基于内在功能连接推定抑郁症脑网络效率的改变

本文研究了在保留最大化内在功能连接条件下抑郁症患者脑网络效率的改变,并探索了改变的拓扑效率和抑郁症病理学之间的关系.为此,我们收集了20例抑郁症患者和20例在年龄、性别和教育水平相匹配的健康被试的静息态功能磁共振图像数据.图论分析显示,与健康对照组比较,抑郁症患者的节点效率减少在左海马旁回、右杏仁核,左颞横回和左颞极(颞中回)减少.减少的节点效率表明,在抑郁症患者脑网络中这些区域传送信息到其他区域的能力减弱.此外,发现局部效率降低在左内侧额上回、左眶部额上回、右回直肌、左杏仁核、右顶上回、左丘脑和左颞极(颞中回).并且发现左内侧额上回、左杏仁核、左丘脑与PHQ-9得分呈负相关.降低的局部效率表明抑郁症患者脑网络中这些区域的局部网络信息传送能力受到抑制.这些结果进一步确认在抑郁症患者中涉及情感信息处理的前额-丘脑-边缘区域被破坏.我们的发现为抑郁症病人的辅助诊断提供了新的潜在生物学标记物.     

Waveform characterization of the soybean stem feeder Edessa meditabunda: overcoming the challenge of wiring pentatomids for EPG

Stink bugs (Hemiptera: Heteroptera: Pentatomidae) are in general robust and restless insects, which makes them difficult to wire for electropenetrograph (EPG) studies. In addition, cuticular lipids may reduce wire effectiveness, and their removal could improve success of wiring. We compared wiring effectiveness for three species of stink bugs, differing in walking behaviour and degree of cuticular waxiness, that is, Piezodorus guildinii (Westwood), Nezara viridula (L.), and Loxa deducta (Walker). Results indicated that removal of cuticular lipids by mechanical abrasion (via sanding) greatly improved attachment success with gold wire. Our hypothesis that heavier and bigger bugs would lose the wire attachment more quickly than lighter and smaller bugs was not confirmed, regardless of the sanding. In contrast, our hypothesis that greater movement of a bug would cause the wire to break more often was supported by extensive testing. Behaviour appears to be more relevant for successful wiring than body weight. We used the sanding and wiring technique to characterize and correlate direct current EPG waveforms for the large and restless stem‐feeding stink bug Edessa meditabunda (Fabricius) on soybean plants. This marks the first published example of pentatomid EPG waveforms. Edessa meditabunda recordings on soybean stems generated eight types of waveforms in three phases and two families, named as follows: non‐probing = Np and Z; pathway phase = Em1; X wave phase = X; ingestion phase, family I = Em2 and Em3; ingestion phase, family N = Em4 and Em5. These eight were described based on their frequencies, relative amplitudes, and level voltages. Histological studies of stylets within salivary sheaths correlated the Em1, Em2, and Em3 waveforms with specific penetration sites. The waveform with the longest duration when feeding was Em2, representing xylem sap ingestion; in addition, waveform Em3 (always preceded by an X wave) was correlated with phloem sap ingestion.     

Regime shifts in marine communities: a complex systems perspective on food web dynamics

Species composition and habitats are changing at unprecedented rates in the world''s oceans, potentially causing entire food webs to shift to structurally and functionally different regimes. Despite the severity of these regime shifts, elucidating the precise nature of their underlying processes has remained difficult. We address this challenge with a new analytic approach to detect and assess the relative strength of different driving processes in food webs. Our study draws on complexity theory, and integrates the network-centric exponential random graph modelling (ERGM) framework developed within the social sciences with community ecology. In contrast to previous research, this approach makes clear assumptions of direction of causality and accommodates a dynamic perspective on the emergence of food webs. We apply our approach to analysing food webs of the Baltic Sea before and after a previously reported regime shift. Our results show that the dominant food web processes have remained largely the same, although we detect changes in their magnitudes. The results indicate that the reported regime shift may not be a system-wide shift, but instead involve a limited number of species. Our study emphasizes the importance of community-wide analysis on marine regime shifts and introduces a novel approach to examine food webs.     

Estimation of a covariance matrix with zeros

We consider estimation of the covariance matrix of a multivariaterandom vector under the constraint that certain covariancesare zero. We first present an algorithm, which we call iterativeconditional fitting, for computing the maximum likelihood estimateof the constrained covariance matrix, under the assumption ofmultivariate normality. In contrast to previous approaches,this algorithm has guaranteed convergence properties. Droppingthe assumption of multivariate normality, we show how to estimatethe covariance matrix in an empirical likelihood approach. Theseapproaches are then compared via simulation and on an exampleof gene expression.     

