Microbially Induced Calcium Carbonate Precipitation by Sporosarcina pasteurii: a Case Study in Optimizing Biological CaCO3 Precipitation.

Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO2 production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on S. pasteurii as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO3 precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on S. pasteurii. Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca2+) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.

Bio-Optics and Bio-Inspired Optical Materials.

Through the use of the limited materials palette, optimally designed micro- and nanostructures, and tightly regulated processes, nature demonstrates exquisite control of light-matter interactions at various length scales. In fact, control of light-matter interactions is an important element in the evolutionary arms race and has led to highly engineered optical materials and systems. In this review, we present a detailed summary of various optical effects found in nature with a particular emphasis on the materials and optical design aspects responsible for their optical functionality. Using several representative examples, we discuss various optical phenomena, including absorption and transparency, diffraction, interference, reflection and antireflection, scattering, light harvesting, wave guiding and lensing, camouflage, and bioluminescence, that are responsible for the unique optical properties of materials and structures found in nature and biology. Great strides in understanding the design principles adapted by nature have led to a tremendous progress in realizing biomimetic and bioinspired optical materials and photonic devices. We discuss the various micro- and nanofabrication techniques that have been employed for realizing advanced biomimetic optical structures.

Plasmonic Biofoam: A Versatile Optically Active Material.

Owing to their ability to confine and manipulate light at the nanoscale, plasmonic nanostructures are highly attractive for a broad range of applications. While tremendous progress has been made in the synthesis of size- and shape-controlled plasmonic nanostructures, their integration with other materials and application in solid-state is primarily through their assembly on rigid two-dimensional (2D) substrates, which limits the plasmonically active space to a few nanometers above the substrate. In this work, we demonstrate a simple method to create plasmonically active three-dimensional biofoams by integrating plasmonic nanostructures with highly porous biomaterial aerogels. We demonstrate that plasmonic biofoam is a versatile optically active platform that can be harnessed for numerous applications including (i) ultrasensitive chemical detection using surface-enhanced Raman scattering; (ii) highly efficient energy harvesting and steam generation through plasmonic photothermal heating; and (iii) optical control of enzymatic activity by triggered release of biomolecules encapsulated within the aerogel. Our results demonstrate that 3D plasmonic biofoam exhibits significantly higher sensing, photothermal, and loading efficiency compared to conventional 2D counterparts. The design principles and processing methodology of plasmonic aerogels demonstrated here can be broadly applied in the fabrication of other functional foams.

Effects of Balsamodendron mukul Gum Resin Extract on Articular Cartilage in Papain-induced Osteoarthritis.

Context • Osteoarthritis (OA) is one of the most prevalent chronic diseases of the musculoskeleton, causing functional disability among older adults. Management of OA includes conventional pharmacological treatments consisting primarily of nonsteroidal anti-inflammatory drugs (NSAIDs), acetaminophen, physiotherapy, and surgical procedures. The medications are not ideal therapeutic agents; NSAIDs in particular can cause serious side effects. Objective • The study was conducted to investigate the effects of Balsamodendron mukul (BDM) gum resin extract on cartilage damage and microstructural changes in the subchondral bone of rats with papain-induced, osteoarthritic knee joints. Design • The authors designed a parallel randomized, controlled study to examine the effects of 3 concentrations of BDM on OA in a murine model. Setting • The present study was undertaken at the research laboratory, Faculty of Biological Engineering, Shobhit University (Modipuram, Meerut, India). Intervention • OA was induced by intra-articular injections of 0.2 mL of 4% papain solution and 0.1 mL of 0.03 M cysteine through the patellar ligament using a 26-gauge, 1.27-cm needle. The rats in the sham group received same volume of isotonic sodium chloride solution. The rats were divided into 6 groups : (1) control group-fresh rats, with ages and genders similar to those of the other groups but with no induction of OA and no treatments; (2) sham group-rats receiving a sham induction of OA using an intra-articular injection of saline of the same volume as the papain given to all OA rats but no treatments; (3) OA group-rats induced with OA but receiving no treatments; (4) OA + BDM (10%) group-rats induced with OA that received a 10% dose of BDM; (5) OA + BDM (20%) group-rats induced with OA that received a 20% dose of BDM; and (6) OA + BDM (40%) group-rats induced with OA that received a 40% dose of BDM. Rats in the treatment groups were fed their respective doses of BDM extract for 30 d. Outcome Measures • The articular cartilages from the knee joints and epiphyseal bones of the femur and tibia were extracted from the right- and left-side limbs to perform the biochemical, microarchitectural, and histological analyses. Results • The total protein and collagen content of the articular cartilage of the knees were significantly higher in all treated groups when compared with the OA group of rats. The histological analysis revealed a thicker cartilage and a higher trabecular density of the subchondral bone (epiphyseal bone) in BDM-treated rats. Conclusions • The oral dose of BDM gum resin extract was shown to relieve OA pain, regenerate the cartilaginous matrix, and increase the subchondral bone components. On the basis of the findings, the research team suggests that the BDM gum resin extract may be used for therapeutic interventions for reversal of OA and reduction in its related inflammatory pain.

