Modification of the butenyl-spinosyns utilizing cross-metathesis

The discovery of a strain of Saccharopolyspora sp. that produced a number of spinosyn analogs that had not before been seen gave an ideal opportunity for extending our knowledge of that SAR of these highly efficacious insecticides. In particular, these compounds contained a butenyl group connected to C-21 which in the regular spinosyns was substituted with a simple ethyl group. The double bond therefore gave us a handle to further modify this position allowing us to substitute different groups there. In this paper we show one of our approaches to this modification using olefin cross-metathesis. Even though the spinosyns were not highly efficient substrates for metathesis reactions, we were nevertheless successful in extending their chemistry accordingly.     

To Imagine an Australian Museum

ABSTRACT

Museums are our memory banks. They tell us where we have come from. They also allow us to imagine where we are heading. Which is why it should trouble us that there has never been a truly Australian museum. Each of our state and federal museums has been built on Aboriginal collections, and each has been built on distinctly Western or European concepts, values, categories and practices. Some of these are unavoidable, but are they all? Are we too far down the path to restump the foundations of our institutions and the narratives they perpetuate in public life? The South Australian Museum holds one of the most important collections of Aboriginal material culture in the world. It is, therefore, given the story it can tell about ancient and enduring cultures, one of the most important collections of human heritage on our planet. What we do with such collections, and what we don’t, defines us. This is the great challenge of contemporary custodianship. These collections are calling us out. In this lecture I examine the South Australian Museum’s response to this challenge. Over the past two years our Museum has undertaken a comprehensive rethink of our policies and practices and the politics of both. We are also transforming the way we work with Aboriginal communities and custodians. This is not simply a question of how collections are displayed or exhibitions are developed. We are rethinking the terms of our custodianship, and the kind of truly Australian Museum that could evolve around those new foundations.     

"SCINT," a Fortran IV program for the analysis of data for doubly labeled and variably quenched liquid scintillation samples

For some time now, we have been using double label techniques in our laboratory. In our work we generate large numbers of samples containing ¹⁴C and ³H and varying amounts of quenching agents. The analysis of this data led us to develop SCINT, a simple and versatile program written in FORTRAN IV for use on our Control Data 1700 computer facility. We feel that such a program may be of use to the many workers now involved with dual isotope procedures who also have access to similar computer facilities.     

Insights into the ultrastructural morphology of novel Planctomycetes

Knowledge of the interesting phylum of Planctomycetes has increased in the last decades both due to cultural and molecular methods. Although a restricted number of species have been described to date, this group presents a much larger diversity that has been mainly revealed by molecular ecology studies. Isolation experiments allowed us to get a number of new Planctomycetes taxa that extend the already described ones. In this work we present the ultrastructural morphological characterization of these new taxa as well as we give new details of Aquisphaera giovannonii ultrastructure. Furthermore, our interpretation on Planctomycetes cell envelope is provided.     

The isotope effects on a hydrogen transfer using path integral instanton method

In our previous work, we have developed an algorithm for calculating the tunnelling splittings using path integral instanton method with the discretised imaginary time approach. Our algorithm has enabled us to take a zero temperature limit, efficiently and accurately. In this paper, we investigate the effect of isotopomers on the tunnelling splittings and semiclassical tunnelling paths of a hydrogen transfer in a model molecular system HO₂.     

How to Get the Most out of Your Curation Effort

Large-scale annotation efforts typically involve several experts who may disagree with each other. We propose an approach for modeling disagreements among experts that allows providing each annotation with a confidence value (i.e., the posterior probability that it is correct). Our approach allows computing certainty-level for individual annotations, given annotator-specific parameters estimated from data. We developed two probabilistic models for performing this analysis, compared these models using computer simulation, and tested each model's actual performance, based on a large data set generated by human annotators specifically for this study. We show that even in the worst-case scenario, when all annotators disagree, our approach allows us to significantly increase the probability of choosing the correct annotation. Along with this publication we make publicly available a corpus of 10,000 sentences annotated according to several cardinal dimensions that we have introduced in earlier work. The 10,000 sentences were all 3-fold annotated by a group of eight experts, while a 1,000-sentence subset was further 5-fold annotated by five new experts. While the presented data represent a specialized curation task, our modeling approach is general; most data annotation studies could benefit from our methodology.     

