Dendrites: bug or feature?

The integrative properties of dendrites are determined by a complex mixture of factors, including their morphology, the spatio-temporal patterning of synaptic inputs, the balance of excitation and inhibition, and neuromodulatory influences, all of which interact with the many voltage-gated conductances present in the dendritic membrane. Recent efforts to grapple with this complexity have focused on identifying functional compartments in the dendritic tree, the number and size of which depend on the aspect of dendritic function being considered. We discuss how dendritic compartments and the interactions between them help to enhance the computational power of the neuron and define the rules for the induction of synaptic plasticity.     

Does neuronal synchrony underlie visual feature grouping?

Previous research suggests that synchronous neural activity underlies perceptual grouping of visual image features. The generality of this mechanism is unclear, however, as previous studies have focused on pairs of neurons with overlapping or collinear receptive fields. By sampling more broadly and employing stimuli that contain partially occluded objects, we have conducted a more incisive test of the binding by synchrony hypothesis in area MT. We find that synchrony in spiking activity shows little dependence on feature grouping, whereas gamma band synchrony in field potentials can be significantly stronger when features are grouped. However, these changes in gamma band synchrony are small relative to the variability of synchrony across recording sites and do not provide a robust population signal for feature grouping. Moreover, these effects are reduced when stimulus differences nearby the receptive fields are eliminated using partial occlusion. Our findings suggest that synchrony does not constitute a general mechanism of visual feature binding.     

Acoustic feature extraction by cross-correlation in crickets?

Common concepts of acoustic feature extraction within the auditory pathway of vertebrates and insects assume temporal filters tuned to particular periodicities. Crickets respond selectively to the conspecific song pattern and reveal a bandpass characteristic, which is thought to arise from a matched filter for a restricted range of periods. Unexpectedly, females of the two sibling species Teleogryllus oceanicus and T. commodus differed in fundamental filter properties. While T. oceanicus revealed a period filter, T. commodus exhibited a pulse duration filter. This finding raises the question of how so distinct properties of homologous neuronal circuits for pattern analysis have evolved during speciation. Evidence is presented that signal analysis by cross-correlation offers a simple explanation for differences in pattern selectivity as well as for the evolutionary transition. By cross-correlation the similarity of an external pattern with an internal template is determined over a certain time window. A comparison of behavioural data and cross-correlation values suggested that both species have similar templates. However, time windows were significantly different between species (T. oceanicus: 180–400 ms, T. commodus: 90–160 ms). Consequently, solely a change in the evaluation time window is required to account for the observed differences in feature extraction that serve to maintain species isolation.Dedicated to Franz Huber, who enriched neuroethology both by his pioneering studies as well as his infectious enthusiasm     

Glycoprotein import: A common feature of complex plastids?

Complex plastids evolved by secondary endosymbiosis and are, in contrast to primary plastids, surrounded by 3 or 4 envelope membranes. Recently, we provided evidence that in diatoms proteins exist that get N-glycosylated during transport across the outermost membrane of the complex plastid. This gives rise to unique questions on the transport mechanisms of these bulky proteins, which get transported across up to 3 further membranes into the plastid stroma. Here we discuss our results in an evolutionary context and speculate about the existence of plastidal glycoproteins in other organisms with complex plastids.     

Immunological tolerance: The key feature in human filariasis?

Filariasis is a widespread tropical disease caused by a group of nematode parasites that can survive for many years in immunocompetent hosts. The paradox of filariasis has always been the inverse association between parasite density, in terms of circulating microfilariae in the blood, and severe pathology. In this review, Rick Maizels and Rachel Lawrence argue that microfilariae and adult parasites induce a form of immunological tolerance which prevents both parasite elimination and progression to disease. The breakdown of this unresponsiveness is seen as the critical step towards pathogenesis. However, not every exposed individual progresses through infection to disease. The authors discuss evidence for protective immunity acting on antigens from the mosquito-borne infective larva, and propose that this stage represents a vulnerable target outside the scope of tolerance and pathogenesis. Stage-specific larval antigens, to which asymptomatic hosts are known to respond, may therefore represent the most effective and safe choice for an anti filarial vaccine.     

