pro-thrombotic state and ultimately atheroma plaque rupture is the main biological mechanism derived from the network. These pilot results may pave the way to future molecular and therapeutic studies to further comprehend the mechanisms between these two conditions.

Prenatal maternal feeding plays an important role in fetal development and has potential to cause long-lasting epigenetic modifications. MicroRNAs (miRNAs) are non-coding, single-stranded RNAs that serve as one epigenetic mechanism. Though miRNAs have crucial roles in fetal programming, growth, and development, there are limited data regarding maternal diet and sheep miRNA expression. Therefore, weanalyzed high and low maternal dietary protein for miRNA expression in sheep fetal longissimus dorsi. Pregnant ewes were fed an isoenergetic high-protein (HP, 160–270 g/day), low-protein (LP, 73–112 g/day), or standard protein diet (SP, 119–198 g/day) during pregnancy. miRNA expression profiles were evaluated using the Affymetrix GeneChip miRNA 4.0 Array. Twelve up-regulated, differentially expressed miRNAs (DE miRNAs) were identified targeting 65 genes. The oar-3957-5p miRNA was highly up-regulated in LP and SP compared to HP. Previous transcriptome analysis identified integrin and non-receptor protein tyrosine phosphatase genes targeted by miRNAs detected in the current experiment. A total of 28 GO terms and 10 pathway-based gene sets were significantly (padj < 0.05) enriched in target genes. Most genes targeted by identified miRNAs are involved in immune and muscle disease pathways. Our study shows dietary protein intake during pregnancy affects fetal skeletal muscle epigenetics via miRNA expression.

Food composition data in the EMR countries are often lacking, obsolete or unreliable. The study aims to provide reliable and up-to-date nutrient data of selected food products consumed in Oman in order to evaluate consistency of nutrition labelling and update the current used food composition database. Contents of total fat, fatty acids, carbohydrates, total nitrogen, sugars and sodium were chemically analyzed in 221 foods and beverages purchased in 2022 and label and corresponding laboratory values were compared using the tolerance levels of the European Union. Food items were classified according their nutritional composition, the extent of processing and coded according FoodEx2 system. Results indicate that the nutrient values stated on a label align with the values obtained in the laboratory with the exception of a 6.3% discrepancy in TFAs content, where the reported values are higher than the appropriate reference values. The category with the highest frequency (71.5%) consisted of ultra-processed foods. In terms of inconsistencies in the nutrition claims, 5.1% of food products with claims did not comply with the statement “sugar free” or “low salt”. These findings underscore the significance of vigilant monitoring of nutritional labels as a means to implement measures that promote the well-being of consumers.

Rationale: The 14-3-3 protein family is known to interact with many proteins in non-cardiac cell types to regulate multiple signaling pathways, particularly those relating to energy and protein homeostasis; and the 14-3-3 network is a therapeutic target of critical metabolic and proteostatic signaling in cancer and neurological diseases. Although the heart is critically sensitive to nutrient and energy alterations, and multiple signaling pathways coordinate to maintain the cardiac cell homeostasis, neither the structure of cardiac 14-3-3 protein interactome, nor potential functional roles of 14-3-3 protein-protein interactions (PPIs) in heart has been explored. Objective: To establish the comprehensive landscape and characterize the functional role of cardiac 14-3-3 PPIs. Methods and Results: We evaluated both RNA expression and protein abundance of 14-3-3 isoforms in mouse heart, followed by co-immunoprecipitation of 14-3-3 proteins and mass spectrometry in left ventricle. We identified 52 proteins comprising the cardiac 14-3-3 interactome. Multiple bioinformatic analyses indicated that more than half of the proteins bound to 14-3-3 are related to mitochondria; and the deduced functions of the mitochondrial 14-3-3 network are to regulate cardiac ATP production via interactions with mitochondrial inner membrane proteins, especially those in mitochondrial complex I. Binding to ribosomal proteins, 14-3-3 proteins likely coordinate protein synthesis and protein quality control. Localizations of 14-3-3 proteins to mitochondria and ribosome were validated via immunofluorescence assays. The deduced function of cardiac 14-3-3 PPIs is to regulate cardiac metabolic homeostasis and proteostasis. Conclusions: Thus, the cardiac 14-3-3 interactome may be a potential therapeutic target in cardiovascular metabolic and proteostatic disease states, as it already is in cancer therapy.

A model that predicts levels of coronavirus (CoV) respiratory/fecal-oral transmission potentials based on the outer shell hardness has been built using neural network (artificial intelligence, AI) analysis of the percentage of disorder (PID) in the nucleocapsid, N, and membrane, M, proteins of the inner and outer viral shells, respectively. Based mainly on the PID of N, SARS-CoV-2 is categorized as having intermediate levels of both respiratory and fecal oral transmission potential. Related to this, other studies have found strong positive correlations between virulence and inner shell disorder among numerous viruses, including Nipah, Ebola, and Dengue viruses. There is some evidence that this is also true for SARS-CoV-2 and SARS-CoV, which have N PIDs of 48% and 50%, and are characterized by case-fatality rates of 7.1% and 10.9%, respectively. The link between levels of respiratory transmission and virulence lies in viral load of body fluids and organ respectively. A virus can be infectious via respiratory modes only if the viral loads in saliva and mucus exceed certain minima. Likewise, a person may die, if the viral load is too high especially in viral organs. Inner shell proteins of viruses play important roles in the replication of viruses, and structural disorder enhances these roles by providing greater efficiency in protein-protein/DNA/RNA/lipid binding. This paper outlines a novel strategy in attenuating viruses involving comparison of disorder patterns of inner shells of related viruses to identify residues and regions that could be ideal for mutation. The M protein of SARS-CoV-2 has one of the lowest M PID values (6%) in its family, and therefore this virus has one of the hardest outer shells, which makes it resistant to antimicrobial enzymes in body fluid. While this is likely responsible for its contagiousness, the risks of creating an attenuated virus with a more disordered M are discussed.

The detection and quantification of protein–protein interactions (PPIs) is a crucial technique that often involves the use of recombinant proteins with fusion-protein tags, such as maltose-binding protein (MBP) and glutathione-S-transferase (GST). In this study, we improved the cohesive and sticky properties of gelatinized starch by supplementing it with agarose, resulting in a harder gel that could coat the bottom of a microtiter plate. The resulting gelatinized starch/agarose mixture allowed for the efficient immobilization of MBP-tagged proteins on the coated plates, enabling the use of indirect ELISA-like PPI assays. By using the enzymatic activity of GST as an indicator, we succeeded in determining the dissociation constants between MBP-tagged and GST-tagged proteins on 96-well microtiter plates and a microplate reader without any expensive specialized equipment.

