bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional stabilisation and partner selection during repeated co-culivation in a methanotrophic interactome
Authors: Kerckhof Frederiek - Maarten , De Rudder Charlotte , Tsilia Varvara , Props Ruben , Ho Adrian , Heylen Kim , Boon Nico
Published: January 2018

Background

Biological oxidation of methane (CH4) is an essential ecosystem function. Accumulating evidence indicated that this function is mediated by associations of methanotrophic bacteria (MOB) with non-methanotrophic partners; together referred to as a methanotrophic interactome. Given the potency of CH4 as a greenhouse gas, a thorough understanding of how these interactomes exert an effect on methane oxidation is of special interest. Furthermore, MOB - non-MOB associations could be exploited for sustainable biotechnological applications in light of the renewed interest in MOB as natural and cost-efficient biocatalysts. The selectivity of MOB for non-MOB partners, as well as the stimulation of MOB activity (CH4 oxidation rate, MOR) with increasing non-MOB richness have both been recently described for a single batch incubation period. Therefore, we hypothesized that during repeated co-cultivation of MOB with non-MOB, ecological sorting would guide the methanotrophic interactome towards its optimal composition, which could additionally boost functionality (MOR).

Methods

Co-cultures of 8 non-MOB partners with a single alpha- or a single gammaproteobacterial MOB were repeatedly sub-cultivated. In every cycle, the headspace CH4 concentration was measured to over time to determine the MOR, while headspace CO2 concentrations and total protein in the culture were determined to track the fate of CH4-derived carbon (catabolism and assimilation respectively). Finally, the relative abundance of each co-culture partner was assessed using a 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE).

Results and Discussion

While no significant improvement of functionality was observed, the biological variability of MOR was stabilized by co-cultivation with non-MOB partners. Overall, higher biomass yields were obtained when MOB were co-cultivated with non-MOB partners and the alphaproteobacterial MOB appeared to be able to support more non-MOB biomass than the gammaproteobacterial MOB, which could be linked to the proposed life-strategies of these clades. A clear partner selection was observed as only 4 out of 8 initial partners were found to persist during repeated cycles of co-cultivation. While 2 of the persisting partners could coexist with either MOB type, the other two were more restricted to a specific MOB. Differential metabolic potential of non-MOB was resolved by genome mining publicly available genomes; our attempt to find clues for the partner selectivity did not reveal a clear link with the potential for C1-compound metabolism. However, genes for sugar metabolism (fructose, mannose, sucrose) were restricted to the persisting partners while genes encoding an ATP-dependent vitamin B12 importer were restricted to the non-persisting partners, underlining the importance of metabolic exchange in the methanotrophic interactome.
epcALGO: a home-grown algorithm for entire proteome comparison
Authors: Kumar Satish , Jena Lingaraja
Published: January 2018

Due to the advancement of bioinformatics and genome sequencing project, entire genome and proteome sequences of different organisms are available in the public domain. These vast data are repeatedly compared and explored to find out identical and similar sequence patterns. In this paper we employed NCBI’s Standalone BLAST program for entire proteome comparison of any two strains / species and illustrate a simple algorithm for the same. The implementation of this epcALGO algorithm is to identify systematically conserved proteins that are missing in a given proteome and also identify proteins unique to a particular species. This algorithm is simple and quick to apply for revealing the species / strain variation among any two closely related species / strains by identifying identical and non-identical proteins in their proteomes and also identifying where there is mutation in the protein sequence. We implemented this algorithm for proteome comparison of two strains of Mycobacterium tuberculosis H37Rv and H37Ra and elucidated the methodology for finding out their proteomic variation.
The reappraisal of Batson’s theory by isolated para-vertebral metastasis of hepatocellular carcinoma
Authors: Liang Po-Chin , Huang Kai-Wen
Published: January 2018

The extra-hepatic metastasis of hepatocellular carcinoma (HCC) usually hints late disease stage and poor prognosis. However, we treated 5 unusual HCC patients with isolated para-vertebral metastasis by tumor excision and the surgical result is satisfactory during 3.5 years follow-up in mean. To explain why the unusual situation of isolated metastasis of HCC occurred, an alternative spreading route of cancer cells bypass pulmonary circulation and avoid pulmonary vascular filtration, the Batson’s plexus, was highly suspected. We supposed that isolated para-vetebral metastases seems not to mean a late disease stage, aggressive management made longer survival possible, and it was confirmed by our clinical experience.
What the future held: Childhood psychosocial adversity is associated with health deterioration through adulthood in a cohort of British women
Authors: Nettle Daniel
Published: January 2018

