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Intracellular macromolecular crowding can lead to increased aggregation of proteins, especially those that lack a natively folded conformation. Crowding may also be mimicked by the addition of polymers like polyethylene glycol (PEG) in vitro. α-Synuclein is an intrinsically disordered protein that exhibits increased aggregation and amyloid fibril formation in a crowded environment. Two hypotheses have been proposed to explain this observation. One is the excluded volume effect positing that reduced water activity in a crowded environment leads to increased effective protein concentration, promoting aggregation. An alternate explanation is that increased crowding facilitates conversion to a non-native form increasing the rate of aggregation. In this work, we have segregated these two hypotheses to investigate which one is operating. We show that mere increase in concentration of α-synuclein is not enough to induce aggregation and consequent fibrillation. In vitro, we find a complex relationship between PEG concentrations and aggregation, in which smaller PEGs delay fibrillation; while, larger ones promote fibril nucleation. In turn, while PEG600 did not increase the rate of aggregation, PEG1000 did and PEG4000 and PEG12000 slowed it but led to a higher overall fibril burden in the latter to cases. In cells, PEG4000 reduces the aggregation of α-synuclein but in a way specific to the cellular environment/due to cellular factors. The aggregation of the similarly sized, globular lysozyme does not increase in vitro when at the same concentrations with either PEG8000 or PEG12000. Thus, natively disordered α-synuclein undergoes a conformational transition in specific types of crowded environment, forming an aggregation-prone conformer.

Designing novel RNA topologies is a challenge, with important therapeutic and industrial applications. We describe a computational pipeline for design of novel RNA topologies based on our coarse-grained RNA-As-Graphs (RAG) framework. RAG represents RNA structures as tree graphs and describes RNA secondary (2D) structure topologies (currently up to 13 vertices, ≈260 nucleotides). We have previously identified novel graph topologies that are RNA-like among these. Here we describe a systematic design pipeline and illustrate design for six broad design problems using recently developed tools for graph-partitioning and fragment assembly (F-RAG). Following partitioning of the target graph, corresponding atomic fragments from our RAG-3D database are combined using F-RAG, and the candidate atomic models are scored using a knowledge-based potential developed for 3D structure prediction. The sequences of the top scoring models are screened further using available tools for 2D structure prediction. The results indicate that our modular approach based on RNA-like topologies rather than specific 2D structures allows for greater flexibility in the design process, and generates a large number of candidate sequences quickly. Experimental structure probing using SHAPE-MaP for two sequences agree with our predictions and suggest that our combined tools yield excellent candidates for further sequence and experimental screening.

Background Caspase-1 knockout mice (Casp1KO) are protected from Acute Kidney Injury (AKI) after warm ischemia/reperfusion injury in non-transplant models. Since Caspase-1 plays a central role as an inflammatory response initiator, we hypothesized that Casp1KO mice would be protected from AKI following transplant. Methods Renal tubular cells (RTECs) were subjected to cold storage and rewarming (CS/REW). C57Bl/6 J wild type or Casp1KO kidneys were subjected to CI for 30 min and then transplanted into wild type recipients (CI + Txp). The recipients underwent bilateral native nephrectomy at the time of transplant. Serum creatinine (sCr) was measured 24 h after native nephrectomy to assess transplant function. Results We found that RTECs subjected to CS/REW had significantly increased expression of the Caspase-1 and inflammasome protein NLRP1. Wild type kidneys subjected to CI + Txp into wild type recipients also demonstrated significantly increased Caspase-1 and NLRP1 protein expression compared to kidneys transplanted from Casp1KO donors into wild type recipients. Caspase-1 deletion results in significantly decreased RTEC apoptosis in transplanted Casp1KO vs WT kidneys. Surprisingly, however, renal function, ATN scores including brush border injury, cast formation and tubular simplification were similar in both groups and not significantly different. Conclusions Our data suggest that other triggers of inflammation and programmed necrosis may need to be inhibited in addition to attenuating Caspase-1 to fully prevent AKI after kidney transplant. Importantly, requirements may be distinct for AKI induced by transplantation as opposed to other transient models such as the clamp model of AKI.

This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.

