Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.     

Ionotropic Receptors as a Driving Force behind Human Synapse Establishment

The origin of nervous systems is a main theme in biology and its mechanisms are largely underlied by synaptic neurotransmission. One problem to explain synapse establishment is that synaptic orthologs are present in multiple aneural organisms. We questioned how the interactions among these elements evolved and to what extent it relates to our understanding of the nervous systems complexity. We identified the human neurotransmission gene network based on genes present in GABAergic, glutamatergic, serotonergic, dopaminergic, and cholinergic systems. The network comprises 321 human genes, 83 of which act exclusively in the nervous system. We reconstructed the evolutionary scenario of synapse emergence by looking for synaptic orthologs in 476 eukaryotes. The Human–Cnidaria common ancestor displayed a massive emergence of neuroexclusive genes, mainly ionotropic receptors, which might have been crucial to the evolution of synapses. Very few synaptic genes had their origin after the Human–Cnidaria common ancestor. We also identified a higher abundance of synaptic proteins in vertebrates, which suggests an increase in the synaptic network complexity of those organisms.     

Using Echo Ultrasound from Schooling Fish to Detect and Classify Fish Types

Fish finders have already been widely available in the fishing market for a number of years.However,the sizes of these fishfinders are too big and their prices are expensive to suit for the research of robotic fish or mini-submarine.The goal of thisresearch is to propose a low-cost fish detector and classifier which suits for underwater robot or submarine as a proximity sensor.With some pre-condition in hardware and algorithms,the experimental results show that the proposed design has good per-formance,with a detection rate of 100 % and a classification rate of 94 %.Both the existing type of fish and the group behaviorcan be revealed by statistical interpretations such as hovering passion and sparse swimming mode.     

An interaction index to predict turtle bycatch in a Mediterranean bottom trawl fishery

Incidental catch is the major threat to the survival of loggerhead turtles (Caretta caretta) in the Mediterranean and the main reason for their decline. More than 100,000 turtles are estimated to be caught annually due to fishing practices; 10–50% die. Bottom trawls are among the fishing gears exerting the worst impact on sea turtle populations, especially in the coastal waters of Tunisia and Libya, northern Adriatic Sea, the Mediterranean coastal areas of Turkey and Egypt, where the continental shelf is large and turtles in the demersal stage are commonly found also in winter. Seven adult-sized loggerhead turtles captured incidentally by bottom trawls in the central-northern Adriatic Sea and treated in rescue centres were tagged with satellite transmitters before release. In this paper Italian bottom trawl track data obtained from vessel monitoring systems (VMSs) were analysed by VMSbase R suite to identify the areas of maximum fishing effort in the Adriatic. These data were combined with satellite information on turtle distribution to provide an interaction index enabling prediction of potential trawl–turtle interaction hotspots and periods. The present pilot study can be considered as a risk-analysis approach directed at identifying the areas and times of possible trawling–turtle interactions in a Mediterranean trawl fishery. By identifying the areas and seasons at highest risk of turtle bycatch, the index here developed has the potential to provide key information to design and implement mitigation strategies. Vessel monitoring system is actually in force in several countries, therefore the approach here studied might have a worldwide application.     

On the Stability of Clathrate Hydrates Encaging Polar Guest Molecules: Contrast in the Hydrogen Bonds of Methylamine and Methanol Hydrates

Abstract

The stability of clathrate hydrates encaging highly polar guests has been investigated in order to explain the experimental observation that some amines form clathrate hydrates but alcohols act as inhibitor to hydrate formation. We choose methylamine and methanol as guest species and examine the stable structure, at which the total potential energy has a minimum value. At the local minima of those two hydrates, the potential energies of water-water and guest-water, and their hydrogen bonded networks are compared. It is found that methanol does not retain the host lattice structure, while the host-network structure is kept in the presence of methylamine. It is shown that the difference in the magnitude of the partial charge on the hydrogen atom between the hydroxyl and amino groups plays a much more significant role on the stability of both clathrate hydrates than the difference in molecular geometry. This is supported from the result of a methylamine-like model that has the same partial charges on the atoms in the hydrophilic site as methanol.     

Adaptive Neural Network-Based ECG Data Compression According to the Morphology

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