Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving Bioinformatics Prediction of microRNA Targets by Ranks Aggregation

microRNAs are non-coding RNAs which down-regulate a large number of target mRNAs and modulate cell activity. Despite continued progress, bioinformatics prediction of microRNA targets remains a challenge since available softwares still suffer from a lack of accuracy and sensitivity. Moreover, these tools show fairly inconsistent results from one another. Thus, in an attempt to circumvent these difficulties, we aggregated all human results of three important prediction algorithms (miRanda, PITA and SVmicrO) showing additional characteristics in order to rerank them into a single list. This database is freely available through a webtool called miRabel (http://bioinfo.univ-rouen.fr/mirabel/) which can take either a list of miRNAs, genes or signaling pathways as search inputs. Receiver Operating Characteristic curves and Precision-Recall curves analysis carried out using experimentally validated data and very large datasets show that miRabel significantly improves the prediction of miRNA targets compared to the three algorithms used separatly. Moreover, using the same analytical methods, miRabel shows significantly better predictions than other popular algorithms such as MBSTAR and miRWalk. Interestingly, a F-score analysis revealed that miRabel also significantly improves the relevance of the top results. The aggregation of results from different databases is therefore a powerful and generalizable approach to many other species to improve miRNA target predictions. Thus, miRabel is an efficient tool to accurately identify miRNA targets and integrate them into a biological context.
Prediction and information integration determine subtle anticipatory fixation biases

A core question underlying neurobiological and computational models of behavior is how individuals learn environmental statistics and use them for making predictions. Treatment of this issue largely relies on reactive paradigms, where inferences about predictive processes are derived by modeling responses to stimuli that vary in likelihood. Here we deployed a novel proactive oculomotor metric to determine how input statistics impact anticipatory behavior, decoupled from stimulus-response. We implemented transition constraints between target locations, and quantified a subtle fixation bias (FB) discernible while individuals fixated a screen center awaiting target presentation. We show that FB is informative with respect the input statistics, reflects learning at different temporal scales, predicts saccade latencies on a trial level, and can be linked to fundamental oculomotor metrics. We also present an extension of this approach to a more complex paradigm. Our work demonstrates how learning impacts strictly predictive processes and presents a novel direction for studying learning and prediction.
Diagnostic Characters within ITS2 DNA Support Molecular Identification of Anastrepha suspensa (Diptera: Tephritidae)

Summary An approximately 220 bp fragment of the internal transcribed spacer 2 (ITS2) was screened as a diagnostic trait of Anastrepha suspensa (Loew) (Diptera: Tephritidae) and other pest fruit fly species in the genus Anastrepha. The majority (96%) of the sites in this fragment were invariant among the test species, but A. suspensa can be separated from other species by using 2 diagnostic characters. Similarly, A. ludens (Loew) and A. obliqua (Macquart) can be distinguished from other species based on 1 fixed character each. There is evidence of intraspecific ITS2 variation in 5 species tested, consistent with species complexes and incomplete homogenization through the process of concerted evolution.
QTL mapping for root vigor and days to flowering in Brassica napus L.

Abstract: A segregating F2 population was developed from a winter and spring type cross to identify quantitative trait loci (QTL) controlling root vigor and days to flowering in canola (Brassica napus). About 3090 polymorphic SNPs derived from genotyping by sequencing were used to develop a linkage map. A final linkage map was constructed with 658 SNPs at LOD 4. One QTL, NRV (Napus Root Vigor) was identified on chromosome A01 (24.7 Mbp) for root vigor explaining 16.3% of the phenotypic variation. GBF Interacting Protein 1 (GIP1) and SAUR-like family proteins are the two candidate genes related to root growth and development identified within this QTL region. Two QTL, DTF1 and DTF2, were identified for days to flowering, accounting for 21.7% and 15% of the phenotypic variation, respectively. DTF1 was assigned on chromosome C08 (9.43 Mbp) and two putative candidate genes, Light Regulated WD1 (LWD1) and FLOWERING BHLH 1 (FBH1) were identified within this QTL region. For DTF2, three putative candidate genes A. thaliana CENTRORDIALIS (ATC), Tetracopeptide Repeat (TPR), and Poly A Binding protein 3 (PAB3) were identified on the chromosome C04 (14.56 Mbp).
Effect of probiotics “Vetlactoflorum-M” and “Vetlactoflorum-C” on some serum blood biochemical parameters of broiler chickens