Cell-penetrating peptides (CPPs), a group of small peptides capable of promoting the transport of molecular cargo across the plasma membrane, have become important tools in promoting the cellular uptake of exogenously delivered macromolecules. GV1001, a peptide derived from a reverse-transcriptase subunit of telomerase (hTERT) and developed as a vaccine against various cancers, reportedly has unexpected CPP properties. Unlike typical CPPs, such as the HIV-1 TAT peptide, GV1001 enabled the cytosolic delivery of macromolecules such as proteins, DNA and siRNA via extracellular heat shock protein 90 (eHSP90) and 70 (eHSP70) complexes. The eHSP-GV1001 interaction may have biological effects in addition to its cytosolic delivery function. GV1001 was originally designed as a MHC class II-binding cancer epitope, but its CPP properties may contribute to its strong anti-cancer immune response relative to other telomerase peptide-based vaccines. Cell signaling via eHSP-GV1001 binding may lead to unexpected biological effects, such as direct anticancer or antiviral effects. In this review, we focus on the CPP effects of GV1001 bound to eHSP90 and ehsp70.

Recent studies supported a clinical association between Parkinson’s Disease (PD) and periodontitis. Hence, investigating possible protein interactions between these two conditions is of interest. In this study, we conducted a protein-protein network interaction analysis with recognized genes encoding proteins for PD and periodontitis. Genes of interest were collected via GWAS database. Then, we conducted a protein interaction analysis using STRING database, with a highest confidence cut-off of 0.9. Our protein network casted a comprehensive analysis of potential protein-protein interactions between PD and periodontitis. This analysis may underpin valuable information for new candidate molecular mechanisms between PD and periodontitis and may serve new potential targets for research purposes. These results should be carefully interpreted giving the limitations of this approach.

Abstract: Aim: Biofields combine many physiological levels both spatially and temporally. These biofields reflect naturally resonant forms of synaptic energy reflected in growing and spreading waves of brain activity. The study desires to theoretically understand better how resonant continuum waves may be reflective of consciousness, memory, and thought. Background: The metabolic processes that maintain animal cellular and physiological function are enhanced by physiological coherence. Internal biological system coordination and sensitivity to particular stimuli and signal frequencies are two aspects of coherent physiology. There exists significant support for the notion that exogenous biologically and non-biologically generated energy entrains human physiological systems. All living things have resonant frequencies that are either comparable or coherent, therefore eventually all species will have a shared resonance. An organism's biofield activity and resonance are what support its life and allow it to react to stimuli. Methods: As the naturally resonant forms of synaptic energy are growing and spreading waves of brain activity, The temporal and spatial frequency of waves are effectively regulated by a time delay (T) in inter-layer signals in a layered structure that mimics the structure of the mammalian cortex. From ubiquitous noise, two different types of waves can arise as a function of T. One is coherent, and as T rises, so does its resonant spatial frequency. Results: Continued growth eventually causes both the wavelength and the temporal frequency to abruptly increase. Two waves expand simultaneously and randomly interfere in an area of T values as a result. Conclusion: We suggest that because of this extraordinary dualism, which has its roots in the phase relationships of amplified waves, coherent waves are essential for memory retrieval whereas random waves represent original cognition.

Obsessive-compulsive disorder (OCD) remains, despite significant scientific progress, a pathological condition that is incomprehensible, due toits paradoxical psychological and behavioral symptoms. The presentwork aims at assessing current phenomenological understandings of this pathology. Among the cognitive models used today, post-rationalist cognitivism and cognitive neuropsychological psychotherapy, which both incorporate a phenomenological approach, seem most effective at grasping OCD patients’ experiences of the world, which are typically characterized by hyper-reflexivity, at the expense of "natural evidence." For OCD patients, the emotional sense of the world becomes a set of sterile rules that determine a suffering life.

The need to regulate the non-exhaust particulate emissions from vehicles has been discussed worldwide due to the toxicity to the human body as well as the atmosphere. In-depth studies have been conducted on precise analysis of the non-exhaust particulates, in particular, accurate measurement of tire-brake-road wear particles, and their proportion in the atmosphere. In this study, the influence of tire and road wear particles (TRWP) on particulate matter (PM) in the atmosphere was investigated through tire and PM samples. PM samples were collected from the atmosphere using a high-volume sampler equipped with a quartz filter. Additionally, polycyclic aromatic hydrocarbons (PAHs) and heavy metals in tire rubber were analyzed as markers by pyrolysis-gas chromatography/mass spectrometry (GC/MS), GC/MS, and inductively coupled plasma/mass spectrometry (ICP/MS). More vinylcyclohexene was detected than dipentene in the markers measured in the samples of tires equipped with vehicles driving on the road with the high-volume sampler installed, while more dipentene was detected in total suspended particles (TSP) samples. Among the PAHs measured in tire samples, pyrene exhibited the highest concentration. In TSP samples, benzo(b)fluoranthene showed the highest concentration. Among the heavy metals, zinc exhibited the highest concentration in all tire samples and calcium in TSP samples.

In Korea’s air pollutant inventory, construction machinery is a major emission source in the non-road sector. Since 2004, the Korean government has introduced and reinforced emission regulations to reduce the air pollutants emitted from their diesel engines. Since the engine dynamometer test method used in emission regulations has limitations in reflecting emission characteristics under the diverse working conditions of construction machinery, it is necessary to examine the effectiveness of emission regulations and the validity of the emission factors applied as inputs to the air pollutants inventory. This could be done by evaluating engine operation and emission characteristics under real-world working conditions. In this study, 14 units were selected among the excavators, wheel loaders, and forklifts that represent approximately 90% of the registered construction machines in Korea. They were equipped with a portable emission measurement system (PEMS) to measure gaseous emissions and collect engine data under various real-world working conditions. With the reinforcement of emission regulations for the construction machinery from K-tier3 to K-tier4 in Korea, exhaust after-treatment technologies, such as selective catalytic reduction and diesel oxidation catalyst, were applied. Real world NOx were reduced by approximately 83%, and THC 77% and CO by 73%, respectively. Real world NOx + THC of the K-tier3 machines exceeded the laboratory emission limit, but the K-tier4 machines considerably improved despite some differences. The emission factors applied to the air pollutant inventory have been developed using the engine dynamometer test method, but they were considerably underestimated compared with emissions under real-world working conditions. The difference was even larger for the K-tier4 machines. In this study, the possibility of developing emission factor equations that use the engine load factor as a parameter was confirmed by using the engine work 1 g/kW·h segment moving averaging window (MAW) method.