Childhood psychosocial adversity is associated with accelerated onset of reproductive effort in women. Adaptive explanations for this phenomenon are built on the assumption that greater childhood psychosocial adversity is statistically associated with having a shorter period of healthy adult life during which reproduction will be possible. However, this critical assumption is never actually tested using individual-level longitudinal data. In this study, I revisit a large, longitudinally-studied cohort of British women. In an earlier paper, we showed that a simple index of psychosocial adversity in the first seven years of life predicted age at first pregnancy in a dose-dependent manner. Here, I show that the same index of adversity also predicts accelerated deterioration of health across the potentially reproductive period, and increased levels of the inflammatory biomarker c-reactive protein at age 44-46. These associations are robust to controlling for adult socioeconomic position, and do not appear to be solely a consequence of accelerated reproductive schedule. I argue that childhood psychosocial adversity may cause latent somatic damage that will, in adulthood, accelerate age-related physical decline. This provides a compelling adaptive rationale for the accelerated reproductive schedules observed in women who experience childhood psychosocial adversity.
Head motion in children with ADHD during resting-state brain imaging
Authors: Kong Xiang-zhen
Published: January 2018

Although head motion during scanning has been largely considered to reflect simply technical artifacts, there is growing evidence showing that the variable of head motion reflects valuable information regarding individual’s psychological and/or clinical factors. Detailed studies would not only help to deal with the head motion biases, but they also help researchers in understanding the mental disorders. In this study, children with ADHD and demographically-matched typically developing control (TDC) participants underwent rs-fMRI examination without any specific task, and six mean single head motion parameters (three translational and three rotational) and a summary motion index for each participant were obtained. We found that patients with ADHD showed specific patterns of head motion during scanning: motion was significantly increased in the ADHD group, which was mainly contributed by the motion around and along the superior-to-inferior direction. Furthermore, the cross-validation classification analyses showed that the head motion could accurately distinguish children with ADHD from the healthy controls. These results suggest that head motion during scanning reflects useful information about the participants and accounting for head motion from MRI data may be helpful for ADHD diagnosing and treatment with neuroimaging.
Self-regulation (locomotion and assessment), well-being (subjective and psychological), and exercise behavior (frequency and intensity) in relation to high school pupils’ academic achievement
Authors: Garcia Danilo , Jimmefors Alexander , Mousavi Fariba , Adrianson Lillemor , Rosenberg Patricia , Archer Trevor
Published: January 2018

Background: Self-regulation is the procedure implemented by an individual striving to reach a goal and consists of two inter-related strategies: assessment and locomotion. Moreover, both subjective and psychological well-being along exercise behavior might also play a role on adolescents academic achievement.

Method: Participants were 160 Swedish high school pupils (111 boys and 49 girls) with an age mean of 17.74 (sd = 1.29). We used the Assessment and Locomotion Scales to measure self-regulation; Ryff’s Psychological Well-Being Scales short version, the Temporal Satisfaction with Life Scale, and the Positive Affect and Negative Affect Schedule to measure well-being and the Archer Ratio to measure exercise behavior. Academic achievement was operationalized through pupils’ the mean value of final grades in Swedish, Mathematics, English, and Physical Education.

Results: Academic achievement was positively associated to assessment, subjective well-being, and frequent/intensive exercise behaviour. Assessment was, however, negatively related to subjective well-being. Locomotion on the other hand was positively associated to subjective and psychological well-being and also to exercise behaviour.

Conclusions: Here we propose a dual (in)direct approach to increase pupils’ academic achievement and well-being—locomotion being related to frequently exercising and well-being, in turn, increasing academic achievement; while assessment being directly related to higher academic achievement.
Association between in-scanner head motion with cerebral white matter microstructure: a multiband diffusion-weighted MRI study
Authors: Kong Xiang-zhen
Published: January 2018