3D Printed Programmable Release Capsules.

The development of methods for achieving precise spatiotemporal control over chemical and biomolecular gradients could enable significant advances in areas such as synthetic tissue engineering, biotic-abiotic interfaces, and bionanotechnology. Living organisms guide tissue development through highly orchestrated gradients of biomolecules that direct cell growth, migration, and differentiation. While numerous methods have been developed to manipulate and implement biomolecular gradients, integrating gradients into multiplexed, three-dimensional (3D) matrices remains a critical challenge. Here we present a method to 3D print stimuli-responsive core/shell capsules for programmable release of multiplexed gradients within hydrogel matrices. These capsules are composed of an aqueous core, which can be formulated to maintain the activity of payload biomolecules, and a poly(lactic-co-glycolic) acid (PLGA, an FDA approved polymer) shell. Importantly, the shell can be loaded with plasmonic gold nanorods (AuNRs), which permits selective rupturing of the capsule when irradiated with a laser wavelength specifically determined by the lengths of the nanorods. This precise control over space, time, and selectivity allows for the ability to pattern 2D and 3D multiplexed arrays of enzyme-loaded capsules along with tunable laser-triggered rupture and release of active enzymes into a hydrogel ambient. The advantages of this 3D printing-based method include (1) highly monodisperse capsules, (2) efficient encapsulation of biomolecular payloads, (3) precise spatial patterning of capsule arrays, (4) "on the fly" programmable reconfiguration of gradients, and (5) versatility for incorporation in hierarchical architectures. Indeed, 3D printing of programmable release capsules may represent a powerful new tool to enable spatiotemporal control over biomolecular gradients.

3D Printed Anatomical Nerve Regeneration Pathways.

An imaging-coupled 3D printing methodology for the design, optimization, and fabrication of a customized nerve repair technology for complex injuries is presented. The custom scaffolds are deterministically fabricated via a microextrusion printing principle which enables the simultaneous incorporation of anatomical geometries, biomimetic physical cues, and spatially controlled biochemical gradients in a one-pot 3D manufacturing approach.

3D printed quantum dot light-emitting diodes.

