High Biological Significance Research Articles

Exploitation of distant Antarctic waters and close neritic waters by short‐tailed shearwaters breeding in South Australia

AbstractIdentifying the primary foraging grounds of abundant top predators is of importance in marine management to identify areas of high biological significance, and to assess the extent of competition with fisheries. We studied the search effort and habitat selection of the highly abundant short‐tailed shearwater Puffinus tenuirostris to assess the search strategies employed by this wide‐ranging seabird. During the chick‐rearing period 52 individuals were tracked performing 39 short foraging trips (1–2 days), and 13 long trips (11–32 days). First‐passage time analysis revealed that 46% of birds performing short trips employed area‐restricted searches, concentrating search effort at an average scale of 14 ± 5 km. Foraging searches were more continuous for the other 54%, who travelled faster to cover greater distances, with little evidence of area‐restricted searches. The prey returned indicated that continuous searchers consumed similar prey mass, but greater prey diversity than area‐restricted search birds. On long trips 23% of birds travelled 500–1000 km to neritic (continental shelf) habitats, showing weak evidence of preference for areas of higher chlorophyll a concentration, and foraged at a similar spatial scale to short trips. The other 76% performed rapid outbound flights of 1000–3600 km across oceanic habitats commuting to regions with higher chlorophyll a. The spatial scale of search effort in oceanic habitat varied widely with some performing broad‐scale searches (260–560 km) followed by finer‐scale nested searches (16–170 km). This study demonstrates that a range of search strategies are employed when exploiting prey across ocean basins. The trade‐offs between different search strategies are discussed to identify the value of these contrasting behaviours to wide‐ranging seabirds.

Well Plate–Coupled Microfluidic Devices Designed for Facile Image-Based Cell Adhesion and Transmigration Assays

Microfluidic devices have become invaluable tools in recent years to model biological phenomena. Here, the authors present a well plate microfluidic (WPM) device for conducting cell biology assays under shear flow. Physiological shear flow conditions of cell-cell and cell-ligand adhesion within this device produce results with higher biological significance than conventional well plates. The WPM format also produced significant work flow advantages such as faster liquid handling compared to static well plate assays. The authors used the VLA-4-VCAM-1 cell adhesion model as the basis for a rapid, higher throughput adhesion inhibition screen of monoclonal antibodies against VLA-4. Using the WPM device, they generated IC(50) dose-response curves 96 times faster than conventional flow cells. The WPM device was also used to study transmigration of mononuclear cells through endothelial cell monolayers. Twenty-four channels of transmigration data were generated in a single experiment.

Efficiently mining local conserved clusters from gene expression data

Extensive studies have shown that mining gene expression data is important for both bioinformatics research and biomedical applications. However, most existing studies focus only on either co-regulated gene clusters or emerging patterns. Factually, another analysis scheme, i.e. simultaneously mining phenotypes and diagnostic genes, is also biologically significant, which has received relative little attention so far. In this paper, we explore a novel concept of local conserved gene cluster (LC-Cluster) to address this problem. Specifically, an LC-Cluster contains a subset of genes and a subset of conditions such that the genes show steady expression values ( instead of the coherent pattern rising and falling synchronously defined by some previous work) only on the subset of conditions but not along all given conditions. To avoid the exponential growth in subspace search, we further present two efficient algorithms, namely FALCONER and E-FALCONER, to mine the complete set of maximal LC-Clusters from gene expression data sets based on enumeration tree. Extensive experiments conducted on both real gene expression data sets and synthetic data sets show: (1) our approaches are efficient and effective, (2) our approaches outperform the existing enumeration tree based algorithms, and (3) our approaches can discover an amount of LC-Clusters, which are potentially of high biological significance.

