Regulation of Growth, Cell Shape, Cell Division, and Gene Expression by Second Messengers (p)ppGpp and Cyclic Di-GMP in Mycobacterium smegmatis

The alarmone (p)ppGpp regulates transcription, translation, replication, virulence, lipid synthesis, antibiotic sensitivity, biofilm formation, and other functions in bacteria. Signaling nucleotide cyclic di-GMP (c-di-GMP) regulates biofilm formation, motility, virulence, the cell cycle, and other functions. In Mycobacterium smegmatis, both (p) ppGpp and c-di-GMP are synthesized and degraded by bifunctional proteins Rel(Msm) and DcpA, encoded by rel(Msm) and dcpA genes, respectively. We have previously shown that the Delta rel(Msm) and Delta dcpA knockout strains are antibiotic resistant and defective in biofilm formation, show altered cell surface properties, and have reduced levels of glycopeptidolipids and polar lipids in their cell wall (K. R. Gupta, S. Kasetty, and D. Chatterji, Appl Environ Microbiol 81:2571-2578, 2015, http://dx.doi.org/10.1128/AEM.03999-14). In this work, we have explored the phenotypes that are affected by both (p) ppGpp and c-di-GMP in mycobacteria. We have shown that both (p) ppGpp and c-di-GMP are needed to maintain the proper growth rate under stress conditions such as carbon deprivation and cold shock. Scanning electron microscopy showed that low levels of these second messengers result in elongated cells, while high levels reduce the cell length and embed the cells in a biofilm-like matrix. Fluorescence microscopy revealed that the elongated Delta rel(Msm) and Delta dcpA cells are multinucleate, while transmission electron microscopy showed that the elongated cells are multiseptate. Gene expression analysis also showed that genes belonging to functional categories such as virulence, detoxification, lipid metabolism, and cell-wall-related processes were differentially expressed. Our results suggests that both (p) ppGpp and c-di-GMP affect some common phenotypes in M. smegmatis, thus raising a possibility of cross talk between these two second messengers in mycobacteria. IMPORTANCE Our work has expanded the horizon of (p) ppGpp and c-di-GMP signaling in Gram-positive bacteria. We have come across a novel observation that M. smegmatis needs (p) ppGpp and c-di-GMP for cold tolerance. We had previously shown that the Delta rel(Msm) and Delta dcpA strains are defective in biofilm formation. In this work, the overproduction of (p) ppGpp and c-di-GMP encased M. smegmatis in a biofilm-like matrix, which shows that both (p) ppGpp and c-di-GMP are needed for biofilm formation. The regulation of cell length and cell division by (p) ppGpp was known in mycobacteria, but our work shows that c-di-GMP also affects the cell size and cell division in mycobacteria. This is perhaps the first report of c-di-GMP regulating cell division in mycobacteria.

A Novel Counter Sheet-Flow Sandwich Cell Culture Device For Mammalian Cell Growth In Space

Cell culture and growth in space is crucial to understand the cellular responses under microgravity. The effects of microgravity were coupled with such environment restrictions as medium perfusion, in which the underlying mechanism has been poorly understood. In the present work, a customer-made counter sheet-flow sandwich cell culture device was developed upon a biomechanical concept from fish gill breathing. The sandwich culture unit consists of two side chambers where the medium flow is counter-directional, a central chamber where the cells are cultured, and two porous polycarbonate membranes between side and central chambers. Flow dynamics analysis revealed the symmetrical velocity profile and uniform low shear rate distribution of flowing medium inside the central culture chamber, which promotes sufficient mass transport and nutrient supply for mammalian cell growth. An on-orbit experiment performed on a recovery satellite was used to validate the availability of the device.

Effects of wall temperature on boundary layer stability over a blunt cone at Mach 7.99

Effects of wall temperature on stabilities of hypersonic boundary layer over a 7-degree half-cone-angle blunt cone are studied by using both direct numerical simulation (DNS) and linear stability theory (LST) analysis. Four isothermal wall cases with Tw/T0= 0.5, 0.7, 0.8 and 0.9, as well as an adiabatic wall case are considered. Results of both DNS and LST indicate that wall temperature has significant effects on the growth of disturbance waves. Cooling the surface accelerates unstable Mack II mode waves and decelerates the first mode (Tollmien–Schlichting mode) waves. LST results show that growth rate of the most unstable Mack II mode waves for the cases of cold wall Tw/T0=0.5 and 0.7 are about 45% and 25% larger than that for the adiabatic wall, respectively. Numerical results show that surface cooling modifies the profiles of rdut/dyn and temperature in the boundary layers, and thus changes the stability haracteristic of the boundary layers, and then effects on the growth of unstable waves. The results of DNS indicate that the disturbances with the frequency range from about 119.4 to 179.1 kHz, including the most unstable Mack modes, produce strong mode competition in the downstream region from about 11 to 100 nose radii. And adiabatic wall enhances the amplitudes of disturbance according to the results of DNS, although the LST indicates that the growth rate of the disturbance of cold wall is larger. That because the growth of the disturbance does not only depend on the development of the second unstable mode.

