High-pressure strengthening in ultrafine-grained metals.

The Hall-Petch relationship, according to which the strength of a metal increases as the grain size decreases, has been reported to break down at a critical grain size of around 10 to 15 nanometres1,2. As the grain size decreases beyond this point, the dominant mechanism of deformation switches from a dislocation-mediated process to grain boundary sliding, leading to material softening. In one previous approach, stabilization of grain boundaries through relaxation and molybdenum segregation was used to prevent this softening effect in nickel-molybdenum alloys with grain sizes below 10 nanometres3. Here we track in situ the yield stress and deformation texturing of pure nickel samples of various average grain sizes using a diamond anvil cell coupled with radial X-ray diffraction. Our high-pressure experiments reveal continuous strengthening in samples with grain sizes from 200 nanometres down to 3 nanometres, with the strengthening enhanced (rather than reduced) at grain sizes smaller than 20 nanometres. We achieve a yield strength of approximately 4.2 gigapascals in our 3-nanometre-grain-size samples, ten times stronger than that of a commercial nickel material. A maximum flow stress of 10.2 gigapascals is obtained in nickel of grain size 3 nanometres for the pressure range studied here. We see similar patterns of compression strengthening in gold and palladium samples down to the smallest grain sizes. Simulations and transmission electron microscopy reveal that the high strength observed in nickel of grain size 3 nanometres is caused by the superposition of strengthening mechanisms: both partial and full dislocation hardening plus suppression of grain boundary plasticity. These insights contribute to the ongoing search for ultrastrong metals via materials engineering.

The Ultimate Guide to Bacterial Swarming: An Experimental Model to Study the Evolution of Cooperative Behavior.

Cooperation has fascinated biologists since Darwin. How did cooperative behaviors evolve despite the fitness cost to the cooperator? Bacteria have cooperative behaviors that make excellent models to take on this age-old problem from both proximate (molecular) and ultimate (evolutionary) angles. We delve into Pseudomonas aeruginosa swarming, a phenomenon where billions of bacteria move cooperatively across distances of centimeters in a matter of a few hours. Experiments with swarming have unveiled a strategy called metabolic prudence that stabilizes cooperation, have showed the importance of spatial structure, and have revealed a regulatory network that integrates environmental stimuli and direct cooperative behavior, similar to a machine learning algorithm. The study of swarming elucidates more than proximate mechanisms: It exposes ultimate mechanisms valid to all scales, from cells in cancerous tumors to animals in large communities.

Iron-inhibited autophagy via transcription factor ZFP27 in Parkinson's disease.

Parkinson's disease (PD) is a challenge because of the ageing of the population and the disease's complicated pathogenesis. Accumulating evidence showed that iron and autophagy were involved in PD. Nevertheless, the molecular mechanism and role of iron and autophagy in PD are not yet elucidated. In the present study, it was shown that PD mice had significant motor dysfunction, increased iron content, less dopamine neurons and more α-synuclein accumulation in the substantia nigra. Meanwhile, PD mice treated with deferoxamine exhibited less iron content, relieved the dyskinesia and had a significant increase in dopamine neurons and a significant decrease in α-synuclein. Autophagy induced by LC3 was inhibited in PD models with iron treatment. Following verification showed that iron aggregation restrained insulin-like growth factor 2 (IGF2) and transcription factor zinc finger protein 27 (ZFP27) in PD models. In addition, LC3-induced autophagy flux was reduced with ZFP27 knockdown. Furthermore, ZFP27 affected autophagy by regulating LC3 promoter activity. These data suggest that iron deposition inhibits IGF2 and ZFP27 to reduce LC3-induced autophagy, and ultimately decrease dopamine neurons, accelerating PD progression. Our findings provide a novel insight that ZFP27-mediated iron-related autophagy and IGF2 may activate the downstream kinase gene to trigger autophagy in the PD model.

A trade-off switch of two immunological memories in Caenorhabditis elegans reinfected by bacterial pathogens.

Recent studies have suggested that innate immune responses exhibit characteristics associated with memory linked to modulations in both vertebrates and invertebrates. However, the diverse evolutionary paths taken, particularly within the invertebrate taxa, should lead to similarly diverse innate immunity memory processes. Our understanding of innate immune memory in invertebrates primarily comes from studies of the fruit fly Drosophila melanogaster, the generality of which is unclear. Caenorhabditis elegans typically inhabits soil harboring a variety of fatal microbial pathogens; for this invertebrate, the innate immune system and aversive behavior are the major defensive strategies against microbial infection. However, their characteristics of immunological memory remains infantile. Here we discovered an immunological memory that promoted avoidance and suppressed innate immunity during reinfection with bacteria, which we revealed to be specific to the previously exposed pathogens. During this trade-off switch of avoidance and innate immunity, the chemosensory neurons AWB and ADF modulated production of serotonin and dopamine, which in turn decreased expression of the innate immunity-associated genes and led to enhanced avoidance via the downstream insulin-like pathway. Therefore, our current study profiles the immune memories during C. elegans reinfected by pathogenic bacteria and further reveals that the chemosensory neurons, the neurotransmitter(s), and their associated molecular signaling pathways are responsible for a trade-off switch between the two immunological memories.

