Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models

With recent advances in single-molecule manipulation techniques, it is now possible to measure the mechanical resistance of proteins to external pulling forces applied at specific positions. Remarkably, such recent studies demonstrated that the pulling/stretching forces required to initiate unfolding vary considerably depending on the location of the application of the forces, unraveling residue/position-specific response of proteins to uniaxial tension. Here we show that coarse-grained elastic network models based on the topology of interresidue contacts in the native state can satisfactory explain the relative sizes of such stretching forces exerted on different residue pairs. Despite their simplicity, such models presumably capture a fundamental property that dominates the observed behavior: deformations that can be accommodated by the relatively lower frequency modes of motions intrinsically favored by the structure require weaker forces and vice versa. The mechanical response of proteins to external stress is therefore shown to correlate with the anisotropic fluctuation dynamics intrinsically accessible in the folded state. The dependence on the overall fold implies that evolutionarily related proteins sharing common structural features tend to possess similar mechanical properties. However, the theory cannot explain the differences observed in a number of structurally similar but sequentially distant domains, such as the fibronectin domains.     

Molecular mapping of the C locus for presence of pungency in Capsicum.

Pungency owing to the presence of capsaicinoids is a unique character of pepper (Capsicum spp.). Capsaicinoids are produced in the placenta and it has long been known that a single dominant gene, C, is required for pungent genotypes to produce capsaicinoids. We mapped C to pepper chromosome 2 in a cross between a pungent Capsicum frutescens wild accession and a non-pungent Capsicum annuum bell pepper. This position confirmed results from earlier studies. The RFLP marker TG 205 cosegregated with C and two additional RFLP markers were also located within 1 cM. The recessive allele at the C locus is used in breeding programs around the world focused on very diverse germplasm, hence any of these tightly linked markers may be of value as potential sources of useful markers for marker-assisted selection. To demonstrate this point, we developed a PCR-based CAPS (cleaved amplified polymorphic sequence) marker linked to C using the sequence of the Capsicum fibrillin gene located 0.4 cM from C. The use of molecular markers for high-throughput screening for the c allele in pepper breeding programs is discussed.     

The influence of scale and patchiness on spider diversity in a semi-arid environment

Semi-arid scrubland in the Middle East consists of a soil crust matrix overlain with patches of perennial shrubs. To understand factors influencing biodiversity in this vulnerable landscape we need to understand how this mosaic of habitats influences associated fauna. Spiders are particularly abundant in this habitat so we asked if spider diversity differed between habitat patches and if different patch types contained either a subset of the regional species pool or specific species guilds. We also asked whether changes in the fractal nature of the microphytic and macrophytic patch mosaic altered spider diversity in this habitat. We found that the semi-arid scrubland at Sayeret Shaked Park (Israel) contains different spider communities that require patches of a certain quality to develop fully. Different patch types contain communities of different species, but the community structure of the patches is similar. We suggest that large-scale environmental factors typical of the site as a whole influence coarse-grained community structure, while small-scale differences between patch types result in the specialisation of species to different patch types.     

Recollection-Based Retrieval Is Influenced by Contextual Variation at Encoding but Not at Retrieval

In this article, we investigated the effects of variations at encoding and retrieval on recollection. We argue that recollection is more likely to be affected by the processing that information undergoes at encoding than at retrieval. To date, manipulations shown to affect recollection were typically carried out at encoding. Therefore, an open question is whether these same manipulations would also affect recollection when carried out at retrieval, or whether there is an inherent connection between their effects on recollection and the encoding stage. We therefore manipulated, at either encoding or retrieval, fluency of processing (Experiment 1)—typically found not to affect recollection—and the amount of attentional resources available for processing (Experiments 2 and 3)—typically reported to affect recollection. We found that regardless of the type of manipulation, recollection was affected more by manipulations carried out at encoding and was essentially unaffected when these manipulations were carried out at retrieval. These findings suggest an inherent dependency between recollection-based retrieval and the encoding stage. It seems that because recollection is a contextual-based retrieval process, it is determined by the processing information undergoes at encoding—at the time when context is bound with the items—but not at retrieval—when context is only recovered.     

