Miracle-dz/UniFAR-FTUs huggingface dataset:
Current knowledge on Coralliophilidae (Gastropoda) and phylogenetic implication of anatomical and reproductive.

EnglishThe current knowledge about feeding, anatomy, sexual strategy, parental care and protoconch of Coralliophilidae (Gastropoda) is reviewed. A preliminary cladistic analysis is carried out in order to unravel the phylogenetic relationship within Coralliophilidae and among Coralliophilidae and Muricidae. Twenty five characters and 55 character states chiefly relative to the anatomy, reproductive biology and larval development has been used in the analysis. The main result of the analysis is the separation of Coralliophilidae and Muricidae into two independent monophyletic clades, and the division of Coralliophilidae into a primitive clade represented by Coralliophila squamosa, with no known synapomorphies, and a more derived one, which give rise to three evolutionary lines represented by the genera Babelomurex, Coralliophila and Leptoconcus. This latter clade is characterised by the synapomorphy of brood care and by further four potential synapomorphies pertaining to the anatomy of the reproductive system. The internal relationships of Muricidae revealed by the present analysis support other current phylogenetic hypotheses obtained by analysis using anatomical or molecular characters. In condusion, the paper stresses the necessity in deepening in the study of the anatomy and biology of coralliophilids, in particular in the reproductive system and reproductive strategy, since these aspects have been shown to be important in establishing internal relationships of coralliophilids. italianoViene riportata una revisione delle conoscenze attualmente disponibili su strategie alimentari e sessuali, anatomia, cure parentali e protoconche delle Coralliophilidae. Un’analisi cladistica preliminare e condotta col fine di dipanare le relazioni filogenetiche all’interno del gruppo e tra le Coralliophilidae e Muricidae. Sono stati usati nell’analisi venticinque caratteri per 55 stati, principalmente relativi all’anatomia, alla biologia riproduttiva e allo sviluppo larvale. Il risultato principale dell’analisi e la separazione di Coralliophilidae e Muricidae in due linee monofiletiche indipendenti, e la divisione delle Coralliophilidae in una linea primitiva rappresentata da Coralliophila squamosa, ed un clado piu evoluto che ha dato origine a tre linee rappresentate dai generi Babelomurex, Coralliophila e Leptoconcus. Quest’ultimo clado e caratterizzato dalla sinapomorfia dell’incubazione delle capsule ovigere e da ulteriori quattro potenziali sinapomorfie riguardanti l’anatomia dell’apparato riproduttore. Le relazioni interne ai Muricidae rivelate da quest’analisi supportano altre ipotesi filogenetiche correnti derivate da dati anatomici e molecolari. In conclusione, il lavoro evidenzia la necessita di un approfondimento nello studio dell’anatomia e della biologia dei coralliofilidi, in particolare per cio che riguarda l’apparato riproduttore e le strategie riproduttive, in quanto questi aspetti hanno dimostrato la loro importanza nello stabilire le relazioni interne tra i coralliofilidi.
Female mate choice and male ornamentation in the stalk-eyed fly, diasemopsis meigenii

Female mate choice is a crucial driver of sexual selection, leading to the evolution of the diverse male sexual ornaments seen in nature. Yet little is known about the factors that cause variation in different components of female preference, or how these components interact to influence the series of choices that exert selection on male ornaments. Likewise, it is not known how the signals of genetic condition revealed by male ornaments, or reproductive capacity, vary across environments. But this variation is important for both the direct and indirect genetic benefits of female mate choice, as well as for the male-driven effects of reproductive investment on ejaculate allocation and sexual selection. Here, I use the sexually dimorphic African stalk-eyed fly species Diasemopsis meigenii to conduct empirical studies to address these issues. First, I manipulate female mating status (virgin versus mated) and use mathematical and statistical techniques to decompose mate choices made in a repeated sequential no-choice design into estimates of preference, and selection on the male ornament. I show that choosiness and selection, but not the preference function, are elevated in mated females. Second, I use larval diet manipulation and a series of crosses within and between a suite of inbred lines to investigate the across-environmental genetic condition dependence of male sexual ornaments relative to nonsexual traits. I find evidence for the heightened condition dependence of the male sexual trait (male eyespan), and for a novel gene-by-environment interaction in which the effects of genetic stress on sexual trait expression are masked in both high and low but not intermediate environments. Finally, I measure the effects of environmental (E) and genetic (G) stress on reproductive, fertility and attractiveness traits, and find evidence for a qualitative alignment of trait responses (all tend to be positive), but a negative integration across traits (traits that respond most to E respond least to G). The results have important implications for the operation of sexual selection in nature.
The effect of introduced Pseudomonas fluorescens strains on nitrogen dynamics in the rhizosphere of crop plants.

