Utility of gel-free,label-free shotgun proteomics approaches to investigate microorganisms

This review will examine the current situation with label-free, quantitative, shotgun-oriented proteomics technology and discuss the advantages and limitations associated with its capability in capturing and quantifying large portions of proteomes of microorganisms. Such an approach allows (1) comparisons between physiological or genetic states of organisms at the protein level, (2) ‘painting’ of proteomic data onto genome data-based metabolic maps, (3) enhancement of the utility of genomic data and finally (4) surveying of non-genome sequenced microorganisms by taking advantage of available inferred protein data in order to gain new insights into strain-dependent metabolic or physiological capacities. The technology essentially is a powerful addition to systems biology with a capacity to be used to ask hypothesis-driven ‘top-down’ questions or for more empirical ‘bottom-up’ exploration.     

Inflammation,Aging, and Cancer: Tumoricidal Versus Tumorigenesis of Immunity

Acute inflammation is a highly regulated defense mechanism of immune system possessing two well-balanced and biologically opposing arms termed apoptosis (‘Yin’) and wound healing (‘Yang’) processes. Unresolved or chronic inflammation (oxidative stress) is perhaps the loss of balance between ‘Yin’ and ‘Yang’ that would induce co-expression of exaggerated or ‘mismatched’ apoptotic and wound healing factors in the microenvironment of tissues (‘immune meltdown’). Unresolved inflammation could initiate the genesis of many age-associated chronic illnesses such as autoimmune and neurodegenerative diseases or tumors/cancers. In this perspective ‘birds’ eye’ view of major interrelated co-morbidity risk factors that participate in biological shifts of growth-arresting (‘tumoricidal’) or growth-promoting (‘tumorigenic’) properties of immune cells and the genesis of chronic inflammatory diseases and cancer will be discussed. Persistent inflammation is perhaps a common denominator in the genesis of nearly all age-associated health problems or cancer. Future challenging opportunities for diagnosis, prevention, and/or therapy of chronic illnesses will require an integrated understanding and identification of developmental phases of inflammation-induced immune dysfunction and age-associated hormonal and physiological readjustments of organ systems. Designing suitable cohort studies to establish the oxido-redox status of adults may prove to be an effective strategy in assessing individual’s health toward developing personal medicine for healthy aging.     

Differences in abscisic acid concentration in roots and leaves of two young Olive (<Emphasis Type="Italic">Olea europaea</Emphasis> L.) cultivars in response to water deficit

Differences in abscisic acid (ABA) accumulation between two olive cultivars were studied by enzyme-linked immunosorbent assay in roots and leaves, leaf water potential (Ψ_l), stomatal conductance (g _s) as well as photosynthetic rate (A) were also determined in well-watered (WW) and water-stressed (WS) plants of two olive cultivars ‘Chemlali’ and ‘Chetoui’. ‘Chemlali’ was able to maintain higher leaf CO₂ assimilation rate and leaf stomatal conductance throughout the drought cycle when compared with ‘Chetoui’. Furthermore, leaf water potential of ‘Chemlali’ decreased in lower extent than in Chetoui in response to water deficit. Interestingly, significant differences in water-stress-induced ABA accumulation were observed between the two olive cultivars and reflect the degree of stress experienced. Chemlali, a drought tolerant cultivar, accumulated lower levels of ABA in their leaves to regulate stomatal control in response to water stress compared to the drought sensitive olive cultivar ‘Chetoui’ which accumulated ABA in large amount.     

