DNA hydrogel-based supercapacitors operating in physiological fluids

A biospecies-derived genomic DNA hybrid gel electrolyte for electrochemical energy storage

Intrinsic impediments, namely weak mechanical strength, low ionic conductivity, low electrochemical performance, and stability have largely inhibited beyond practical applications of hydrogels in electronic devices and remains as a significant challenge in the scientific world. Here, we report a biospecies-derived genomic DNA hybrid gel electrolyte with many synergistic effects, including robust mechanical properties (mechanical strength and elongation of 6.98 MPa and 997.42%, respectively) and ion migration channels, which consequently demonstrated high ionic conductivity (73.27 mS/cm) and superior electrochemical stability (1.64 V). Notably, when applied to a supercapacitor the hybrid gel-based devices exhibit a specific capacitance of 425 F/g. Furthermore, it maintained rapid charging/discharging with a capacitance retention rate of 93.8% after ∼200,000 cycles while exhibiting a maximum energy density of 35.07 Wh/kg and a maximum power density of 193.9 kW/kg. This represents the best value among the current supercapacitors and can be immediately applied to minicars, solar cells, and LED lightning. The widespread use of DNA gel electrolytes will revolutionize human efforts to industrialize high-performance green energy.

Evolutionarily related host and microbial pathways regulate fat desaturation

Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression1-4, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, whose activity mimics that of microbiota-dependent becyp#1, but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.

Yolk-deprived Caenorhabditis elegans secure brood size at the expense of competitive fitness

Oviparous animals support reproduction via the incorporation of yolk as a nutrient source into the eggs. In Caenorhabditis elegans, however, yolk proteins seem dispensable for fecundity, despite constituting the vast majority of the embryonic protein pool and acting as carriers for nutrient-rich lipids. Here, we used yolk protein-deprived C. elegans mutants to gain insight into the traits that may yet be influenced by yolk rationing. We show that massive yolk provisioning confers a temporal advantage during embryogenesis, while also increasing early juvenile body size and promoting competitive fitness. Opposite to species that reduce egg production under yolk deprivation, our results indicate that C. elegans relies on yolk as a fail-safe to secure offspring survival, rather than to maintain offspring numbers.

Aged Breast Matrix Bound Vesicles Promote Breast Cancer Invasiveness

Aging is one of the inherent risk factors for breast cancer. Although the influence of age-related cellular alterations on breast cancer development has been extensively explored, little is known about the alterations in the aging breast tissue microenvironment, specifically the extracellular matrix (ECM). Here, for the first time in literature, we have identified tissue resident matrix bound vesicles (MBVs) within the healthy mouse breast ECM, investigated and compared their characteristics in young and aged healthy breast tissues, and studied the effects of these MBVs on normal (KTB21) and cancerous (MDA-MB-231) human mammary epithelial cells with respect to the tissue age that they are extracted from. Using vesicle labeling technology, we were able to visualize cellular uptake of the MBVs directly from the native decellularized tissue sections, showing that these MBVs have regulatory roles in the tissue microenvironment. We mimicked the ECM by embedding the MBVs in collagen gels, and showed that MBVs could be taken up by the cells. The miRNA and cytokine profiling showed that MBVs shifted towards a more tumorigenic and invasive phenotype with age, as evidenced by the more pronounced presence of cancer-associated cytokines, and higher expression levels of oncomiRs miR-10b, miR-30e, and miR-210 in MBVs isolated from aged mice. When treated with MBVs or these upregulated factors, KTB21 and MDA-MB-231 cells showed significantly higher motility and invasion compared to untreated controls. Treatment of cells with a cocktail of miRNAs (miR-10b, miR-30e, and miR-210) or with the agonist of adiponectin (AdipoRon), which both were enriched in the aged MBVs, recapitulated the effect of aged MBVs on cells. This study shows for the first time that the MBVs have a regulatory role in the tissue microenvironment and that the MBV contents change towards cancer-promoting upon aging. Studying the effects of MBVs and their cargos on cellular behavior could lead to a better understanding of the critical roles of MBVs played in breast cancer progression and metastasis.

Biochemical Properties of Naturally Occurring Human Bloom Helicase Variants

Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human BLM cause Bloom syndrome (BS), an autosomal recessive disorder that leads to myriad negative health impacts including a predisposition to cancer. BS-causing mutations in BLM often negatively impact BLM ATPase and helicase activity. While BLM mutations that cause BS have been well characterized both in vitro and in vivo , there are other less studied BLM mutations that exist in the human population that do not lead to BS. Two of these non-BS mutations, encoding BLM P868L and BLM G1120R, when homozygous, increase sister chromatid exchanges in human cells. To characterize these naturally occurring BLM mutant proteins in vitro , we purified the BLM catalytic core (BLM core , residues 636-1298) with either the P868L or G1120R substitution. We also purified a BLM core K869A K870A mutant protein, which alters a lysine-rich loop proximal to the P868 residue. We found that BLM core P868L and G1120R proteins were both able to hydrolyze ATP, bind diverse DNA substrates, and unwind G-quadruplex and duplex DNA structures. Molecular dynamics simulations suggest that the P868L substitution weakens the DNA interaction with the winged-helix domain of BLM and alters the orientation of one lobe of the ATPase domain. Because BLM core P868L and G1120R retain helicase function in vitro , it is likely that the increased genome instability is caused by specific impacts of the mutant proteins in vivo . Interestingly, we found that BLM core K869A K870A has diminished ATPase activity, weakened binding to duplex DNA structures, and less robust helicase activity compared to wild-type BLM core . Thus, the lysine-rich loop may have an important role in ATPase activity and specific binding and DNA unwinding functions in BLM.