The primary aim of this study was to investigate the effects of seed inoculation with the biocontrol agent Pseudomonas fluorescens strain F113 (producing the antibiotic DAPG) and its modified derivative strain F113G22 (with DAPG production disrupted) on the uptake of nitrogen by pea and wheat plants. Uptake of N by the two plant species was investigated in soil microcosms amended with 15N-labelled fertilisers (urea or ammonium nitrate) or 15N-labelled plant residues. Uptake of fertiliser-N was unaffected by inoculation. However, uptake of N derived from organic residues was enhanced in pea inoculated with either strain. In contrast, uptake of N by wheat was reduced in the presence of either strain F113 or F113G22, suggesting that the effects of these microbial inocula on N-mineralisation in the rhizosphere were dependent on plant species. It was subsequently found that microfaunal populations, especially soil nematodes in the rhizosphere of inoculated pea were significantly larger than those associated with the rhizosphere of non-inoculated controls. In wheat, however, microfaunal populations in the rhizosphere of inoculated plants were lower than those associated with noninoculated controls. These trends were repeated using simple sand microcosms into which soil bacteria and the bacterial-feeding nematode Caenorhabditis elegans were introduced. This suggested that effects on N-mineralisation were mediated by changes in populations of microbial-feeding microfauna. As a possible explanation for the increased nematode populations in the rhizosphere of inoculated pea plants, the nematicidal effects of pea seed exudates on C. elegans were investigated in small-scale sand systems. It was found that exposure to non-inoculated pea seeds reduced the short-term survival of C. elegans as compared to unamended sand, and that survival was greater in the presence of pea seeds inoculated with either strain than non-inoculated seeds, suggesting that nematicidal compounds released by germinating pea seeds were utilised by the P.fluorescens strains. No such effects were observed for wheat.
Determination of Keystone Species that Influences the Diversity of Birds Species in the Land of Reclamation and Revegetation of Post-Coal Mining

Restoration of biodiversity is one of the successful assessments in the ecological restoration efforts on reclamation and revegetation land. The objective of this study is to determine the relationship between fauna diversity and role of vegetation as a producer. The selected fauna included bird species and the selected vegetation included the fast growing plant of revegetation as well as the lower vegetation growing among the staple crops. The analysis used was DCCA for sub-factor of bird species, shrub species and vegetation role clusters as fauna food producers. The result of the analysis shows that the highest Index Shannon in H 4 ( Sengon-rambutan ) habitat and in H9 habitat (Oil Palm) is 2.33, while the lowest index is in H 1 that is only one bird species. The species richness from the lowest to the highest is in H 1 ( Akasia-plantan [-]), H 10 ( Ponds [0.6]), H 5 ( Trembesi-johar [0.86]), H 6 ( Karamunting-shrubs [0.95]), H11 (Fern-Rice [1.36]), H7 ( Sengon-karamunting [1.85]), H 2 ( Akasia-karamunting [1.94]), H 8 (Rubber [2.01]), H 9 (Oil Palm [ 2.30]), and H 4 (Sengon-rambutan [2.33]). H 6 and H 11 have a better visible kind of richness than the P3 & P8 factors. H 5 is more closely influenced by P 2 factor. H 2 , H 7 and H 9 are strongly influenced by P 6 and P 7 , H 8 and H 3 are strongly influenced by P 4 and are weakly affected by P 2 and P 1 . H 4 is strongly influenced by P 1 and less influenced by P 4 .
Analysis and engineering of biomolecules and microorganisms: from genome-scale study of pathogens to programming of DNA and cells