Do fluctuations in the somatic growth rate of rock lobster (Jasus lalandii) encompass all size classes? A re-assessment of juvenile growth

Catch rates in the South African rock lobster (Jasus lalandii) fishery declined after 1989 in response to reduced adult somatic growth rates and a consequent reduction in recruitment to the fishable population. Although spatial and temporal trends in adult growth are well described, little is known about how juvenile growth rates have been affected. In our study, growth rates of juvenile rock lobster on Cape Town harbor wall were compared with those recorded at the same site more than 25 years prior to our study, and with those on a nearby natural nursery reef. We found that indices of somatic growth measured during 1996–97 at the harbor wall had declined significantly since 1971–72. Furthermore, growth was slower among juvenile J. lalandii at the harbor wall than those at the natural nursery reef. These results suggest that growth rates of juvenile and adult J. lalandii exhibit similar types of spatiotemporal patterns. Thus, the recent coastwide decline in adult somatic growth rates might also encompass smaller size classes.

A comparative study on effects of Immunoster and Immunowall as immunostimulants on some hematological, biochemical and growth indices of farmed great sturgeon juveniles (Huso huso)

Prebiotics are non-digestible food ingredients that profitably affect the host by selectively stimulating the growth and /or activation of one or a limited number of bacteria in the intestine that can enhance host health status. Immunoster (IS) and Immunowall (IW) are prebiotics and immunostimulants derived from the outer cell wall of brewers yeast, Saccharomyces cerevisiae. These substances contain MOS and �-glucans. After a four-week acclimatization period to rearing conditions and basal diet, 450 farmed great sturgeon juveniles weighing 95.58 ± 9.38 g were randomly distributed into 15 fiberglass tanks (2 × 2 × 0.53 m) in five treatments (Control, IS 1%, IW 1%, IS 3%, and IW 3%) in three replicates (completely randomized design) and kept at a density of 30 fish per tank for a period of 8 weeks at water temperature 20.55 ± 5.11ºC, dissolved oxygen 6.73 ± 0.35 mg L-1 and pH 7.92 ± 0.09. IS and IW were added at two levels of 1% and 3% to the basal diet in place of cellulose, except the control. At the beginning, in the middle and at the end of the trial, carcass analysis was done to determine the moisture, protein, fat, ash, and total carbohydrate. Also, blood samples were collected to measure hematological, biochemical and immune indices. At the end of the trial, final weight, final length, body weight increase (BWI), specific growth rate (SGR), average daily growth (ADG), protein efficiency ratio (PER), feed conversion ratio (FCR), and condition factor (CF) in fish fed on IS and IW in both levels 1% and 3% showed some differences. These differences were significant in IS 3% and IW 1% and 3% compared with the control (P<0.05). HSI showed no significant difference (P>0.05) and survival rate was 100% in all treatments. Crude protein of carcass in fish fed on IS and IW at 1% and 3% showed an increase in comparison with the control. There was significant difference between IS 3% and the control in crude protein of carcass (P<0.05). Fish fed on IS and IW at 1% and 3% showed various results in hematological and biochemical factors. It was observed significant difference in MCV between IW 1% and IS 3% compared with the control (P<0.05). Although there was an increase in values of hematocrit, hemoglobin (except IS 1%), WBC (except IW 3%), MCH, neutrophil, total protein, albumin (except IS 3%), K+, and lysozyme in fish fed on IS and IW compared with the control, it was no significant (P>0.05). The maximum count of WBC and the highest value of Ca2+ were seen in IW 1%. The maximum count of lymphocyte, the highest values of total protein, albumin and IgM were recorded in IW 3%. IS 1% had the maximum count of neutrophil and the highest concentration of lysozyme. Based on obtained results, it can be declared that IS and IW at two levels of 1% and 3% can enhance growth performance and feed efficiency and also improve some hematological, biochemical, and immune indices in farmed great sturgeon juveniles.

