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Autophagy is a critical cellular process by which biomolecules and cellular organelles are degraded in an orderly manner inside lysosomes. This process is particularly important in neurons: these post-mitotic cells cannot divide or be easily replaced and are therefore especially sensitive to the accumulation of toxic proteins and damaged organelles. Dysregulation of neuronal autophagy is well documented in a range of neurodegenerative diseases. However, growing evidence indicates that autophagy also critically contributes to neurodevelopmental cellular processes, including neurogenesis, maintenance of neural stem cell homeostasis, differentiation, metabolic reprogramming, and synaptic remodelling. These findings implicate autophagy in neurodevelopmental disorders. In this review we discuss the current understanding of the role of autophagy in neurodevelopment and neurodevelopmental disorders, as well as currently available tools and techniques that can be used to further investigate this association., Research in the P.B. lab is supported by grant (PGC2018-098557-B-I00) from Spain’s Ministerio Ciencia e Innovación, the Agencia Estatal de Investigación (AEI), the Fondo Europeo de Desarrollo Regional (FEDER), and funding from the European Union’s Horizon 2020 Research and Innova-tion Programme under grant agreement No. 765912, Fundación Tatiana Pérez de Guzmán el Bueno Proyectos en Neurociencia 2018, and Redes de BioMedicina de la Co-munidad de Madrid, BMD-3813. JZM is a recipient of a FPU fellowship (Ministerio de Universidades).

INTRODUCTION: Central nervous system (CNS) diseases affect a large portion of the population, however, few therapeutic options are available. Furthermore, to date, clinical trials have been largely unsuccessful due to difficulty in targeting the undruggable, toxic proteins that underly many CNS disorders. PROteolysis Targeting Chimeras (PROTACs) are a rapidly emerging technology that has been proposed as a potential treatment option for various CNS diseases by hijacking the endogenous protein degradation process. AREAS COVERED: Herein, the authors discuss how the application of PROTACs may be beneficial in the treatment of major CNS diseases. They further discuss the main advantages and disadvantages of using PROTACs in the CNS, focusing on potential limitations such as their transient nature, localization, blood-brain barrier permeability and proteasome dysfunction. EXPERT OPINION: It is evident that PROTACs have significant potential as a therapeutic tool for the treatment of CNS diseases and there is preliminary evidence suggesting that PROTACs could be successful in a clinical setting. Nevertheless, numerous limitations exist that must be overcome before this technology can be applied as a successful therapeutic for CNS disorders. Importantly, more in vivo studies are needed to determine the feasibility and effectiveness of using PROTACs in the brain.

Background We successfully captured a kind of gelatinous organism DA-6 from Antarctic water, extracted its total RNAs and proteins, and performed species identification through a combination of transcriptomics and proteomics in this study. Methods The gelatinous organism DA-6 was captured 200 m underwater in Antarctica. Total RNA was extracted to construct the transcriptome and the proteins were identified by LC-MS/MS. Results DA-6 was identified as an Antarctic Salpa sp. through morphological examination and MT-CO1 phylogenetic analysis. A total of 47,183 unigenes were harvested through transcriptome. We also successfully annotated 11,954 (25.34%), 10,006 (22.21%), 4469 (9.47%) and 4901 (9.71%) unigenes with NR, SwissProt, GO and KEGG databases, respectively. In the proteomic analysis, a total of 4680 peptides and 1280 proteins were harvested using the transcriptome as the reference database. A number of both 549 (31.98%) proteins reannotated against the GO and KEGG databases. Moreover, a number of 5 toxic proteins matched from the 89 toxin-related unigenes were successfully screened, including 2 metalloproteinases, 1 serine protease, 1 serine protease inhibitor and 1 aflatoxin. Conclusion Our study is the first to identify an Antarctic Salpa sp. according to the combination of de novo transcriptomics and proteomics, which can further be served as a public database for the identification of potential polar Salpa-derived lead compounds. In addition to morphology and CO1, the combined analysis of transcriptome and proteome can also be used as a value method for new species identify e.g. Salpa sp.

Traditional Chinese medicine (TCM) has become a crucial cause of drug-induced liver injury (DILI). Differ from chemical medicines, TCM feature more complex and mostly indefinite components. This review aimed to clarify the classification, underlying mechanisms and targets of the risk components in TCM-induced liver injury to further guide the secure application of TCM. Relevant studies or articles published on the PubMed database from January 2008 to December 2019 were searched. Based on the different chemical structures of the risk ingredients in TCM, they are divided into alkaloids, glycosides, toxic proteins, terpenoids and lactones, anthraquinones, and heavy metals. According to whether drug metabolism is activated or hepatocytes are directly attacked during TCM-induced liver injury, the high-risk substances can be classified into metabolic activation, non-metabolic activation, and mixed types. Mechanisms of the hepatotoxic ingredients in TCM-induced hepatotoxicity, including cytochrome P450 (CYP450) induction, mitochondrial dysfunction, oxidative damage, apoptosis, and idiosyncratic reaction, were also summarized. The targets involved in the risk ingredient-induced hepatocellular injury mainly include metabolic enzymes, nuclear receptors, transporters, and signaling pathways. Our periodic review and summary on the risk signals of TCM-induced liver injury must be beneficial to the integrated analysis on the multi-component, multi-target, and multi-effect characteristics of TCM-induced hepatotoxicity.