This thesis is consisted of three major but different parts with the general aims of systems level evaluation and engineering of biomolecules and biological systems. In the first part of this thesis, comparative genomic studies of mutans streptococci strains, which are involved in the development of dental caries, were performed for better understanding their pathogenicity at the level of systems biology. A mosaic-like structure of genome arrangement was revealed by genome alignment analysis. Genes related to pathogenicity were found to have high variations among the strains, whereas genes for oxidative stress resistance are well conserved, indicating the importance of this trait in the dental biofilm community. Genome-scale metabolic network analysis revealed significant differences in 42 pathways. A striking dissimilarity is the unique presence of two lactate oxidases in S. sobrinus DSM 20742, probably indicating an unusual capability of this strain in producing H2O2 and expanding its ecological niche. In addition, lactate oxidases may form a unique energy-producing pathway with other enzymes in S. sobrinus DSM 20742 that can remedy its deficiency in citrate utilization pathway. An "open" pan-genome was inferred by pan-genome analysis using 67 S. mutans genomes currently available including the strains sequenced in this study. An online regulation database for S. mutans, named StrepReg, was constructed by integrating a transcription factor-based gene regulatory network, which was derived from time-series transcriptome analysis, with STRING protein-protein interaction information and KEGG pathway information (http://biosystem.bt1.tu-harburg.de:1555/homes/). Although systems biology is a powerful tool in understanding the system level behaviors of biological systems, the establishment of predictive, multiscale models in systems biology is still a challenge due to the complexity of biological systems. For the same reason, mathematical models often fail in applications under physiological conditions, such as for identification of targets in metabolic engineering for the development of highly production strains. In the second part of this thesis, a novel multiple input-output (I/O) system was therefore proposed and verified, which allows the identification of limiting bioreactions or key enzymes in metabolic pathways and even the optimization of biomolecules in vivo. The basic idea is to design a multiple I/O system which can introduce various genetic manipulations (perturbations) into the cells and record the specific intracellular signal changes
Adherence Assay of Uropathogenic Escherichia coli In Vivo and In Vitro

Purpose: This study aims to investigate the specific pathogenic properties or virulent determinant characteristics of uropathogenic Escherichia coli (UPEC) as bacterial adherence in tissue culture cells in vitro and the pathogenicity in animal model in vivo. Materials and Methods: Thirty strains of E. coli were isolated from urine of patients with acute pyelonephritis. Four cell lines—HeLa cells, HEp-2 cells, A-498 cells, and J-82 cells—were used for bacterial adherence assay. Histologic examination and scanning electron microscopy examination of pyelonephritis or cystitis, which was caused by E. coli, in mice was performed. Results: Sixteen (53.3%) strains of E. coli appeared to adhere to at least one or more kinds of four cell lines, and seven strains were able to adhere to all four cell lines. All of the tested E. coli strains were adhered to the mouse bladder and kidneys. The number of bacteria colonized in the kidney was greater than that of bladders in the following 5 strains of E. coli: TME104, TME107, TME113, TME306, and TME119. There was no difference in the number of bacteria colonized in the bladder and kidneys in the aspects of adherence patterns to tissue culture cells. Conclusions: Although there was no best choice cell lines in the adherence assay to identify the adherence patterns, combined assays of in vitro cell culture and in vivo model of mouse urinary tract infection appeared to be efficient methods to investigate the role of bacterial adherence in the pathogenesis of UPEC.
Adipose-Derived Adult Stem Cells as Trophic Mediators of Tendon Regeneration

The adipose-derived stromal vascular fraction (SVF) is a promising new therapy for equine flexor tendonitis. This heterogeneous population of cells may improve tendon healing via the production of growth and chemotactic factors capable of recruiting endogenous stem cells and increasing extracellular matrix production by tendon fibroblasts (TFBL). The purpose of this study was to evaluate the ability of adipose-derived cells (ADC) culture expanded from the SVF to act as trophic mediators in vitro. We hypothesized that ADCs would produce growth and chemotactic factors important in tendon healing and capable of inducing cell migration and matrix protein gene expression. Superficial digital flexor tendons and adipose tissue were harvested from eight adult horses and processed to obtain SVF cells, ADCs and TFBLs. Adipose-derived cells and TFBLs were grown in monolayer culture for growth factor quantification, to produce conditioned media for microchemotaxis, and in co-culture for quantification of matrix protein gene expression by TFBLs. Growth factor gene expression by SVF cells was significantly greater than in ADCs or TFBLs. Co-culture of TFBLs and ADCs resulted in modest up-regulation of matrix protein expression (collagen types I and III, decorin, and cartilage oligomeric matrix protein) by TFBLs. Media conditioned by ADCs induced ADC migration in a dose dependent manner. These findings support the role of both SVF and ADCs as trophic mediators in tendon regeneration. The differences detected in gene expression between SVF cells and ADCs indicate that additional studies are needed to evaluate the changes that occur during culture of these cells.
Effects of bamboo charcoal powder including vinegar supplementation on performance, eggshell quality, alterations of intestinal villi and intestinal pathogenic bacteria populations of aged laying hens

