Miracle-dz/UniFAR-FTUs huggingface dataset:
Pre-Sowing Seed Treatment with some Organic Compounds for Controlling Root Rot Disease and Improving Faba Bean Productivity under Salinity Affected Soil Conditions

Greenhouse experiment was conducted to evaluate the pathogenicity of root rot fungi on faba bean plant. Lab. experiment was also conducted to study the effect of organic compounds and fungicide Rizolex-T50 on the linear growth of the tested pathogenic fungi. Two field experiments were also carried out to study the effect of organic compounds with different concentrations and fungicide Rizolex-T50 on reduction of root rot and enhancing some morphological, physiological characteristics and productivity of faba bean under saline affected soil conditions during 2013/2014 and 2014/2015 seasons. The results under greenhouse conditions indicated that all tested pathogenic fungi caused emergence damping-off. Rhizoctonia solani was the most effective in pre-emergence damping-off while, Fusarium solani gave the highest percentage of post-emergence damping-off. The pathogenic fungi caused anatomically deformation in root structure. Infected root with F. solani caused complete destruction of epidermal cells followed by degradation of cell wall in the cells of cortex. In vitro, Rizolex-T50 completely inhibited the growth of the tested pathogenic fungi. On the other hand, chitosan at 8 g/L was the most effective in reducing fungal growth followed by proline at 200 ppm. In vivo, the application of organic compounds counteracted the harmful effects of salinity. Humic acid highly reduced preand post-emergence damping-off and subsequently increased field emergence %. The high level of proline (200 ppm) was more effective in increasing morphological measurements (plant height, No. of branches and leaves/plant) and photosynthetic pigments i.e. chlorophyll a, b and carotenoids. While, the high concentration of HA (2000 ppm) significantly increased No. of pods/plant, seed yield/plant and 100-seed weight. Chitosan gave the highest phenols content followed by proline treatment. The high increase in carbohydrate content occurred under low level of HA (1000 ppm), followed by high level of proline (200 ppm). The efficacy of the tested organic compounds in control of root rot disease was reflected on the plant causing increase in yield components. It is suggested that pre-sowing seed soaking with HA (2000 ppm) or chitosan (8 g/L) or proline (200 ppm) could be considered as alternative fungicide for controlling root rot disease and increasing productivity of faba bean under salinity and natural infection conditions in the field.
Fluctuations in the homeostatic neural circuitry influence consistency in choices between cultural goods

Preferences for primary goods, such as food items, are variable and depend on current physiological state. Decisions on cultural goods, entailing no direct physiological consequence, rely on the same neural underpinnings of valuation and choice than primary goods. Here, we test whether subjective preferences for cultural goods inherit a functional link with the neural circuitry monitoring physiological variables. Using magnetoencephalography in human participants choosing between two movies, we measured heartbeat-evoked responses (HERs), which index the cortical monitoring of cardiac contractions. Trial-by-trial fluctuations in HERs, measured before option presentation, influenced the subsequent neural encoding of subjective value in ventro-medial prefrontal cortex - a region involved both in valuation and cardiac monitoring. The neural interaction between HERs and value encoding enhanced trial-by-trial choice precision and predicted inter-individual differences in choice consistency. The enhanced monitoring of physiological variables thus supports more stable representations of subjective, self-related cognitive information.
Structural organization of the C1a-e-c supercomplex within the ciliary central apparatus

Nearly all motile cilia contain a central apparatus (CA) composed of two connected singlet-microtubules with attached projections that play crucial roles in regulating ciliary motility. Defects in CA assembly usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of the CA projections are largely unknown. Here, we integrated biochemical and genetic approaches with cryo-electron tomography to compare the CA of wild type Chlamydomonas with CA mutants. We identified a large (>2 MDa) complex, the C1a-e-c supercomplex, that requires the PF16 protein for assembly and contains the CA components FAP76, FAP81, FAP92, and FAP216. We localized these subunits within the supercomplex using nanogold-labeling and show that loss of any one of them results in impaired ciliary motility. These data provide insight into the subunit organization and three-dimensional (3D) structure of the CA, which is a prerequisite for understanding the molecular mechanisms by which the CA regulates ciliary beating. Summary Fu et al. use a wild-type vs. mutant comparison and cryo-electron tomography of Chlamydomonas flagella to identify central apparatus (CA) subunits and visualize their location in the native 3D CA structure. The study provides a better understanding of the CA and how it regulates ciliary motility.
Fractalkine (CX3CL1) and its receptor (CX3CR1) in children with hypertrophic adenoid and chronic otitis media with effusion