Efficiently Mining Time-Delayed Gene Expression Patterns

Unlike pattern-based biclustering methods that focus on grouping objects in the same subset of dimensions, in this paper, we propose a novel model of coherent clustering for time-series gene expression data, i.e., time-delayed cluster (td-cluster). Under this model, objects can be coherent in different subsets of dimensions if these objects follow a certain time-delayed relationship. Such a cluster can discover the cycle time of gene expression, which is essential in revealing gene regulatory networks. This paper is the first attempt to mine time-delayed gene expression patterns from microarray data. A novel algorithm is also presented and implemented to mine all significant td-clusters. Our experimental results show following two results: 1) the td-cluster algorithm can detect a significant amount of clusters that were missed by previous models, and these clusters are potentially of high biological significance and 2) the td-cluster model and algorithm can easily be extended to 3-D gene x sample x time data sets to identify 3-D td-clusters.

Personality counts: the effect of boldness on shoal choice in three-spined sticklebacks

The grouping behaviour of fish is a widespread phenomenon of high biological significance but little is known as to how consistent individual behavioural differences may affect group joining preferences. When given the option to join either a shy or a bold shoal of three-spined sticklebacks, Gasterosteus aculeatus, both shy and bold individuals showed a strong preference for associating with bold fish. Personality type interacted with individual hunger levels to affect the extent of association, suggesting important strategy variation by focal fish in a competitive foraging environment. Furthermore, shoals modified their behaviour in relation to the focal individual. Individual behavioural differences were shown to have a complex role in influencing association preferences as well as driving previously unrecognized behavioural modifications in foraging groups.

AMP-activated protein kinase (AMPK) in the rock crab,Cancer irroratus: an early indicator of temperature stress

Exposure of marine invertebrates to high temperatures leads to a switch from aerobic to anaerobic metabolism, a drop in the cellular ATP concentration ([ATP]), and subsequent death. In mammals, AMP-activated protein kinase (AMPK) is a major regulator of cellular [ATP] and activates ATP-producing pathways, while inhibiting ATP-consuming pathways. We hypothesized that temperature stress in marine invertebrates activates AMPK to provide adequate concentrations of ATP at increased but sublethal temperatures and that AMPK consequently can serve as a stress indicator (similar to heat shock proteins, HSPs). We tested these hypotheses through two experiments with the rock crab, Cancer irroratus. First, crabs were exposed to a progressive temperature increase (6 degrees C h(-1)) from 12 to 30 degrees C. AMPK activity, total AMPK protein and HSP70 levels, reaction time, heart rate and lactate accumulation were measured in hearts at 2 degrees C increments. AMPK activity remained constant between 12 and 18 degrees C, but increased up to 9.1(+/-1.5)-fold between 18 and 30 degrees C. The crabs' reaction time also decreased above 18 degrees C. By contrast, HSP70 (total and inducible) and total AMPK protein expression levels did not vary significantly over this temperature range. Second, crabs were exposed for up to 6 h to the sublethal temperature of 26 degrees C. This prolonged exposure led to a constant elevation of AMPK activity and levels of HSP70 mRNA. AMPK mRNA continuously increased, indicating an additional response in gene expression. We conclude that AMPK is an earlier indicator of temperature stress in rock crabs than HSP70, especially during the initial response to high temperatures. We discuss the temperature-dependent increase in AMPK activity in the context of Shelford's law of tolerance. Specifically, we describe AMPK activity as a cellular marker that indicates a thermal threshold, called the pejus temperature, T(p). At T(p) the animals leave their optimum range and enter a temperature range with a limited aerobic scope for exercise. This T(p) is reached periodically during annual temperature fluctuations and has higher biological significance than earlier described critical temperatures, at which the animals switch to anaerobic metabolism and HSP expression is induced.

