Miracle-dz/UniFAR-FTUs huggingface dataset:
A biological source of marine sedimentary iron oxides

The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although reductive biological processes that bridge the iron cycle to other element cycles are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments—resulting in the formation of iron oxides. Here, we show that a major source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, stimulated by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments and would equate to an annual production of approximately 7.9 x 1015 grams of sedimentary iron oxides—twenty-five times larger than the annual flux of iron oxides by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments given their low numerical abundance; yet exert a profound impact via the production of iron oxides.
Genome-wide association analysis of 350 000 Caucasians from the UK Biobank identifies novel loci for asthma, hay fever and eczema.

Even though heritability estimates suggest that the risk of asthma, hay fever and eczema is largely due to genetic factors, previous studies have not explained a large part of the genetics behind these diseases. In this genome-wide association study, we include 346 545 Caucasians from the UK Biobank to identify novel loci for asthma, hay fever and eczema and replicate novel loci in three independent cohorts. We further investigate if associated lead single nucleotide polymorphisms (SNPs) have a significantly larger effect for one disease compared to the other diseases, to highlight possible disease-specific effects. We identified 141 loci, of which 41 are novel, to be associated (P ≤ 3 × 10-8) with asthma, hay fever or eczema, analyzed separately or as disease phenotypes that includes the presence of different combinations of these diseases. The largest number of loci was associated with the combined phenotype (asthma/hay fever/eczema). However, as many as 20 loci had a significantly larger effect on hay fever/eczema only compared to their effects on asthma, while 26 loci exhibited larger effects on asthma compared with their effects on hay fever/eczema. At four of the novel loci, TNFRSF8, MYRF, TSPAN8, and BHMG1, the lead SNPs were in Linkage Disequilibrium (LD) (>0.8) with potentially casual missense variants. Our study shows that a large amount of the genetic contribution is shared between the diseases. Nonetheless, a number of SNPs have a significantly larger effect on one of the phenotypes, suggesting that part of the genetic contribution is more phenotype specific.
The effect of roads on spider monkeys’ home range and mobility in a heterogeneous regenerating forest

Arboreal fauna living in tropical ecosystems may be particularly affected by roads given their dependency on forest cover and the high vulnerability of such ecosystems to changes. Over a period of 4 yr, we followed subgroups of spider monkeys living in a regenerating dry tropical forest with 8.2 km of roads within their home range. We aimed to understand whether roads shaped the home range of spider monkeys and which road features affected their movement. Only 18 percent (3 km) of the spider monkeys’ home range perimeter bordered with roads; these roads had greater habitat disparity between road sides than roads inside the home range. Although monkeys were reluctant to be close to roads, and roadside habitat contained low proportions of mature forest, spider monkeys crossed roads at 69 locations (7.5 crossings per kilometer). The main road characteristic affecting crossings was canopy opening size, with greater probability of crossing where canopy openings were smaller. Our findings support the importance of canopy opening size for road crossing of arboreal taxa, but they also indicate the relevant role roadside forest structure may have. Minimizing canopy opening size and forest disturbance along roads can facilitate the movement of arboreal fauna and preserve the important role of spider monkeys and other arboreal taxa in seed dispersal and thus the maintenance and regeneration of forest diversity.
Potential Use of Umbilical Cord Blood Cells in Spinal Cord Injury