The aims of this study were to evaluate effect of using liquid preparation "Vetlactoflorum-M" (dissolved in diluted milk) and "Vetlactoflorum-C" (dissolved in whey) on some parameters such as concentration of cholesterol, triglyceride, glucose and uric acidin blood of broiler chickens. One hundred fifty broilers chicken breed "Ross-308" used in one day old, divided into three groups (each of 50 chicks as follow: (control" un supplemented probiotic" , first treatment group received “Vetlactoflorum-C” and second treatment group received “Vetlactoflorum-M”). Blood samples were taken in 7, 14, 21, 28, 35 and 42 day-old. The results showed that the selected probiotics ("Vetlactoflorum-M" and "Vetlactoflorum-C") are able to reduce uric acid, increase glucose. Lower concentrations of serum cholesterol and triglycerides were observed in the treatment groups. So the results were improved by using probiotic.
High efficient protocol for Callus induction and Regeneration of a medicinal plant Orthosiphon stamineus

Callus induction and indirect organogenesis protocol were developed using different explants of Orthosiphon stamineus such as leaf, petiole, and internode on MS medium supplemented with different plant growth regulators. For callus induction, MS medium with 2, 4-D, NAA and IBA alone or in combinations with BAP were used. High-efficiency callus induction was obtained (100%) in petiole compared with other explants at the concentrations of 5mg/l 2, 4-D hormone, and 99% callus induction was obtained in leaf and internode at the concentration of 4.0 mg/l 2,4-D hormone. Similarly, 100% callus induction was obtained at the concentrations of 4.0 mg/l NAA with 0.5 mg/l BAP combinations in petiole and internode whereas 99% of callus induction was obtained from the same concentration. The induced callus of leaf, petiole, and internode was transferred to shooting medium fortified with plant growth regulators at 5.0 mg/l BAP and 0.5 mg/l NAA. Among these, internode has shown maximum percentage of the shoot (60%) regeneration than petiole and leaf callus. Shoot regenerated plantlets were then transferred to 1⁄4MS medium fortified with 1.0 mg/l NAA hormone results in high efficient rooting (20) in vitro plantlets without inducing basal callus. Further, root-induced healthy plantlets were subjected to hardening in the greenhouse and established in natural environmental condition with a survival rate of 95% without any morphological changes of true type plants. Hence the developed protocol was optimized to yield a high frequency of callus induction and regeneration in different explants of O.stamineus with different concentrations of plant growth regulator.
Impaired phloem loading in genome-edited triple knock-out mutants of SWEET13 sucrose transporters

Crop yield depends on efficient allocation of sucrose from leaves to seeds. In Arabidopsis, phloem loading is mediated by a combination of SWEET sucrose effluxers and subsequent uptake by SUT1/SUC2 sucrose/H+ symporters. ZmSUT1 is essential for carbon allocation in maize, but the relative contribution to apoplasmic phloem loading and retrieval of sucrose leaking from the translocation path is not known. We therefor tested whether SWEETs are important for phloem loading in maize. Here we identified three leaf-expressed SWEET sucrose transporters as key components of apoplasmic phloem loading in Zea mays L. Notably, ZmSWEET13 paralogs (a, b, c) are among the highest expressed genes in the leaf vasculature. Genome-edited triple knock-out mutants are severely stunted. Photosynthesis of mutants was impaired and leaves accumulated starch and soluble sugars. RNA-seq revealed profound transcriptional deregulation of genes associated with the photosynthetic apparatus and carbohydrate metabolism. GWAS analyses may indicate that variability in ZmSWEET13s is correlated with agronomical traits, specifically flowering time and leaf angle. This work provides support for cooperation of three ZmSWEET13s with ZmSUT1 in phloem loading in Zea mays L. Our study highlights these three ZmSWEET13 sucrose transporters as possible candidates for the engineering of crop yield. One Sentence Summary Three SWEET sucrose transporter paralogs are necessary for phloem loading in maize.
Distribution of Batillaria multiformis and B. attramentaria (Batillariidae) in Southern Kyushu

