Perceptual Processes and the Maintenance of Polymorphism Through Frequency-dependent Predation

One of the key challenges of both ecology and evolutionary biology is to understand the mechanisms that maintain diversity. Negative frequency-dependent selection is a powerful mechanism for maintaining variation in the population as well as species diversity in the community. There are a number of studies showing that this type of selection, where individuals of a rare type (i.e. a rare morph or a rare species) experience higher survival than those of more common type(s). However, it is still not clear how frequency-dependent selection operates. Search image formation has been invoked as a possible, proximate explanation. Although the conceptual link between search image and frequency-dependent predation is often assumed in ecological and evolutionary studies, a review of the literature reveals a paucity of evidence demonstrating the occurrence of both in a natural predator-prey system. Advances in the field of psychology strongly support the existence of search image, yet these findings are not fully recognized in the realm of ecology and evolutionary biology, in part, we feel because of confusion and inconsistencies in terminology. Here we try to simplify the language, clarify the advances in the study of frequency-dependent predation and search image, and suggest avenues for future research. We feel that the investigations of both proximate (perceptual mechanisms) and ultimate (pattern of predation) processes are necessary to fully understand the importance of individual behavioural processes for mediating evolutionary and ecological diversity.Co-ordinating editor: O. Leimar     

The role of liquid–liquid phase separation in regulating enzyme activity

Liquid–liquid phase separation (LLPS) is now recognized as a common mechanism underlying regulation of enzyme activity in cells. Insights from studies in cells are complemented by in vitro studies aimed at developing a better understanding of mechanisms underlying such control. These mechanisms are often based on the influence of LLPS on the physicochemical properties of the enzyme's environment. Biochemical mechanisms underlying such regulation include the potential for concentrating reactants together, tuning reaction rates, and controlling competing metabolic pathways. LLPS is thus a powerful tool with extensive utilities at the cell's disposal, e.g. for consolidating cell survival under stress or rerouting metabolic pathways in response to the energy state of the cell. Here, we examin the evidence for how LLPS affects enzyme catalysis and begin to understand emerging concepts and expand our understanding of enzyme catalysis in living cells.     

Intrinsic aging-related mortality in birds

Actuarial senescence in captive populations of 28 species of bird was quantified by estimating the parameters of Weibull models fitted to survival curves constructed from data obtained from zoos. Samples of natural and captive populations were compared using phylogenetically independent contrasts, which revealed that extrinsic mortality rates in captive populations are, on average, less than 30% of those of natural populations but that the component of mortality related to aging does not differ significantly between natural and captive birds. This result supports the hypothesis that aging-related mortality is associated with intrinsic causes of death that kill independently of the external environment. A logical implication of this result is that birds in natural populations maintain a high level of physical fitness into old age and do not become more vulnerable to extrinsic mortality factors with increasing age. Additional comparisons showed that the rate of aging in this sample of birds is correlated with body mass, but not with embryonic or postnatal growth rate. These analyses suggest that studies of aging in captive populations can provide powerful tools to help us understand senescence in natural populations.     

A model-based statistic for detecting molecular markers associated with complex survival patterns in early-stage cancer

ABSTRACT: BACKGROUND: : In early-stage of cancer, primary treatment can be considered as effective at eliminating the tumor for a non-negligible proportion of patients whereas for the others it leads to a lower tumor burden and thereby potentially prolonged survival. In this mixed population of patients, it is of great interest to detect complex differences in survival distributions associated with molecular markers that potentially activate latent downstream pathways implicated in tumor progression. METHOD: : We propose a novel model-based score test designed for identifying molecular markers with complex effects on survival in early-stage cancer. From a biological point of view, the proposed score test allows to detect complex changes in the survival distributions linked to either the tumor burden or its dynamic growth. RESULTS: : Simulation results show that the proposed statistic is powerful at identifying departure from the null hypothesis of no survival difference. The practical use of the proposed statistic is exemplified by analyzing the prognostic impact of Kras mutation in early-stage of lung adenocarcinomas. This analysis leads to the conclusion that Kras mutation has a significant negative prognostic impact on survival. Moreover, it emphasizes that the complex role of Kras mutation on survival would have been overlooked by considering results from the classical logrank test. CONCLUSION: With the growing number of biological markers to be tested in early-stage cancer, the proposed score test statistic is a powerful tool for detecting molecular markers associated with complex survival patterns.     

