Conjugated linoleic acids: are they beneficial or detrimental to health?

Conjugated linoleic acids (CLAs) comprise a family of positional and geometric isomers of linoleic acid (18:2n − 6; LA) that are formed by biohydrogenation and oxidation processes in nature. The major dietary sources of these unusual fatty acids are foods derived from ruminant animals, in particular dairy products. The main form of CLA, cis-9, trans-11-18:2, can be produced directly by bacterial hydrogenation in the rumen or by delta-9 desaturation of the co-product vaccenic acid (trans-11-18:1) in most mammalian tissues including man. The second most abundant isomer of CLA is the trans-10, cis-12-18:2 form. Initially identified in grilled beef as a potential anti-carcinogen a surprising number of health benefits have subsequently been attributed to CLA mixtures and more recently to the main individual isoforms. It is also clear from recent studies that the two main isoforms can have different effects on metabolism and cell functions and can act through different cell signalling pathways. The majority of studies on body compositional effects (i.e. fat loss, lean gain), on cancer and cardiovascular disease attenuation, on insulin sensitivity and diabetes and on immune function have been conducted with a variety of animal models. Observations clearly emphasise that differences exist between mammalian species in their response to CLAs with mice being the most sensitive. Recent studies indicate that some but not all of the effects observed in animals also pertain to human volunteers. Reports of detrimental effects of CLA intake appear to be largely in mice and due mainly to the trans-10, cis-12 isomer. Suggestions of possible deleterious effects in man due to an increase in oxidative lipid products (isoprostanes) with trans-10, cis-12 CLA ingestion require substantiation. Unresponsiveness to antioxidants of these non-enzymatic oxidation products casts some doubt on their physiological relevance. Recent reports, albeit in the minority, that CLAs, particularly the trans-10, cis-12 isomer, can elicit pro-carcinogenic effects in animal models of colon and prostate cancer and can increase prostaglandin production in cells also warrant further investigation and critical evaluation in relation to the many published anti-cancer and anti-prostaglandin effects of CLAs.     

Bacterial EPIYA effectors – Where do they come from? What are they? Where are they going?

Recent studies have revealed a distinct class of bacterial effectors defined by the presence of EPIYA or EPIYA‐related motif. These bacterial EPIYA effectors are delivered into host cells via type III or IV secretion, where they undergo tyrosine phosphorylation at the EPIYA motif and thereby manipulate host signalling by promiscuously interacting with multiple SH2 domain‐containing proteins. Up to now, nine EPIYA effectors have been identified from various bacteria. These effectors do not share sequence homology outside the EPIYA motif, arguing against the idea that they have common ancestors. A search of mammalian proteomes revealed the presence of a mammalian EPIYA‐containing protein, Pragmin, which potentiates Src family kinase (SFK) activity by binding and sequestrating the SFK inhibitor Csk upon EPIYA phosphorylation. As several bacterial EPIYA effectors also target Csk, they may have evolved through generation of sequences that mimic the Pragmin EPIYA motif. EPIYA motifs are often diverged through multiple duplications in each bacterial effector. Such a structural plasticity appears to be due to intrinsic disorder of the EPIYA‐containing region, which enables the bacterial effectors to undergo efficient phosphorylation and mediate promiscuous interaction with multiple host proteins. Given the functional versatility of the EPIYA motif, many more bacterial EPIYA effectors will soon be emerging.     

Density dependence tests,are they?

