An LC–MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology

Introduction

Given a raw LC–MS dataset, it is often required to rapidly generate initial hypotheses, in conjunction with other ‘omics’ datasets, without time-consuming lipid verifications. Furthermore, for meta-analysis of many datasets, it may be impractical to conduct exhaustive confirmatory analyses. In other cases, samples for validation may be difficult to obtain, replicate or maintain. Thus, it is critical that the computational identification of lipids is of appropriate accuracy, coverage, and unbiased by a researcher’s experience and prior knowledge.

Objectives

We aim to prescribe a systematic framework for lipid identifications, without usage of their characteristic retention-time by fully exploiting their underlying mass features.

Results

Initially, a hybrid technique, for deducing both common and distinctive daughter ions, is used to infer parent lipids from deconvoluted spectra. This is followed by parent confirmation using basic knowledge of their preferred product ions. Using the framework, we could achieve an accuracy of ~?80% by correctly identified 101 species from 18 classes in Chinese hamster ovary (CHO) cells. The resulting inferences could explain the recombinant-producing capability of CHO-SH87 cells, compared to non-producing CHO-K1 cells. For comparison, a XCMS-based study of the same dataset, guided by a user’s ad-hoc knowledge, identified less than 60 species of 12 classes from thousands of possibilities.

Conclusion

We describe a systematic LC–MS-based framework that identifies lipids for rapid hypothesis generation.

     

Variation in gaze-following between two Asian colobine monkeys

Gaze-following is a basic cognitive ability found in numerous primate and nonprimate species. However, little is known about this ability and its variation in colobine monkeys. We compared gaze-following of two Asian colobines—François’ langurs (Trachypithecus francoisi) and golden snub-nosed monkeys (Rhinopithecus roxellana). Although both species live in small polygynous family units, units of the latter form multilevel societies with up to hundreds of individuals. François’ langurs (N = 15) were less sensitive to the gaze of a human experimenter than were golden snub-nosed monkeys (N = 12). We then tested the two species using two classic inhibitory control tasks—the cylinder test and the A-not-B test. We found no difference between species in inhibitory control, which called into question the nonsocial explanation for François’ langur’s weaker sensitivity to human gaze. These findings are consistent with the social intelligence hypothesis, which predicted that golden snub-nosed monkeys would outperform François’ langurs in gaze-following because of the greater size and complexity of their social groups. Furthermore, our results underscore the need for more comparative studies of cognition in colobines, which should provide valuable opportunities to test hypotheses of cognitive evolution.     

Coarse-to-Fine Construction for High-Resolution Representation in Visual Working Memory

Background

This study explored whether the high-resolution representations created by visual working memory (VWM) are constructed in a coarse-to-fine or all-or-none manner. The coarse-to-fine hypothesis suggests that coarse information precedes detailed information in entering VWM and that its resolution increases along with the processing time of the memory array, whereas the all-or-none hypothesis claims that either both enter into VWM simultaneously, or neither does.

Methodology/Principal Findings

We tested the two hypotheses by asking participants to remember two or four complex objects. An ERP component, contralateral delay activity (CDA), was used as the neural marker. CDA is higher for four objects than for two objects when coarse information is primarily extracted; yet, this CDA difference vanishes when detailed information is encoded. Experiment 1 manipulated the comparison difficulty of the task under a 500-ms exposure time to determine a condition in which the detailed information was maintained. No CDA difference was found between two and four objects, even in an easy-comparison condition. Thus, Experiment 2 manipulated the memory array’s exposure time under the easy-comparison condition and found a significant CDA difference at 100 ms while replicating Experiment 1′s results at 500 ms. In Experiment 3, the 500-ms memory array was blurred to block the detailed information; this manipulation reestablished a significant CDA difference.

Conclusions/Significance

These findings suggest that the creation of high-resolution representations in VWM is a coarse-to-fine process.     