Developing the ability to 3D print various classes of materials possessing distinct properties could enable the freeform generation of active electronics in unique functional, interwoven architectures. Achieving seamless integration of diverse materials with 3D printing is a significant challenge that requires overcoming discrepancies in material properties in addition to ensuring that all the materials are compatible with the 3D printing process. To date, 3D printing has been limited to specific plastics, passive conductors, and a few biological materials. Here, we show that diverse classes of materials can be 3D printed and fully integrated into device components with active properties. Specifically, we demonstrate the seamless interweaving of five different materials, including (1) emissive semiconducting inorganic nanoparticles, (2) an elastomeric matrix, (3) organic polymers as charge transport layers, (4) solid and liquid metal leads, and (5) a UV-adhesive transparent substrate layer. As a proof of concept for demonstrating the integrated functionality of these materials, we 3D printed quantum dot-based light-emitting diodes (QD-LEDs) that exhibit pure and tunable color emission properties. By further incorporating the 3D scanning of surface topologies, we demonstrate the ability to conformally print devices onto curvilinear surfaces, such as contact lenses. Finally, we show that novel architectures that are not easily accessed using standard microfabrication techniques can be constructed, by 3D printing a 2 × 2 × 2 cube of encapsulated LEDs, in which every component of the cube and electronics are 3D printed. Overall, these results suggest that 3D printing is more versatile than has been demonstrated to date and is capable of integrating many distinct classes of materials.

A novel association of ocular neuromyotonia with brainstem demyelination: two case reports.

Ocular neuromyotonia (ONM) is a rare disorder of ocular mal-alignment in which painless, transient spontaneous or gaze-induced abnormal deviation of the eye manifests as episodic diplopia. With only a few cases reported in the literature, ONM mostly follows months to years after cranial irradiation for sellar or suprasellar lesions. Here we present two patients with this rare ocular condition, secondary to brainstem demyelination, the association of which is hitherto unreported in the literature. Both patients were 15-year-old girls who presented to us with episodic forced-eye deviation with diplopia. Examination during these attacks revealed ONM involving the superior rectus and medial rectus in the first and second patient, respectively. There was clinical evidence of intrinsic brainstem involvement with downbeat nystagmus and skew deviation in one patient without any other cerebellar or long tract signs. MRI showed evidence of demyelination involving the brainstem in both, with CSF showing positive immunological markers and with positive aquaporin-4 antibody in one patient. Both patients responded remarkably to immunomodulatory therapy and are asymptomatic at follow-up. That ONM can occur with brainstem demyelination has not been reported in the literature. This association may help in explaining the pathophysiology of ONM as secondary to segmental demyelination.

A robust and facile approach to assembling mobile and highly-open unfrustrated triangular lattices from ferromagnetic nanorods.

A simple and widely applicable approach to assemble long-range two-dimensional mobile arrays of functionalized nickel nanorods with tunable and "highly open" lattice structures is presented. The magnetic assembly of uniformly oriented nanorods in triangular lattices was achieved by a phase separation of the surface confined yet mobile vertical nanorods driven by a gradient magnetic field. In contrast to known approaches, the unfrustrated lattices can be further locked in place allowing for the removal of the applied magnetic field and processing without disrupting the initial order with different symmetries precisely assembled and locked in their position on the same substrate. We suggest that the tunable assemblies of magnetic nanorods provide a versatile platform for downstream handling of open lattice arrays for eventual device integration.

Cell-Free Protein Expression in Polymer Materials.

While synthetic biology has advanced complex capabilities such as sensing and molecular synthesis in aqueous solutions, important applications may also be pursued for biological systems in solid materials. Harsh processing conditions used to produce many synthetic materials such as plastics make the incorporation of biological functionality challenging. One technology that shows promise in circumventing these issues is cell-free protein synthesis (CFPS), where core cellular functionality is reconstituted outside the cell. CFPS enables genetic functions to be implemented without the complications of membrane transport or concerns over the cellular viability or release of genetically modified organisms. Here, we demonstrate that dried CFPS reactions have remarkable tolerance to heat and organic solvent exposure during the casting processes for polymer materials. We demonstrate the utility of this observation by creating plastics that have spatially patterned genetic functionality, produce antimicrobials in situ, and perform sensing reactions. The resulting materials unlock the potential to deliver DNA-programmable biofunctionality in a ubiquitous class of synthetic materials.

Surface assembly and plasmonic properties in strongly coupled segmented gold nanorods.