Background The widespread usage of protein expression systems in Escherichia coli (E. coli) is a workhorse of molecular biology research that has practical applications in biotechnology industry, including the production of pharmaceutical drugs. Various factors can strongly affect the successful construction and stable maintenance of clones and the resulting biosynthesis levels. These include an appropriate selection of recombinant hosts, expression systems, regulation of promoters, the repression level at an uninduced state, growth temperature, codon usage, codon context, mRNA secondary structure, translation kinetics, the presence/absence of chaperons and others. However, optimization of the growth medium’s composition is often overlooked. We systematically evaluate this factor, which can have a dramatic effect on the expression of recombinant proteins, especially those which are toxic to a recombinant host. Results Commonly used animal tissue- and plant-based media were evaluated using a series of clones in pET vector, containing expressed Open Reading Frames (ORFs) with a wide spectrum of toxicity to the recombinant E. coli: (i) gfpuv (nontoxic); (ii) tp84_28—which codes for thermophilic endolysin (moderately toxic); and (iii) tthHB27IRM—which codes for thermophilic restriction endonuclease-methyltransferase (REase-MTase)—RM.TthHB27I (very toxic). The use of plant-derived peptones (soy peptone and malt extract) in a culture medium causes the T7-lac expression system to leak. We show that the presence of raffinose and stachyose (galactoside derivatives) in those peptones causes premature and uncontrolled induction of gene expression, which affects the course of the culture, the stability of clones and biosynthesis levels. Conclusions The use of plant-derived peptones in a culture medium when using T7-lac hybrid promoter expression systems, such as Tabor-Studier, can lead to uncontrolled production of a recombinant protein. These conclusions also extend to other, lac operator-controlled promoters. In the case of proteins which are toxic to a recombinant host, this can result in mutations or deletions in the expression vector and/or cloned gene, the death of the host or highly decreased expression levels. This phenomenon is caused by the content of certain saccharides in plant peptones, some of which (galactosides) may act as T7-lac promoter inducer by interacting with a Lac repressor. Thus, when attempting to overexpress toxic proteins, it is recommended to either not use plant-derived media or to use them with caution and perform a pilot-scale evaluation of the derepression effect on a case-by-case basis.

Reconstituted cell-free protein synthesis systems (e.g., the PURE system) allow the expression of toxic proteins, hetero-oligomeric protein subunits, and proteins with noncanonical amino acids with high levels of homogeneity. In these systems, an artificial ATP/GTP regeneration system is required to drive protein synthesis, which is accomplished using three kinases and phosphocreatine. Here, we demonstrate the replacement of these three kinases with one bifunctional Cytophaga hutchinsonii polyphosphate kinase that phosphorylates nucleosides in an exchange reaction from polyphosphate. The optimized single-kinase system produced a final sfGFP concentration (∼530 μg/mL) beyond that of the three-kinase system (∼400 μg/mL), with a 5-fold faster mRNA translation rate in the first 90 min. The single-kinase system is also compatible with the expression of heat-sensitive firefly luciferase at 37 °C. Potentially, the single-kinase nucleoside triphosphate regeneration approach developed herein could expand future applications of cell-free protein synthesis systems and could be used to drive other biochemical processes in synthetic biology which require both ATP and GTP.

Background While the rapidly increasing global population has led to a dramatically increased demand for the agricultural production, there have been heavy economic losses owing to various pest attacks on different food crops. The advancement of various biotechnological techniques have come as a boon in addressing the global concern and leads to the development of novel varieties that have proven to be highly economical, pesticide resistant and environmentally safe. Main body The present review was aimed to update the recent developments that have taken place in the field of crop production. Major focus was laid predominantly on such genes that have demonstrated positive effects and proved to be of commercial success at the market primarily due to the development of pest-resistant transgenic food crops with expression of Bacillus thuringiensis toxins. This technology has been effective against a wide range of pests including coleopterans, lepidopterans, hemipterans, dipterans, strongylida (nematodes) and rhabditida. In similar lines various plant derived toxic proteins were also discussed along with different genes that code for insect resistant proteins such as δ-endotoxins and secreted toxins. This article also helps in understanding the structural features of the genes that are endowed with insect resistance followed by their mechanism of action on pests. Further the role of secondary metabolites in controlling the pests was addressed. The Pros and Cons of existing tools of insect pest management were demonstrated. Conclusions Novel technologies are necessary in crop improvement to progress the pace of the breeding programs, to confer insect resistance in crop plants. Therefore, the future aim of crop biotechnology is to engineer a sustainable, multi-mechanistic resistance to insect pests considering the diversity of plant responses to insect attack.

Exosomes are secreted by every cell in our body under both physiological and pathological conditions. They travel in the blood, CSF, and all studied biofluids. Their biological roles have been reported to include delivery of important physiological cargo between organs and cells, clearance of toxic proteins; maintenance of cellular stasis, and the propagation of disease pathology. In the case of Alzheimer’s disease (AD) exosomes have been shown to carry pathological proteins such as amyloid, yet the specificity of this association of amyloid and exosomes is unclear. To address this deficiency, we utilized Isothermal Titration Calorimetry (ITC) to measure the binding of amyloid to exosomes. Here we report that Aβ40 and Aβ42 bind to exosomes in a saturable and endothermic manner, a phenomenon not observed with the scrambled versions of either peptide. This points to this interaction being more specific than previously understood, and to amyloid associated with exosomes as an important pool of this peptide in the plasma.

