Enzyme-assisted self-assembly under thermodynamic control

The production of functional molecular architectures through self-assembly is commonplace in biology, but despite advances^{1, 2, 3}, it is still a major challenge to achieve similar complexity in the laboratory. Self-assembled structures that are reproducible and virtually defect free are of interest for applications in three-dimensional cell culture^{4, 5}, templating⁶, biosensing⁷ and supramolecular electronics⁸. Here, we report the use of reversible enzyme-catalysed reactions to drive self-assembly. In this approach, the self-assembly of aromatic short peptide derivatives^{9, 10} provides a driving force that enables a protease enzyme to produce building blocks in a reversible and spatially confined manner. We demonstrate that this system combines three features: (i) self-correction—fully reversible self-assembly under thermodynamic control; (ii) component-selection—the ability to amplify the most stable molecular self-assembly structures in dynamic combinatorial libraries^{11, 12, 13}; and (iii) spatiotemporal confinement of nucleation and structure growth. Enzyme-assisted self-assembly therefore provides control in bottom-up fabrication of nanomaterials that could ultimately lead to functional nanostructures with enhanced complexities and fewer defects.

Fresh and cultured buccal cells as a source of mRNA and protein for molecular analysis

We developed a method for obtaining viable buccal cells from mouthwash samples for use as a source of mRNA and protein. Immunofluorescent analysis showed that most cells were derived from nonkeratinized parabasal epithelia, with a minor proportion of proliferative cells. Gene expression was detected in buccal cells using reverse transcription PCR, Western blot analysis, and immunofluorescence. Using a keratinocyte-specific medium, buccal cells could be cultured on Matrigel™-coated permeable filters for up to 2 weeks while maintaining the expression of some epithelial-specific markers, including cytokeratin 13, cytokeratin 10, transferrin receptor, and β-integrin. The basal marker cytokeratin 14 and Ki67, an indicator of cellular proliferation, were detected in a few cells. We show that buccal cells can be obtained from a noninvasive procedure for use as a source of material for biochemical analyses. A population of the buccal cells can be maintained in culture for up to 2 weeks using keratinocyte-specific medium in combination with extracellular matrix.

Myoepithelial molecular markers in human breast carcinoma PMC42-LA cells are induced by extracellular matrix and stromal cells

The microenvironment plays a key role in the cellular differentiation of the two main cell lineages of the human breast, luminal epithelial, and myoepithelial. It is not clear, however, how the components of the microenvironment control the development of these cell lineages. To investigate how lineage development is regulated by 3-D culture and microenvironment components, we used the PMC42-LA human breast carcinoma cell line, which possesses stem cell characteristics. When cultured on a two-dimensional glass substrate, PMC42-LA cells formed a monolayer and expressed predominantly luminal epithelial markers, including cytokeratins 8, 18, and 19; E-cadherin; and sialomucin. The key myoepithelial-specific proteins alpha-smooth muscle actin and cytokeratin 14 were not expressed. When cultured within Engelbreth-Holm- Swarm sarcoma-derived basement membrane matrix (EHS matrix), PMC42-LA cells formed organoids in which the expression of luminal markers was reduced and the expression of other myoepithelial-specific markers (cytokeratin 17 and P-cadherin) was promoted. The presence of primary human mammary gland fibroblasts within the EHS matrix induced expression of the key myoepithelial-specific markers, alpha-smooth muscle actin and cytokeratin 14. Immortalized human skin fibroblasts were less effective in inducing expression of these key myoepithelial-specific markers. Confocal dual-labeling showed that individual cells expressed luminal or myoepithelial proteins, but not both. Conditioned medium from the mammary fibroblasts was equally effective in inducing myoepithelial marker expression. The results indicate that the myoepithelial lineage is promoted by the extracellular matrix, in conjunction with products secreted by breast-specific fibroblasts. Our results demonstrate a key role for the breast microenvironment in the regulation of breast lineage development.

