What makes Allium species effective against pathogenic microbes?

The antimicrobial activity of garlic (Allium sativum L.) has been known since ancient times. The first citation dates back to the Egyptian period of fifteenth century BC when garlic was reported to be used in folk medicine as a remedy for microbial infections. Scientific investigations on garlic started in 1858 with the work of Pasteur who first noted antibacterial properties of garlic extracts. From that date to the discovery of antibiotics, garlic has been used against amoebic dysentery and epidemic diseases such as typhus, cholera, diphtheria, and tuberculosis. But what makes garlic and Allium species effective against pathogenic microbes? The volatile allicin and other thiosulfinates, giving pungency to Allium plants, are well-studied antimicrobial agents. The thiosulfinates can decompose to form additional sulfur constituents, including diallyl, methyl allyl, and dipropyl mono-, di-, tri- e tetra-sulfides, and (E)- and (Z)-ajoene without losing antimicrobial activity. Besides these compounds, onion and garlic are characterized by polar compounds of steroidal and phenolic origin, often glycosilated, not pungent and more stable during cooking, showing also antimicrobial activity. Recently, there has been increasing scientific attention given to such compounds. Nitrogen organic compounds, like alkaloids and polypeptides, have also been isolated from these plants and have shown antimicrobial activity. In this paper, the literature about the major volatile and non-volatile organic compounds of garlic and other Allium plants has been reviewed. Particular attention is given to the compounds possessing antimicrobial activity and to the correlation between the observed activity and the chemical structure of the tested compounds.     

What makes a cell face selective? The importance of contrast

Faces are robustly detected by computer vision algorithms that search for characteristic coarse contrast features. Here, we investigated whether face-selective cells in the primate brain exploit contrast features as well. We recorded from face-selective neurons in macaque inferotemporal cortex, while presenting?a face-like collage of regions whose luminances were changed randomly. Modulating contrast combinations between regions induced activity changes ranging from no response to a response greater than that to a real face in 50% of cells. The critical stimulus factor determining response magnitude was contrast polarity, for example, nose region brighter than left eye. Contrast polarity preferences were consistent across cells, suggesting a common computational strategy across the population, and matched features used by computer vision algorithms for face detection. Furthermore, most cells were tuned both for contrast polarity and for the geometry of facial features, suggesting cells encode information useful both for detection and recognition.     

What makes vessels grow with exercise training?

Exercise and muscle contractions create a powerful stimulus for structural remodeling of the vasculature. An increase in flow velocity through a vessel increases shear stress, a major stimulus for enlargement of conduit vessels. This leads to an endothelial-dependent, nitric oxide-dependent enlargement of the vessel. Increased flow within muscle, in the absence of contractions, leads to an enhanced capillarity by intussusceptive angiogenesis, a process of capillary splitting by intraluminal longitudinal divide. In contrast, sprouting angiogenesis requires extensive endothelial cell proliferation, with degradation of the extracellular matrix to permit migration and tube formation. This occurs during muscle adaptations to chronic contractions and/or muscle overload. The angiogenic growth factor VEGF appears to be an important element in angiogenesis. Recent advances in research have identified hemodynamic and mechanical stimuli that upregulate angiogenic processes, demonstrated a complexity of potent growth factors and interactions with their corresponding receptors, detected an interaction of cellular signaling events, and identified important tissue reorganization processes that must be coordinated to effect vascular remodeling. It is likely that much of this information is applicable to the vascular remodeling that occurs in response to exercise and/or muscle contractions.     

What makes some species of milk snakes more attractive to humans than others?

Animals are ancestrally important stimuli for humans who pay disproportional attention to animal objects and exhibit an outstanding ability to categorize animal species, especially those most relevant to them. Humans as well as other primates perceive snakes as ambivalent stimuli that elicit unspecific arousal and attention. We assessed human aesthetic preferences toward milk snakes, the traditional model for studies of Batesian mimicry. The genus is fairly uniform in size and shape, but includes a great variety of color forms; some possessing aposematic patterns while others being rather cryptic. This provides an opportunity to test which features are responsible for positive aesthetic evaluation of the species. We asked the respondents to rank 34 pictures of milk snakes according to perceived beauty. The sets (whole bodies, heads, and skin fragments) covered most of naturally occurring variation in milk snake appearance. While ranking the beauty, the respondents spontaneously classified the species according to two dimensions. In each set, one of the dimensions corresponds to perceived beauty. The respondents’ ranking revealed several distinct clusters of species instead of a continuous gradient. The species clustered in a similar way irrespective of evaluated set. One dimension of the ranking associated with the relative representation of red color and the number of transversal stripes, the other corresponded to a low proportion of red and a high proportion of black color. When the whole body of the snake is evaluated, aposematic coloration contributes to its perceived beauty. In conclusion, humans showed a surprising ability to classify milk snake patterns; they repeatedly formed the same distinct groups of species, thus completing a process that resembles unsupervised categorization.     