Label-free metabolic imaging for sensitive and robust monitoring of anti-CD47 immunotherapy response in triple-negative breast cancer

Background

Immunotherapy is revolutionizing cancer treatment from conventional radiotherapies and chemotherapies to immune checkpoint inhibitors which use patients’ immune system to recognize and attack cancer cells. Despite the huge clinical success and vigorous development of immunotherapies, there is a significant unmet need for a robust tool to identify responders to specific immunotherapy. Early and accurate monitoring of immunotherapy response is indispensable for personalized treatment and effective drug development.

Methods

We established a label-free metabolic intravital imaging (LMII) technique to detect two-photon excited autofluorescence signals from two coenzymes, NAD(P)H (reduced nicotinamide adenine dinucleotide (phosphate) hydrogen) and FAD (flavin adenine dinucleotide) as robust imaging markers to monitor metabolic responses to immunotherapy. Murine models of triple-negative breast cancer (TNBC) were established and tested with different therapeutic regimens including anti-cluster of differentiation 47 (CD47) immunotherapy to monitor time-course treatment responses using the developed metabolic imaging technique.

Results

We first imaged the mechanisms of the CD47-signal regulatory protein alpha pathway in vivo, which unravels macrophage-mediated antibody-dependent cellular phagocytosis and illustrates the metabolism of TNBC cells and macrophages. We further visualized the autofluorescence of NAD(P)H and FAD and found a significant increase during tumor growth. Following anti-CD47 immunotherapy, the imaging signal was dramatically decreased demonstrating the sensitive monitoring capability of NAD(P)H and FAD imaging for therapeutic response. NAD(P)H and FAD intravital imaging also showed a marked decrease after chemotherapy and radiotherapy. A comparative study with conventional whole-body bioluminescence and fluorescent glucose imaging demonstrated superior sensitivity of metabolic imaging. Flow cytometry validated metabolic imaging results. In vivo immunofluorescent staining revealed the targeting ability of NAD(P)H imaging mainly for tumor cells and a small portion of immune-active cells and that of FAD imaging mainly for immunosuppressive cells such as M2-like tumor-associated macrophages.

Conclusions

Collectively, this study showcases the potential of the LMII technique as a powerful tool to visualize dynamic changes of heterogeneous cell metabolism of cancer cells and immune infiltrates in response to immunotherapy thus providing sensitive and complete monitoring. Leveraged on ability to differentiate cancer cells and immunosuppressive macrophages, the presented imaging approach provides particularly useful imaging biomarkers for emerged innate immune checkpoint inhibitors such as anti-CD47 therapy.

Peptidic microarchitecture-trapped tumor vaccine combined with immune checkpoint inhibitor or PI3Kγ inhibitor can enhance immunogenicity and eradicate tumors

Background

With the rapid development of immune checkpoint inhibitors and neoantigen (NeoV)-based personalized tumor vaccines, tumor immunotherapy has shown promising therapeutic results. However, the limited efficacy of available tumor vaccines impedes the development of personalized tumor immunotherapy. In this study, we developed a novel tumor vaccine system and proposed combined therapeutic strategies for improving treatment effects.

Methods

We developed a novel tumor vaccine system comprising a newly synthesized peptidic microarchitecture (PMA) with high assembly efficacy. The PMA-trapped neoantigen vaccine was developed to codeliver tumor neoantigen and the Toll-like receptor 9 agonist CpG (NeoV), abbreviated as PMA-NeoV. A microfluidic chip was used to produce PMA particles in a uniform and precise manner. Vaccine effectiveness was investigated both in vitro and in vivo. The combined immunotherapeutic effect of PMA-NeoV with anti-programmed cell death ligand 1 antibody (aPD-L1) or with the phosphatidylinositol 3‑kinase γ (PI3Kγ) inhibitor IPI-549 was further tested in MC38 mouse tumor model.