A large number of time series of abundances of insects and birds from a variety of data sets were submitted to a new density dependence test. The results varied enormously between data sets, but the relation between the frequency of statistically significant density dependence (SSDD) and the length of the series was similar to that of the power curve of the test, making the results consistent with the hypothesis of the density-dependent model being universally applicable throughout the data used. Pest and non-pest species did not differ in the incidence of SSDD. The more sampling error present in the data, the higher the percentages of SSDD. This was expected given that the power of the test increases with increasing sampling error in the data. Many of the data used here, as well as in the literature, clearly violate the basic assumption of the test that the organism concerned should be univoltine and semelparous. Yet the incidence of SSDD was the same in univoltine as in bi/polyvoltine species and the same in semelparous organisms as in birds that are reproductively active in more than one year. The seasonal migrant Autographa gamma in Britain and Czechoslovakia and even rainfall data were found to have SSDD. Statistical significance, however, does not automatically lead to the conclusion of density-dependent regulation. Any series of random variables which are in a stochastic equilibrium, such as a series of independent, identically distributed, random variables, is typically described better by the alternative (density-dependent) model than by the null (density-independent) model. Significant test results were often obtained with sloppy data, with data that clearly violate the basic assumptions of the test and with other data where an interpretation of the results in terms of densitydependent regulation was absurd. Given the fact that other explanations have to be found for significant test results for all these cases, mechanisms other than regulation may very well be applicable too where the data are entirely appropriate for the test. The test is simply a data-based choice between a model without and one with a stochastic equilibrium. A time series as such does not contain any information about the causes of the fluctuation pattern, so that one cannot expect statistics to produce such information from that time series. A significant test result using suitable data is entirely consistent with the hypothesis of density-dependent regulation, but also with any other suitable hypotheses. Because the test results were generally consistent with the hypothesis of a universal applicability of the density-dependence model, a negative test result may only mean that the time series was not long enough for the density dependence that was present to become statistically significant. Positive results are difficult to interpret, but so are negative results. A final decision needs to be based not so much on the test result as on much detailed information about the population concerned. Because the density-dependence test does not test for the presence of the mechanism of density-dependent regulation and because of the loaded, multiple meanings of the term density-dependence, calling the test a test of statistical density dependence may be preferable.     

Whose turtles are they,anyway?

The hawksbill turtle (Eretmochelys imbricata), listed since 1996 by the IUCN as Critically Endangered and by the Convention on International Trade in Endangered Species (CITES) as an Appendix I species, has been the subject of attention and controversy during the past 10 years due to the efforts of some nations to re-open banned international trade. The most recent debate has centred on whether it is appropriate for Cuba to harvest hawksbills from shared foraging aggregations within her national waters. In this issue of Molecular Ecology, Bowen et al. have used molecular genetic data to show that such harvests are likely to have deleterious effects on the health of hawksbill populations throughout the Caribbean.     

Viruses: are they living entities?

The essence (living or nonliving entities) of viruses has today become an aporia, i.e. a difficulty inherent in reasoning because they shared four fundamental characteristics with livings (multiplication, genetic information, mutation and evolution) without having the capacity to have an independent life. For much time, however, they were considered minuscule pathogenetic micro-organisms in observance of Koch and Pasteur's 'germ theory' albeit no microbiologist could show their existence except their filterability and pathogenetic action. Only some voices based on experimental results raised against this dogmatic view, in particular those of Beijerinck, Baur and Mrowka, without dipping effectively into the dominant theory. The discovery relative to their nucleoprotein nature made between 1934 and 1936 (Schlesinger as for the phage, and Bawden and co-operators as for Tobacco mosaic virus; TMV), together with the first demonstrations of their structures thanks to electron microscopy (from 1939 onwards) started on casting a new light on their true identity, which could be more clearly identified when, from 1955 onwards, phage and TMV proved to be decisive factors to understand the strategies of replication of the genetic material. Following the new knowledge, the theoretical view relative to viruses changed rather radically and the current view looks on these pathogenetic agents as nonliving aggregates of macromolecules provided with biological properties. There is, however, a current of thought, made explicitly by Lwoff that places viruses as compromise between living and non living and, perhaps, as primitive forms of life which have had great importance for the evolution of cellular life. At any rate, viruses are peculiar entities whose importance cannot be unacknowledged.     

Late-onset porphyrias: what are they?