The influence of plant growth regulators and storage on root induction and growth in <Emphasis Type="Italic">Pelargonium zonale</Emphasis> cuttings

The effects of post harvest application of ethylene, abscisic acid (ABA), indole-3-butyric acid (IBA) treatments or dark storage on root induction and continued growth of regenerated roots in Pelargonium cuttings were investigated using hydroponics in the greenhouse. Ethylene markedly increased rooting percentage in ‘Greco’ and ‘Surfing’, reduced the number of roots per cutting in ‘Surfing’ and had no effect on the total root lengths in the two cultivars. Ethylene treatment reduced fresh root mass in ‘Surfing’, increased dry root mass and reduced root water content in both cultivars. ABA (50 μM) enhanced rooting percentage in ‘Greco’, reduced the number of roots per cutting, reduced total root lengths and fresh root mass in both cultivars. ABA increased dry root mass and reduced root water content in ‘Surfing’ but this effect was not apparent in ‘Greco’. Storing cuttings in the dark for 4 days had no effect on rooting percentage and number of roots per cutting in ‘Greco’ and ‘Surfing’. However, dark storage reduced total root lengths in ‘Surfing’ and reduced fresh root mass in ‘Greco’. Dark storage had no effect on dry root mass and water content in both cultivars. Applying 4 μl l⁻¹ IBA in the rooting solution induced maximum (100%) root induction in ‘Surfing’. However, IBA reduced the number of roots per cutting in ‘Greco’, reduced total root lengths and fresh root mass in the two cultivars. IBA treatment profoundly increased and reduced dry root mass and root water content, respectively, in ‘Greco’ and ‘Surfing’. The enhanced root induction observed after IBA and ABA applications could be ascribed to their influence on ethylene biosynthesis, since ethylene treatment increased rooting percentage in both cultivars. However, high ABA (100 μM) and IBA (12 μl l⁻¹) levels or dark storage reduced the ability of induced roots to continue growth. We attribute our results to plant stress-response mechanism and ethylene appears to play an important role in the process of root initiation and root growth in Pelargonium cuttings.     

Darwin without borders? Looking at ‘generalised Darwinism’ through the prism of the ‘hourglass model’

This article critically analyzes the arguments of the ‘generalized Darwinism’ recently proposed for the analysis of social-economical systems. We argue that ‘generalized Darwinism’ is both restrictive and empty. It is restrictive because it excludes alternative (non-selectionist) evolutionary mechanisms such as orthogenesis, saltationism and mutationism without any examination of their suitability for modeling socio-economic processes and ignoring their important roles in the development of contemporary evolutionary theory. It is empty, because it reduces Darwinism to an abstract triple-principle scheme (variation, selection and inheritance) thus ignoring the actual structure of Darwinism as a complex and dynamic theoretical structure inseparable from a very detailed system of theoretical constraints. Arguing against ‘generalised Darwinism’ we present our vision of the history of evolutionary biology with the help of the ‘hourglass model’ reflecting the internal dynamic of competing theories of evolution.     

ABA and proline accumulation in leaves and roots of wild (<Emphasis Type="Italic">Hordeum spontaneum</Emphasis>) and cultivated (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> ‘Maresi’) barley genotypes under water deficit conditions

The purpose of the study was to examine water stress-induced changes in the ABA and proline contents in roots and leaves of a potentially more resistant wild accession of Hordeum spontaneum and the modern cultivar Maresi (Hordeum vulgare). Leaves of H. spontaneum had higher contents of constitutive ABA and proline in comparison to those of ‘Maresi’. A moderate water deficit resulted only in root dehydration, which was higher in ‘Maresi’. Increases of water deficit in roots coincided with an increase of ABA content in roots, followed by that in leaves. The level of proline increased only in leaves and only in the case of H. spontaneum. Under conditions of severe water stress, the root dehydration levels were similar in the both genotypes, whereas leaf dehydration was higher in ‘Maresi’. H. spontaneum, as compared to ‘Maresi’ showed an earlier increase of ABA content in the roots and accumulated more ABA in the leaves. Free proline levels in the roots increased in both genotypes but H. spontaneum exhibited a 2-fold higher proline accumulation than ‘Maresi’. In H. spontaneum the accumulation of proline in the leaves occurred noticeably earlier and to a higher extent than in ‘Maresi’. A possible connection of these modifications with water stress resistance of the investigated genotypes is discussed in this paper.     