Emerging structural biology of TRPM subfamily channels

TRPM family (Transient receptor potential channels, M for melastatin) is a group of intrinsic plasma membrane ion channels which are widely expressed throughout human body. It has been identified as a potent entry point of working desperate diseases out in a new way with newfangled ideas and safer technological means. In our review, we discussed the common and unique properties of TRPM family with the elaborate narrate in their overall structures, different states and the underlying activation mechanism. Thus, this review can help to consummate the limited work of TRPM family and provide novel therapeutic targets of certain diseases.     

Species assembly in model ecosystems, I: Analysis of the population model and the invasion dynamics

Recently we have introduced a simplified model of ecosystem assembly (Capitán et al., 2009) for which we are able to map out all assembly pathways generated by external invasions in an exact manner. In this paper we provide a deeper analysis of the model, obtaining analytical results and introducing some approximations which allow us to reconstruct the results of our previous work. In particular, we show that the population dynamics equations of a very general class of trophic-level structured food-web have an unique interior equilibrium point which is globally stable. We show analytically that communities found as end states of the assembly process are pyramidal and we find that the equilibrium abundance of any species at any trophic level is approximately inversely proportional to the number of species in that level. We also find that the per capita growth rate of a top predator invading a resident community is key to understand the appearance of complex end states reported in our previous work. The sign of these rates allows us to separate regions in the space of parameters where the end state is either a single community or a complex set containing more than one community. We have also built up analytical approximations to the time evolution of species abundances that allow us to determine, with high accuracy, the sequence of extinctions that an invasion may cause. Finally we apply this analysis to obtain the communities in the end states. To test the accuracy of the transition probability matrix generated by this analytical procedure for the end states, we have compared averages over those sets with those obtained from the graph derived by numerical integration of the Lotka-Volterra equations. The agreement is excellent.     

From a crisis to an opportunity: Eight insights for doing science in the COVID‐19 era and beyond

The COVID‐19 crisis has forced researchers in Ecology to change the way we work almost overnight. Nonetheless, the pandemic has provided us with several novel components for a new way of conducting science. In this perspective piece, we summarize eight central insights that are helping us, as early career researchers, navigate the uncertainties, fears, and challenges of advancing science during the COVID‐19 pandemic. We highlight how innovative, collaborative, and often Open Science‐driven developments that have arisen from this crisis can form a blueprint for a community reinvention in academia. Our insights include personal approaches to managing our new reality, maintaining capacity to focus and resilience in our projects, and a variety of tools that facilitate remote collaboration. We also highlight how, at a community level, we can take advantage of online communication platforms for gaining accessibility to conferences and meetings, and for maintaining research networks and community engagement while promoting a more diverse and inclusive community. Overall, we are confident that these practices can support a more inclusive and kinder scientific culture for the longer term.     

Responsiveness of the interrenal tissue of Jundiá (Rhamdia quelen) to an in vivo ACTH test following acute exposure to sublethal concentrations of agrichemicals

As in many aquatic environments, pollution is a widespread problem in Southern Brazil. In our previous work, we demonstrated that sublethal contamination with some agrichemicals impairs the capacity of fishes to elevate cortisol levels in response to an additional acute stressor. In earlier experiments, the experimental design did not allow us to conclude where this effect occurs. In the present work, we used the adrenocorticotropic hormone (ACTH) challenge test to help us identify if the impairment occur in the interrenal tissue. For this purpose, five experiments were conducted, each with one specific agrichemical (methyl-parathion, atrazine+simazine, atrazine, tebuconazole, and glyphosate) in sublethal concentrations of 16.6% of the LC(50-96h), as previously determined. Fish were subjected to the ACTH challenge test protocol as follows: group 1, were non-injected and maintained as the specific control group; group 2 received an injection of the vehicle alone (the saline group); and group 3 receive an injection of ACTH. One hour later, blood samples were taken from the caudal plexus, using sterile syringes. In all specific control groups, the injection of ACTH induced a strong rise in plasma cortisol, compared with the fish injected only with the vehicle and the non-injected group. Fish exposed to methyl-parathion and tebuconazole did not elevate cortisol in response to the ACTH injection, with values significantly lower than the control fish. Fish exposed to sublethal concentrations of atrazine+simazine, atrazine, and glyphosate showed a rise in plasma cortisol very similar to the control fish. We conclude that the ACTH challenge test revealed that R. quelen exposed to sublethal concentrations of tebuconazole and methyl-parathion had a reduced ability to elevate plasma cortisol in response to an intraperitoneal (i.p.) injection of exogenous ACTH, indicating that the interrenal tissue is the site of the impairment within the HPI axis. These ACTH challenge tests also revealed that the impairment of the cortisol response verified in fish exposed to atrazine+simazine and glyphosate, as shown in our previous work, seems to be related to steps of cortisol secretion in higher levels within the HPI axis.     