Porphyrias are inherited disorders of heme biosynthesis. ALA dehydratase porphyria (ADP) and congenital erythropoietic porphyria (CEP) are autosomal recessive porphyrias, and are typically expressed at birth or in childhood. However, a few cases of late-onset recessive porphyrias have been reported. Recently we encountered a late-onset ADP patient who developed symptoms of acute porphyria when he was 63 years old. This was accompanied by polycythemia vera. It was concluded that he developed the porphyria because an abnormal ALAD allele was clonally expanded by polycythemia vera. Upon reviewing the literature, a few cases of late-onset CEP were found to be also associated with hematologic abnormalities suggestive of myelodysplastic syndrome (MDS), another clonal disorder. These findings suggest that these late-onset porphyrias may be heterozygous for their gene defects, but clinical expression may be elicited if there is a loss of heterozygosity, either by a clonal expansion of the porphyric allele or by a loss of function mutation in the other allele.     

Functionally and structurally relevant residues of enzymes: are they segregated or overlapping?

There is a delicate balance between stability and flexibility needed for enzyme function. To avoid undesirable alteration of the functional properties during the evolutionary optimization of the structural stability under certain circumstances, and vice versa, to avoid unwanted changes of stability during the optimization of the functional properties of proteins, common sense would suggest that parts of the protein structure responsible for stability and parts responsible for function developed and evolved separately. This study shows that nature did not follow this anthropomorphic logic: the set of residues involved in function and those involved in structural stabilization of enzymes are rather overlapping than segregated.     

The genomes and transposable elements in plants: are they friends or foes?

Transposable elements (TEs) are mobile genetic elements that are present in prokaryotes and eukaryotes. The ubiquity and abundance of these self-replicating entities, bereft of cellular function, had earned them the label of ‘genomic parasites’. However, the status of TEs has been revised, with ample genomic and biological evidence now portraying them as “genomic gold”. They are perceived as a major participant in the evolution of species. This review addresses the classification of TEs as well as their role and significance in the evolution of genomes, genetic diversity, gene regulation, and exaptation of contemporary species of the plant and animal kingdoms.     

Vetulicolians—are they deuterostomes? chordates?

A recent paper by Shu et al.(1) reinterprets the fossil Vetulicola and related forms, all from the Lower Cambrian, as basal deuterostomes, assigning them their own phylum, Vetulicolia. Their conclusion is based on the presence of structures resembling gill slits and a trunk-like region that shows evidence of segmentation. This report summarizes the fossil evidence for their interpretation and evaluates a possible alternative, that vetulicolians may instead be tunicate-like chordates. Implications for our understanding of the nature of the primitive deuterostome (and chordate) body plan are discussed. .     

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.     

Nuclear grooves. How specific are they?

OBJECTIVE: To study the significance of nuclear grooves in thyroid and extrathyroid benign and malignant lesions. STUDY DESIGN: In this retrospective study, 26 cases were selected randomly, consisting of papillary carcinoma of the thyroid (7), papillary adenocarcinoma (9), normal cervical smear (5) and benign bronchioalveolar lavage (BAL) (5). In all cases hematoxylin and eosin- and Papanicolaou-stained smears were studied for nuclear grooves. RESULTS: Except for one case of papillary adenocarcinoma, nuclear grooves were discernible in all cases. The highest number of nuclear grooves was seen in normal cervical smears, followed by papillary carcinoma of the thyroid, papillary adenocarcinoma and BAL smears. CONCLUSION: The number of grooves did not correlate with either benign or malignant conditions. These findings cast serious doubt about the diagnostic significance of nuclear grooves. Probably nuclear grooves are nonspecific findings and should be considered only in association with other diagnostic features.     

Human supernumeraries: are they B chromosomes?

