A Quantitative Analysis of Growth and Size Regulation in Manduca sexta: The Physiological Basis of Variation in Size and Age at Metamorphosis.

Body size and development time are important life history traits because they are often highly correlated with fitness. Although the developmental mechanisms that control growth have been well studied, the mechanisms that control how a species-characteristic body size is achieved remain poorly understood. In insects adult body size is determined by the number of larval molts, the size increment at each molt, and the mechanism that determines during which instar larval growth will stop. Adult insects do not grow, so the size at which a larva stops growing determines adult body size. Here we develop a quantitative understanding of the kinetics of growth throughout larval life of Manduca sexta, under different conditions of nutrition and temperature, and for genetic strains with different adult body sizes. We show that the generally accepted view that the size increment at each molt is constant (Dyar's Rule) is systematically violated: there is actually a progressive increase in the size increment from instar to instar that is independent of temperature. In addition, the mass-specific growth rate declines throughout the growth phase in a temperature-dependent manner. We show that growth within an instar follows a truncated Gompertz trajectory. The critical weight, which determines when in an instar a molt will occur, and the threshold size, which determines which instar is the last, are different in genetic strains with different adult body sizes. Under nutrient and temperature stress Manduca has a variable number of larval instars and we show that this is due to the fact that more molts at smaller increments are taken before threshold size is reached. We test whether the new insight into the kinetics of growth and size determination are sufficient to explain body size and development time through a mathematical model that incorporates our quantitative findings.

Quantitative model of the phase behavior of recombinant pH-responsive elastin-like polypeptides.

Quantitative models are required to engineer biomaterials with environmentally responsive properties. With this goal in mind, we developed a model that describes the pH-dependent phase behavior of a class of stimulus responsive elastin-like polypeptides (ELPs) that undergo reversible phase separation in response to their solution environment. Under isothermal conditions, charged ELPs can undergo phase separation when their charge is neutralized. Optimization of this behavior has been challenging because the pH at which they phase separate, pHt, depends on their composition, molecular weight, concentration, and temperature. To address this problem, we developed a quantitative model to describe the phase behavior of charged ELPs that uses the Henderson-Hasselbalch relationship to describe the effect of side-chain ionization on the phase-transition temperature of an ELP. The model was validated with pH-responsive ELPs that contained either acidic (Glu) or basic (His) residues. The phase separation of both ELPs fit this model across a range of pH. These results have important implications for applications of pH-responsive ELPs because they provide a quantitative model for the rational design of pH-responsive polypeptides whose transition can be triggered at a specified pH.

Phase transfer catalysts drive diverse organic solvent solubility of single-walled carbon nanotubes helically wrapped by ionic, semiconducting polymers.

Use of phase transfer catalysts such as 18-crown-6 enables ionic, linear conjugated poly[2,6-{1,5-bis(3-propoxysulfonicacidsodiumsalt)}naphthylene]ethynylene (PNES) to efficiently disperse single-walled carbon nanotubes (SWNTs) in multiple organic solvents under standard ultrasonication methods. Steady-state electronic absorption spectroscopy, atomic force microscopy (AFM), and transmission electron microscopy (TEM) reveal that these SWNT suspensions are composed almost exclusively of individualized tubes. High-resolution TEM and AFM data show that the interaction of PNES with SWNTs in both protic and aprotic organic solvents provides a self-assembled superstructure in which a PNES monolayer helically wraps the nanotube surface with periodic and constant morphology (observed helical pitch length = 10 ± 2 nm); time-dependent examination of these suspensions indicates that these structures persist in solution over periods that span at least several months. Pump-probe transient absorption spectroscopy reveals that the excited state lifetimes and exciton binding energies of these well-defined nanotube-semiconducting polymer hybrid structures remain unchanged relative to analogous benchmark data acquired previously for standard sodium dodecylsulfate (SDS)-SWNT suspensions, regardless of solvent. These results demonstrate that the use of phase transfer catalysts with ionic semiconducting polymers that helically wrap SWNTs provide well-defined structures that solubulize SWNTs in a wide range of organic solvents while preserving critical nanotube semiconducting and conducting properties.