Diffusion-weighted Magnetic Resonance Imaging (DW-MRI) has emerged as the most popular neuroimaging technique used to depict the biological microstructural properties of human brain white matter. However, like other MRI technique, traditional DW-MRI data remains subject to head motion artifacts during scanning. For example, previous studies have indicated that, with traditional DW-MRI data, head motion artifacts significantly affect the evaluation of diffusion metrics. Actually, DW-MRI data scanned with higher sampling rate are important for accurately evaluating diffusion metrics because it allows for full-brain coverage through the acquisition of multiple slices simultaneously and more gradient directions. Here, we employed a publicly available multiband DW-MRI dataset to investigate the association between motion and diffusion metrics with the standard pipeline, tract-based spatial statistics (TBSS). The diffusion metrics used in this study included not only the commonly used metrics (i.e., FA and MD) in DW-MRI studies, but also newly proposed inter-voxel metric, local diffusion homogeneity (LDH). We found that the motion effects in FA and MD seems to be mitigated to some extent, but the effect on MD still exists. Furthermore, the effect in LDH is much more pronounced. These results indicate that researchers shall be cautious when conducting data analysis and interpretation. Finally, the motion-diffusion association is discussed.
A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life
Authors: Huerta-Cepas Jaime , Marcet-Houben Marina , Gabaldón Toni
Published: January 2018

Assembling the Tree Of Life (TOL) faces the pressing challenge of incorporating a rapidly growing number of sequenced genomes. This problem is exacerbated by the fact that different sets of genes are informative at different evolutionary scales. Here, we present a novel phylogenetic approach ( N ested P hylogenetic R econstruction) in which each tree node is optimized based on the genes shared at that taxonomic level. We apply such procedure to reconstruct a 216-species eukaryotic TOL and compare it with a standard concatenation-based approach. The resulting topology is highly accurate, and reveals general trends such as the relationship between branch lengths and genome content in eukaryotes. The approach lends itself to continuous update, and we show this by adding 29 and 173 newly-sequenced species in two consecutive steps. The proposed approach, which has been implemented in a fully-automated pipeline, enables the reconstruction and continuous update of highly-resolved phylogenies of sequenced organisms.
Close connections between open science and open-source software
Authors: Chen Youhua , Lu Xueke , Chen You-Fang
Published: January 2018

Open science is increasingly gaining attention in recent years. In this mini-review, we briefly discuss and summarize the reasons of introducing open science into academic publications for scientists. We argue that open-source software (like R and Python software) can be the universal and important platforms for doing open science because of their appealing features: open source, easy-reading document, commonly used in various scientific disciplines like statistics, chemistry and biology. At last, the challenges and future perspectives of performing open science are discussed.
How the flow and processing of information shapes the cerebrum
Authors: de Lussanet Marc H.E.
Published: January 2018

The cerebrum of mammals spans a vast range of sizes and yet has a very regular structure. The amount of folding of the cortical surface and the proportion of white matter gradually increase with size, but the underlying mechanisms remain elusive. Here, two laws are derived to fully explain these cerebral scaling relations. The two general laws are derived from the notion that total processing power of the cortex is determined by the total cortical surface (i.e., the number of neurons), whereas the most efficient over-all flow of information is governed by the size of local networks (cortical columns). Since information is transferred by axonal connections which have a definite volume, a trade-off can be formulated from theoretical considerations between local, inter-gyral information transfer and long-range information transfer. It can be shown that this trade-off is governed by a single parameter describing the size of local networks, tlocal. Despite having just one free parameter, the first law fits the mammalian cerebrum better than any existing function, both across species and within humans. According to the second law, the scaling of white matter volume is also determined by the information principles. It follows that large cerebrums have much local processing and little global information flow. Moreover, paradoxically, a further increase in long-range connections would decrease the efficiency of information flow. These theoretical scaling principles help to compare the cerebrums across mammals regardless their size.
Castration modulates singing patterns and electrophysiological properties of ra projection neurons in adult male zebra finches
Authors: Li Dongfeng , Wang Songhua , Liao Congshu , Liu Shaoyi , Li Fengling , Meng Wei
Published: January 2018

Castration can change levels of plasma testosterone. Androgens such as testosterone play an important role in stabilizing birdsong. The robust nucleus of the arcopallium (RA) is an important premotor nucleus critical for singing. In this study, we investigated the effect of castration on singing patterns and electrophysiological properties of projection neurons (PNs) in the RA of adult male zebra finches.Adult male zebra finches were castrated and the changes in bird song assessed. We also recorded the electrophysiological changes from RA PNs using patch clamp recording. We found that the plasma levels of testosterone were significantly decreased, song syllable’s entropy was increased and the similarity of motif was decreased after castration. Spontaneous and evoked firing rates, membrane time constants, and membrane capacitance of RA PNs in the castration group were lower than those of the control and the sham groups. Afterhyperpolarization（AHP）time to peak of spontaneous action potential (AP) was prolonged after castration.These findings suggest that castration decreases song stereotypy and excitability of RA PNs in male zebra finches.
Observations of a naturalized Gazania population & fruit morphology of a Baccharis species
Authors: Baznekian Aleksi
Published: January 2018

