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.

Application of enthalpy method for moving boundary problem in laser surface melting

A numerical analysis was carried out to study the moving boundary problem in the physical process of pulsed Nd-YAG laser surface melting prior to vaporization. The enthalpy method was applied to solve this two-phase axisymmetrical melting problem Computational results of temperature fields were obtained, which provide useful information to practical laser treatment processing. The validity of enthalpy method in solving such problems is presented.

Direct Numerical Simulation of a Spatially Evolving Supersonic Turbulent Boundary Layer at Ma=6

Direct numerical simulation is carried out for a spatially evolving supersonic turbulent boundary layer at free-stream Mach number 6. To overcome numerical instability, the seventh-order WENO scheme is used for the convection terms of Navier-Stokes equations, and fine mesh is adopted to minimize numerical dissipation. Compressibilty effects on the near-wall turbulent kinetic energy budget are studied. The cross-stream extended self-similarity and scaling exponents including the near-wall region are studied. In high Mach number flows, the coherence vortex structures are arranged to be smoother and streamwised, and the hair-pin vortices are less likely to occur.

Boundary knot method for 2D and 3D Helmholtz and convection-diffusion problems under complicated geometry

The boundary knot method (BKM) of very recent origin is an inherently meshless, integration-free, boundary-type, radial basis function collocation technique for the numerical discretization of general partial differential equation systems. Unlike the method of fundamental solutions, the use of non-singular general solution in the BKM avoids the unnecessary requirement of constructing a controversial artificial boundary outside the physical domain. The purpose of this paper is to extend the BKM to solve 2D Helmholtz and convection-diffusion problems under rather complicated irregular geometry. The method is also first applied to 3D problems. Numerical experiments validate that the BKM can produce highly accurate solutions using a relatively small number of knots. For inhomogeneous cases, some inner knots are found necessary to guarantee accuracy and stability. The stability and convergence of the BKM are numerically illustrated and the completeness issue is also discussed.

Experimental Study on Vortex-Induced Vibrations of a Pipeline Near a Plane Boundary in Steady Flow

对单向水流作用下近壁管道横向涡激振动进行了实验模拟,重点探讨了管道与壁面间隙比(e/D)对管道涡激振动幅值和涡激振动频率响应特性的影响规律.实验结果表明,管道与壁面间隙宽度对管道涡激振动特性有较明显影响.在较大间隙比(e/D＞0.66)下,管道振幅随着Vr数的增大先快速增长到最大值,然后平缓下降;在振动初期(即Vr数较小时),管道振动频率变化基本符合Strouhal规律;在振动中后期(即Vr数较大时),管道振动频率变化不符合Strouhal规律,而在管道固有频率附近缓慢增长.在较小间隙比(e/D＜0.30)下,管道振幅随Vr数的增大先平缓上升到最大值,随后较快速下降;在振动初期,管道振动频率变化不遵循Strouhal规律;在整个振动范围内,与较大间隙比情况相比,随着Vr数增加,管道振动频率增长幅度明显较大.

Influence of grain boundary on melting

The temperature behaviour of an Al bicrystal with surfaces consisting of (110) and (111) crystals is simulated using molecular dynamics. The result shows that the (110) crystal losses its crystalline order at 820K, whereas the disorder does not propagate through the (111) crystal at this temperature. Instead, some disordered atoms are recrystallized into the (111) crystal and the initial grain boundary changes into a stable order-disorder interface. Thus, it was discovered that at a temperature near its melting point, the (111) crystal grew and obstructed the propagation of disorder. Such an obstruction is helpful for understanding melting.

Correct biological timing in Arabidopsis requires multiple light-signaling pathways.

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in the timing of circadian outputs require light regulation via feed-forward loops, combining rapid light-signaling pathways with entrained circadian oscillators. Linear time-invariant models of circadian rhythms were computed for 3,503 circadian-regulated genes and for the concentration of cytosolic-free calcium to quantify the magnitude and timing of regulation by circadian oscillators and light-signaling pathways. Bioinformatic and experimental analysis show that rapid light-induced regulation of circadian outputs is associated with seasonal rephasing of the output rhythm. We identify that external coincidence is required for rephasing of multiple output rhythms, and is therefore important in general phase control in addition to specific photoperiod-dependent processes such as flowering and hypocotyl elongation. Our findings uncover a fundamental design principle of circadian regulation, and identify the importance of rapid light-signaling pathways in temporal control.

Flow Characteristics and Its Friction Coefficient of Laminar Near-Wall Boundary Layer in Dusty Atmosphere

采用双向耦合的双流体模型,研究了大气悬浮沙尘的存在对大气边界层中层流底层流动特性及摩阻系数的影响,计算并讨论了不同沙尘含量下含尘大气相对于无尘大气摩阻系数的变化。结果表明：摩阻系数的变化取决于悬浮沙尘的初始运动状态和质量载荷率。