Applications of weighted association networks applied to compositional data in biology

Next-generation sequencing technologies have generated, and continue to produce, an increasingly large corpus of biological data. The data generated are inherently compositional as they convey only relative information dependent upon the capacity of the instrument, experimental design and technical bias. There is considerable information to be gained through network analysis by studying the interactions between components within a system. Network theory methods using compositional data are powerful approaches for quantifying relationships between biological components and their relevance to phenotype, environmental conditions or other external variables. However, many of the statistical assumptions used for network analysis are not designed for compositional data and can bias downstream results. In this mini-review, we illustrate the utility of network theory in biological systems and investigate modern techniques while introducing researchers to frameworks for implementation. We overview (1) compositional data analysis, (2) data transformations and (3) network theory along with insight on a battery of network types including static-, temporal-, sample-specific- and differential-networks. The intention of this mini-review is not to provide a comprehensive overview of network methods, rather to introduce microbiology researchers to (semi)-unsupervised data-driven approaches for inferring latent structures that may give insight into biological phenomena or abstract mechanics of complex systems.     

Enzyme-Linked Immunoassay-Based Quantitative Measurement of Apolipoprotein B (ApoB) in Dried Blood Spots,a Biomarker of Cardiovascular Disease Risk

Apolipoprotein B (ApoB) is a strong predictor of cardiovascular disease, which remains the leading cause of mortality in both higher and lower income countries. Here, we adapted an enzyme-linked immunosorbent assay (ELISA) development kit for quantitative determination of ApoB levels in serum and plasma for use with dried blood spots (DBS). After confirming the dilution linearity of the assay for DBS, we measured ApoB in 208 venous DBS samples. Then, using Passing-Bablok regression analysis and Spearman rank correlation analysis, we evaluated the correspondence in ApoB values between matched plasma and finger-prick DBS samples from 40 individuals who had ApoB values spanning the range of ApoB values observed in the 208 vDBS samples. We also evaluated assay precision and recovery, the effects of hematocrit, number of freeze-thaw cycles, and different storage temperatures on ApoB levels in DBS. There was a strong, significant correlation between plasma and DBS ApoB levels with little bias. Assay precision and recovery were within the range recommended by the U.S. government’s industry guidelines for bioanalytical assay validation. The assay was not affected by the DBS matrix or physiological hematocrit levels. This DBS-based ELISA assay will facilitate population-scale assessment of cardiovascular risk in previously unexplored populations.     

Intracellular Recording,Sensory Field Mapping,and Culturing Identified Neurons in the Leech,Hirudo medicinalis

The freshwater leech, Hirudo medicinalis, is a versatile model organism that has been used to address scientific questions in the fields of neurophysiology, neuroethology, and developmental biology. The goal of this report is to consolidate experimental techniques from the leech system into a single article that will be of use to physiologists with expertise in other nervous system preparations, or to biology students with little or no electrophysiology experience. We demonstrate how to dissect the leech for recording intracellularly from identified neural circuits in the ganglion. Next we show how individual cells of known function can be removed from the ganglion to be cultured in a Petri dish, and how to record from those neurons in culture. Then we demonstrate how to prepare a patch of innervated skin to be used for mapping sensory or motor fields. These leech preparations are still widely used to address basic electrical properties of neural networks, behavior, synaptogenesis, and development. They are also an appropriate training module for neuroscience or physiology teaching laboratories.     

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus)

Intestinal microbial communities from 362 anadromous Arctic char (Salvelinus alpinus) from the high Arctic Kitikmeot region, Nunavut, Canada, were characterized using high-throughput 16S rRNA gene sequencing. The resulting bacterial communities were compared across four seasonal habitats that correspond to different stages of annual migration. Arctic char intestinal communities differed by sampling site, salinity and stages of freshwater residence. Although microbiota from fish sampled in brackish water were broadly consistent with taxa seen in other anadromous salmonids, they were enriched with putative psychrophiles, including the nonluminous gut symbiont Photobacterium iliopiscarium that was detected in >90% of intestinal samples from these waters. Microbiota from freshwater-associated fish were less consistent with results reported for other salmonids, and highly variable, possibly reflecting winter fasting behaviour of these char. We identified microbiota links to age for those fish sampled during the autumn upriver migration, but little impact of the intestinal content and water microbiota on the intestinal community. The strongest driver of intestinal community composition was seasonal habitat, and this finding combined with identification of psychrophiles suggested that water temperature and migratory behaviour are key to understanding the relationship between Arctic char and their symbionts.     

Facial diplegia with hyperreflexia-a mild Guillain-Barre Syndrome variant, to treat or not to treat?

Schwannomas are common, benign nerve tumors originating from the sheath of peripheral nerves. In this article, a 54 year old woman suffered from sudden onset motor and sensory deficit at her first radial three fingers on her right hand. Radiological investigations were normal. Electromyography diagnosed a median nerve entrapment neuropathy and urgent surgery was performed. Interestingly, a hemorrhaged mass was detected in the median nevre at the proximal end of the carpal ligament and was resected totally. Histopathological diagnosis was Schwannoma. The patient maintained a healthy status for five years.     

Substrate-Specific Clades of Active Marine Methylotrophs Associated with a Phytoplankton Bloom in a Temperate Coastal Environment

Marine microorganisms that consume one-carbon (C₁) compounds are poorly described, despite their impact on global climate via an influence on aquatic and atmospheric chemistry. This study investigated marine bacterial communities involved in the metabolism of C₁ compounds. These communities were of relevance to surface seawater and atmospheric chemistry in the context of a bloom that was dominated by phytoplankton known to produce dimethylsulfoniopropionate. In addition to using 16S rRNA gene fingerprinting and clone libraries to characterize samples taken from a bloom transect in July 2006, seawater samples from the phytoplankton bloom were incubated with ¹³C-labeled methanol, monomethylamine, dimethylamine, methyl bromide, and dimethyl sulfide to identify microbial populations involved in the turnover of C₁ compounds, using DNA stable isotope probing. The [¹³C]DNA samples from a single time point were characterized and compared using denaturing gradient gel electrophoresis (DGGE), fingerprint cluster analysis, and 16S rRNA gene clone library analysis. Bacterial community DGGE fingerprints from ¹³C-labeled DNA were distinct from those obtained with the DNA of the nonlabeled community DNA and suggested some overlap in substrate utilization between active methylotroph populations growing on different C₁ substrates. Active methylotrophs were affiliated with Methylophaga spp. and several clades of undescribed Gammaproteobacteria that utilized methanol, methylamines (both monomethylamine and dimethylamine), and dimethyl sulfide. rRNA gene sequences corresponding to populations assimilating ¹³C-labeled methyl bromide and other substrates were associated with members of the Alphaproteobacteria (e.g., the family Rhodobacteraceae), the Cytophaga-Flexibacter-Bacteroides group, and unknown taxa. This study expands the known diversity of marine methylotrophs in surface seawater and provides a comprehensive data set for focused cultivation and metagenomic analyses in the future.     

Exploring the causes and consequences of cooperative behaviour in wild animal populations using a social network approach

Understanding why individuals carry out behaviours that benefit others, especially genetically unrelated others, has been a major undertaking in many fields and particularly in biology. Here, we focus on the cooperation literature from natural populations and present the benefits of a social network approach in terms of how it can help to identify and understand factors that influence the maintenance and spread of cooperation, but are not easily captured when solely considering independent dyadic interactions. We describe how various routes to cooperation can be tested within the social network framework. Applying the social network approach to data from natural populations can help to uncover the evolutionary and ecological pressures that lead to differences in cooperation and other social processes.