An assembly strategy is reported such that segmented nanorods fabricated through template-assisted methods can be robustly transferred and tethered to a pre-functionalized substrate with excellent uniformity over large surface areas. After embedding the rods, sacrificial nickel segments were selectively etched leaving behind strongly coupled segmented gold nanorods with gaps between rods below 40 nm and as small as 2 nm. Hyper-spectral imaging is utilized to measure Rayleigh scattering spectra from individual and coupled nanorod elements in contrast to common bulk measurements. This approach discerns the effects of not only changing segment and gap size but also the presence of characteristic defects on the plasmonic coupling between closely spaced nanorods. Polarized hyper-spectral measurements are conducted to provide direct observation of the anisotropic plasmonic resonance modes in individual and coupled nanorods, which are close to those predicted by computer simulations for nanorods with ideal shapes. Some common deviations from ideal shape such as non-flat facets and asymmetric tails are demonstrated to result in the appearance of characteristic plasmon resonances, which have not been considered before. The large-scale assembly of coupled noble nanostructures with fine control over geometry and high uniformity provides means to strongly tune the scattering, absorption, and near-field plasmonic properties through the geometric arrangement of precisely controlled nanorod segments.

Genetic and epigenetic alterations in MGMT gene and correlation with concomitant chemoradiotherapy (CRT) in cervical cancer.

PURPOSE: The MGMT (O6-methylguanine-DNA methyltransferase) gene plays a crucial role in repairing DNA damage caused by alkylating agents, including those used in chemotherapy. Genetic and epigenetic alterations can influence the regulation of MGMT gene, which in turn may impact the response to concomitant chemoradiotherapy (CRT) in cervical cancer. The present study was undertaken to evaluate the correlation of such variations in MGMT gene with the treatment outcome of concomitant chemoradiotherapy (CRT) in cervical cancer. METHODS: A total of 460 study subjects (240 controls and 220 patients) were subjected to genotypic analysis of MGMT gene variants rs12917(T/C) and rs2308327(A/G) by Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR). Out of them, 48 each of controls and patients were analyzed for promoter methylation and expression by methylation-specific PCR and real-time PCR, respectively. Patients (n = 48) were followed up and evaluated for treatment (CRT) outcome. Statistical analyses were done using GraphPad (9.0) and SPSS version 18.0. RESULTS: Individuals with GG genotype, G allele of rs2308327, and haplotype 'TA' of both variants showed a significant increase in the development of cervical cancer (P ≤ 0.05). In epigenetic regulation, there was a significant hypermethylation of MGMT gene and down-regulation of their expression in patients compared to control individuals. In treatment outcome of CRT, GG genotype of rs2308327(A/G) gene variant showed better response and GG + AG was significantly associated with vital status (alive). Unmethylated MGMT gene showed better median overall survival up to 25 months significant in comparison to methylated MGMT promoter. CONCLUSION: Gene variant rs2308327(A/G) and promoter hypermethylation regulated MGMT gene can be a good prognostic for treatment response in cervical cancer patients.

Iridescent biofilms of Cellulophaga lytica are tunable platforms for scalable, ordered materials.

Nature offers many examples of materials which exhibit exceptional properties due to hierarchical assembly of their constituents. In well-studied multi-cellular systems, such as the morpho butterfly, a visible indication of having ordered submicron features is given by the display of structural color. Detailed investigations of nature's designs have yielded mechanistic insights and led to the development of biomimetic materials at laboratory scales. However, the manufacturing of hierarchical assemblies at industrial scales remains difficult. Biomanufacturing aims to leverage the autonomy of biological systems to produce materials at lower cost and with fewer carbon emissions. Earlier reports documented that some bacteria, particularly those with gliding motility, self-assemble into biofilms with polycrystalline structures and exhibit glittery, iridescent colors. The current study demonstrates the potential of using one of these bacteria, Cellulophaga lytica, as a platform for the large scale biomanufacturing of ordered materials. Specific approaches for controlling C. lytica biofilm optical, spatial and temporal properties are reported. Complementary microscopy-based studies reveal that biofilm color variations are attributed to changes in morphology induced by cellular responses to the local environment. Incorporation of C. lytica biofilms into materials is also demonstrated, thereby facilitating their handling and downstream processing, as would be needed during manufacturing processes. Finally, the utility of C. lytica as a self-printing, photonic ink is established by this study. In summary, autonomous surface assembly of C. lytica under ambient conditions and across multiple length scales circumvent challenges that currently hinder production of ordered materials in industrial settings.

