Miracle-dz/UniFAR-FTUs huggingface dataset:
TOL proteins mediate vacuolar sorting of the borate transporter BOR1 in Arabidopsis thaliana

Boron (B) is an essential micronutrient for plants, however, it shows cytotoxicity at high concentrations. A borate transporter BOR1 is required for efficient transport of boron (B) toward the root stele in Arabidopsis thaliana. BOR1 shows polar localization in the plasma membrane of various root cells toward the stele-side under B limitation. To avoid over-accumulation of B, BOR1 in the plasma membrane is rapidly internalized and transported into the vacuole for proteolysis after high-B supply in an ubiquitination-dependent manner. Although BOR1 has been predicted to be transported into multi-vesicular bodies/late endosomes (MVB/LEs) via the endosomal sorting complex required for transport (ESCRT) machinery, experimental evidence was absent so far. In this study, we investigated the intracellular localization of BOR1 by visualizing endomembrane compartments, and tested the involvement of ESCRT-0-like proteins TOM1-LIKEs (TOLs) in the vacuolar sorting of BOR1. Under low-B conditions, a large portion of cytoplasmic BOR1 was localized in the trans-Golgi networks/early endosomes (TGN/EEs) labeled with VHA-a1 subunit. Pharmacological interference of endosomal recycling using brefeldin A induced colocalization of BOR1 with RabA5D, which labels recycling vesicles associated with the TGN. These data suggest that BOR1 cycles between plasma membrane and TGN/EE via RabA5D-positive endomembrane compartments under low-B conditions. On the other hand, under high-B conditions, BOR1 was localized in the inside of TOL5-positive MVB/LEs. To examine the roles of TOL proteins in intracellular trafficking of BOR1, we analyzed BOR1-GFP localization in the TOL quintuple mutant (tolQ; tol2-1tol3-1tol5-1tol6-1tol9-1) after high-B supply. In the tolQ mutant, vacuolar sorting of BOR1 was delayed, while the polar localization of BOR1 was not disturbed. Taken together, BOR1 is constantly transported to the TGN/EE by endocytosis and recycled to the plasma membrane likely via RabA5D-positive endomembrane compartments under low-B conditions. On the other hand, BOR1 is transported to the vacuole via TOL5-positive MVB/LEs under high-B conditions. TOL proteins are required for sorting of ubiquitinated BOR1 into MVB/LE for vacuolar degradation but not for the polar trafficking of BOR1.
O-fucosylation of thrombospondin-like repeats is required for processing of MIC2 and for efficient host cell invasion by Toxoplasma gondii tachyzoites

Toxoplasma gondii is an intracellular parasite that causes disseminated infections which can lead to neurological damage in fetuses and immunocompromised individuals. Microneme protein 2 (MIC2)2, a member of the thrombospondin-related anonymous protein (TRAP) family, is a secreted protein important for motility, host cell attachment, invasion, and egress. MIC2 contains six thrombospondin type I repeats (TSRs) that are modified by C-mannose and O-fucose in Plasmodium spp. and mammals. Here we used mass spectrometry to show that the four TSRs in T. gondii MIC2 with protein O-fucosyltransferase 2 (POFUT2) acceptor sites are modified by a dHexHex disaccharide, while Trp residues within three TSRs are also modified with C-mannose. Disruption of genes encoding either pofut2 or nucleotide sugar transporter 2 (nst2), the putative GDP-fucose transporter, results in loss of MIC2 O-fucosylation, as detected by an antibody against the GlcFuc disaccharide, and markedly reduced cellular levels of MIC2. Furthermore, in 10-15% of the Δpofut2 or Δnst2 vacuoles, MIC2 accumulates earlier in the secretory pathway rather than localizing to micronemes. Dissemination of tachyzoites in human foreskin fibroblasts is reduced in these knockouts, which both show defects in attachment to and invasion of host cells comparable to the phenotype observed in the Βmic2. These results, which show O-fucosylation of TSRs is required for efficient processing of MIC2 and for normal parasite invasion, are consistent with the recent demonstration that P. falciparum Δpofut2 has decreased virulence and support a conserved role for this glycosylation pathway in quality control of TSR-containing proteins in eukaryotes.
White matter connectivity disruptions in the pre-clinical continuum of psychosis: A connectome study