Gazania linearis is reported to be naturalized in California (amongst a host of cultivated Gazania hybrids and species), and the fruits of Baccharis salicifolia ssp. salicifolia are reported to have 5 ribs. By carrying out a morphological study of a naturalized Gazania population, and fruits of a B. s. ssp. salicifolia individual, I was able to conclude that G. linearis may not be the only naturalized Gazania species in the population studied here (and perhaps across California), and that the number of ribs on the fruits of B. s. ssp. salicifolia are not restricted to 5, and in fact, vary in numbers.
The UK vs Sweden: Is the NHS really so bad?
Authors: Lazaridis Emmanuel N , Gavalova Lucia , Jones Simon , Quinn Tom , Weston Clive
Published: January 2018

Sheng-Chia Chung and colleagues report in The Lancet (23 January 2014) an international comparison of cardiovascular patient mortality between the UK and Sweden. They suggest that “more than 10000 deaths at 30 days would have been prevented or delayed had UK patients experienced the care of their Swedish counterparts.” Further, they estimate that 1741 deaths would have been prevented in the UK had the Swedish pattern of primary percutaneous coronary intervention (PCI) and beta-blocker use been replicated in the NHS from 2004 to 2010. However, their study does not provide convincing evidence that faster uptake of primary PCI or beta-blockers on discharge would have had an effect on cardiovascular patient mortality in the UK.
The effect of the required current/frequency combinations (EC 1099/2009) on the incidence of cardiac arrest in broilers stunned and slaughtered for the halal market
Authors: Wotton Steve S.B. , Zhang Xiaofan , McKinstry Justin J.L. , Velarde Antonio , Knowles Toby G
Published: January 2018

Multi-bird water bath stunning is the only method permitted for stunning broilers in halal plants in the UK. The electrocardiogram (ECG) was measured in broilers that were stunned electrically in a commercial water bath using four of the frequency/current parameters permitted under EU Regulation (1099/2009) plus a control treatment (pulsed DC waveform). The results showed that there were no differences between the treatments in that all the birds displayed a rhythmic heart beat following stunning and before slaughter. An opportunity to observe recovery in a small number of broilers (nine) in a Spanish processing plant suggested that AC at 1000 Hz applied at 200 mA per bird would also meet both the legislative requirements and the needs of the halal market, in that all birds recovered from the stun.
Human Motion Project - Overview
Authors: Daumer Martin
Published: January 2018

The vision of the Human Motion Project is to become a successful analogue of the Human Genome Project: improving human health by an open collaborative technology platform for the mobile medical monitoring of human motion. The basis is a growing “critical path toolbox” and a biomedical data warehouse for collecting, archiving, analysing, and disseminating human motion data including a library of validated algorithms.

The "human accelerom", i.e. objective long term information about a person's physical activity, carries information about health status and disease risk. It can be used to define novel outcome measures for clinical trials. Physical inactivity should be understood as a modifiable risk factor.
Extreme inequalities of citation counts in environmental sciences
Authors: Chimalakonda Deepthi , Cook Alex R , Carrasco L Roman
Published: January 2018

Well-established scientists are expected to be more likely to have their work recognised than early-career individuals and thus receive more citations. Estimating the degree of inequality in citation counts in environmental sciences can help identify the dynamics behind citation inequalities. Using the scientific profiles of researchers in the Google Scholar database, we estimated the inequality in the distribution of citations in the disciplines of evolutionary biology, conservation biology and ecology. The data were modelled using short-tailed (exponential) and long-tailed power-law (Pareto) distributions. The inequality in performance in each distribution was assessed using Gini coefficients. Citations counts per researcher presented Gini coefficients of 0.83–0.84, indicating extreme inequality. The results suggest that the reinforcement in citation counts due to seniority and previous success might be very strong. To produce meaningful comparisons of actual research impact using citation counts, factors such as lab size, collaborations or role in articles should ideally be controlled for.
The spectacular human nose: an amplifier of individual quality?
Authors: Mikalsen Åse Rognmo , Folstad Ivar , Yoccoz Nigel G , Laeng Bruno
Published: January 2018

Background: Amplifiers are signals that improve the perception of underlying differences in quality. They are cost free and advantageous to high quality individuals, but disadvantageous to low quality individuals, as poor quality is easier perceived because of the amplifier. For an amplifier to evolve, the average fitness benefit to the high quality individuals should be higher than the average cost for the low quality individuals. The human nose is, compared to the nose of most other primates, extraordinary large, fragile and easily broken – especially in male-male interactions. May it have evolved as an amplifier, allowing easy assessment of individual quality and influencing the perception of attractiveness?