The monotreme genome: a patchwork of reptile, mammal and unique features?

The first specimen of platypus (Ornithorhynchus anatinus) that reached Britain in the late 18th century was regarded a scientific hoax. Over decades the anatomical characteristics of these unique mammals, such as egg laying and the existence of mammary glands, were hotly debated before they were accepted. Within the last 40 years, more and more details of monotreme physiology, histology, reproduction and genetics have been revealed. Some show similarities with birds or reptiles, some with therian mammals, but many are very specific to monotremes. The genome is no exception to monotreme uniqueness. An early opinion was that the karyotype, composed of a few large chromosomes and many small ones, resembled bird and reptile macro- and micro-chromosomes. However, the platypus genome also features characteristics that are not present in other mammals, such as a complex translocation system. The sex chromosome system is still not resolved. Nothing is known about dosage compensation and, unlike in therian mammals, there seems to be no genomic imprinting. In this article we will recount the mysteries of the monotreme genome and describe how we are using recently developed technology to identify chromosomes in mitosis, meiosis and sperm, to map genes to chromosomes, to unravel the sex chromosome system and the translocation chain and investigate X inactivation and genomic imprinting in monotremes.     

What makes a species central in a cleaning mutualism network?

Mutualisms often form networks of interacting species, characterized by the existence of a central core of species that potentially drive the ecology and the evolution of the whole community. Centrality measures allow quantification of how central or peripheral a species is within a network, thus informing about the role of each species in network organization, dynamics, and stability. In the present study we addressed the question whether the structural position of species in the network (i.e. their topological importance) relates to their ecological traits. We studied interactions between cleaner and client reef fishes to identify central and peripheral species within a mutualistic network, and investigated five ecological correlates. We used three measures to estimate the level of centrality of a species for distinct structural patterns, such as the number of interactions and the structural proximity to other species. Through the use of a principal component analysis (PCA) we observed that the centrality measures were highly correlated (92.5%) in the studied network, which indicates that the same species plays a similar role for the different structural patterns. Three cleaner and ten client species had positive values of centrality, which suggests that these species are modulating ecological and evolutionary dynamics within the network. Higher centralities were related to higher abundances and feeding habits for client fishes, but not for cleaners. The high correlation between centrality measures in the present study is likely related to the nested structure of the cleaning network. The cleaner species’ set, by having central species that are not necessarily the most abundant ones, bears potentially more vulnerable points for network cohesiveness. Additionally, the present study generalizes previous findings for plant–animal mutualisms, as it shows that the structure of marine mutualisms is also related to a complex interplay between abundance and niche‐related features.     

What makes a species vulnerable to extinction? Comparative life-history traits of two sympatric snakes

Although it is well known that species vary in their vulnerability to extinction, the reasons are poorly understood. Theory predicts that long-lived species with slow life histories (small litters, slow growth, late maturation) should be at greater risk than short-lived species with high potential rates of increase. This hypothesis was tested by comparing life-history traits of two species of sympatric, elapid snakes: the endangered broad-headed snake, Hoplocephalus bungaroides, and common small-eyed snake, Cryptophis nigrescens. From 1992 to 2000 a mark–recapture study of both species was undertaken in Morton National Park, south-eastern Australia, and this information was used to construct transition matrices for each species. The endangered H. bungaroides was found to mature late (6 years of age), had a high juvenile (54.7%) and adult (81.6%) survival rate, and a long generation length (10.4 years). In striking contrast, the common C. nigrescens matured early (within 3 years), had a lower juvenile (30.4%) and adult (74.4%) survival rate (but higher recruitment rate), and a substantially shorter generation length (5.9 years). Elasticity analyses revealed that H. bungaroides was considerably more sensitive to survival past the age of 2 years (68.6%) than C. nigrescens (37.4%). These results provide support for the hypothesis that species with slow life histories are more vulnerable to extinction.     

What makes a mitochondrion?