The present study investigated the distribution of Batillaria multiformis and B. attramentaria in the tidal flats of Southern Kyushu. These two species are the dominant inhabitants of tidal flats and play an important role in conserving the environmental condition of the coastal area. Since it is difficult to distinguish between the two species based on shell morphology, the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) technique was used for identification. Among the 55 tidal flats surveyed, Batillaria species were found in 32, mainly along the coasts of Kagoshima Bay and East China Sea. Furthermore, these species were not observed in certain tidal flats, although their presence in these tidal flats was confirmed from 1999 to 2003. The reason for their absence or decline has been discussed here. Batillaria multiformis was distributed along the neighboring tidal flats of inner Kagoshima Bay and around Nagashima Island, whereas B. attramentaria was isolated along a few scattered tidal flats facing to the Pacific Ocean or East China Sea. The difference in the distribution of two species might be attributed to their developmental system̶B. multiformis and B. attramentaria employ planktonic and direct developmental systems, respectively.
The Role of Prebiotics and Probiotics in Human Health

There has recently been a significant increase in research on the potential health benefi ts associated with probiotics and prebiotics. Some effects attributed to selected probiotics or prebiotics have been proved by clinical trials, while others have been acquired on the basis of in vitro tests which need to be replicated in vivo in order to be validated. Clinical reports in the literature for the application of probiotics have been done for the treatment of infectious diseases including viral, bacterial or antibiotic associated diarrhea, lowering of serum cholesterol, decreased risk of colon cancer, improved lactose digestion, and altered intestinal microbiota. However, information on probiotic species, a specific strain-therapeutic application, and adequate dosages, is not yet sufficient to allow rational consumption. Moreover, prebiotic oligosaccharides are poorly understood in regard to their fermentation profi les and dosages required for health effects. The present review summarizes some of the literature in regard to clinical or therapeutic trials of probiotics and prebiotics.
The regulation of translesion synthesis through the binding and activation of polymerases by PCNA

b i o c h e m . u i o w a . e d u Individuals with disabilities are encouraged to attend all University of Iowa-sponsored events. If you are a person with a disability who requires an accommodation in order to attend this program, please contact the Biochemistry Department in advance at 335-7932 or email Biochem@uiowa.edu Elizabeth Boehm Graduate Student Department of Biochemistry University of Iowa
Performance and some physiological indices of broiler chicks fed urea-containing grower diets

The present study was undertaken to investigate the effects of feeding ureacontaining grower diets on growth performance, nutrient digestibility, carcass traits and some blood parameters of broiler chicks. Three hundred sixty 3-wk-old unsexed (Cobb-500) broiler chicks were randomly divided into five equal treatments; each consisted of 6 equal replications, and kept in conventional wire-floored growing batteries. Five experimental diets [of similar crude protein (18.9%) and metabolizable energy (about 3136 kcal/kg) contents] having five graded levels of urea (0.00, 0.345, 0.69, 1.035 and 1.38%) were formulated and used from 3 to 6 weeks of age. All birds had free access to feed and water and were reared under similar managerial and environmental conditions. The response of chicks to feeding the urea-containing diets included growth performance [in terms of feed intake (FI), live body weight (LBW), body weight gain (BWG), feed conversion (FC), economic efficiency of growth (EEG), mortality rate, nutrient digestibility [including dry matter (DM), organic matter (OM), crude protein (CP), ether extract (EE), crude fiber (CF) and nitrogen-free extract, and ash and nitrogen retention], certain carcass traits, and some blood parameters. The obtained results could be summarized as follows: There were significant depressions in final LBW, BWG and FI of birds fed the urea-containing diets as compared to their control group; however, FC and EEG were not significantly affected. With the exception of slight reductions in crude protein digestibility and rate of nitrogen retention in birds fed the 1.38% urea in their diet while the other experimental groups (fed diets containing 0.345, 0.69 and 1.035% urea) exhibited means of digestibility for DM, OM, EE, CF and NFE as well as ash retention comparable to those of the control birds. Feeding the urea-containing diets had no significant effects on either carcass traits or blood parameters but urea concentrations in blood plasma of broilers fed the diets containing 0.69, 1.035 and 1.38% urea were significantly higher compared with their control counterparts. Because of the depressed growth performance and poor economic efficiency of growth resulting from feeding the urea-containing diets, it can be concluded that urea addition as a source of non-protein nitrogen in broiler chick diets is nutritionally invaluable and not recommended.
Caloscyphaceae, a new family of the Pezizales