Host genetics and HIV-1: the final phase?

This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.

The effect of differences in methodology among some recent applications of shearing quotients.

A shearing quotient (SQ) is a way of quantitatively representing the Phase I shearing edges on a molar tooth. Ordinary or phylogenetic least squares regression is fit to data on log molar length (independent variable) and log sum of measured shearing crests (dependent variable). The derived linear equation is used to generate an 'expected' shearing crest length from molar length of included individuals or taxa. Following conversion of all variables to real space, the expected value is subtracted from the observed value for each individual or taxon. The result is then divided by the expected value and multiplied by 100. SQs have long been the metric of choice for assessing dietary adaptations in fossil primates. Not all studies using SQ have used the same tooth position or crests, nor have all computed regression equations using the same approach. Here we focus on re-analyzing the data of one recent study to investigate the magnitude of effects of variation in 1) shearing crest inclusion, and 2) details of the regression setup. We assess the significance of these effects by the degree to which they improve or degrade the association between computed SQs and diet categories. Though altering regression parameters for SQ calculation has a visible effect on plots, numerous iterations of statistical analyses vary surprisingly little in the success of the resulting variables for assigning taxa to dietary preference. This is promising for the comparability of patterns (if not casewise values) in SQ between studies. We suggest that differences in apparent dietary fidelity of recent studies are attributable principally to tooth position examined.

Ground and Electronic Excited States from Pairing Matrix Fluctuation and Particle-Particle Random Phase Approximation

The accurate description of ground and electronic excited states is an important and challenging topic in quantum chemistry. The pairing matrix fluctuation, as a counterpart of the density fluctuation, is applied to this topic. From the pairing matrix fluctuation, the exact electron correlation energy as well as two electron addition/removal energies can be extracted. Therefore, both ground state and excited states energies can be obtained and they are in principle exact with a complete knowledge of the pairing matrix fluctuation. In practice, considering the exact pairing matrix fluctuation is unknown, we adopt its simple approximation --- the particle-particle random phase approximation (pp-RPA) --- for ground and excited states calculations. The algorithms for accelerating the pp-RPA calculation, including spin separation, spin adaptation, as well as an iterative Davidson method, are developed. For ground states correlation descriptions, the results obtained from pp-RPA are usually comparable to and can be more accurate than those from traditional particle-hole random phase approximation (ph-RPA). For excited states, the pp-RPA is able to describe double, Rydberg, and charge transfer excitations, which are challenging for conventional time-dependent density functional theory (TDDFT). Although the pp-RPA intrinsically cannot describe those excitations excited from the orbitals below the highest occupied molecular orbital (HOMO), its performances on those single excitations that can be captured are comparable to TDDFT. The pp-RPA for excitation calculation is further applied to challenging diradical problems and is used to unveil the nature of the ground and electronic excited states of higher acenes. The pp-RPA and the corresponding Tamm-Dancoff approximation (pp-TDA) are also applied to conical intersections, an important concept in nonadiabatic dynamics. Their good description of the double-cone feature of conical intersections is in sharp contrast to the failure of TDDFT. All in all, the pairing matrix fluctuation opens up new channel of thinking for quantum chemistry, and the pp-RPA is a promising method in describing ground and electronic excited states.

Whole-cell-analysis of live cardiomyocytes using wide-field interferometric phase microscopy.

We apply wide-field interferometric microscopy techniques to acquire quantitative phase profiles of ventricular cardiomyocytes in vitro during their rapid contraction with high temporal and spatial resolution. The whole-cell phase profiles are analyzed to yield valuable quantitative parameters characterizing the cell dynamics, without the need to decouple thickness from refractive index differences. Our experimental results verify that these new parameters can be used with wide field interferometric microscopy to discriminate the modulation of cardiomyocyte contraction dynamics due to temperature variation. To demonstrate the necessity of the proposed numerical analysis for cardiomyocytes, we present confocal dual-fluorescence-channel microscopy results which show that the rapid motion of the cell organelles during contraction preclude assuming a homogenous refractive index over the entire cell contents, or using multiple-exposure or scanning microscopy.