Biosynthetic potentials of metabolites and their hierarchical organization

A major challenge in systems biology is to understand how complex and highly connected metabolic networks are organized. The structure of these networks is investigated here by identifying sets of metabolites that have a similar biosynthetic potential. We measure the biosynthetic potential of a particular compound by determining all metabolites than can be produced from it and, following a terminology introduced previously, call this set the scope of the compound. To identify groups of compounds with similar scopes, we apply a hierarchical clustering method. We find that compounds within the same cluster often display similar chemical structures and appear in the same metabolic pathway. For each cluster we define a consensus scope by determining a set of metabolites that is most similar to all scopes within the cluster. This allows for a generalization from scopes of single compounds to scopes of a chemical family. We observe that most of the resulting consensus scopes overlap or are fully contained in others, revealing a hierarchical ordering of metabolites according to their biosynthetic potential. Our investigations show that this hierarchy is not only determined by the chemical complexity of the metabolites, but also strongly by their biological function. As a general tendency, metabolites which are necessary for essential cellular processes exhibit a larger biosynthetic potential than those involved in secondary metabolism. A central result is that chemically very similar substances with different biological functions may differ significantly in their biosynthetic potentials. Our studies provide an important step towards understanding fundamental design principles of metabolic networks determined by the structural and functional complexity of metabolites.     

Discrete hierarchical organization of social group sizes

The 'social brain hypothesis' for the evolution of large brains in primates has led to evidence for the coevolution of neocortical size and social group sizes, suggesting that there is a cognitive constraint on group size that depends, in some way, on the volume of neural material available for processing and synthesizing information on social relationships. More recently, work on both human and non-human primates has suggested that social groups are often hierarchically structured. We combine data on human grouping patterns in a comprehensive and systematic study. Using fractal analysis, we identify, with high statistical confidence, a discrete hierarchy of group sizes with a preferred scaling ratio close to three: rather than a single or a continuous spectrum of group sizes, humans spontaneously form groups of preferred sizes organized in a geometrical series approximating 3-5, 9-15, 30-45, etc. Such discrete scale invariance could be related to that identified in signatures of herding behaviour in financial markets and might reflect a hierarchical processing of social nearness by human brains.     

A functional hierarchical organization of the protein sequence space

Background

It is a major challenge of computational biology to provide a comprehensive functional classification of all known proteins. Most existing methods seek recurrent patterns in known proteins based on manually-validated alignments of known protein families. Such methods can achieve high sensitivity, but are limited by the necessary manual labor. This makes our current view of the protein world incomplete and biased. This paper concerns ProtoNet, a automatic unsupervised global clustering system that generates a hierarchical tree of over 1,000,000 proteins, based solely on sequence similarity.

Results

In this paper we show that ProtoNet correctly captures functional and structural aspects of the protein world. Furthermore, a novel feature is an automatic procedure that reduces the tree to 12% its original size. This procedure utilizes only parameters intrinsic to the clustering process. Despite the substantial reduction in size, the system's predictive power concerning biological functions is hardly affected. We then carry out an automatic comparison with existing functional protein annotations. Consequently, 78% of the clusters in the compressed tree (5,300 clusters) get assigned a biological function with a high confidence. The clustering and compression processes are unsupervised, and robust.

Conclusions

We present an automatically generated unbiased method that provides a hierarchical classification of all currently known proteins.

     

Grooming in crickets: Timing and hierarchical organization

The variations in structural and timing principles underlying grooming are examined in the cricket Teleogryllus oceanicus. Two situations were studied: normal grooming and grooming that appears with locomotion in an unfamiliar environment. Normal grooming appears to be controlled by a hierarchy of random processes. Transitions between grooming acts are based on anatomical proximity, while hierarchical clusters are based on body regions. Acts per bout, acts per cluster, and clusters per bout are all random variables that follow geometric distributions; pauses between acts are also randomly distributed. In the unfamiliar environment, time-sharing appears to control the transition between locomotion and grooming. The study shows how a hierarchy can account for timing as well as structure in a behavioural sequence and how control principles change with variations in functional priority.     