Spinal cord injury (SCI) pathophysiology occurs as a primary traumatic event followed by secondary injury, resulting in the loss of neurons, oligodendrocytes and demyelination of residual axons. Unfortunately, endogenous spontaneous regeneration of oligodendrocytes is minimal. Previously, a method to generate multi-potential stem cells (MPSC) from umbilical cord blood (UCB) has been reported using lineage negative cells (Lin neg ) grown in fibroblast growth factor 4 (FGF4), stem cell factor (SCF) and fms-like tyrosine kinase receptor-3 ligand (Flt-3l) supplemented serum free medium. These MPSC have the ability to differentiate into bone, muscle and endothelial cells. In this thesis, the ability of MPSC to differentiate into oligodendrocytes was investigated as a potential treatment for SCI. Culturing MPSC under conditions that mimic normal timing of oligodendrocyte differentiation resulted in cells that expressed oligodendrocyte markers in vitro and were morphologically similar to them. I next investigated the ability of MPSC to improve functional recovery in a SCI compression injury model. Although the cells did not differentiate into oligodendrocytes in vivo as we initially hypothesised, a modest but significant improvement in hindlimb function was observed. A cytokine assay revealed that MPSC secrete elevated levels of anti-inflammatory, angiogenic and neurotrophic factors, possibly contributing to indirect mechanisms of repair by reducing iii secondary injury. Shiverer mouse neonates were next used as an alternative non-injury model to investigate the differentiation potential of MPSC. We hypothesised that transplanting MPSC into a host with an immature immune system and an actively myelinating environment would lead to engraftment and differentiation into oligodendrocytes. However no MPSC that differentiated into oligodendrocytes could be detected. Altogether, our in vitro data adds support for the reprogramming of cells, with further studies needed to test the functionality of resulting oligodendrocyte-like cells. Although MPSC failed to differentiate in both in vivo models, several potential therapeutic targets to treat SCI were found.
Unreported catch and tourist demand on local fisheries of small island states: the case of The Bahamas, 1950-2010.

The views and opinions expressed or implied in this article are those of the author (or authors) and do not necessarily reflect the position of the National Marine Fisheries Service, NOAA. Abstract—Tourism is vital to the economy of small island states like The Bahamas and is closely linked to fisheries. Fish is a protein source for tourists and residents, and both groups expect to catch and eat local fish. To adequately manage these dual demands, we need to know total removals of fish, as well as patterns of demand by tourists and residents in the past and present. Using a reconstruction approach, we performed a comprehensive accounting of fisheries catches in The Bahamas from commercial and noncommercial sectors for 1950–2010 and estimated the demand from tourism over the same period. Our results distinctly contrast with national data supplied to the Food and Agriculture Organization of the United Nations (FAO), which presents only commercial landings. Reconstructed total catches (i.e., reported catches and estimates of unreported catches) were 2.6 times the landings presented by the FAO for The Bahamas. This discrepancy was primarily due to unreported catches from the recreational and subsistence fisheries in the FAO data. We found that recreational fishing accounted for 55% of reconstructed total catches. Furthermore, 75% of reconstructed total catches were attributable to tourist demand on fisheries. Incomplete accounting for catches attributed to the tourist industry, therefore, makes it difficult to track potentially unsustainable pressures on fisheries resources. Tourism is one of the largest and fastest growing industries globally (UNWTO, 2014a), and is vital to many small island developing states in which it can account for more than one-quarter of gross domestic product (GDP) (UNWTO, 2014b). In addition to its influence on island economies, tourism can have large effects on the extraction of natural resources like fisheries, particularly in the Caribbean, where visitors can greatly outnumber resident populations (Table 1, Fig. 1). Tourism, through recreational fishing and the consumption of local seafood by tourists, increases the demand on local fisheries. Consider the case of the Commonwealth of The Bahamas, a nation of small islands, for which tourism is the primary industry, which accounted for 51% of GDP in 2003 (Sacks1). Located in the northern Caribbean east of Florida and northeast of Cuba,
A New Suite of Pathogenesis-Induced Gene Expression Markers in Arabidopsis thaliana

Plant immunity comprises of two main branches. In one branch, plants recognize microbial molecules called pathogen-associated molecular patterns (PAMPs); inducing PAMP-triggered immunity (PTI). Successful pathogens suppress PTI using effector proteins. These effectors can be recognized by the plant causing effector-triggered immunity (ETI); causing cell death to prevent further infection. Pathogenesis-Related genes are markers of pathogen infection but do not distinguish between PTI, ETI or susceptibility. Using available transcriptomic data for the interaction between Arabidopsis thaliana and Pseudomonas syringae, I identified 2 genes induced during a susceptible interaction, 1 gene induced by ETI and 4 genes induced by PTI. These genes characterized using protein interaction data from the Proteomics Standards Initiative Common QUery InterfaCe using the BAR’s interactive database; the Arabidopsis Interactions Viewer. This analysis produced networks of protein interactions
High contrast staining for serial block face scanning electron microscopy without uranyl acetate