Experimental analyses of the proteins found in the mitochondria of yeast, humans and Arabidopsis have confirmed some expectations but given some surprises and some insights into the evolutionary origins of mitochondrial proteins.     

What makes a plant species specialist in mixed broad-leaved deciduous forests?

Knowledge about relationships between specialization degree of species, i.e. the width of their realized niche and functional traits, may have important implications for the assessment of future population developments under environmental change. In this study, we used a recently introduced method to calculate ecological niche widths of plant species in mixed broad-leaved deciduous forests and to investigate the dependence between niche widths of plants and their functional traits and Ellenberg indicator values. The research is based on a dataset of 4556 phytosociological relevés of mixed broad-leaved deciduous forests in Slovenia. We calculated theta indices for 326 species, which ranks them along a continuous gradient of habitat specialization. For 272 species, we compiled 26 functional traits and Ellenberg indicator values. We found some significant correlations between theta indices of species and their functional traits and Ellenberg indicator values; habitat specialists thrive primarily on the highest altitudes, on colder, dry sites and achieve the age of first flowering later than generalists. They also have smaller seed diameter, lower leaf dry matter content, lower mean canopy height and bigger specific leaf area than generalists. Two species groups, chamaephytes and spring green species, are particularly characterized as specialist species. The added value of our work is in complementing the knowledge about the niche differentiating along different environmental gradients and species coexistence in mixed broad-leaved deciduous forests.     

What makes us human?

The sequence of chimpanzee chromosome 22 is starting to help us to define the set of genetic attributes that are unique to humans, but interpreting the biological consequences of these remains a major challenge.     

What makes desiccation tolerable?

A comparison of drought tolerance in plants at extreme ends of the evolutionary spectrum is beginning to show the mechanisms involved.     

Centromeric chromatin: what makes it unique?

Centromeres represent the final frontier of eukaryotic genomes. Although they are defining features of chromosomes--the points at which spindle microtubules attach--the fundamental features that distinguish them from other parts of the chromosome remain mysterious. The function of centromeres is conserved throughout eukaryotic biology, but their DNA sequences are not. Rather, accumulating evidence favors chromatin-based centromeric identification. To understand how centromeric identity is maintained, researchers have studied DNA-protein interactions at native centromeres and ectopic "neocentromeres". Other studies have taken a comparative approach focusing on centromere-specific proteins, of which mammalian CENP-A and CENP-C are the prototypes. Elucidating the assembly and structure of chromatin at centromeres remain key challenges.     

Selenoproteins—What unique properties can arise with selenocysteine in place of cysteine?

The defining entity of a selenoprotein is the inclusion of at least one selenocysteine (Sec) residue in its sequence. Sec, the 21st naturally occurring genetically encoded amino acid, differs from its significantly more common structural analog cysteine (Cys) by the identity of a single atom: Sec contains selenium instead of the sulfur found in Cys. Selenium clearly has unique chemical properties that differ from sulfur, but more striking are perhaps the similarities between the two elements. Selenium was discovered by Jöns Jacob Berzelius, a renowned Swedish scientist instrumental in establishing the institution that would become Karolinska Institutet. Written at the occasion of the bicentennial anniversary of Karolinska Institutet, this mini review focuses on the unique selenium-derived properties that may potentially arise in a protein upon the inclusion of Sec in place of Cys. With 25 human genes encoding selenoproteins and in total several thousand selenoproteins yet described in nature, it seems likely that the presence of that single selenium atom of Sec should convey some specific feature, thereby explaining the existence of selenoproteins in spite of demanding and energetically costly Sec-specific synthesis machineries. Nonetheless, most, if not all, of the currently known selenoproteins are also found as Cys-containing non-selenoprotein orthologues in other organisms, wherefore any potentially unique properties of selenoproteins are yet a matter of debate. The pK_a of free Sec (approximately 5.2) being significantly lower than that of free Cys (approximately 8.5) has often been proposed as one of the unique features of Sec. However, as discussed herein, this pK_a difference between Sec and Cys can hardly provide an evolutionary pressure for maintenance of selenoproteins. Moreover, the typically 10- to 100-fold lower enzymatic efficiencies of Sec-to-Cys mutants of selenoprotein oxidoreductases, are also weak arguments for the overall existence of selenoproteins. Here, it is however emphasized that the inherent high nucleophilicity of Sec and thereby its higher chemical reaction rate with electrophiles, as compared to Cys, seems to be a truly unique property of Sec that cannot easily be mimicked by the basicity of Cys, even within the microenvironment of a protein. The chemical rate enhancement obtained with Sec can have other consequences than those arising from a low redox potential of some Cys-dependent proteins, typically aiming at maintaining redox equilibria. Another unique aspect of Sec compared to Cys seems to be its efficient potency to support one-electron transfer reactions, which, however, has not yet been unequivocally shown as a Sec-dependent step during the natural catalysis of any known selenoprotein enzyme.     