System boundary selection in life-cycle inventories using hybrid approaches

Life-cycle assessment (LCA) is a method for evaluating the environmental impacts of products holistically, including direct and supply chain impacts. The current LCA methodologies and the standards by the International Organization for Standardization (ISO) impose practical difficulties for drawing system boundaries; decisions on inclusion or exclusion of processes in an analysis (the cutoff criteria) are typically not made on a scientific basis. In particular, the requirement of deciding which processes could be excluded from the inventory can be rather difficult to meet because many excluded processes have often never been assessed by the practitioner, and therefore, their negligibility cannot be guaranteed. LCA studies utilizing economic input−output analysis have shown that, in practice, excluded processes can contribute as much to the product system under study as included processes; thus, the subjective determination of the system boundary may lead to invalid results. System boundaries in LCA are discussed herein with particular attention to outlining hybrid approaches as methods for resolving the boundary selection problem in LCA. An input−output model can be used to describe at least a part of a product system, and an ISO-compatible system boundary selection procedure can be designed by applying hybrid input−output-assisted approaches. There are several hybrid input−output analysis-based LCA methods that can be implemented in practice for broadening system boundary and also for ISO compliance.

Stat5 as a diagnostic marker for leukemia

The Jak-Stat-Socs pathway is an important component of cytokine receptor signaling. Not surprisingly, perturbation of this pathway is implicated in diseases of hematopoietic and immune origin, including leukemia, lymphoma and immune deficiencies. This review examines the role of a key component of this pathway, Stat5. This has been shown to be activated in a variety of leukemias and myeloproliferative disorders, including downstream of a range of key oncogenes where it has been shown to play an important role in mediating their effects. Therefore, Stat5 represents a useful pan-leukemia/myeloproliferative disorder diagnostic marker and key therapeutic end point, as well as representing an attractive therapeutic target for these disorders.

Molecular analysis of Australian Newcastle disease virus isolates

The results presented demonstrate that outbreaks of virulent Newcastle disease in Australia arose from the emergence of virulent virus from an endemic avirulent quasispecies. Environmental selection pressures, or industrial practices, led to the emergence of this species and its dominance in several distinct ourbreaks from 1998-2002.

Permanent genetic resources added to molecular ecology resources database 1 August 2010 – 30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis · Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Photoinduced reversible shape conversion of silver nanoparticles assisted by TiO₂.

Silver nanoprisms were transformed into nanodecahedra through photoinduction of ultraviolet (UV) light in the presence of titanium dioxide (TiO2) quantum dots (QDs). Subsequently, the silver nanodecahedra were reconverted to silver nanoprisms under sodium lamp if there was sufficient citrate in the reaction system. The localized surface plasmon resonance (LSPR) optical properties of silver nanoparticles were tuned during photoinduced shape conversion. The photocatalytic activity of TiO2 QDs assisted the conversion of prisms to decahedra upon UV light irradiation. Nevertheless, the presence of TiO2 did not inhibit the photoinduced reconversion from decahedra to prisms by sodium light. It was demonstrated that citrate was indispensable in the photoinduction process. In addition, oxygen in solution played a vital role in the reversible shape conversion of silver nanoparticles. Moreover, simulated sunlight can convert silver nanoprisms to nanodecahedra instead of UV light with assistance of TiO2 QDs, which would promote the photoinduced reaction of silver nanoparticles based on a natural light source.

Effects of Mitochondrial DNA Rate Variation on Reconstruction of Pleistocene Demographic History in a Social Avian Species, Pomatostomus superciliosus

Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (TMRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in TMRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of TMRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade.

Morphological and molecular investigations of the holocephalan elephant fish nephron: the existence of a countercurrent-like configuration and two separate diluting segments in the distal tubule