Endosperm Balance Number and the polar-nuclei activation hypotheses for endosperm development in interspecific crosses of Solanaceae and Gramineae,respectively

The Endosperm Balance Number (EBN) and the polar-nuclei activation (PNA) hypotheses have been developed to interpret, explain and predict interspecific and interploidy crossabilities in the Solanums and the Gramineae, respectively. Although these two hypotheses evolved independently, they share a number of common features. Assignment of EBNs and activation/response values (AVs/RVs) depend on plumpness, size, and germinability of hybrid seeds. Also, both hypotheses emphasize the importance of a balanced parental genic contribution for the normal development of endosperm. However, in the EBN hypothesis a 2 maternal1 paternal EBN ratio is a prerequisite for successful interspecific crossability, while the PNA hypothesis is based on the stimulative strength of the male nuclei to initiate mitotic divisions in the primary endosperm nucleus and is idependent on a 21 ratio between the RV of the polar nuclei and the AV of the male gamete. Differences and similarities betweeen the EBN and PNA hypotheses are summarized and contrasted. It is proposed that EBN and PNA be considered as the same concept.     

Gender differences and a new adult eukaryotic record for upper thermal tolerance in the desert moss Syntrichia caninervis

1.

Two competing hypotheses relating to thermostress were proposed to understand skewed sex ratios in Syntrichia caninervis, a reproductive investment hypothesis and a wildfire selection hypothesis.     

Homologous recombination is unlikely to play a major role in influenza B virus evolution

Background

The role of migratory birds and of poultry trade in the dispersal of highly pathogenic H5N1 is still the topic of intense and controversial debate. In a recent contribution to this journal, Flint argues that the strict application of the scientific method can help to resolve this issue.

Discussion

We argue that Flint's identification of the scientific method with null hypothesis testing is misleading and counterproductive. There is far more to science than the testing of hypotheses; not only the justification, bur also the discovery of hypotheses belong to science. We also show why null hypothesis testing is weak and that Bayesian methods are a preferable approach to statistical inference. Furthermore, we criticize the analogy put forward by Flint between involuntary transport of poultry and long-distance migration.

Summary

To expect ultimate answers and unequivocal policy guidance from null hypothesis testing puts unrealistic expectations on a flawed approach to statistical inference and on science in general.     

A bayesian method for evaluating and discovering disease loci associations

Background

A genome-wide association study (GWAS) typically involves examining representative SNPs in individuals from some population. A GWAS data set can concern a million SNPs and may soon concern billions. Researchers investigate the association of each SNP individually with a disease, and it is becoming increasingly commonplace to also analyze multi-SNP associations. Techniques for handling so many hypotheses include the Bonferroni correction and recently developed Bayesian methods. These methods can encounter problems. Most importantly, they are not applicable to a complex multi-locus hypothesis which has several competing hypotheses rather than only a null hypothesis. A method that computes the posterior probability of complex hypotheses is a pressing need.

Methodology/Findings

We introduce the Bayesian network posterior probability (BNPP) method which addresses the difficulties. The method represents the relationship between a disease and SNPs using a directed acyclic graph (DAG) model, and computes the likelihood of such models using a Bayesian network scoring criterion. The posterior probability of a hypothesis is computed based on the likelihoods of all competing hypotheses. The BNPP can not only be used to evaluate a hypothesis that has previously been discovered or suspected, but also to discover new disease loci associations. The results of experiments using simulated and real data sets are presented. Our results concerning simulated data sets indicate that the BNPP exhibits both better evaluation and discovery performance than does a p-value based method. For the real data sets, previous findings in the literature are confirmed and additional findings are found.

Conclusions/Significance

We conclude that the BNPP resolves a pressing problem by providing a way to compute the posterior probability of complex multi-locus hypotheses. A researcher can use the BNPP to determine the expected utility of investigating a hypothesis further. Furthermore, we conclude that the BNPP is a promising method for discovering disease loci associations.     

The Role of Ontogeny in the Evolution of Human Cooperation

To explain the evolutionary emergence of uniquely human skills and motivations for cooperation, Tomasello et al. (2012, in Current Anthropology 53(6):673–92) proposed the interdependence hypothesis. The key adaptive context in this account was the obligate collaborative foraging of early human adults. Hawkes (2014, in Human Nature 25(1):28–48), following Hrdy (Mothers and Others, Harvard University Press, 2009), provided an alternative account for the emergence of uniquely human cooperative skills in which the key was early human infants’ attempts to solicit care and attention from adults in a cooperative breeding context. Here we attempt to reconcile these two accounts. Our composite account accepts Hrdy’s and Hawkes’s contention that the extremely early emergence of human infants’ cooperative skills suggests an important role for cooperative breeding as adaptive context, perhaps in early Homo. But our account also insists that human cooperation goes well beyond these nascent skills to include such things as the communicative and cultural conventions, norms, and institutions created by later Homo and early modern humans to deal with adult problems of social coordination. As part of this account we hypothesize how each of the main stages of human ontogeny (infancy, childhood, adolescence) was transformed during evolution both by infants’ cooperative skills “migrating up” in age and by adults’ cooperative skills “migrating down” in age.     

