Biology subjects

Browse preprints

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

At least 667 records · Page 37Linked to original sources

bioRxiv2018

How non-veridical perception drives actions in healthy humans - Evidence from Synaesthesia

We continually perform actions driven by our perception and it is commonly held that only objectively perceived changes within the real world affect behaviour. Exceptions are usually only made for clinical conditions associated with hallucinations, where objectively non-existent percepts can influence behavior. Using synaesthesia as a model condition, we show that even in healthy populations irrelevant non-veridical precepts exert an effect on action. By non-veridical we refer to stimulus dimensions that are only subjectively perceived to be there. Applying electrophysiological (EEG) methods, we show that although these examined peculiarities are perceptual in nature, not primarily perceptual processes underlie the effects of irrelevant non-veridical perceptions on actions. Rather, high-order processes linking perceptions and motor control in medial frontal cortices reflect the underlying mechanism how irrelevant non-veridical perceptions modulate behaviour. Our results challenge assumptions about the determinants of healthy human behaviour but can be embedded within existing frameworks detailing perception action interactions.

neuroscience↗

bioRxiv2018

SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology

Genome sequencing is revolutionising infectious disease epidemiology, providing a huge step forward in sensitivity and specificity over more traditional molecular typing techniques. However, the complexity of genome data often means that its analysis and interpretation requires high-performance compute infrastructure and dedicated bioinformatics support. Furthermore, current methods have limitations that can differ between analyses and are often opaque to the user, and their reliance on multiple external dependencies makes reproducibility difficult. Here I introduce SKA, a toolkit for analysis of genome sequence data from closely-related, small, haploid genomes. SKA uses split kmers to rapidly identify variation between genome sequences, making it possible to analyse hundreds of genomes on a standard home computer. Tests on publicly available simulated and real-life data show that SKA is both faster and more efficient than the gold standard methods used today while retaining similar levels of accuracy for epidemiological purposes. SKA can take raw read data or genome assemblies as input and calculate pairwise distances, create single linkage clusters and align genomes to a reference genome or using a reference-free approach. SKA requires few decisions to be made by the user, which, along with its computational efficiency, allows genome analysis to become accessible to those with only basic bioinformatics training. The limitations of SKA are also far more transparent than for current approaches, and future improvements to mitigate these limitations are possible. Overall, SKA is a powerful addition to the armoury of the genomic epidemiologist. SKA source code is available from Github (https://github.com/simonrharris/SKA).

genomics↗

bioRxiv2018

Characterizing noncompliance in conservation: a multidimensional Randomized Response Technique for multinomial responses.

Rule violation is critical for biological conservation worldwide. Conventional questionnaires are not suitable to survey these violations and specialized questioning techniques that preserve respondents privacy, like the forced-response RRT, have been increasingly adopted by conservationists. However, most of these approaches do not measure multinomial answers and conservationists need a specialized questioning technique for real-world settings where non-compliance could occur in different forms. We developed a multidimensional, statistically-efficient, RRT which is suitable for multinomial answers (mRRT) and which allows researchers to test for respondents noncompliance during completion. Then, we applied it to measure the frequency of the various forms of illegal restocking of European catfish from specialized anglers in Italy, developing an operational code for the statistical software R. A total of 75 questionnaires were administered at a large fishing fair in Northern Italy, in winter 2018. Our questionnaires were easily compiled and the multinomial model revealed that around 6% of respondents had moved catfish across public freshwater bodies and private ponds. Future studies should better address their characteristics, and the mRRT could allow for modeling the effect of co-variates over restocking behavior. The multinomial mRRT could be adopted to measure many forms of rule violation in conservation that could take different forms, like various forms of fish restocking or different modes of wildlife persecution.

ecology↗

bioRxiv2018

Predictive coding with neural transmission delays: a real-time temporal alignment hypothesis

