Microarray results: how accurate are they?

Background  

DNA microarray technology is a powerful technique that was recently developed in order to analyze thousands of genes in a short time. Presently, microarrays, or chips, of the cDNA type and oligonucleotide type are available from several sources. The number of publications in this area is increasing exponentially.     

Plant hormone interactions: how complex are they?

Models describing plant hormone interactions are often complex and web-like. Here we assess several suggested interactions within one experimental system, elongating pea internodes. Results from this system indicate that at least some suggested interactions between auxin, gibberellins (GAs), brassinosteroids (BRs), abscisic acid (ABA) and ethylene do not occur in this system or occur in the reverse direction to that suggested. Furthermore, some of the interactions are relatively weak and may be of little physiological relevance. This is especially true if plant hormones are assumed to show a log-linear response curve as many empirical results suggest. Although there is strong evidence to support some interactions between hormones (e.g. auxin stimulating ethylene and bioactive GA levels), at least some of the web-like complexities do not appear to be justified or are overstated. Simpler and more targeted models may be developed by dissecting out key interactions with major physiological effects.     

Genetic instability and rapid speciation: are they coupled?

Models of rapid speciation by fixation of underdominant chromosomal rearrangements are constrained by multiple conditions on population structure and chromosomal performance. Realistic population conditions impose long periods of time to fixation or reproductive isolation, even under a model of accumulation of successive advantageous slightly underdominant rearrangements. However, when increased mutation rates are considered, fixation time is significantly reduced. Evidence is presented of high rates of chromosomal rearrangement production under genomic stress, such as in inbred and interspecific crosses. These episodes of high instability are most probably the result of mobile element transpositions, since transposition is also increased under genomic stress. Nonetheless, the evolutionary value of mobile elements to speed up speciation will be only significant if their mutagenic potential is activated in concert with population scenarios favorable to speciation events. Although this coupling needs to be demonstrated, many models of rapid speciation are carried out under population conditions favoring inbreeding and/or hybridization.     

Functional protein microarrays: just how functional are they?

Arrays of immobilized proteins have been developed for the discovery and characterization of protein functions ranging from molecular recognition to enzymatic activity. The success of these applications is highly dependent upon the maintenance of protein structure and function while in an immobilized state - a largely untested hypothesis. However, the immobilization of functional proteins is not without precedent. Active enzymes have been successfully immobilized for industrial applications for several decades. Furthermore, a survey of recent protein microarray literature reveals that an even wider range of proteins can maintain 'proper' function while immobilized. These reports help to validate the functionality of so-called functional protein microarrays.     

Nectar and pollination drops: how different are they?

Background

Pollination drops and nectars (floral nectars) are secretions related to plant reproduction. The pollination drop is the landing site for the majority of gymnosperm pollen, whereas nectar of angiosperm flowers represents a common nutritional resource for a large variety of pollinators. Extrafloral nectars also are known from all vascular plants, although among the gymnosperms they are restricted to the Gnetales. Extrafloral nectars are not generally involved in reproduction but serve as ‘reward’ for ants defending plants against herbivores (indirect defence).

Scope

Although very different in their task, nectars and pollination drops share some features, e.g. basic chemical composition and eventual consumption by animals. This has led some authors to call these secretions collectively nectar. Modern techniques that permit chemical analysis and protein characterization have very recently added important information about these sugary secretions that appear to be much more than a ‘reward’ for pollinating (floral nectar) and defending animals (extrafloral nectar) or a landing site for pollen (pollination drop).

Conclusions

Nectar and pollination drops contain sugars as the main components, but the total concentration and the relative proportions are different. They also contain amino acids, of which proline is frequently the most abundant. Proteomic studies have revealed the presence of common functional classes of proteins such as invertases and defence-related proteins in nectar (floral and extrafloral) and pollination drops. Invertases allow for dynamic rearrangement of sugar composition following secretion. Defence-related proteins provide protection from invasion by fungi and bacteria. Currently, only few species have been studied in any depth. The chemical composition of the pollination drop must be investigated in a larger number of species if eventual phylogenetic relationships are to be revealed. Much more information can be provided from further proteomic studies of both nectar and pollination drop that will contribute to the study of plant reproduction and evolution.Key words: Nectar, pollination drop, ovular secretion, plant reproduction, proteins, sugars, gymnosperms, angiosperms, plant–animal interaction     

Ciliary subcompartments: how are they established and what are their functions?