Methods: We tested whether nose tip centrality had a particular influence on attractiveness by manipulating the position of the nose tip or, as a control, the mouth in facial pictures and had the pictures rated for attractiveness.

Results: Our results show that facial attractiveness is not influenced by mouth manipulations. Yet, facial attractiveness increased when the nose tip was artificially centered according to other facial features. Conversely, facial attractiveness decreased when the nose tip was displaced away from its central position.

Discussion: Our results suggest that the centering of the nose tip is important for evaluation of attractiveness, maybe because it has a particularly strong effect on our perception of facial symmetry or averageness. However, whether such centering is related to individual quality remains unclear.
A call for virtual experiments: accelerating the scientific process
Authors: Cooper Jonathan , Vik Jon Olav , Waltemath Dagmar
Published: January 2018

Experimentation is fundamental to the scientific method, whether for exploration, description or explanation. In the exploration of a novel system, children and researchers alike will mess about with things just to see what happens. More formalized experimental protocols ensure reproducible results and form a basis for comparing systems in terms of their response to a specific stimulus. Finally, experiments can be carefully designed to distinguish between competing causal hypotheses based on their different testable predictions about the outcome of the experimental manipulation. One would therefore expect experiments to be central in computational biology too.

Indeed, a mathematical model embodies a thought experiment, a causal hypothesis, and its falsifiable predictions. It is easy to ask "what if" we were to change a parameter, an initial state, or the model structure. Papers in computational biology focus on describing and analyzing the effects of such changes, and on confronting models with experimental data. This confrontation often generates new hypotheses, and many if not most new models arise by modification of existing ones. However, most virtual experiments are not built to be reproducible, and thus die with the paper they are published in. This inhibits the critical scrutiny of models, as models are seldom subjected to the same simulation experiments as their predecessors, or revisited later in the light of new data. Perhaps worse, the status quo fails to take full advantage of experiments as a common language between modellers and experimentalists. Despite the growing availability of data and model repositories, there has been only a slow uptake of emerging tools and standards for documenting and sharing the protocols for simulation experiments and their results.

We argue that promoting the reuse of virtual experiments would vastly improve the usefulness and relevance of computational models, including in biomedical endeavours such as the Virtual Physiological Human and the Human Brain Project. We review the benefits of reusable virtual experiments: in specifying, assaying, and comparing the behavioural repertoires of models; as prerequisites for reproducible research; to guide model reuse and composition; and for quality assurance in the application of computational biology models. Next, we discuss potential approaches for implementing virtual experiments, arguing that models and experimental protocols should be represented separately, but annotated so as to facilitate the linking of models to experiments and data. We follow with some consideration of open questions and challenges that remain before the use of virtual experiments can become widespread. Lastly, we outline a vision for how the rigorous, streamlined confrontation between experimental datasets and candidate models would enable a "continuous integration" of biological knowledge, akin to the strategy used in software development.
Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss
Authors: Pique Lynn M , Brennan Marie-Luise , Davidson Colin J , Schaefer Frederick , Greinwald Jr. John , Schrijver Iris
Published: January 2018

Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4-6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype.
Culture of equine fibroblast-like synoviocytes on synthetic tissue scaffolds towards meniscal tissue engineering: a preliminary cell-seeding study
Authors: Warnock Jennifer J , Fox Derek B , Stoker Aaron M , Beatty Mark , Cockrell Mary K , Janicek John C , Cook James L
Published: January 2018

