ProDCoNN: Protein design using a convolutional neural network

Designing protein sequences that fold to a given three-dimensional (3D) structure has long been a challenging problem in computational structural biology with significant theoretical and practical implications. In this study, we first formulated this problem as predicting the residue type given the 3D structural environment around the C _α atom of a residue, which is repeated for each residue of a protein. We designed a nine-layer 3D deep convolutional neural network (CNN) that takes as input a gridded box with the atomic coordinates and types around a residue. Several CNN layers were designed to capture structure information at different scales, such as bond lengths, bond angles, torsion angles, and secondary structures. Trained on a very large number of protein structures, the method, called ProDCoNN (protein design with CNN), achieved state-of-the-art performance when tested on large numbers of test proteins and benchmark datasets.     

Morphometric and phylogenetic analysis of theDaviesia ulicifolia complex (Fabaceae, Mirbelieae)

Daviesia ulicifolia is a widespread species that exhibits complex variation throughout its range. Using ordination and cluster analysis of morphometric characters we resolved ten terminal taxa for phylogenetic analysis. A data set including these and five closely related species was coded for a combination of morphometric and qualitative characters and analysed using parsimony. This revealed thatD. ulicifolia is paraphyletic by inclusion ofD. acicularis, D. arenaria andD. microcarpa. One terminal cluster is more similar to an outgroup species (D. arthropoda) than toD. ulicifolia and should be treated as a new species. Given recent theoretical and empirical studies showing paraphyly to be both expected and observed at species level, we propose that all existing species in this group continue to be recognised taxonomically. We suggest subdividingD. ulicifolia into several subspecies.     

Genetic analysis of risk in clonal populations of forest trees

Summary A major concern arising from the culture of clonally propagated crops of forest trees is risk of catastrophic loss due to an agent or event not anticipated at the time of population establishment. Since danger of such a catastrophe depends to some degree on the genetic variability within clonal mixtures, attention has been focused on the number of clones needed to keep the risk of catastrophic loss below specified levels. In this paper, we describe a genetical analysis of susceptibility to a destructive agent and the effect that frequency of genes for susceptibility have on the number of clones needed to effectively manage this risk. As a part of the analysis, parameters representing the minimum unacceptable mortality rates in plantations () and acceptable levels of risk () are defined, and their effects on the number of single-pair matings needed for the production of clonal stock are evaluated. Dominance and recessive gene action models for a single two-allele genetic locus are investigated. Probabilities for plantation failure are functions of the gene frequency for the allele conferring susceptibility. These functions converge to zero for allele frequencies less than but to one for frequencies greater than or equal to . This convergence is periodic rather than monotonie, since probabilities for plantation failure increase rather than decrease over restricted ranges of increasing numbers of clones. Recessive and dominance gene actions are found to have different effects on the minimum number of clones needed to attain acceptable risk levels. For conditions in which substantial numbers of clones are required, selecting multiple clones per mating is an effective method for reducing the number of matings necessary to achieve acceptable risks.Paper No. 12480 of the Journal Series of the North Carolina Agriculture Research Service, Raleigh, NC 27695-7643, USA     

Benchmark Dose Profiles for Joint‐Action Quantal Data in Quantitative Risk Assessment

Summary Benchmark analysis is a widely used tool in public health risk analysis. Therein, estimation of minimum exposure levels, called Benchmark Doses (BMDs), that induce a prespecified Benchmark Response (BMR) is well understood for the case of an adverse response to a single stimulus. For cases where two agents are studied in tandem, however, the benchmark approach is far less developed. This article demonstrates how the benchmark modeling paradigm can be expanded from the single‐dose setting to joint‐action, two‐agent studies. Focus is on response outcomes expressed as proportions. Extending the single‐exposure setting, representations of risk are based on a joint‐action dose–response model involving both agents. Based on such a model, the concept of a benchmark profile (BMP) – a two‐dimensional analog of the single‐dose BMD at which both agents achieve the specified BMR – is defined for use in quantitative risk characterization and assessment. The resulting, joint, low‐dose guidelines can improve public health planning and risk regulation when dealing with low‐level exposures to combinations of hazardous agents.     

Cimicifuga racemosa extract BNO 1055 inhibits proliferation of the human prostate cancer cell line LNCaP

Extracts from black cohosh (Cimicifuga racemosa, CR) exert an anti-proliferative action in human breast cancer cell cultures, which has been attributed to an anti-estrogenic effect. However, CR constituents do not bind to either of the known estrogen receptors. Thus, the anti-tumor effect of CR me be mediated by mechanisms not involving these receptors. Polycyclic aromatic hydrocarbons are toxic environmental pollutants, which indirectly act as anti-estrogens by activating the aryl hydrocarbon receptor (AhR). The AhR is widely expressed in mammalian tissues and tumors. A recent screening study demonstrated activation of the AhR by a variety of herbal extracts, among others, CR. Since activation of the AhR causes inhibition of growth of prostate cancer cells, we addressed the question, whether CR may not only inhibit growth of breast cancer--but also of prostate cancer cells. In the AhR ligand assay, the CR extract BNO 1055 reduced tracer binding to 71% of the control demonstrating interaction of constituents of this extract with the receptor. Under basal as well as under estradiol- and dihydrotestosterone stimulated conditions, the CR extract dose dependently inhibited proliferation of LNCaP cells. A significant reduction of cell growth was observed at a concentration as low as 50 ng/ml. Thus, it is demonstrated for the first time that CR compounds potently inhibit the growth of human prostate cancer cells in vitro. This anti-proliferative effect may be mediated via the AhR.     