Hierarchical predictive coding is an influential model of cortical organization, in which sequential hierarchical layers are connected by feedback connections carrying predictions, as well as feedforward connections carrying prediction errors. To date, however, predictive coding models have neglected to take into account that neural transmission itself takes time. For a time-varying stimulus, such as a moving object, this means that feedback predictions become misaligned with new sensory input. We present an extended model implementing both feed-forward and feedback extrapolation mechanisms that realigns feedback predictions to minimize prediction error. This realignment has the consequence that neural representations across all hierarchical stages become aligned in real-time. Using visual motion as an example, we show that the model is neurally plausible, that it is consistent with evidence of extrapolation mechanisms throughout the visual hierarchy, that it predicts several known motion-position illusions, and that it provides a solution to the temporal binding problem.

neuroscience↗

bioRxiv2018

Reporting of \"dialysis adequacy\" as an outcome in randomised trials conducted in adults on haemodialysis: a systematic review

BackgroundClinical trials are most informative for evidence-based decision-making when they consistently measure and report outcomes of relevance to stakeholders, especially patients, clinicians, and policy makers. However, sometimes terminology used is interpreted differently by different stakeholders, which might lead to confusion during shared decision making. The construct dialysis adequacy is frequently used, suggesting it is an important outcome both for health care professionals as for patients.\n\nObjectiveTo assess the scope and consistency of the construct dialysis adequacy as reported in randomised controlled trials in hemodialysis, and evaluate whether these align to the insights and understanding of this construct by patients.\n\nMethodsTo assess scope and consistency of dialysis adequacy by professionals, we performed a systematic review searching the Cochrane Central Register of Controlled Trials (CENTRAL) up to July 2017. We identified all randomised controlled trails (RCT) including patients on hemodialysis and reporting dialysis adequacy, adequacy or adequacy of dialysis and extracted and classified all reported outcomes. To explore interpretation and meaning of the construct of adequacy by patients, we conducted 10 semi-structured interviews with HD patients using thematic analysis. Belgian registration number B670201731001.\n\nFindingsFrom the 31 included trials, we extracted and classified 98 outcome measures defined by the authors as adequacy of dialysis, of which 94 (95%) were biochemical, 3 (3%) non-biochemical surrogate and 2 (2%) patient-relevant. The three most commonly reported measures were all biochemical. None of the studies defined adequacy of dialysis as a patient relevant outcome such as survival or quality of life.\n\nPatients had a substantially different understanding of the construct dialysis adequacy than the biochemical interpretation reported in the literature. Being alive, time spent while being on dialysis, fatigue and friendliness of staff were the most prominent themes that patients linked to the construct of dialysis adequacy.\n\nConclusion Adequacy of dialysis as reported in the literature refers to biochemical outcome measures, most of which are not related with patient relevant outcomes. For patients, adequate dialysis is a dialysis that enables them to spend as much quality time in their life as possible.

epidemiology↗

bioRxiv2018

Fair allocation of healthcare research funds by the European Union?

This study aimed to investigate the distribution of European Union (EU) healthcare research grants across EU countries, and to study the effect of the potential influencing factors on grant allocation. We analysed publicly available data on healthcare research grants from the 7th Framework Programme and the Horizon 2020 Programme allocated to beneficiaries between 2007 and 2016. Grant allocation was analysed at the beneficiary-, country-, and country group-level (EU-15 versus newer Member States, defined as EU-13). The investigated country-level explanatory variables included GDP per capita, population size, overall disease burden, and healthcare research excellence. Grant amounts per 100,000 inhabitants was used as an outcome variable in the regression analyses.\n\nResearch funds were disproportionally allocated to EU-15 versus the EU-13, as 96.9% of total healthcare grants were assigned to EU-15 countries. At the beneficiary level, EU funding was positively influenced by participating in previous grants. The average grant amount per beneficiary was higher for EU-15 organizations. In univariate regression analyses at the country level, higher GDP per capita (p<0.001) and better medical research excellence (p<0.001) were associated with more EU funding, and a higher disease burden was associated with less EU funding (p=0.003). In the multiple regression analysis GDP per capita (p=0.002) and research excellence (p<0.001) had a significant positive association with EU funding. Population size had an inverted U-shaped relationship with EU funding for healthcare research, having the largest per capita funding in second and the third quartiles (p=0.03 and p=0.02).\n\nThe uneven allocation of healthcare research funds across EU countries was influenced by GDP per capita, medical research excellence and population size. Wealthier countries with an average population size and strong research excellence in healthcare had more EU funding for healthcare research. Higher disease burden apparently was not associated with more EU research funding.

