Directed cell migration towards softer environments.

How cells sense tissue stiffness to guide cell migration is a fundamental question in development, fibrosis and cancer. Although durotaxis-cell migration towards increasing substrate stiffness-is well established, it remains unknown whether individual cells can migrate towards softer environments. Here, using microfabricated stiffness gradients, we describe the directed migration of U-251MG glioma cells towards less stiff regions. This 'negative durotaxis' does not coincide with changes in canonical mechanosensitive signalling or actomyosin contractility. Instead, as predicted by the motor-clutch-based model, migration occurs towards areas of 'optimal stiffness', where cells can generate maximal traction. In agreement with this model, negative durotaxis is selectively disrupted and even reversed by the partial inhibition of actomyosin contractility. Conversely, positive durotaxis can be switched to negative by lowering the optimal stiffness by the downregulation of talin-a key clutch component. Our results identify the molecular mechanism driving context-dependent positive or negative durotaxis, determined by a cell's contractile and adhesive machinery.

Photocatalytic removal of toxic dyes, liquorice and tetracycline wastewaters by a mesoporous photocatalyst under irradiation of different lamps and sunlight.

Simple recyclable K5CoW12O40/TiO2 was synthesized and used to remove methyl orange, rhodamine B, direct red 16 and crystal violet toxic organic dyes, liquorice industrial wastewater and tetracycline (TC) as an antibiotic. Photoactivity of the catalyst was checked out under irradiation of various lamps (such as 18 W fluorescent, 300 W Xenon, LED and IR lamps). The best efficiency was obtained by fluorescent lamp at catalyst loading of 3 g/L, initial pH of 5, initial dye concentration of 5 ppm, complete degradation was achieved after 30 min contact time. Mechanistic investigation showed that·O2 radicals and h+ are majorly responsible for photodegradation in this process. Electrochemical investigation, Nyquist, Bode, Mott-Schottky, Tauc plots and photoluminescence proved that using this photocatalyst delay the electron-hole recombination, increase the lifetime of excited electron, extend light absorption to visible region and improve the light absorption capacity. This photocatalyst work well under winter sunlight. Also 97% and 84% dye removal was obtained for liquorice with 300 and 1000 COD at optimal condition. This catalyst showed similar activity for TC wastewater. Photocatalyst was characterized by FE-SEM, EDX, AFM, FT-IR, XRD, PL, DRS, EIS, BJH and BET.

4K-memristor analog-grade passive crossbar circuit.

The superior density of passive analog-grade memristive crossbar circuits enables storing large neural network models directly on specialized neuromorphic chips to avoid costly off-chip communication. To ensure efficient use of such circuits in neuromorphic systems, memristor variations must be substantially lower than those of active memory devices. Here we report a 64 × 64 passive crossbar circuit with ~99% functional nonvolatile metal-oxide memristors. The fabrication technology is based on a foundry-compatible process with etch-down patterning and a low-temperature budget. The achieved <26% coefficient of variance in memristor switching voltages is sufficient for programming a 4K-pixel gray-scale pattern with a <4% relative tuning error on average. Analog properties are also successfully verified via experimental demonstration of a 64 × 10 vector-by-matrix multiplication with an average 1% relative conductance import accuracy to model the MNIST image classification by ex-situ trained single-layer perceptron, and modeling of a large-scale multilayer perceptron classifier based on more advanced conductance tuning algorithm.

Combinatorial optimization by weight annealing in memristive hopfield networks.