Abstract Background Adenoid hypertrophy (AH) is one of the possible causes of chronic inflammation in the middle ear. It has been suggested that CX3CL1 and its specific receptor (CX3CR1) could be related with the pathogenesis of some inflammatory diseases. The aim of the present study was to evaluate the role of CX3CL1 and CX3CR1 in the pathogenesis of AH with chronic otitis media with effusion (COME) in children. Materials and methods Adenoid tissue samples were obtained from 91 pediatric patients and divided into two groups: adenoidectomy only for AH (n: 47) and adenoidectomy in conjunction with ventilation tube insertion for AH + COME (n: 44). Expression levels of CX3CL1 and CX3CR1 genes were compared. Results Expression levels of CX3CL1 and CX3CR1 in hypertrophic adenoid tissue were not significantly different between the AH + COME and AH only groups. Although no significant difference was detected in the expression of CX3CL1 in the adenoid samples, the expression of CX3CR1 was higher in children older than 48 months. Conclusions When allergy, atopy and chronic adenoiditis does not exist to obstructive adenoid hypertrophy, inflammatory fractalkine chemokine expression levels in adenoid tissue was not observed to be increased in children with COME.
A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer

Lysosomal enzymes are synthesized in the endoplasmic reticulum (ER) and transferred to the Golgi complex by interaction with the Batten disease protein CLN8. Here we investigated the relationship of this pathway with CLN6, an ER-associated protein of unknown function that is defective in a different Batten disease subtype. Experiments focused on protein interaction and trafficking identified CLN6 as an obligate component of a CLN6-CLN8 complex (herein referred to as EGRESS: ER-to-Golgi relaying of enzymes of the lysosomal system) which recruits lysosomal enzymes at the ER to promote their Golgi transfer. Simultaneous deficiency of CLN6 and CLN8 did not aggravate mouse pathology compared to the single deficiencies, indicating that the EGRESS complex works as a functional unit. Mutagenesis experiments showed that the second luminal loop of CLN6 is required for the interaction of CLN6 with the enzymes but dispensable for interaction with CLN8, and in vitro and in vivo studies showed that CLN6 deficiency results in inefficient ER export of lysosomal enzymes and diminished levels of the enzymes at the lysosome. These results identify CLN6 and the EGRESS complex as key players in lysosome biogenesis and shed light on the molecular etiology of Batten disease caused by defects in CLN6.
fCite: a fractional citation tool to quantify an individual’s scientific research output

Here, I present the fCite web service (fcite.org) a tool for the in-depth analysis of an individual’s scientific research output. While multiple existing tools (e.g., Google Scholar, iCite, Microsoft Academic) focus on the total number of citations and the H-index, I propose the analysis of the research output by considering multiple metrics to provide greater insight into a scientist’s multifaceted profile. The most distinguishing feature of fCite is its ability to calculate fractional scores for most of the metrics currently in use. Thanks to the division of citations (and RCR scores) by the number of authors, the tool provides a more detailed analysis of a scholar’s portfolio. fCite is based on PUBMED data (∼18 million publications), and the statistics are calculated with respect to ORCID data (∼600,000 user profiles).
The Biocontrol Ability Test of Trichoderma harzianum Toward Damping Off Desease On Soybean Seedlings