scientific communication and education↗

bioRxiv2018

Chronosequence and direct observation approaches reveal complementary community dynamics in a novel ecosystem

Non-native, early-successional plants have been observed to maintain dominance for decades, particularly in semi-arid systems. Here, two approaches were used to detect potentially slow successional patterns in an invaded semi-arid system: chronosequence and direct observation. Plant communities in 25 shrub-steppe sites that represented a 50-year chronosequence of agricultural abandonment were monitored for 13 years. Each site contained a field abandoned from agriculture (ex-arable) and an adjacent never-tilled field. Ex-arable fields were dominated by short-lived, non-native plants. These weedy communities had lower species richness, diversity and ground cover, and greater annual and forb cover than communities in never-tilled fields. Never-tilled fields were dominated by long-lived native plants. Across the chronosquence, plant community composition remained unchanged in both ex-arable and never-tilled fields. In contrast, 13 years of direct observation detected directional changes in plant community composition in both field types. Despite changes in community composition in both field types during direct observation, there was little evidence that native plants were invading ex-arable fields or that non-native plants were invading never-tilled fields. The more-controlled, direct observation approach was more sensitive to changes in community composition, but the chronosequence approach suggested that these changes are unlikely to manifest over longer time periods, at least in part because of disturbances in the system. Results highlight the long-term consequences of soil disturbance and the difficulty of restoring native perennials in disturbed semi-arid systems.\n\nNomenclature: Hitchcock and Cronquist (1973) for plants.

ecology↗

bioRxiv2018

Ethnobotanical and nutritional study of quelites sold in two traditional markets of Oaxaca, Mexico

Background.In Mexico, it is called quelites to certain edible vegetables (young plants, germ, shoots or flowers). Since pre-Hispanic times, quelites have been eaten as a source of vitamins, minerals and proteins. Now, its traditional and healthy consumption has decreased. We studied the quelites of two traditional markets in the Valles Centrales of Oaxaca state, Mexico using an ethnobotanical and nutritional approach.\n\nMethodsFrom July 2017 to July 2018, weekly ethnobotanical interviews were conducted with 26 collectors-sellers of the Zimatlan market and 36 in the Zaachila market. The vegetal supply was acquired, herborized and identified by through dichotomous keys. There were determined the proximal composition, phenolic compounds, flavonoids, antioxidant capacity and mineral content of the floral structures of two quelites types. The statistical analysis was performed through a one-way analysis of variance (ANOVA) of Tukey HSD.\n\nResultsIn two sampled markets, 23 species belonging to 11 botanical families were registered, from which leaves, branches, stems, flowers and fruits are eaten. The flowers of the species Diphysa americana (Q1) and Phaseolus coccineus (Q2) are the most used for human consumption of the communities involved in the sale of the sampled quelites. Both flowers had important amounts of proteins (2.66-3.29%) and fiber (1.66-2.43%). Q1 had higher content of phenols and flavonoids and therefore higher antioxidant capacity than Q2 (p <0.05). When we talk about Q2 minerals, it presented a greater amount of Zn, Ca and Mg in comparison to Q1 (p> 0.05).\n\nConclusionsIn local markets of the state of Oaxaca, a wide variety of quelites are usually found, where their botanical structures, such as flowers, are widely eaten. The flowers of Q1 and Q2 proved to be a rich source of proteins and bioactive compounds, as well as minerals. Showing thus to be a food alternative to enrich the human diet.

plant biology↗

bioRxiv2018

Mortality in trauma patients admitted during, before, and after national academic emergency medicine and trauma surgery meeting dates in Japan