The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts.

Host-associated microbiota help defend against bacterial pathogens; however, the mechanisms by which pathogens overcome this defense remain largely unknown. We developed a zebrafish model and used live imaging to directly study how the human pathogen Vibrio cholerae invades the intestine. The gut microbiota of fish monocolonized by symbiotic strain Aeromonas veronii was displaced by V. cholerae expressing its type VI secretion system (T6SS), a syringe-like apparatus that deploys effector proteins into target cells. Surprisingly, displacement was independent of T6SS-mediated killing of A. veronii, driven instead by T6SS-induced enhancement of zebrafish intestinal movements that led to expulsion of the resident microbiota by the host. Deleting an actin cross-linking domain from the T6SS apparatus returned intestinal motility to normal and thwarted expulsion, without weakening V. cholerae's ability to kill A. veronii in vitro. Our finding that bacteria can manipulate host physiology to influence intermicrobial competition has implications for both pathogenesis and microbiome engineering.

Origin of Plasticity in Nanostructured Silicon.

The mechanism of plasticity in nanostructured Si has been intensively studied over the past decade but still remains elusive. Here, we used in situ high-pressure radial x-ray diffraction to simultaneously monitor the deformation and structural evolution of a large number of randomly oriented Si nanoparticles (SiNPs). In contrast to the high-pressure ß-Sn phase dominated plasticity observed in large SiNPs (∼100 nm), small SiNPs (∼9 nm) display a high-pressure simple hexagonal phase dominated plasticity. Meanwhile, dislocation activity exists in all of the phases, but significantly weakens as the particle size decreases and only leads to subtle plasticity in the initial diamond cubic phase. Furthermore, texture simulations identify major active slip systems in all of the phases. These findings elucidate the origin of plasticity in nanostructured Si under stress and provide key guidance for the application of nanostructured Si.

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection.

Pseudomonas aeruginosa, a main cause of human infection, can gain resistance to the antibiotic aztreonam through a mutation in NalD, a transcriptional repressor of cellular efflux. Here we combine computational analysis of clinical isolates, transcriptomics, metabolic modeling and experimental validation to find a strong association between NalD mutations and resistance to aztreonam-as well as resistance to other antibiotics-across P. aeruginosa isolated from different patients. A detailed analysis of one patient's timeline shows how this mutation can emerge in vivo and drive rapid evolution of resistance while the patient received cancer treatment, a bone marrow transplantation, and antibiotics up to the point of causing the patient's death. Transcriptomics analysis confirmed the primary mechanism of NalD action-a loss-of-function mutation that caused constitutive overexpression of the MexAB-OprM efflux system-which lead to aztreonam resistance but, surprisingly, had no fitness cost in the absence of the antibiotic. We constrained a genome-scale metabolic model using the transcriptomics data to investigate changes beyond the primary mechanism of resistance, including adaptations in major metabolic pathways and membrane transport concurrent with aztreonam resistance, which may explain the lack of a fitness cost. We propose that metabolic adaptations may allow resistance mutations to endure in the absence of antibiotics and could be targeted by future therapies against antibiotic resistant pathogens.

Carbide Formation in Refractory Mo15Nb20Re15Ta30W20 Alloy under a Combined High-Pressure and High-Temperature Condition.

In this work, the formation of carbide with the concertation of carbon at 0.1 at.% in refractory high-entropy alloy (RHEA) Mo15Nb20Re15Ta30W20 was studied under both ambient and high-pressure high-temperature conditions. The x-ray diffraction of dilute carbon (C)-doped RHEA under ambient pressure showed that the phases and lattice constant of RHEA were not influenced by the addition of 0.1 at.% C. In contrast, C-doped RHEA showed unexpected phase formation and transformation under combined high-pressure and high-temperature conditions by resistively employing the heated diamond anvil cell (DAC) technique. The new FCC_L12 phase appeared at 6 GPa and 809 °C and preserved the ambient temperature and pressure. High-pressure and high-temperature promoted the formation of carbides Ta3C and Nb3C, which are stable and may further improve the mechanical performance of the dilute C-doped alloy Mo15Nb20Re15Ta30W20.