A two-sample test sensitive to crossing hazards in uncensored and singly censored data

Savage score statistics are employed to develop a test for comparing survival distributions with right-hand singly censored data. The procedure is motivated by the interest in developing a powerful method for determining differences when true survival distributions cross. Examination of small-sample characteristics under the null hypothesis indicate that asymptotic critical values yield a slightly conservative test. Power of the test compares favorably with other criteria, including the modified Smirnov procedure, particularly if there is a single crossing of the survival curves.     

Complex patterns of local adaptation in heat tolerance in Drosophila simulans from eastern Australia

Latitudinal clines are considered a powerful means of investigating evolutionary responses to climatic selection in nature. However, most clinal studies of climatic adaptation in Drosophila have involved species that contain cosmopolitan inversion polymorphisms that show clinal patterns themselves, making it difficult to determine whether the traits or inversions are under selection. Further, although climatic selection is unlikely to act on only one life stage in metamorphic organisms, a few studies have examined clinal patterns across life stages. Finally, clinal patterns of heat tolerance may also depend on the assay used. To unravel these potentially confounding effects on clinal patterns of thermal tolerance, we examined adult and larval heat tolerance traits in populations of Drosophila simulans from eastern Australia using static and dynamic (ramping 0.06 °C min^?1) assays. We also used microsatellites markers to clarify whether demographic factors or selection are responsible for population differentiation along clines. Significant cubic clinal patterns were observed for adult static basal, hardened and dynamic heat knockdown time and static basal heat survival in larvae. In contrast, static, hardened larval heat survival increased linearly with latitude whereas no clinal association was found for larval ramping survival. Significant associations between adult and larval traits and climatic variables, and low population differentiation at microsatellite loci, suggest a role for climatic selection, rather than demographic processes, in generating these clinal patterns. Our results suggest that adaptation to thermal stress may be species and life‐stage specific, complicating our efforts to understand the evolutionary responses to selection for increasing thermotolerance.     

Recognition of translation initiation sites of eukaryotic genes based on an EM algorithm.

With the rapid increase of DNA databases of human and other eukaryotic model organisms, a large great number of genes need to be distinguished from the DNA databases. Exact recognition of translation initiation sites (TISs) of eukaryotic genes is very important to understand the translation initiation process, predict the detailed structure of eukaryotic genes, and annotate uncharacterized sequences. The problem has not been solved satisfactorily, especially for recognizing TISs of the eukaryotic genes with shorter first exons. It is an important task for extracting new features and finding new powerful algorithms for recognizing TISs of eukaryotic genes. In this paper, the important characteristics of shorter flanking fragments around TISs are extracted and an expectation-maximization (EM) algorithm based on incomplete data is used to recognize TISs of eukaryotic genes. The accuracy is up to 87.8% over a six-fold cross-validation test. The result shows that the identification variables are effectively extracted and the EM algorithm is a powerful tool to predict the TISs of eukaryotic genes. The algorithm also can be applied to other classification or clustering tasks in bioinformatics.     

DGGE/TGGE技术在土壤微生物分子生态学研究中的应用

传统的微生物生态学研究方法只限于环境样品中极少部分(0.1%￣1%)可培养的微生物类群,极大程度地限制了对土壤微生物群落结构的研究。综述了以16S rDNA为主要研究对象的DGGE/TGGE(Denaturing gradientgel electrophoresis,DGGE/Temperature gradient gel electrophoresis,TGGE)技术原理,以其为主要手段结合PCR扩增、克隆建库、序列测定以及种系分析对土壤微生物的群落结构和多样性研究的最新动态。DGGE/TGGE技术极大地推动了土壤微生物分子生态学的发展,同时也为实际问题的诊断、作物生长跟踪监测等提供了技术支撑,在土壤微生物分子生态学研究和生产实践中起着越来越重要的作用。     

基于蛋白质组芯片的结核分枝杆菌系统生物学研究进展

近些年全球结核病疫情愈发严重,耐药性结核病使其雪上加霜。一个重要原因是结核病新药的匮乏以及结核分枝杆菌相关基础研究的不足。因此迫切需要开发新的技术以促进结核病系统生物学基础研究,并在此基础上研究新机制,发现新靶标,开发新药物。结核分枝杆菌功能蛋白质组芯片的出现旨在促进结核病相关研究工作。考虑到结核分枝杆菌高毒力、复制周期长和需要在生物安全三级实验室中开展研究等特点和难点,该工具为结核病相关研究人员提供了一个强有力的武器。目前这一技术手段的应用已经使我们对结核分枝杆菌-宿主相互作用、小分子-蛋白结合以及抗生素耐药性机制等关键生物过程有了更深入的了解。为了更好地帮助同行了解这一有效的工具,本文综述了结核分枝杆菌功能蛋白组芯片的几种主要应用,期望同行专家能更好地将其应用于结核病相关的基础研究中。     