Results

PMA-NeoV not only promoted codelivery of the tumor vaccine but also potentiated vaccine immunogenicity. Moreover, compared with free NeoV, PMA-NeoV significantly increased the number of tumor-infiltrating lymphocytes, promoted the neoantigen-specific systemic immune response, and suppressed murine colon MC38 tumor growth. Furthermore, PMA-NeoV increased the expression of programmed cell death receptor-1 on T lymphocytes, and in combination with aPD-L1 eradicated seven of eight MC38 tumors by rescuing exhausted T lymphocytes. Moreover, we combined the PMA-NeoV with the IPI-549, a molecular switch that controls immune suppression, and found that this combination significantly suppressed tumor growth and eradicated five of eight inoculated tumors, by switching suppressive macrophages to their active state and activating T cells to prime a robust tumor immune microenvironment.

Conclusions

We developed a tumor vaccine delivery system and presented a promising personalized tumor vaccine-based therapeutic regimen in which a tumor vaccine delivery system is combined with an aPD-L1 or PI3Kγ inhibitor to improve tumor immunotherapy outcomes.

Association Between Occupational Exposure to Formaldehyde and Cognitive Impairment

OBJECTIVE

To our knowledge, no study has investigated the effect of exposure to formaldehyde on cognition in the general population. Our objective was to examine the association between occupational exposure to formaldehyde and cognitive impairment in middle-aged and young- old adults (≥45 years).

METHODS

In the French CONSTANCES cohort, cognitive function was assessed with a standardized battery of seven cognitive tests to evaluate global cognitive function, episodic verbal memory, language abilities and executive functions (e.g., Digit Symbol Substitution Test, DSST). A global cognitive score was created using principal component analysis. Cognitive impairment was assessed in reference to norms of neuropsychological battery according to age, sex and education. Lifetime exposure to formaldehyde was assessed using a French job-exposure matrix created in the framework of the Matgéné project. After performing multiple imputation, separate modified Poisson regression models were used to evaluate the association between cognitive impairment (<25^th percentile) and formaldehyde exposure (exposed/never exposed), exposure duration, cumulative exposure index (CEI), and combination of CEI and time of last exposure.

RESULTS

Among 75 322 participants (median age: 57.5 years, women: 53%), 8% were exposed to formaldehyde during their professional life. These participants were at higher risk of global cognitive impairment (for global cognitive score: adjusted relative risk, aRR, 1.17, 95% confidence interval, CI: 1.11-1.23), after adjusting for confounders (age, sex, education, income, solvent exposure, Effort-Reward Imbalance, night-shift, repetitive, and noisy work). They were at higher risk of cognitive impairment for all cognitive domains explored. Longer exposure duration and high CEI were associated with cognitive impairment, with a dose-effect relationship for exposure duration. Recent exposure was associated with impairment in all cognitive domains. Time did not fully attenuate formaldehyde-associated cognitive deficits especially in highly exposed individuals (for DSST: high past exposure aRR 1.23, 95%CI: 1.11-1.36; high recent exposure: aRR 1.24, 95%CI: 1.13-1.35).

CONCLUSION

Our findings highlight the long-term detrimental effect of formaldehyde exposure on cognitive health in a relatively young population.

Implantable Biosupercapacitor Inspired by the Cellular Redox System

The carbon nanotube (CNT) yarn supercapacitor has high potential for in vivo energy storage because it can be used in aqueous environments and stitched to inner parts of the body, such as blood vessels. The biocompatibility issue for frequently used pseudocapacitive materials, such as metal oxides, is controversial in the human body. Here, we report an implantable CNT yarn supercapacitor inspired by the cellular redox system. In all living cells, nicotinamide adenine dinucleotide (NAD) is a key redox biomolecule responsible for cellular energy transduction to produce adenosine triphosphate (ATP). Based on this redox system, CNT yarn electrodes were fabricated by inserting a twist in CNT sheets with electrochemically deposited NAD and benzoquinone for redox shuttling. Consequently, the NAD/BQ/CNT yarn electrodes exhibited the maximum area capacitance (55.73 mF cm^-2 ) under physiological conditions, such as phosphate-buffered saline and serum. In addition, the yarn electrodes showed a negligible loss of capacitance after 10 000 repeated charge/discharge cycles and deformation tests (bending/knotting). More importantly, NAD/BQ/CNT yarn electrodes implanted into the abdominal cavity of a rat's skin exhibited the stable in vivo electrical performance of a supercapacitor. Therefore, these findings demonstrate a redox biomolecule-applied platform for implantable energy storage devices.

3D DNA nanonet structure coupled with target-catalyzed hairpin assembly for dual-signal synergistically amplified electrochemical sensing of circulating microRNA

DNA nanomaterials are reliable and powerful tools in the development of a variety of biosensors owing to their notable self-assembly ability and precise recognition capability. Here, we propose a DNA nanomaterial-based system for the dual-amplified electrochemical sensing of circulating microRNAs by a coupled cascade of catalyzed hairpin assembly (CHA) and three-dimensional (3D) DNA nanonet structure. In the target-assisted CHA process, the stable hairpin structures H1 and H2 act as probes for the recognition and recycling of circulating microRNAs, leading to the formation of abundant H1-H2 duplexes with tails. Subsequently, a 3D DNA nanonet structure was introduced, which was assembled using three DNA strands constructed X-DNA monomers as the building blocks, and hybridized to the tails of H1-H2 duplexes. The successful integration of target-assisted CHA and 3D DNA nanonet structure induced the second signal amplification. The designed biosensor performed under optimized experimental conditions, and exposed admirable analytical performance for the detection of circulating miR-21, with a wide linear range from 10 fM to 1 nM, high sensitivity of limit of detection (LOD) of 3.6083 fM, good specificity in the face of single nucleotides and other microRNAs, satisfactory stability and reproducibility for practical analysis. Furthermore, the clinical applicability for circulating miR-21 detection was verified in human serum samples without additional treatment. We hope that this elaborated biosensor will provide new opportunities for bioassays based on DNA nanomaterials.