Cilia are conserved subcellular organelles with diverse sensory and developmental roles. Recently, they have emerged as crucial organelles whose dysfunction causes a wide spectrum of disorders called ciliopathies. Recent studies on the pathological mechanisms underlying ciliopathies showed that the ciliary compartment is further divided into subdomains with specific roles in the biogenesis, maintenance and function of cilia. Several conserved sets of molecules that play specific roles in each subcompartment have been discovered. Here we review recent progress on our understanding of ciliary subcompartments, especially focusing on the molecules required for their structure and/or function. [BMB Reports 2015; 48(7): 380-387]     

Search tactics of desert lizards: how polarized are they?

The patterns of foraging movements of the teiid species Cnemidophorus tigris (western whiptail) and four iguanid species, Gambelia wislizeni (leopard lizard), Uta stansburiana (side-blotched lizard), Phrynosoma platyrhinos (desert horned lizard), and Callisaurus draconoides (zebra-tailed lizard), were investigated between 1978 and 1981. Rates and frequencies of movement while foraging, based on more than 44 000 minutes of observation of over 500 different lizards, were analysed with respect to temporal variation on yearly, seasonal and daily time scales and compared to expectations froma dichotomous view of foraging modes. The notion of polarized foragiing tactics among lizards was partially supported. Among the iguanid species, only Gambelia exhibited rates of foraging movements that were not always significantly less than those of the active forager, Cnemidophorus. Nevertheless, the analyses also revealed temporal variation in the search tactics of iguanid species. Gambelia exhibited a seasonal decline in foraging movements during three out of four years. Phrynosoma, Callisaurus and Uta all exhibited seasonal declines in their foraging movements in some years, but not in others. The foraging movements of all iguanid species increased during the early-season of 1978, corresponding to a marked increase in late winter/early spring rainfall that year. Uta showed diurnal shifts in foraging movements during most years. Such diurnal variation was also apparent in Callisaurus in some years. Despite consistent differences between Cnemidophorus and most iguanid species, the presence of temporal variability in foraging movements of iguanid lizards indicates a capacity for shifts in tactics in these species. Thus, this variability more realistically reflects a continuum of foraging tactics than it does dichotomous strategies.     

Individual aging and mortality rate: how are they related?

Many researchers working in the area of aging and longevity base their conclusions on the behavior of empirical age trajectories of mortality rates. In such analyses, changes in the slope of the logarithm of the mortality curve are often associated with changes in the rate of individual aging. We show that such interpretation may be incorrect: the changes in the slope of this curve do not necessarily correspond to the changes in the rate of individual aging. We use three models of mortality and aging to illustrate this statement. The first one is based on the idea of frailty. We show that changes in frailty distribution alone may be responsible for changes in the slope. The second model exploits the idea of saving lives. It evaluates changes in mortality rate after elimination of lethal stressful events. The third model uses the idea of Strehler and Mildvan (1960). It shows that changes in the rate of individual aging may take place without changes in the slope of the logarithm of the mortality curve.     

Cell-penetrating peptides and antimicrobial peptides: how different are they?

Some cationic peptides, referred to as CPPs (cell-penetrating peptides), have the ability to translocate across biological membranes in a non-disruptive way and to overcome the impermeable nature of the cell membrane. They have been successfully used for drug delivery into mammalian cells; however, there is no consensus about the mechanism of cellular uptake. Both endocytic and non-endocytic pathways are supported by experimental evidence. The observation that some AMPs (antimicrobial peptides) can enter host cells without damaging their cytoplasmic membrane, as well as kill pathogenic agents, has also attracted attention. The capacity to translocate across the cell membrane has been reported for some of these AMPs. Like CPPs, AMPs are short and cationic sequences with a high affinity for membranes. Similarities between CPPs and AMPs prompted us to question if these two classes of peptides really belong to unrelated families. In this Review, a critical comparison of the mechanisms that underlie cellular uptake is undertaken. A reflection and a new perspective about CPPs and AMPs are presented.     

Radiation-induced bystander effects: what are they, and how relevant are they to human radiation exposures?

The term radiation-induced bystander effect is used to describe radiation-induced biological changes that manifest in unirradiated cells remaining within an irradiated cell population. Despite their failure to fit into the framework of classical radiobiology, radiation-induced bystander effects have entered the mainstream and have become established in the radiobiology vocabulary as a bona fide radiation response. However, there is still no consensus on a precise definition of radiation-induced bystander effects, which currently encompasses a number of distinct signal-mediated effects. These effects are classified here into three classes: bystander effects, abscopal effects and cohort effects. In this review, the data have been evaluated to define, where possible, various features specific to radiation-induced bystander effects, including their timing, range, potency and dependence on dose, dose rate, radiation quality and cell type. The weight of evidence supporting these defining features is discussed in the context of bystander experimental systems that closely replicate realistic human exposure scenarios. Whether the manifestation of bystander effects in vivo is intrinsically limited to particular radiation exposure scenarios is considered. The conditions under which radiation-induced bystander effects are induced in vivo will ultimately determine their impact on radiation-induced carcinogenic risk.     