Analysis of selected phenolic acids and flavonoids inAmaranthus cruentusandChenopodium quinoaseeds and sprouts by HPLC

Summary Red amaranth (Amaranthus cruentus) and quinoa (Chenopodium quinoa) are pseudocereals with particularly highly regarded nutritional value. Because of the high biological significance of the flavonoids and phenolic acids in these plants, qualitative and quantitative analysis has been performed by HPLC. Extracts from the seeds of two amaranth varieties (A. cruentus v. Rawa and v. Aztek) and quinoa seeds, and their sprouts grown in natural conditions and in the dark were analyzed. The main phenolic acid found both in seeds and sprouts was gallic acid. p-Hydroxybenzoic acid, vanillic acid, p-coumaric acid, caffeic acid, and cinnamic acid were also found in the seeds and p-coumaric acid, syringic acid, and ferulic acid in the sprouts. The main flavonoid found in the sprouts was rutin. Vitexin, isovitexin, and morin were also detected in the sprouts, and orientin, vitexin, isovitexin, morin, and traces of hesperidin and neohesperidin in the seeds. Although sprouting conditions (daylight or darkness) had no effect on gallic acid content, light caused an increase in the amount of rutin and darkness resulted in increased amounts of isovitexin and vitexin.

Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles

Cluster analysis (of gene-expression data) is a useful tool for identifying biologically relevant groups of genes that show similar expression patterns under multiple experimental conditions. Various methods have been proposed for clustering gene-expression data. However most of these algorithms have several shortcomings for gene-expression data clustering. In the present article, we focus on several shortcomings of conventional clustering algorithms and propose a new one that is able to produce better clustering solution than that produced by some others. We present the Divisive Correlation Clustering Algorithm (DCCA) that is suitable for finding a group of genes having similar pattern of variation in their expression values. To detect clusters with high correlation and biological significance, we use the correlation clustering concept introduced by Bansal et al. Our proposed algorithm DCCA produces a clustering solution without taking number of clusters to be created as an input. DCCA uses the correlation matrix in such a way that all genes in a cluster have highest average correlation with genes in that cluster. To test the performance of the DCCA, we have applied DCCA and some well-known conventional methods to an artificial dataset, and nine gene-expression datasets, and compared the performance of the algorithms. The clustering results of the DCCA are found to be more significantly relevant to the biological annotations than those of the other methods. All these facts show the superiority of the DCCA over some others for the clustering of gene-expression data. The software has been developed using C and Visual Basic languages, and can be executed on the Microsoft Windows platforms. The software may be downloaded as a zip file from http://www.isical.ac.in/~rajat. Then it needs to be installed. Two word files (included in the zip file) need to be consulted before installation and execution of the software.

Second SH3 Domain of Ponsin Solved from Powder Diffraction

Determination of protein crystal structures is dependent on the growth of high-quality single crystals, a process that is not always successful. Optimum crystallization conditions must be systematically sought for, and microcrystalline powders are frequently obtained in failed attempts to grow the desired crystal. In materials science, structures of samples ranging from ceramics, pharmaceuticals, zeolites, etc., can nowadays be solved, almost routinely, from powdered samples, and there seems to be no fundamental reason, except the sheer size and complexity of the structures involved, why powder diffraction should not be employed to solve structures of small proteins. Indeed, recent work has shown that the high-quality powder diffraction data can be used in the study of protein crystal structures. We report the solution, model building, and refinement of a 67-residue protein domain crystal structure, with a cell volume of 64 879 A3, from powder diffraction. The second SH3 domain of ponsin, a protein of high biological significance due to its role in cellular processes, is determined and refined to resolution limits comparable to single-crystal techniques. Our results demonstrate the power and future applicability of the powder technique in structural biology.

That baby caught my eye... Attention capture by infant faces.

An alternative to the view that during evolution the human brain became specialized to preferentially attend to threat-related stimuli is to assume that all classes of stimuli that have high biological significance are prioritized by the attention system. Newborns are highly biologically relevant stimuli for members of a species, as their survival is important for reproductive success. The authors examined whether the Kindchenschema (baby schema) as described by Lorenz (1943) captures attention in the dot probe task. The results confirm attentional capture by photos of human infants presented to the left visual field, suggesting right hemisphere advantage. The magnitude of the attentional modulation was highly correlated with subjective arousal ratings of the photos. The findings show that biologically significant positive stimuli are prioritized by the attention system.