The increasing utility of specialized circuits and growing applications of optimization call for the development of efficient hardware accelerator for solving optimization problems. Hopfield neural network is a promising approach for solving combinatorial optimization problems due to the recent demonstrations of efficient mixed-signal implementation based on emerging non-volatile memory devices. Such mixed-signal accelerators also enable very efficient implementation of various annealing techniques, which are essential for finding optimal solutions. Here we propose a "weight annealing" approach, whose main idea is to ease convergence to the global minima by keeping the network close to its ground state. This is achieved by initially setting all synaptic weights to zero, thus ensuring a quick transition of the Hopfield network to its trivial global minima state and then gradually introducing weights during the annealing process. The extensive numerical simulations show that our approach leads to a better, on average, solutions for several representative combinatorial problems compared to prior Hopfield neural network solvers with chaotic or stochastic annealing. As a proof of concept, a 13-node graph partitioning problem and a 7-node maximum-weight independent set problem are solved experimentally using mixed-signal circuits based on, correspondingly, a 20 × 20 analog-grade TiO2 memristive crossbar and a 12 × 10 eFlash memory array.

Two-photon uncaging of bioactive thiols in live cells at wavelengths above 800 nm.

Photoactivatable protecting groups (PPGs) are useful for a broad range of applications ranging from biology to materials science. In chemical biology, induction of biological processes via photoactivation is a powerful strategy for achieving spatiotemporal control. The importance of cysteine, glutathione, and other bioactive thiols in regulating protein structure/activity and cell redox homeostasis makes modulation of thiol activity particularly useful. One major objective for enhancing the utility of photoactivatable protecting groups (PPGs) in living systems is creating PPGs with longer wavelength absorption maxima and efficient two-photon (TP) absorption. Toward these objectives, we developed a carboxyl- and dimethylamine-functionalized nitrodibenzofuran PPG scaffold (cDMA-NDBF) for thiol photoactivation, which has a bathochromic shift in the one-photon absorption maximum from λmax = 315 nm with the unfunctionalized NDBF scaffold to λmax = 445 nm. While cDMA-NDBF-protected thiols are stable in the presence of UV irradiation, they undergo efficient broad-spectrum TP photolysis at wavelengths as long as 900 nm. To demonstrate the wavelength orthogonality of cDMA-NDBF and NDBF photolysis in a biological setting, caged farnesyltransferase enzyme inhibitors (FTI) were prepared and selectively photoactivated in live cells using 850-900 nm TP light for cDMA-NDBF-FTI and 300 nm UV light for NDBF-FTI. These experiments represent the first demonstration of thiol photoactivation at wavelengths above 800 nm. Consequently, cDMA-NDBF-caged thiols should have broad applicability in a wide range of experiments in chemical biology and materials science.

Versatile stochastic dot product circuits based on nonvolatile memories for high performance neurocomputing and neurooptimization.

The key operation in stochastic neural networks, which have become the state-of-the-art approach for solving problems in machine learning, information theory, and statistics, is a stochastic dot-product. While there have been many demonstrations of dot-product circuits and, separately, of stochastic neurons, the efficient hardware implementation combining both functionalities is still missing. Here we report compact, fast, energy-efficient, and scalable stochastic dot-product circuits based on either passively integrated metal-oxide memristors or embedded floating-gate memories. The circuit's high performance is due to mixed-signal implementation, while the efficient stochastic operation is achieved by utilizing circuit's noise, intrinsic and/or extrinsic to the memory cell array. The dynamic scaling of weights, enabled by analog memory devices, allows for efficient realization of different annealing approaches to improve functionality. The proposed approach is experimentally verified for two representative applications, namely by implementing neural network for solving a four-node graph-partitioning problem, and a Boltzmann machine with 10-input and 8-hidden neurons.

Correlation between expression of CatSper1,2 and sperm parameters in the gamma irradiated adult mouse testis.