Disturbance–diversity models: what do they really predict and how are they tested?

The intermediate disturbance hypothesis (IDH) and the dynamic equilibrium model (DEM) are influential theories in ecology. The IDH predicts large species numbers at intermediate levels of disturbance and the DEM predicts that the effect of disturbance depends on the level of productivity. However, various indices of diversity are considered more commonly than the predicted number of species in tests of the hypotheses. This issue reaches beyond the scientific community as the predictions of the IDH and the DEM are used in the management of national parks and reserves. In order to compare responses with disturbance among measures of biodiversity, we used two different approaches of mathematical modelling and conducted an extensive meta-analysis. Two-thirds of the surveyed studies present different results for different diversity measures. Accordingly, the meta-analysis showed a narrow range of negative quadratic regression components for richness, but not evenness. Also, the two models support the IDH and the DEM, respectively, when biodiversity is measured as species richness, but predict evenness to increase with increasing disturbance, for all levels of productivity. Consequently, studies that use compound indices of diversity should present logical arguments, a priori, to why a specific index of diversity should peak in response to disturbance.     

Hollow spheroids in ascites of ovarian clear cell carcinoma: how are they formed and how do they behave?

N. Kato, K. Narutomi, M. Fukase and T. Motoyama Hollow spheroids in ascites of ovarian clear cell carcinoma: how are they formed and how do they behave? Objective: Although the multicellular aggregates (spheroids) in malignant ascites are usually solid throughout, they sometimes have acellular hollow spaces, especially in ascites of ovarian clear cell carcinoma. The purpose of this study is to analyse the origin and behaviour of hollow spheroids. Methods: Archival cytological and histological specimens of 32 ovarian carcinomas, including 12 clear cell carcinomas, were reviewed. HAC‐2, a clear cell carcinoma cell line, was injected into the abdominal cavity of nude mice for direct comparison of ascitic cytology and tumour histology. Spheroids that were collected from nude mice ascites were cultured in vitro to observe their behaviour. Results: Five of six clear cell carcinomas with hollow spheroids showed spherule‐like hyaluronan‐rich stroma in their tumour tissue, whereas those without hollow spheroids did not. After heterotransplantation, both ascites and tumour imprints showed small or large hollow spheroids. Hyaluronan was detected in the former but not in the latter. The abdominal tumours showed compact spherule‐like hyaluronan‐rich stroma, enlarged oedematous stroma or intermediate stroma. In both size and hyaluronan status, small and large hollow spheroids were approximately comparable to spherule‐like hyaluronan‐rich stroma and oedematous stroma, respectively. During culture in vitro, hollow spheroids were maintained as hollow spheroids in suspension, and produced daughter hollow spheroids. Conclusions: The hollow space in the spheroids originates from spherule‐like hyaluronan‐rich stroma, where water trapping by hyaluronan causes enlargement of the space. The matrix within the hollow space serves as a scaffold that regulates cell polarity and matrix production.     

Proteome signatures—how are they obtained and what do they teach us?

The dawn of a new Proteomics era, just over a decade ago, allowed for large-scale protein profiling studies that have been applied in the identification of distinctive molecular cell signatures. Proteomics provides a powerful approach for identifying and studying these multiple molecular markers in a vast array of biological systems, whether focusing on basic biological research, diagnosis, therapeutics, or systems biology. This is a continuously expanding field that relies on the combination of different methodologies and current advances, both technological and analytical, which have led to an explosion of protein signatures and biomarker candidates. But how are these biological markers obtained? And, most importantly, what can we learn from them? Herein, we briefly overview the currently available approaches for obtaining relevant information at the proteome level, while noting the current and future roles of both traditional and modern proteomics. Moreover, we provide some considerations on how the development of powerful and robust bioinformatics tools will greatly benefit high-throughput proteomics. Such strategies are of the utmost importance in the rapidly emerging field of immunoproteomics, which may play a key role in the identification of antigens with diagnostic and/or therapeutic potential and in the development of new vaccines. Finally, we consider the present limitations in the discovery of new signatures and biomarkers and speculate on how such hurdles may be overcome, while also offering a prospect for the next few years in what could be one of the most significant strategies in translational medicine research.     

Bruises in culled cows: when,where and how are they inflicted?