New Technology for Noninvasive Evaluation of Coronary Artery Disease

Cardiac computed tomography (CT) and positron emission tomography (PET) are emerging as powerful noninvasive imaging tools for the evaluation of atherosclerosis in patients with known or suspected coronary artery disease (CAD). Unlike invasive coronary angiography, CT coronary angiography (CTA) not only assesses disease within the coronary lumen but can also provide direct qualitative and quantitative information about nonobstructive atherosclerotic plaque burden within the vessel wall. Thus, it is possible that CTA-based patient evaluation may provide more clinically relevant information on which to base risk assessments compared with conventional “lumenography.” On the other hand, PET is rapidly growing as a powerful and efficient alternative to conventional single-photon emission CT (SPECT) imaging to evaluate regional myocardial perfusion and metabolism in patients with CAD. In addition, PET scanners are now being converted to hybrid PET/CT devices, which, in the setting of CAD, offer the potential for a comprehensive noninvasive cardiac evaluation of anatomy and function. This review will discuss current and potential future applications of cardiovascular CT, PET, and hybrid PET/CT, with a particular focus on ischemic heart disease. The information provided by noninvasive imaging generally falls into 1 of 3 categories: myocardial perfusion, left ventricular (LV) function, or coronary artery anatomy. The clinical utility, value, and role of a noninvasive modality are based on 2 test characteristics: What type of information is provided (eg, stress perfusion, stress and/or rest LV function, coronary anatomy), and what is the accuracy of the information provided. For example, SPECT and PET both provide stress and rest perfusion information, but the latter will be a superior clinical tool if the imaging data better represent the actual defect size and are subject to less artifact. The advantage of PET over SPECT will be further enhanced, as will be discussed later, if it provides additional clinically relevant information not …

A Novel Approach to Revealing Positive and Negative Co-Regulated Genes

As explored by biologists, there is a real and emerging need to identify co-regulated gene clusters, which include both positive and negative regulated gene clusters. However, the existing pattern-based and tendency-based clustering approaches are only designed for finding positive regulated gene clusters. In this paper, a new subspace clustering model called g-Cluster is proposed for gene expression data. The proposed model has the following advantages: 1) find both positive and negative co-regulated genes in a shot, 2) get away from the restriction of magnitude transformation relationship among co-regulated genes, and 3) guarantee quality of clusters and significance of regulations using a novel similarity measurement gCode and a user-specified regulation threshold δ, respectively. No previous work measures up to the task which has been set. Moreover, MDL technique is introduced to avoid insignificant g-Clusters generated. A tree structure, namely GS-tree, is also designed, and two algorithms combined with efficient pruning and optimization strategies to identify all qualified g-Clusters. Extensive experiments are conducted on real and synthetic datasets. The experimental results show that 1) the algorithm is able to find an amount of co-regulated gene clusters missed by previous models, which are potentially of high biological significance, and 2) the algorithms are effective and efficient, and outperform the existing approaches.

The effect of autumn treatment of potato tubers with protecting-stimulating preparations on storability and future harvest

The effect of protecting-stimulating preparations has been evaluated when laying for storage potato tubers of the varieties Udacha, Nevskii, and Belosnezhka. High biological and economic significance of autumn treatment of tubers with the preparation Colfugo-super and a mixture of Sprout-stop and Vist was demonstrated.