Propose: CatSper protein channels are responsible for the entry of Ca2+ into sperm cells. These proteins play an important role in motility and male fertility. So it is important to find out whether or not environmental factors, such as gamma radiation, have an effect on the expression of Catsper genes. In this study, we investigated the effects of gamma radiation on the expression of CatSper1 and CatSper2 genes. Materials and methods: Twenty-one male NMRI mice were divided into three groups: a control group without gamma radiation, and two experimental groups; Group 1 treated with 1 Gy of gamma radiation, and Group 2 treated with a higher dose of 2 Gy gamma radiation. Testes were removed from all groups of animals 35 days following irradiation and the testicular tissue, processed and embedded in paraffin blocks for sectioning and histological examination. Sperm samples were also taken from the epididymis for microscopic. Sperm parameters such as sperm count, morphology, motility, and viability rates were analyzed. Expression of CatSper genes was evaluated using Real-time PCR. Data were analyzed using the SPSS software and ANOVA test. Results: Our results showed that after treatment with gamma radiation, testes morphology was changed. Epididymal sperm count, motility, and morphology rates were significantly affected in both experimental groups compared to the control group. The relative expressions of CatSper 1 and 2 genes were significantly reduced in the irradiated mice (1 Gy and 2 Gy) than non-irradiated ones. Conclusions: Gamma radiations not only change testes histology and sperm parameters, but also decrease the expression of CatSper 1 and 2 genes in male mice.

Vitamin C ameliorates the adverse effects of dexamethasone on sperm motility, testosterone level, and spermatogenesis indexes in mice.

BACKGROUND:: Dexamethasone (DEX) is a common medicine that is capable of causing malformation in the male reproductive system. The aim of this study was to investigate the effect of vitamin C (Vit-C) on spermatogenesis indexes and daily sperm production (DSP) in adult mice treated with DEX. METHODS:: Male Naval Medical Research Institute (NMRI) mice were divided into four groups: Control, DEX (7 mg/kg/day), Vit-C (100 mg/kg/day), and DEX +Vit-C and treated for 7 days with intraperitoneal injection. RESULTS:: A significant increase in the mean levels of serum and tissue malondialdehyde (MDA) and apoptosis of Leydig cells was found in the DEX group compared to the control group. Sperm motility, DSP, tubular differentiation index, meiotic index, spermatogenesis index, the mean number of spermatocytes, round and long spermatids, and Leydig cells, and also serum testosterone level decreased in the DEX group compared to the control group. The results of this study indicate that Vit-C can significantly prevent the adverse effects of DEX on the mean number of spermatocyte, spermatid, and Leydig cells, tubular differentiation, meiotic and spermatogenesis index, DSP, sperm motility, and the mean levels of serum MDA. CONCLUSION:: In conclusion, our results showed that coadministration of Vit-C and DEX prevents the adverse effects of DEX on the spermatogenesis indexes and DSP.

Spike-timing-dependent plasticity learning of coincidence detection with passively integrated memristive circuits.

Spiking neural networks, the most realistic artificial representation of biological nervous systems, are promising due to their inherent local training rules that enable low-overhead online learning, and energy-efficient information encoding. Their downside is more demanding functionality of the artificial synapses, notably including spike-timing-dependent plasticity, which makes their compact efficient hardware implementation challenging with conventional device technologies. Recent work showed that memristors are excellent candidates for artificial synapses, although reports of even simple neuromorphic systems are still very rare. In this study, we experimentally demonstrate coincidence detection using a spiking neural network, implemented with passively integrated metal-oxide memristive synapses connected to an analogue leaky-integrate-and-fire silicon neuron. By employing spike-timing-dependent plasticity learning, the network is able to robustly detect the coincidence by selectively increasing the synaptic efficacies corresponding to the synchronized inputs. Not surprisingly, our results indicate that device-to-device variation is the main challenge towards realization of more complex spiking networks.

Molecular epidemiology of environmental Cryptococcus species isolates based on amplified fragment length polymorphism.

OBJECTIVE: Cryptococcosis is a major opportunistic fungal infection caused by members of the genus Cryptococcus, mainly those belonging to the Cryptococcus neoformans/Cryptococcus gattii species complexes. Here, we report a comprehensive molecular epidemiological study of the environmental distribution of Cryptococcus isolates in Shiraz, Iran with review of litreature. METHOD: A total of 406 samples were obtained from Eucalyptus trees and 139 samples from pigeon droppings. Cryptococcus species identification and genotyping were performed by amplified fragment length polymorphism (AFLP) fingerprinting sequencing and sequencing of the ITS rDNA region. RESULTS: Majority of the isolates belonged to the Naganishia taxon (n=69) including N. albida (formerly C. albidus, n=62), N. globosa (formerly C. saitoi, n=4), N. adeliensis (formerly C. adeliensis, n=2), N. diffluens (formerly C. diffluens, n=1), and the identified C. neoformans isolates (n=25) belonged to genotype AFLP1/VNI (n=22) and AFLP1B/VNII (n=3). CONCLUSION: More research efforts should be employed to isolate C. gattii species complex from environmental niches in Iran and provide additional evidence related to novel molecular types.