Toxins are widely produced by different organisms to disrupt the physiology of other organisms, and support their own existence. Their study is useful to understand protein evolution, environmental adaptation and survival competition. In-silico predictions of toxic proteins can support empirical frameworks, and help in the safety measurements needed for various industrial related processes. Some in-silico methods are slow, hard to implement or lack taxa representation in their training datasets. Here we present a deep learning model to classify protein toxins, through the use of Convolutional Neural Networks (ConvTOX). ConvTOX is able to accurately identify toxic proteins across the domains of life, with accuracies over 80% for animal and plant toxins, and over 50% for bacterial toxins. Moreover, ConvTOX is able to generalize the identification of differences among toxin types, such as neurotoxins and myotoxins, and to accurately identify structural similarities between different protein toxins. ConvTOX overcomes limitations from previous models by being able to predict toxin proteins from across all domains of life, and by not being limited to only short toxin peptides. Limitations are still clear in terms of lower accuracies for specific phylogenetic groups (such as bacterial toxins), but still this works presents itself as a one step forward for the universal use, classification and study of toxic proteins.

Botulinum neurotoxins (BoNTs) are among the most toxic proteins. Vaccination is an effective strategy to prevent botulism. To generate a vaccine suitable for human use, a recombinant non-His-tagged isoform of the Hc domain of botulinum neurotoxin serotype E (rEHc) was expressed in Escherichia coli and purified by sequential chromatography. The immunogenicity of rEHc was evaluated in mice and dose- and time-dependent immune responses were observed in both antibody titers and protective potency. Then, the pilot-scale expression and purification of rEHc were performed, and its immunological activity was characterized. Our results showed rEHc has good immunogenicity and can elicit strong protective potency against botulinum neurotoxin serotype E (BoNT/E) in mice, indicating that rEHc is an effective botulism vaccine candidate. Further, we developed a novel antitoxin against BoNT/E by purifying F(abʹ)(2) from pepsin-digested serum IgG of rEHc-inoculated horses. The protective effect of the F(abʹ)(2) antitoxin was determined in vitro and in vivo. The results showed that our F(abʹ)(2) antitoxin can prevent botulism in BoNT/E-challenged mice and effectively alleviate the progression of paralysis caused by BoNT/E to achieve therapeutic effects. Therefore, our results provide valuable experimental data for the production of a novel antitoxin, which is a promising candidate for the treatment of BoNT/E-induced botulism.

During the production and application of Bacillus thuringiensis (Bt) transgenic crops, large doses of insecticidal Bt toxic proteins are expressed continuously. The multi-interfacial behaviors of Bt proteins entering the environment in multi-media affects their states of existence transformation, transport and fate as well as biological and ecological impacts. Because both soil matrix and organisms will be exposed to Bt proteins to a certain extent, knowledge of the multi-interfacial behaviors and affecting factors of Bt proteins are vital not only for understanding the source-sink distribution mechanisms, predicting their bio-availability, but also for exploring the soil safety and environmental problems caused by the interaction between Bt proteins and soil matrix. This review summarized and analyzed various internal and external factors that affect the adsorption/ desorption and degradation of Bt proteins in the environment, so as to understand the multi-interfacial behaviors of Bt proteins. In addition, the reasons of concentration changes of Bt proteins in soil are discussed. This review will also discuss the existing knowledge of the combined effects of Bt proteins and other pollutants in environment. Finally, discussing the factors that should be considered when assessing the environmental risk of Bt proteins, thus to further improve the understanding of the environmental fate of Bt proteins.

Neurodegenerative diseases are frequently associated with aggregation and propagation of toxic proteins. In particular, it is well known that along with amyloid-beta, the tau protein is also driving Alzheimer’s disease. Multiscale reaction-diffusion models can assist in our better understanding of the evolution of the disease. We have modified the heterodimer model in such a way that it can now capture some of critical characteristics of this evolution such as the conversion time from healthy to toxic proteins. We have analyzed the modified model theoretically and validated the theoretical findings with numerical simulations.

Neurodegenerative diseases are frequently associated with aggregation and propagation of toxic proteins. In particular, it is well known that along with amyloid-beta, the tau protein is also driving Alzheimer’s disease. Multiscale reaction-diffusion models can assist in our better understanding of the evolution of the disease. Based on a coarse-graining procedure of the continuous model and taking advantage of the brain data connectome, a computationally challenging network mathematical model has been described where the edges of the network are the axonal bundles in white-matter tracts. Further, we have modified the heterodimer model in such a way that it can now capture some of the critical characteristics of this evolution such as the conversion time from healthy to toxic proteins. Finally, we have analyzed the modified model theoretically and validated the theoretical findings with numerical simulations.

The lytic phage, fHe-Kpn01 was isolated from sewage water using an extended-spectrum beta-lactamase-producing strain of Klebsiella pneumoniae as a host. The genome is 43,329 bp in size and contains direct terminal repeats of 222 bp. The genome contains 56 predicted genes, of which proteomics analysis detected 29 different proteins in purified phage particles. Comparison of fHe-Kpn01 to other phages, both morphologically and genetically, indicated that the phage belongs to the family Podoviridae and genus Drulisvirus. Because fHe-Kpn01 is strictly lytic and does not carry any known resistance or virulence genes, it is suitable for phage therapy. It has, however, a narrow host range since it infected only three of the 72 tested K. pneumoniae strains, two of which were of capsule type KL62. After annotation of the predicted genes based on the similarity to genes of known function and proteomics results on the virion-associated proteins, 22 gene products remained annotated as hypothetical proteins of unknown function (HPUF). These fHe-Kpn01 HPUFs were screened for their toxicity in Escherichia coli. Three of the HPUFs, encoded by the genes g10, g22, and g38, were confirmed to be toxic.

Introduction Heat shock proteins (Hsp) are a family of proteins and the major chaperons of the cells. Hsp70 assists in folding and correct misfolded protein, improve the cellular transportation of proteins, reducing toxic proteins aggregation and act as a buffering system against cellular stressors either extrinsic or intrinsic stimuli.