Reproductive biology of the European Cuckoo Cuculus canorus: early insights, persistent errors and the acquisition of knowledge

The brood parasitic habits of the European Cuckoo Cuculus canorus have excited wonder, disbelief and speculation since the fourth century BC. Accurate knowledge of cuckoo biology, however, accumulated only slowly and mostly since 1700. The aim of this study is to review six main topics: (1) the placement of cuckoo eggs in host nests; (2) cuckoo ‘clutch’ size; (3) cuckoo egg characteristics, mimicry and rejection; (4) choice of hosts; (5) eviction of eggs and chicks; and (6) the reasons why cuckoos are brood parasites and are incapable of rearing their own young. Early errors in reporting cuckoo biology were often a consequence of poor or incomplete observations leading to erroneous interpretations. Many of the early observers were egg collectors who focussed almost exclusively on the egg-laying period, thus ignoring cuckoo chick biology. Major landmarks in cuckoo studies included the facts that: (1) cuckoo eggs often resembled those of their hosts (1760s) and that this mimicry was adaptive (1850s); (2) hosts sometimes evicted cuckoo eggs (1770s); (3) female cuckoos laid individually distinctive eggs and that specific cuckoo gentes may exist (1850s); and (4) although well recognised that cuckoo chicks were reared alone, prior to Jenner’s work in the 1780s female cuckoo parents were thought to either eat or evict the host eggs or young. Jenner’s results was more readily accepted in Britain than in Germany. Between 1700 and 1859, cuckoo brood parasitism was difficult to reconcile with the prevalent conceptual framework of physico-theology (later known as the argument from design). Thereafter, Darwin’s idea of natural selection provided a superior conceptual framework, which in conjunction with experimental testing of specific hypotheses has continued to advance our understanding of brood parasitism. Our knowledge of cuckoo biology is far from complete, however, and we predict that continuing research often incorporating new technologies will refine and extend our understanding of the cuckoo’s extraordinary biology.     

Cryopreservation of horse-chestnut (Aesculus hippocastanum L. ) somatic embryos using three different freezing methods

Cryopreservation of somatic embryos of Aesculus hippocastanum L. cultured on nutritive media containing abscisic acid (ABA) at concentrations of 0.75 μM, 7.5 μM and 75.0 μM was evaluated for three cooling methods: (i) slow freezing with cryoprotectants, (ii) fast freezing with cryoprotectants, and (iii) fast freezing with desiccation techniques. The ‘cryoprotectant’ freezing techniques included the embryo pretreatment on ABA containing medium for 4 days, followed by cryoprotective treatment in liquid medium containing 0.5 M dimethylsulfoxide, 0.5 M glycerol, 1.0 M sucrose, and cooled at slow, and rapid rates. Embryos pretreated on a medium containing 0.75 μM ABA, and cooled to −35 °C at 1°C /min, held for 30 min at this transfer temperature and then immersed in liquid nitrogen (LN) had the best embryo recovery (43%). The ‘desiccation’ method involved an air drying step of similar ABA-pretreated, non-cryoprotected embryos followed by rapid cooling. Embryos precultured on 0.75 μM ABA, then subjected to a 4 h period of air desiccation (water content reduction to 13%) showed about the same level of survival (46%) as found with the ‘cryoprotectant’ slow freezing technique. The air-dry ‘desiccation’ method is easier to apply than the more complicated ‘cryoprotectant’ method. This revised version was published online in June 2006 with corrections to the Cover Date.     

Integrating biotechnology into a non-majors biology curriculum

A general education biology course entitled ‘Biotechnology Transforms Our World’ has been developed to illustrate biological concepts with advances from biotechnology. The contributions of molecular biology to understanding human genetics, evolution, plant and animal (including human) biology and ecology are illustrated with specific case studies. Journal of Industrial Microbiology & Biotechnology (2000) 24, 308–309. Received 02 April 1999/ Accepted in revised form 11 November 1999     

Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut?

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement.     