Background Widespread white matter disruptions in schizophrenia have been commonly reported, but it remains unanswered whether these abnormalities are associated with schizophrenia specifically or whether they range along a psychotic continuum into the healthy population. Investigating the extent of white matter connectivity disruptions specific to psychotic-like experiences in healthy individuals is insofar important as it is a necessary first step towards the development of prodromal psychosis biomarkers. Methods High resolution, multi-shell diffusion-weighted magnetic resonance images were acquired from 89 healthy individuals. Whole-brain white matter fiber tracking was performed to quantify the strength of white matter connections. Network-based statistics were applied to white matter connections in a regression model in order to test for a linear relationship between streamline count and psychotic-like experiences. Results A significant subnetwork was identified whereby streamline count declined with increasing quantity of psychotic-like experiences. This network of significant connectivity reductions affected all cortical lobes, subcortical structures and the cerebellum. Conclusion A widespread network of linearly declining connectivity strength with increasing number of psychotic-like experiences was identified in healthy individuals. This finding is in line with white matter connectivity reductions reported from early to chronic stages of schizophrenia. We suggest that these white matter changes might be a potential biomarker for the identification of individuals at high risk for transitioning to psychosis.
Future state prediction errors guide active avoidance behavior by adult zebrafish

Human predicts future. To ask if fish also has this capacity, we established the virtual reality training system with live imaging of the telencephalic neurons of adult zebrafish in the active avoidance and found that, at the onset of the trial, learned fish conceives two future conditions as the favorable status on its way to the safe goal, i.e. one with the backwardly moving landscape and the other with the color of the safe goal. And the two different neural ensembles monitor the discrepancy between these predictions and the perceived real external status. Once fish reaches the goal, another ensemble is set to work to monitor whether fish keeps staying in the safe goal. The manipulation to artificially enhance these prediction errors elevated the activities of these ensembles and induced fish to behave to correct errors, revealing that fish sets behavioral strategy to actively realize these predictions.
Discharge Trajectories of Bulk Solids

Theoretical formulae are defined for underside and topside limits of material path discharge trajectories. To predict the trajectory path for real conditions, divergent coefficients have been introduced to the theoretical functions which enable the shape of the trajectory to be modelled. An example prediction of trajectory calculation is illustrated and compared with that of other methods.
ESTIMATION OF SYNCHRONOUS MOTOR EXCITATION CURRENT USING MULTIPLE LINEAR REGRESSION MODEL OPTIMIZED BY SYMBIOTIC ORGANISMS SEARCH ALGORITHM

Bu belgede guc faktoru duzeltme islemi icin senkron motor (SM) uyartim akiminin tahminine yonelik etkili ve basit bir yol sunulmustur. Bu islem icin ilk olarak motor yuk akimi, gercek guc faktoru, guc faktoru hatasi ve uyartim akiminin degisimi karar degiskenleri olarak ele alinarak coklu dogrusal regresyon modeli olusturulmustur. Ardindan hazirlanan deneysel duzenekten toplanan veriler kullanilarak bu modeldeki regresyon katsayilarinin iyilestirilmesi amaciyla yeni ortaya konulan simbiyotik organizmalar arama algoritmasindan faydalanilmistir. Bu algoritmanin benzer kompanzasyon islemi icin genetik algoritma, yapay ari kolonisi ve yercekimi algoritmasi gibi yakin zamanda yayinlanan algoritmalara olan ustunlugu karsilastirmali bilgisayar simulasyonlari ile gosterilmistir. Bu makalede sergilenen sonuclar, sunulan teknigin bahsi gecen literaturdeki algoritmalara gore basitlik, gurbuzluk ve dogruluk acilarindan daha iyi performans verdigini gostermistir. Bu baglamda coklu dogrusal regresyon model katsayilarin onerilen sekilde ayari onceki calismalardan daha iyi SM uyartim akimi tahmin performansi saglamistir.
Key terms and issues in open and distance learning

This volume raises the issues that must be considered before creating an open or distance learning system. It explains how to define, locate and reach the learner, how to produce quality learning materials, how to make the best use of teaching media and how to assess the learning experience. The second half of the text is a glossary of terms, with brief explanations and suggestions for discovering further advice and information.
A method for genome editing in the anaerobic magnetotactic bacterium Desulfovibrio magneticus RS-1