Protein aggregates result from altered structural conformations and they can perturb cellular homeostasis. Prevention mechanisms, which function against protein aggregation by modulatory processes, are diverse and redundant. In this study, we have characterized Huntingtin interacting protein K (HYPK) as a global aggregation-regulatory protein. We report the mechanistic details of how HYPK's aggregation-prone regions allow it to sense and prevent other toxic protein's aggregation by forming unique annular-shaped sequestration complexes. Screenings for interacting partners of different aggregation-prone proteins identify HYPK as a global interacting partner/regulator of Huntingtin97Qexon1, α-Synuclein-A53T and Superoxide dismutase1-G93A. C-terminal hydrophobic region in HYPK makes direct contacts with aggregates to initiate the formation of sequestration complexes. HYPK acts as aggregate sensor by existing in a seeded amyloid-like state which also favors its own concentration-dependent self-oligomerization. Oligomerization of HYPK leads to annular and non-fibrillar/amorphous aggregates. Two hydrophobic segments in the C-terminus of HYPK are responsible for its own aggregations. Self-association of HYPK follows seed nucleation, in which oligomeric HYPK seeds nucleate to annular structures. Annular oligomers of HYPK fuse with each other to form amorphous aggregates. HYPK shows differential interactions with aggregation-prone and non-aggregating proteins, as it preferentially binds to aggregation-prone proteins with higher affinity than native/non-aggregating proteins. This favors the formation of HYPK's sequestration complexes both in cytosol and in ribosome. Besides having aggregation-preventive property, HYPK also reduces the cellular level of toxic proteins. In vivo, HYPK sequestration complexes prevent the formation of toxic protein aggregates to physiologically show positive impact on cell survival and restoration of normal cell physiology.

Sarah Palmer discusses a recent study that looked into the property of the drug felodipine in inducing cells to clear up toxic proteins. The study found that there is some scope to repurpose the drug as a treatment for neurodegenerative diseases.

Botulinum neurotoxins (BoNTs) are the most toxic proteins in nature. Endopeptidase-mass-spectrometry (Endopep-MS) is used as a specific and rapid in-vitro assay to detect BoNTs. In this assay, immunocaptured toxin cleaves a serotype-specific-peptide-substrate, and the cleavage products are then detected by MS. Here we describe the design of a new peptide substrate for improved detection of BoNT type A (BoNT/A). Our strategy was based on reported BoNT/A-SNAP-25 interactions integrated with analysis method efficiency considerations. Integration of the newly designed substrate led to a 10-fold increase in the assay sensitivity both in buffer and in clinically relevant samples.

For the proteins that cannot be expressed exactly by cell expression technology (e.g., proteins with multiple posttranslational modifications or toxic proteins), chemical synthesis is an important substitute. Given the limited peptide length offered by solid-phase peptide synthesis invented by Professor Merrifield, peptide ligation plays a key role in long peptide or protein synthesis by ligating two small peptides to a long one. Moreover, high-molecular-weight proteins must be synthesized using two or more peptide ligation steps, and sequential peptide ligation is such an efficient way. In this paper, we reviewed the development of chemical protein synthesis, including solid-phase peptide synthesis, chemical ligation, and sequential chemical ligation.

With advancements in synthetic biology, the cost and the time needed for designing and synthesizing customized gene products have been steadily decreasing. Many research laboratories in academia as well as industry routinely create genetically engineered proteins as a part of their research activities. However, manipulation of protein sequences could result in unintentional production of toxic proteins. Therefore, being able to identify the toxicity of a protein before the synthesis would reduce the risk of potential hazards. Existing methods are too specific, which limits their application. Here, we extended general function prediction methods for predicting the toxicity of proteins. Protein function prediction methods have been actively studied in the bioinformatics community and have shown significant improvement over the last decade. We have previously developed successful function prediction methods, which were shown to be among top-performing methods in the community-wide functional annotation experiment, CAFA. Based on our function prediction method, we developed a neural network model, named NNTox, which uses predicted GO terms for a target protein to further predict the possibility of the protein being toxic. We have also developed a multi-label model, which can predict the specific toxicity type of the query sequence. Together, this work analyses the relationship between GO terms and protein toxicity and builds predictor models of protein toxicity.

Instead of only focusing on the targeted drug delivery system, researchers have a great interest in developing peptide-based therapies for the procurement of numerous class of diseases. The main idea behind this is to anchor the properties of the receptor to design peptide-based therapeutics. As these macromolecules have distinct physicochemical properties over small molecules, it becomes an obligatory field for the treatment of diseases. For this, various in silico models have been developed to speculate the proteins by virtue of the application of machine learning and artificial intelligence. By analysing the properties and structural alert of toxic proteins, researchers aim to dissert some of the mechanisms of protein toxicity from which therapeutic insights may be drawn. Numerous models already exist worldwide emphasizing themselves as leading paramount for toxicity prediction in protein macromolecules. Few of them comparatively compete with the other predictive protein toxicity models and convincingly give a high-performance result in terms of accuracy. But their foundation is quite ambiguous, and varying approaches are found at the level of toxicoproteomic data utilization while building a machine learning model. In this review work, we present the contribution of artificial intelligence and machine learning approaches in prediction of protein toxicity using proteomics data.

In a recent paper by Dvela-Levitt et al., chemical screening using an immunofluorescent assay identified a compound that caused removal of a dominant-inherited misfolded secretory protein, mucin1-frameshifted, from an intracellular location in immortalized renal epithelial cells of a patient affected with progressive medullary cystic kidney disease. This illustrates the power of chemical screening at the cellular level to address specific proteinopathies and the utility of such compounds to illuminate novel cellular pathways that can clear toxic proteins.