Evolution of early determinate tomato cultivars during the last three decades as a result of research conducted at Warsaw Agricultural University

Earliness is a crucial factor of tomato field production in Poland. A. Michalska and B. Kubicki (1978) conducted the first investigations on tomato earliness at the Department of Plant Genetics and Breeding. The main conclusions from these studies indicated that it was possible to obtain varieties earlier than ‘New Yorker’ as a result of transgression. The two new varieties (‘Alfa’ and ‘Akord F₁’) proved to be two weeks earlier than ‘New Yorker’. However, earliness was correlated with smaller fruit weight (30–40 g). At the next stage of experiment some improvement was achieved both in the size of fruit (45 g for ‘Beta’ up to 70 g for ‘Alka’) as well as colour intensity and good flavour. With the next few years fruit weight was still increased (up to 100 g for ‘Maskarena’) and a higher level of firmness was obtained (mid firm fruits for ‘Maskarena’ and ‘Delta’). At present, the Polish Research Centre for Cultivar Testing recommends our varieties ‘Betalux’, ‘Promyk’ and ‘Delta’ as standards.     

Stress-induced changes important for effective androgenic induction in isolated microspore culture of triticale (×<Emphasis Type="Italic">Triticosecale</Emphasis> Wittm.)

The accumulation of abscisic acid (ABA) and the activities of antioxidative enzymes along with cell metabolic activity were monitored during androgenesis induction in triticale (×Triticosecale Wittm.). Tested cultivars ‘Mieszko’ and ‘Wanad’ were selected due to their significantly different responses to androgenic induction. Significant variation was observed in respect of superoxide dismutase activity and endogenous ABA content in anthers isolated from freshly cut tillers. For both cultivars, tillers pretreatment with low temperature decreased peroxidase activity by 36%, highly accelerated respiration rate and reduced heat production. At the same time, the level of ABA in ‘Mieszko’ was increased to the level measured in ‘Wanad’. This effect was associated with higher microspore culture viability and increased stress tolerance in ‘Mieszko’. Low temperature and metabolic starvation during 4-day anther preculture did not influence activities of antioxidative enzymes, while it resulted in slight decrease in respiration rate and heat emission. The importance of these changes for effective androgenesis induction is discussed.     

Populations under microevolutionary scrutiny: what will we gain?

Understanding the evolution of biodiversity and the function of biological systems are burning and linked questions in biology. Evolution of biodiversity begins at the level of microevolution, with the differentiation of individuals in populations. The study of this process splits into two conceptually different approaches (1) the concept of functional biology of testing hypothesis by precisely controlled and forward-directed experiments (digital and experimental evolution), and (2) the concept of a theory-based historical narrative (testing hypothesis on events in the past for their suitability to best explain the present). Here, I discuss and emphasize the benefits of the study of natural bacterial populations for a deeper understanding of prokaryotic biology. Also, I adress current problems in taxonomy at the ‘species’ level which obviously need discussion and clarification. I exemplify this with a natural model population for such studies, Bacillus simplex from “Evolution Canyon”, Israel.     

Assaying polymorphism at DNA level for genetic diversity diagnostics of the safflower (Carthamus tinctorius L.) world germplasm resources

Carthamus tinctorius (2n = 2x = 24), commonly known as safflower, is widely cultivated in agricultural production systems of Asia, Europe, Australia, and the Americas as a source of high quality vegetable and industrial oil. Twenty-two RAPD primers, 18 SSR primers, and 10 AFLP primer combinations were used to assess: (1) the genetic diversity of 85 accessions (originating from 24 countries) representing global germplasm variability of safflower and (2) the interrelationships among safflower ‘centers of similarity’ or ‘regional gene pools’ proposed earlier. The RAPD and SSR primers and AFLP primer combinations revealed 57.6, 68.0, and 71.2% polymorphism, respectively, among 111, 72, and 330 genetic loci amplified from the accessions. The sum of effective number of alleles (66.44), resolving power (59.16), and marker index (51.3) explicitly revealed the relative superiority of AFLP as a marker system in uncovering variation in safflower. Overall, AFLP markers could recognize ‘centers of similarity’ or ‘regional gene pools’. Analysis of molecular variance and Shannon’s information index provided corroborating evidences for the present and previous studies that concluded fragmentation of safflower gene pool into many gene pools. Divergent directional selection is likely to have played an important role in shaping the diversity. From the practical applications standpoint, the diversity of Iran–Afghanistan gene pool is very high, equivalent to the total diversity of the species. The Far East gene pool is the least diverse. The present comprehensive input, first of its own kind in safflower, will assist marker based improvement programmes in the crop.     