Serial block face scanning electron microscopy (SBFSEM) is an increasingly popular method for investigating the three-dimensional ultrastructure of large biological samples. Prior to imaging, samples are typically chemically fixed, stained with osmium and uranyl acetate, and subsequently embedded in resin. The purpose of staining is to provide image contrast and reduce specimen charging under the electron beam, which is detrimental to the quality of imaging. Obtaining, using, and disposing of uranyl acetate is getting increasingly cumbersome in many countries due to new regulations on the handling of radioactive substances. Therefore, we developed an alternative staining procedure that does not rely on the use of uranium or any other radioactive substance. This procedure provides excellent contrast and efficiently reduces specimen charging.
Population Genetic Structure of Pacific White Shrimp (Litopenaeus vannamei) from Mexico to Panama

Genetic variation and population structure of wild white shrimp (Litopenaeus vannamei) from 4 geographic locations from Mexico to Panama were investigated using 5 microsatellite DNA loci. The genetic diversity between populations was indicated by the mean number of alleles per locus and mean observed heterozygosity, which ranged from 7.4 to 8.6 and from 0.241 to 0.388, respectively. Significant departures from Hardy-Weinberg equilibrium were found at most locations at each locus, with the exception Guatemala at Pvan0013, and were caused by high heterozygote deficiencies. Genetic differences between localities were detected by pairwise comparison based on allelic and genotypic frequencies, with the exception of locus Pvan1003. Significant pairwise FST values between locations and total FST showed that the white shrimp population is structured into subpopulations. However, population differentiation does not follow an isola- tion-by-distance model. Knowledge of the genetic diversity and structure of L.vannamei populations will be of interest for aquaculture and fisheries management to utilize and preserve aquatic biodiversity.
Valvular Heart Disease-Related Feed-Forward Loop Network Reveals Some Biological Features for Disease Development

This study is to uncover VHD-related important biological features for understanding molecular of this disease. The system analysis strategy is applied to generate the first VHD-related FFL network. Then, the network topology is mapped into the biological space to refine the biological features of VHD. 4 miRNA, 4 TF and 34 gene hubs are identified and confirmed to play important roles in the occurrence and development of VHD. The signal pathways mediated by miRNA hubs are also predicted, where the processes that MAPK pathway mediated by has-let-7c induces VHD are explained. This study provides some new computational evidences for the understanding of VHD molecular mechanism, and also has important implications in terms of improving current therapeutic strategies of VHD. Introduction The miRNAs, TFs and genes interact to form a network system, in which miRNAs and TFs are major regulators and they are closely linked to regulate common target genes and to participate in many important biological processes, including cell proliferation, differentiation, apoptosis, etc. Many complex diseases are associated with disorders of TFs and miRNAs [1], which will cause that the biological regulatory system of an organism appears to adjust abnormal, the internal homeostasis of system is broken and the symptoms of the disease in vitro are shown. So far, a lot of efforts have been made to construct the regulatory network associated with an objective disease based on interaction relationships among miRNA, TF and their target genes, such as the ovarian cancer [2], the glioblastoma multiforme [3], the osteosarcomas [4], etc. The existing studies showed that: (i) the analysis of complex diseases can benefit from systems biological approaches; (ii) FFLs are conservative and have basic biological functions in the complex regulatory relationships among miRNAs, TFs and genes, meanwhile it can be used as a basic unit to construct a regulatory network. VHD is the function or structural abnormality of one or more valve structures due to 90 This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/). Copyright © 2017, the Authors. Published by Atlantis Press. 2nd International Conference on Biomedical and Biological Engineering 2017 (BBE 2017) Advances in Biological Sciences Research (ABSR), volume 4
Impact of fishing activities on different coralligenous assemblages of Gulf of Naples (Italy)