The dentate gyrus (DG) principal cells are glutamatergic granule cells (GCs), and they are located in a compact cell layer. However, GCs are also present in the adjacent hilar region, but have been described in only a few studies. Therefore, we used the transcription factor prospero homeobox 1 (Prox1) to quantify GCs at postnatal day (PND) 16, 30, and 60 in a common mouse strain, C57BL/6J mice. At PND16, there was a large population of Prox1-immunoreactive (ir) hilar cells, with more in the septal than temporal hippocampus. At PND30 and 60, the size of the hilar Prox1-ir cell population was reduced. Similar numbers of hilar Prox1-expressing cells were observed in PND30 and 60 Swiss Webster mice. Prox1 is usually considered to be a marker of postmitotic GCs. However, many Prox1-ir hilar cells, especially at PND16, were not double-labeled with NeuN, a marker typically found in mature neurons. Most hilar Prox1-positive cells at PND16 co-expressed doublecortin (DCX) and calretinin, markers of immature GCs. Double-labeling with a marker of actively dividing cells, Ki67, was not detected. These results suggest that, surprisingly, a large population of cells in the hilus at PND16 are immature GCs (Type 2b and Type 3 cells). We also asked whether hilar Prox1-ir cell numbers are modifiable. To examine this issue, we conditionally deleted the proapoptotic gene BAX in Nestin-expressing cells at a time when there are numerous immature GCs in the hilus, PND2-8. When these mice were examined at PND60, the numbers of Prox1-ir hilar cells were significantly increased compared to control mice. However, deletion of BAX did not appear to change the proportion that co-expressed NeuN, suggesting that the size of the hilar Prox1-expressing population is modifiable. However, deleting BAX, a major developmental disruption, does not appear to change the proportion that ultimately becomes neurons.

SUMMARY The sparse activity of hippocampal dentate gyrus (DG) granule cells (GCs) is thought to be critical for cognition and behavior, whereas excessive DG activity may contribute to disorders such as temporal lobe epilepsy (TLE). Glutamatergic mossy cells (MCs) of the DG are potentially critical to normal and pathological functions of the DG because they can regulate GC activity through innervation of GCs or indirectly through GABAergic neurons. Here, we test the hypothesis that MC excitation of GCs is normally weak, but under pathological conditions, MC excitation of GCs is dramatically strengthened. We show that selectively inhibiting MCs during severe seizures reduced manifestations of those seizures, hippocampal injury, and chronic epilepsy. In contrast, selectively activating MCs was pro-convulsant. Mechanistic in vitro studies using optogenetics further demonstrated the unanticipated ability of MC axons to excite GCs under pathological conditions. These results demonstrate an excitatory and epileptogenic effect of MCs in the DG., In Brief Dentate gyrus (DG) mossy cells (MCs) have glutamatergic synapses on the DG principal cells, granule cells (GCs), but many studies suggest that MCs inhibit GCs by exciting local GABAergic interneurons. Botterill et al. show that MC excitation of GCs is robust during status epilepticus, which contributes to excitotoxicity and epileptogenesis., Graphical Abstract

Diabetes mellitus is considered as a main risk factor for vascular dementia. In the past, we have reported the induction of vascular dementia by experimental diabetes. This study investigates the efficacy of a ruthenium red, a ryanodine receptor antagonist and pioglitazone in the pharmacological interdiction of pancreatectomy diabetes (PaD) induced vascular endothelial dysfunction and subsequent vascular dementia in rats. Attentional set shifting and Morris water-maze test were used for assessment of learning and memory. Vascular endothelial function, blood brain barrier permeability, serum glucose, serum nitrite/nitrate, oxidative stress (viz. aortic superoxide anion, brain thiobarbituric acid reactive species and brain glutathione), brain calcium and inflammation (myeloperoxidase) were also estimated. PaD rats have shown impairment of endothelial function, blood brain barrier permeability, learning and memory along with an increase in brain inflammation, oxidative stress and calcium. Administration of ruthenium red and pioglitazone has significantly attenuated PaD induced impairment of learning, memory, blood brain barrier permeability, endothelial function and biochemical parameters. It may be concluded that ruthenium red, a ryanodine receptor antagonist and pioglitazone, a PPAR-γ agonist may be considered as potent pharmacological agent for the management of PaD induced endothelial dysfunction and subsequent vascular dementia. Ryanodine receptor may be explored further for their possible benefits in vascular dementia.