Introduction: Tissue Engineering is a new methodology for addressing meniscal injury or loss. Synovium may be an ideal source of cells for in vitro meniscal fibrocartilage formation, however, favorable in vitro culture conditions for synovium must be established in order to achieve this goal. The objective of this study was to determine cellularity, cell distribution, and extracellular matrix (ECM) formation of equine fibroblast-like synoviocytes (FLS) cultured on synthetic scaffolds, for potential application in synovium-based meniscal tissue engineering. Scaffolds included open-cell poly-L-lactic acid (OPLA) sponges and polyglycolic acid (PGA) scaffolds cultured in static and dynamic culture conditions, and PGA scaffolds coated in poly-L-lactic (PLLA) in dynamic culture conditions. Materials and Methods: Equine FLS were seeded on OPLA and PGA scaffolds, and cultured in a static environment or in a rotating bioreactor for 12 days. Equine FLS were also seeded on PGA scaffolds coated in 2% or 4% PLLA and cultured in a rotating bioreactor for 14 and 21 days. Three scaffolds from each group were fixed, sectioned and stained with Masson’s Trichrome, Safranin-O, and Hematoxylin and Eosin, and cell numbers and distribution were analyzed using computer image analysis. Three PGA and OPLA scaffolds from each culture condition were also analyzed for extracellular matrix (ECM) production via di-methylmethylene blue (sulfated glycosaminoglycan) assay and hydroxyproline (collagen) assay. PLLA coated PGA scaffolds were analyzed using double stranded DNA quantification as a reflection of cellularity and confocal laser microscopy in a fluorescent cell viability assay. Results: The highest cellularity occurred in PGA constructs cultured in a rotating bioreactor, which also had a mean sulfated glycosaminoglycan content of 22.3μg per scaffold. PGA constructs cultured in static conditions had the lowest cellularity. Cells had difficulty adhering to OPLA and the PLLA coating of PGA scaffolds; cellularity was inversely proportional to the concentration of PLLA used. PLLA coating did not prevent dissolution of the PGA scaffolds. All cell scaffold types and culture conditions produced non-uniform cellular distribution. Discussion/ Conclusion: FLS-seeding of PGA scaffolds cultured in a rotating bioreactor resulted in the most optimal cell and matrix characteristics seen in this study. Cells grew only in the pores of the OPLA sponge, and could not adhere to the PLLA coating of PGA scaffold, due to the hydrophobic property of PLA. While PGA culture in a bioreactor produced measureable GAG, no culture technique produced visible collagen. For this reason, and due to the dissolution of PGA scaffolds, the culture conditions and scaffolds described here are not recommended for inducing fibrochondrogenesis in equine FLS for meniscal tissue engineering.
Immune stimulation reduces sleep and memory ability in Drosophila melanogaster
Authors: Mallon Eamonn B , Alghamdi Akram , Holdbrook Robert T.K. , Rosato Ezio
Published: January 2018

Psychoneuroimmunology studies the increasing number of connections between neurobiology, immunology and behaviour. We establish Drosophila melanogaster as a tractable model in this field by demonstrating the effects of the immune response on two fundamental behaviours: sleep and memory ability. We used the Geneswitch system to upregulate peptidoglycan receptor protein (PGRP) expression, thereby stimulating the immune system in the absence of infection. Geneswitch was activated by feeding the steroid RU486, to the flies. We used an aversive classical conditioning paradigm to quantify memory and measures of activity to infer sleep. Immune stimulated flies exhibited reduced levels of sleep, which could not be explained by a generalised increase in waking activity. The effects on sleep were more pronounced for day compared to night sleep. Immune stimulated flies also showed a reduction in memory abilities. These results establish Drosophila as a model for immune-neural interactions and suggest a possible role for sleep in the interplay between the immune response and memory.
Ferritin is required at multiple stages during the embryonic development of Drosophila melanogaster
Authors: González-Morales Nicanor , Missirlis Fanis , Mendoza-Ortíz Miguel Ángel , Blowes Liisa M , Riesgo-Escovar Juan R
Published: January 2018

In Drosophila, iron is stored in the endomembrane system of cells inside a protein cavity formed by 24 ferritin subunits of two types (Fer1HCH and Fer2LCH) in a 1:1 stoichiometry. Ferritin accumulates in the midgut, nervous system, hemolymph and nephrocytes of Drosophila larvae. Here, we show that mutation of either ferritin gene product or deletion of both genes resulted in a similar set of phenotypes of embryonic lethality, ranging from non-deposition of cuticle to developmental defects associated with germ band retraction, dorsal closure and head involution. Maternal contribution of ferritin, which varied reflecting the mother’s iron stores, is used in early development, but zygotic ferritin mutants died with ectopic apoptotic events and disrupted intestinal morphology. The embryonic nervous system of ferritin mutants presented ventral nerve cord disruptions, misguided axonal projections and brain malformations. Finally, ferritin accumulation was also observed in embryonic hemocytes. One ferritin mutant showed no hemocyte ferritin accumulation and this expression was also lost by genetic inhibition of the secretory pathway. Our work suggests that insect ferritin functions in iron storage, intercellular iron transport and protection from oxidative stress at multiple times during the embryonic development of Drosophila melanogaster.
Continental variation in wing pigmentation in Calopteryx damselflies is related to the presence of heterospecifics
Authors: Hassall Christopher
Published: January 2018

