Bioconjugation of Meldrum's acid activated furan: A detergent compatible assay for protein quantitation.

A simple yet efficient assay for the quantitation of proteins ranging from plasma proteins to purified proteins from whole cell lysate, based on the bioconjugation reaction between protein and Meldrum's acid Activated Furan (MAF) is described. This easy to use, sensitive method is based on the conjugation of amine functionalities present on the protein with MAF to form the corresponding Donor Acceptor Stenhouse Adducts (DASAs) with characteristic absorption in the visible region. The reaction is rapid as well as reproducible and shows a proportionate increase in color change over a broad range of protein concentration. The assay was found to be sensitive up to 0.125 mg/mL concentration of the protein and was compatible with most of the commonly employed detergents and isolation protocols which makes it ideal for the estimation of protein samples containing detergents. Another striking feature of this protocol is its tolerance towards other major interference contributors such as chelating agents, reducing agents, carbohydrates and protease inhibitors.

Effects of liquid cultivation on gene expression and phenotype of C. elegans.

BACKGROUND: Liquid cultures have been commonly used in space, toxicology, and pharmacology studies of Caenorhabditis elegans. However, the knowledge about transcriptomic alterations caused by liquid cultivation remains limited. Moreover, the impact of different genotypes in rapid adaptive responses to environmental changes (e.g., liquid cultivation) is often overlooked. Here, we report the transcriptomic and phenotypic responses of laboratory N2 and the wild-isolate AB1 strains after culturing P0 worms on agar plates, F1 in liquid cultures, and F2 back on agar plates. RESULTS: Significant variations were found in the gene expressions between the N2 and AB1 strains in response to liquid cultivation. The results demonstrated that 8-34% of the environmental change-induced transcriptional responses are transmitted to the subsequent generation. By categorizing the gene expressions for genotype, environment, and genotype-environment interactions, we identified that the genotype has a substantial impact on the adaptive responses. Functional analysis of the transcriptome showed correlation with phenotypical changes. For example, the N2 strain exhibited alterations in both phenotype and gene expressions for germline and cuticle in axenic liquid cultivation. We found transcript evidence to approximately 21% of the computationally predicted genes in C. elegans by exposing the worms to environmental changes. CONCLUSIONS: The presented study reveals substantial differences between N2 and AB1 strains for transcriptomic and phenotypical responses to rapid environmental changes. Our data can provide standard controls for future studies for the liquid cultivation of C. elegans and enable the discovery of condition-specific genes.

Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay.

Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll-dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30 to 60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems are limited. Here, we use total internal reflection fluorescence microscopy to show that the number of free-living microbes that produce rhodopsins increases along the salinity gradient in the Chesapeake Bay. We correlate this functional data with environmental data to show that rhodopsin abundance is positively correlated with salinity and with indicators of active heterotrophy during the day. Metagenomic and metatranscriptomic data suggest that the microbial rhodopsins in the low-salinity samples are primarily found in Actinobacteria and Bacteroidetes, while those in the high-salinity samples are associated with SAR-11 type AlphaproteobacteriaIMPORTANCE Microbial rhodopsins are common light-activated ion pumps in heterotrophs, and previous work has proposed that heterotrophic microbes use them to conserve energy when organic carbon is limiting. If this hypothesis is correct, rhodopsin-producing cells should be most abundant where nutrients are most limited. Our results indicate that in the Chesapeake Bay, rhodopsin gene abundance is correlated with salinity, and functional rhodopsin production is correlated with nitrate, bacterial production, and chlorophyll a We propose that in this environment, where carbon and nitrogen are likely not limiting, heterotrophs do not need to use rhodopsins to supplement ATP synthesis. Rather, the light-generated proton motive force in nutrient-rich environments could be used to power energy-dependent membrane-associated processes, such as active transport of organic carbon and cofactors, enabling these organisms to more efficiently utilize exudates from primary producers.

Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry.