Annually, many physicians attend national academic meetings. While participating in these meetings can have a positive impact on daily medical practice, attendance may result in reduced medical staffing during the meeting dates. We sought to examine whether there were differences in mortality after trauma among patients admitted to the hospital during, before, and after meeting dates. Using the Japan Trauma Data Bank, we analyzed in-hospital mortality in patients with traumatic injury admitted to the hospital from 2004 to 2015 during the dates of two national academic meetings - the Japanese Association for Acute Medicine (JAAM) and the Japanese Association for the Surgery of Trauma (JAST). We compared the data with that of patients admitted with trauma during identical weekdays in the weeks before and after the meetings, respectively. We used multiple logistic regression analysis to compare outcomes among the three groups. A total of 7,491 patients were included in our analyses, with 2,481, 2,492, and 2,518 patients in the during, before, and after meeting dates groups, respectively; their mortality rates were 7.3%, 8.0%, and 8.5%, respectively. After adjusting for covariates, no significant differences in in-hospital mortality were found among the three groups (adjusted odds ratio [95% CI] of the before meeting dates and after meeting dates groups; 1.18 [0.89-1.56] and 1.23 [0.93-1.63], respectively, with the during meeting dates group as the reference category). No significant differences in in-hospital mortality were found among trauma patients admitted during, before, and after the JAAM and JAST meeting dates.

epidemiology↗

bioRxiv2018

Hypothalamic transcriptome analysis reveals the neuroendocrine mechanisms in controlling broodiness of Muscovy duck (Cairina moschata)

Broodiness, one of the maternal behaviors and instincts for natural breeding in birds, is an interesting topic in reproductive biology. Broodiness in poultry is characterized by persistent nesting, usually associated with cessation of egg laying. The study of avian broodiness is essential for bird conservation breeding and commercial poultry industry. In this study, we examined the hypothalamus transcriptome of Muscovy duck in three reproductive stages, including egg-laying anaphase (LA), brooding prophase (BP) and brooding metaphase (BM). Differences in gene expression during the transition from egg-laying to broodiness were examined, and 155, 379, 292 differently expressed genes (DEGs) were obtained by pairwise comparisons of LA-vs-BP, LA-vs-BM and BP-vs-BM, respectively (fold change[≥] 1.5, P < 0.05). Gene Ontology Term (GO) enrichment analysis suggested a possible role of oxidative stress in the hypothalamus might invoke reproductive costs that potentially change genes expression. KEGG analysis revealed glutamatergic synapse, dopaminergic synapse, serotonergic synapse and GABAergic synapse pathway were significantly enriched, and regulator genes were identified. Eight gene expression patterns were illustrated by trend analysis and further clustered into three clusters. Additional six hub genes were identified through combining trend analysis and protein-protein interaction (PPI) analysis. Our results suggested that the cyclical mechanisms of reproductive function conversion include effects of oxidative stress, biosynthesis of neurotransmitters or their receptors, and interactions between glucocorticoids and thyroid hormones and regulatory genes. These candidate genes and biological pathways may be used as targets for artificial manipulation and marker-assisted breeding in the reproductive behavior.

animal behavior and cognition↗

bioRxiv2018

Modeling Edar expression reveals the hidden dynamics of tooth signaling center patterning

The generation of patterns during development is generally viewed as a direct process. In the mouse jaw, however, the sequential patterning of molars initiates with abortive tooth signaling centers called MS and R2, thought to be vestiges of the lost rodent premolars. Moreover, the mature signaling center of the first molar (M1) is formed from the fusion of two signaling centers (R2 and early M1). Here, we report that Edar expression reveals the hidden dynamics of signalling centers patterning. First, Edar expression evidenced a hidden two-step patterning process that we modelled with a single activator-inhibitor pair: the epithelium is initially broadly activated, then activation becomes restricted in space to give rise to the signalling centers. Second, Edar expression unveils successive phases of pattern making and pattern erasing events, a phenomenon that we called a developmental palimpsest. MS is erased by a broad activation for the benefit of R2, which itself is erased before it recovers when the first molar signaling center forms. In the lower but not the upper jaw, the two neighboring signaling centers then fuse into a single elongated center. Our model recapitulated the erasure of the R2 signaling center by the wave of activation that precedes the formation of M1 signaling center, and predicted the surprising rescue of R2 in the context of an Edar mutant with reduced activation. It suggested that R2 was not intrinsically defective, but actively outcompeted by M1 formation. We confirmed this by cultivating R2 separately from the posterior tissue and showing it could then generate a tooth. Finally, by introducing chemotaxis as a secondary process of tooth germ maturation, we recapitulated the fusion of R2 and M1 in the lower jaw only, and the loss of fusion when Edar function is impaired in organ cultures. In conclusion, we have uncovered a highly indirect and dynamic nature of pattern formation in the molar field that could nevertheless be simulated with simple mathematical models. Our study argues for viewing embryonic patterns as dynamical objects rather than as fixed endpoints, where dynamics is essential to the outcome of the patterning process.