Elevation of inflammatory S100A8/S100A9 complexes in intracranial aneurysms

BACKGROUND

Inflammation-related factors might give further insight into the pathophysiology of vessel wall inflammation and intracranial aneurysm (IA) rupture. One of these factors is the protein complex S100A8/A9, which is released by neutrophils, monocytes, and activated macrophages and is known for its role in cardiovascular disease.

OBJECTIVE

To determine if venous S100A8/A9 levels in patients with a ruptured IA (rIA) or unruptured IA (uIA) are elevated compared with a control group. Second, to assess differences between venous and intra-aneurysmal S100A8/A9 levels of rIA and uIA patients.

METHODS

A prospective case study was performed between June 2016 and May 2017 in patients harboring a ruptured or unruptured saccular IA. Primary outcome measures were individual S100A8/A9 serum concentrations as measured in venous and intra-aneurysmal blood samples during endovascular treatment. Venous serum S100A8/A9 concentrations from a healthy control group served as a reference.

RESULTS

We included 16 patients with either a rIA or uIA and 47 healthy controls. Venous S100A8/A9 concentrations were higher in aneurysm patients (rIA and uIA) than those of healthy controls (P≤0.001). S100A8/A9 concentrations were higher in intra-aneurysmal samples than in venous samples of rIA patients (P=0.011). This difference was not found in uIA patients (P=0.054). Intra-aneurysmal S100A8/A9 levels were higher in rIAs than in uIAs (P=0.04).

CONCLUSIONS

Venous S100A8/A9 levels are elevated in patients with both rIAs and uIAs compared with healthy controls and likely represents aneurysm wall inflammation. S100A8/A9 causes macrophage-induced inflammation and degeneration of the vessel wall which might explain higher intra-aneurysmal S100A8/A9 levels found in rIAs than in uIAs.

Tailoring DNA Self-assembly to Build Hydrogels

DNA hydrogels are crosslinked polymeric networks in which DNA is used as the backbone or the crosslinker. These hydrogels are novel biofunctional materials that possess the biological character of DNA and the framed structure of hydrogels. Compared with other kinds of hydrogels, DNA hydrogels exhibit not only high mechanical strength and controllable morphologies but also good recognition ability, designable responsiveness, and programmability. The DNA used in this type of hydrogel acts as a building block for self-assembly or as a responsive element due to its sequence recognition ability and switchable structural transitions, respectively. In this review, we describe recent developments in the field of DNA hydrogels and discuss the role played by DNA in these hydrogels. Various synthetic strategies for and a range of applications of DNA hydrogels are detailed.

MRI brain lesions in asymptomatic boys with X-linked adrenoleukodystrophy

OBJECTIVE

To describe the brain MRI findings in asymptomatic patients with childhood cerebral adrenoleukodystrophy (CCALD).

METHODS

We retrospectively reviewed a series of biochemically or genetically confirmed cases of adrenoleukodystrophy followed at our institution between 2001 and 2015. We identified and analyzed 219 brain MRIs from 47 asymptomatic boys (median age 6.0 years). Patient age, MRI scan, and brain lesion characteristics (e.g., contrast enhancement, volume, and Loes score) were recorded. The rate of lesion growth was estimated using a linear mixed effect model.

RESULTS

Sixty percent of patients (28/47) showed brain lesions (median Loes score of 3.0 points; range 0.5-11). Seventy-nine percent of patients with CCALD (22/28) had contrast enhancement on first lesional or subsequent MRI. Lesion progression (Loes increase of ≥0.5 point) was seen in 50% of patients (14/28). The rate of lesion growth (mL/mo) was faster in younger patients (r = -0.745; p < 0.0001). Older patients (median age 14.4 y/o) tended to undergo spontaneous arrest of disease. Early lesions grew 46× faster when still limited to the splenium, genu of the corpus callosum, or the brainstem (p = 0.001).

CONCLUSION

We provide a description of CCALD lesion development in a cohort of asymptomatic boys. Understanding the early stages of CCALD is crucial to optimize treatments for children diagnosed by newborn screening.