Brain rhythms reveal a hierarchical network organization

Recordings of ongoing neural activity with EEG and MEG exhibit oscillations of specific frequencies over a non-oscillatory background. The oscillations appear in the power spectrum as a collection of frequency bands that are evenly spaced on a logarithmic scale, thereby preventing mutual entrainment and cross-talk. Over the last few years, experimental, computational and theoretical studies have made substantial progress on our understanding of the biophysical mechanisms underlying the generation of network oscillations and their interactions, with emphasis on the role of neuronal synchronization. In this paper we ask a very different question. Rather than investigating how brain rhythms emerge, or whether they are necessary for neural function, we focus on what they tell us about functional brain connectivity. We hypothesized that if we were able to construct abstract networks, or "virtual brains", whose dynamics were similar to EEG/MEG recordings, those networks would share structural features among themselves, and also with real brains. Applying mathematical techniques for inverse problems, we have reverse-engineered network architectures that generate characteristic dynamics of actual brains, including spindles and sharp waves, which appear in the power spectrum as frequency bands superimposed on a non-oscillatory background dominated by low frequencies. We show that all reconstructed networks display similar topological features (e.g. structural motifs) and dynamics. We have also reverse-engineered putative diseased brains (epileptic and schizophrenic), in which the oscillatory activity is altered in different ways, as reported in clinical studies. These reconstructed networks show consistent alterations of functional connectivity and dynamics. In particular, we show that the complexity of the network, quantified as proposed by Tononi, Sporns and Edelman, is a good indicator of brain fitness, since virtual brains modeling diseased states display lower complexity than virtual brains modeling normal neural function. We finally discuss the implications of our results for the neurobiology of health and disease.     

Distinct actin-dependent nanoscale assemblies underlie the dynamic and hierarchical organization of E-cadherin

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Selective priming of syntactic processing by event-related transcranial magnetic stimulation of Broca's area

It remains controversial whether Broca's aphasia is an articulatory deficit, a lexical-access problem, or agrammatism. In spite of recent neuroimaging studies, the causal link between cortical activity and linguistic subcomponents has not been elucidated. Here we report an experiment with event-related transcranial magnetic stimulation (TMS) to clarify the role of Broca's area, more specifically, the left inferior frontal gyrus (F3op/F3t), in syntactic processing. An experimental paradigm contrasted sentences requiring syntactic decisions with those requiring semantic decisions. We found selective priming effects on syntactic decisions when TMS was administered to the left F3op/F3t at a specific timing, but not to the left middle frontal gyrus (F2). Our results provide direct evidence of the involvement of the left F3op/F3t in syntactic processing.     

Assessment of asymmetry of the Broca's area through C.A.T. imagery

It is the purpose of this study to demonstrate the lateral asymmetry, if any, in the region of the Broca's speech area in a circumscribed group of humans. Linguists espouse an all-encompassing definition of «Language». For the purpose of this study, language is construed as articulated words in proper syntax in response to one's perception, i.e., human speech.     

A complex experimental assessment for objective description of hierarchical psychophysiological behavior as human regulatory phenotype

For the objective and valid identification of different human regulatory phenotypes it should be useful to analyze the behavior of different regulatory subsystems (Anochin 1976) in one multivariate design. Therefore in a DARA supported project a fully computerized and reliable laboratory assessment was developed and tested. We used a set of electrophysiological parameters that should indicate the activity of different functional regulation systems on different "behavioral levels". Skin conductance, skin temperature and voice pitch were used as indicators of sympathico-parasympathical activity. Breathing, heart rate variability and bloodpressure should indicate cardiovascular activity and electromyogram and mimic variablity were thought as indicators of locomotional external behavioral activity. To identify physiological reactions which are influenced by emotional stress we used voice stress measures. Even in the field of aviation and space medicine there exist data about the correlation of voice pitch with emotional excitation (Hecker et. al. 1968, Williams et.al. 1969, Friedrich, Vaic 1978, Vaic et.al. 1981,1982, Griffin, Williams 1987). In our former study (MOSAIC-study, Johannes 1990) the voice pitch and its variation range correlated with perceived emotional excitation but were independent of real bloodpressure variations. Two different types of pitch reaction to this experimental design were correlated to psychological personality scales and assigned subjects to "sensitizers" and "suppressors".     

Statistics of weighted brain networks reveal hierarchical organization and Gaussian degree distribution

Whole brain weighted connectivity networks were extracted from high resolution diffusion MRI data of 14 healthy volunteers. A statistically robust technique was proposed for the removal of questionable connections. Unlike most previous studies our methods are completely adapted for networks with arbitrary weights. Conventional statistics of these weighted networks were computed and found to be comparable to existing reports. After a robust fitting procedure using multiple parametric distributions it was found that the weighted node degree of our networks is best described by the normal distribution, in contrast to previous reports which have proposed heavy tailed distributions. We show that post-processing of the connectivity weights, such as thresholding, can influence the weighted degree asymptotics. The clustering coefficients were found to be distributed either as gamma or power-law distribution, depending on the formula used. We proposed a new hierarchical graph clustering approach, which revealed that the brain network is divided into a regular base-2 hierarchical tree. Connections within and across this hierarchy were found to be uncommonly ordered. The combined weight of our results supports a hierarchically ordered view of the brain, whose connections have heavy tails, but whose weighted node degrees are comparable.     