Utilizing conformational changes for patterning thin films of recombinant spider silk proteins.

Recombinant spider silk proteins mimicking the properties of dragline silk proteins represent a class of materials that hold great potential for future high-performance applications. Here we explore the self-assembly behavior of a recombinantly produced spider silk protein based on the dragline silk of the Araneus diadematus , eADF4 (C16), by selectively patterning its secondary structure using capillary transfer lithography and solvent-assisted microcontact molding. Two conformational transitions were observed, influenced by initial solvent composition: α-helix/random coil conformation to a more densely packed ß-sheet conformation (by casting from 1,1,1,3,3,3-hexafluoro-propanol) and moderate initial ß-sheet content to higher ß-sheet content (casting from formic acid). Furthermore, by using the solvent-assisted microcontact molding technique, we were able to achieve a submicrometer spatial resolution and reveal fine details of morphological and mechanical changes in patterned regions and at interfaces.

Particle-Based Microrheology As a Tool for Characterizing Protein-Based Materials.

Microrheology based on video microscopy of embedded tracer particles has the potential to be used for high-throughput protein-based materials characterization. This potential is due to a number of characteristics of the techniques, including the suitability for measurement of low sample volumes, noninvasive and noncontact measurements, and the ability to set up a large number of samples for facile, sequential measurement. In addition to characterization of the bulk rheological properties of proteins in solution, for example, viscosity, microrheology can provide insight into the dynamics and self-assembly of protein-based materials as well as heterogeneities in the microenvironment being probed. Specifically, passive microrheology in the form of multiple particle tracking and differential dynamic microscopy holds promise for applications in high-throughput characterization because of the lack of user interaction required while making measurements. Herein, recent developments in the use of multiple particle tracking and differential dynamic microscopy are reviewed for protein characterization and their potential to be applied in a high-throughput, automatable setting.

Higher order genes interaction in DNA repair and cytokine genes polymorphism and risk to lung cancer in North Indians.

Context: Lung cancer pathological process involves cumulative effects exerted by gene polymorphism(s), epigenetic modifications, and alterations in DNA repair machinery. Further, DNA damage due to oxidative stress, chronic inflammation, and the interplay between genetic and environmental factors is also an etiologic milieu of this malignant disease. Aims: The present study aims to assess the prognostic value of DNA repair, cytokines, and GST gene polymorphism in lung cancer patients who had not received any neoadjuvant therapy. Materials and Methods: In this case-control study, 127 cases and 120 controls were enrolled. DNA from the blood samples of both patients and controls was used to genotype XRCC1Arg399Gln, XPDLys751Gln, and interleukin-1 (IL-1ß) genes by polymerase chain reaction (PCR)-restriction fragment length polymorphism method, whereas multiplex PCR was performed to genotype GSTT1 and GSTM1. Results: Binary logistic regression analysis showed that XRCC1Arg399Gln-mutant genotype (Gln/Gln, odds ratio [OR] = 4.6, 95% confidence interval [CI]: 2.2-9.6) and GSTT1 null (OR = 2.7, 95% CI: 1.6-4.5) were linked to cancer susceptibility. Generalized multidimensional reduction analysis of higher order gene-gene interaction using cross-validation testing (CVT) accuracy showed that GSTT1 (CVT 0.62, P = 0.001), XPD751 and IL-1ß (CVT 0.6, P = 0.001), and XRCC1399, XPD751, and interleukin-1 receptor antagonists (IL-1RN) (CVT 0.98, P = 0.001) were single-, two-, and three-factor best model predicted, respectively, for lung cancer risk. Classification and regression tree analysis results showed that terminal nodes which contain XRCC1399-mutant genotype (AA) had increased the risk to lung cancer. Conclusion: The present study demonstrated that XRCC1399 (Gln/Gln), GSTT1, and IL-1RN allele I, I/II served as the risk genotypes. These genes could serve as the biomarkers to predict lung cancer risk.

