A framework for studying behavioral evolution by reconstructing ancestral repertoires

Although extensive behavioral changes often exist between closely related animal species, our understanding of the genetic basis underlying the evolution of behavior has remained limited. Here, we propose a new framework to study behavioral evolution by computational estimation of ancestral behavioral repertoires. We measured the behaviors of individuals from six species of fruit flies using unsupervised techniques and identified suites of stereotyped movements exhibited by each species. We then fit a Generalized Linear Mixed Model to estimate the suites of behaviors exhibited by ancestral species, as well as the intra- and inter-species behavioral covariances. We found that much of intraspecific behavioral variation is explained by differences between individuals in the status of their behavioral hidden states, what might be called their "mood." Lastly, we propose a method to identify groups of behaviors that appear to have evolved together, illustrating how sets of behaviors, rather than individual behaviors, likely evolved. Our approach provides a new framework for identifying co-evolving behaviors and may provide new opportunities to study the genetic basis of behavioral evolution

Microcantilever Sensors for In-Situ Subsurface Characterization

Real-time, in-situ analysis is critical for decision makers in environmental monitoring, but current techniques for monitoring and characterizing radionuclides rely primarily on liquid scintillation counting, ICP-MS, and spectrofluorimetry, which require sample handling and labor intensive lengthy analytical procedures. Other problems that accompany direct sampling include adherence to strict holding times and record maintenance for QA/QC procedures. Remote, automated sensing with direct connection to automated data management is preferred

Light-limited photosynthesis under energy-saving film decreases eggplant yield

Glasshouse films with adjustable light transmittance and energy-efficient designs have the potential to reduce (up to 80%) the high energy cost for greenhouse horticulture operations. Whether these films compromise the quantity and quality of light transmission for photosynthesis and crop yield remains unclear. A “Smart Glass” film ULR-80 (SG) was applied to a high-tech greenhouse horticulture facility, and two experimental trials were conducted by growing eggplant (Solanum melongena) using commercial vertical cultivation and management practices. SG blocked 85% of ultraviolet (UV), 58% of far-red, and 26% of red light, leading to an overall reduction of 19% in photosynthetically active radiation (PAR, 380–699 nm) and a 25% reduction in total season fruit yield. There was a 53% (season mean) reduction in net short-wave radiation (radiometer range, 385–2,105 nm upward; 295–2,685 nm downward) that generated a net reduction of 8% in heat load and reduced water and nutrient consumption by 18%, leading to improved energy and resource use efficiency. Eggplant adjusted to the altered SG light environment via decreased maximum light-saturated photosynthetic rates (Amax) and lower xanthophyll de-epoxidation state. The shift in light characteristics under SG led to reduced photosynthesis, which may have reduced source (leaf) to sink (fruit) carbon distribution, increased fruit abortion and decreased fruit yield, but did not affect nutritional quality. We conclude that SG increases energy and resource use efficiency, without affecting fruit quality, but the reduction in photosynthesis and eggplant yield is high. The solution is to re-engineer the SG to increase penetration of UV and PAR, while maintaining blockage of glasshouse heat gain

A novel cover material improves cooling energy and fertigation efficiency for glasshouse eggplant production

Glasshouses hold the potential to improve global food security, but high energy costs are an ongoing challenge in bringing them to the forefront of agriculture in warm climates. Here, the energy-saving potential of a ‘Smart Glass’ (SG), diffuse glass fitted with ULR-80 film which permits transmission of 85% of photosynthetically-active light and blocks heat-generating radiation, was characterised for a warm-climate glasshouse. Two consecutive 6-month trials of eggplant crops were grown in a high-tech glasshouse to compare SG to standard diffuse glass (control) in both cool and warm climate conditions. The SG reduced cooling energy use by 4.4% and fertigation demand by 29% in cooler months, and reduced cooling energy use by 4.4% and fertigation demand by 18% in warmer months. The SG did not significantly affect ventilation or heating energy use, but substantially reduced fruit yield. SG may be beneficial for reducing nutrient/water use alongside minor energy savings in commercial glasshouses. However, re-engineering the spectral characteristics of SG could improve eggplant fruit yield while maintaining reductions in energy, nutrient, and water use in the glasshouse

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes

Strength of Hydrogen Bond Network Takes Crucial Roles in the Dissociation Process of Inhibitors from the HIV-1 Protease Binding Pocket