Growth rates of Tilapia esculenta (Graham) and Tilapia zillii (Gervais) under cultivation in ponds at Nyegezi, Tanzania

Aquaculture in Tanzania is still on a subsistence level and most of the ponds are maintained as part time job. The ponds are too small, shallow and over crowded with stunted Tilapia spp. In the present paper the results of experiments conducted in ponds at Nyegezi with T. esculenta and T. zillii are presented. This was part of an overall project of developing techniques of fish cultures with Tilapia under the limited existing conditions at Nyegezi. In a mono - species culture experiement with Tilapia zillii in nine month's time an average size of 172.8 mm/115.0 g was attained. In another experiment with T. zillii and T. esculenta in thirteen month's time, T. zillii attained an average size of 180.2mm/106.6 g and T. esculenta 193.6 mm/118.8 g. In another experiment with intensive feeding schedule an average size of 179.3 mm/126.6 g was attained by T. zillii and 191.0 mm/125.0 g by T. esculenta in four month's time. A locally prepared supplimentary feed with local Brewery Waste and Fish Meal (10:1) was readily accepted by both species of Tilapia. T. zillii voraciously fed on Cabbage leaves, Cauliflower leaves, Chinese cabbage leaves, Cassava leaves and on the common weed Comalina sp. Though all the items mentioned above were readily accepted by T. zillii feeding with Comaltna sp. was the easiest and most convenient because of its availability. In an intensive feeding experiment with vegetable leaves/Comalina sp. and the locally prepared supplimentary feed the fishes attained table size in four months time. Cement cistens of 5 X 3 X 1½ m size could be conveniently used for breeding both species of Tilapia. T. zillii had semi adhesive eggs and they were deposited on the sides of the cement wall. The number of young ones in a brood ranged from 160 to 314 in T. esculenta and 687 to 4,356 in T. zillii.

Cold-gas chemical vapor deposition to identify the key precursor for rapidly growing vertically-aligned single-wall and few-wall carbon nanotubes from pyrolyzed ethanol

Vertically-aligned carbon nanotubes (VA-CNTs) were rapidly grown from ethanol and their chemistry has been studied using a "cold-gas" chemical vapor deposition (CVD) method. Ethanol vapor was preheated in a furnace, cooled down and then flowed over cobalt catalysts upon ribbon-shaped substrates at 800 °C, while keeping the gas unheated. CNTs were obtained from ethanol on a sub-micrometer scale without preheating, but on a millimeter scale with preheating at 1000 °C. Acetylene was predicted to be the direct precursor by gas chromatography and gas-phase kinetic simulation, and actually led to millimeter-tall VA-CNTs without preheating when fed with hydrogen and water. There was, however a difference in CNT structure, i.e. mainly few-wall tubes from pyrolyzed ethanol and mainly single-wall tubes for unheated acetylene, and the by-products from ethanol pyrolysis possibly caused this difference. The "cold-gas" CVD, in which the gas-phase and catalytic reactions are separately controlled, allowed us to further understand CNT growth. © 2012 Elsevier Ltd. All rights reserved.

Carbon nanotube growth for through silicon via application.

Through silicon via (TSV) technology is key for next generation three-dimensional integrated circuits, and carbon nanotubes (CNT) provide a promising alternative to metal for filling the TSV. Three catalyst preparation methods for achieving CNT growth from the bottom of the TSV are investigated. Compared with sputtering and evaporation, catalyst deposition using dip-coating in a FeCl2 solution is found to be a more efficient method for realizing a bottom-up filling of the TSV (aspect ratio 5 or 10) with CNT. The CNT bundles grown in 5 min exceed the 50 μm length of the TSV and are multi-wall CNT with three to eight walls. The CNT bundles inside the TSV were electrically characterized by creating a direct contact using a four-point nanoprober setup. A low resistance of the CNT bundle of 69.7 Ω (297 Ω) was measured when the CNT bundle was contacted midway along (over the full length of) the 25 μm deep TSV. The electrical characterization in combination with the good filling of the TSV demonstrates the potential use of CNT in fully integrated TSV applications.

Spectroscopic characterization of protein-wrapped single-wall carbon nanotubes and quantification of their cellular uptake in multiple cell generations

We study the spectral characteristics of bovine serum albumin (BSA) protein conjugated single-wall carbon nanotubes (SWNTs), and quantify their uptake by macrophages. The binding of BSA onto the SWNT surface is found to change the protein structure and to increase the doping of the nanotubes. The G-band Raman intensity follows a well-defined power law for SWNT concentrations of up to 33 μg ml-1 in aqueous solutions. Subsequently, in vitro experiments demonstrate that incubation of BSA-SWNT complexes with macrophages affects neither the cellular growth nor the cellular viability over multiple cell generations. Using wide spot Raman spectroscopy as a fast, non-destructive method for statistical quantification, we observe that macrophages effectively uptake BSA-SWNT complexes, with the average number of nanotubes internalized per cell remaining relatively constant over consecutive cell generations. The number of internalized SWNTs is found to be ∼30 × 106 SWNTs/cell for a 60 mm-2 seeding density and ∼100 × 10 6 SWNTs/cell for a 200 mm-2 seeding density. Our results show that BSA-functionalized SWNTs are an efficient molecular transport system with low cytotoxicity maintained over multiple cell generations. © 2013 IOP Publishing Ltd.