Gastrodin protects dopaminergic neurons via insulin-like pathway in a Parkinson's disease model.

BACKGROUND: Recently, the use of traditional Chinese medicine (TCM) has become more generally accepted, including by the Food and Drug Administration. To expand the use of TCM worldwide, it is important to study the molecular mechanisms by which TCM and its active ingredients produce effects. Gastrodin is an active ingredient from Gastrodia elata Blume. It is reported that gastrodin has neuroprotective function in Parkinson's disease. But its mechanisms of neuroprotection remain not clear in PD. Here, we build two C. elegans PD model using 6-OHDA and transgenic animal to observe the changes of PD worms treated with or without gastrodin to confirm the function of gastrodin, then utilize mutant worms to investigate DAF-2/DAF-16 signaling pathway, and finally verify the mechanism of gastrodin in PD. RESULTS: Gastrodin attenuates the accumulation of α-synuclein and the injury of dopaminergic neurons, improves chemotaxis behavior in Parkinson's disease models, then recovers chemotaxis behavior by insulin-like pathway. DAF-2/DAF-16 is required for neuroprotective effect of dopamine neuron in PD. CONCLUSIONS: Our study demonstrated that gastrodin rescued dopaminergic neurons and reduced accumulation of α-synuclein protein, and the activity of gastrodin against Parkinson's disease depended on the insulin-like DAF-2/DAF-16 signaling pathway. Our findings revealed that this insulin-like pathway mediates neuroprotection of gastrodin in a Parkinson's disease model.

Metabolism and the Evolution of Social Behavior.

How does metabolism influence social behavior? This fundamental question at the interface of molecular biology and social evolution is hard to address with experiments in animals, and therefore, we turned to a simple microbial system: swarming in the bacterium Pseudomonas aeruginosa. Using genetic engineering, we excised a locus encoding a key metabolic regulator and disrupted P. aeruginosa's metabolic prudence, the regulatory mechanism that controls expression of swarming public goods and protects this social behavior from exploitation by cheaters. Then, using experimental evolution, we followed the joint evolution of the genome, the metabolome and the social behavior as swarming re-evolved. New variants emerged spontaneously with mutations that reorganized the metabolome and compensated in distinct ways for the disrupted metabolic prudence. These experiments with a unicellular organism provide a detailed view of how metabolism-currency of all physiological processes-can determine the costs and benefits of a social behavior and ultimately influence how an organism behaves towards other organisms of the same species.

Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network.

Bacteria of many species rely on a simple molecule, the intracellular secondary messenger c-di-GMP (Bis-(3'-5')-cyclic dimeric guanosine monophosphate), to make a vital choice: whether to stay in one place and form a biofilm, or to leave it in search of better conditions. The c-di-GMP network has a bow-tie shaped architecture that integrates many signals from the outside world-the input stimuli-into intracellular c-di-GMP levels that then regulate genes for biofilm formation or for swarming motility-the output phenotypes. How does the 'uninformed' process of evolution produce a network with the right input/output association and enable bacteria to make the right choice? Inspired by new data from 28 clinical isolates of Pseudomonas aeruginosa and strains evolved in laboratory experiments we propose a mathematical model where the c-di-GMP network is analogous to a machine learning classifier. The analogy immediately suggests a mechanism for learning through evolution: adaptation though incremental changes in c-di-GMP network proteins acquires knowledge from past experiences and enables bacteria to use it to direct future behaviors. Our model clarifies the elusive function of the ubiquitous c-di-GMP network, a key regulator of bacterial social traits associated with virulence. More broadly, the link between evolution and machine learning can help explain how natural selection across fluctuating environments produces networks that enable living organisms to make sophisticated decisions.

The Signaling Pathway of Caenorhabditis elegans Mediates Chemotaxis Response to the Attractant 2-Heptanone in a Trojan Horse-like Pathogenesis.