Brain Response to Visceral Aversive Conditioning: A Functional Magnetic Resonance Imaging Study

Brain-imaging studies to date have confounded visceral pain perception with anticipation. We used functional magnetic resonance imaging of the human brain to study the neuroanatomic network involved in aversive conditioning of visceral pain and, thus, anticipation. Eight healthy volunteers (5 male) participated in the study. We used a classic conditioning paradigm in which 3 neutral stimuli (differently colored circles) that acted as conditioned stimuli were paired with painful esophageal distention, air puff to the wrist, or nothing, which acted as unconditioned stimuli. Neural activity was measured during learning, anticipation (pairing only 50% of conditioned stimuli with their unconditioned stimuli), and extinction (unpaired conditioned stimuli) phases. For magnetic resonance imaging, axial slices depicting blood oxygen level-dependent contrast were acquired with a 1.5-T system. Neural responses during the learning phase included areas commonly associated with visceral pain (anterior cingulate cortex, insula, and primary and secondary somatosensory cortices) and innocuous somatosensory perception (primary and secondary somatosensory cortices and insula). During the anticipation and extinction phases of aversive stimulation, brain activity resembled that seen during actual painful esophageal stimulation. In contrast, anticipation and extinction of the innocuous somatic stimulus failed to show that effect. We have shown that actual and anticipated visceral pain elicit similar cortical responses. These results have implications for the design and interpretation of brain-imaging studies of visceral pain. They not only contribute to our understanding of the processing of visceral pain, but also have clinical implications for the management of chronic pain states.

The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery

Recurring RNA structural motifs are important sites of tertiary interaction and as such, are integral to RNA macromolecular structure. Although numerous RNA motifs have been classified and characterized, the identification of new motifs is of great interest. In this study, we discovered four new conformationally recurring motifs: the pi-turn, the Omega-turn, the alpha-loop and the C2'-endo mediated flipped adenosine motif. Not only do they have complex and interesting structures, but they participate in contacts of high biological significance. In a first for the RNA field, new motifs were discovered by a fully automated algorithm. This algorithm, COMPADRES, utilized a reduced representation of the RNA backbone and was highly successful at discerning unique structural relationships. This study also shows that recurring RNA substructures are not necessarily accompanied by consistent primary or secondary structure.

Profiling treatment-specific post-translational modifications in a complex proteome with subtractive substrate phage display.

Proteolytic activation of zymogens or controlled degradation of inhibitory factors is part of a major regulatory system on the post-translational level to regulate treatment induced cellular stress responses. The identification of differential activity based substrates is thus of high interest to prioritize and validate candidate targets for drug discovery. Here we present a novel subtractive substrate phage display screening method for the selection of treatment induced post-translational peptide modifications in complex proteomes. We investigated this approach with tumor cells in response to a protease activating anticancer treatment modality using subtractive and iterative screening of cellular extracts derived from control and treated cells. Specific phage were identified that served as substrates for proteolytic activities in response to treatment related activity changes and could be distinguished from substrates for unspecific proteolytic background activities. Novel, selected peptide substrates were investigated in vitro and in vivo and showed high substrate specificity and functional biological significance.

The UNESCO biosphere reserve concept as a tool for urban sustainability: the CUBES Cape Town case study.

The Cape Town Case Study (CTCS) was a multi-institutional collaborative project initiated by CUBES, a knowledge networking initiative of UNESCO's Ecological Sciences Division and the Earth Institute at Columbia University. Cape Town was selected as a CUBES site on the basis of its high biological and cultural significance, together with its demonstrated leadership in promoting urban sustainability. The CTCS was conducted by the Cape Town Urban Biosphere Group, a cross-disciplinary group of specialists drawn from national, provincial, municipal, and civil society institutions, mandated to examine the potential value of the UNESCO Biosphere Reserve concept as a tool for environmental management, social inclusion, and poverty alleviation in Cape Town. This article provides a contextualization of the CTCS and its collaborative process. It also reviews the biosphere reserve concept relative to urban sustainability objectives and proposes a more functional application of that concept in an urban context. A detailed analysis of key initiatives at the interface of conservation and poverty alleviation is provided in table format. Drawing on an examination of successful sustainability initiatives in Cape Town, specific recommendations are made for future application of the biosphere reserve concept in an urban context, as well as a model by which urban areas might affiliate with the UNESCO World Network of Biosphere Reserves, and criteria for such affiliation.