Phylogeographic analysis of the true lemurs (genus <Emphasis Type="Italic">Eulemur</Emphasis>) underlines the role of river catchments for the evolution of micro-endemism in Madagascar

Introduction

Due to its remarkable species diversity and micro-endemism, Madagascar has recently been suggested to serve as a biogeographic model region. However, hypothesis-based tests of various diversification mechanisms that have been proposed for the evolution of the island’s micro-endemic lineages are still limited. Here, we test the fit of several diversification hypotheses with new data on the broadly distributed genus Eulemur using coalescent-based phylogeographic analyses.

Results

Time-calibrated species tree analyses and population genetic clustering resolved the previously polytomic species relationships among eulemurs. The most recent common ancestor of eulemurs was estimated to have lived about 4.45 million years ago (mya). Divergence date estimates furthermore suggested a very recent diversification among the members of the “brown lemur complex”, i.e. former subspecies of E. fulvus, during the Pleistocene (0.33-1.43 mya). Phylogeographic model comparisons of past migration rates showed significant levels of gene flow between lineages of neighboring river catchments as well as between eastern and western populations of the redfronted lemur (E. rufifrons).

Conclusions

Together, our results are concordant with the centers of endemism hypothesis (Wilmé et al. 2006, Science 312:1063–1065), highlight the importance of river catchments for the evolution of Madagascar’s micro-endemic biota, and they underline the usefulness of testing diversification mechanisms using coalescent-based phylogeographic methods.

     

A Bird in the Hand Versus Two in the Bush? The Specialist Leafhopper <Emphasis Type="Italic">Dalbulus maidis</Emphasis> (Hemiptera: Cicadellidae) Does Not Discriminate Against Sub-optimal Host Plants (<Emphasis Type="Italic">Zea</Emphasis> spp.)

The corn leafhopper [Dalbulus maidis (DeLong & Wolcott)] is a specialist on Zea (Poaceae) that coevolved with maize (Zea mays mays) and its teosinte (Zea spp.) relatives. This study tested the hypothesis that host acceptance by females varies among Zea hosts, and is correlated with variation in defensive levels across those hosts. Prior studies revealed differences in plant defenses among Zea hosts and corresponding differences in corn leafhopper performance. Thus, host acceptance was expected to be correlated with defensive levels and offspring performance across Zea hosts, following the hypothesis that offspring performance mediates host preference. In parallel, host acceptance was expected to be correlated with transitions in life history strategy (perennial to annual life cycle), domestication status (wild to domesticated), and breeding intensity (landrace to hybrid variety) in Zea because variation in defensive levels and corn leafhopper performance were shown in prior studies to be correlated with those transitions. The study’s hypotheses were tested by comparing, under no-choice conditions, host acceptance by corn leafhopper of a suite of Zea hosts encompassing those transitions: perennial teosinte (Zea diploperennis), Balsas teosinte (Zea mays parviglumis), and landrace and commercial hybrid maize. The results did not show differences in host acceptance for oviposition or feeding among the hosts. Thus, under no-choice conditions, all Zea hosts may be similarly acceptable for feeding and oviposition, despite marked ovipositional preferences under choice conditions and poorer offspring performance on teosintes relative to maize shown previously. The results suggested also that oviposition frequency per plant by females was not correlated with their offspring’s performance.     

Limiting similarity and Darwin’s naturalization hypothesis: understanding the drivers of biotic resistance against invasive plant species