Resolving distinct biochemical interaction states when analyzing the trajectories of diffusing proteins in live cells on an individual basis remains challenging because of the limited statistics provided by the relatively short trajectories available experimentally. Here, we introduce a novel, machine-learning based classification methodology, which we call perturbation expectation-maximization (pEM), that simultaneously analyzes a population of protein trajectories to uncover the system of diffusive behaviors which collectively result from distinct biochemical interactions. We validate the performance of pEM in silico and demonstrate that pEM is capable of uncovering the proper number of underlying diffusive states with an accurate characterization of their diffusion properties. We then apply pEM to experimental protein trajectories of Rho GTPases, an integral regulator of cytoskeletal dynamics and cellular homeostasis, in vivo via single particle tracking photo-activated localization microscopy. Remarkably, pEM uncovers 6 distinct diffusive states conserved across various Rho GTPase family members. The variability across family members in the propensities for each diffusive state reveals non-redundant roles in the activation states of RhoA and RhoC. In a resting cell, our results support a model where RhoA is constantly cycling between activation states, with an imbalance of rates favoring an inactive state. RhoC, on the other hand, remains predominantly inactive.

Detection and estimation of liquid flow through a pipe in a tissue-like object with ultrasound-assisted diffuse correlation spectroscopy.

Using coherent light interrogating a turbid object perturbed by a focused ultrasound (US) beam, we demonstrate localized measurement of dynamics in the focal region, termed the region-of-interest (ROI), from the decay of the modulation in intensity autocorrelation of light. When the ROI contains a pipe flow, the decay is shown to be sensitive to the average flow velocity from which the mean-squared displacement (MSD) of the scattering centers in the flow can be estimated. While the MSD estimated is seen to be an order of magnitude higher than that obtainable through the usual diffusing wave spectroscopy (DWS) without the US, it is seen to be more accurate as verified by the volume flow estimated from it. It is further observed that, whereas the MSD from the localized measurement grows with time as τ(α) with α≈1.65, without using the US, α is seen to be much less. Moreover, with the local measurement, this super-diffusive nature of the pipe flow is seen to persist longer, i.e., over a wider range of initial τ, than with the unassisted DWS. The reason for the super-diffusivity of flow, i.e., α<2, in the ROI is the presence of a fluctuating (thermodynamically nonequilibrium) component in the dynamics induced by the US forcing. Beyond this initial range, both methods measure MSDs that rise linearly with time, indicating that ballistic and near-ballistic photons hardly capture anything beyond the background Brownian motion.

Oral candidosis in relation to oral immunity.

Symptomatic oral infection with Candida albicans is characterized by invasion of the oral epithelium by virulent hyphae that cause tissue damage releasing the inflammatory mediators that initiate and sustain local inflammation. Candida albicans triggers pattern-recognition receptors of keratinocytes, macrophages, monocytes and dendritic cells, stimulating the production of IL-1ß, IL-6 and IL-23. These cytokines induce the differentiation of Th17 cells and the generation of IL-17- and/or IL-22-mediated antifungal protective immuno-inflammatory responses in infected mucosa. Some immune cells including NKT cells, γδ T cells and lymphoid cells that are innate to the oral mucosa have the capacity to produce large quantities of IL-17 in response to C. albicans, sufficient to mediate effective protective immunity against C. albicans. On the other hand, molecular structures of commensal C. albicans blastoconidia, although detected by pattern-recognition receptors, are avirulent, do not invade the oral epithelium, do not elicit inflammatory responses in a healthy host, but induce regulatory immune responses that maintain tissue tolerance to the commensal fungi. The type, specificity and sensitivity of the protective immune response towards C. albicans is determined by the outcome of the integrated interactions between the intracellular signalling pathways of specific combinations of activated pattern-recognition receptors (TLR2, TLR4, Dectin-1 and Dectin-2). IL-17-mediated protective immune response is essential for oral mucosal immunity to C. albicans infection.

Noma (cancrum oris) in the South African context.

Noma (cancrum oris) is a destructive necrotising disease affecting orofacial tissues predominantly of malnourished young children. It is characterised by a rapid acute onset which usually starts in the mouth, spreads intra-orally destroying soft tissue and bone and progresses to perforate the facial skin, causing disfigurement. Polybacterial anaerobic infection is critical too, but is not alone sufficient for the initiation of noma. Cofactors, first and foremost malnutrition, but also systemic viral and bacterial infections are crucial to the development of noma. A patient with necrotising stomatitis or noma must be admitted to hospital for antibiotic treatment, fluid and electrolytes as well as nutritional supplementation and general supportive treatment. The epidemiology of noma in the South African population is unknown, and the clinicopathological features are poorly characterised. Although worldwide there is no evidence that HIV infection is a strong risk factor for noma, HIV infection may play a substantial role in the pathogenesis of noma in South Africa.