This study aims to determine the controlling power of Trichoderma harzianum against the activity of damping off pathogen (Rhizoctonia solani isolate Rs-Clkt-01) on soybean during the period of attack. The first phase of research is descriptive research that explains the potential of damping off pathogen attack isolated from pine seeds in forest land on soybean plant which is part of pine-based agroforestry system. The experimental research are arranged in complete randomized design using 5 kinds of seedlings inoculation treatment ie: without inoculation, inoculated by pathogens, inoculated by Trichoderma and 6 hours later inoculated by pathogens, inoculated by pathogens and 6 hours later inoculated by Trichoderma, inoculated by pathogens and Trichoderma simultaneously. Each treatment was repeated 4 times. For this research observed the damping off disease index. The observed data were analyzed using a variance test followed by a 5% HSD test to determine the differences between treatments. The results showed that T. harzianum is able to control the damping off pathogen both at 6 hours before and after and simultaneously inoculate with pathogens so as to suppress the disease index up to 5-10 (100) during the period of soybean cultivation. T. harzianum Tc-JJr-02 isolate can be used to control the damping off disease caused by R. solani in soybean cultivation.
Characterization of the complete mitochondrial genome of the Seron yak (Bos grunniens)

Abstract In this study, we assembled the mitochondrial genome for Seron yak (Bos grunniens), a local yak breed with strong adaptation to marshy grasslands. The resultant mitochondrial genome is 16,325 bp long with an A + T-biased base composition (61.0% A + T) and harbours the typical set of 37 mitochondrial genes and 1 non-coding control region. The PCGs start with the typical ATA or ATG codons and are terminated with TAA, TAG or the incomplete stop codon T. Phylogenetic analysis supports the inclusion of Bison within the genus Bos, and suggests that Seron yak is most closely related to Datong yak and polled yak.
Mechanical Stimuli Affect E. Coli Heat Stable Enterotoxin (ST)-Cyclic GMP Signaling in a Human Enteroid Intestine-Chip Diarrhea Model

Modeling host-pathogen interactions with human intestinal epithelia using enteroid monolayers on permeable supports (such as Transwells) represents an alternative to animal studies or use of colon cancer-derived cell lines. However, the static monolayer model does not expose epithelial cells to mechanical forces normally present in the intestine, including luminal flow and serosal blood flow (shear force) or peristaltic forces. To determine the contribution of mechanical forces in the functional response of human small intestine to a pathogen virulence factor, human jejunal enteroids were cultured as monolayers in microengineered fluidic-based Organ-Chips (Intestine-Chips), exposed to enterotoxigenic E. coli heat-stable enterotoxin A (ST), and evaluated under conditions of static fluid, apical and basolateral flow, and flow plus repetitive stretch. Application of flow increased epithelial cell height, transcription of the cyclic nucleotide transporting protein MRP4, and apical and basolateral secretion of cGMP under baseline, unstimulated conditions. Addition of ST under flow conditions increased apical and basolateral secretion of cGMP relative to static conditions, but did not enhance intracellular cGMP accumulation. Cyclic stretch did not have any significant effect beyond that contributed by flow. This study demonstrates that fluid flow application initiates changes in intestinal epithelial cell characteristics relative to static culture conditions under both baseline conditions and with exposure to ST enterotoxin, and suggests that further investigations of application of these mechanical forces will provide insights into physiology and pathophysiology that more closely resembles intact intestine than study under static conditions.
The complete mitochondrial genome of Erromyzon sinensis (Cypriniformes: Gastromyzontidae) and phylogenetic implications

Abstract In this study, we first determined the complete mitochondrial genome of Erromyzon sinensis. It was 16,560 bp in length and contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a light strand origin of replication (OL), and a control region (D-loop). In addition, its overall nucleotide composition was 29.4% of A, 16.8% of G, 25.7% of T, and 28.1% of C, with a total of 55.1% A + T content. Phylogenetic analysis based on 13 protein-coding genes revealed that E. sinensis had the closest relationship with E. kalotaenia. Our study aimed at providing basic information for molecular systematics and conservation genetics research of E. sinensis.
High throughput photogrammetric measurement of morphological traits in free-ranging phototropic insects