Abstract This study examined the supplementation level effects of bamboo charcoal powder including vinegar (BCV) on performance, eggshell quality, alterations of intestinal villi and intestinal pathogenic bacteria populations, in aged laying hens. A total of 200 laying hens (60 weeks of age) were randomly allotted into four treatment groups, with five replicates per treatment and 10 hens per replicate. Hens were fed a basal diet, supplemented with BCV at 0, 0.5, 1.0 or 1.5% level, ad libitum for 12 weeks. Egg production, egg weight, egg mass, feed intake and feed efficiency were not affected by the dietary treatment (p > .05). Damaged egg rate decreased in the hens fed the 1.0 and 1.5% BCV diets during the late feeding stage (69 to 72 weeks of age), and eggshell thickness increased in the 1.5% BCV group (p < .05). In the ileal content, population of Escherichia coli decreased with BCV in the diet, while colony counts of Salmonella spp. were comparatively low with 1.0 and 1.5% BCV (p < .01). Villus height and villus area of duodenum were higher in hens fed with 1.0 and 1.5% diets (p < .01), while villus size of jejunum was higher in hens fed with BCV diets (p < .05). The results of this study demonstrate that a level of 1.0% BCV in a layer’s diet is sufficient for decreasing pathogenic bacteria and stimulating intestinal functions; and that dietary supplementation of BCV at 1.5% can improve eggshell thickness in aged laying hens.
On the Evolutionary Significance of the Mantle Margin in Pteriomorphian Bivalves

Abstract: The bivalve mantle margin comprises the free portion of the pallial lobes, and often bears muscular, sensory or secretory structures located on extensions of the mantle, called mantle folds. In the bivalve Infraclass Pteriomorphia, which underwent an extensive adaptive radiation in epifaunal habitats, the mantle margin exhibits an enormous diversity in mantle fold organization and associated structures. The present work reviews the current knowledge of the mantle margin in Pteriomorphia and discusses how the mantle margin can be used as a model for investigating the evolution of the marine epifaunal benthos as many species in this community have undergone similar selective pressures and developed comparable morphological adaptations, such as ciliated tentacular organs. Herein, we stress how additional investigations are necessary to cover the huge diversity seen in this taxonomic group. Given the scarcity of broad comparative studies of bivalves, including Pteriomorphia, the homology of their pallial features is still not clear. Moreover, although it is suspected that mantle margin diversification is correlated with transitions in pteriomorphian life habits, no hypotheses have been tested within a phylogenetic framework. To address these questions requires extensive comparative analyses of mantle margin diversity in Pteriomorphia that focuses on: 1) genetic expression and molecular dynamics in the mantle margin; 2) mantle margin morphogenesis, 3) assessment and test of hypotheses on homology, convergent and parallel evolution of mantle margin characters, and 4) testing possible correlations between mantle margin morphological diversity and lifestyle transitions. In a broader sense, by using Pteriomorphia as a model clade, we will gain insight into the macroecology of the marine epifauna.
Emerging sandfly-borne Phleboviruses in Balkan countries : virus isolation, characterization, evolution and seroepidemiology