Coralligenous bioconstructions are among the most important Mediterranean habitats for biodiversity maintenance. However some characteristic and sensitive organisms, such as the fan corals, are considered endangered in the international community; indeed, they may be severely damaged by fishing activities causing mechanical damage and increasing sedimentation rate. ROV (Remotely Operated Vehicle) investigations were carried out in order to characterize different morphological types of coralligenous habitat (rim, bank and shoal) located in the southern Bay of Naples (Italy), and to assess the presence of lost fishing gears and their impact on these benthic communities. A rapid classification of different fishing pressures and impacts was obtained through the development of new, representative and synthetic categories. Image analysis revealed the presence of rich and diversified communities, characterized by several fan coral colonies. However, fishing activity dramatically affects these coralligenous habitats, entangling and covering benthic assemblages and leading to necrosis and to parasitic epibionts growth especially on branched organisms. Monitoring programmes may provide a detailed assessment of coralligenous habitats characterization, distribution and health status. An accurate evaluation of fishing pressure and impact may be considered a useful tool to improve sustainable management of these valuable habitats.
Genealogical Properties of Subsamples in Highly Fecund Populations

We consider some genealogical properties of nested samples. The complete sample is assumed to have been drawn from a natural population characterised by high fecundity and sweepstakes reproduction (abbreviated HFSR). The random gene genealogies of the samples are—due to our assumption of HFSR—modelled by coalescent processes which admit multiple mergers of ancestral lineages looking back in time. Among the genealogical properties we consider are the probability that the most recent common ancestor is shared between the complete sample and the subsample nested within the complete sample; we also compare the lengths of ‘internal’ branches of nested genealogies between different coalescent processes. The results indicate how ‘informative’ a subsample is about the properties of the larger complete sample, how much information is gained by increasing the sample size, and how the ‘informativeness’ of the subsample varies between different coalescent processes.
Molecular characterization of duck (Anas platyrynhos) Toll-like receptors, mRNA expressions profile in day-old duckling’s tissues and cytokine response to in vitro TLR agonsists stimulation

TLR repertoire of duck, profiling of their mRNA expression in a range of duckling tissues and cytokine gene expressions upon TLR agonists stimulation in in vitro assay have been investigated. All ten TLR genes orthologous to chicken TLR repertoire were found in duck. Duck TLR genes showed 77-83% similarity at amino acid level to their chicken counterparts. All ten TLRs-TLR1LA, 1LB, 2A, 2B, 3, 4, 5, 7, 15 and 21 mRNA expressions were significantly higher in bursa than other tissues studied, whereas in muscle all TLRs mRNA expressions were significantly lower except for TLR15 (P<0.01). TLR7 gene expression was significantly higher in spleen, bursa and also in lung tissues (P<0.01). The cytokine gene expression levels in duck PBMCs upon LPS and poly I:C stimulation have been quantified. IL-1g gene expression level in LPS stimulated duck PBMC culture was significantly higher at both 12 h and 24 h time intervals (P<0.05). However, there were no significant changes in IFN-a gene expression levels in poly I:C stimulated duck PBMC culture at both the intervals. TLR gene expression in young ducklings together with cytokine response upon LPS stimulation demonstrates the innate preparedness of younger birds to encounter pathogens and their functional ability to respond to their ligands.
The Role of Bacterial Products and Intestinal Microbiota in Non-Alcoholic Fatty Liver Disease