Real-world optimization problems are often gov- erned by one or more constraints. Over the last few decades, extensive research has been performed in Constrained Opti- mization Problems (COPs) fueled by advances in computational power. In particular, Evolutionary Algorithms (EAs) are a preferred tool for practitioners for solving these COPs within practicable time limits. We propose a novel hybrid Evolutionary Algorithm based on the Differential Evolution algorithm and Adaptive Parameter Gaining Sharing Knowledge-based algo- rithm to solve global real-world constrained parameter space. The proposed CHAGSKODE algorithm leverages the power of multiple adaptation strategies concerning the control parameters, search mechanisms, as well as uses knowledge sharing between junior and senior phases. We test our method on the benchmark functions taken from the CEC2020 special session & competition on real-world constrained optimization. Experimental results indicate that CHAGSKODE is able to achieve state-of-the- art performance on real-world constrained global optimization when compared against other well-known real-world constrained optimizers.

The "best of all possible worlds" theory (hereinafter the "possible world theory") was presented by Leibniz many centuries ago, and provided an opportunity for metaphysics to understand the ontological meaning of the world in an in-depth way. Furthermore, the theory has multiple impacts on the multiverse theory of modern physics. However, considering the ontological questions of the world solely on linguistics logic leads to basing the possible world theory or the multiverse theory on relatively uncertain inferential reasons. In this study, symbolic logic was used to consider the possible world theory on a more solid foundation. The entire world was made into oneness, and tracking the existential process at the beginning of the world, realized the existential necessity of the world, even though the initial causal point of the world was assumed to be completely void (null set). The existential system in this study, was generalized without specific elements, apart from existence and non-existence. It was discovered that existential possibility and existential necessity are logically equivalent.

Indirect effects of global change via changing species interactions have been largely ignored in studies predicting global change impacts on ecosystems. Antagonistic biotic interactions, however, can strongly affect ecosystems and are likely to be affected by global change drivers themselves. We synthesize current knowledge on the impact of invertebrate herbivores and pathogens on plant productivity, diversity and community composition, and outline theory and expectations on how important global change drivers – nitrogen enrichment, climate change and elevated CO², and plant and insect diversity loss, may affect enemy impact on plant communities. We illustrate that our ability to predict global change impact requires a holistic perspective, taking into account direct as well as indirect effects via the biotic component of ecosystems.

There are now a wide variety of global metrics. To find the degree of overlap between these different measures, we employ a principal components analysis (PCA) to 15 indices across 145 countries. Our results demonstrate that the most important underlying dimension highlights that economic development and social progress go hand in hand with state stability. The results are used to produce categorical divisions of the world. The threefold division identifies a world composed of what we describe and map as Rich, Poor and Middle countries. A five-group classification provided a more nuanced categorization described as; The Very Rich, Free and Stable, Affluent and Free, Upper Middle, Lower Middle, and Poor and Not Free.

As we approach the 135th anniversary of the automobile, two industry trends, automation and digitalization, are rapidly revolutionizing the thus far, relatively unchanged automotive user experience. This paper describes the development of the Valeo MyMobius user interface concept. The goal of this project was to explore how to achieve an intuitive driving experience as the automotive industry undergoes transition from primarily analog to primarily digital interfaces and from physical buttons to multimodal interactions. To achieve the perception of intuitiveness, designers must understand their users, find and reduce physical and cognitive friction points, and bridge knowledge gaps with interface designs that facilitate discovery and learnability. The Valeo MyMobius concept featured steering wheel touch displays that supported quick, frequent menu selections using swiping gestures (common in smartphone interactions) and reinforcing icons (to facilitate learnability). Learning algorithms personalized the experience by tailoring suggestions, while more complex interactions were handled with a conversational voice assistant, which also served as a driving copilot, capable of contextually suggesting when Advanced Driving Assistance System (ADAS) features such as ACC could be utilized. The visual design aesthetic embodied Kenya Hara’s design philosophy of “Emptiness,” reducing visual clutter and creating spaces that are ready to receive inspiration and information. Altogether, the Valeo MyMobius concept demonstrated an attainable future where the perception of intuitiveness can be achieved with today’s technologies.

Protein tyrosine sulfation (PTS), a vital post-translational modification, facilitates protein–protein interactions and regulates many physiological and pathological responses. Monitoring PTS has been difficult owing to the instability of sulfated proteins and the lack of a suitable method for detecting the protein sulfate ester. In this study, we combined an in situ PTS system with an ultra-high-sensitivity polysilicon nanowire field-effect transistor (pSNWFET)-based sensor to directly monitor PTS formation. A peptide containing the tyrosine sulfation site of P-selectin glycoprotein ligand (PSGL)-1 was immobilized onto the surface of the pSNWFET by using 3-aminopropyltriethoxysilane and glutaraldehyde as linker molecules. A coupled enzyme sulfation system consisting of tyrosylprotein sulfotransferase and phenol sulfotransferase was used to catalyze PTS of the immobilized PSGL-1 peptide. Enzyme-catalyzed sulfation of the immobilized peptide was readily observed through the shift of the drain current–gate voltage curves of the pSNWFET before and after PTS. To the best of our knowledge, this is the first study to describe in situ PTS and its direct observation by using semiconductor devices. We expect that this approach can be developed as a next generation biochip for biomedical research and industries.

SARS-CoV-2 is a novel and highly pathogenic coronavirus, which was first diagnosed in Wuhan city, China, in 2019, and spread to 185 countries and territories, and as of April 29, 2020, more than 3.11 million cases were recorded, and more than 217,000 people were killed. Despite all worldwide efforts, there is currently no vaccine, any drugs available to protect people against deadly SARS-CoV-2 coronavirus. The world urgently needs a SARS-CoV-2 coronavirus vaccine or effective antiviral drugs to relieve the human suffering associated with the pandemic that kills thousands of people every day. The SARS-CoV-2 genome encode a non-structural proteins named as ORF1a/b, and structural proteins such as spike (S) glycoprotein, nucleocapsid protein (N), small envelop protein (E) and matrix protein (M). A number of studies have been shown that CoV spike (S) glycoprotein and nucleocapsid protein (N) could be promising targets for vaccine, antibodies and therapeutic drug development to combat with deadly, pandemic SARS-CoV-2. Purposes of the present paper is the sequence analysis and amino acid variations of structural proteins deduced from novel coronavirus SARS-CoV-2 strains, isolated in different countries. Multiple sequence alignment of S, N and E proteins from four different coronavirus species, are also described. It is expected that the data from these studies will be very useful for the the designing and development of vaccines, antibodies and therapeutic agents that can be used to combat with the highly pathogenic SARS-CoV-2 coronavirus worldwide.