Engineering Gelation Kinetics in Living Silk Hydrogels by Differential Dynamic Microscopy Microrheology and Machine Learning.

Microbes embedded in hydrogels comprise one form of living material. Discovering formulations that balance potentially competing for mechanical and biological properties in living hydrogels-for example, gel time of the hydrogel formulation and viability of the embedded organisms-can be challenging. In this study, a pipeline is developed to automate the characterization of the gel time of hydrogel formulations. Using this pipeline, living materials comprised of enzymatically crosslinked silk and embedded E. coli-formulated from within a 4D parameter space-are engineered to gel within a pre-selected timeframe. Gelation time is estimated using a novel adaptation of microrheology analysis using differential dynamic microscopy (DDM). In order to expedite the discovery of gelation regime boundaries, Bayesian machine learning models are deployed with optimal decision-making under uncertainty. The rate of learning is observed to vary between artificial intelligence (AI)-assisted planning and human planning, with the fastest rate occurring during AI-assisted planning following a round of human planning. For a subset of formulations gelling within a targeted timeframe of 5-15 min, fluorophore production within the embedded cells is substantially similar across treatments, evidencing that gel time can be tuned independent of other material properties-at least over a finite range-while maintaining biological activity.

SERS effects in silver-decorated cylindrical nanopores.

Optimization of pore diameter, the placement of nanoparticles, and the transmission of surface-enhanced Raman scattering (SERS) substrates are found to be very critical for achieving high SERS activity in porous alumina-membrane-based substrates. SERS substrates with a pore diameter of 355 nm incorporating silver nanoparticles show very high SERS activity with enhancement factors of 10(10) .

Adenoma detection rate increases with each decade of life after 50 years of age.

BACKGROUND: The adenoma detection rate (ADR) has recently been used as a quality measure for screening colonoscopy. We hypothesize that the ADR will increase with each decade of life after 50 years of age. OBJECTIVE: The aim of this study was to define age-based goals for the ADR and advanced neoplasia to improve the quality of colonoscopy. METHODS: Using the Clinical Outcomes Research Initiative database, we identified patients who underwent screening colonoscopy between 2005 and 2006. Pathology of polyp findings was reviewed, and the ADR and the prevalence of advanced neoplasia were calculated based on age and sex. RESULTS: A total of 7756 polypectomies (44.9%) were performed on 17,275 patients between 2005 and 2006. Of these polyps, 56.3% (4363) were adenomas or more advanced lesions. The ADR was higher in men than women and increased with age. The ADR in men younger than age 50 was 24.7 (95% CI, 18.2-31.2); for those 50 to 59 years of age, it was 27.8 (95% CI, 26.5-29.1); for those 60 to 69 years of age, it was 33.6 (95% CI, 31.7-35.4); for those 70 to 79 years of age, it was 34.3 (95% CI, 31.5-37.1); and for those older than 80 years of age, it was 40.0 (95% CI, 32.9-47.1). The ADR in women younger than 50 years old was 12.6 (95% CI, 6.8-18.4); in those 50 to 59 years of age, it was 17.0 (85% CI, 15.9-18.1); for those 60 to 69 years of age, it was 22.4 (95% CI, 20.8-24.0); for those 70 to 79 years of age, it was 26.1 (95% CI, 23.7-28.5); and for those older than 80 years of age, it was 26.9 (95% CI, 21.4-32.5). LIMITATIONS: The Clinical Outcomes Research Initiative database offers access to demographic information as well as endoscopy and pathology data, but there is limited clinical information about patients in the database. CONCLUSION: The ADR, and, importantly, the rate of advanced neoplasia increased with each decade of life after the age of 50 and are higher in men than women in each decade of life.