The Hippocampus and Social Impairment in Psychiatric Disorders

Social deficits, such as poor social skills (i.e., the inability to engage in appropriate and effective social interactions) and social withdrawal, are prevalent across psychiatric disorders and often co-occur with hippocampal structural and functional abnormalities. The centrality of both social and hippocampal dysfunction in psychiatric research prompts the question: Are they linked? The social cognitive map framework provides a clue: The hippocampus tracks social information in the physical environment, maps others along social dimensions, and supports social memory and decision-making. Hippocampal dysfunction might disrupt social map representation and contribute to commonly seen social behavioral symptoms. This review summarizes evidence for the role of the hippocampus in social cognitive mapping, followed by evidence that hippocampal dysfunction and social dysfunction co-occur in psychiatric disorders. We argue that the co-occurrence of hippocampal and social impairment may be related via hippocampal social cognitive mapping.

Flexibility defines structure in crystals of amphiphilic DNA nanostars

DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and bond directionality have been recognised as key design features for DNA motifs to sustain long-range order in 3D, but the practical challenges associated with prescribing building-block geometry with sufficient accuracy have limited the variety of available designs. We have recently introduced a novel platform for the one-pot preparation of crystalline DNA frameworks supported by a combination of Watson-Crick base pairing and hydrophobic forces (Brady et al 2017 Nano Lett. 17 3276-81). Here we use small angle x-ray scattering and coarse-grained molecular simulations to demonstrate that, as opposed to available all-DNA approaches, amphiphilic motifs do not rely on structural rigidity to support long-range order. Instead, the flexibility of amphiphilic DNA building-blocks is a crucial feature for successful crystallisation.

Fabrication of Flexible, Fully Organic, Degradable Energy Storage Devices Using Silk Proteins

Flexible and thin-film devices are of great interest in epidermal and implantable bioelectronics. The integration of energy storage and delivery devices such as supercapacitors (SCs) with properties such as flexibility, miniaturization, biocompatibility, and degradability are sought for such systems. Reducing e-waste and using sustainable materials and processes are additional desirable qualities. Herein, a silk protein-based biocompatible and degradable thin-film microSC (μSC) is reported. A protein carrier with the conducting polymer poly(3,4-ethylenedioxythiophene) polystyrene sulfonate and reduced graphene oxide dopant is used as a photopatternable biocomposite ink. Active electrodes are fabricated using photolithography under benign conditions, using only water as the solvent. These electrodes are printed on flexible protein sheets to form degradable, organic devices with a benign agarose-NaCl gel electrolyte. High capacitance, power density, cycling stability over 500 cycles, and the ability to power a light-emitting diode are shown. The device is flexible, can sustain cyclic mechanical stresses over 450 cycles, and retain capacitive properties over several days in liquid. Significantly, the μSCs are cytocompatible and completely degraded over the period of ∼1 month. By precise control of the device configuration, these silk protein-based, all-polymer organic devices can be designed to be tunably transient and provide viable alternatives for powering flexible and implantable bioelectronics.

Impaired striatal dopamine release in homozygous Vps35 D620N knock-in mice

Point mutations in the vacuolar protein sorting 35 gene (VPS35) have been associated with an autosomal dominant form of late-onset Parkinson disease (PARK17), but there has been considerable debate over whether it is caused by a loss- or gain-of-function mechanism and over the intracellular target site of neurotoxicity. To investigate the pathogenesis of PARK17 in vivo, we generated Vps35 D620N knock-in (KI) mice, expressing the homologous mutant protein with endogenous patterns of expression, simultaneously with Vps35 deletion 1 (Del1) mice, which carry 1bp deletion in the exon15 of Vps35, by CRISPR/Cas9-mediated genome engineering. Neither homozygous nor heterozygous Vps35 D620N KI mice suffered from premature death or developed clear neurodegeneration up to 70 weeks of age. Vps35 Del1 allele appeared to be a null or at least severely hypomorphic allele and homozygous Vps35 Del1 showed early embryonic lethality. Heterozygous crossings between Del1 and D620N knock-in mice revealed that the D620N/Del1 compound heterozygous mice, but not heterozygous Del1 mice, suffered from survival disadvantage. In vivo microdialysis showed that DA release evoked by 120 mM potassium chloride was significantly reduced in the caudate putamen of adult homozygous Vps35 D620N KI mice. Taken together, these results suggest that Vps35 D620N allele is a partial-loss-of-function allele and that such a genetic predisposition and age-related alterations in the nigrostriatal dopamine system cooperatively influence the pathogenesis of PARK17.

Macroscopic assembly of oppositely charged polyelectrolyte hydrogels

Stimulus-responsive hydrogels are assembled into soft devices that transform their shape upon external stimuli.