The nematode Caenorhabditis elegans exhibits behavioral responses to a wide range of odorants associated with food and pathogens. A previous study described a Trojan Horse-like strategy of pathogenesis whereby the bacterium Bacillus nematocida B16 emits the volatile organic compound 2-heptanone to trap C. elegans for successful infection. Here, we further explored the receptor for 2-heptanone as well as the pathway involved in signal transduction in C. elegans Our experiments showed that 2-heptanone sensing depended on the function of AWC neurons and a GPCR encoded by str-2 Consistent with the above observation, the HEK293 cells expressing STR-2 on their surfaces showed a transient elevation in intracellular Ca2+ levels after 2-heptanone applications. After combining the assays of RNA interference and gene mutants, we also identified the Gα subunits and their downstream components in the olfactory signal cascade that are necessary for responding to 2-heptanone, including Gα subunits of egl-30 and gpa-3, phospholipase C of plc-1and egl-8, and the calcium channel of cmk-1 and cal-1. Our work demonstrates for the first time that an integrated signaling pathway for 2-heptanone response in C. elegans involves recognition by GPCR STR-2, activation by Gα subunits of egl-30/gpa-3 and transfer to the PLC pathway, indicating that a potentially novel olfactory pathway exists in AWC neurons. Meanwhile, since 2-heptanone, a metabolite from the pathogenic bacterium B. nematocida B16, can be sensed by C. elegans and thus strongly attract its host, our current work also suggested coevolution between the pathogenic microorganism and the chemosensory system in C. elegans.

Reversal in the Size Dependence of Grain Rotation.

The conventional belief, based on the Read-Shockley model for the grain rotation mechanism, has been that smaller grains rotate more under stress due to the motion of grain boundary dislocations. However, in our high-pressure synchrotron Laue x-ray microdiffraction experiments, 70 nm nickel particles are found to rotate more than any other grain size. We infer that the reversal in the size dependence of the grain rotation arises from the crossover between the grain boundary dislocation-mediated and grain interior dislocation-mediated deformation mechanisms. The dislocation activities in the grain interiors are evidenced by the deformation texture of nickel nanocrystals. This new finding reshapes our view on the mechanism of grain rotation and helps us to better understand the plastic deformation of nanomaterials, particularly of the competing effects of grain boundary and grain interior dislocations.

Detecting grain rotation at the nanoscale.

It is well-believed that below a certain particle size, grain boundary-mediated plastic deformation (e.g., grain rotation, grain boundary sliding and diffusion) substitutes for conventional dislocation nucleation and motion as the dominant deformation mechanism. However, in situ probing of grain boundary processes of ultrafine nanocrystals during plastic deformation has not been feasible, precluding the direct exploration of the nanomechanics. Here we present the in situ texturing observation of bulk-sized platinum in a nickel pressure medium of various particle sizes from 500 nm down to 3 nm. Surprisingly, the texture strength of the same-sized platinum drops rapidly with decreasing grain size of the nickel medium, indicating that more active grain rotation occurs in the smaller nickel nanocrystals. Insight into these processes provides a better understanding of the plastic deformation of nanomaterials in a few-nanometer length scale.

Deformation Behavior across the Zircon-Scheelite Phase Transition.

The pressure effects on plastic deformation and phase transformation mechanisms of materials are of great importance to both Earth science and technological applications. Zircon-type materials are abundant in both nature and the industrial field; however, there is still no in situ study of their deformation behavior. Here, by employing radial x-ray diffraction in a diamond anvil cell, we investigate the dislocation-induced texture evolution of zircon-type gadolinium vanadate (GdVO_{4}) in situ under pressure and across its phase transitions to its high-pressure polymorphs. Zircon-type GdVO_{4} develops a (001) compression texture associated with dominant slip along ⟨100⟩{001} starting from 5 GPa. This (001) texture transforms into a (110) texture during the zircon-scheelite phase transition. Our observation demonstrates a martensitic mechanism for the zircon-scheelite transformation. This work will help us understand the local deformation history in the upper mantle and transition zone and provides fundamental guidance on material design and processing for zircon-type materials.

A novel role for the alcohol sensitive ring/PHD finger protein Asr1p in regulating cell cycle mediated by septin-dependent assembly in yeast.

Septin is a conserved eukaryotic family of GTP-binding filament-forming proteins with functions in cytokinesis and other processes. It has been suggested that the dynamic assembly of septin, including the processes from septin initially localizing to the presumptive bud site to the septin collar finally splitting into two cells, coordinates closely with the checkpoint response of cell cycle. Here, we discovered that over-expression of Alcohol sensitive Ring/PHD finger 1 protein (Asr1p) in Saccharomyces cerevisiae triggered the Swe1p-dependent cell cycle checkpoint for a G2/M transition delay, and this G2/M transition delay was caused by the septin defect. Since it was shown that Asr1p affected actin dynamics through the interaction with Crn1p and crn1 should be epistatic to asr1 in the regulation of actin, the gene knockout of crn1 in the Asr1p over-expression strain restored the defects in septin and cell cycle along with the disordered actin dynamics. Our investigation further showed that the disturbed septin assembly caused by abnormal Asr1p lead to the abnormal localization of the checkpoint proteins such as Gla4/PAK and Cdc5/Polo, and finally triggered the Swe1p-dependent G2/M transition arrest. Additionally, the Ring finger/PHD domains of Asr1p were illustrated to be required but not sufficient for its role in septin. Taken together, our current data suggested a close relationship in the assembly between septin and actin cytoskeleton, which also partially explained how actin cytoskeleton participated in the regulation of the checkpoint of G2/M.