ABSTRACT Magnetosomes are complex bacterial organelles that serve as model systems for studying cell biology, biomineralization, and global iron cycling. Magnetosome biogenesis is primarily studied in two closely related Alphaproteobacterial Magnetospirillum spp. that form cubooctahedral-shaped magnetite crystals within a lipid membrane. However, chemically and structurally distinct magnetic particles have also been found in physiologically and phylogenetically diverse bacteria. Due to a lack of molecular genetic tools, the mechanistic diversity of magnetosome formation remains poorly understood. Desulfovibrio magneticus RS-1 is an anaerobic sulfate-reducing Deltaproteobacterium that forms bullet-shaped magnetite crystals. A recent forward genetic screen identified ten genes in the conserved magnetosome gene island of D. magneticus that are essential for its magnetic phenotype. However, this screen likely missed many interesting mutants with defects in crystal size, shape, and arrangement. Reverse genetics to target the remaining putative magnetosome genes using standard genetic methods of suicide vector integration has not been feasible due to low transconjugation efficiency. Here, we present a reverse genetic method for targeted mutagenesis in D. magneticus using a replicative plasmid. To test this method, we generated a mutant resistant to 5-fluorouracil by making a markerless deletion of the upp gene that encodes uracil phosphoribosyltransferase. We also used this method for targeted marker exchange mutagenesis by replacing kupM, a gene identified in our previous screen as a magnetosome formation factor, with a streptomycin resistance cassette. Overall, our results show that targeted mutagenesis using a replicative plasmid is effective in D. magneticus and may also be applied to other genetically recalcitrant bacteria. IMPORTANCE Magnetotactic bacteria (MTB) are a group of organisms that form small, intracellular magnetic crystals though a complex process involving lipid and protein scaffolds. These magnetic crystals and their lipid membrane, termed magnetosomes, are model systems for studying bacterial cell biology and biomineralization as well as potential platforms for biotechnological applications. Due to a lack of genetic tools and unculturable representatives, the mechanisms of magnetosome formation in phylogenetically deeply-branching MTB remain unknown. These MTB contain elongated bullet-/tooth-shaped magnetite and greigite crystals that likely form in a manner distinct from the cubooctahedral-shaped magnetite crystals of the genetically tractable Alphaproteobacteria MTB. Here, we present a method for genome editing in the anaerobic Deltaproteobacterium Desulfovibrio magneticus RS-1, the first cultured representative of the deeply-branching MTB. This marks a crucial step in developing D. magneticus as a model for studying diverse mechanisms of magnetic particle formation by MTB.
Using Autotagging for Classification of Vocals in Music Signals

Modern society has drastically changed the way it consumes music. During these last recent years, listeners have become more demanding in how many songs they want to have accessible and require to access them faster than ever before. The modern listener got used to features like automatic music recommendation and searching for songs that, for example, have “female vocals” and “ambient” characteristics. This has only been possible due to sophisticated autotagging algorithms. However, there has been an increasing belief in the research community that these algorithms often report over optimistic results. This work approaches this issue, in the context of automatic vocal detection, using evaluation methods that are rarely seen in literature. Three methods are conducted for the evaluation of the classification model developed: same dataset validation, cross dataset validation and filtering. The cross dataset experiment shows that the concept of vocals is generally specific per dataset rather than universal as expected. The filtering experiment, which consists of iteratively applying a random filterbank, shows drastic performance drops, in some cases, from a global f-score of 0.72 to 0.27. However, these filters have been showed not to affect the human ear’s ability to distinguish vocals, by conducting a listening experiment with over 150 candidates. Additionally, a comparison between two binarization algorithms maximum and dynamic threshold is performed and shows no significance difference. The results are reported on three datasets that have been widely used within the research community, on which a mapping from its original tags to the vocals domain was performed and which is made available to other researchers.
The European Microwave Signature Laboratory

The following paper describes in short a new research facility which has been installed at the Joint Research Centre of the Commission of the European Communities in Ispra, Italy. This unique measurement laboratory for signature research has been inaugurated and presented to the public in April 1992. At this occasion the JRC also distributed an announcement of research and experiment opportunities to potential customers world-wide. The paper summarises the key features of this facility and provides an overview about its potential.
Analogue optoelectronic implementation of a neural network with in-situ learning

We present an implementation of a neural network using specially designed ferroelectric liquid crystal on silicon (FLC/Si) spatial light modulators. The spatial light modulators act as a somatic and a synaptic plane, and provide analogue weight multiplication. A learning algorithm is implemented locally in every synapse. The optoelectronic system therefore realises a fully interconnected neural network with a truly in-situ learning capability.
A Taxonomic Study on Zooplankton Fauna of Kıgı Dam Lake (Bingol-Turkey)