Cyclic dipeptides from rhabditid entomopathogenic nematode-associated Bacillus cereus have antimicrobial activities.

The cell free culture filtrate of Bacillus cereus associated with an entomopathogenic nematode, Rhabditis (Oscheius) sp. exhibited strong antimicrobial activity. The ethyl acetate extract of the bacterial culture filtrate was purified by silica gel column chromatography to obtain four bioactive compounds. The structure and absolute stereochemistry of these compounds were determined based on extensive spectroscopic analyses (FABMS, (1)H NMR, (13)C NMR, (1)H-(1)H COSY, (1)H-(13)C HMBC) and Marfey's method. The compounds were identified as cyclic dipeptides (CDPs): cyclo(L-Pro-L-Trp), cyclo(L-Leu-L-Val), cyclo(D-Pro-D-Met), and cyclo(D-Pro-D-Phe), respectively. Compounds recorded significant antibacterial activity against all the test bacteria (Staphylococcus epidermidis, Staphylococcus aureus, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa and methicillin-resistant S. aureus) except cyclo(L-Leu-L-Val). Cyclo(L-Leu-L-Val) recorded activity only against Gram positive bacteria. Best antibacterial activity was recorded by cyclo(L-Pro-L-Trp) against S. aureus (4 µg/ml). The four compounds were active against all the five fungi tested (Trichophyton rubrum, Aspergillus flavus, Candida albicans, Candida tropicalis and Cryptococcus neoformans) and the activity was compared with amphotericin B, the standard fungicide. The highest activity of 1 µg/ml by cyclo(L-Pro-L-Trp) was recorded against T. rubrum, a human pathogen responsible for causing athlete's foot, jock itch, and ringworm. The activity of cyclo(L-Pro-L-Trp) against T. rubrum, C. neoformans and C. albicans were better than amphotericin B, the standard antifungal agent. To our knowledge, this is the first report of antifungal activity of CDPs against the human pathogenic fungi T. rubrum and C. neoformans. The four CDPs are nontoxic to healthy human cell line up to 200 µg/ml. We conclude that the bacterium associated with entomopathogenic nematode is promising sources of natural antimicrobial secondary metabolites, which may receive greater benefit as potential sources of new drugs in the pharmaceutical industry.

Osseointegration: biological events in relation to characteristics of the implant surface.

Osseointegration of titanium implants is a complex biological process involving interactions between immuno-inflammatory responses, angiogenesis and osteogenesis, all of which are influenced by the physical and chemical characteristics of the implant surface. An implant surface with moderately rough topography and high surface energy influences cellular activities, enhancing peri-implant bone wound healing. Primary mechanical stability of the implant is essential for osseointegration. In this article we review some of the more important biological events of peri-implant bone wound healing in the process of osseointegration, and discuss how the biophysical properties of implant surfaces influence cellular responses.

Acute successful management of a chainsaw injury to the roof of the left chest.

This case report chronicles the experience of prompt resuscitation, beginning with the patient, and immediate surgery following the fatal malfunction of a chainsaw. The injuries were atypical for chainsaw injuries and involved total transection of the left subclavian artery and vein, total transection of the left brachial plexus and laceration to the apex of the left lung, among other injuries. A coordinated effort allowed for successful repair of the life- and limb-threatening injuries so that the patient could return to his young family in time for his 40th birthday.

Neural network auto-segmentation of serial-block-face scanning electron microscopy images exhibit collagen fibril structural differences with tendon type and health.