Non-alcoholic fatty liver disease (NAFLD) includes simple steatosis (SS) and non-alcoholic steatohepatitis (NASH), which can progress to cirrhosis. NAFLD pathogenesis is complex. Recent research suggests a role for the intestinal microbiota (IM) with various potential mechanisms involving bacterial metabolism and products. This cross-sectional study compared bacterial products and metabolites in the blood and feces, and fecal levels of total bacteria, Bacteroidetes, C. coccoides, C. leptum, Bifidobacteria, Lactobacilli, E. coli and Archaea in biopsy confirmed SS, NASH, and healthy controls (HC). NAFLD patients (SS+NASH) had higher levels of bacterial fecal metabolites, including choline, trimethylamine, total short-chain fatty acids, propionate, isobutyric acid, and higher serum 2-hydroxybutyrate than HC. NASH patients had lower proportions of fecal C. leptum and higher amounts of E. coli than HC. Several bacterial metabolites correlated with histological findings, and with specific bacteria and diet. These findings suggest a potential role for bacteria and bacterial metabolism in NAFLD
Population and Evolutionary Genetics Subfamily-specific functionalization of diversified immune receptors in wild barley

Gene-for-gene immunity between plants and host-adapted pathogens is often linked to population-level diversification of immune receptors encoded by disease resistance (R) genes. The complex barley (Hordeum vulgare L.) R gene locus Mildew Locus A (Mla) provides isolate-specific resistance against the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) and has been introgressed into modern barley cultivars from diverse germplasms, including the wild relative H. spontaneum. Known Mla disease resistance specificities to Bgh appear to encode allelic variants of the R Gene Homolog 1 (RGH1) family of nucleotide-binding domain and leucine-rich repeat (NLR) proteins. To gain insights into Mla diversity in wild barley populations, we here sequenced and assembled the transcriptomes of 50 accessions of H. spontaneum representing nine populations distributed throughout the Fertile Crescent. The assembled Mla transcripts exhibited rich sequence diversity, which is linked neither to geographic origin nor population structure. Mla transcripts in the tested H. spontaneum accessions could be grouped into two similar-sized subfamilies based on two major N-terminal coiled-coil signaling domains that are both capable of eliciting cell death. The presence of positively selected sites, located mainly in the C-terminal leucine-rich repeats of both MLA subfamilies, together with the fact that both coiled-coil signaling domains mediate cell death, implies that the two subfamilies are actively maintained in the host population. Unexpectedly, known MLA receptor variants that confer Bgh resistance belong exclusively to one subfamily. Thus, signaling domain divergence, potentially to distinct pathogen populations, is an evolutionary signature of functional diversification of an immune receptor.
The production and fate of picoplankton and protozoa in the pelagic food web of Napoleon Gulf, Lake Victoria, East Africa

The importance of the microbial food web and how it interplays with the classical food chain has gained considerable attention in temperate lakes. However its role in carbon transfer from picoand nanoplankton to zooplankton and planktivores is relatively unknown in tropical lakes. Sampling of the microbial food web and experiments to estimate the growth rate and fate of its components were performed in Lake Victoria, East Africa, during the mixing season (May to August) 2002. Bacterioplankton and ciliate densities in Napoleon Gulf ranged from 6.2 to 14.9 cells x 106·mL-1 and 51.9 to 75.2 cells·mL-1, respectively. Flagellate abundance was high, ranging from 70.4 to 127.9 cells x 103·mL-1. Small flagellates, tentatively called Choanoflagellida, dominated the flagellate community by abundance and biomass. Bacterial growth rates were low, yet high abundance and cell size resulted in high bacterial production representing 24 to 38% of phytoplankton production. Protozoan growth rates and production are similar to values reported for other African lakes and the Laurentian Great Lakes. Protozoa were the dominant grazers of bacteria with grazing pressure switching from protozoa > 5 μm in June to protozoa < 5 μm (presumably flagellates) in July. In July, grazing on flagellates was from predators < 40 μm, probably ciliates, while the ciliate community was grazed by > 40-μm plankton. Given that plankton of Lake Victoria is dominated by colonial cyanobacteria and raptorial zooplankton, protozoa could be an important pathway in the pelagic food web of Lake Victoria, East Africa.