In humans, the presence of supernumerary chromosomes is an unusual phenomenon, which is often associated with developmental abnormalities and malformations. In contrast to most animal and plant species, the extensive knowledge of the human genome and the ample set of molecular and cytogenetic tools available have permitted to ascertain not only that most human supernumerary chromosomes (HSCs) derive from the A chromosome set, but also the specific A chromosome from which most of them arose. These extra chromosomes are classified into six types on the basis of morphology and size. There are both heterochromatic and euchromatic HSCs, the latter being more detrimental. Most are mitotically stable, except some producing individual mosaicism. No information is available on the HSC transmission rate since extensive familial studies are not usually performed generally because of death of the relatives or lack of cooperation. The main B chromosome property failing in HSCs seems to be their population spread as polymorphisms, since most HSCs seem to correspond to extra A chromosomes or centric fragments spontaneously arisen in the analysed individual or one of his/her parents. However, we cannot rule out at this moment, that more intensive studies on population distribution and frequency of those HSCs most closely resembling B chromosomes (i.e. those heterochromatic and thus less detrimental) would reveal possible HSCs polymorphisms. Although HSCs cannot be considered B chromosomes, some of them might be a source for future B chromosomes. The best candidates would be heterochromatic HSCs, which might manage to drive in either sex. To ascertain this possibility, research on inheritance and population studies would be very helpful in combination with the powerful cytogenetic and molecular tools available for our species.     

Histone variants: are they functionally heterogeneous?

In most eukaryotes, histones, which are the major structural components of chromatin, are expressed as a family of sequence variants encoded by multiple genes. Because different histone variants can contribute to a distinct or unique nucleosomal architecture, this heterogeneity can be exploited to regulate a wide range of nuclear functions, and evidence is accumulating that histone variants do indeed have distinct functions.     

Dark septate endophytes – are they mycorrhizal?

Dark septate endophytes (DSE) are a miscellaneous group of ascomycetous anamorphic fungi that colonize root tissues intracellularly and intercellularly. The limited selection of studies quoted here exemplifies the range of host responses to symbiotic DSE fungi. Like mycorrhizal associations, DSE associations vary from negative to neutral and positive when measured by host performance or host tissue nutrient concentrations. This range of host responses is partially attributable to variation between different fungus taxa and strains. Similarly, hosts differ in their responses to a single DSE strain. Experimental conditions may also govern the nature of the symbiotic association. It is concluded that DSE are capable of forming mutualistic associations functionally similar to mycorrhizas. If the variation in host response to mycorrhizal fungi is considered to represent a continuum ranging from parasitism to mutualism, DSE symbiosis must be considered mycorrhizal, at least under some conditions.     

Foraging strategies by omnivores: are black bears actively searching for ungulate neonates or are they simply opportunistic predators?

Omnivores feed on animals with dynamic distributions and on plants with static distributions. The search tactics they adopt will not only define the risk for the targeted prey, but also for other prey that may be consumed when encountered. The potential impact of omnivores on the dynamics of multi‐prey systems thus depends on resource selection and on the tactics used to find their prey. We present an approach that can clarify the foraging decisions of omnivores by combining analyses of habitat selection, local residency time, and interpatch movements. We use this framework to evaluate whether predation by omnivorous black bears on ungulate neonates resulted from an active search or from incidental encounters. We monitored 12 bears, 22 forest‐dwelling caribou, and 36 moose during calving seasons. We estimated the spatial patterns in relative occurrence probability of ungulate neonates using Resource Selection Functions (RSFs). We also mapped plant abundance from vegetation surveys. RSF were then built to assess the link between bear distribution and the distribution of these three food types (vegetation, moose calves, caribou fawns). We further evaluated the search tactic used by bears that led to this spatial dependency by exploring patterns of residency times and interpatch movements. Bears did not select areas with a high probability of encounter with neonates, but selected areas with abundant vegetation. Surprisingly, bears displayed shorter residency times in vegetation‐rich areas. The selection for vegetation‐rich areas was therefore achieved by moving preferentially, but frequently, between areas offering abundant vegetation. Such frequent interpatch movements could result in high rates of fortuitous encounters with neonates, even if bears are not actively searching for them. To mitigate the impacts of forest harvesting on threatened caribou populations, vegetation‐rich areas selected by bears (e.g. roadsides) should be segregated from large patches of mature conifer forest suitable for caribou.