Xanthusbase after five years expands to become Openmods.

Xanthusbase (http://www.xanthusbase.org), a model organism database for the bacterium Myxococcus xanthus, functions as a collaborative information repository based on Wikipedia principles. It was created more than 5 years ago to serve as a cost-effective reference database for M. xanthus researchers, an education tool for undergraduate students to learn about genome annotation, and a means for the community of researchers to collaboratively improve their organism's annotation. We have achieved several goals and are seeking creative solutions to ongoing challenges. Along the way we have made several important improvements to Xanthusbase related to stability, security and usability. Most importantly, we have designed and implemented an installer that enables other microbial model organism communities to use it as a MOD. This version, called Openmods, has already been used to create Xenorhabdusbase (http://xenorhabdusbase.bact.wisc.edu), Caulobacterbase (http://caulobacterbase.bsd.uchicago.edu) and soon Bdellovibriobase.

Valeric acid reduction by chitosan oligosaccharide induces autophagy in a Parkinson's disease mouse model.

Parkinson's disease (PD) is a central nervous system disease with the highest disability and mortality rate worldwide, and it is caused by a variety of factors. The most common medications for PD have side effects with limited therapeutic outcomes. Many studies have reported that chitosan oligosaccharide (COS) crossed blood-brain barrier to achieve a neuroprotective effect in PD. However, the role of COS in PD remains unclear. The present study demonstrated that COS increased dopaminergic neurons in the substantia nigra (SN) and ameliorated dyskinesia in a PD mouse model. Moreover, COS reduced gut microbial diversity and faecal short-chain fatty acids. Valeric acid supplementation enhanced the inflammatory response in the colon and SN, and it reversed COS - suppressed dopamine neurons damage. Autophagy was involved in COS modulating inflammation through valeric acid. These results suggest that COS reduces bacterial metabolites - valeric acid, which diminishes inflammation via activating autophagy, ultimately alleviating PD.

Chitosan alleviates symptoms of Parkinson's disease by reducing acetate levels, which decreases inflammation and promotes repair of the intestinal barrier and blood-brain barrier.

ABSTRACT: Studies have shown that chitosan protects against neurodegenerative diseases. However, the precise mechanism remains poorly understood. In this study, we administered chitosan intragastrically to an MPTP-induced mouse model of Parkinson's disease and found that it effectively reduced dopamine neuron injury, neurotransmitter dopamine release, and motor symptoms. These neuroprotective effects of chitosan were related to bacterial metabolites, specifically short-chain fatty acids, and chitosan administration altered intestinal microbial diversity and decreased short-chain fatty acid production in the gut. Furthermore, chitosan effectively reduced damage to the intestinal barrier and the blood-brain barrier. Finally, we demonstrated that chitosan improved intestinal barrier function and alleviated inflammation in both the peripheral nervous system and the central nervous system by reducing acetate levels. Based on these findings, we suggest a molecular mechanism by which chitosan decreases inflammation through reducing acetate levels and repairing the intestinal and blood-brain barriers, thereby alleviating symptoms of Parkinson's disease.

High-pressure studies of size dependent yield strength in rhenium diboride nanocrystals.

The superhard ReB2 system is the hardest pure phase diboride synthesized to date. Previously, we have demonstrated the synthesis of nano-ReB2 and the use of this nanostructured material for texture analysis using high-pressure radial diffraction. Here, we investigate the size dependence of hardness in the nano-ReB2 system using nanocrystalline ReB2 with a range of grain sizes (20-60 nm). Using high-pressure X-ray diffraction, we characterize the mechanical properties of these materials, including bulk modulus, lattice strain, yield strength, and texture. In agreement with the Hall-Petch effect, the yield strength increases with decreasing size, with the 20 nm ReB2 exhibiting a significantly higher yield strength than any of the larger grained materials or bulk ReB2. Texture analysis on the high pressure diffraction data shows a maximum along the [0001] direction, which indicates that plastic deformation is primarily controlled by the basal slip system. At the highest pressure (55 GPa), the 20 nm ReB2 shows suppression of other slip systems observed in larger ReB2 samples, in agreement with its high yield strength. This behavior, likely arises from an increased grain boundary concentration in the smaller nanoparticles. Overall, these results highlight that even superhard materials can be made more mechanically robust using nanoscale grain size effects.