Background: Staphylococcus aureus (S. aureus) is an opportunistic pathogen and a predominant cause of life-threatening nosocomial infections. Drug resistance in S. aureus is attributed to production of biofilm, which is controlled largely by bacterial quorum sensing (QS) systems. Methodology: In vitro analysis of biofilm inhibition assay was performed using crystal violet staining assay, swarming motility, light microscopy and growth curve analyses. Identification of the major constituents of I. verum fruit extract was performed by GC-MS. Ligand-protein interaction was analyzed by molecular docking investigations. Results: The methanol extract of I. verum inhibited the growth of MRSA at the concentration of 4.8 mg/ml. At the sub-inhibitory concentration (2.4mg/ml), the extract showed significant reduction in biofilmogenesis. Light microscopy analysis confirmed the antibiofilm activity as well as the efficacy in disturbing biofilm architecture. A reduced swarming motility was observed at the lowest concentration of 2.4mg/ml. GC-MS analysis revealed anethol (AL) as the major constituent. The molecular docking analysis attributes the antibiofilm activity to an active ligand AL, which strongly interacted with the active site residues of AgrA and SarA proteins of S. aureus. Conclusion: We report the activities of I. verum to be immensely interfering with QS system and biofilm formation in MRSA.

(1) Background: Aim was to investigate real-world effectiveness (hypothesizing non-inferiority) and safety profile of risdiplam in paediatric and adult nusinersen-risdiplam spinal muscular atrophy (SMA) switch cohort. (2) Methods: A retrospective and anonymous collection of relevant demographic and clinical data for all Croatian SMA patients switched from nusinersen to risdiplam up to September 2023 (reimbursed by Croatian Health Insurance Fund – CHIF) was performed using CHIF database and associated reimbursement documentation. Patients were included in effectiveness and safety analysis if they met the following inclusion criteria: i) risdiplam reimbursed by CHIF; ii) patient received at least 6 doses of nusinersen before switch to risdiplam; iii) no relevant pause between the latter disease modifying drugs (DMDs); iv) availability of all prespecified studied data and parameters. (3) Results: 17 patients met inclusion criteria [58.9% female; median age 12.75 (3.0-44.5) yr.]. In our ‘switch’ cohort, we have demonstrated a non-inferiority of risdiplam to nusinersen, in SMA 1 (+1.0 in CHOP INTEND; p=0.067), SMA 3p (+0.7 in HFMSE; p=0.897) and SMA 3a (+0.8 in RHS; p=0.463) subpopulations, during a one-year follow-up period. There were no reports on respiratory function worsening, feeding worsening, and no lethal events. No new safety concerns were identified, except of the weight gain that arose as a new potential adverse drug reaction ‘signal’ in two patients. (4) Conclusions: We have reported a pivotal real-world findings on switching SMA patients from nusinersen to risdiplam and demonstrated its effectiveness (non-inferiority), safety and tolerability in a heterogenous paediatric and adult ‘switch’ cohort, which will further increase the quality and standards of care as well as safety of a notable portion of SMA patients; especially for those who demand switch from nusinersen to other DMDs from clinical or personal reasons.

Taxanes have been shown to be the most effective treatment for recurrent or metastatic breast cancer. However, for patients pretreated with taxanes, more active and possibly less toxic drugs are needed. In this retrospective study, we investigated on the effectiveness and safety of eribulin mesylate in 91 taxane-refractory subjects, extracted from the ESEMPIO database, which included 497 metastatic breast cancer patients treated with eribulin allover the Italy. This analysis included only those patients who have shown disease progression while receiving taxane therapy (primary refractory), or those who achieved a response followed by progression while still on therapy (taxane failure). Overall, 41/91 patients (45.2%) showed a clinical benefit; 1 complete response (2.2%) and 16 partial responses (17.6%) were observed. The median progression free survival was 3.1 months (95% CI: 2.8–3.5) and the median overall survival was 11.6 months (95% CI: 8.7–16.7). With regard to toxicity, 53 patients (58%) experienced asthenia/fatigue, 23 (25%) showed peripheral neurotoxicity, 18 (20%) alopecia, 12 (13%) mild constipation and 27 (30%) neutropenia. The toxicity related to the treatment led to eribulin dose reduction in 19 (21%) and discontinuation in 9 (10%) patients, respectively. In conclusion, this study suggests that eribulin is effective and well tolerated also in taxane-refractory patient.

In this work, we explore the intrinsic disorder status of the three members of the synuclein family of proteins - α-, β-, and γ-synucleins. We also analyzed the peculiarities of the amino acid sequences and modeled 3D structures of the human synuclein family members to find potential effects of pathological mutations. Furthermore, we conducted a comparative sequence-based analysis of the synuclein proteins from various evolutionary distant species and evaluated their levels of intrinsic disorder using a set of commonly used bioinformatics tools. Next, we conducted a detailed functional disorder analysis of the proteins in the interactomes of the human synuclein family members using various web-based disorder analysis and prediction tools, such as RIDAO, D2P2 and FuzDrop. We identify that the interactome of human α-synuclein has relatively higher levels of intrinsic disorder, as compared to the interactomes of human β- and γ- synucleins. These observations highlight the critical importance of intrinsic disorder of human α-synuclein and its interactors in neuronal processes as compared to other proteins of the synuclein family.