Effect of Capacity for Care on cat admission trends at the Guelph Humane Society, 2011–2015

In recent years, there has been a growing concern regarding populations of cats who are homeless. Shelters are constantly overwhelmed by the influx of cats without caregivers and are seeking solutions to enhance positive outcomes for them. In 2014, the Guelph Humane Society implemented a population management program to expedite the movement of cats through the shelter by decreasing the average nonhuman animal’s length of stay using scheduled intakes to control for overcrowding and by implementing strategies to increase adoption rates. This study investigated the time trends in admission rates of cats to the Guelph Humane Society to assess the effectiveness of a population management program called Capacity for Care using a generalized linear autoregressive moving average model. From January 2011 to December 2015, a total of 3295 live cats were admitted to the Guelph Humane Society. When the analysis was adjusted to account for admissions of kittens, there was a significant reduction in admissions for adult cats (p < .01) following the introduction of the population management program. The results also showed a strong seasonal peak in total admissions during the summer months.     

Recombinant human bone morphogenetic protein-2 stimulates differentiation in primary cultures of fetal rat calvarial osteoblasts

Molecular mechanisms of lipid synthesis and their controls in hepatic stellate cells are not known. We have previously proposed that, in contrast to other fat storing cells, hepatic stellate cells are not involved in energy storage, but they represent a particular cell population specialized in storage of lipid-soluble substances, the major one being probably retinol. In agreement with this hypothesis, induction of the lipocyte phenotype in stellate cells is not under the control of insulin, but responds to retinoids and other molecules that modify the gene expression program in these cells. In the present study we have monitored the activity of the two major enzymes involved in lipid synthesis during the induction of the lipocyte phenotype in hepatic stellate cells: glycerol-3-phosphate dehydrogenase (GPDH) that mediates the de novo lipid synthesis, and lipoprotein lipase that mediates incorporation of plasma lipids. In early stages of lipocyte induction, both pathways of lipid synthesis are activated. When lipocytes have already constituted the lipid droplets, lipoprotein lipase pathway is downregulated, while GPDH activity remains high. Adult liver has been reported to lack lipoprotein lipase, but under stress, lipase activity was detected around and at the surface of the intrahepatic vasculature. We have now shown that the lipase activity can be induced in the hepatic stellate cells, located in the Disse's space. The high lipoprotein lipase activity under acute induction of lipocyte phenotype, followed by the low activity under conditions of metabolic equilibrium, are in compass with the increased activity of this enzyme under stress, and its low activity in adult liver parenchyma under normal conditions.     

Development of polyclonal antibodies for detection of aflatoxigenic molds involving culture filtrate and chimeric proteins expressed in Escherichia coli.

Polyclonal antibodies (PAb) were raised against an aflatoxigenic strain of Aspergillus parasiticus by using two different sources for antibody elicitation: (i) filtrate of a culture on which the fungus had been grown (ii) and two chimeric proteins, expressed in Escherichia coli as separate products, of the genes ver-1 and apa-2, which are involved in aflatoxin biosynthesis. The gene products were amplified by PCR, and each was cloned into the E. coli expression vector pGEX2T. Upon induction, the bacteria overexpressed 38- and 33-kDa chimeric proteins corresponding to the N-terminal domains of the genes ver-1 and apa-2, respectively. The chimeric proteins were isolated and affinity purified for use as antigens. The specificity of the raised antibodies was examined by enzyme-linked immunosorbent assay (ELISA). The PAbs raised against the culture filtrate reacted with all the species of Aspergillus and Penicillium tested but not with Fusarium species or corn gain. However, the PAbs elicited against the chimeric proteins were highly specific, showing significantly higher ELISA absorbance values (A405) against A. parasiticus and A. flavus than against the other fungi tested and the corn grain. The approach of utilizing gene products associated with aflatoxin biosynthesis for antibody production therefore appears to be feasible. Such a multiantibody system combined with the PCR technique, could provide a useful tool for the rapid, sensitive, and accurate detection of aflatoxin producers present in grains and foods.