Remote measurement of morphological traits in free-ranging animals is very useful for many studies, but such non-invasive photogrammetric methods are limited to large mammals and have yet to be successfully applied to insects which dominate terrestrial ecosystem diversity and dynamics. Currently, insect traits are measured using collected specimens; the process of collection and maintenance of specimens can impose a heavy and unnecessary cost when such specimens themselves are not needed for the study. We propose a rapid, simple, accurate, and semi-automated method for high-throughput morphometric measurements of phototropic insects from shape and size calibrated digital images without having to collect a specimen. The method only requires inexpensive, off-the-shelf, consumer equipment and freely available programming (R) and image processing (ImageMagick) tools. We demonstrate the efficacy of the method using a data set of 3675 images of free-ranging hawkmoths (Lepidoptera: Sphingidae) attracted to a light screen. Comparison of trait values from a subset of these images with direct measurements of specimens using a scale showed a high degree of correspondence. We have also identified several error metrics which help in assessing the method in an objective manner. Although this method was developed for nocturnal phototropic insects, it can be used for any other (small) animal that can be imaged on a simple graph paper. While this technique will be generally useful for a variety of studies of insect traits, we suggest that it is particularly suited as a commensal on multi-epoch and multi-location population monitoring of insects in the context of climate and land-use change, where repeated sampling obviates the necessity of collecting specimen every time. It will help in accumulating a large amount of reliable trait data on hundreds of thousands of individual insects without an overwhelming expenditure on collection, handling, and maintenance of specimens.
Development of new cultivation strategies to enhance heterologous protein production in Pichia pastoris

5 Impact statement . 6 Table of content . 7 List of figures . 11 List of tables . 14 Nomenclature . 15 Greek symbols . 17 Abbreviations and symbols . 18 Chapter
Analysis of primitive genetic interactions for the design of a genetic signal differentiator

Abstract We study the dynamic and static input–output behavior of several primitive genetic interactions and their effect on the performance of a genetic signal differentiator. In a simplified design, several requirements for the linearity and time-scales of processes like transcription, translation and competitive promoter binding were introduced. By experimentally probing simple genetic constructs in a cell-free experimental environment and fitting semi-mechanistic models to these data, we show that some of these requirements can be verified, while others are only met with reservations in certain operational regimes. Analyzing the linearized model of the resulting genetic network, we conclude that it approximates a differentiator with relative degree one. Taking also the discovered nonlinearities into account and using a describing function approach, we further determine the particular frequency and amplitude ranges where the genetic differentiator can be expected to behave as such.
Candidate Animal Disease Model of Elizabethkingia Spp. Infection in Humans, Based on the Systematic Pathology and Oxidative Damage Caused by E. miricola in Pelophylax nigromaculatus

Most species of the genus Elizabethkingia are pathogenic to humans and animals, most commonly causing meningitis. However, our understanding of the pathogenic mechanisms involved is poor and there have been few pathological studies of Elizabethkingia spp. in animals. To understand the host injury induced by Elizabethkingia spp. , we established a model of E. miricola infection in the black-spotted frog (Pelophylax nigromaculatus). The systematic pathology in and oxidative damage in the infection model were investigated. Our results show that recently isolated E. miricola is a bacterium that mainly parasitizes the host brain and that neurogenic organs are the predominant sites of damage. Infection mainly manifested as severe brain abscesses, meningoencephalitis, necrotic spondylitis, and necrotic retinitis. The liver, spleen, kidney, gastrointestinal tract, and lung were also affected to varying degrees, with bacterial necrotic inflammation. P. nigromaculatus also suffered enormous damage to its oxidative system during E. miricola infection, which may have further aggravated its disease state. Our results provide a preliminary reference for the study and treatment of Elizabethkingia spp. -induced neurological diseases in animals.
Role of Reef-Building, Ecosystem Engineering Polychaetes in Shallow Water Ecosystems

