The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content.

Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis

Undetected Blooms in Prince William Sound: Using Multiple Techniques to Elucidate the Base of the Summer Food Web

© 2015, Coastal and Estuarine Research Federation. Prince William Sound supports many commercially and culturally important species. The phytoplankton community dynamics which support and sustain the high biomass and diversity of this ecosystem are largely unknown. The aim of this study was to describe the phytoplankton community composition during the summer, the time at which this system supports many additional migrants and commercially important fisheries. Phytoplankton community composition (pigments), dissolved nutrients, Secchi depth, total and particulate organic carbon and nitrogen, and export to deep water were measured during the summers of 2008–2010. In addition, natural abundance stable isotopes (δ13C and δ15N) of particulate organic matter (POM) and faunal samples were measured in 2010. The analysis of the phytoplankton community composition using multivariate statistics showed that changes over the summer were driven by changes in the proportion of the dominant groups: diatoms, dinoflagellates, cyanobacteria, cryptophytes, chlorophytes, and prasinophytes. These changes were driven by changes in nutrients including an organic nitrogen source, phosphate, and silica and correspond to shifts in particulate concentrations. A consistent pattern was observed each year: a large Noctiluca sp. bloom in June concurrent with low nutrients, low diversity, and high particulate organic carbon (POC) concentrations was followed by a shift in the phytoplankton community to a more diverse smaller size class community in July and equilibrating in August. This annual summer bloom could be an important contributor to the energy and nutrient inputs at the base of the regional marine food web

Validating two-dimensional leadership models on three-dimensionally structured fish schools

Identifying leader–follower interactions is crucial for understanding how a group decides where or when to move, and how this information is transferred between members. Although many animal groups have a three-dimensional structure, previous studies investigating leader–follower interactions have often ignored vertical information. This raises the question of whether commonly used two-dimensional leader–follower analyses can be used justifiably on groups that interact in three dimensions. To address this, we quantified the individual movements of banded tetra fish (Astyanax mexicanus) within shoals by computing the three-dimensional trajectories of all individuals using a stereo-camera technique. We used these data firstly to identify and compare leader–follower interactions in two and three dimensions, and secondly to analyse leadership with respect to an individual's spatial position in three dimensions. We show that for 95% of all pairwise interactions leadership identified through two-dimensional analysis matches that identified through three-dimensional analysis, and we reveal that fish attend to the same shoalmates for vertical information as they do for horizontal information. Our results therefore highlight that three-dimensional analyses are not always required to identify leader–follower relationships in species that move freely in three dimensions. We discuss our results in terms of the importance of taking species' sensory capacities into account when studying interaction networks within groups

Potential impact of a maternal vaccine for RSV: a mathematical modelling study

Respiratory syncytial virus (RSV) is a major cause of respiratory morbidity and one of the main causes of hospitalisation in young children. While there is currently no licensed vaccine for RSV, a vaccine candidate for pregnant women is undergoing phase 3 trials. We developed a compartmental age-structured model for RSV transmission, validated using linked laboratory-confirmed RSV hospitalisation records for metropolitan Western Australia. We adapted the model to incorporate a maternal RSV vaccine, and estimated the expected reduction in RSV hospitalisations arising from such a program. The introduction of a vaccine was estimated to reduce RSV hospitalisations in Western Australia by 6-37% for 0-2month old children, and 30-46% for 3-5month old children, for a range of vaccine effectiveness levels. Our model shows that, provided a vaccine is demonstrated to extend protection against RSV disease beyond the first three months of life, a policy using a maternal RSV vaccine could be effective in reducing RSV hospitalisations in children up to six months of age, meeting the objective of a maternal vaccine in delaying an infant's first RSV infection to an age at which severe disease is less likely

Dynamic Environmental Photosynthetic Imaging Reveals Emergent Phenotypes.