developmental biology↗

bioRxiv2018

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways

Endogenous small RNAs (sRNAs) and Argonaute proteins are ubiquitous regulators of gene expression in germline and somatic tissues. sRNA-Argonaute complexes are often expressed in gametes and are consequently inherited by the next generation upon fertilization. In Caenorhabditis elegans, 26G-RNAs are primary endogenous sRNAs that trigger the expression of downstream secondary sRNAs. Two subpopulations of 26G-RNAs exist, each of which displaying strongly compartmentalized expression: one is expressed in the spermatogenic gonad and associates with the Argonautes ALG-3/4; plus another expressed in oocytes and in embryos, which associates with the Argonaute ERGO-1. The determinants and dynamics of gene silencing elicited by 26G-RNAs are largely unknown. Here, we provide diverse new insights into these endogenous sRNA pathways of C. elegans. Using genetics and deep sequencing, we dissect a maternal effect of the ERGO-1 branch sRNA pathway. We find that maternal primary sRNAs can trigger the production of zygotic secondary sRNAs that are able to silence targets, even in the absence of zygotic primary triggers. Thus, the interaction of maternal and zygotic sRNA populations, assures target gene silencing throughout animal development. Furthermore, we find that sRNA abundance, the pattern of origin of sRNA and 3 UTR length are predictors of the regulatory outcome by the Argonautes ALG-3/4. Lastly, we discovered that ALG-3- and ALG-4-bound 26G-RNAs are dampening the expression of their own mRNAs, revealing a negative feedback loop. Altogether, we provide several new regulatory insights on the dynamics, target regulation and self-regulation of the endogenous RNAi pathways of C. elegans.\n\nAuthor SummarySmall RNAs (sRNAs) and their partner Argonaute proteins regulate the expression of target RNAs. When sperm and egg meet upon fertilization, a diverse set of proteins and RNA, including sRNA-Argonaute complexes, is passed on to the developing progeny. Thus, these two players are important to initiate specific gene expression programs in the next generation. The nematode Caenorhabditis elegans expresses several classes of sRNAs. 26G-RNAs are a particular class of sRNAs that are divided into two subpopulations: one expressed in the spermatogenic gonad and another expressed in oocytes and in embryos. In this work, we describe the dynamics whereby oogenic 26G-RNAs setup gene silencing in the next generation. We also show several ways that spermatogenic 26G-RNAs and their partner Argonautes, ALG-3 and ALG-4, use to regulate their targets. Finally, we show that ALG-3 and ALG-4 are fine-tuning their own expression, a rare role of Argonaute proteins. Overall, we provide new insights into how sRNAs and Argonautes are regulating gene expression.

molecular biology↗

bioRxiv2018

Strongyloides stercoralis: spatial distribution of a highly prevalent and ubiquitous soil-transmitted helminth in Cambodia