Although the effect of ecosystem engineers in structuring communities is common in several systems, it is seldom as evident as in shallow marine soft-bottoms. These systems lack abiotic three-dimensional structures but host biogenic structures that play critical roles in controlling abiotic conditions and resources. Here I review how reef-building polychaetes (RBP) engineer their environment and affect habitat quality, thus regulating community structure, ecosystem functioning, and the provision of ecosystem services in shallow waters. The analysis focuses on different engineering mechanisms, such as hard substrate production, effects on hydrodynamics, and sediment transport, and impacts mediated by filter feeding and biodeposition. Finally, I deal with landscape-level topographic alteration by RBP. In conclusion, RBP have positive impacts on diversity and abundance of many species mediated by the structure of the reef. Additionally, by feeding on phytoplankton and decreasing water turbidity, RBP can control primary production, increase light penetration, and might alleviate the effects of eutrophication affecting supporting ecosystem services, such as nutrient cycling. They can also modulate cultural ecosystem services by affecting recreational activities (e.g., negative impacts on boating and angling, increased value of sites as birdwatching sites). Acknowledging the multiplicity of synergistic and antagonistic effects of RBP on ecosystems and linking changes in habitat structure, filter-feeding activities, and biodeposition to ecosystem services are essential for effective decision-making regarding their management and restoration.
Specific mitochondrial ss-tRNAs in phylum Chaetognatha

Chaetognaths are marine invertebrate organisms that constitute a small phylum of very abundant animals. Chaetognaths exhibit several morphological, physiological, anatomical and molecular peculiarities. In all known chaetognath mitochondrial (mt) genomes, the number of genes encoding tRNAs is always small. In addition, the primary sequences and secondary structures of chaetognath tRNAs are not conventional. Several metazoan mt-trn genes (encoding tRNAs) exhibit nucleotide triplets corresponding to stop codons (TAG/TAA) and/or start codons (ATG/ATA) at specific conserved positions. The products of genes that bear one or both types of these codons are known as ss-tRNAs (ss for stop/start). Indirect analyses strongly suggest that in chaetognath mt genomes, some of these start and stop codons could be functional. Moreover, taking these codons into account in the algorithms predicting tRNAs makes it possible to identify and correct several potential annotation errors. Furthermore, a type of ss-trn gene appears to have emerged by duplication in order Aphragmophora.
Endoplasmic reticulum-mitochondria associations and amyotrophic lateral sclerosis

Damage to both mitochondria and the endoplasmic reticulum (ER) involving ER stress and the unfolded protein response (UPR) are characteristic features in amyotrophic lateral sclerosis (ALS). However, how these two pathological features might be linked in a common disease pathway is unclear. Approximately 5-20% of the mitochondrial surface is closely apposed to ER and tethers linking the two organelles can be visualised via electron microscopy. These regions mediate a number of physiological processes including Ca and phospholipid exchange between ER and mitochondria, ER and mitochondrial stress responses and apoptosis. Moreover, defects in ER-mitochondria associations are now known to contribute to neurodegenerative diseases. To properly investigate the role of ER-mitochondria associations in physiological processes and disease situations, the identity of the molecular tethers that physically link ER with mitochondria needs to be established. Previous work from our research group identified the outer mitochondrial membrane protein, protein tyrosine phosphatase-interacting protein 51 (PTPIP51) as a binding partner for the resident ER protein vesicle-associated membrane protein-associated protein-B (VAPB). As such, VAPB and PTPIP51 represent plausible candidates for mediating ER-mitochondria associations. In order to test this possibility, ER and mitochondria associations were quantified following the experimental manipulation of VAPB and/or PTPIP51 expression. The results strongly support a role for VAPB and PTPIP51 in controlling ER-mitochondria associations. TAR DNA-binding protein-43 (TDP-43) is strongly linked to ALS and mutations in TARDBP, the gene encoding TDP-43, are the cause of some familial forms of the disease. The effects of TDP-43 expression on ER-mitochondria associations and