A U-Net machine learning algorithm was adapted to automatically segment tendon collagen fibril cross-sections from serial block face scanning electron microscopy (SBF-SEM) and create three-dimensional (3D) renderings. We compared the performance of routine Otsu thresholding and U-Net for a positional tendon that has low fibril density (rat tail tendon), an energy-storing tendon that has high fibril density (rat plantaris tendon), and a high fibril density tendon hypothesized to have disorganized 3D ultrastructure (degenerated rat plantaris tendon). The area segmentation of the tail and healthy plantaris tendon had excellent accuracy for both the Otsu and U-Net, with an Intersection over Union (IoU) of 0.8. With degeneration, only the U-Net could accurately segment the area, whereas Otsu IoU was only 0.45. For boundary validation, the U-Net outperformed Otsu segmentation for all tendons. The fibril diameter from U-Net was within 10% of the manual segmentation, however, the Otsu underestimated the fibril diameter by 39% in healthy plantaris and by 84% in the degenerated plantaris. Fibril geometry was averaged across the entire image stack and compared across tendon types. The tail had a lower fibril area fraction (58%) and larger fibril diameter (0.31 µm) than the healthy plantaris (67% and 0.21 µm) and degenerated plantaris tendon (66% and 0.19 µm). This method can be applied to a large variety of tissues to quantify 3D collagen fibril structure.

Hyaluronic acid-based hydrogels containing covalently integrated drug depots: implication for controlling inflammation in mechanically stressed tissues.

Synthetic hydrogels containing covalently integrated soft and deformable drug depots capable of releasing therapeutic molecules in response to mechanical forces are attractive candidates for the treatment of degenerated tissues that are normally load bearing. Herein, radically cross-linkable block copolymer micelles (xBCM) assembled from an amphiphilic block copolymer consisting of hydrophilic poly(acrylic acid) (PAA) partially modified with 2-hydroxyethyl acrylate, and hydrophobic poly(n-butyl acryclate) (PnBA) were employed as the drug depots and the microscopic cross-linkers for the preparation of hyaluronic acid (HA)-based, hydrogels. HA hydrogels containing covalently integrated micelles (HAxBCM) were prepared by radical polymerization of glycidyl methacrylate (GMA)-modified HA (HAGMA) in the presence of xBCMs. When micelles prepared from the parent PAA-b-PnBA without any polymerizable double bonds were used, hydrogels containing physically entrapped micelles (HApBCM) were obtained. The addition of xBCMs to a HAGMA precursor solution accelerated the gelation kinetics and altered the hydrogel mechanical properties. The resultant HAxBCM gels exhibit an elastic modulus of 847 ± 43 Pa and a compressive modulus of 9.2 ± 0.7 kPa. Diffusion analysis of Nile Red (NR)-labeled xBCMs employing fluorescence correlation spectroscopy confirmed the covalent immobilization of xBCMs in HA networks. Covalent integration of dexamethasone (DEX)-loaded xBCMs in HA gels significantly reduced the initial burst release and provided sustained release over a prolonged period. Importantly, DEX release from HAxBCM gels was accelerated by intermittently applied external compression in a strain-dependent manner. Culturing macrophages in the presence of DEX-releasing HAxBCM gels significantly reduced cellular production of inflammatory cytokines. Incorporating mechano-responsive modules in synthetic matrices offers a novel strategy to harvest mechanical stress present in the healing wounds to initiate tissue repair.

Effect of W-TiO2 composite to control microbiologically influenced corrosion on galvanized steel.

Microorganisms tend to colonize on solid metal/alloy surface in natural environment leading to loss of utility. Microbiologically influenced corrosion or biocorrosion usually increases the corrosion rate of steel articles due to the presence of bacteria that accelerates the anodic and/or cathodic corrosion reaction rate without any significant change in the corrosion mechanism. An attempt was made in the present study to protect hot-dip galvanized steel from such attack of biocorrosion by means of chemically modifying the zinc coating. W-TiO2 composite was synthesized and incorporated into the zinc bath during the hot-dipping process. The surface morphology and elemental composition of the hot-dip galvanized coupons were analyzed by scanning electron microscopy and energy dispersive X-ray spectroscopy. The antifouling characteristics of the coatings were analyzed in three different solutions including distilled water, seawater, and seawater containing biofilm scrapings under immersed conditions. Apart from electrochemical studies, the biocidal effect of the composite was evaluated by analyzing the extent of bacterial growth due to the presence and absence of the composite based on the analysis of total extracellular polymeric substance and total biomass using microtiter plate assay. The biofilm-forming bacteria formed on the surface of the coatings was cultured on Zobell Marine Agar plates and studied. The composite was found to be effective in controlling the growth of bacteria and formation of biofilm thereafter.