Because no living cells are involved, the open cell-free biosystems can be flexibly regulated to produce proteins in a few hours. In the open system, the transcription and translation process can be directly controlled on demand by adjusting the temperature, salts, and redox environment and adding nature or human-made materials. Therefore, cell-free biosystem could be well adopted to produce proteins which are difficult to synthesize in living cells, such as membrane proteins and toxic proteins.

The ipd072Aa gene from Pseudomonas chlororaphis encodes the IPD072Aa protein which confers protection against certain coleopteran pests when expressed in genetically modified (GM) plants. A weight of evidence approach was used to assess the safety of the IPD072Aa protein. This approach considered the history of safe use of the source organism and bioinformatic comparison of the protein sequence with known allergenic and toxic proteins. The IPD072Aa protein was assessed for resistance to degradation in the presence of simulated gastric fluid containing pepsin as well as heat stability. There was no hazard identified with the IPD072Aa protein. Furthermore, an acute oral toxicity study found no evidence of adverse effects. Collectively, these studies support the human health safety assessment of the IPD072Aa protein.

Multivalent binding interactions are commonly found throughout biology to enhance weak monovalent binding such as between glycoligands and protein receptors. Designing multivalent polymers to bind to viruses and toxic proteins is a promising avenue for inhibiting their attachment and subsequent infection of cells. Several studies have focused on oligomeric multivalent inhibitors and how changing parameters such as ligand shape and size, and linker length and flexibility affect binding. However, experimental studies of how larger structural parameters of multivalent polymers such as degree of polymerization affect binding avidity to targets have mixed results with some finding an improvement with longer polymers and some finding no effect. Here, we use Brownian dynamics simulations to provide a theoretical understanding of how degree of polymerization affects the binding avidity of multivalent polymers. We show that longer polymers increase binding avidity to multivalent targets, but reach a limit in binding avidity at high degrees of polymerization. We also show that when interacting with multiple targets simultaneously, longer polymers are able to use inter-target interactions to promote clustering and improve binding efficiency. We expect our results to narrow the design space for optimizing the structure and effectiveness of multivalent inhibitors, as well as be useful to understand biological design strategies for multivalent binding.

Efficient quality control mechanisms are essential for a healthy, functional neuron. Recognition and degradation of misfolded, damaged, or potentially toxic proteins, is a crucial aspect of protein quality control. Tau is a protein that is highly expressed in neurons, and plays an important role in modulating a number of physiological processes. Maintaining appropriate levels of tau is key for neuronal health; hence perturbations in tau clearance mechanisms are likely significant contributors to neurodegenerative diseases such as Alzheimer's disease and frontotemporal lobar degeneration. In this chapter we will first briefly review the two primary degradative mechanisms that mediate tau clearance: the proteasome system and the autophagy-lysosome pathway. This will be followed by a discussion about what is known about the contribution of each of these pathways to tau clearance. We will also present recent findings on tau degradation through the endolysosomal system. Further, how deficits in these degradative systems may contribute to the accumulation of dysfunctional or toxic forms of tau in neurodegenerative conditions is considered.

Neurodegenerative diseases are closely associated with the amplification and invasion of toxic proteins. In particular Alzheimer's disease is characterized by the systematic progression of amyloid-$\beta$ and $\tau$-proteins in the brain. These two protein families are coupled and it is believed that their joint presence greatly enhances the resulting damage. Here, we examine a class of coupled chemical kinetics models of healthy and toxic proteins in two spatial dimensions. The anisotropic diffusion expected to take place within the brain along axonal pathways is factored in the models and produces a filamentary, predominantly one-dimensional transmission. Nevertheless, the potential of the anisotropic models towards generating interactions taking advantage of the two-dimensional landscape is showcased. Finally, a reduction of the models into a simpler family of generalized Fisher-Kolmogorov-Petrovskii-Piskunov (FKPP) type systems is examined. It is seen that the latter captures well the qualitative propagation features, although it may somewhat underestimate the concentrations of the toxic proteins., Comment: 11 pages, 8 figures

The freshwater snails Pomacea Perry, 1810 lay conspicuous aerial egg clutches that are ignored by most predators. Egg biochemical defenses in the apple snail Pomacea canaliculata (Lamarck, 1822) are provided by multifunctional proteins. We analyzed the eggs of a sympatric species, Pomacea maculata Perry, 1810, studying the gross composition, toxicity, hemagglutinating activity, and its antinutritive and antidigestive properties. Eggs are mostly composed of polysaccharides (mainly galactogen) and proteins, followed by lipids and nonsoluble calcium. Two perivitellins account for ∼85% dry mass of the egg protein. The major lipids are phospholipids and sterols. A suite of potential defenses was determined, including strong lethal neurotoxicity on mice and moderate antidigestive and lectin activities. Remarkably, their polysaccharides were refractive to in vitro digestion by digestive glycosidases. This study characterized ∼99% of egg composition and identified multiple potential defenses, provided not only by proteins but also by polysaccharides. This is the first evidence to our knowledge that reserve sugars may be involved in defenses, giving further insight into the unusual reproductive strategy of these well-defended snail eggs.