Photo-immobilized EGF chemical gradients differentially impact breast cancer cell invasion and drug response in defined 3D hydrogels.

Breast cancer cell invasion is influenced by growth factor concentration gradients in the tumor microenvironment. However, studying the influence of growth factor gradients on breast cancer cell invasion is challenging due to both the complexities of in vivo models and the difficulties in recapitulating the tumor microenvironment with defined gradients using in vitro models. A defined hyaluronic acid (HA)-based hydrogel crosslinked with matrix metalloproteinase (MMP) cleavable peptides and modified with multiphoton labile nitrodibenzofuran (NDBF) was synthesized to photochemically immobilize epidermal growth factor (EGF) gradients. We demonstrate that EGF gradients can differentially influence breast cancer cell invasion and drug response in cell lines with different EGF receptor (EGFR) expression levels. Photopatterned EGF gradients increase the invasion of moderate EGFR expressing MDA-MB-231 cells, reduce invasion of high EGFR expressing MDA-MB-468 cells, and have no effect on invasion of low EGFR-expressing MCF-7 cells. We evaluate MDA-MB-231 and MDA-MB-468 cell response to the clinically tested EGFR inhibitor, cetuximab. Interestingly, the cellular response to cetuximab is completely different on the EGF gradient hydrogels: cetuximab decreases MDA-MB-231 cell invasion but increases MDA-MB-468 cell invasion and cell number, thus demonstrating the importance of including cell-microenvironment interactions when evaluating drug targets.

Production of pectinases for quality apple juice through fermentation of orange pomace.

Production of pectinases by Aspergillus niger was successfully carried out through solid state fermentation. Orange pomace was used as substrate to produce pectinases using a wild type of A. niger isolated from a rotten orange texture. Some of the important parameters affecting exo- and endo-pectinases activities such as temperature, moisture, C/N ratio were optimized. The results indicated that the produced pectinases exhibited maximum activity in temperature range of 45-55 °C and the maximum enzyme productivity occurred at 70% moisture content and C/N ratio of 10. The enzyme kinetic was studied using Michaelis-Menten and Logistic model and the equation were fitted to experimental data for both exo- and endo-pectinases activities. In evaluation of kinetic model, it was found that Monod model presented perfectly fitted with experimental data. Monod kinetic parameters [Formula: see text] for exo-pectinase activities were [Formula: see text] mM, respectively. The Monod kinetic parameters [Formula: see text] for endo-pectinase activity were [Formula: see text] and [Formula: see text] respectively. Finally, the performances of the produced pectinases were evaluated on natural apple juice. It was confirmed that concentration of soluble sugar, clarity and viscosity of the juice and the yield of extracted juice were significantly improved by the enzymatic hydrolysis activity of pectinases.

Regulatory effects of the novel synthesized Indole-3-carbaldehyde on expression of cell cycle genes: A study on Cyclin D and P21 expression by acute promylocytic leukemia cell line (NB4)

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Effect of passive transport of water through plasma membrane in production of extracellular enzyme.

In this article, availability and control of water in solid-state fermentation (SSF) were investigated. Based on passive transport of water through plasma membranes, a new model was proposed for calculation and control of water activities in the mixture of solids. The validity of theoretical model and accuracy of the proposed model were proved by experimental data. This model was used for production of pectinases via mixed-SSF with the aid of a rotary drum bioreactor. It was found that in case of extracellular enzyme production, the new model is in good agreement with experimental data for the control of water activities in the mixed-SSF. Exact control of water activity in SFF, the production of endo- and exo-pectinases was relatively enhanced. Based on theoretical view point, the prominence of this new model in control of water activity was also proved.