Sparse energy functions that ignore long range interactions between residue pairs are frequently used by protein design algorithms to reduce computational cost. Current dynamic programming algorithms that fully exploit the optimal substructure produced by these energy functions only compute the GMEC. This disproportionately favors the sequence of a single, static conformation and overlooks better binding sequences with multiple low-energy conformations. Provable, ensemble-based algorithms such as A* avoid this problem, but A* cannot guarantee better performance than exhaustive enumeration. We propose a novel, provable, dynamic programming algorithm called Branch-Width Minimization* (BWM*) to enumerate a gap-free ensemble of conformations in order of increasing energy. Given a branch-decomposition of branch-width w for an n-residue protein design with at most q discrete side-chain conformations per residue, BWM* returns the sparse GMEC in O(\documentclass{aastex}\usepackage{amsbsy}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{bm}\usepackage{mathrsfs}\usepackage{pifont}\usepackage{stmaryrd}\usepackage{textcomp}\usepackage{portland, xspace}\usepackage{amsmath, amsxtra}\pagestyle{empty}\DeclareMathSizes{10}{9}{7}{6}\begin{document} $$nw^2 q^ { \frac { 3 } { 2 } w } $$ \end{document}) time and enumerates each additional conformation in merely O(\documentclass{aastex}\usepackage{amsbsy}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{bm}\usepackage{mathrsfs}\usepackage{pifont}\usepackage{stmaryrd}\usepackage{textcomp}\usepackage{portland, xspace}\usepackage{amsmath, amsxtra}\pagestyle{empty}\DeclareMathSizes{10}{9}{7}{6}\begin{document} $$n \log q$$ \end{document}) time. We define a new measure, Total Effective Search Space (TESS), which can be computed efficiently a priori before BWM* or A* is run. We ran BWM* on 67 protein design problems and found that TESS discriminated between BWM*-efficient and A*-efficient cases with 100% accuracy. As predicted by TESS and validated experimentally, BWM* outperforms A* in 73% of the cases and computes the full ensemble or a close approximation faster than A*, enumerating each additional conformation in milliseconds. Unlike A*, the performance of BWM* can be predicted in polynomial time before running the algorithm, which gives protein designers the power to choose the most efficient algorithm for their particular design problem.

Robust incorporation of new principal cells into pre-existing circuitry in the adult mammalian brain is unique to the hippocampal dentate gyrus (DG). We asked if adult-born granule cells (GCs) might act to regulate processing within the DG by modulating the substantially more abundant mature GCs. Optogenetic stimulation of a cohort of young adult-born GCs (0 to 7 weeks post-mitosis) revealed that these cells activate local GABAergic interneurons to evoke strong inhibitory input to mature GCs. Natural manipulation of neurogenesis by aging-to decrease it-and housing in an enriched environment-to increase it-strongly affected the levels of inhibition. We also demonstrated that elevating activity in adult-born GCs in awake behaving animals reduced the overall number of mature GCs activated by exploration. These data suggest that inhibitory modulation of mature GCs may be an important function of adult-born hippocampal neurons. (c) 2015 Wiley Periodicals, Inc.

With a death toll of over one million worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has become the most devastating humanitarian catastrophe in recent decades. The fear of acquiring infection and spreading to vulnerable people has severely impacted society’s socio-economic status. To put an end to this growing number of infections and deaths as well as to switch from restricted to everyday living, an effective vaccine is desperately needed. As a result, enormous efforts have been made globally to develop numerous vaccine candidates in a matter of months. Currently, over 30 vaccine candidates are under assessment in clinical trials, with several undergoing preclinical studies. Here, we reviewed the major vaccine candidates based on the specific vaccine platform utilized to develop them. We also discussed the immune responses generated by these candidates in humans and preclinical models to determine vaccine safety, immunogenicity, and efficacy. Finally, immune responses induced in recovered COVID-19 patients and their possible vaccine development implications were also briefly reviewed.

RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking pseudoknots. We report 56 subgraph blocks up to nine vertices, among them, 22 are frequently occurring, 15 of which contain pseudoknots. We then catalog atomic fragments corresponding to the subgraph blocks to define a library of building blocks that can be used for RNA design, which we call RAG-3Dual, as we have done for tree graphs. As an application, we analyze the distribution of these subgraph blocks within ribosomal RNAs of various prokaryotic and eukaryotic species to identify common subgraphs and possible ancestry relationships. Other applications of dual graph partitioning and motif library can be envisioned for RNA structure analysis and design.

Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications.

Background Hibernators, such as the 13-lined ground squirrel, endure severe hypothermia during torpor followed by periodic rewarming (REW) during interbout arousal (IBA), proapoptotic conditions that are lethal to nonhibernating mammals. We have previously shown that 13-lined ground squirrel tubular cells are protected from apoptotic cell death during IBA. To understand the mechanism of protection, we developed an in vitro model of prolonged cold storage (CS) followed by REW, which is akin to the in vivo changes of hypothermia followed by REW observed during IBA. We hypothesized that renal tubular epithelial cells (RTECs) isolated from hibernating ground squirrels would be protected against apoptosis during CS/REW versus nonhibernating mouse RTECs. Methods Isolated hibernating ground squirrel and mouse RTECs were subjected to CS at 4°C for 24 hours followed by REW to 37°C for 24 hours (CS/REW). Results Ground squirrel RTECs had significantly less apoptosis compared to mouse RTECs when subjected to CS/REW. Next, we hypothesized that the mechanism of protection was related to the antiapoptotic proteins X-linked inhibitor of apoptosis (XIAP), phospho-Akt (pAkt), and phospho-BAD. There was a significantly increased pAkt and pBAD expression in ground squirrel versus mouse RTECs subjected to CS/REW. The XIAP expression was maintained in ground squirrel RTECs but was significantly decreased in mouse RTECs after CS/REW. Ground squirrel RTECs in which gene expression of Akt1 and XIAP was silenced lost their protection and demonstrated increased apoptosis and cleaved caspase-3 expression after CS/REW. Conclusions Our findings suggest that ground squirrel RTECs are protected against apoptosis during prolonged CS/REW by the "prosurvival" factors XIAP and pAkt.

Researchers have created a wealth of knowledge about the mechanisms that regulate food intake, appetite and therefore weight control. The control of appetite is a complex mechanism and involves the coordination of inputs from both physiological and environmental sources. Early theoretical approaches were based on the idea that the control mechanism was dedicated exclusively to signals from glucose metabolism, amino acids or proteins, or adipose tissue. However, a complex system of biologic and environmental factors regulates our appetite. The brain integrates chemical and nervous signals to control hunger and satiety. These controls include sensory and gastrointestinal signals, neurotransmitters and neuropeptides. This review paper summarizes the existing plethora of the highly convoluted process of appetite regulation and food intake.

Mohammad F Anwar,1 Deepak Yadav,2 Swati Jain,3 Sumeet Kapoor,4 Shweta Rastogi,5 Indu Arora,6 Mohammed Samim1 1Department of Chemistry, Faculty of Science, 2Faculty of Medicine, Jamia Hamdard University, New Delhi, 3Amity Institute of Nanotechnology, Amity University, Noida, Uttar Pradesh, 4Centre for Biomedical Engineering, Indian Institute of Technology, Delhi, 5Department of Chemistry, Hans Raj College, 6Department of Biomedical Sciences, Rajguru College of Applied Sciences for Women, University of Delhi, Delhi, India Abstract: Dandruff is a prominent scalp problem caused by the growth of fungus Malassezia furfur, potentially cascading into dermal inflammation, itching, and tissue damage. The present work outlines a detailed analysis of the treatment of scalp infection using silver nanomaterials (Ag NMs), and focuses on biocidal activity owing to manipulation of size, shape, and structure. Monodisperse silver spherical nanoparticles (NPs) and nanorods (NRs) were synthesized by chemical routes that were characterized using analytical and spectroscopic techniques. Ag NMs demonstrated enhanced biocidal tendencies compared to market available drugs, itracanozole and ketoconazole, showing greater zones of inhibition. The obtained 20nm and 50nm spherical-shaped NPs and 50nm NRs showed concentration-, size-, and shape-dependent antifungal activity, with 20nm spherical-shaped NPs exhibiting excellent potency. Minimum inhibitory concentration for 20nm was lowest at 0.2mg/mL in comparison to 0.3mg/mL for NRs. Primary irritation index was 0.33 and 0.16 for 20nm and 50nm spherical-shaped NPs, respectively, while 50nm rod-shaped NMs exhibited negligible redness. An in vivo model for M. furfur infection was generated by passing fungi subcutaneously in rats’ skin. Again, 20nm particles showed best normalization of skin after 10days on regular dosing, in comparison with bigger and rod-shaped particles. The statistical clinical score was highest for Ag nanorods, followed by 50nm Ag NPs-treated animals. It was observed that 20nm spherical particles exhibited the lowest score (0) compared with others as well as with antifungal drugs. Biochemical analysis performed by checking antioxidant enzymatic activities indicated tissue repair and normalization of enzymes and protein concentration by Ag NPs. Keywords: Malassezia furfur, nanorods, in vivo analysis, Wistar rat model

Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation (GMEC). To efficiently find the GMEC, protein design algorithms must methodically reduce the conformational search space. By applying distance and energy cutoffs, the protein system to be designed can thus be represented using a sparse residue interaction graph, where the number of interacting residue pairs is less than all pairs of mutable residues, and the corresponding GMEC is called the sparse GMEC. However, ignoring some pairwise residue interactions can lead to a change in the energy, conformation, or sequence of the sparse GMEC vs. the original or the full GMEC. Despite the widespread use of sparse residue interaction graphs in protein design, the above mentioned effects of their use have not been previously analyzed. To analyze the costs and benefits of designing with sparse residue interaction graphs, we computed the GMECs for 136 different protein design problems both with and without distance and energy cutoffs, and compared their energies, conformations, and sequences. Our analysis shows that the differences between the GMECs depend critically on whether or not the design includes core, boundary, or surface residues. Moreover, neglecting long-range interactions can alter local interactions and introduce large sequence differences, both of which can result in significant structural and functional changes. Designs on proteins with experimentally measured thermostability show it is beneficial to compute both the full and the sparse GMEC accurately and efficiently. To this end, we show that a provable, ensemble-based algorithm can efficiently compute both GMECs by enumerating a small number of conformations, usually fewer than 1000. This provides a novel way to combine sparse residue interaction graphs with provable, ensemble-based algorithms to reap the benefits of sparse residue interaction graphs while avoiding their potential inaccuracies., Author summary Computational structure-based protein design algorithms have successfully redesigned proteins to fold and bind target substrates in vitro, and even in vivo. Because the complexity of a computational design increases dramatically with the number of mutable residues, many design algorithms employ cutoffs (distance or energy) to neglect some pairwise residue interactions, thereby reducing the effective search space and computational cost. However, the energies neglected by such cutoffs can add up, which may have nontrivial effects on the designed sequence and its function. To study the effects of using cutoffs on protein design, we computed the optimal sequence both with and without cutoffs, and showed that neglecting long-range interactions can significantly change the computed conformation and sequence. Designs on proteins with experimentally measured thermostability showed the benefits of computing the optimal sequences (and their conformations), both with and without cutoffs, efficiently and accurately. Therefore, we also showed that a provable, ensemble-based algorithm can efficiently compute the optimal conformation and sequence, both with and without applying cutoffs, by enumerating a small number of conformations, usually fewer than 1000. This provides a novel way to combine cutoffs with provable, ensemble-based algorithms to reap the computational efficiency of cutoffs while avoiding their potential inaccuracies.

Calorie restriction can occur as a consequence of food shortage due to natural calamities, war like situations or voluntarily for health benefits. This state of negative energy balance leads to decrease in performance and increase in feeling of hunger. A normal individual can sustain himself on stored energy in form of body fat for a period of time. It was hypothesised that use of an appetite suppressant like Hoodia gordonii along with L-carnintine, which helps in fat oxidation can be used as strategy for coping adverse situation without compromising physical performance. The aim of the study was to evaluate the combined effect of H. gordonii and L-carnitine supplementation on metabolic changes and appetite regulatory peptides during calorie restriction. Male albino rats were divided into two groups (n=12 in each) i.e. control (without treatment) and treated (H. gordonii organic solvent extract and L-carnitine, orally for 5 days at a dose of 100 mg/kg under 25 per cent calorie restriction). Biochemical variables including regulatory peptides were estimated along with physical efficiency tests. Significant changes in ghrelin, leptin, corticosterone and thyroid hormones were observed in comparison to control. While blood glucose, AMP kinase decreased significantly in the treated group, an increase in CPT-1 activity was observed compared with controls. It is concluded that approach could be practically suitable and effective in emergency situations of combat or food shortage.Defence Science Journal, Vol. 66, No. 1, January 2016, pp. 11-18, DOI: http://dx.doi.org/10.14429/dsj.66.9178