Understanding and improving the productivity and robustness of plant photosynthesis requires high-throughput phenotyping under environmental conditions that are relevant to the field. Here we demonstrate the dynamic environmental photosynthesis imager (DEPI), an experimental platform for integrated, continuous, and high-throughput measurements of photosynthetic parameters during plant growth under reproducible yet dynamic environmental conditions. Using parallel imagers obviates the need to move plants or sensors, reducing artifacts and allowing simultaneous measurement on large numbers of plants. As a result, DEPI can reveal phenotypes that are not evident under standard laboratory conditions but emerge under progressively more dynamic illumination. We show examples in mutants of Arabidopsis of such "emergent phenotypes" that are highly transient and heterogeneous, appearing in different leaves under different conditions and depending in complex ways on both environmental conditions and plant developmental age. These emergent phenotypes appear to be caused by a range of phenomena, suggesting that such previously unseen processes are critical for plant responses to dynamic environments

Collapse of a Bose gas: kinetic approach

We have analytically explored temperature dependence of critical number of particles for the collapse of a harmonically trapped attractively interacting Bose gas below the condensation point by introducing a kinetic approach within the Hartree-Fock approximation. The temperature dependence obtained by this easy approach is consisted with that obtained from the scaling theory.Comment: Brief Report, 4 pages, 1 figure, Accepted in Pramana-Journal of Physic

Freezing and water availability structure the evolutionary diversity of trees across the Americas

The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are still a subject of debate. We unveil the evolutionary structure of tree species assemblages across the Americas to assess whether an inability to move or an inability to evolve is the predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity. Our study establishes the pervasive importance of niche conservatism to community assembly even at intercontinental scales

Security Implications of Running Windows Software on a Linux System Using Wine

Linux is considered to be less prone to malware compared to other operating systems, and as a result Linux users rarely run anti-malware. However, many popular software applications released on other platforms cannot run natively on Linux. Wine is a popular compatibility layer for running Windows programs on Linux. The level of security risk that Wine poses to Linux users is largely undocumented. This project was conducted to assess the security implications of using Wine, and to determine if any specific types of malware or malware behavior have a significant effect on the malware being successful in Wine. Dynamic analysis (both automated and manual) was applied to 30 malware samples both in a Windows environment and Linux environment running Wine. Behavior analyzed included file system, registry, and network access, and the spawning of processes, and services. The behavior was compared to determine malware success in Wine. The study results provide evidence that Wine can pose serious security implications when used to run Windows software in a Linux environment. Five samples of Windows malware were run successfully through Wine on a Linux system. No significant relationships were discovered between the success of the malware and its high-level behavior or malware type. However, certain API calls could not be recreated in a Linux environment, and led to failure of malware to execute via Wine. This suggests that particular malware samples that utilize these API calls will never run completely successfully in a Linux environment. As a consequence, the success of some samples can be determined from observing the API calls when run within a Windows environment

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota.

Human milk oligosaccharides (HMOs) play an important role in the health of an infant as substrate for beneficial gut bacteria. Little is known about the effects of HMO composition and its changes on the morbidity and growth outcomes of infants living in areas with high infection rates. Mother's HMO composition and infant gut microbiota from 33 Gambian mother/infant pairs at 4, 16, and 20 weeks postpartum were analyzed for relationships between HMOs, microbiota, and infant morbidity and growth. The data indicate that lacto-N-fucopentaose I was associated with decreased infant morbidity, and 3'-sialyllactose was found to be a good indicator of infant weight-for-age. Because HMOs, gut microbiota, and infant health are interrelated, the relationship between infant health and their microbiome were analyzed. While bifidobacteria were the dominant genus in the infant gut overall, Dialister and Prevotella were negatively correlated with morbidity, and Bacteroides was increased in infants with abnormal calprotectin. Mothers nursing in the wet season (July to October) produced significantly less oligosaccharides compared to those nursing in the dry season (November to June). These results suggest that specific types and structures of HMOs are sensitive to environmental conditions, protective of morbidity, predictive of growth, and correlated with specific microbiota

Isolation of a wide range of minerals from a thermally treated plant: Equisetum arvense, a Mare’s tale

Silica is the second most abundant biomineral being exceeded in nature only by biogenic CaCO3. Many land plants (such as rice, cereals, cucumber, etc.) deposit silica in significant amounts to reinforce their tissues and as a systematic response to pathogen attack. One of the most ancient species of living vascular plants, Equisetum arvense is also able to take up and accumulate silica in all parts of the plant. Numerous methods have been developed for elimination of the organic material and/or metal ions present in plant material to isolate biogenic silica. However, depending on the chemical and/or physical treatment applied to branch or stem from Equisetum arvense; other mineral forms such glass-type materials (i.e. CaSiO3), salts (i.e. KCl) or luminescent materials can also be isolated from the plant material. In the current contribution, we show the chemical and/or thermal routes that lead to the formation of a number of different mineral types in addition to biogenic silica