Balancing life and death in the ischemic brain: SIK and TORC weigh in

Activation of NMDA receptors during cerebral ischemia triggers signaling pathways that promote both neuronal death and survival. In this issue of Neuron, Sasaki et al. present evidence for a new endogenous survival pathway involving the kinase SIK2 and the CREB coactivator TORC1. The powerful neuroprotection conferred by this pathway has considerable translational potential for stroke therapy.     

A comparison of life‐history and parental care in temperate and tropical wrens

Comparing closely related species that live in different environments is a powerful way to understand selective pressures that influence life‐history evolution. We examined a suite of life‐history traits and parental care in neotropical buff‐breasted wrens Cantorchilus leucotis and north‐temperate Carolina wrens Thryothorus ludovicianus (Family Troglodytidae), to test hypotheses about life‐history evolution. As expected, buff‐breasted wrens exhibited smaller clutch sizes and higher annual adult survival than Carolina wrens. We found minimal support for the nest predation hypothesis, as nest survival and age‐corrected provisioning rates to whole broods were similar between species, and number of breeding attempts and breeding season length were greater in temperate wrens. Critical predictions of the food limitation hypothesis were not supported; in particular age‐corrected provisioning rates per nestling were higher in the tropical than temperate species. The adult survival and offspring quality hypothesis garnered the most support, as buff‐breasted wrens exhibited greater age‐corrected provisioning rates per nestling, a longer nestling period, longer re‐nesting intervals following nest success, and lower annual fecundity than Carolina wrens. Despite similarly prolonged breeding seasons, reproductive strategies differ between species with buff‐breasted wrens investing considerably in single broods to optimize first‐year survival and Carolina wrens investing in multiple small broods to optimize annual fecundity.     

Lateral genomics

More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.     

Lateral genomics

More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.     

Lateral genomics

More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.     

A minimum version of log-rank test for testing the existence of cancer cure using relative survival data

Cancer survival is one of the most important measures to evaluate the effectiveness of treatment and early diagnosis. The ultimate goal of cancer research and patient care is the cure of cancer. As cancer treatments progress, cure becomes a reality for many cancers if patients are diagnosed early and get effective treatment. If a cure does exist for a certain type of cancer, it is useful to estimate the time of cure. For cancers that impose excess risk of mortality, it is informative to understand the difference in survival between cancer patients and the general cancer-free population. In population-based cancer survival studies, relative survival is the standard measure of excess mortality due to cancer. Cure is achieved when the survival of cancer patients is equivalent to that of the general population. This definition of cure is usually called the statistical cure, which is an important measure of burden due to cancer. In this paper, a minimum version of the log-rank test is proposed to test the equivalence of cancer patients' survival using the relative survival data. Performance of the proposed test is evaluated by simulation. Relative survival data from population-based cancer registries in SEER Program are used to examine patients' survival after diagnosis for various major cancer sites.     

Semi-supervised methods to predict patient survival from gene expression data

An important goal of DNA microarray research is to develop tools to diagnose cancer more accurately based on the genetic profile of a tumor. There are several existing techniques in the literature for performing this type of diagnosis. Unfortunately, most of these techniques assume that different subtypes of cancer are already known to exist. Their utility is limited when such subtypes have not been previously identified. Although methods for identifying such subtypes exist, these methods do not work well for all datasets. It would be desirable to develop a procedure to find such subtypes that is applicable in a wide variety of circumstances. Even if no information is known about possible subtypes of a certain form of cancer, clinical information about the patients, such as their survival time, is often available. In this study, we develop some procedures that utilize both the gene expression data and the clinical data to identify subtypes of cancer and use this knowledge to diagnose future patients. These procedures were successfully applied to several publicly available datasets. We present diagnostic procedures that accurately predict the survival of future patients based on the gene expression profile and survival times of previous patients. This has the potential to be a powerful tool for diagnosing and treating cancer.