Objective: The aim of study is to find key genes and enriched pathways associated with lung cancer. Participants and Methods: Differentially expressed genes (DEGs) data of 54674 genes based on stage, tumor and status of lung cancer was taken from 66 patients of African American (AAs) origin. 2392 DEGs were found based on stage, 13502 DEGs were found based on tumor, 2927 DEGs were found based on status having p value (p<0.05). Results: Total 33 common DEGs were found from stage, tumor and status of lung cancer. Gene ontology (GO) and KEGG pathway enrichment analysis was performed and 49 significant pathways were obtained, out of which 10 pathways were found to be exclusively involved in lung cancer development. Protein-protein interaction (PPI) network analysis found 69 nodes and 324 edges and identified 10 hub genes based on their highest degrees. Module analysis of PPI found that ‘Viral carcinogenesis’, ‘pathways in cancer’, ‘notch signaling pathway’, ‘AMPK signaling pathways’ had a close association with lung cancer. Conclusion: These identified DEGs regulate other genes which play important role in growth of lung cancer. The key genes and enriched pathways identified can thus help in better identification and prediction of lung cancer.

regulating translational speed and accuracy. Threonylcarbamoyl adenosine (t6A37) and 5-methoxycarbonylmethyl-thiouridine (mcm5s2U34) are critical ASL modifications that have been linked to several human diseases. The model yeast Saccharomyces cerevisiae is viable despite the absence of both modifications, growth is however greatly impaired. The major observed consequence is a subsequent increase in protein aggregates and aberrant morphology. Proteomic analysis of the t6A-deficient strain revealed a global mistranslation leading to protein aggregation without regard to physicochemical properties or t6A-dependent or biased codon usage in parent genes. However, loss of sua5 led to increased expression of soluble proteins for mitochondrial function, protein quality processing/trafficking, oxidative stress response, and energy homeostasis. These results point to a global function for t6A in protein homeostasis very similar to mcm5/s2U modifications.

Intrinsically Disordered Proteins (IDPs) play crucial roles in signal transduction, cell differentiation, and transcriptional regulation. Many disrupted genes associated with mental disorders are identified as IDPs, and emerging evidence suggests the functional role of IDPs in neuropsychiatric disorders. However, few studies comprehensively explore the functional association between protein disorder properties and different mental diseases. To address this gap, we collected disrupted gene sets for seven mental diseases (MDD, SCZ, BP, ID, AD, ADHD, ASD) and a control gene set from normal brains using DisGeNET and GeneCards databases. The state-of-the-art predictor IUPred2A was then utilized to calculate the disorder properties , followed by a thorough comparison between the disordered proteins in mental diseases and healthy controls. Functional enrichment analysis and protein-protein interaction networks were conducted to investigate the IDPs’ functional roles in psychiatric diseases. Additionally, we demonstrated the role of IDPs in protein binding formations through a case study of alpha-synuclein using protein docking. Our findings reveal that differentially expressed proteins in mental disorders, especially in ASD and ADHD, exhibit more IDPs than those in healthy controls. IDPs in psychiatric disorders are significantly enriched in neurodevelopmental pathways and play an important role in in gene expression regulation. Our results indicate distinct functional patterns of disorder proteins among mental diseases and healthy controls. When comparing the IDPs between ASD and ADHD, we observed that IDPs in ADHD are more likely linked to the synaptic signaling and regulation, while IDPs in ASD are more tendentiously related to diverse and complex biological processes. Our work offers valuable insights into the important functions of IDPs in psychiatric disorders, enhancing our understanding of the molecular mechanisms involved in psychiatric disorders.

This study aimed to investigate the appearance and frequencies of the booroola polymorphism of the bone morphogenetic protein receptor 1b (BMPR1B) gene (FecB) and the embrapa polymorphism of the growth differentiation factor 9 (GDF9) gene (FecGE) in sheep in Thailand. A total of 454 cross-bred sheep blood samples were collected from four provinces in Thailand during August 2022 to July 2023. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to identify the FecB and FecGE genotype. The history of ewe birth types was collected from the owners to analyze the association between Fecundity (Fec) genotypes and the history of birth types. The genotypic frequencies of FecB for homozygous genotype (B/B), heterozygous genotype (+/B) and wild-type (+/+) were 0.22%, 1.54%, and 98.24%, respectively. Meanwhile, the genotypic frequencies of FecGE for homozygous genotype (E/E), heterozygous genotype (+/E), and wildtype (+/+) were 0.00%, 2.42%, and 97.58%, respectively. Furthermore, three ewes exhibited both FecB and FecGE genotypes. Fisher’s exact test revealed that the possessor of FecB genotype was associated with multiple births (p&lt;0.01). Both FecB and FecGE mutations were identified in crossbred sheep in Thailand. Sheep containing FecB allele is a better candidate to be selected to improve the prolificacy of crossbred sheep in Thailand.

This study aimed to elucidate the similarities and differences between amyloid-forming corpora amylacea (CA) in the prostate and lung, examine the nature of CAs in cystic tumors of the atrioventricular node (CTAVN), and clarify the distinctions between amyloid-forming CA and spheroid-type amyloid deposition. We conducted proteomics analyses using liquid chromatography–tandem mass spectrometry with laser microdissection and immunohistochemistry to validate the characteristics of CAs in the lung and prostate. Our findings revealed that CAs in these organs primarily consist of common proteins (β2-microglobulin and lysozyme) and locally produced proteins. Moreover, we observed a discrepancy between the histopathological and proteomic analysis results in CTAVN-associated CAs. In addition, while the histopathological appearance of amyloid-forming CAs and spheroid-type amyloid deposits were nearly identical, the latter deposition lacked β2-microglobulin and lysozyme, and exhibited evident destruction of surrounding tissue. A literature review further supported these findings. These results suggest that amyloid-forming CAs in the lung and prostate are formed through a shared mechanism, serving as waste containers (wasteosomes) and/or storage for excess proteins (functional amyloids). In contrast, we hypothesize that while amyloid-forming CA and spheroid-type amyloid deposits are formed, in part, through common mechanisms, the latter are pathological.

Matrix Metaloproteinase-2 (MMP-2) is an extracellular Zn²⁺ protease specific to type I and IV collagens. Its expression is associated with several inflammatory, degenerative, and malignant diseases. Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation. Dihedral principle component analysis revealed 10 families of conformations with the greatest degree of variability occurring in the link region connecting the catalytic and hemopexin domains. Dynamics cross correlation analysis indicated domain movements corresponding to opening and closing of the hemopexin domain in relation to the fibronectin and catalytic domains facilitated by the link region. Interaction energies were calculated using the MMPBSA-interaction entropy analysis method and revealed strong binding energies for the catalytic Zn²⁺ ion 1, Ca²⁺ ion 1, and Ca²⁺ ion 3 with significant conformational stability at the binding sites of Zn²⁺ ion 1 and Ca²⁺ ion 1. Ca²⁺ ion 2 diffuses freely away from its crystallographically defined binding site. Zn²⁺ ion 2 plays a minor role in conformational stability of the catalytic domain while Ca²⁺ ion 3 is strongly attracted to the highly electronegative sidechains of the Asp residues around the central β-sheet core of the hemopexin domain.