Several hypotheses have been proposed to explain biotic resistance of a recipient plant community based on reduced niche opportunities for invasive alien plant species. The limiting similarity hypothesis predicts that invasive species are less likely to establish in communities of species holding similar functional traits. Likewise, Darwin’s naturalization hypothesis states that invasive species closely related to the native community would be less successful. We tested both using the invasive alien Ambrosia artemisiifolia L. and Solidago gigantea Aiton, and grassland species used for ecological restoration in central Europe. We classified all plant species into groups based on functional traits obtained from trait databases and calculated the phylogenetic distance among them. In a greenhouse experiment, we submitted the two invasive species at two propagule pressures to competition with communities of ten native species from the same functional group. In another experiment, they were submitted to pairwise competition with native species selected from each functional group. At the community level, highest suppression for both invasive species was observed at low propagule pressure and not explained by similarity in functional traits. Moreover, suppression decreased asymptotically with increasing phylogenetic distance to species of the native community. When submitted to pairwise competition, suppression for both invasive species was also better explained by phylogenetic distance. Overall, our results support Darwin’s naturalization hypothesis but not the limiting similarity hypothesis based on the selected traits. Biotic resistance of native communities against invasive species at an early stage of establishment is enhanced by competitive traits and phylogenetic relatedness.     

Animal signals: A reply to Hinde

Hinde has criticized articles by Dawkins & Krebs (1978) and Caryl (1979) in which supposedly traditional ethological views about agonistic display were contrasted with those arising from games theory. It is argued here that the views that we contrasted with those from games theory were not ‘straw men’: in particular, Cullen's view is completely incompatible with the predictions from games theory, and is well supported by ethological evidence (as conventionally interpreted). But an unusually detailed analysis of the ethological data, which raises many points for future studies, shows that the evidence actually favours the games theoretic view. Hinde argues that the conflict hypothesis of threat display implies that displays could not and should not carry precise information. The arguments he used in this context are not wholly satisfactory: in particular, explanations in terms of interaction are of little value unless details of the interaction can be specified. Clear hypotheses are needed in the analysis of animal communication, and ideas from games theory can be of help to ethology in this respect.     

Functional response of the fungus <Emphasis Type="Italic">Hirsutella rhossiliensis</Emphasis> to the nematode, <Emphasis Type="Italic">Heterodera glycines</Emphasis>

Functional response is a key index in determining the population fluctuation in predation. However, the lack of operable research system limits the studies on functional response of fungal predators. Hirsutella rhossiliensis is a dominant parasite of the soybean cyst nematode, Heterodera glycines. In a soil microcosm bioassay, we determined fungal biomass at different days within 21 days after inoculation, and parasitism rate of H. glycines by the fungus was determined. The functional response of H. rhossiliensis to H. glycines was established and found to be Holling’s type III, which was influenced by mycelial densities. Meanwhile, we conducted anti-fungal analysis of metabolic fractions extracted from H. rhossiliensis to explain the potential mechanism of the intraspecific competition illustrated by functional response. The result of anti-fungal experiments indicated that the fungal predators had more complicated interaction at population level than expected, which might be regulated by self-inhibition metabolite(s). This study was the first functional response study of fungal predators in microcosm. With the increasing recognition of emerging fungal threats to animal, plant, and ecosystem health, the methodologies and hypotheses proposed in this study might inspire further research in fungal ecology.     

Assessing the typology of person portmanteaus

This paper reports the results of a typological study evaluating two different claims from the transitive agreement literature: that portmanteau affixes which mark a specific combination of subject and object agreement, show a cross-linguistic preference for certain paradigm parts viz. ‘local’ contexts where both arguments are first or second person (e.g. Heath 1991, 1998), or ‘direct’ contexts where the subject outranks the object on a 1?2?3 person hierarchy (e.g. Lakämper and Wunderlich 1998). According to automatic procedures to analyze unsegmented transitive agreement paradigms and identify portmanteau markers, only the hypothesis of direct portmanteaus is supported.     

Effect of low salinity on ion accumulation, gas exchange and postharvest drought resistance and habit of Coriandrum sativum L.

Aims

Drought resistance of crops is one of the great challenges for the world’s agricultural systems. Although the concept of ‘drought hardening’ has been known for many years, very little has been done on pre-harvest treatment that can help leafy vegetable crops resist drought stress on a retailer’s shelf. Our hypothesis was that for pot-grown vegetables a saline treatment could be found that would reduce transpiration pre- and post-harvest, but not harvestable yield.

Methods

Coriander (Coriandrum sativum L.) was used as a model plant; several accessions (k-4, k-43, k-52, k-60 and k-62) from N.I. Vavilov Research Institute of Plant Industry, Russia and two commercial cultivars—Kashmir and Americanum—were studied. Plant growth, weight, transpiration, net CO2 assimilation, respiration, wilting, apparent petioles rigidity, leaf sodium content, elemental analysis and osmotic potential were assessed.

