Traveling EEG slow oscillation along the dorsal attention network initiates spontaneous perceptual switching

An ambiguous figure such as the Necker cube causes spontaneous perceptual switching (SPS). The mechanism of SPS in multistable perception has not yet been determined. Although early psychological studies suggested that SPS may be caused by fatigue or satiation of orientation, the neural mechanism of SPS is still unknown. Functional magnetic resonance imaging (fMRI) has shown that the dorsal attention network (DAN), which mainly controls voluntary attention, is involved in bistable perception of the Necker cube. To determine whether neural dynamics along the DAN cause SPS, we performed simultaneous electroencephalography (EEG) and fMRI during an SPS task with the Necker cube, with every SPS reported by pressing a button. This EEG–fMRI integrated analysis showed that (a) 3–4 Hz spectral EEG power modulation at fronto-central, parietal, and centro-parietal electrode sites sequentially appeared from 750 to 350 ms prior to the button press; and (b) activations correlating with the EEG modulation traveled along the DAN from the frontal to the parietal regions. These findings suggest that slow oscillation initiates SPS through global dynamics along the attentional system such as the DAN.     

Detecting nonculturable bacteria in the active mycorrhizal zone of the pine mushroom <Emphasis Type="Italic">Tricholoma matsutake</Emphasis>

The fungus Tricholoma matsutake forms an ectomycorrhizal relationship with pine trees. Its sporocarps often develop in a circle, which is commonly known as a fairy ring. The fungus produces a solid, compact, white aggregate of mycelia and mycorrhizae beneath the fairy ring, which in Japanese is called a ’shiro’. In the present study, we used soil dilution plating and molecular techniques to analyze the bacterial communities within, beneath, and outside the T. matsutake fairy ring. Soil dilution plating confirmed previous reports that bacteria and actinomycetes are seldom present in the soil of the active mycorrhizal zone of the T. matsutake shiro. In addition, the results showed that the absence of bacteria was strongly correlated with the presence of T. matsutake mycorrhizae. The results demonstrate that bacteria, especially aerobic and heterotrophic forms, and actinomycetes, are strongly inhibited by T. matsutake. Indeed, neither bacteria nor actinomycetes were detected in 11.3% of 213 soil samples from the entire shiro area by culture-dependent methods. However, molecular techniques demonstrated that some bacteria, such as individual genera of Sphingomonas and Acidobacterium, were present in the active mycorrhizal zone, even though they were not detected in soil assays using the dilution plating technique.     

Grasses and browsers reinforce landscape heterogeneity by excluding trees from ecosystem hotspots

Spatial heterogeneity in woody cover affects biodiversity and ecosystem function, and may be particularly influential in savanna ecosystems. Browsing and interactions with herbaceous plants can create and maintain heterogeneity in woody cover, but the relative importance of these drivers remains unclear, especially when considered across multiple edaphic contexts. In African savannas, abandoned temporary livestock corrals (bomas) develop into long-term, nutrient-rich ecosystem hotspots with unique vegetation. In central Kenya, abandoned corral sites persist for decades as treeless ‘glades’ in a wooded matrix. Though glades are treeless, areas between adjacent glades have higher tree densities than the background savanna or areas near isolated glades. The mechanisms maintaining these distinctive woody cover patterns remain unclear. We asked whether browsing or interactions with herbaceous plants help to maintain landscape heterogeneity by differentially impacting young trees in different locations. We planted the mono-dominant tree species (Acacia drepanolobium) in four locations: inside glades, far from glades, at edges of isolated glades and at edges between adjacent glades. Within each location, we assessed the separate and combined effects of herbivore exclusion (caging) and herbaceous plant removal (clearing) on tree survival and growth. Both caging and clearing improved tree survival and growth inside glades. When herbaceous plants were removed, trees inside glades grew more than trees in other locations, suggesting that glade soils were favorable for tree growth. Different types of glade edges (isolated vs. non-isolated) did not have significantly different impacts on tree performance. This represents one of the first field-based experiments testing the separate and interactive effects of browsing, grass competition and edaphic context on savanna tree performance. Our findings suggest that, by excluding trees from otherwise favorable sites, both herbaceous plants and herbivores help to maintain functionally important landscape heterogeneity in African savannas.     

GPCR-MPredictor: multi-level prediction of G protein-coupled receptors using genetic ensemble