Mapping the organization of axis of motion selective features in human area MT using high-field fMRI

Functional magnetic resonance imaging (fMRI) at high magnetic fields has made it possible to investigate the columnar organization of the human brain in vivo with high degrees of accuracy and sensitivity. Until now, these results have been limited to the organization principles of early visual cortex (V1). While the middle temporal area (MT) has been the first identified extra-striate visual area shown to exhibit a columnar organization in monkeys, evidence of MT's columnar response properties and topographic layout in humans has remained elusive. Research using various approaches suggests similar response properties as in monkeys but failed to provide direct evidence for direction or axis of motion selectivity in human area MT. By combining state of the art pulse sequence design, high spatial resolution in all three dimensions (0.8 mm isotropic), optimized coil design, ultrahigh field magnets (7 Tesla) and novel high resolution cortical grid sampling analysis tools, we provide the first direct evidence for large-scale axis of motion selective feature organization in human area MT closely matching predictions from topographic columnar-level simulations.     

白蚁的社会组织和社会行为

白蚁属于等翅目昆虫,共有7科2 750种,这是昆虫纲中唯一的一个目,其所有的种类都靠消化道内共生的鞭毛类、原生动物利用和消化纤维素。介绍了白蚁社会组织和社会存为的特点,比较了白蚁与蚂蚁的异同,并指出两者相似是由于趋同进化,而两者不同是由于亲缘关系相距甚远,各来自不同祖先。     

Contribution of the frontal lobe secondary motor area to organization of postural components in human voluntary movement

A total of 225 patients with local verified brain lesions were investigated with a view to identifying the brain regions contributing to organizing postural aspects of voluntary movement. Impaired postural adjustment movements associated with voluntary deep breathing were found in patients with damage primarily to the posterior section of the frontal lobe inferior convolution. Impaired activation of leg and trunk muscles accompanying arm movements were revealed in patients with damage chiefly to the posterior section of the superior convolution of the lobe, including the accessory motor area. It was deduced that postural movements differing in their functional purpose are controlled, like other learned tasks, by different sections of the secondary motor zone of the frontal lobe of the brain.Institute for Information Transmission Studies, Academy of Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 20, No. 1, pp. 7–15, January–February, 1988.     

Angiotensin II in the organization of rat feeding behavior

Intraventricular injection of angiotensin-II (100 ng) increased the latency period and decreased the amount of food intake in the hungry rats. Preliminary administration of saralasin (100 ng) blocked the inhibitory effect of angiotensin-II on food consumption. In contrast to the above mentioned intraperitoneal injection of angiotensin-II (10 ng/kg) 10 min before food and water admission results in the tendency to increase the food intake. And the same application of angiotensin-II 60 min before food and water admission increased by 49% of food intake in hungry rats. Saralasin (50 ng/kg) given prior to the angiotensin-II administration blocked the angiotensin-II effects. Moreover a significant decrease in the food intake was found after intraperitoneal injection of saralasin only. No significant changes in the drinking behavior in response to the intraventricular and intraperitoneal drugs administration were registered.     

HiNO: an approach for inferring hierarchical organization from regulatory networks

Background

Gene expression as governed by the interplay of the components of regulatory networks is indeed one of the most complex fundamental processes in biological systems. Although several methods have been published to unravel the hierarchical structure of regulatory networks, weaknesses such as the incorrect or inconsistent assignment of elements to their hierarchical levels, the incapability to cope with cyclic dependencies within the networks or the need for a manual curation to retrieve non-overlapping levels remain unsolved.

Methodology/Results

We developed HiNO as a significant improvement of the so-called breadth-first-search (BFS) method. While BFS is capable of determining the overall hierarchical structures from gene regulatory networks, it especially has problems solving feed-forward type of loops leading to conflicts within the level assignments. We resolved these problems by adding a recursive correction approach consisting of two steps. First each vertex is placed on the lowest level that this vertex and its regulating vertices are assigned to (downgrade procedure). Second, vertices are assigned to the next higher level (upgrade procedure) if they have successors with the same level assignment and have themselves no regulators. We evaluated HiNO by comparing it with the BFS method by applying them to the regulatory networks from Saccharomyces cerevisiae and Escherichia coli, respectively. The comparison shows clearly how conflicts in level assignment are resolved in HiNO in order to produce correct hierarchical structures even on the local levels in an automated fashion.

Conclusions

We showed that the resolution of conflicting assignments clearly improves the BFS-method. While we restricted our analysis to gene regulatory networks, our approach is suitable to deal with any directed hierarchical networks structure such as the interaction of microRNAs or the action of non-coding RNAs in general. Furthermore we provide a user-friendly web-interface for HiNO that enables the extraction of the hierarchical structure of any directed regulatory network.

Availability

HiNO is freely accessible at http://mips.helmholtz-muenchen.de/hino/.