In Chile, cow carcasses present the highest bruise prevalence compared with other cattle categories; however, the causes of the bruises are frequently unknown. In this study, 52 cull cows were transported to the slaughterhouse in three batches under identical transport conditions. A combination of direct observation and video analyses was used to determine moment, pre-slaughter stage and cause of potential bruising events during the period from loading on the farm until stunning at the slaughterhouse. After slaughter, number of bruises, location on the carcass and characteristics of the bruises were assessed. Seventy-eight bruises were observed on 37 carcasses. Fifty-two bruises were linked back to their causal event. Results showed that 46% of these bruises were a result of interactions between animal and facility, and most of them were inflicted in the stunning box, 27% of the bruises originated from animal–animal interactions and were mostly inflicted during lairage, another 27% was a result of human–animal interactions and were mostly inflicted during loading and unloading of animals. The percentages of potential bruising events resulting in a bruise were 43%, 9% and less than 1% for animal–facility, human–animal and animal–animal interactions, respectively. Most bruises on the back site were inflicted when the animal was in the stunning box (91.2%), whereas bruises on the pin site were mostly (75%) inflicted during loading at the farm. One may conclude that in relative short journeys (⩽4 h) directly from farm to the slaughterhouse and long lairage times (>12 h), most bruises are the result of circumstances at the slaughterhouse. A substantial amount of these bruises could be avoided by proper animal handling and adequate stunning facilities.     

Palms as rainforest resources: how evenly are they distributed in Peruvian Amazonia?

The distribution and the abundance of a species define the limits of itspotential use. Despite this simple fact, there are only a few studies thathave quantified the actual abundance and the distribution of species/resourcesin Amazonian rainforests, especially within unflooded (tierra firme) forests.The present study focused on the distributions and the abundances of palms,since they are both structurally important and widely utilized in the forests ofAmazonia. The similarity of the palm communities at eight different sites intierra firme forests of Peruvian Amazonia were examined, and the eighteconomically most important palm species were selected for more detailed studieson abundance and population structure. The results showed that both the overallpalm community composition and the abundances of the eight focal palm speciesvaried among the sites, and that these differences in abundances were related tothe amount of exchangeable cations in the soils. Population structure differedbetween growth forms: large, solitary palm species were mainly represented byseedlings and juveniles, whereas small, clonal palm species had very fewseedlings. The great variability in abundance of palm species should be takeninto account when estimating the availability of palm resources, as well as inconservation planning of the palm species in an area of interest.     

Bird community responses to habitat fragmentation: how consistent are they across landscapes?

Aim The woodland ecosystems of south‐eastern Australia have been extensively disturbed by agriculture and urbanization. Herein, the occurrence of birds in woodland remnants in three distinct landscapes was analysed to examine the effects of different types of landscape matrices on species richness vs. area and species richness vs. isolation relationships and individual species responses to woodland fragmentation. Location The study system comprised three distinct woodland landscapes of the northern Australian Capital Territory and bordering areas of New South Wales. These landscapes (termed agricultural, peri‐urban and urban) are located within 50 km of each other, have remnant fragments of similar age, size, isolation, woodland cover, elevation and climates. The major distinguishing feature of the three landscapes was the properties of the habitats surrounding the numerous woodland remnants. Methods Bird surveys, using an area‐search methodology, were conducted in 1999 and 2000 in 127 remnants in the three landscapes to determine bird species presence/absence. Each remnant was characterized by measures of remnant area, isolation and habitat complexity. To characterize differences between each landscape, we conducted an analysis of the amount of tree cover and human disturbance in each landscape using SPOT imagery and aerial photographs. Linear regressions of woodland‐dependent species richness vs. remnant area and remnant isolation for the three different landscapes were calculated to see if there were any apparent differences. Binomial logistic regressions were used to determine the relationships between the occurrence of each species and the size and isolation of woodland habitat, in each landscape. Results All the landscapes displayed a significant (P < 0.01) species vs. area relationship, but the slope of the urban relationship was significantly greater than those of the other landscapes. In contrast, only the agricultural landscape displayed a significant (P < 0.01) species richness vs. isolation relationship. When individual species were investigated, we found species that were: (1) apparently insensitive to reduction in remnant area and increase in isolation across all landscapes, (2) absent in small remnants in all landscapes, (3) absent in small remnants in all landscapes and also absent in isolated remnants in the agricultural landscape, (4) absent in isolated remnants in the agricultural landscape, and (5) absent in small remnants in the urban landscape. Threshold values (50% probability of occurrence) for area and isolation for individual species were highly variable across the three landscapes. Main conclusions These results indicate that woodland bird communities have a varying response to habitat fragmentation in different landscapes. Whilst we cannot be sure how representative our chosen landscapes are of other similarly composed landscapes, these results suggest that the type of landscape matrix may have a considerable influence on how bird species are affected by woodland fragmentation in the region. For instance, the properties of a matrix may influence both the resources available in the landscape as a whole for different bird species, and the connectivity (dispersal of birds), between woodland remnants. We encourage further research that examines these hypotheses and argue that the management of the matrix should be included in conservation strategies for fragmented landscapes.