Ultrathin Graphene-Protein Supercapacitors for Miniaturized Bioelectronics

Nearly all implantable bioelectronics are powered by bulky batteries which limit device miniaturization and lifespan. Moreover, batteries contain toxic materials and electrolytes that can be dangerous if leakage occurs. Herein, an approach to fabricate implantable protein-based bioelectrochemical capacitors (bECs) employing new nanocomposite heterostructures in which 2D reduced graphene oxide sheets are interlayered with chemically modified mammalian proteins, while utilizing biological fluids as electrolytes is described. This protein-modified reduced graphene oxide nanocomposite material shows no toxicity to mouse embryo fibroblasts and COS-7 cell cultures at a high concentration of 1600 μg mL^-1 which is 160 times higher than those used in bECs, unlike the unmodified graphene oxide which caused toxic cell damage even at low doses of 10 μg mL^-1. The bEC devices are 1 μm thick, fully flexible, and have high energy density comparable to that of lithium thin film batteries. COS-7 cell culture is not affected by long-term exposure to encapsulated bECs over 4 d of continuous charge/discharge cycles. These bECs are unique, protein-based devices, use serum as electrolyte, and have the potential to power a new generation of long-life, miniaturized implantable devices.

Investigation into Pseudo-Capacitance Behavior of Glycoside-Containing Hydrogels

Electrochemical pseudocapacitors are an attractive choice for energy storage applications because they offer higher energy densities than electrostatic or electric double layer capacitors. They also offer higher power densities in shorter durations of time, as compared to batteries. Recent efforts on pseudocapacitors include biocompatible hydrogel electrolytes and transition metal electrodes for implantable energy storage applications. Pseudocapacitive behavior in these devices has been attributed to the redox reactions that occur within the electric double layer, which is formed at the electrode-electrolyte interface. In the present study, we describe a detailed investigation on redox reactions responsible for pseudocapacitive behavior in glycoside-containing hydrogel formulations. Pseudocapacitive behavior was compared among various combinations of biocompatible hydrogel electrolytes, using carbon tape electrodes and transition metal electrodes based on fluorine-doped tin oxide. The hydrogels demonstrated a pseudocapacitive response only in the presence of transition metal electrodes but not in the presence of carbon electrodes. Hydrogels containing amine moieties showed greater energy storage than gels based purely on hydroxyl functional groups. Furthermore, energy storage increased with greater amine content in these hydrogels. We claim that the redox reactions in hydrogels are largely based on Lewis acid-base interactions, facilitated by amine and hydroxyl side groups along the electrolyte chain backbones, as well as hydroxylation of electrode surfaces. Water plays an important role in these reactions, not only in terms of providing ionic radicals but also in assisting ion transport. This understanding of redox reactions will help determine the choice of transition metal electrodes, Lewis acid-base pairs in electrolytes, and medium for ionic transport in future biocompatible pseudocapacitors.

RADIATION DOSE MEASUREMENTS FOR HIGH-INTENSITY LASER INTERACTIONS WITH SOLID TARGETS AT SLAC

A systematic study of photon and neutron radiation doses generated in high-intensity laser-solid interactions is underway at SLAC National Accelerator Laboratory. These laser-solid experiments are being performed using a 25 TW (up to 1 J in 40 fs) femtosecond pulsed Ti:sapphire laser at the Linac Coherent Light Source's (LCLS) Matter in Extreme Conditions (MEC) facility. Radiation measurements were performed with passive and active detectors deployed at various locations inside and outside the target chamber. Results from radiation dose measurements for laser-solid experiments at SLAC MEC in 2014 with peak intensity between 10¹⁸ and 7.1 × 10¹⁹ W cm^-2 are presented.

Finding optimal interaction interface alignments between biological complexes

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a ‘blackbox preprocessing’ to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory.

Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein–DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the ‘blackbox preprocessing’). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein–DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein–protein complex and a protein–RNA complex, which is biologically known as a protein–RNA mimicry case.

Availability and implementation: The PROSTA-inter web-server is publicly available at http://www.cbrc.kaust.edu.sa/prosta/.

Contact:xin.gao@kaust.edu.sa

A Smart Colorful Supercapacitor with One Dimensional Photonic Crystals

To meet the pressing demands for portable and flexible equipment in contemporary society, developing flexible, lightweight, and sustainable supercapacitor systems with large power densities, long cycle life, and ease of strongly required. However, estimating the state-of-charge of existing supercapacitors is difficult, and thus their service life is limited. In this study, we fabricate a flexible color indicative supercapacitor device with mesoporous polyaniline (mPANI)/Poly(N-Isopropyl acrylamide-Graphene Oxide-Acrylic Acid) (P(NiPPAm-GO-AA)) one dimensional photonic crystals (1DPCs) as the electrode material through a low-cost, eco-friendly, and scalable fabrication process. We found that the state-of-charge could be monitored by the structural color oscillation due to the change in the photonic band gap position of the 1DPCs. The flexible 1DPCs supercapacitor is thin at 3 mm and exhibits good specific capacitance of 22.6 F g⁻¹ with retention of 91.1% after 3,000 cycles. This study shows the application of the 1DPCs supercapacitor as a visual ultrathin power source. The technology may find many applications in future wearable electronics.