Kigi Baraj Golu’nun zooplankton faunasini belirlemek icin Eylul 2012 - Agustos 2013 arasinda yapilan mevsimsel calismada zooplankton ornekleri, 55 µm goz acikligina sahip plankton kepcesi yardimiyla horizontal olarak toplanmis ve %4’luk formolde tespit edilmistir. Baraj Golu’nde toplam 22 takson (16 Rotifera, 4 Cladocera ve 2 Copepoda) teshis edilmistir Rotiferlerden Ascomorpha saltans, Asplanchna priodonta, Brachionus angularis, Cephalodella gibba, Euchlanis dilatata, Kellicottia longispina, Keratella cochlearis, Keratella quadrata, Lecane luna, Lecane lunaris, Notholca squamula, Polyarthra dolichoptera, Rotaria rotatoria, Synchaeta pectinata, Synchaeta oblonga, Trichocerca capucina; kladoserlerden Bosmina longirostris, Chydorus sphaericus, Daphnia cucullata, Daphnia longispina; kopepodlardan Acanthodiaptomus denticornis, Cyclops vicinus bu baraj golu icin yeni kayittir. Zooplanktonik organizmalarin % 72,7’sini Rotifera, % 18,2’sini Cladocera ve % 9,1’ini Copepoda olusturmustur.
Which results of the standard test in community weighted mean approach are too optimistic?

Questions Community weighted mean (CWM) approach analyses the relationship species attributes (like traits or Ellenberg-type indicator values) to sample attributes (environmental variables). Recently it has been shown to suffer from inflated Type I error rate if tested by standard parametric or (row-based) permutation test. Results of many published studies are likely influenced, reporting overly optimistic relationships that are in fact merely a numerical artefact. Can we evaluate results of which studies are likely to be influenced and how much? Methods I suggest that hypotheses commonly tested by CWM approach are classified into three categories, which differ by assumption they make about the link of species composition to either species or sample attributes. I used a set of simulated and one simple real dataset to show how is the inflated Type I error rate influenced by data characteristics. Results For hypotheses assuming the link of species composition to species attributes, CWM approach with standard test returns correct Type I error rate. However, for the other two categories (assuming link of species composition to sample attributes or not assuming any link) it returns inflated Type I error rate and requires alternative tests to control for it (column-based and max test, respectively). Inflation index is negatively related to the beta diversity of species composition and positively to the strength of species composition-sample attributes relationship and the number of samples in the dataset. Inflation index is also influenced by modifying species composition matrix (by transformation or removal of species). The relationship of CWM with intrinsic species attributes is a case of spurious correlation and can be tested by column-based (modified) permutation test. Conclusions The concept of three hypothesis categories offers a simple tool to evaluate whether given study reports correct or inflated Type I error rate, and how inflated the rate can be.
Widespread inter-individual gene expression variability in Arabidopsis thaliana

A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in plants. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24 hour time-course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.
Molecular fingerprinting of Botrytis cinerea population structure from different hosts

Botrytis cinerea (teleomorph: Botryotinia fuckeliana ) ortualti sebze yetistiriciliginde kursuni kuf hastaligi etmenidir. Patojende olusan farkliliklarin bilinmesi hastalikla mucadelenin etkinligini arttirmaktadir. Calismada, Turkiye’nin Antalya ilinde yer alan 36 farkli seradan 42 adet izolat kullanilmistir. On iki SRAP (sequence-related amplified polymorphism) primer kombinasyonu ve 18 ISSR (inter simple sequence repeat) primeri dereotu, feslegen, marul, fasulye, hiyar, domates, biber ve patlicandan elde edilen B. cinerea izolatlarinin genetik farkliliklarinin belirlenmesinde oldukca yuksek polimorfizm saglamislardir. ISSR ve SRAP markirlardan elde edilen sonuclar UPGMA (The unweighted pair-group method with arithmetic average analysis) analizine gore izolatlar arasinda 0.15-0.90 oraninda degisen benzerlik elde edilmistir. Ayrica, cophenetic correlation degeri r=0.93 ile oldukca yuksek bulunmustur. Cluster analizi sonuclari degerlendirildiginde marul izolatlari diger izolatlara gore oldukca uzak kumelenmistir. Ayrica, tum izolatlar icin tranpozabl elementler ( Flipper ve Boty ) arastirilmis ve sadece Flipper element tespit edilmistir. Elde edilen genetik karakterizasyon sonuclarina gore, B. cinerea populasyonunda oldukca yuksek seviyede genetik farkliliklar bulunmustur. Bu durum, B. cinerea’ nin evrimsellesme potensiyeli ve gen akislarindan kaynaklanabilir. Farkli konukculardan elde edilen bu patojenin genetik farkliliklarinin belirlenmesinde kullanilan molekuler markirlar, ileride yapilacak calismalara da isik tutmaktadir.
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.
Extensive transmission of microbes along the gastrointestinal tract

The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.