G protein-coupled receptors (GPCRs) are transmembrane proteins, which transduce signals from extracellular ligands to intracellular G protein. Automatic classification of GPCRs can provide important information for the development of novel drugs in pharmaceutical industry. In this paper, we propose an evolutionary approach, GPCR-MPredictor, which combines individual classifiers for predicting GPCRs. GPCR-MPredictor is a web predictor that can efficiently predict GPCRs at five levels. The first level determines whether a protein sequence is a GPCR or a non-GPCR. If the predicted sequence is a GPCR, then it is further classified into family, subfamily, sub-subfamily, and subtype levels. In this work, our aim is to analyze the discriminative power of different feature extraction and classification strategies in case of GPCRs prediction and then to use an evolutionary ensemble approach for enhanced prediction performance. Features are extracted using amino acid composition, pseudo amino acid composition, and dipeptide composition of protein sequences. Different classification approaches, such as k-nearest neighbor (KNN), support vector machine (SVM), probabilistic neural networks (PNN), J48, Adaboost, and Naives Bayes, have been used to classify GPCRs. The proposed hierarchical GA-based ensemble classifier exploits the prediction results of SVM, KNN, PNN, and J48 at each level. The GA-based ensemble yields an accuracy of 99.75, 92.45, 87.80, 83.57, and 96.17% at the five levels, on the first dataset. We further perform predictions on a dataset consisting of 8,000 GPCRs at the family, subfamily, and sub-subfamily level, and on two other datasets of 365 and 167 GPCRs at the second and fourth levels, respectively. In comparison with the existing methods, the results demonstrate the effectiveness of our proposed GPCR-MPredictor in classifying GPCRs families. It is accessible at .     

The effects of riparian forest disturbance on stream temperature,sedimentation, and morphology

Forested headwater streams rely on their riparian areas for temperature regulation, woody debris inputs, and sediment retention. These products and services may be altered by disturbances such as timber harvest, windthrow, or development. This study investigated the effects of riparian forest disturbance by removing trees using 50 and 90% basal area harvests and by directly felling some trees into eight streams in eastern West Virginia. On summer afternoons, water temperature increased in the 50 and 90% BAH treatments at average rates of 0.18 and 0.79°C/100 m, respectively. The 90% BAH treatments had the potential to disrupt fish and invertebrate communities via increased water temperature. New roads and log landings associated with the riparian logging had no detectable effect on sedimentation or turbidity. Large woody debris (LWD) additions increased habitat complexity but no net increase in pool area was observed. Greater morphological instability was observed within the LWD addition sections as pools were both created and destroyed at significantly higher rates. Experimentally manipulating small riparian patches may be an analog for small-scale natural and anthropogenic disturbances. These common events are assumed to alter streams, but there are few experimental studies quantifying their effects.     

Paravascular pathways contribute to vasculitis and neuroinflammation after subarachnoid hemorrhage independently of glymphatic control

Subarachnoid hemorrhage (SAH) is a devastating disease with high mortality. The mechanisms underlying its pathological complications have not been fully identified. Here, we investigate the potential involvement of the glymphatic system in the neuropathology of SAH. We demonstrate that blood components rapidly enter the paravascular space following SAH and penetrate into the perivascular parenchyma throughout the brain, causing disastrous events such as cerebral vasospasm, delayed cerebral ischemia, microcirculation dysfunction and widespread perivascular neuroinflammation. Clearance of the paravascular pathway with tissue-type plasminogen activator ameliorates the behavioral deficits and alleviates histological injury of SAH. Interestingly, AQP4^−/− mice showed no improvements in neurological deficits and neuroinflammation at day 7 after SAH compared with WT control mice. In conclusion, our study proves that the paravascular pathway dynamically mediates the pathological complications following acute SAH independently of glymphatic control.Cerebral aneurysm rupture causes subarachnoid hemorrhage (SAH), which is associated with a high mortality due to its secondary complications, including hemorrhage, hydrocephalus and delayed cerebral ischemia (DCI).^{1, 2, 3} Therapeutic interventions against the secondary complications, especially DCI, are yet limited, as the pathological mechanism underlying that is not fully understood.^{2, 3, 4, 5, 6, 7} Current hypotheses of the development of the secondary complications mainly include cerebral vasospasm (CVS) and the microcirculation disturbance, as well as parenchymal arterial lesions, microthrombosis and neuroinflammation.^{1, 2, 4, 7, 8, 9}Previous studies have shown that the blockade of cerebral lymphatic drainage deteriorated the secondary cerebral ischemia after SAH, suggesting that the cerebral lymphatic drainage pathway could be involved in the pathological mechanism of SAH.^{10, 11} However, the central nervous system (CNS) was considered lack of a conventional lymphatic drainage system in the past. Recently, several studies have shown that the brain has in fact the proper lymphatic system, including sinus-associated lymphatic vessels and the glymphatic system (GS).^{12, 13, 14, 15} Sinus-associated lymphatic vessels express all of the molecular hallmarks of lymphatic endothelial cells, contain cerebrospinal fluid (CSF) and immune cells, and drain into the deep cervical lymph nodes.^{12, 13}There is a histologically defined space in the brain, the Virchow–Robin space, where the subarachnoid space meets the paravascular space (or perivascular space in somewhere, PVS).¹⁶ The GS is a specialized brain-wide anatomic structure locating at the PVS surrounding the brain vasculature, which is ensheathed with the astroglial endfeet and astroglial water channel aquaporin-4 (AQP4).^{14, 15} The GS facilitates the efficient lymphatic clearance of extracellular solutes and fluid in the brain through astroglial-mediated interstitial fluid bulk flow.¹⁴Impairment of GS involves neurological conditions including traumatic brain injuries,¹⁷ ischemic stroke¹⁸ and aged brain.¹⁹ Interestingly, brain imaging study with magnetic resonance imaging reported weakened GS perfusion following acute stroke or SAH.^{18, 20} However, little is known about whether the GS is involved in the secondary complications of SAH. Here, we examined the potential involvement of GS in SAH-associated pathology progression with in vivo two-photon microscopy and CLARITY technique.^{21, 22} Our data showed that subarachnoid blood flowed into the brain parenchyma rapidly through the PVS, causing CVS, vasculitis, widespread microinfraction and neuroinflammation in the animal model of SAH and SAH patients. Prevention of CVS with Fasudil²³ did not improve the neurological impairment nor alleviated the pathology, while the PVS clearance with tissue-type plasminogen activator (tPA) infusion improved the behavioral recovery and reduced neuroinflammation in the brain. Interestingly, AQP4^−/− mice showed no improvements in neurological deficits and neuroinflammation at day 7 after SAH compared with WT control mice. Our study therefore suggested that the paravacular pathway dynamically mediates the pathological complications following acute SAH independently of glymphatic control.     