Two-step cross-entropy feature selection for microarrays—power through complementarity

Current feature selection methods for supervised classification of tissue samples from microarray data generally fail to exploit complementary discriminatory power that can be found in sets of features. Using a feature selection method with the computational architecture of the cross-entropy method, including an additional preliminary step ensuring a lower bound on the number of times any feature is considered, we show when testing on a human lymph node data set that there are a significant number of genes that perform well when their complementary power is assessed, but “pass under the radar” of popular feature selection methods that only assess genes individually on a given classification tool. We also show that this phenomenon becomes more apparent as diagnostic specificity of the tissue samples analysed increases.     

Automated feature engineering improves prediction of protein–protein interactions

Amino Acids - Over the last decade, various machine learning (ML) and statistical approaches for protein–protein interaction (PPI) predictions have been developed to help annotating...     

Why is entry exclusion an essential feature of conjugative plasmids?

Entry exclusion is a property of plasmids by which the cells that contain them become bad recipients in additional conjugation rounds. This work reviews entry exclusion essential features and analyzes the mechanisms of action of the best studied systems. We searched for homologs of the proteins responsible for experimentally known exclusion systems. Results were used to classify exclusion systems in families of related elements. We arrive to the conclusion that all conjugative plasmids contain at least one entry exclusion gene. Although entry exclusion genes seem to be part of the plasmid conjugative machinery, they are systematically absent in phylogenetically related type IV protein exporting machines involved in virulence for plants and animals. We infer from this fact that entry exclusion is an essential feature of conjugative plasmid biology. Mathematical models suggest that plasmids expressing entry exclusion selectively eliminate plasmids lacking it, reinforcing its essential character and suggesting that entry exclusion plays a direct role in plasmid survival. Other experimental results confirm that entry exclusion is essential for the stability of a conjugative plasmid. We suggest that entry exclusion limits the damage of lethal zygosis (bacterial death produced by excessive rounds of conjugation). Additionally, it avoids competition in a host among identical plasmid backbones. Conversely, the lack of entry exclusion in conjugative transposons can be understood as a means of generating rapid evolutionary change.     

Steryl glycosides: a characteristic feature of the Helicobacter spp.?

The lipids of different species of Helicobacter (H.felis, H. muridarum, H. mustelae, H. fennelliae, and H. cinaedi) were studied. Different types of cholesteryl glucosides were found in all of the species studied except H. cinaedi. The total amount of cholesteryl glucosides varied from 14.8% of total lipids in H. mustelae to 33.1% of total lipids in H. felis. The different types of cholesteryl glucosides and their species distribution are cholesteryl-6-O-acyl-alpha-D-glucopyranoside (cholesteryl-6-O-tetradecanoyl-alpha-D-glucopyranoside in H. felis and cholesteryl-6-O-dodecanoyl-alpha-D-glucopyranoside in H. muridarum), cholesteryl-alpha-D-glucopyranoside (H. felis, H. muridarum, H. mustelae, and H. fennelliae), and cholesteryl-6-O-phosphatidyl-alpha-D-glucopyranoside (H. fennelliae). The neutral lipid fractions showed a high percentage of cholesterol, with selective accumulation of free cholesterol. The study thus shows that the characteristic presence of steryl glycosides in Helicobacter spp. may be an important chemotaxonomic marker for many of the species, and the helicobacters show a selective accumulation of free cholesterol from the media.     

Volatilisation of metals and metalloids: An inherent feature of methanoarchaea?