Results

We found that minor salinity (12.5?mM Na2SO4) triggered both drought and salt resistance mechanisms, which regulate appearance and shelf-life of pot-grown coriander.

Conclusion

We found that the drought avoidance mechanisms (i.e. decreased transpiration and increased water use efficiency) and salt tolerance mechanisms induced by pre-harvest treatment could significantly postpone wilting and improve post-harvest habit of a leafy vegetable crop.     

Pollen grain size, stigma depth, and style length: the relationships revisited

I examine data and review information in the literature to test hypotheses proposed by Delpino and Darwin to explain the source of nutrients utilized by pollen tubes. In 1867, Delpino, in his discussion of distyly, suggested that the positive relationship between pollen grain size and style length was based on the pollen grains containing sufficient nutrients to sustain the growth of their pollen tubes through their respective styles. Darwin (The different forms of flowers on plants of the same species, 2nd edn. J. Murray, London, 1884) rejected Delpino’s suggestion based on his examination of distylous species whose morphs produced pollen grains whose sizes were not proportionate to the lengths of their respective styles. Darwin then proposed that pollen tubes first grow autotrophically, i.e., through the stigma, then heterotrophically in the style. This should result in a positive relationship between pollen grain size and stigma depth, if pollen tubes grow autotrophically through the stigma. I examined 15 species in Fabaceae and 20 species in Proteaceae to test the two hypotheses. Pollen grain size was correlated with stigma depth among the Fabaceae, i.e., consistent with Darwin’s hypothesis, and was not correlated with style length in either family, i.e., inconsistent with Delpino’s proposal. Comparisons of related species, in general, were consistent with Darwin’s hypothesis. In addition, information in the literature provided no evidence that pollen tubes obtain resources on or in the stigma, i.e., pollen tube growth from the stigmatic surface to the style was autotrophic. In contrast, pollen tubes obtain an array of resources from the transmission tissue, thus there is little reason for pollen grains to contain those resources. In addition, I suggest that positive correlations between pollen grain size and style/pistil length may be a result of both being correlated with stigma depth.     

From mutations to mechanisms and dysfunction via computation and mining of protein energy landscapes

Background

The protein energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. Reconstructing a protein’s energy landscape holds the key to characterizing a protein’s equilibrium conformational dynamics and its relationship to function. Many pathogenic mutations in protein sequences alter the equilibrium dynamics that regulates molecular interactions and thus protein function. In principle, reconstructing energy landscapes of a protein’s healthy and diseased variants is a central step to understanding how mutations impact dynamics, biological mechanisms, and function.

Results

Recent computational advances are yielding detailed, sample-based representations of protein energy landscapes. In this paper, we propose and describe two novel methods that leverage computed, sample-based representations of landscapes to reconstruct them and extract from them informative local structures that reveal the underlying organization of an energy landscape. Such structures constitute landscape features that, as we demonstrate here, can be utilized to detect alterations of landscapes upon mutation.

Conclusions

The proposed methods detect altered protein energy landscape features in response to sequence mutations. By doing so, the methods allow formulating hypotheses on the impact of mutations on specific biological activities of a protein. This work demonstrates that the availability of energy landscapes of healthy and diseased variants of a protein opens up new avenues to harness the quantitative information embedded in landscapes to summarize mechanisms via which mutations alter protein dynamics to percolate to dysfunction.

     

A supertree approach to shorebird phylogeny

Background

Order Charadriiformes (shorebirds) is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species. Here we use the matrix representation with parsimony method to produce the first fully inclusive supertree of Charadriiformes. We also provide preliminary estimates of ages for all nodes in the tree.

Results

Three main lineages are revealed: i) the plovers and allies; ii) the gulls and allies; and iii) the sandpipers and allies. The relative position of these clades is unresolved in the strict consensus tree but a 50% majority-rule consensus tree indicates that the sandpiper clade is sister group to the gulls and allies whilst the plover group is placed at the base of the tree. The overall topology is highly consistent with recent molecular hypotheses of shorebird phylogeny.

Conclusion

The supertree hypothesis presented herein is (to our knowledge) the only complete phylogenetic hypothesis of all extant shorebirds. Despite concerns over the robustness of supertrees (see Discussion), we believe that it provides a valuable framework for testing numerous evolutionary hypotheses relating to the diversity of behaviour, ecology and life-history of the Charadriiformes.