Les phlebovirus presentent sont presents dans toutes les regions du globe. Certains phlebovirus transmis par phlebotomes provoquent une maladie febrile et des infections du systeme nerveux central. Depuis, de plus en plus de donnees montrent que la peninsule des Balkans joue un role majeur dans l'emergence de maladies a transmission vectorielle. Au debut de ce travail, on comptait un nombre tres limite de phlebovirus identifies et isoles dans cette region. Une etude integree et transdisciplinaire en vue d'un inventaire des virus circulant dans pays des Balkans. (i) Un total de 3,850 phlebotomes sont ete recueillis dans sept pays des Balkans en 2014 et 2015. Ils ont ete testes pour la presence d'ARN viral et inocule sur des cellules VERO afin d'isoler le virus detecte; (ii) des etudes de seroprevalence utilisant des tests de neutralisation ont ete effectuees sur des echantillons de bovins et de moutons pour evaluer a deux agents pathogenes humains : le virus Toscana (TOSV) et le virus Sandfly fever Sicilian virus (SFSV). Nos resultats se composent de (i) la decouverte et le sequencage de 3 nouveaux phlebovirus appartenant a 2 especes differentes, (ii) la premiere identification du genotype B de TOSV en Croatie, (iii) la preuve de la co-circulation de deux genotypes (B et C) de TOSV, (iv) des taux d'anticorps neutralisants qui sont beaucoup plus eleves chez les bovins et les moutons pour le SFSV que pour TOSV. En conclusion, les resultats obtenus au cours de ce travail demontrent qu’es les Balkans representent une zone de tres importante activite pour les phlebovirus et donc merite une surveillance particuliere a cause du risque d’emergence et de dissemination.
Effects of postharvest methyl jasmonate treatment on aromatic volatile biosynthesis by ‘Nanguoli’ fruit at different harvest maturity stages

ABSTRACT The ripe fruit of Pyrus ussuriensis ‘Nanguoli’ is favoured by people for its attractive colour, exquisite flesh and pleasant flavour. However, its flavour is negatively affected by early harvest. Therefore, this study aimed to determine whether exogenous methyl jasmonate (MJ) can help to regulate aromatic volatiles biosynthesis in pre-climacteric ‘Nanguoli’ fruit at different maturity stages (135 days after full bloom (DAFB) or ‘early harvested’ and 145 DAFB or ‘normal harvested’). MJ promoted aromatic volatile biosynthesis in normal harvested fruit, with the number of volatile compounds increasing from 43 in untreated fruit to 51 and 57 in fruit that had been treated with 1 and 5 mM MJ, respectively. By contrast, MJ had little effect on early harvested fruit, which exhibited an increase from 41 to 49 and 44 volatile compounds following treatment with 1 and 5 mM MJ, respectively. The total content of aromatic volatiles also increased by 53.75% and 66.82% in normal harvested fruit treated with 1 and 5 mM MJ, respectively, whereas early harvested fruit exhibited only slight increases. There was no significant difference between the effects of 1 and 5 mM MJ on aromatic volatile biosynthesis, indicating that the observed effects were dependent on the maturity stage of the fruit rather than the exogenous MJ concentration within the range tested. The ethylene production rate exhibited similar changes to those observed for the aromatic volatile content and there were no significant differences in the aromatic volatile contents of ‘Nanguoli’ fruits that had been treated with 1-methylcyclopropene (1-MCP) + MJ at different maturity stages. Therefore, it is deduced that ethylene may trigger aromatic volatile biosynthesis.
Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community

The gut microbiome is strongly interwoven with human health. Conventional gut microbiome analysis generally involves 16S rRNA gene targeting next generation sequencing (NGS) of stool microbial communities, and correlation of results with clinical parameters. However, some microorganisms may not be alive at the time of sampling, and thus their impact on the human health is potentially less significant. As conventional NGS methods do not differentiate between viable and dead microbial components, retrieved results provide only limited information. Propidium monoazide (PMA) is frequently used in food safety monitoring and other disciplines to discriminate living from dead cells. PMA binds to free DNA and masks it for subsequent procedures. In this article we show the impact of PMA on the results of 16S rRNA gene-targeting NGS from human stool samples and validate the optimal applicable concentration to achieve a reliable detection of the living microbial communities. Fresh stool samples were treated with a concentration series of zero to 300 μM PMA, and were subsequently subjected to amplicon-based NGS. The results indicate that a substantial proportion of the human microbial community is not intact at the time of sampling. PMA treatment significantly reduced the diversity and richness of the sample depending on the concentration and impacted the relative abundance of certain important microorganisms (e.g. Akkermansia, Bacteroides). Overall, we found that a concentration of 100 μM PMA was sufficient to quench signals from disrupted microbial cells. The optimized protocol proposed here can be easily implemented in classical microbiome analyses, and helps to retrieve an improved and less blurry picture of the microbial community composition by excluding signals from background DNA.