The structural alignment between two proteins: is there a unique answer?

Structurally similar but sequentially unrelated proteins have been discovered and rediscovered by many researchers, using a variety of structure comparison tools. For several pairs of such proteins, existing structural alignments obtained from the literature, as well as alignments prepared using several different similarity criteria, are compared with each other. It is shown that, in general, they differ from each other, with differences increasing with diminishing sequence similarity. Differences are particularly strong between alignments optimizing global similarity measures, such as RMS deviation between C alpha atoms, and alignments focusing on more local features, such as packing or interaction pattern similarity. Simply speaking, by putting emphasis on different aspects of structure, different structural alignments show the unquestionable similarity in a different way. With differences between various alignments extending to a point where they can differ at all positions, analysis of structural similarities leads to contradictory results reported by groups using different alignment techniques. The problem of uniqueness and stability of structural alignments is further studied with the help of visualization of the suboptimal alignments. It is shown that alignments are often degenerate and whole families of alignments can be generated with almost the same score as the "optimal alignment." However, for some similarity criteria, specially those based on side-chain positions, rather than C alpha positions, alignments in some areas of the protein are unique. This opens the question of how and if the structural alignments can be used as "standards of truth" for protein comparison.     

What is an edge species? The implications of sensitivity to habitat edges

For decades, researchers have categorized species as “edge‐loving” or “edge‐avoiding”, but recent studies that show inconsistencies in responses have called these labels into question and led to a sense that edge effects are idiosyncratic and difficult to understand. We suggest that species would be better categorized according to their sensitivity to edges, not the direction of observed responses because no species should be expected to show the same response to all edge types. Measures of edge sensitivity will apply widely across taxa and landscapes and allow metrics that are broadly comparable, making generalities easier to discern. Finally, while the direction of observed edge responses remains a critical (but largely understood) dynamic, most reported edge responses are neutral, so discovering when species are least likely to respond to edges will increase our understanding of edge ecology and associated fragmentation effects. We offer a case study that measures edge sensitivity of 15 butterfly species at 12 edge types. We found that sensitivity is weakly related to vulnerability to predation, but more importantly we show how our results generate new predictions about edge sensitivity that can be explored in future studies.     

What makes wild rabbits drink?

Wild rabbits Oryctolagus cuniculus (L) introduced to Australia over a century ago successfully colonized diverse environments in a large part of the continent varying from arid desert, alps, to lush grasslands and coastline where water and salt may be either abundant or very scarce. Wild rabbits caught in Northern Victoria were studied under laboratory conditions, where they adapted to dry pelleted food and drank regularly water and a cafeteria of electrolyte solutions offered. Intracerebroventricular (IVT) infusion of angiotensin II (AII) in doses 10, 50 and 500 ng/h did not increase their water drinking, but increased salt appetite, although it was delayed one or more days after the beginning of AII infusion. IVT infusion of AII 500 ng/h for one day caused a halving in water intake and a tenfold increase in sodium excretion. These were followed by compensatory changes in water and 0.5 M NaCl intake on the consecutive days. IVT infusion of AII 50 ng/h for one day induced an increased urinary sodium excretion, a negative sodium balance which was not followed by an increased salt appetite. IVT infusion of AII 10 ng/h for five days caused a progressive increase in sodium excretion and salt appetite which were significant on the fourth day of infusion and both remained eight-ten times greater than control levels for three days after the cessation of infusion. Water intake was unchanged. IVT infusion of 0.3 M Na-CSF for two days reduced water and food intake, and caused a negative sodium balance on the second day of infusion which was not followed by increase in salt appetite.(ABSTRACT TRUNCATED AT 250 WORDS)     

What makes the cell differentiate?

In the present paper, I propose a hypothesis whereby the necessity to maintain the permanent energy-dissipating metabolic flux represents the primary force that determines the eukaryotic cell's choice to grow, divide and/or differentiate. This view is based on the universal structure and the strict redox neutrality of the core metabolic network. I propose that the direct substrate level coupling between metabolism and gene expression through epigenetic mechanisms provides a mechanistic explanation of how this control is implemented.