Oral leukoplakia in a South African sample: a clinicopathological study.

OBJECTIVE: This study analysed differences in clinicopathological features of oral leukoplakia in different racial groups in the greater Johannesburg area of South Africa, with emphasis on the black population. MATERIAL AND METHODS: The retrospective review included cases diagnosed clinically as oral leukoplakia and histologically as hyperkeratosis without dysplasia, hyperkeratosis with mild, moderate or severe dysplasia, and carcinoma in situ from 1990 to 2010. Age, gender, ethnicity, clinical appearance, site of lesion and tobacco smoking habit were recorded. RESULTS: Fourteen per cent of oral leukoplakia occurred in black South Africans compared with 80% in white South Africans. In contrast to whites, blacks were diagnosed with oral leukoplakia at a younger age; there were more men affected than women; and the proportion of idiopathic leukoplakia was greater. There were significantly more blacks (23%) than whites (13%) with non-homogenous leukoplakia and significantly more whites (51%) than blacks (23%) with dysplastic oral leukoplakia. CONCLUSION: This study suggests that oral leukoplakia, especially non-homogenous and idiopathic forms affects South African blacks less frequently than white South Africans; and in the former, it occurs more in men and at a younger age. These findings may provide some guidance in establishing screening policies for oral cancer, particularly suited for blacks.

Assessment of well water quality in Tsunami affected regions of south-west coast of Kerala, India.

The quality of well waters, based on 23 parameters of water, at 12 stations of south-west coast of Kerala, India, was assessed during monsoon, 2009 and summer, 2010, to determine their suitability for drinking and other domestic purposes. The stations selected were grouped into four regions viz. least, slightly, moderately and severely affected ones based on the severity of 2004 Asian Tsunami at each station. The depths of wells showed variations depending on the seasons and on their distance from the seacoast. The average water temperatures during monsoon and summer seasons were 28.5 degrees C and 30.2 degrees C respectively. The pH of well waters were below 6.5 in least and slightly affected regions and above this value in moderately and severely affected regions. In all the four regions, the well water parameters of electrical conductivity, hardness, fluoride, free chlorine, copper, zinc, calcium and nickel were below, and phosphorus, lead, iron cadmium and manganese were above the standard permissible levels set for them in drinking water. The values of salinity, sodium and potassium in the well waters of moderately and severely affected regions, and the values of nitrate-nitrogen, nitrate and magnesium in the well waters of severely affected regions were above the permissible limits set for them in drinking water. Water quality index calculated on the basis of drinking water standards revealed that the well waters of least and slightly affected regions were moderately polluted in both monsoon and summer seasons and the same of moderately affected region were excessively polluted during monsoon and severely polluted during summer seasons, whereas the well waters of severely affected regions were severely polluted in both seasons. Suitable recommendations were made to improve the quality of well waters of least and slightly affected regions.

Alcohol and oral squamous cell carcinoma.

Alcohol is a risk factor for oral squamous cell carcinoma. It enhances the permeability of the oral epithelium, acts as a solvent for tobacco carcinogens, induces basal-cell proliferation, and generates free radicals and acetaldehyde, which have the capacity to cause DNA damage. Alcohol-associated malnutrition and immune suppression may further promote carcinogenesis. However, acetaldehyde, the first metabolite of ethanol, is the critical agent by which prolonged and excessive consumption of alcoholic beverages increases the risk of oral squamous cell carcinoma. Alcohol also acts synergistically with the products of tobacco combustion in the pathogenesis of oral squamous cell carcinoma.

Transcriptomic Signature of the Simulated Microgravity Response in Caenorhabditis elegans and Comparison to Spaceflight Experiments.