A top-down approach for fabricating free-standing bio-carbon supercapacitor electrodes with a hierarchical structure

Biomass has delicate hierarchical structures, which inspired us to develop a cost-effective route to prepare electrode materials with rational nanostructures for use in high-performance storage devices. Here, we demonstrate a novel top-down approach for fabricating bio-carbon materials with stable structures and excellent diffusion pathways; this approach is based on carbonization with controlled chemical activation. The developed free-standing bio-carbon electrode exhibits a high specific capacitance of 204 F g⁻¹ at 1 A g⁻¹; good rate capability, as indicated by the residual initial capacitance of 85.5% at 10 A g⁻¹; and a long cycle life. These performance characteristics are attributed to the outstanding hierarchical structures of the electrode material. Appropriate carbonization conditions enable the bio-carbon materials to inherit the inherent hierarchical texture of the original biomass, thereby facilitating effective channels for fast ion transfer. The macropores and mesopores that result from chemical activation significantly increase the specific surface area and also play the role of temporary ion-buffering reservoirs, further shortening the ionic diffusion distance.

Capacitive Energy Storage: Current and Future Challenges

Capacitive energy storage devices are receiving increasing experimental and theoretical attention due to their enormous potential for energy applications. Current research in this field is focused on the improvement of both the energy and the power density of supercapacitors by optimizing the nanostructure of porous electrodes and the chemical structure/composition of the electrolytes. However, the understanding of the underlying correlations and the mechanisms of electric double layer formation near charged surfaces and inside nanoporous electrodes is complicated by the complex interplay of several molecular scale phenomena. This Perspective presents several aspects regarding the experimental and theoretical research in the field, discusses the current atomistic and molecular scale understanding of the mechanisms of energy and charge storage, and provides a brief outlook to the future developments and applications of these devices.

Band edge engineering of TiO2@DNA nanohybrids and implications for capacitive energy storage devices

Novel mesoporous TiO2@DNA nanohybrid electrodes, combining covalently encoded DNA with mesoporous TiO2 microbeads using dopamine as a linker, were prepared and characterised for application in supercapacitors. Detailed information about donor density, charge transfer resistance and chemical capacitance, which have an important role in the performance of an electrochemical device, were studied by electrochemical methods. The results indicated the improvement of electrochemical performance of the TiO2 nanohybrid electrode by DNA surface functionalisation. A supercapacitor was constructed from TiO2@DNA nanohybrids with PBS as the electrolyte. From the supercapacitor experiment, it was found that the addition of DNA played an important role in improving the specific capacitance (Cs) of the TiO2 supercapacitor. The highest Cs value of 8 F g(-1) was observed for TiO2@DNA nanohybrids. The nanohybrid electrodes were shown to be stable over long-term cycling, retaining 95% of their initial specific capacitance after 1500 cycles.

Transcriptome dynamics of the microRNA inhibition response

We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line—the first such dynamic study of the microRNA inhibition response—revealing both general and specific aspects of the physiological response. We show miR-9 inhibition inducing a multiphasic transcriptome response, with a direct target perturbation before 4 h, earlier than previously reported, amplified by a downstream peak at ∼32 h consistent with an indirect response due to secondary coherent regulation. Predictive modelling indicates a major role for miR-9 in post-transcriptional control of RNA processing and RNA binding protein regulation. Cluster analysis identifies multiple co-regulated gene regulatory modules. Functionally, we observe a shift over time from mRNA processing at early time points to translation at later time points. We validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies.

DNA-Assisted Solubilization of Carbon Nanotubes and Construction of DNA-MWCNT Cross-Linked Hybrid Hydrogels

A simple method for preparation of DNA-carbon nanotubes hybrid hydrogel based on a two-step procedure including: (i) solubilization of multi-walled carbon nanotubes (MWCNT) in aqueous solution of DNA, and (ii) chemical cross-linking between solubilized MWCNT via adsorbed DNA and free DNA by ethylene glycol diglycidyl ether is reported. We show that there exists a critical concentration of MWCNT below which a homogeneous dispersion of MWCNT in hybrid hydrogel can be achieved, while at higher concentrations of MWCNT the aggregation of MWCNT inside hydrogel occurs. The strengthening effect of carbon nanotube in the process of hydrogel shrinking in solutions with high salt concentration was demonstrated and significant passivation of MWCNT adsorption properties towards low-molecular-weight aromatic binders due to DNA adsorption on MWCNT surface was revealed.

Light-responsible DNA hydrogel–gold nanoparticle assembly for synergistic cancer therapy

A DNA hydrogel based delivery vehicle that combines assembled gold nanoparticles and Doxorubicins showed light-triggered and synergistic combination cancer therapy at the in vitro and in vivo levels.