As shown by recent studies, anaerobic members of Archaea and Bacteria are involved in processes that transform ionic species of metals and metalloids (arsenic, antimony, bismuth, selenium, tellurium and mercury) into volatile and mostly toxic derivatives (mainly methyl derivatives or hydrides). Since the fact that these transformations proceed in both environmental settings and in parts of the human body, we have to consider that these processes also interfere directly with human health. The diversity of the volatile derivatives produced and their emission rates were significantly higher in methanoarchaeal than in bacterial strains, which supports the pivotal role of methanoarchaea in transforming metals and metalloids (metal(loid)s) into their volatile derivatives. Compared with methanoarchaea, 14 anaerobic bacterial strains showed a significantly restricted spectrum of volatilised derivatives and mostly lower production rates of volatile bismuth and selenium derivatives. Since methanoarchaea isolated from the human gut (Methanosphaera stadtmanae, Methanobrevibacter smithii) showed a higher potential for metal(loid) derivatisation compared to bacterial gut isolates, we assume that methanoarchaea in the human gut are mainly responsible for the production of these volatile derivatives. The observation that trimethylbismuth ((CH(3))(3)Bi), the main volatile derivative of bismuth produced in human feces, inhibited growing cultures of Bacteroides thetaiotaomicron, a representative member of the human physiological gut flora, suggests that these volatiles exert their toxic effects on human health not only by direct interaction with host cells but also by disturbing the physiological gut microflora.     

Primary auditory cortex of cats: feature detection or something else?

Neurons in sensory cortices are often assumed to be feature detectors, computing simple and then successively more complex features out of the incoming sensory stream. These features are somehow integrated into percepts. Despite many years of research, a convincing candidate for such a feature in primary auditory cortex has not been found. We argue that feature detection is actually a secondary issue in understanding the role of primary auditory cortex. Instead, the major contribution of primary auditory cortex to auditory perception is in processing previously derived features on a number of different timescales. We hypothesize that, as a result, neurons in primary auditory cortex represent sounds in terms of auditory objects rather than in terms of feature maps. According to this hypothesis, primary auditory cortex has a pivotal role in the auditory system in that it generates the representation of auditory objects to which higher auditory centers assign properties such as spatial location, source identity, and meaning.Abbreviations A1 primary auditory cortex - MGB medical geniculate body - IC inferior coliculus - STRF spectrotemporal receptive field     

One common structural feature of “words” in protein sequences and human texts

Frequently discussed analogy between genetic and human texts is explored by comparison of alternation of polar and non-polar amino-acid residues in proteins and alternation of consonants and vowels in human texts. In human languages, the usage of possible combinations of consonants and vowels is influenced by pronounceability of the combinations. Similarly, oligopeptide composition of proteins is influenced by requirements of protein folding and stability. One special type of structure often present in proteins is amphipathic α-helices in which polar and non-polar amino acids alternate with the period 3.5 residues, not unlike alternation of consonants and vowels. In this study, we evaluated the contribution made by amphipathic alternations to the protein sequence texts (20–24%). Their proportion is lower than respective values for alternating words in human texts (57–89%). The proteomes (full sets of proteins for selected organisms) were transformed into ranked sequences of n-grams (words of length n), including periodical amphipathic structures. Similarly, human texts were transformed into sequences of alternating consonants and vowels. Analysis of the vocabularies shows that in both types of texts (human languages and proteins) the alternating words are dominant or highly preferred, thus, strengthening the analogy between these two types of texts. The contribution of amphipathic words in the upper parts of the ranked lists for 10 analyzed proteomes varies between 58 and 74%. In human texts respective values range between 90 and 100%.     

Prediction of protein–protein interactions based on PseAA composition and hybrid feature selection

Based on pseudo amino acid (PseAA) composition and a novel hybrid feature selection frame, this paper presents a computational system to predict the PPIs (protein–protein interactions) using 8796 protein pairs. These pairs are coded by PseAA composition, resulting in 114 features. A hybrid feature selection system, mRMR–KNNs–wrapper, is applied to obtain an optimized feature set by excluding poor-performed and/or redundant features, resulting in 103 remaining features. Using the optimized 103-feature subset, a prediction model is trained and tested in the k-nearest neighbors (KNNs) learning system. This prediction model achieves an overall accurate prediction rate of 76.18%, evaluated by 10-fold cross-validation test, which is 1.46% higher than using the initial 114 features and is 6.51% higher than the 20 features, coded by amino acid compositions. The PPIs predictor, developed for this research, is available for public use at http://chemdata.shu.edu.cn/ppi.     

Response variability in the mammalian auditory cortex: an objection to feature detection?