Artificial diet delivery system for Philaenus spumarius,the European vector of Xylella fastidiosa

Artificial diets represent an essential tool for investigations on the intimate relationship between plant pathogens and their vectors. Previous research failed in devising an artificial diet delivery system for the meadow spittlebug Philaenus spumarius, to date considered the most important vector of the bacterium Xylella fastidiosa in Europe. Here, we describe a new delivery “tube system” by which we succeeded in artificial feeding of P. spumarius with holidic diets (one sucrose diet and two amino acids diets). Spittlebug probing and feeding behaviour on either the tube system or a traditional “flat system” realized out of a small Petri dish filled with diet and covered with stretched Parafilm^® were observed in real time by video‐EPG (Electrical Penetration Graph), in order to assess the occurrence of ingestion and excretion. Moreover, we evaluated P. spumarius survival on either the tube system filled with the two holidic diets that gave the best EPG results or an empty tube system serving as control. Contrary to the flat system, where just brief stylet insertions through the Parafilm^® were recorded, the spittlebug ingested the artificial diets when delivered with the tube system. Survival on the diets provided with the tube system was significantly greater than the control, with no differences between the diets tested. Furthermore, the tube system was suitable also for another spittlebug species shown to be a competent vector of X. fastidiosa, that is Neophilaenus campestris. The tool we devised opens new perspectives for investigations on X. fastidiosa/spittlebugs interactions, as well as for the functional analysis of mutant X. fastidiosa strains in respect to insect colonization and transmission.     

Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids

Many large protein-nucleic acid complexes exhibit allosteric regulation. In these systems, the propagation of the allosteric signaling is strongly coupled to conformational dynamics and catalytic function, challenging state-of-the-art analytical methods. Here, we review established and innovative approaches used to elucidate allosteric mechanisms in these complexes. Specifically, we report network models derived from graph theory and centrality analyses in combination with molecular dynamics (MD) simulations, introducing novel schemes that implement the synergistic use of graph theory with enhanced simulations methods and ab-initio MD. Accelerated MD simulations are used to construct “enhanced network models”, describing the allosteric response over long timescales and capturing the relation between allostery and conformational changes. “Ab-initio network models” combine graph theory with ab-initio MD and quantum mechanics/molecular mechanics (QM/MM) simulations to describe the allosteric regulation of catalysis by following the step-by-step dynamics of biochemical reactions. This approach characterizes how the allosteric regulation changes from reactants to products and how it affects the transition state, revealing a tense-to-relaxed allosteric regulation along the chemical step. Allosteric models and applications are showcased for three paradigmatic examples of allostery in protein-nucleic acid complexes: (i) the nucleosome core particle, (ii) the CRISPR-Cas9 genome editing system and (iii) the spliceosome. These methods and applications create innovative protocols to determine allosteric mechanisms in protein-nucleic acid complexes that show tremendous promise for medicine and bioengineering.     

EDENetworks: A user‐friendly software to build and analyse networks in biogeography,ecology and population genetics

The recent application of graph‐based network theory analysis to biogeography, community ecology and population genetics has created a need for user‐friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy‐to‐use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray‐Curtis or Sorensen distance, or population genetic metrics such as F_ST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.     

Diurnal feeding as a potential mechanism of osmoregulation in aphids

Diurnal variation in phloem sap composition has a strong infuence on aphid performance.The sugar-rich phloem sap serves as the sole diet for aphids and a suite of physiological mechanisms and behaviors allowv them to tolerate the high osmotic stress.Here,we tested the hypothesis that night-time feeding by aphids is a behavior that takes advantage of the low sugar diet in the night to compensate for osmotic stress incurred while feeding on high sugar diet during the day.Using the electrical penetration graph(EPG)technique.we examined the eiects of diurmal rhythm on feeding behaviors of bird cherry-oat aphid(Rhopalosiphurm padi L.)on wheat.A strong diurmal rhythm in aphids as indicated by the presence of a cyclical pattern of expression in a core clock gene did not impact aphid feeding and similar feeding behaviors were observed during day and night.The major difference observed between day and night feeding was that aphids spent significantly longer time in phloem salivation during the night compared to the day.In contrast,aphid hydration was reduced at the end of the day-time feeding compared to end of the night-time fepding.Gene expression analysis of R.padi osmoregulatory genes indicated that sugar break down and water transport into the aphid gut was reduced at night.These data suggest that while diumal variation occurs in phloem sap composition,aphids use night time feeding to overcome the high osmotic stress incurred while feeding on sugar-rich phloem sap during the day.     

Methods for analyzing neuronal structure and activity in Caenorhabditis elegans

The model research animal Caenorhabditis elegans has unique properties making it particularly advantageous for studies of the nervous system. The nervous system is composed of a stereotyped complement of neurons connected in a consistent manner. Here, we describe methods for studying nervous system structure and function. The transparency of the animal makes it possible to visualize and identify neurons in living animals with fluorescent probes. These methods have been recently enhanced for the efficient use of neuron-specific reporter genes. Because of its simple structure, for a number of years, C. elegans has been at the forefront of connectomic studies defining synaptic connectivity by electron microscopy. This field is burgeoning with new, more powerful techniques, and recommended up-to-date methods are here described that encourage the possibility of new work in C. elegans. Fluorescent probes for single synapses and synaptic connections have allowed verification of the EM reconstructions and for experimental approaches to synapse formation. Advances in microscopy and in fluorescent reporters sensitive to Ca²⁺ levels have opened the way to observing activity within single neurons across the entire nervous system.