To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions

Novel Evolved Immunoglobulin (Ig)-Binding Molecules Enhance the Detection of IgM against Hepatitis C Virus

Detection of specific antibodies against hepatitis C virus (HCV) is the most widely available test for viral diagnosis and monitoring of HCV infections. However, narrowing the serologic window of anti-HCV detection by enhancing anti-HCV IgM detection has remained to be a problem. Herein, we used LD5, a novel evolved immunoglobulin-binding molecule (NEIBM) with a high affinity for IgM, to develop a new anti-HCV enzyme-linked immunosorbent assay (ELISA) using horseradish peroxidase-labeled LD5 (HRP-LD5) as the conjugated enzyme complex. The HRP-LD5 assay showed detection efficacy that is comparable with two kinds of domestic diagnostic kits and the Abbott 3.0 kit when tested against the national reference panel. Moreover, the HRP-LD5 assay showed a higher detection rate (55.9%, 95% confidence intervals (95% CI) 0.489, 0.629) than that of a domestic diagnostic ELISA kit (Chang Zheng) (53.3%, 95% CI 0.463, 0.603) in 195 hemodialysis patient serum samples. Five serum samples that were positive using the HRP-LD5 assay and negative with the conventional anti-HCV diagnostic ELISA kits were all positive for HCV RNA, and 4 of them had detectable antibodies when tested with the established anti-HCV IgM assay. An IgM confirmation study revealed the IgM reaction nature of these five serum samples. These results demonstrate that HRP-LD5 improved anti-HCV detection by enhancing the detection of anti-HCV IgM, which may have potential value for the early diagnosis and screening of hepatitis C and other infectious diseases

Hydrogen Peroxide Acts on Sensitive Mitochondrial Proteins to Induce Death of a Fungal Pathogen Revealed by Proteomic Analysis

How the host cells of plants and animals protect themselves against fungal invasion is a biologically interesting and economically important problem. Here we investigate the mechanistic process that leads to death of Penicillium expansum, a widespread phytopathogenic fungus, by identifying the cellular compounds affected by hydrogen peroxide (H2O2) that is frequently produced as a response of the host cells. We show that plasma membrane damage was not the main reason for H2O2-induced death of the fungal pathogen. Proteomic analysis of the changes of total cellular proteins in P. expansum showed that a large proportion of the differentially expressed proteins appeared to be of mitochondrial origin, implying that mitochondria may be involved in this process. We then performed mitochondrial sub-proteomic analysis to seek the H2O2-sensitive proteins in P. expansum. A set of mitochondrial proteins were identified, including respiratory chain complexes I and III, F1F0 ATP synthase, and mitochondrial phosphate carrier protein. The functions of several proteins were further investigated to determine their effects on the H2O2-induced fungal death. Through fluorescent co-localization and the use of specific inhibitor, we provide evidence that complex III of the mitochondrial respiratory chain contributes to ROS generation in fungal mitochondria under H2O2 stress. The undesirable accumulation of ROS caused oxidative damage of mitochondrial proteins and led to the collapse of mitochondrial membrane potential. Meanwhile, we demonstrate that ATP synthase is involved in the response of fungal pathogen to oxidative stress, because inhibition of ATP synthase by oligomycin decreases survival. Our data suggest that mitochondrial impairment due to functional alteration of oxidative stress-sensitive proteins is associated with fungal death caused by H2O2

Rime length, stress, and association domains

Every regular Chinese syllable has a syllable tone (the tone we get when the syllable is read in isolation). In some Chinese languages, the tonal pattern of a multisyllabic expression is basically a concatenation of the syllable tones. In other Chinese languages, the tonal pattern of a multisyllabic expression is determined solely by the initial syllable. I call the former M -languages (represented by Mandarin) and the latter S -languages (represented by Shanghai). I argue that there is an additional difference in rime structures between the two language groups. In S-languages, all rimes are simple, i.e., there are no underlying diphthongs or codas. In M-languages, all regular rimes are heavy. I further argue that a syllable keeps its underlying tones only if it has stress. Independent metrical evidence tells us that heavy rimes may carry inherent stress. Thus, in M-languages, all regular syllables are stressed and retain their underlying tones (which may or may not undergo further changes). In contrast, in S-languages, regular rimes do not carry inherent stress; instead, only those syllables that are assigned stress by rule can keep their underlying tones and hence head a multisyllabic tonal domain.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42998/1/10831_2005_Article_BF01440582.pd