Neurodegenerative diseases such as Alzheimer’s or Parkinson’s are associated with the prion-like propagation and aggregation of toxic proteins. A long standing hypothesis that amyloid-beta drives Alzheimer’s disease has proven the subject of contemporary controversy; leading to new research in both the role of tau protein and its interaction with amyloid-beta. Conversely, recent work in mathematical modeling has demonstrated the relevance of nonlinear reaction-diffusion type equations to capture essential features of the disease. Such approaches have been further simplified, to network-based models, and offer researchers a powerful set of computationally tractable tools with which to investigate neurodegenerative disease dynamics. Here, we propose a novel, coupled network-based model for a two-protein system that includes an enzymatic interaction term alongside a simple model of aggregate transneuronal damage. We apply this theoretical model to test the possible interactions between tau proteins and amyloid-beta and study the resulting coupled behavior between toxic protein clearance and proteopathic phenomenology. Our analysis reveals ways in which amyloid-beta and tau proteins may conspire with each other to enhance the nucleation and propagation of different diseases, thus shedding new light on the importance of protein clearance and protein interaction mechanisms in prion-like models of neurodegenerative disease., Author summary In 1906 Dr. Alois Alzheimer presented the case of Ms. Auguste Deter; her symptoms would help to define Alzheimer’s disease (AD). Over a century later, with an aging world population, AD is at the fore of global neurodegenerative disease research. Previously, toxic amyloid-beta protein (Aβ) was thought to be the primary driver of AD development. Recent research suggests that another protein, tau, plays a fundamental role. Toxic tau protein contributes to cognitive decline and appears to interact with toxic Aβ; research suggests that toxic Aβ may further increase the effects of toxic tau. Theoretical mathematical models are an important part of neurodegenerative disease research. Such models: enable extensible computational exploration; illuminate emergent behavior; and reduce research costs. We have developed a novel, theoretical mathematical model of two interacting species of proteins within the brain. We analyze the mathematical model and demonstrate a computational implementation in the context of Aβ-tau interaction in the brain. Our model clearly suggests that: the removal rate of toxic protein plays a critical role in AD; and the Aβ-tau ‘conspiracy theory’ is a nuanced, and exciting path forward for Alzheimer’s disease research.

Ribosome-associated Quality Control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to the degradation of the faulty mRNA and partially synthesized polypeptide. Here, we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific inhibition of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP. Both model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs, and subsequent accumulation of partially synthesized polypeptides, could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.

The threat of biological and chemical terror acts remains a growing worldwide concern. There is therefore a need to develop appropriate technology for the detection of chemical and biological warfare agents, with early identification intended for use by first responders. Here, we disclose the developed autonomous air sampling and detection system for evaluation of the presence of chemical and biological warfare agents that can be harmful to the population. The current device utilizes the designed mist generator-assisted air collection system (338 l min−1) and biosensing chip technologies, such as electrochemical measurement, Au nanoparticle-based localized surface plasmon resonance, and rapid microfluidic chip PCR for detection of minute concentrations lower than the mean lethal dose (LD50) of nerve gases (sarin and VX), toxic proteins (BTX/A/Hc and ricin), and pathogens (anthrax simulant). An operation time of only 5–15 min is needed for the collection and detection; sample preparation is already integrated into the system without the need for direct human intervention. In addition to the system’s sensitivity and ease of use, its portability makes it highly beneficial for first responders, which could aid in immediate risk assessment and mitigation of on-site events. A portable device that can detect dangerous chemical and biological warfare agents at less than the mean lethal dose has been developed. Chemical and biological terrorism represents an increasing threat worldwide. Although various sensors have been developed for detecting toxins and pathogenic agents, there remains a need for a portable device that first responders can use to perform initial risk assessments. Masato Saito of Osaka University in Japan and co-workers have achieved this by combining three detection strategies in one device. The device samples air from the environment and then uses electrochemical measurements to detect nerve gases, gold nanoparticles to detect toxic proteins, and a PCR chip to detect pathogens. Molecules of interest can be detected in 5 to 15 minutes, and the device can be transported in a 30-centimeter cubic case.

Traditional Chinese Medicine (TCM) has been practiced in China for thousands of years. As a complementary and alternative treatment, herbal medicines that are frequently used in the TCM are the most accepted in the Western world. However, animal materials, which are equally important in the TCM practice, are not well-known in other countries. On the other hand, the Chinese doctors had documented the toxic profiles of hundreds of animals and plants thousand years ago. Furthermore, they saw the potential benefits of these materials and used their toxic properties to treat a wide variety of diseases, such as heavy pain and cancer. Since the 50s of the last century, efforts of the Chinese government and societies to modernize TCM have achieved tremendous scientific results in both laboratory and clinic. A number of toxic proteins have been isolated and their functions identified. Although most of the literature was written in Chinese, this review provide a summary, in English, regarding our knowledge of the clinical use of the toxic proteins isolated from a plant, Tian Hua Fen, and an animal, scorpion, both of which are famous toxic prescriptions in TCM.

Compounds that tether toxic proteins with polyglutamine expansions to autophagosomes promote their autophagic clearance and might, in principle, be suitable for the treatment of associated neurodegenerative diseases.

The toxic proteins of Bacillus thuringiensis israelinsis (Bti) and Bacillus sphaericus 2362 (Bs) were tested either singly or in combination with plant oils and chemical insecticides against the la...

Phagocytes are the main component of innate immunity. They remove pathogens and particles from organisms using their bactericidal tools in the form of both reactive oxygen species and degrading enzymes—contained in granules—that are potentially toxic proteins. Therefore, it is important to investigate the possible interactions between phages and immune cells and avoid any phage side effects on them. Recent progress in knowledge concerning the influence of phages on phagocytes is also important as such interactions may shape the immune response. In this review we have summarized the current knowledge on phage interactions with phagocytes described so far and their potential implications for phage therapy. The data suggesting that phage do not downregulate important phagocyte functions are especially relevant for the concept of phage therapy.