In marine cartilaginous fish, reabsorption of filtered urea by the kidney is essential for retaining a large amount of urea in their body. However, the mechanism for urea reabsorption is poorly understood due to the complexity of the kidney. To address this problem, we focused on elephant fish (Callorhinchus milii) for which a genome database is available, and conducted molecular mapping of membrane transporters along the different segments of the nephron. Basically, the nephron architecture of elephant fish was similar to that described for elasmobranch nephrons, but some unique features were observed. The late distal tubule (LDT), which corresponded to the fourth loop of the nephron, ran straight near the renal corpuscle, while it was convoluted around the tip of the loop. The ascending and descending limbs of the straight portion were closely apposed to each other and were arranged in a countercurrent fashion. The convoluted portion of LDT was tightly packed and enveloped by the larger convolution of the second loop that originated from the same renal corpuscle. In situ hybridization analysis demonstrated that co-localization of Na(+),K(+),2Cl(-) cotransporter 2 and Na(+)/K(+)-ATPase α1 subunit was observed in the early distal tubule and the posterior part of LDT, indicating the existence of two separate diluting segments. The diluting segments most likely facilitate NaCl absorption and thereby water reabsorption to elevate urea concentration in the filtrate, and subsequently contribute to efficient urea reabsorption in the final segment of the nephron, the collecting tubule, where urea transporter-1 was intensely localized.

The relative importance of spatial proximity, kin selection and potential ‘greenbeard’ signals on provisioning behaviour among helpers in a cooperative bird

© 2015 Springer-Verlag Berlin Heidelberg Many hypotheses have been proposed to account for cooperative behaviour, with those favouring kin selection receiving the greatest support to date. However, the importance of relatedness becomes less clear in complex societies where interactions can involve both kin and non-kin. To help clarify this, we examined the relative effect of indirect versus key direct benefit hypotheses in shaping cooperative decisions. We assessed the relative importance of likely reciprocal aid (as measured by spatial proximity between participants), kin selection (using molecular-based relatedness indices) and putative signals of relatedness (vocal similarity) on helper/helper cooperative provisioning dynamics in bell miners (Manorina melanophrys), a species living in large, complex societies. Using network analysis, we quantified the extent of shared provisioning (helping at the same nests) among individual helpers (excluding breeding pairs) over three seasons and 4290 provisioning visits, and compared these with the location of individuals within a colony and networks built using either genetic molecular relatedness or call similarity indices. Significant levels of clustering were observed in networks; individuals within a cluster were more closely related to each other than other colony members, and cluster membership was stable across years. The probability of a miner helping at another’s nest was not simply a product of spatial proximity and thus the potential for reciprocal aid. Networks constructed using helping data were significantly correlated to those built using molecular data in 5 of 10 comparisons, compared to 8 of 10 comparisons for networks constructed using call similarity. This suggests an important role of kinship in shaping helping dynamics in a complex cooperative society, apparently determined via an acoustic ‘greenbeard’ signal in this system.

Widespread convergence in toxin resistance by predictable molecular evolution

The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na(+)/K(+)-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na(+)/K(+)-ATPase H1-H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na(+)/K(+)-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses.

Selection and characterization of probiotic culture of Streptococcus thermophilus from dahi

For the isolation of probiotic cultures of Streptococcus thermophilus from dahi, we collected 120 samples from the southern regions of Punjab, Pakistan. Eleven isolates were obtained, and six were scrutinized for antibacterial activities against food-borne pathogens. The carbohydrate fermentation profile of these six strains was determined by the API50 CHL system. Additionally, these strains were amplified for their 16S rRNA regions to confirm their genotypic relationship. Furthermore, phenotypic characteristics among these strains were established by S-layer protein analysis of their cell walls by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and by plasmid profiling. The outer cell wall layers of these strains have 6-14 different sizes of protein bands of 27, 34, 37, 40, 45 and 60 kDa molecular weight. Similarly, except S02FT, all strains have a single prominent plasmid of 23 kbp, whereas S02FT has an additional plasmid of 9 kbp. On the basis of this unique feature and a wide spectrum of killing patterns against pathogenic bacteria, S. thermophilus S02FT was further characterized. This culture showed an optimum antibacterial activity of 800 AU/ml at pH 5.0-5.5 and a temperature of 30-37°C. It grows well in in vitro acidic conditions and tolerates bile salt up to 2% concentration. It was resistant to nalidixic acid, ciprofloxacin, gentamicin and sulphamethoxazol, but showed intermediate behaviour to vancomycin and erythromycin.