DNA materials: bridging nanotechnology and biotechnology

CONSPECTUS: In recent decades, DNA has taken on an assortment of diverse roles, not only as the central genetic molecule in biological systems but also as a generic material for nanoscale engineering. DNA possesses many exceptional properties, including its biological function, biocompatibility, molecular recognition ability, and nanoscale controllability. Taking advantage of these unique attributes, a variety of DNA materials have been created with properties derived both from the biological functions and from the structural characteristics of DNA molecules. These novel DNA materials provide a natural bridge between nanotechnology and biotechnology, leading to far-ranging real-world applications. In this Account, we describe our work on the design and construction of DNA materials. Based on the role of DNA in the construction, we categorize DNA materials into two classes: substrate and linker. As a substrate, DNA interfaces with enzymes in biochemical reactions, making use of molecular biology's "enzymatic toolkit". For example, employing DNA as a substrate, we utilized enzymatic ligation to prepare the first bulk hydrogel made entirely of DNA. Using this DNA hydrogel as a structural scaffold, we created a protein-producing DNA hydrogel via linking plasmid DNA onto the hydrogel matrix through enzymatic ligation. Furthermore, to fully make use of the advantages of both DNA materials and polymerase chain reaction (PCR), we prepared thermostable branched DNA that could remain intact even under denaturing conditions, allowing for their use as modular primers for PCR. Moreover, via enzymatic polymerization, we have recently constructed a physical DNA hydrogel with unique internal structure and mechanical properties. As a linker, we have used DNA to interface with other functional moieties, including gold nanoparticles, clay minerals, proteins, and lipids, allowing for hybrid materials with unique properties for desired applications. For example, we recently designed a DNA-protein conjugate as a universal adapter for protein detection. We further demonstrate a diverse assortment of applications for these DNA materials including diagnostics, protein production, controlled drug release systems, the exploration of life evolution, and plasmonics. Although DNA has shown great potential as both substrate and linker in the construction of DNA materials, it is still in the initial stages of becoming a well-established and widely used material. Important challenges include the ease of design and fabrication, scaling-up, and minimizing cost. We envision that DNA materials will continue to bridge the gap between nanotechnology and biotechnology and will ultimately be employed for many real-world applications.

Acquisition and structuring of midgut bacterial communities in gypsy moth (Lepidoptera: Erebidae) larvae

Insects are associated with a diversity of bacteria that colonize their midguts. The extent to which these communities reflect maternal transmission, environmental acquisition, and subsequent structuring by the extreme conditions within the insect gut are poorly understood in many species. We used gypsy moth (Lymantria dispar L.) as a model to investigate interactions between egg mass and environmental sources of bacteria on larval midgut communities. Egg masses were collected from several wild and laboratory populations, and the effects of diet, initial egg mass community, and internal host environment were evaluated using 454 16S-rRNA gene pyrosequencing. Wild populations were highly diverse, while laboratory-maintained egg masses were associated with few operational taxonomic units. As larvae developed, their midgut bacterial communities became more similar to each other and the consumed diet despite initial differences in egg mass-associated bacteria. Subsequent experiments revealed that while midgut membership was more similar to bacteria associated with diet than with egg mass-associated bacteria, we were unable to detect distinct, persistent differences attributable to specific host plants. The differences between foliar communities and midgut communities of larvae that ingested them were owing to relative changes in populations of several bacteria phylotypes. We conclude that gypsy moth has a relatively characteristic midgut bacterial community that is reflective of, but ultimately distinct from, its foliar diet. This work demonstrates that environmental acquisition of diverse microbes can lead to similar midgut bacterial assemblages, underscoring the importance of host physiological environment in structuring bacterial communities.

DNA hydrogel as a template for synthesis of ultrasmall gold nanoparticles for catalytic applications

DNA cross-linked hydrogel was used as a matrix for synthesis of gold nanoparticles. DNA possesses a strong affinity to transition metals such as gold, which allows for the concentration of Au precursor inside a hydrogel. Further reduction of HAuCl4 inside DNA hydrogel yields well dispersed, non-aggregated spherical Au nanoparticles of 2-3 nm size. The average size of these Au nanoparticles synthesized in DNA hydrogel is the smallest reported so far for in-gel metal nanoparticles synthesis. DNA hybrid hydrogel containing gold nanoparticles showed high catalytic activity in the hydrogenation reaction of nitrophenol to aminophenol. The proposed soft hybrid material is promising as environmentally friendly and sustainable material for catalytic applications.

Robust analysis of synthetic label-free DNA junctions in solution by X-ray scattering and molecular simulation

Structural analysis of branched DNA molecules (BDM) is important as model systems for DNA junctions and also as building units for DNA assembly. Although there have been efforts to study the structures of BDM, label-free solution structures have not been well determined yet. Here, we used a combination of synchrotron-based experimental tools and computational simulation to study the global structures of label-free BDM in solution. Overall structures of 3-arm and 4-arm BDM were revealed as an asymmetric T(or Y)-shape and a distorted X-shape, respectively. The internal structures of the DNA double helix were shown to have a canonical B-form for both the BDM. We also reconstructed the thermal denaturation process of BDM by determining the transient global structures over a wide range of temperatures. The proposed high-resolution structures of BDM are expected to provide fundamental information for studies of the biological function of junction DNAs and DNA assembly.