The origins of belonging: social motivation in infants and young children

Our reliance on our group members has exerted a profound influence over our motivation: successful group functioning requires that we are motivated to interact, and engage, with those around us. In other words, we need to belong. In this article, I explore the developmental origins of our need to belong. I discuss existing evidence that, from early in development, children seek to affiliate with others and to form long-lasting bonds with their group members. Furthermore, when children are deprived of a sense of belonging, it has negative consequences for their well-being. This focus on social motivation enables us to examine why and in what circumstances children engage in particular behaviours. It thus provides an important complement to research on social cognition. In doing so, it opens up important questions for future research and provides a much-needed bridge between developmental and social psychology.     

The selenocysteine insertion sequence binding protein SBP is different from the Y-box protein dbpB

In eukaryotes, translation of internal UGA selenocysteine codons requires the SECIS stem-loop structure in the 3'UTR of selenoprotein mRNAs. In an earlier work, we identified SBP as a selenocysteine insertion sequence (SECIS)-binding protein. Here, the yeast three-hybrid screen was employed to capture the cDNA of SBP. One candidate, satisfying the genetic screens, was identified as the already known dbpB protein. Although it was also found by another group, but with a different strategy, to carry SECIS-binding activity, further experiments enabled us to show that dbpB was unable to bind the SECIS element in vitro. Altogether, our findings led us to conclude that, under our conditions, dbpB and SBP are two distinct proteins.     

Discussion on “Adaptive enrichment designs with a continuous biomarker” by Nigel Stallard

We congratulate Dr. Nigel Stallard on his stimulating paper on adaptive enrichment designs with a continuous biomarker. Dr. Stallard details a framework for a large and interesting class of enrichment procedures. His work has motivated us to offer some thoughts in response. Dr. Stallard's strategy is to use the maximum of a test statistic over a set of possible threshold values to define the enriched population to be sampled in a second stage. This reminds us of procedures for identifying a change point, a biomarker value beyond which the effect of treatment is increased. For simplicity we focus our comments on Dr. Stallard's Rule 1 for selecting the second-stage sampling threshold. Using this rule, we present the likelihood ratio approach for adaptive testing and compare it to Dr. Stallard's approach for a few scenarios.     

Development of an efficient semisynthetic modification of FR901459 via a novel regioselective N,O-acyl migration

HCV utilizes cellular protein cyclophilins in the virus replication cycle and cyclophilin inhibitors have become a new class of anti-HCV agents. In our screening of natural products, we identified a unique cyclosporin analogue, FR901459, as a cyclophilin inhibitor with potent anti-HCV activity. In this work, we developed an efficient synthetic methodology to prepare FR901459 derivatives via an N, O-acyl migration reaction. This method allows us to efficiently manipulate the amino acid residues at the 3 position while avoiding lengthy total synthesis for each compound. By using this methodology, we discovered 4, which has superior anti-HCV activity and decreased immunosuppressive activity compared to FR901459.     

Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations, for observables that explicitly enter the coarse-grained Hamiltonian. We show that this requirement leads to equivalency of the corresponding partition functions, resulting in a one-step renormalization. Compared to prior works exploiting similar ideas, the main novelty of this work is the introduction of a highly compact set of Hamiltonian basis functions, based on molecular interaction potentials. We demonstrate that such compactification allows us to reproduce many-body effects, generated by one-step renormalization, at low computational cost. In addition, compact Hamiltonians greatly increase the likelihood of finding unique solutions for the coarse-grained force-field parameter values. By successfully applying our molecular renormalization group coarse-graining technique to double-stranded DNA, we solved, for the first time, a long-standing problem in coarse-graining polymer systems, namely, how to accurately capture the correlations among various polymeric degrees of freedom. Excellent agreement is found among atomistic and coarse-grained distribution functions for various structural observables, including those not included in the Hamiltonian. We also suggest higher-order generalization of this method, which may allow capturing more subtle correlations in biopolymer dynamics.     