Given the growing interest in human exploration of space, it is crucial to identify the effects of space conditions on biological processes. Here, we analyze the transcriptomic response of Caenorhabditis elegans to simulated microgravity and observe the maintained transcriptomic response after returning to ground conditions for four, eight, and twelve days. We show that 75% of the simulated microgravity-induced changes on gene expression persist after returning to ground conditions for four days while most of these changes are reverted after twelve days. Our results from integrative RNA-seq and mass spectrometry analyses suggest that simulated microgravity affects longevity-regulating insulin/IGF-1 and sphingolipid signaling pathways. Finally, we identified 118 genes that are commonly differentially expressed in simulated microgravity- and space-exposed worms. Overall, this work provides insight into the effect of microgravity on biological systems during and after exposure.

Burkholderia cepacia Bacteremia Complicated by Intracranial Abscesses and Immune Reconstitution Inflammatory Syndrome in a Renal Transplantation Recipient.

Burkholderia cepacia is almost always a colonizing organism rather than an infecting organism, but it may be pathogenic in immunocompromised individuals when isolated from body fluids that are ordinarily sterile. When recovered from blood culture it may present infection, pseuedo infection, or actual infection from contaminated intravenous fluids. We present a case of a renal transplant recipient patient who developed B. cepacia bacteremia following central venous cannulation. The subsequent clinical course was of worsening quadriparesis, which on neuroimaging revealed multiple brain and spinal abscesses. Following two weeks of intravenous antibiotics, his clinical features further worsened and the size of lesions further increased, which was suggestive of immune reconstitution inflammatory syndrome. With an increased steroid dose and continuation of the same anti-biotics, there was a regression of the lesions and significant clinical improvement.

Drug infused Al2O3-bioactive glass coatings toward the cure of orthopedic infection.

A unique implant coated substrate with dual-drug-eluting system exhibiting antibacterial, anti-inflammatory, and bone regenerative capacity has been fabricated using spray pyrolysis deposition (SPD) method. Bioglass (BG) and BG-alumina (BG-Al) composites coatings with different concentrations of Al incorporated on BG network over the Cp-Ti substrate were fabricated using SPD technique. Phase purity of BG and BG-Al composites were analyzed by XRD in which Na2Ca2Si3O9 and ß-Na2Ca4(PO4)2SiO4) and Na7.15(Al7.2Si8.8O32) phases were formed. Surface morphology of the coated substrates was analyzed by SEM. Uniformity of the coatings were evaluated by surface profilometer and the uniform distribution the nanoparticles were confirmed with Elemental mapping. Systematically, each apatite layer formation on coated substrate was confirmed by immersing the samples for 1, 3, and 7 days in simulated body fluid and the needle-like structure was characterized using SEM. Cumulative release of Tetracycline hydrochloride (Tet) antibiotic and Dexamethasone (Dex) anti-inflammatory drug-loaded BG-Al and BG-Al composite-coated substrate were studied for 24 h. Antibacterial activity of the coated substrates were evaluated by time-dependent growth inhibition and minimal inhibitory concentration (MIC) assays in which BG-Al and BG-Al composite loaded with Tet showed considerable growth inhibition against S. aureus. Osteoblast-like cells (MG-63) exhibited profound proliferation with no cytotoxic effects which was due to release of Dex drug-coated substrates. Thus, surface modification of Cp-Ti substrate with BG, BG-Al composites coatings loaded with Tet and Dex drug can be considered for post-operative orthopedic implant infection application.

Ultrasound modulated optical tomography: Young's modulus of the insonified region from measurement of natural frequency of vibration.

We demonstrate a method to recover the Young's modulus (E) of a tissue-mimicking phantom from measurements of ultrasound modulated optical tomography (UMOT). The object is insonified by a dual-beam, confocal ultrasound transducer (US) oscillating at frequencies f0 and f0 + Δf and the variation of modulation depth (M) in the autocorrelation of light traversed through the focal region of the US transducer against Δf is measured. From the dominant peaks observed in the above variation, the natural frequencies of the insonified region associated with the vibration along the US transducer axis are deduced. A consequence of the above resonance is that the speckle fluctuation at the resonance frequency has a higher signal-to-noise to ratio (SNR). From these natural frequencies and the associated eigenspectrum of the oscillating object, Young's modulus (E) of the material in the focal region is recovered. The working of this method is confirmed by recovering E in the case of three tissue-mimicking phantoms of different elastic modulus values.