Studies on Protein-Protein interactions (PPI) can be helpful for the annotation of unknown protein function and for the understanding of cellular processes, such as specific virulence mechanisms developed by bacterial pathogens. In that context, several methods have been extensively used in recent years for the characterization of Mycobacterium tuberculosis PPI to further decipher TB pathogenesis. This review aims at compiling the most striking results based on in vivo methods (yeast and bacterial two-hybrid systems, protein complementation assays) for the specific study of PPI in mycobacteria. Moreover, newly developed methods, such as in-cell native mass resonance and proximity-dependent biotinylation identification, will have a deep impact on future mycobacterial research, as they are able to perform dynamic (transient interactions) and integrative (multiprotein complexes) analyses.

Tumor necrosis factor (TNF) inhibitors (anti-TNFs) represent a cornerstone of the treatment of various immune-mediated inflammatory diseases and are among the most commercially successful therapeutic agents. Knowledge of TNF binding partners is critical for identification of the factors able to affect clinical efficacy of the anti-TNFs. Here we report that among eighteen representatives of the multifunctional S100 protein family only S100A11, S100A12 and S100A13 interact with the soluble form of TNF (sTNF) in vitro. The lowest equilibrium dissociation constants (Kd) for the complexes with monomeric sTNF determined using surface plasmon resonance spectroscopy range from 2 nM to 28 nM. The apparent Kd values for the complexes of multimeric sTNF with S100A11/A12 estimated from fluorimetric titrations are 0.1-0.3 µM. S100A12/A13 suppress the cytotoxic activity of sTNF against Huh-7 cells, as evidenced by the MTT assay. Structural modeling indicates that the sTNF-S100 interactions may interfere with the sTNF recognition by the therapeutic anti-TNFs. Bioinformatic analysis reveals dysregulation of TNF and S100A11/A12/A13 in numerous disorders. Overall, we have shown a novel potential regulatory role of the extracellular forms of specific S100 proteins that may affect efficacy of anti-TNF treatment in various diseases.

Long-term potentiation (LTP) is a molecular basis of memory formation. Here, we demonstrate that LTP critically depends on muscle fructose 1,6-bisphosphatase 2 (Fbp2) – a glyconeogenic enzyme and moonlighting protein protecting mitochondria against stress. We show that LTP induction regulates Fbp2 association with neuronal mitochondria and Camk2, and that the Fbp2-Camk2 interaction correlates with Camk2 autophosphorylation. Silencing of Fbp2 expression or simultaneous inhibition and tetramerization of the enzyme with a synthetic effector mimicking the action of physiological inhibitors (NAD⁺ and AMP) abolishes Camk2 autoactivation and blocks formation of the early phase of LTP and expression of the late phase LTP markers. Astrocyte-derived lactate reduces NAD⁺/NADH ratio in neurons and thus, diminishes the pool of tetrameric and increases the fraction of dimeric Fbp2. We therefore hypothesize that this NAD⁺-level-dependent increase of the Fbp2 dimer/tetramer ratio might be a crucial mechanism in which astrocyte-neuron lactate shuttle stimulates LTP formation.

Streptococcus pneumoniae is an pathogenic and opportunistic Gram-positive bacteria that is the leading cause of community acquired respiratory diseases, varying from mild- to deathly- infections. Appearance of antibiotic resistant isolates has prompted the search for novel targets. One of the most promising approaches is the structure-based knowledge of possible targets in conjunction to rational design and docking of inhibitors of the chosen targets. A useful technique to help solving protein structures is to label them with a heavy atom, like selenium, that facilitates tracing of the some of the amino acid residues. We have chosen two pneumococcal DNA-binding proteins, namely the relaxase domain of MobM protein from plasmid pMV158, and the RelB-RelE antitoxin-toxin protein complex. Through the update of a previous protocol [1] that uses seleno-L-methionine, we could achieve 100% labelling of the proteins. Furthermore, the labelled proteins retained full activity as judged from relaxation of supercoiled plasmid DNA and from gel-retardation assays.

Proteins play a major role in biosensors in which they provide catalytic activity and specificity in molecular recognition. The immobilization process is however far from straightforward as it often affects the protein functionality. An extensive interaction of the protein with the surface or a significant surface crowding can lead to changes in the mobility and conformation of the protein structure. This review will provide an insight of how the analysis of the physico-chemical features of the protein surface features before the immobilization process can help to identify the optimal immobilization approach to preserve the functionality of the protein when on the surface of the biosensor.

This study used established biomarkers of death due to ischemic stroke (IS) and performed network, enrichment, and annotation analysis. Protein-protein interaction (PPI) network analysis revealed that the backbone of the highly connective network of IS death consisted of IL6, ALB, TNF, SERPINE1, VWF, VCAM1, TGFB1, and SELE. Cluster analysis revealed immune and hemostasis subnetworks, which were strongly interconnected through the major switches ALB and VWF. Enrichment analysis revealed that the PPI immune subnetwork of death due to IS was highly associated with TLR2/4, TNF, JAK-STAT, NOD, IL10, IL13, IL4, and TGF-β1/SMAD pathways. The top biological and molecular functions and pathways enriched in the hemostasis network of death due IS were platelet degranulation and activation, the intrinsic pathway of fibrin clot formation, the urokinase-type plasminogen activator pathway, post-translational protein phosphorylation, integrin cell surface interactions, and the proteoglycan-integrin-extra cellular matrix complex (ECM). Regulation Explorer analysis of transcriptional factors shows: a) that NFKB1, RELA and SP1 were the major regulating actors of the PPI network; and b) hsa-mir-26-5p and hsa-16-5p were the major regulating microRNA actors. In conclusion, prevention of death due to IS should consider that current IS treatments may be improved by targeting VWF, VEGFA, proteoglycan-integrin-ECM complex, NFKB/RELA and SP1.