6-Bromo-7-hydroxy-3-methylcoumarin (mBhc) is an efficient multi-photon labile protecting group for thiol caging and three-dimensional chemical patterning.

The photochemical release of chemical reagents and bioactive molecules provides a useful tool for spatio-temporal control of biological processes. However, achieving this goal requires the development of highly efficient one- and two-photon sensitive photo-cleavable protecting groups. Thiol-containing compounds play critical roles in biological systems and bioengineering applications. While potentially useful for sulfhydryl protection, the 6-bromo-7-hydroxy coumarin-4-ylmethyl (Bhc) group can undergo an undesired photoisomerization reaction upon irradiation that limits its uncaging efficiency. To address this issue, here we describe the development of 6-bromo-7-hydroxy-3-methylcoumarin-4-ylmethyl (mBhc) as an improved group for thiol-protection. One- and two-photon photolysis reactions demonstrate that a peptide containing a mBhc-caged thiol undergoes clean and efficient photo-cleavage upon irradiation without detectable photoisomer production. To test its utility for biological studies, a K-Ras-derived peptide containing an mBhc-protected thiol was prepared by solid phase peptide synthesis using Fmoc-Cys(mBhc)-OH for the introduction of the caged thiol. Irradiation of that peptide using either UV or near IR light in presence of protein farnesyltransferase (PFTase), resulted in generation of the free peptide which was then recognized by the enzyme and became farnesylated. To show the utility of this caging group in biomaterial applications, we covalently modified hydrogels with mBhc-protected cysteamine. Using multi-photon confocal microscopy, highly defined volumes of free thiols were generated inside the hydrogels and visualized via reaction with a sulfhydryl-reactive fluorophore. The simple synthesis of mBhc and its efficient removal by one- and two-photon processes make it an attractive protecting group for thiol caging in a variety of applications.

Nitrodibenzofuran: A One- and Two-Photon Sensitive Protecting Group That Is Superior to Brominated Hydroxycoumarin for Thiol Caging in Peptides.

Photoremovable protecting groups are important for a wide range of applications in peptide chemistry. Using Fmoc-Cys(Bhc-MOM)-OH, peptides containing a Bhc-protected cysteine residue can be easily prepared. However, such protected thiols can undergo isomerization to a dead-end product (a 4-methylcoumarin-3-yl thioether) upon photolysis. To circumvent that photoisomerization problem, we explored the use of nitrodibenzofuran (NDBF) for thiol protection by preparing cysteine-containing peptides where the thiol is masked with an NDBF group. This was accomplished by synthesizing Fmoc-Cys(NDBF)-OH and incorporating that residue into peptides by standard solid-phase peptide synthesis procedures. Irradiation with 365 nm light or two-photon excitation with 800 nm light resulted in efficient deprotection. To probe biological utility, thiol group uncaging was carried out using a peptide derived from the protein K-Ras4B to yield a sequence that is a known substrate for protein farnesyltransferase; irradiation of the NDBF-caged peptide in the presence of the enzyme resulted in the formation of the farnesylated product. Additionally, incubation of human ovarian carcinoma (SKOV3) cells with an NDBF-caged version of a farnesylated peptide followed by UV irradiation resulted in migration of the peptide from the cytosol/Golgi to the plasma membrane due to enzymatic palmitoylation. Overall, the high cleavage efficiency devoid of side reactions and significant two-photon cross-section of NDBF render it superior to Bhc for thiol group caging. This protecting group should be useful for a plethora of applications ranging from the development of light-activatable cysteine-containing peptides to the development of light-sensitive biomaterials.

Chorionic morphine, naltrexone and pentoxifylline effect on hypophyso-gonadal hormones of male rats.