Research strategy in the auditory system has tended to parallel that in the visual system, where neurons have been shown to respond selectively to specific stimulus parameters. Auditory neurons have been shown to be sensitive to changes in acoustic parameters, but only rarely have neurons been reported that respond exclusively to only one biologically significant sound. Even at higher levels of the auditory system very few cells have been found that could be described as "vocalization detectors." In addition, variability in responses to artificial sounds have been reported for auditory cortical neurons similar to the response variability that has been reported in the visual system. Recent evidence indicates that the responses of auditory cortical neurons to species-specific vocalizations can also be labile, varying in both strength and selectivity. This is especially true of the secondary auditory cortex. This variability, coupled with the lack of extreme specificity in the secondary auditory cortex, suggests that secondary cortical neurons are not well suited for the role of "vocalization detectors."     

Stress and fitness in parthenogens: is dormancy a key feature for bdelloid rotifers?

Background

Bdelloid rotifers are the most common and abundant group of animals that reproduce by ameiotic parthenogenesis, only. They are common in temporally ephemeral habitats, and it is unclear if they dwell in unstable habitats because are excluded from better conditions by stronger competitors, or because they need unstable conditions for their success. We tested the hypothesis that bdelloids 'require' stressful conditions for their persistence by comparing fitness-related traits of stressed (desiccated, D) and unstressed (hydrated, H) lines of two species, Adineta ricciae and Macrotrachela quadricornifera.

Results

For both bdelloid species, fecundity was significantly lower in H than in parallel D line. Fitness components decreased with time progressively in the H line but not in the D line. Recovery rates of D lines were recorded after every desiccation and did not reveal any trend in time, suggesting that no selection was operating.

Conclusion

Stress in the form of reiterated desiccations seemed to help both bdelloid species to keep fitness stable; in contrast under stable conditions, like permanent hydration, these bdelloid species had poorer performances. Bdelloids, although aquatic animals, are not only efficient in tolerating desiccation, but seem somehow dependent on anhydrobiosis, a circumstance that might represent a key event in their life cycle. If this is true, life in unpredictable habitats should not be seen as the result of competitive exclusion from 'easier' habitats, but a requirement for long-term survival of these parthenogenetic animals.

     

Terminal disorder: a common structural feature of the axial proteins of bacterial flagellum?

We report, based on proteolytic experiments and high resolution 1H nuclear magnetic resonance studies that the terminal regions of the monomeric hook protein are highly mobile and exposed to the solvent. The disordered parts of the hook protein span approximately the first 70 and the last 30 amino acid residues. Although the amino acid sequences of flagellin and hook protein do not resemble each other at all, both proteins have now been shown to contain large disordered terminal regions. Sequential similarities of flagellin and hook protein, especially near the NH2 and COOH termini, to other axial components of bacterial flagellum suggest that terminal disorder may be a common structural feature of the axial proteins of the bacterial flagellum.     

Using feature optimization-based support vector machine method to recognize the β-hairpin motifs in enzymes

β-Hairpins in enzyme, a kind of special protein with catalytic functions, contain many binding sites which are essential for the functions of enzyme. With the increasing number of observed enzyme protein sequences, it is of especial importance to use bioinformatics techniques to quickly and accurately identify the β-hairpin in enzyme protein for further advanced annotation of structure and function of enzyme. In this work, the proposed method was trained and tested on a non-redundant enzyme β-hairpin database containing 2818 β-hairpins and 1098 non-β-hairpins. With 5-fold cross-validation on the training dataset, the overall accuracy of 90.08% and Matthew’s correlation coefficient (Mcc) of 0.74 were obtained, while on the independent test dataset, the overall accuracy of 88.93% and Mcc of 0.76 were achieved. Furthermore, the method was validated on 845 β-hairpins with ligand binding sites. With 5-fold cross-validation on the training dataset and independent test on the test dataset, the overall accuracies were 85.82% (Mcc of 0.71) and 84.78% (Mcc of 0.70), respectively. With an integration of mRMR feature selection and SVM algorithm, a reasonable high accuracy was achieved, indicating the method to be an effective tool for the further studies of β-hairpins in enzymes structure. Additionally, as a novelty for function prediction of enzymes, β-hairpins with ligand binding sites were predicted. Based on this work, a web server was constructed to predict β-hairpin motifs in enzymes (http://202.207.29.251:8080/).