Two related tumor suppressor genes, Brca1 and Brca2, attract a lot of attention from both fundamental and clinical points of view. Oncogenic hereditary mutations in these genes are firmly linked to the early onset of breast and ovarian cancers. However, the molecular mechanisms that drive extensive mutagenesis in these genes are not known. In this review we hypothesize that one of the potential mechanisms behind this phenomenon can be mediated by Alu mobile genomic elements. Linking mutations in the BRCA1 and BRCA2 genes to the general mechanism(s) of genome stability and DNA repair is critical to ensure the rationalized choice of anti-cancer therapy. Accordingly, we review the literature available on mechanisms of DNA damage repair where these proteins are involved in and how the inactivating mutations in these genes (BRCAness) can be exploited in anti-cancer therapy. We also propose a hypothesis that explains why breast and ovarian epithelial tissues are preferentially susceptible to mutations in BRCA genes. Finally, we discuss perspectives of novel therapeutic approaches for treating BRCAness cancers.

DNA Topoisomerase IIa (Top2A) is a nuclear enzyme that is a cancer drug target, and there is interest in identifying novel sites on the enzyme to inhibit cancer cells more selectively and to reduce off-target toxicity. The C-terminal domain (CTD) is one potential target, but it is an intrinsically disordered domain, which prevents structural analysis. Therefore, we set out to analyze the sequence of Top2A from 105 species using bioinformatic analysis including the PSICalc algorithm, entropy analysis, and other approaches. Our results demonstrate that large (10th-order) interdependent clusters are found including non-proximal positions across the major domains of Top2A. Further, CTD-specific clusters of 3rd, 4th, and 5th-order were identified that included positions that had been previously analyzed via mutation and biochemical assays. Some of these clusters coincided with positions that when mutated either increased or decreased relaxation activity. Finally, sites of low entropy (i.e., high information content) were identified and mapped as key positions in the CTD. Included in the low entropy sites are phosphorylation sites and charged positions. Together, these results help to build a clearer picture of the critical positions in the CTD and provide potential sites/regions for further analysis.

In this study we used a recently developed ex vivo-in vitro model to assess the effect of feeding older adults a casein protein hydrolysate (CPH) compared with non-bioactive non-essential amino acid (NEAA) supplement on Muscle Protein Synthesis (MPS) and Breakdown (MPB). Serum from six healthy older males following overnight fast and 60 min postprandial ingestion of CPH or NEAA (0.33 g.kg^-1 body mass) was used to condition C2C12 myotube media. CPH-fed serum significantly increased MPS compared to fasted serum. In addition, CPH-fed serum induced myotube growth and markedly suppressed atrogin-1, but not MuRF1, expression. Comparatively, no change in MPS, myotube growth and gene expression was observed following NEAA-fed serum treatment. CPH-fed serum from older adults stimulated de novo MPS, suppressed markers of protein breakdown and resulted in myotube growth, indicating a potential role for CPH as a dietary protein source to prevent age-related sarcopenia.

Background/Aim: Baricitinib (BAR) is the first oral selective Janus kinase inhibitor approved in Europe for rheumatoid arthritis (RA). Real-world data are still needed to clarify its long-term benefit/risk profile. This study aimed to evaluate the effectiveness, persistence, adherence, and safety of BAR in a real-world setting. Methods: An ambispective study was conducted between October 2017 and December 2021 in RA patients starting BAR. Effectiveness was evaluated by change from baseline in the Disease Activity Score using 28-joint counts-C reactive protein (DAS28CRP), and achievement of low disease activity/remission. Drug persistence was evaluated by Kaplan-Meier analysis. Adherence was estimated by medication possession ratio (MPR) and the 5-item Compliance Questionnaire for Rheumatology. Safety was assessed by global incidence proportion and adjusted incidence rates of adverse events. Results: 61/64 recruited patients were finally analyzed, 83.6% female, 78.7% seropositive, mean age of 58.1 (15.4) years, and disease duration of 13.9 (8.3) years. 32.8% were naïve to biologics and 16.4% received BAR on monotherapy. After a median exposure to BAR of 12.4 (6.6-31.2) months (range 3.1-51.4), a significant change in DAS28CRP was observed (difference -1.2, p=0.000). A total of 70.5% and 60.7% patients achieved low disease activity or remission, respectively and 50.8% (31/61) patients remained on BAR during follow-up with a median persistence of 31.2 (9.3-53.1) months. The average MPR was 0.96 (0.08) and all patients were “good adherents” by questionnaire. 21.3% patients discontinued baricitinib due to toxicity. Conclusion: In our real-world practice, BAR demonstrated effectiveness, large persistence, high adherence to treatment and acceptable safety profile.

This publication delves into the intricate world of human communication, extending beyond the realm of spoken and written language to explore the profound influence of non-verbal communication. Focusing on body language—comprising gestures, facial expressions, postures, and movements—it reveals the pivotal role it plays in conveying emotions, intentions, and psychological states. The rapidly evolving fields of neuroscience and cognitive science are investigating the neural mechanisms and cognitive processes that underpin the interpretation and utilization of these non-verbal cues. Notably, the amygdala's involvement in processing emotional facial expressions has provided a neurological foundation for our emotional understanding in non-verbal communication. Concurrently, cognitive psychology sheds light on how perception, attention, and memory influence our interpretation of non-verbal cues and communication strategies.In our modern, technologically advancing society characterized by global interconnectivity and cultural diversity, the significance of non-verbal communication, especially in digital and virtual contexts, is paramount. The transformation of non-verbal expression into digital symbols like emoticons and emojis raises questions regarding its ability to maintain authenticity and emotional understanding. This publication endeavors to comprehensively explore the fundamental role of body language and non-verbal communication in contemporary society. By integrating insights from psychology, neuroscience, social sciences, and digital technologies, it aims to elucidate the underlying mechanisms guiding non-verbal communication. Additionally, it delves into the implications of non-verbal communication across diverse domains, including interpersonal communication, the workplace, politics, advertising, and the virtual world.The research presented herein strives to offer a thorough understanding of interpersonal dynamics, relationships, and social behavior, with the goal of promoting the development of more effective, conscious, and ethically guided communication strategies. Ultimately, this analysis aspires to inspire further interdisciplinary research and reflection, addressing emerging challenges and fully leveraging the potential of non-verbal communication in modern society. This, in turn, guides our path towards a communication landscape that is more inclusive, authentic, and empathetic.