Antennal responses to floral scents in the butterfly Heliconius melpomene.

Floral scent, together with visual floral cues, are important signals to adult butterflies searching for food-rewarding plants. To identify which compounds in a floral scent are more attractive and, thus, of biological importance to foraging butterflies, we applied electrophysiological methods. Antennal responses of male and female adults of the tropical butterfly Heliconius melpomene L. (Lepidoptera: Nymphalidae: Heliconiinae) to individual compounds of natural floral scents and synthetic floral scent mixtures were investigated using gas chromatography-electroantennographic detection (GC-EAD). The natural floral scents included those of two tropical plant species, Lantana camara L. (Verbenaceae) and Warszewiczia coccinea (Vahl) Kl. (Rubiaceae), and two temperate species, Buddleja davidii Franchet (Loganiaceae) and Cirsium arvense (L.) Scop. (Asteraceae). The two synthetic floral scent mixtures contained many of the compounds found in the natural scents, but all in equal quantities. Compounds both present in relatively high abundance in the floral scents and detected exclusively in the floral parts of the plant, such as linalool, linalool oxide (furanoid) I and II, oxoisophoroneoxide, and phenylacetaldehyde, elicited the strongest antennal responses, suggesting that they may reflect adaptations by the plant to attract butterfly pollinators. However, other compounds also present in high abundance in the floral scent, but detected in the vegetative as well as floral plant parts, either elicited strong antennal responses, such as trans-beta-ocimene and benzaldehyde, or failed to elicit antennal responses, such as the sesquiterpenes beta-caryophyllene and alpha-humulene from L. camara. The most volatile monoterpene alkenes in the synthetic scent mixtures elicited only low or no responses. Furthermore, the overall antennal responses were stronger in females than in males. The findings suggest that several floral scent volatiles, especially those of exclusively floral origin, are of high biological significance to H. melpomene butterflies. These include compounds of different biosynthetic origins belonging to the benzenoids, monoterpenoids, and irregular terpenoids.

Valence-related vigilance biases in anxiety studied through event-related potentials

Introduction: Behavioral experiments on reaction time indicate that anxious subjects’ vigilance-related attention is biased towards threatening words, though direct data on cerebral activity associated to this bias are conspicuously scarce. Methods: In the present study, event-related potentials (ERPs) were recorded from 30 subjects, grouped according to their scores in trait and state anxiety questionnaires. The specific role of the arousal and valence content of the stimulation in the vigilance bias was investigated by blocking the arousal content. Stimulation with high biological significance was employed. An S1 (sound)–S2 (emotional picture) task ensured that subjects were vigilant towards positive, negative or control (neutral) images. Results: Only subjects presenting high state scores and high state–trait combination scores showed significantly higher amplitudes in the Early Contingent Negative Variation during vigilance towards negative stimuli. This ERP component typically appears between S1 and S2 and reflects the intensity of vigilance. Conclusions: ERP activity detects cerebral indices that confirm the presence of valence-related vigilance biases in anxiety.

An expanded view of bacterial DNA replication.

A protein-interaction network centered on the replication machinery of Bacillus subtilis was generated by genome-wide two-hybrid screens and systematic specificity assays. The network consists of 91 specific interactions linking 69 proteins. Over one fourth of the interactions take place between homologues of proteins known to interact in other organisms, indicating the high biological significance of the other interactions we report. These interactions provide insights on the relations of DNA replication with recombination and repair, membrane-bound protein complexes, and signaling pathways. They also lead to the biological role of unknown proteins, as illustrated for the highly conserved YabA, which is shown here to act in initiation control. Thus, our interaction map provides a valuable tool for the discovery of aspects of bacterial DNA replication.