<Emphasis Type="Italic">Alona alsafadii</Emphasis> n. sp. from Yemen,a primitive,groundwater-dwelling member of the <Emphasis Type="Italic">A. karua</Emphasis>-group

The effect of algae on the production of musty-smelling compounds by actinomycetes was studied. Streptomyces spp., causing intensive musty odor, were isolated from hypertrophic Lake Kasumigaura and cultured in association with algae from the same lake. Isolate E and I effectively utilized the cyanobacteria, Microcystis aeruginosa and Anabaena spiroides, and the diatom, Synedra acus, as a carbon source and produced a musty-smelling 2-methylisoborneol in the shaken sediment cultures. High populations of algae and actinomycetes, and aerobic condition in the sediment seem responsible for the occurrence of musty odor in Lake Kasumigaura.     

补肾益气活血方对胎儿宫内生长迟缓胎盘组织一氧化氮合酶活性的影响

为了探讨补肾益气活血方对胎儿宫内生长迟缓（ＩＵＧＲ）胎盘组织一氧化氮（ＮＯ）生成的影响,本文对正常孕妇、ＩＵＧＲ患者及补肾益气活血中药治疗后患者各１２例,采用ＮＡＤＰＨ黄递酶法研究了一氧化氮合酶（ＮＯＳ）在胎盘组织的分布,应用化学发光法测定胎盘组织ＮＯＳ活性。结果表明：正常孕妇胎盘绒毛合体滋养层细胞ＮＯＳ呈强阳性反应,绒毛干血管壁呈阳性反应,终末绒毛毛细血管壁呈阴性反应;ＩＵＧＲ患者绒毛合体滋养层细胞和绒毛干血管壁ＮＯＳ染色明显变浅,而终末绒毛毛细血管壁呈阳性反应;中药治疗后合体滋养层细胞和绒毛干血管壁ＮＯＳ染色明显加深。ＮＯＳ活性测定中药组较ＩＵＧＲ未治疗组显著增高,与正常孕妇相比其差异无显著性。结果提示：ＮＯ参与ＩＵＧＲ的病理生理过程,补肾益气活血方通过增强ＮＯＳ活性促进胎盘组织ＮＯ的产生     

HMPAS: Human Membrane Protein Analysis System

Background

Membrane proteins perform essential roles in diverse cellular functions and are regarded as major pharmaceutical targets. The significance of membrane proteins has led to the developing dozens of resources related with membrane proteins. However, most of these resources are built for specific well-known membrane protein groups, making it difficult to find common and specific features of various membrane protein groups.

Methods

We collected human membrane proteins from the dispersed resources and predicted novel membrane protein candidates by using ortholog information and our membrane protein classifiers. The membrane proteins were classified according to the type of interaction with the membrane, subcellular localization, and molecular function. We also made new feature dataset to characterize the membrane proteins in various aspects including membrane protein topology, domain, biological process, disease, and drug. Moreover, protein structure and ICD-10-CM based integrated disease and drug information was newly included. To analyze the comprehensive information of membrane proteins, we implemented analysis tools to identify novel sequence and functional features of the classified membrane protein groups and to extract features from protein sequences.

Results

We constructed HMPAS with 28,509 collected known membrane proteins and 8,076 newly predicted candidates. This system provides integrated information of human membrane proteins individually and in groups organized by 45 subcellular locations and 1,401 molecular functions. As a case study, we identified associations between the membrane proteins and diseases and present that membrane proteins are promising targets for diseases related with nervous system and circulatory system. A web-based interface of this system was constructed to facilitate researchers not only to retrieve organized information of individual proteins but also to use the tools to analyze the membrane proteins.

Conclusions

HMPAS provides comprehensive information about human membrane proteins including specific features of certain membrane protein groups. In this system, user can acquire the information of individual proteins and specified groups focused on their conserved sequence features, involved cellular processes, and diseases. HMPAS may contribute as a valuable resource for the inference of novel cellular mechanisms and pharmaceutical targets associated with the human membrane proteins. HMPAS is freely available at http://fcode.kaist.ac.kr/hmpas.

     

Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.