Poultry eggs are a critical source of protein, vitamins, and minerals for people worldwide; facing the current global egg shortage is a significant concern. The shortage results from various factors, including avian flu outbreaks, changes in consumer demand, and supply chain disruptions caused by the COVID-19 pandemic. The economic crisis caused by the pandemic has also impacted the availability and affordability of eggs, particularly in low-income countries. The global egg shortage has implications for public health, particularly for vulnerable populations who rely on eggs for essential nutrients. One Health, an approach that recognizes the interconnectedness of human, animal, and environmental health, provides a useful framework for understanding and addressing the egg shortage. One Health approaches to the egg shortage involve collaboration between agriculture and environmental sectors to address the root causes of the lack and ensure the sustainable production and distribution of eggs. Addressing the global egg shortage requires a multifaceted approach considering the complex social, economic, and environmental factors. One Health perspectives offer a way to understand and address the interconnected factors contributing to the shortage to ensure access to affordable, nutritious eggs for all in a healthy way

This paper aims to contribute to the advancement of scientific knowledge about the impact of the COVID-19 pandemic on social workers and the social work profession in Romania. Research has shown that social work is a profession at high risk for developing the burnout syndrome, which has many detrimental effects on both social workers and the clients that they serve. Two conceptual models are used to frame the discussion: the theoretical framework of VUCA (volatility, uncer-tainty, complexity, and ambiguity) to discuss the challenges of the unprecedented context the COVID-19 pandemic has created for social workers; stress and burnout to explain the negative impact of this period of time. Based on convergent mixt methods, the study sample consisted of 83 social workers employed in statutory and private social services in Romania, from different fields of intervention. Results show that 25,3% of respondents suffer from a high level of burnout and 44.6% scored in a range that indicate a medium level of burnout. A group of 31.1% have managed to handle stress factors in a healthy manner. Main stressors found are especially personal (fear of contamination, personal and family) and work-related factors (workload, new legislative rules and decisions, inconsistency, instability, ambiguity of managerial decisions, or even their absence or non-assumption, lack of clarity of working procedures, limited managerial and supervisory support, limited financial resources), less than client related factors (lack of direct contact, risk of contami-nation in two ways, managing beneficiaries fears, difficulties related to technology and digital skills). Study results point to the importance of organizational support and developing a self-care plan that help protect against occupational stress and burnout. Recommendations are made putting forward the voice of fieldworkers and managers fostering initiatives and applications of sustainability-based measures and activities designed to deal with the challenges of the VUCA environment.

Protein import into the endoplasmic reticulum (ER) is the first step in the biogenesis of about 10,000 different soluble and membrane proteins in humans. It involves co- or post-translational targeting of precursor polypeptides to the ER and their subsequent membrane insertion or translocation. So far, three pathways for ER targeting of precursor polypeptides plus four pathways for ER targeting of mRNAs were described. Typically, these pathways deliver their substrates to the Sec61 polypeptide-conducting channel in the ER membrane. Next, the precursor polypeptides are inserted into the ER membrane or translocated into the ER lumen, which may involve auxiliary translocation components, such as the TRAP and Sec62/Sec63 complexes, or auxiliary membrane protein insertases, such as EMC and the TMCO1 complex. Recently, the PEX19/PEX3-dependent pathway, which has a well-known function in targeting and inserting various peroxisomal membrane proteins into pre-existent peroxisomal membranes, was also found to act in targeting and, putatively, inserting monotopic hairpin proteins into the ER. These either remain in the ER as resident ER membrane proteins or are pinched off from the ER as components of new lipid droplets. Therefore, the question arose if this pathway may play a more general role in ER protein targeting, i.e. represents a fourth pathway for ER targeting of precursor polypeptides. Thus, we addressed the client spectrum of the PEX19/PEX3-dependent pathway in both PEX3-depleted HeLa cells and PEX3-deficient Zellweger patient fibroblasts by an established approach, which involves label-free quantitative mass spectrometry of the total proteome of depleted or deficient cells and differential protein abundance analysis. The negatively affected proteins included twelve peroxisomal proteins and two hairpin proteins of the ER, thus confirming two previously identified classes of putative PEX19/PEX3-clients in human cells. Interestingly, fourteen collagen-related proteins with signal peptides or N-terminal transmembrane helices and belonging to the secretory pathway were also negatively affected by PEX3-deficiency, which may suggest compromised collagen biogenesis as a hitherto unknown contributor to organ failures in the respective Zellweger patients.

With its sights set on sustainable development, transport policy finds itself confronted with the challenge of convincing people to abandon the current path of growth and instead use small, slower vehicles with a reduced range in the future. The problem with this goal is that people's mental structures are shaped by the car ensconced in their heads. Thinking in other terms hardly seems possible; moreover, many of the products classified as vehicles, but smaller in scale than the "car" and that already exist, remain unknown, nor can they be tried out - they are quite literally nowhere to be seen. In light of this situation, the German Federal Environmental Foundation has commissioned a feasibility study to explore the establishment of a World of Experience (Erlebniswelt) of sustainable urban mobility - the EcoMobileum®. Here, the aim is to open up the horizons of a new culture of mobility in order to get people excited about the transformation of mobility.

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.

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 &lt; 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.

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 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.

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.

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.

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.

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.

Multiple myeloma (MM) accounts for about 10 to 15% of all diagnosed hematologic malignancies and about 1-2% of all cancer cases. Approximately 80-90% of MM patients develop bone disease and the changes rarely regress. It is only possible to stop or slow their progression. A major role in bone destruction in MM is attributed to the Wnt signaling pathway, and its action can be modified by various types of interventions including training and diet. Therefore, the aim of this project was to evaluate the effects of a Nordic Walking (NW) training cycle and intermittent fasting (IF) on the levels of selected bone turnover markers associated with the Wnt pathway in patients with MM. Results from 35 patients divided into training (NW and IF NW) and non-training (IF and control) groups were included in the analysis. A 6-week training cycle involving 60-minute workouts 3 times a week was conducted. Body mass and composition and the levels of: vitamin D, calcium and phosphorus, beta2-microglobulin and albumin were examined before and after completion of training cycle. Markers of bone turnover were also determined: sclerostin (SOST), Dickkopf-related protein 1 (DKK-1), osteoprotegrin (OPG), osteopontin (OPN) and Tartrate-resistant acid phos-phatase 5b (TRACP 5b). There was no negative effect of IF or combined training and fasting on the nutritional status of the patients (the level of albumines was unchanged). Both training groups showed an increase in serum concentrations of the active metabolite of vitamin D (IF NW and NW: p=0.001 and p=0.022, re-spectively). The change in the concentration of this vitamin negatively correlated with the con-centration of TRACP 5b (r=-0.413, p=0.014). Evaluating the concentrations of markers related to bone turnover, a reduction in the concentrations of SOST (time: p=0.026, time vs. group: p=0.033) and TRACP 5b (time: p

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.