Inhibition of yeast tRNATrp aminoacylation by 4-methyltryptophan

The effect of the tryptophan analogue 4-methyltryptophan in Saccharomyces cerevisiae has been investigated. 4-Methyltryptophan inhibits the aminoacylation of tryptophan specific transfer ribonucleic acid (tRNA^Trp). The mode of inhibition is competitive and the analogue is not charged onto tRNA^Trp. Thus 4-methyltryptophan application depletes the cells from charged tRNA^Trp. As a consequence cell growth and protein synthesis are strongly reduced. 4-Methyltryptophan is degraded efficiently in culture media inoculated with the wild type strain; the effects of 4-methyltryptophan were therefore found to be transient.     

Fluorescence changes accompanying short-term light adaptations in photosystem I and photosystem II of the cyanobacterium <Emphasis Type="Italic">Synechocystis</Emphasis> sp. PCC 6803 and phycobiliprotein-impaired mutants: State 1/State 2 transitions and carotenoid-induced quenching of phycobilisomes

The features of the two types of short-term light-adaptations of photosynthetic apparatus, State 1/State 2 transitions, and non-photochemical fluorescence quenching of phycobilisomes (PBS) by orange carotene-protein (OCP) were compared in the cyanobacterium Synechocystis sp. PCC 6803 wild type, CK pigment mutant lacking phycocyanin, and PAL mutant totally devoid of phycobiliproteins. The permanent presence of PBS-specific peaks in the in situ action spectra of photosystem I (PSI) and photosystem II (PSII), as well as in the 77 K fluorescence excitation spectra for chlorophyll emission at 690 nm (PSII) and 725 nm (PSI) showed that PBS are constitutive antenna complexes of both photosystems. The mutant strains compensated the lack of phycobiliproteins by higher PSII content and by intensification of photosynthetic linear electron transfer. The detectable changes of energy migration from PBS to the PSI and PSII in the Synechocystis wild type and the CK mutant in State 1 and State 2 according to the fluorescence excitation spectra measurements were not registered. The constant level of fluorescence emission of PSI during State 1/State 2 transitions and simultaneous increase of chlorophyll fluorescence emission of PSII in State 1 in Synechocystis PAL mutant allowed to propose that spillover is an unlikely mechanism of state transitions. Blue–green light absorbed by OCP diminished the rout of energy from PBS to PSI while energy migration from PBS to PSII was less influenced. Therefore, the main role of OCP-induced quenching of PBS is the limitation of PSI activity and cyclic electron transport under relatively high light conditions.     

Management of threatened insect species in Australia, with particular reference to butterflies

Abstract   Advances in determination of conservation status of insects through evaluation of threats (rather than simple 'rarity' alone) help to set priorities for allocation of conservation resources, and formulate effective legislative treatment and field management for the most needy species. Summaries of several recent conservation studies on butterflies exemplify the variety of practical needs, amongst which habitat protection and enhancement is paramount. However, the paucity of biological and distributional information on most Australian insects necessitates considerable flexibility in approach, so that perceptions of conservation need may be highly subjective. Listing species for protection and conservation priority must be viewed as a dynamic process, with opportunity for rapid action, either to list or de-list taxa as research and recovery actions lead to change in perceived or real status and conservation need.     

Effects of phorbol esters on insulin receptor function and insulin action in hepatocytes: evidence for heterogeneity

We investigated the effect of phorbol 12-myristate 13-acetate (PMA), a protein kinase C (PKC) activator on insulin receptors and insulin action in freshly isolated and primary cultures of rat hepatocytes. PMA (1 x 10^–7 M) did not alter insulin receptor numbers or affinity either acutely or chronically but within 60 minute inactivated insulin stimulated tyrosine kinase of the insulin receptor. PKC activation inhibitied insulin (1 x 10^–7M) stimulation of glycogen and lipid synthesis with a decrease or no change in basal glycogenesis and lipogenesis respectively. However, PKC activation did not alter insulin stimulated or basal amino acid transport even though PCK activation inhibited insulin stimulation of the insulin. receptor tyrosine kinase. Thus, within one tissue, PKC activation has differential effect on insulin action depending on which pathway is examined. Furthermore, insulin stimulation of the insulin receptor tyrosine kinase may not be a necessary step for all insulin signaling pathways.     

Inhibitory effects and mechanisms of physiological conditions on the activity of enantiomeric forms of an α-helical antibacterial peptide against bacteria

Enantiomeric amphipathic α-helical antibacterial peptides were synthesized and their biophysical and biological properties under different physiological conditions were studied. In the absence of physiological factors, the l- and d-peptides exhibited similar antimicrobial activities against a broad spectrum of bacteria, even against clinical isolates with resistance to traditional antibiotics. However, in the presence of NaCl, CaCl₂ or human serum albumin (HSA) at physiological concentrations, the enantiomers revealed bacterium-species dependent attenuations in antibacterial activity. In the presence of salts the electrostatic interaction between the peptides and the biomembrane was inhibited. Salts, especially CaCl_2, weakened the ability of the peptides to permeabilize the outer membrane of Gram-negative bacteria, as determined by a 1-N-phenylnaphthylamine uptake assay. HSA exhibited variable inhibitory effects on the activity of the peptides when incubated with different bacterial strains. The peptides showed different binding association abilities to HSA at different molar ratios, regardless of their chirality, resulting in reduced peptide biological activity. The d-peptide performed better than its l-enantiomer in all conditions tested because of its resistance to proteolysis, and may therefore represent a promising candidate for development as a therapeutic agent.