Growth kinetics and uniform scaling-up of graphene synthesis

Chemical vapor deposition on copper is the most widely used method to synthesize graphene at large scale. However, the clear understanding of the fundamental mechanisms that govern this synthesis is lacking. Using a vertical-flow, cold-wall reactor with short gas residence time we observe the early growths to study the kinetics of chemical vapor deposition of graphene on copper foils and demonstrate uniform synthesis at wafer scale. Our results indicate that the growth is limited by the catalytic dissociative dehydrogenation on the surface and copper sublimation hinders the graphene growth. We report an activation energy of 3.1 eV for ethylene-based graphene synthesis. © The Electrochemical Society.

Diameter and wall number control of carbon nanotubes by chemical vapor deposition

We analyze the relationship between the average wall number (N) and the diameter (d) for carbon nanotubes (CNTs) grown by chemical vapour deposition. It is found that N depends linearly on d for diameters in the range of 2.5-10 nm, while single wall nanotubes predominate for diameters under about 2.1 nm. The linear relationship is found to depend somewhat on the growth conditions. It is also verified that the mean diameter depends on the diameter of the originating catalyst nanoparticle, and thus on the initial catalyst thickness where a thin film catalyst is used. This simplifies the characterisation of CNTs by electron microscopy. We also find a linear relationship between nanotube diameter and initial catalyst film thickness. © 2013 AIP Publishing LLC.

Carbon nanotube forests growth using catalysts from atomic layer deposition

We have grown carbon nanotubes using Fe and Ni catalyst films deposited by atomic layer deposition. Both metals lead to catalytically active nanoparticles for growing vertically aligned nanotube forests or carbon fibres, depending on the growth conditions and whether the substrate is alumina or silica. The resulting nanotubes have narrow diameter and wall number distributions that are as narrow as those grown from sputtered catalysts. The state of the catalyst is studied by in-situ and ex-situ X-ray photoemission spectroscopy. We demonstrate multi-directional nanotube growth on a porous alumina foam coated with Fe prepared by atomic layer deposition. This deposition technique can be useful for nanotube applications in microelectronics, filter technology, and energy storage. © 2014 AIP Publishing LLC.

High epitaxial growth rate of 4H-SiC using TCS as silicon precursor

High homoepitaxial growth of 4H-SiC has been performed in a home-made horizontal hot wall CVD reactor on n-type 4H-SiC 8 degrees off-oriented substrates in the size of 10 mm x 10 mm, using trichlorosilane (TCS) as silicon precursor source together with ethylene as carbon precursor source. Cross-section Scanning Electron Microscopy (SEM), Raman scattering spectroscopy and Atomic Force Microscopy (AFM) were used to determine the growth rate, structural property and surface morphology, respectively. The growth rate reached to 23 mu m/h and the optimal epilayer was obtained at 1600 degrees C with TCS flow rate of 12 seem in C/Si of 0.42, which has a good surface morphology with a low Rms of 0.64 nm in 10 mu mx10 mu m area.

In-Situ Boron and Aluminum Doping and Their Memory Effects in 4H-SiC Homoepitaxial Layers Grown by Hot-Wall LPCVD

The in-situ p-type doping of 4H-SiC grown on off-oriented (0001) 4H-SiC substrates was performed with trimethylaluminum (TMA) and/or diborane (B2H6) as the dopants. The incorporations of Al and B atoms and their memory effects and the electrical properties of p-type 4H-SiC epilayers were characterized by secondary ion mass spectroscopy (SIMS) and Hall effect measurements, respectively. Both Al- and B-doped 4H-SiC epilayers were p-type conduction. It was shown that the profiles of the incorporated boron and aluminum concentration were in agreement with the designed TMA and B2H6 flow rate diagrams. The maximum hole concentration for the Al doped 4H-SiC was 3.52x10(20) cm(-3) with Hall mobility of about 1 cm(2)/Vs and resistivity of 1.6 similar to 2.2x10(-2) Omega cm. The heavily boron-doped 4H-SiC samples were also obtained with B2H6 gas flow rate of 5 sccm, yielding values of 0.328 Omega cm for resistivity, 5.3x10(18) cm(-3) for hole carrier concentration, and 7 cm(2)/VS for hole mobility. The doping efficiency of Al in SiC is larger than that of B. The memory effects of Al and B were investigated in undoped 4H-SiC by using SIMS measurement after a few run of doped 4H-SiC growth. It was clearly shown that the memory effect of Al is stronger than that of B. It is suggested that p-type 4H-SiC growth should be carried out in a separate reactor, especially for Al doping, in order to avoid the join contamination on the subsequent n-type growth. 4H-SiC PiN diodes were fabricated by using heavily B doped epilayers. Preliminary results of PiN diodes with blocking voltage of 300 V and forward voltage drop of 3.0 V were obtained.