Wing pigmentation in Calopteryx damselflies, caused by the deposition of melanin, is energetically expensive to produce and enhances predation risk. However, patterns of melanisation are used in species identification, greater pigmentation is an accurate signal of male immune function in at least some species, and there may be a role for pigment in thermoregulation. This study tested two potential hypotheses to explain the presence of, and variation in, this pigmentation based on these three potential benefits using 907 male specimens of Calopteryx maculata collected from 49 sites (34 discrete populations) across the geographical range of the species in North America: (i) pigmentation varies with the presence of the closely related species, Calopteryx aequabilis, and (ii) pigment increases at higher latitudes as would be expected if it enhances thermoregulatory capacity. No gradual latitudinal pattern was observed, as might be expected if pigmentation was involved in thermoregulation. However, strong variation was observed between populations that were sympatric or allopatric with C. aequabilis. This variation was characterised by dark wings through allopatry in the south of the range and then a step change to much lighter wings at the southern border of sympatry. Pigmentation then increased further north into the sympatric zone, finally returning to allopatry levels at the northern range margin. These patterns are qualitatively similar to variation in pigmentation in C. aequabilis, meaning that the data are consistent with what would be expected from convergent character displacement. Overall, the results corroborate recent research that has suggested sexual selection as a primary driver behind the evolution of wing pigmentation in this group.
Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes
Authors: Dohms Kimberly M , Burg Theresa M
Published: January 2018

The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.
Automated analysis of invadopodia dynamics in live cells
Authors: Berginski Matthew E , Creed Sarah J , Cochran Shelly , Roadcap David W , Bear James E , Gomez Shawn M
Published: January 2018

Multiple cell types form specialized protein complexes, podosomes or invadopodia and collectively referred to as invadosomes, which are used by the cell to actively degrade the surrounding extracellular matrix. Due to their potential importance in both healthy physiology as well as in pathological conditions such as cancer, the characterization of these structures has been of increasing interest. Following early descriptions of invadopodia, assays were developed which labelled the matrix underneath metastatic cancer cells allowing for the assessment of invadopodia activity in motile cells. However, characterization of invadopodia using these methods has traditionally been done manually with time-consuming and potentially biased quantification methods, limiting the number of experiments and the quantity of data that can be analysed. We have developed a system to automate the segmentation, tracking and quantification of invadopodia in time-lapse fluorescence image sets at both the single invadopodia level and whole cell level. We rigorously tested the ability of the method to detect changes in invadopodia formation and dynamics through the use of well-characterized small molecule inhibitors, with known effects on invadopodia. Our results demonstrate the ability of this analysis method to quantify changes in invadopodia formation from live cell imaging data in a high throughput, automated manner.
Moral action as cheater suppression in human super organisms: Testing the human superorganism approach to morality
Authors: Aunger Robert , Greenland Katie
Published: January 2018

Large-scale human groups cannot rely on shared genetic interests or dyadic reciprocity to ensure social cohesion as genetic similarity is low and indirect reciprocity is rife; nevertheless, such societies continue to cohere, due to the evolution of novel regulatory mechanisms that inhibit defaulting on social obligations: moral sentiments and actions. The present paper argues that the extent of moral concern can be most usefully identified by defining the set of functions required to sustain a human ‘superorganism’. These functions are determined to be boundary, production, distribution, storage, control, structure, enforcement, signaling, memory, excretion, perception and reproductive functions. Moral obligations to act arise when individuals default on contributing to these functions. To test this approach, roughly 80,000 respondents from over 200 countries completed a web-based experiment hosted by the British Broadcasting Corporation (BBC). This experiment elicited a suite of responses to a set of 33 short scenarios derived from the 13 domains of superorganism function. Results indicate that all functions are moralized, while violations falling outside this domain (social conventions and individual decisions) are not. People living in larger communities exhibited stronger moral sentiments and action propensities, consistent with the greater interdependence of living in groups with more social roles. Such people were also more likely to see the function of the justice system as supporting group-level protection rather than personal recrimination or restitution, were more willing to engage in punishment of those who failed to punish cheaters, and more offended by those who choose not to contribute to social welfare. These results support the contention of Human Superorganism Theory that large-scale human groups strongly rely on moral propensities to regulate those who fail to perform superorganismal functions. Given this supporting evidence, we believe this new approach to defining the moral domain has implications for fields ranging from psychology to legal theory.
How male signaling intensity influences phonotaxis in virgin female Jamaican field crickets (Gryllus assimilis)
Authors: Bertram Susan M , Pacheco Karen
Published: January 2018