BackgroundStrongyloides stercoralis is a neglected soil-transmitted helminth that occurs worldwide and can cause long-lasting and potentially fatal infections due to its ability to replicate within its host. S. stercoralis causes gastrointestinal and dermatological morbidity. The objective of this study was to assess the S. stercoralis infection risk, and using geostatistical models, to predict its geographical distribution in Cambodia.\n\nMethodology / Principal FindingsA nation-wide community-based parasitological survey was conducted among the population aged 6 years and above. S. stercoralis was diagnosed using a serological diagnostic test detecting antigens in urine. Data on demography, hygiene and knowledge about helminth infection were collected. S. stercoralis prevalence among 7,246 participants with complete data record was 30.5% and ranged across provinces between 10.9% and 48.2%. The parasite was ubiquitous in Cambodia, with prevalence rates below 20% only in five south-eastern provinces. Infection risk increased with age both in men and women although girls aged less than 13 years and women aged 50 years and above had lower odds of infection than their male counterparts. Open defecation was associated with higher odds of infection while declaring having some knowledge about health problems caused by worms was protective. Infection risk was positively associated with night maximum temperature, minimum rainfall, and distance to water, and negatively associated with land occupied by rice fields.\n\nConclusions / SignificanceS. stercoralis infection is ubiquitous and rampant in Cambodia. The parasite needs to be addressed by control programs delivering ivermectin. However the high cost of this drug in Cambodia currently precludes control implementation. Donations, subsidization or the production of affordable generic production are needed so S. stercoralis, which infests almost a third of the Cambodian population, can be addressed by an adequate control program.\n\nAuthors SummaryThe threadworm, Strongyloides stercoralis, is a most neglected worm infection transmitted through infective larvae on the soil. Threadworms occur worldwide and particularly in tropical climates. It may cause long-lasting and potentially fatal infections due to its ability to replicate within its host. This study aimed to assess the risk of threadworm infection in at the national level in Cambodia.\n\nWe conducted a nation-wide community-based parasitological survey among the population aged 6 years and above. The threadworm was diagnosed using a serological diagnostic test detecting antigens in urine. Data on demography, hygiene and knowledge about helminth infection were collected. The threadworm infection risk was calculated by using geostatistical models to predict its geographical distribution in Cambodia. About one third (30.5%) of the enrolled study participants (n=7,246) were infected with threadworms. The lowest and hightest infection rates a province level was 10.9% and 48.2%, respectively. Prevalence rates below 20% were found only in five south-eastern provinces. The risk of an infection with threadworms increased with age in men and women. Open defecation was associated with higher risk of infection while declaring having some knowledge about health problems caused by worms was protective. Furthermore, the threadworm infection risk was positively associated with environmental factors such as night maximum temperature, minimum rainfall, and distance to water, and negatively associated with land occupied by rice fields.\n\nThreadworm infection is highly prevalent in Cambodia and adequate control measures are warranted, including access to treatment, in order to address the burden of this NTD in Cambodia.

epidemiology↗

bioRxiv2018

Universal antibiotic tolerance arising from antibiotic-triggered accumulation of redox metabolites

Pseudomonas aeruginosa is an opportunistic pathogen that often infects open wounds or patients with cystic fibrosis. Once established, P. aeruginosa infections are notoriously difficult to eradicate. This difficulty is in part due to the ability of P. aeruginosa to tolerate antibiotic treatment at the individual-cell level or through collective behaviors. Here we describe a new mechanism by which P. aeruginosa tolerates antibiotic treatment by modulating its global cellular metabolism. In particular, treatment of P. aeruginosa with sublethal concentrations of antibiotics covering all major classes promoted accumulation of the redox-sensitive phenazine - pyocyanin (PYO). PYO in turn conferred general tolerance against diverse antibiotics for both P. aeruginosa and other Gram-negative and Gram-positive bacteria. We show that PYO promotes energy generation to enhance the activity of efflux pumps, leading to enhanced antibiotic tolerance. This property is shared by other redox-active phenazines produced by P. aeruginosa. Our discovery sheds new insights into the physiological functions of phenazines and has implications for designing effective antibiotic treatment protocols.\n\nAuthor SummaryAntibiotic tolerance can facilitate the evolution of resistance, and here we describe a previously unknown mechanism of collective antibiotic tolerance in Pseudomonas aeruginosa. In particular, P. aeruginosa treated with sublethal concentrations of antibiotics covering all major classes promotes accumulation of pyocyanin (PYO), an important virulence factor. In turn, PYO confers general tolerance against diverse antibiotics for both P. aeruginosa and other bacteria. Our discovery is a perfect example of what Nietzsche once said: That which does not kill me makes me stronger.

microbiology↗

bioRxiv2018

The Ca2+-activated Cl- current ensures robust and reliable signal amplification in vertebrate olfactory receptor neurons