Fungi establish a complex network of biological interactions with other organisms in nature. In many cases, these involve the production of toxins for survival or colonization purposes. Among these toxins, ribotoxins stand out as promising candidates for their use in biotechnological applications. They constitute a group of highly specific extracellular ribonucleases that target a universally conserved sequence of RNA in the ribosome, the sarcin-ricin loop. The detailed molecular study of this family of toxic proteins over the past decades has highlighted their potential in applied research. Remarkable examples would be the recent studies in the field of cancer research with promising results involving ribotoxin-based immunotoxins. On the other hand, some ribotoxin-producer fungi have already been studied in the control of insect pests. The recent role of ribotoxins as insecticides could allow their employment in formulas and even as baculovirus-based biopesticides. Moreover, considering the important role of their target in the ribosome, they can be used as tools to study how ribosome biogenesis is regulated and, eventually, may contribute to a better understanding of some ribosomopathies.

Pathogene Bakterien uberwinden unsere Abwehrmechanismen durch Ausbildung so genannter Virulenzfaktoren. Dabei handelt es sich in der Regel um toxische Proteine, aggressive Enzyme oder tauschende Oberflachenstrukturen. Deren Synthese ist energie- und materialaufwandig, daher werden Virulenzfaktoren erst gebildet, wenn das Zielgewebe erreicht ist. Dazu mussen Informationen uber die Umgebung mit Hilfe spezifischer Proteine gesammelt werden. Weiterhin hangt der Erfolg einer Infektion zumindest in den ersten Stadien davon ab, dass eine genugend grose Anzahl an Angreifern prasent ist, die dann wie ein multizellularer Organismus kooperieren, in kurzer Zeit grose Mengen an Virulenzfaktoren bilden und das Wirtsgewebe uberrumpeln. Der Infektionsweg lasst sich meistens unterscheiden in: 1. Uberwindung der ersten Schranken, 2. Adhasion an das Zielgewebe, 3. Invasion, 4. Behebung des Eisenmangels, 5. Abwehr unserer Immunsysteme. How bacteria overcome our defence systems Pathogenic bacteria overcome our defence systems by synthesis of virulence factors, among them toxic proteins, aggressive enzymes or deceiving surface structures. Their synthesis requires an additional recruitment of building blocks and energy. Therefore virulence factors are produced only when the target tissue has been reached. This requires collection of information about the environment with the help of specific proteins. In addition the first stages of a successful infection require presence of a sufficient number of attackers, which act like a multi-cellular organism, producing high amounts of virulence factors that take by surprise the target tissue. The route of infection generally can be divided into: 1. surpassing the first barriers, 2. adhesion at the target tissue, 3. Invasion, 4. acquisition of iron, 5. counteracting our immune systems.

Despite its small size, the brain consumes 25% of the body’s energy, generating its own weight in potentially toxic proteins and biological debris each year. The brain is also the only organ lacking lymph vessels to assist in removal of interstitial waste. Over the past 50 years, a picture has been developing of the brain’s unique waste removal system. Experimental observations show cerebrospinal fluid, which surrounds the brain, enters the brain along discrete pathways, crosses a barrier into the spaces between brain cells, and flushes the tissue, carrying wastes to routes exiting the brain. Dysfunction of this cerebral waste clearance system has been demonstrated in Alzheimer’s disease, traumatic brain injury, diabetes, and stroke. The activity of the system is observed to increase during sleep. In addition to waste clearance, this circuit of flow may also deliver nutrients and neurotransmitters. Here, we review the relevant literature with a focus on transport processes, especially the potential role of diffusion and advective flows.

Merck & Co. will spend up to $576 million to acquire Calporta Therapeutics, a San Diego–based start-up that is developing small molecules to boost autophagy, the process of cellular self-renewal. Calporta was founded in 2015 at COI Pharmaceuticals, a start-up incubator funded by GlaxoSmithKline and the venture capital firm Avalon Ventures. Today, Calporta is one of more than a dozen start-ups developing drugs that alter autophagy. Studies in cells and animals show that boosting autophagy helps brain cells clean up cellular debris, including the toxic proteins that accumulate in neurodegenerative conditions such as Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis. Calporta says its drug candidates could help these diseases, but its initial focus will be on Niemann-Pick disease type C, a lysosomal storage disease. Its candidates are small-molecule agonists of TRPML1, a calcium channel found in lysosomes, the enzyme-filled sacs that break down cellular debris. TRPML1 is important for lysosomal health

The article discusses how a chain reaction of toxic proteins may help explain neurodegenerative disorders such as Alzheimer's, Parksinson's, and amyotrophic lateral sclerosis (ALS). Topics include an overview of proteinaceous infectious particle (PrP), called prions, research in the 1980s by Stanley B. Prusiner of the University of California, San Francisco that provided evidence that an infectious agent responsible for the animal diseases, called spongiform encephalopathies, led to the misfolding of a protein called PrP, and the impact of knowledge about how proteins fold into a form that causes others to undergo similar transformations on the prevention and treatment of neurological illnesses.

The chapter reviews several aspects related to the mechanism of action of toxic proteins used as biological warfare agents, together with the latest advances in immunosensor development. Emphasis will be put on the role played by the nanoparticle technology in the sensing and transduction design. The potential applications of the nanostructured immunosensors in point-of-care systems and the amenability of these devices for detection on-the-field will be critically commented.