BACKGROUND: Knowledge about harmful effects of morphine on hormone secretion seems to be necessary. The aim of the present study was to evaluate the effect of pentoxifylline on side effects derived by morphine on hypophyso-gonadal hormones of male rats. METHODS: 32 male rats were divided into the 4 groups of OSS: control (received 40 g Sucrose/l drinking water and intraperitoneal injection of 1 l/kg normal saline), OMS: morphine group (received 0.4 mg/l + 40 g Sucrose/l in drinking water and intraperitoneal injection of 1 l/kg normal saline), NMS: morphine+naltrexane group (received 0.4 mg/l + 40 g Sucrose/l in drinking water and IP injection dose of 10 mg/kg/ml/day Naltrexane) and PMS: morphine + pentoxifylline group (received 0.4 mg/dl + 40 g Sucrose/l in drinking water and IP injection dose of 12 mg/kg/ml/day Pentoxifylline) for 56 days, respectively. RESULTS: Serum levels of testosterone, LH, FSH hormones were measured. Pentoxifylline increased serum levels of testosterone, LH, FSH hormones compared to control, morphine and morphine-naltrexane groups. CONCLUSION: Pentoxifylline has a significant efficacy for increasing serum levels of sexual hormones. Considering that Pentoxifylline is safe and cheap, with easy application, we suggest for the usage of this drug for improving semen parameter's quality before performing ART for the treatment of morphine addicts (Fig. 1, Ref. 31).

Predicting CCHF incidence and its related factors using time-series analysis in the southeast of Iran: comparison of SARIMA and Markov switching models.

Crimean-Congo haemorrhagic fever (CCHF) is endemic in the southeast of Iran. This study aimed to predict the incidence of CCHF and its related factors and explore the possibility of developing an empirical forecast system using time-series analysis of 13 years' data. Data from 2000 to 2012 were obtained from the Health Centre of Zahedan University of Medical Sciences, Climate Organization and the Veterinary Organization in the southeast of Iran. Seasonal autoregressive integrated moving average (SARIMA) and Markov switching models (MSM) were performed to examine the potential related factors of CCHF outbreaks. These models showed that the mean temperature (°C), accumulated rainfall (mm), maximum relative humidity (%) and legal livestock importation from Pakistan (LIP) were significantly correlated with monthly incidence of CCHF in different lags (P < 0·05). The modelling fitness was checked with data from 2013. Model assessments indicated that the MSM had better predictive ability than the SARIMA model [MSM: root mean square error (RMSE) 0·625, Akaike's Information Criterion (AIC) 266·33; SARIMA: RMSE 0·725, AIC 278·8]. This study shows the potential of climate indicators and LIP as predictive factors in modelling the occurrence of CCHF. Our results suggest that MSM provides more information on outbreak detection and can be a better predictive model compared to a SARIMA model for evaluation of the relationship between explanatory variables and the incidence of CCHF.

Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots.

Many genetic epidemiology resources have collected dried blood spots (predominantly as Guthrie Cards) as an economical and efficient means of archiving sources of DNA, conferring great value to genetic screening methods that are compatible with this medium. We applied Hi-Plex to screen the breast cancer predisposition gene PALB2 in 93 Guthrie Card-derived DNA specimens previously characterized for PALB2 genetic variants via DNA derived from lymphoblastoid cell lines, whole blood, and buffy coat. Of the 93 archival Guthrie Card-derived DNAs, 92 (99%) were processed successfully and sequenced using approximately half of a MiSeq run. From these 92 DNAs, all 59 known variants were detected and no false-positive variant calls were yielded. Fully 98.13% of amplicons (5417/5520) were represented within 15-fold of the median coverage (2786 reads), and 99.98% of amplicons (5519/5520) were represented at a depth of 10 read-pairs or greater. With Hi-Plex, we show for the first time that a High-Plex amplicon-based massively parallel sequencing (MPS) system can be applied effectively to DNA prepared from dried blood spot archival specimens and, as such, can dramatically increase the scopes of both method and resource.