Activation of most primary sensory neurons results in transduction currents that are carried by cations. One notable exception is the vertebrate olfactory receptor neuron (ORN), where the transduction current is carried largely by the anion Cl-. However, it remains unclear why ORNs use an anionic current for signal amplification. We have sought to provide clarification on this topic by studying the so far neglected dynamics of Na+, Ca2+, K+ and Cl- in the small space of olfactory cilia during an odorant response. Using computational modeling and simulations we compared the outcomes of signal amplification based on either Cl- or Na+ currents. We found that amplification produced by Na+ influx instead of a Cl- efflux is problematic due to several reasons: First, the Na+ current amplitude varies greatly depending on mucosal ion concentration changes. Second, a Na+ current leads to a large increase in the ciliary Na+ concentration during an odorant response. This increase inhibits and even reverses Ca2+ clearance by Na+/Ca2+/K+ exchange, which is essential for response termination. Finally, a Na+ current increases the ciliary osmotic pressure, which could cause swelling to damage the cilia. By contrast, a transduction pathway based on Cl- efflux circumvents these problems and renders the odorant response robust and reliable.

neuroscience↗

bioRxiv2018

Genetic distance and social compatibility in the aggregation behavior of Japanese toad tadpoles

From microorganism to vertebrates, living things often exhibit social aggregation. One of anuran larvae, dark-bodied toad tadpoles (genus Bufo) are known to aggregate against predators. When individuals share genes from a common ancestor for whom social aggregation was a functional trait, they are also likely to share common recognition cues regarding association preferences, while greater genetic distances make cohesive aggregation difficult. In this study, we conducted quantitative analyses to examine aggregation behavior among three lineages of toad tadpoles: Bufo japonicus japonicus, B. japonicus formosus, and B. gargarizans miyakonis. To determine whether there is a correlation between cohesiveness and genetic similarity among group members, we conducted an aggregation test using 42 cohorts consisting of combinations drawn from a laboratory-reared set belonging to distinct clutches. As genetic indices, we used mitochondrial DNA (mtDNA) and major histocompatibility complex (MHC) class II alleles. The results clearly indicated that aggregation behavior in toad tadpoles is directly influenced by genetic distances based on mtDNA sequences and not on MHC haplotypes. Cohesiveness among heterogeneous tadpoles is negatively correlated with the geographic dispersal of groups. Our findings suggest that social incompatibility among toad tadpoles reflects phylogenetic relationships.

animal behavior and cognition↗

bioRxiv2018

A new method for enamel amino acid racemization dating: a closed system approach

Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables age estimation over the Quaternary. We postulate that enamel is a suitable biomineral for the long-term survival of endogenous amino acids. Analysis of multiple amino acids for geochronological studies is typically achieved using a RP-HPLC method. However, the low concentrations of amino acids coupled with high concentrations of inorganic species make accurate determination of amino concentrations challenging. We have developed a method for the routine preparation of multiple enamel samples using biphasic separation. Furthermore, we have shown that amino acids that exhibit effectively closed system behaviour can be isolated from enamel through an exposure time of 72 h to bleach. Elevated temperature experiments investigating the processes of intra-crystalline protein degradation (IcPD) do not appear to match the patterns from fossil samples, reinforcing the need for a comprehensive understanding of the underlying mechanisms of protein degradation. This novel preparative method isolates intra-crystalline amino acids suitable for the development of mammalian geochronologies based on enamel protein degradation. The lower rates of racemisation in enamel (cf. Bithynia opercula) suggest that the enamel AAR may be able to be used as a relative dating technique over time scales > 2.8 Ma. Enamel AAR has the potential to estimate the age of mammalian remains past the limit of all other current direct dating methods, providing an invaluable tool for geochronological studies.

paleontology↗

bioRxiv2018

The Sicilian wolf: genetic identity of a recently extinct insular population

During historical times many local grey wolf (Canis lupus) populations underwent a substantial reduction of their sizes or became extinct. Among these, the wolf population once living in Sicily, the biggest island of the Mediterranean Sea, was completely eradicated by human persecution in the early decades of the XX century.\n\nIn order to understand the genetic identity of the Sicilian wolf, we applied ancient DNA techniques to analyse the mitochondrial DNA of six specimens actually stored in Italian museums.\n\nWe successfully amplified a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Results showed that two samples shared the same haplotype, that differed by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a wolf-like haplotype never described before and the fourth a haplotype commonly found in dogs.\n\nFurthermore, all the wolf haplotypes detected in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations.\n\nUnfortunately, this endemic island population, bearing unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.

genetics↗