Traditional Chinese medicine (TCM) is widely used around the world. However, with its wide use has been the identification of a number of toxicological issues that have severely restricted its use in clinical treatment. The identification of these toxic substances within TCM has become somewhat of a hot topic in recent years.This article reviews literature published on professional authoritative journals in the last 10 years on the toxic constituents and toxicology of TCM, including chemical structures, absorption and metabolism. The literature search for this article was based, but not limited to, toxic constituents including: alkaloids, glycosides, toxic proteins, polypeptide, amino acids, phenols or organic acids, terpenes and lactones. The authors discuss the toxic substances referring to their toxicity on organs, tissues and systems.More and more toxic constituents from different TCMs have been identified, in addition to information on how they act in the body at a molecular level. However, the toxicology of TCMs is very complex, and although some progress has been made, a lot work is still needed in order to put an end to toxic incidents.

Celiac disease is a food intolerance triggered by the ingestion of gluten-containing cereals; the only therapy is a strict gluten-free diet for life. In recent years, amaranth flour has received considerable attention as an interesting source for the formulation of gluten-free products due to its high nutritional value and low content of prolamins, the toxic proteins for celiacs. The aim of this study was to characterize 40 amaranth varieties using both SDS-PAGE/immunoblotting and ELISA to assess their possible tolerance by celiac subjects. All of the amaranth samples studied showed similar binding affinities for both specific anti-gliadin antibodies and human IgAs. In most amaranth grains, the content of gluten-like proteins measured by ELISA was

The cassava mealybug Phenacoccus herreni (Sternorryncha: Pseudococcidae) is a pest of cassava, Manihot esculenta Crantz (Euphorbiaceae), in South America. Proteins, representing direct gene products, are prime candidates in genetic engineering manipulations for host plant resistance. Jatropha gossypiifolia L. (Euphorbiaceae), a plant species known to contain proteins toxic to insects, exhibited insecticidal properties to P. herreni. The toxic compounds consisting of proteins around 101.02 kDa appeared to be mostly located in the mature leaves. Further studies are needed to identify the proteins and to ensure that they are not toxic to mammals.

Proteins are important biomaterials and are generally produced in living cells. Here, we show a novel DNA hydrogel that is capable of producing functional proteins without any living cells. This protein-producing gel (termed 'the P-gel system' or 'P-gel') consists of genes as part of the gel scaffolding. This is the first time that a hydrogel has been used to produce proteins. The efficiency was about 300 times higher than current, solution-based systems. In terms of volumetric yield, the P-gel produced up to 5 mg ml(-1) of functional proteins. The mechanisms behind the high efficiency and yield include improved gene stability, higher local concentration and a faster enzyme turnover rate due to a closer proximity of genes. We have tested a total of 16 different P-gels and have successfully produced all 16 proteins including membrane and toxic proteins, demonstrating that the P-gel system can serve as a general protein production technology.

A toxic accumulation of proteins is the hallmark pathology of several neurodegenerative disorders. Protein accumulation is regularly prevented by the network of molecular chaperone proteins, including and especially Hsp90. For reasons not yet elucidated, Hsp90 and the molecular chaperones interact with, but do not degrade, these toxic proteins resulting in the pathogenic accumulation of proteins such as tau, in Alzheimer's Disease, and α-synuclein, in Parkinson's Disease. In this review, we describe the associations between Hsp90 and the pathogenic and driver proteins of several neurodegenerative disorders. We additionally describe how the inhibition of Hsp90 promotes the degradation of both mutant and pathogenic protein species in models of neurodegenerative diseases. We also examine the current state of Hsp90 inhibitors capable of crossing the blood-brain barrier; compounds which may be capable of slowing, preventing, and possible reversing neurodegenerative diseases.

Storage proteins from wheat kernels are the base of a wide variety of homemade and industrial food products. Nonetheless, for a group of individuals (celiac disease (CD) patients), these proteins are toxic. Gliadins and glutenins from wheat, as well as their counterparts in barley and rye, also called prolamins, are evolutionary related, and present a high degree of homology. Polyclonal and monoclonal antibodies raised against prolamins have been a very useful tool to characterise structural and conformational features of prolamins, and particularly, for gluten analysis based on immunochemical techniques. Complete adherence to a gluten-free diet is required to recover the normal histology of the small intestine in CD patients. To this end, the use of certified gluten-free products is mandatory. Aqueous solvents such as 60-70% ethanol, have been used for extraction of prolamins from flours and food. This method is not selective and, therefore, results in complex mixtures of proteins which together with their low solubility in aqueous solutions, high degree of homology, and consequently crossreactivity, produce some drawbacks in gluten analysis by immunoassays. Prolamins drive an exacerbated immune response in intestinal mucosa of CD patients. T lymphocytes are a central piece in CD pathogenesis. However, new insights in the knowledge of innate immunity point out to some gliadin peptides which can also produce structural changes in the intestine as well as inflammatory reactions. Instituto de Estudios Inmunológicos y Fisiopatológicos

The previously found wide range in the ratios of avenin or methanol-precipitated fractions to residual proteins was revisited by studying 75 oat varieties, mainly representing landraces from Finland, and included old varieties or selections, cv. Kyto, synthetic hexaploid oats and an Avena strigosa line (HA 71–87). The means of the fraction ratios ranged from 4.17 to 6.46 with significant differences. Samples of 10 narrow-ratio and 10 wide-ratio oats were compared more closely. The wide-ratio sample had significantly higher total protein content and significantly lower content of the methanol-precipitated protein fraction. Therefore, both fractions in general appear to contribute to the ratio of the protein fractions. The wide-ratio sample had significantly lower grain mass and husk-free karyopsis mass. Samples of the extreme ends in the ratios of the protein fractions showed different electrophoretic protein patterns, which was also seen in samples representing the same population of origin. It is evident that polymorphisms in the protein fractions would allow breeding of oat cultivars showing further lowering of proteins putatively toxic to coeliacs assuming oats contain these toxic proteins.