Understanding female mate preference is important for determining the strength and the direction of sexual trait evolution. Male signalling intensity is often an important predictor of mating success because higher intensity (louder) signallers are detectable at greater distances. However, if females are simultaneously more attracted to higher signalling intensities, then the potential fitness impacts of higher intensity signalling should be elevated beyond what would be expected from detection distance alone. Here we manipulated the signal intensity of cricket mate attraction signals to determine how female phonotaxis was influenced. We examined female phonotaxis using two common methodologies: spherical treadmills and open arenas. Both methodologies showed similar results, with females exhibiting highest phonotaxis towards loud (X̅+1 SD = 69 dB) mate attraction signals but showing reduced phonotaxis towards the loudest (X̅+2 SD = 77 dB) signals. Reduced phonotaxis towards supernormal stimuli may occur for several reasons including elevating the females’ perceived predation risk, invoking females’ acoustic startle response, or exceeding females’ perceptual limits.
The Shape of Color: Retinal Cones and Spectral Dispersion
Authors: Medeiros John A , Medeiros Nancy E
Published: January 2018

Why are the retinal color receptors cone-shaped? This is not a trivial question: the cone shape is evidently a universal feature of the color receptors while the achromatic rod receptors are always rod-shaped. What might be behind this dichotomy has not previously been explored in any meaningful way. We suggest here that the cone shape is not an incidental feature, but actually integral to cone function. We describe a waveguide mode cut-off effect that can physically separate light into its spectral colors along the length of a small, tapered waveguide, i.e., a cone. This effect converts the spectrum of incident light into position-dependent information along a tapered fiber; long-wavelength red light is excluded from the cone first, and the shortest-wavelength, blue light last. The retinal cone optical dimensions are apparently ideally tuned to exhibit this spectral dispersion. Converting this length-correlated information into a readable color code can be accomplished through translation into a time-correlated code through the microsaccadic movements of the eye to synchronize the time-delayed electrical signal generated by photoabsorption events from different positions along the receptor. Such a time code explains the existence of subjective color effects such as that induced by Benham’s Top. Detecting color information through such a waveguide effect also explains the Stiles-Crawford Effect of the Second Kind (SC II) whereby the apparent color of monochromatic light depends on its angle of incidence at the retina. The long puzzling similarity of violet and purple is directly explained by excitation of second-order waveguide mode propagation for short-wavelength light in this model. This dynamic model of color vision also accounts for the breakdown of statically-established metameric color matches under dynamic presentation, a feature of color vision that contradicts the basic assumptions of the standard Young-Helmholtz trichromatic model. Further underscoring the utility of the our proposed model is that it explains the major features of common forms of color blindness as a consequence of “mistuning” of the cone parameters.
Modeling the population dynamics of lemon sharks
Authors: White Easton R , Nagy John D , Gruber Samuel H
Published: January 2018

Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population dynamics. In particular, factors such as age-structure, density-dependent feedbacks on reproduction, and demographic stochasticity are important for understanding population trends, but are often difficult to assess. Lemon sharks (Negaprion brevirostris) have a pelagic adult phase that makes them logistically difficult to study. However, juveniles use coastal nursery areas where their densities can be high. Thus, we use a stage-structured, Markov-chain stochastic model to describe lemon shark population dynamics from a 17-year longitudinal dataset at a coastal nursery area at Bimini, Bahamas. We found that the interaction between delayed breeding and demographic stochasticity accounts for 33 to 49% of the variance. Demographic stochasticity contributed all random effects in this model, suggesting that the existence of unmodeled environmental factors may be driving the majority of interannual population fluctuations. In addition, we are able to use our model to estimate the natural mortality rate of older age classes of lemon sharks that are difficult to study. Further, we use our model to examine what effect the length of a time series plays on deciphering ecological patterns. We find that — even with a relatively long time series — our sampling still misses important rare events. Our approach can be used more broadly to infer population dynamics of other large vertebrates in which age structure and demographic stochasticity are important.
BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
Authors: Luo Ruibang , Wong Yiu-Lun , Law Wai-Chun , Lee Lap-Kei , Liu Chi-Man , Cheung Jeanno , Lam Tak-Wah
Published: January 2018

This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 hours to process 50-fold whole genome sequencing (~750 million 100bp paired-end reads), or just 25 minutes for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses.

BALSA is available at: http://sourceforge.net/p/balsa