Punish and Voice: Punishment Enhances Cooperation when Combined with Norm-Signalling

Material punishment has been suggested to play a key role in sustaining human cooperation. Experimental findings, however, show that inflicting mere material costs does not always increase cooperation and may even have detrimental effects. Indeed, ethnographic evidence suggests that the most typical punishing strategies in human ecologies (e.g., gossip, derision, blame and criticism) naturally combine normative information with material punishment. Using laboratory experiments with humans, we show that the interaction of norm communication and material punishment leads to higher and more stable cooperation at a lower cost for the group than when used separately. In this work, we argue and provide experimental evidence that successful human cooperation is the outcome of the interaction between instrumental decision-making and the norm psychology humans are provided with. Norm psychology is a cognitive machinery to detect and reason upon norms that is characterized by a salience mechanism devoted to track how much a norm is prominent within a group. We test our hypothesis both in the laboratory and with an agent-based model. The agent-based model incorporates fundamental aspects of norm psychology absent from previous work. The combination of these methods allows us to provide an explanation for the proximate mechanisms behind the observed cooperative behaviour. The consistency between the two sources of data supports our hypothesis that cooperation is a product of norm psychology solicited by norm-signalling and coercive devices.     

The logical structure of dreams and their relation to reality.

The contradictions and non sequiturs often found in dreams (or, equivalently, dream-narratives) are not in fact logical errors, but express and work with a type of logic that characterizes the deepest dimensions of our waking reality. These are the dimensions in which we deal with ourselves as a whole, our lives as a whole, or with the sense of reality as a whole. We do so, for example, in situations of deep personal transformation, or of recognition of deep difference of outlook. The paper argues that the logic of these situations is validly one of contradiction and non sequitur, that dreams sometimes express and work with these kinds of situations, and that these kinds of dreams therefore validly involve the same kind of logic. These kinds of dreams consequently also express insight into the sense that our lives or existence as a whole has for us. In achieving that insight, they actively orient, situate, or resituate us in our relation to our lives or existence as a whole. In this respect they are in themselves a practice of philosophy. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A protocol for analysing thermal stress in insects using infrared thermography

The study of insect responses to thermal stress has involved a variety of protocols and methodologies that hamper the ability to compare results between studies. For that reason, the development of a protocol to standardize thermal assays is necessary. In this sense, infrared thermography solves some of the problems allowing us to take continuous temperature measurements without handling the individuals, an important fact in cold-blooded organisms like insects. Here, we present a working protocol based on infrared thermography to estimate both cold and heat thermal stress in insects. We analyse both the change in the body temperature of individuals and their behavioural response. In addition, we used partial least squares regression for the statistical analysis of our data, a technique that solves the problem of having a large number of variables and few individuals, allowing us to work with rare or endemic species. To test our protocol, we chose two species of congeneric, narrowly distributed dung beetles that are endemic to the southeastern part of the Iberian Peninsula. With our protocol we have obtained five variables in the response to cold and twelve in the response to heat. With this methodology we discriminate between the two flightless species of Jekelius through their thermal response. In response to cold, Jekelius hernandezi showed a higher rate of cooling and reached higher temperatures of stupor and haemolymph freezing than Jekelius punctatolineatus. Both species displayed similar thermoregulation ranges before reaching lethal body temperature with heat stress. Overall, we have demonstrated that infrared thermography is a suitable method to assess insect thermal responses with a high degree of sensitivity, allowing for the discrimination between closely related species.     

Use of monoclonal antibody 225.28S in the study of nevus cells in culture

The aim of this work is to identify and purify cultured nevus cells. We used for our study monoclonal antibody 225.28S. This antibody reacts with a surface antigen which is expressed by nevus cells and melanoma cells, but it does not react with normal melanocytes. We studied 10 dermic nevi and we observed that antigenic determinant survives in cultured nevus cells. These results allowed us to employ the method of panning for purify cultured nevus cells.     

Configurational-bias sampling technique for predicting side-chain conformations in proteins

Prediction of side-chain conformations is an important component of several biological modeling applications. In this work, we have developed and tested an advanced Monte Carlo sampling strategy for predicting side-chain conformations. Our method is based on a cooperative rearrangement of atoms that belong to a group of neighboring side-chains. This rearrangement is accomplished by deleting groups of atoms from the side-chains in a particular region, and regrowing them with the generation of trial positions that depends on both a rotamer library and a molecular mechanics potential function. This method allows us to incorporate flexibility about the rotamers in the library and explore phase space in a continuous fashion about the primary rotamers. We have tested our algorithm on a set of 76 proteins using the all-atom AMBER99 force field and electrostatics that are governed by a distance-dependent dielectric function. When the tolerance for correct prediction of the dihedral angles is a <20 degrees deviation from the native state, our prediction accuracies for chi1 are 83.3% and for chi1 and chi2 are 65.4%. The accuracies of our predictions are comparable to the best results in the literature that often used Hamiltonians that have been specifically optimized for side-chain packing. We believe that the continuous exploration of phase space enables our method to overcome limitations inherent with using discrete rotamers as trials.