Living Rivers: Trends and Challenges in Science and Management

This paper discusses and summarizes the major conclusions of the special issue entitled ‘Living rivers: trends and challenges in science and management’ of Hydrobiologia/Developments in Hydrobiology. It is structured along three lines: (1) Functioning of river systems; (2) Ecological rehabilitation of river systems; (3) Challenges and obstacles to sustainable management. Sustainable river basin management requires a thorough understanding of natural, physical, chemical and ecological processes as well as socio-economic functioning. Environmental rehabilitation of river systems inevitably requires an ecosystem-based approach involving solutions supported by the public. The challenge is to combine ecological and socio-economic sustainability. Rethinking our efforts in both directions must lead to more innovative solutions than those available at present.     

Two strategies for investigating the evolution of behavior

In this paper I distinguish and characterize two strategies, both prominent in contemporary biology, for investigating the evolution of behavior. The ‘Lorenzian Strategy’ is taxon-focused, holistic, and particularistic, and relies heavily on naturalistic observation as well as careful experimental manipulation of target systems; it tends to produce detailed knowledge of concrete historical instances of the evolution of behavior in particular lineages. The ‘Analytic Strategy’ is principle-focused, generative, and taxonomically universal; it relies on the development of mathematical principles (simple analytic models) of the evolution of behavior at an abstract level, and uses experimentation to garner support for the empirical relevance for these. The strategies hence employ different methods and produce different sorts of knowledge, hence they are neither inconsistent nor redundant, but complementary, and indeed they both play important roles in the contemporary biology of animal behavior.     

Signaling mechanisms in abscisic acid-mediated stomatal closure

The plant hormone abscisic acid (ABA) plays a central role in the regulation of stomatal movements under water-deficit conditions. The identification of ABA receptors and the ABA signaling core consisting of PYR/PYL/RCAR ABA receptors, PP2C protein phosphatases and SnRK2 protein kinases has led to studies that have greatly advanced our knowledge of the molecular mechanisms mediating ABA-induced stomatal closure in the past decade. This review focuses on recent progress in illuminating the regulatory mechanisms of ABA signal transduction, and the physiological importance of basal ABA signaling in stomatal regulation by CO₂ and, as hypothesized here, vapor-pressure deficit. Furthermore, advances in understanding the interactions of ABA and other stomatal signaling pathways are reviewed here. We also review recent studies investigating the use of ABA signaling mechanisms for the manipulation of stomatal conductance and the enhancement of drought tolerance and water-use efficiency of plants.     

Effects of ethylene and 1-MCP (1-methylcyclopropene) on bud and flower drop in mini <Emphasis Type="Italic">Phalaenopsis</Emphasis> cultivars

Phalaenopsis frequently exhibits bud drop during production and in response to adverse postharvest conditions. The effect of exogenous ethylene on bud drop of mini Phalaenopsis was studied and ethylene sensitivity of four cultivars was compared. Water content, membrane permeability and ABA (abscisic acid) content in floral buds and flowers were determined after ethylene treatment. Exogenous ethylene induced flower bud drop in all tested Phalaenopsis cultivars and the different cultivars showed distinct differences in ethylene sensitivity. The cultivar Sogo ‘Vivien’ exhibited the highest bud drop, water loss and change in membrane permeability in floral petals, while Sogo ‘Berry’ showed the lowest sensitivity. The ethylene inhibitor 1-MCP (1-methylcyclopropene) reduced ethylene-induced floral bud drop in the cultivar Sogo ‘Yenlin’. ABA content in floral buds was increased in response to ethylene and 1-MCP pretreatment inhibited the ethylene-induced increase in ABA levels efficiently. This finding suggests that the observed increase in ABA content during bud drop was mediated by ethylene. The interaction between ABA and ethylene is discussed.