The genus Caloscypha Boud. , with its only species C. fulgens (Pers . : Fr.) Boud. , has usually been included in the family Pyronemataceae (Pezizales). However, since a rather long time the genus been considered taxonomically isolated without having close relatives (see e.g. Korf 1972). This status was strengthened as the spores of C. fulgens were reported to belong to an infrequent kind as to their wall structure (Harmaja 1974). As I also observed that the ascus wall is often somewhat thickened upwards (up to 3.0 mm in Melzer's reagent; unpublished until now), I even prepared a manuscript in the 1970's to describe a new family for Caloscypha. After those times, two additional special characteristics of Caloscypha have been detected: (i) the nutrition mode: Geniculodendron pyriforme G. A. Salt, pathogenic to the seeds of Abies, Picea and Pinus, was found to be the anamorph of C. fit! gens (see e.g. Sutherland 1979), (ii) according to Landvik et al. ( 1997) the genus unexpectedly is phylogenetically distinct from the other cupulate, carotenoid-containing taxa with uninucleate spores: of the three main lineages of the Pezizales the genus clusters with one that comprises the families Helvellaceae, Morchellaceae and Tuberaceae (and obviously also Discinaceae and Rhizinaceae; see O'Donnell & al. 1997). In these families, the apothecia are non-bright in colour, devoid of carotenoid pigments, and the spores are multinucleate. The genus clearly deserves a family of its own. Below, the new family Caloscyphaceae is described. The characters that appear to be diagnostic at the family le el are given in the English description; these are partly a matter of personal judgement. Detailed features of the genus Caloscypha and its only species have been described e.g. by Eckblad (1968); see also Harmaja (1974) for some spore characters.
Dendra2-tagged Lifeact and MAP4 as exchangeable probes for single-molecule fluorescence imaging of cytoskeleton in live cells

Recently, a new method called image reconstruction by integrating exchangeable single-molecule localization (IRIS) was developed (Kiuchi et al., Nat. Methods 2015, 12, 743-746). IRIS ensures high-density labeling for super-resolution microscopy but can be applied for fixed cells only. Here, we extended the IRIS conception to live cell imaging. We applied Lifeact and MAP4 transiently binding to microfilaments and microtubules, respectively. Green-to-red photoconvertible fluorescent protein Dendra2 was chosen as an efficient tag for single-molecule localization microscopy. Live-cell single-molecule localization imaging with Dendra2-Lifeact and Dendra2-MAP4 was performed. As a result, super-resolved images of actin and tubulin in dynamics in living cells were reconstructed. Importantly, Dendra2-Lifeact provided a higher number of individual localizations and denser labeling of microfilaments in comparison with commonly used Dendra2-actin.
Life history evolution in three-spined stickleback

A main challenge in evolutionary ecology is to elaborate the main ecological factors that vary in a study system and analyse how those factors shape the phenotype of organisms in their natural environment. These ecological variables can have complex effects since most life history traits are correlated. Here I examined the effects of ecological factors on life history traits, and the relationship among life history traits of North Uist three-spined stickleback, Gasterosteus aculeatus (hereafter stickleback). Both abiotic and biotic factors that are commonly measured in aquatic systems, and are known to vary greatly between North Uist lochs, were examined. The traits analysed were body size, age and size at maturation, proportion of fish over one year old, and the fecundity rate. My results showed that there was strong variation in water chemistry and inter-specific competition among the lochs on North Uist. Lochs on the west side of the island were characterised by higher sodium and calcium ion concentrations, higher pH and conductivity, and increased inter-specific competition. As a result, western populations had a faster absolute growth rate, larger body size, and a higher proportion of older fish, indicative of a longer life span. Although western populations had a larger body size, they tended to mature later with a smaller gonadosomatic index. They also favoured a larger number of eggs, but with a smaller egg size. Variations within population showed that larger females had greater fecundity but small egg size. Both plasticity and evolution appear to have contributed to these life history variations. Overall, variation in life history of North Uist stickleback was largely related to measures of resources availability and interspecific competition, except for egg size which was mostly associated with variation in predator density.
Candidate urine biomarker discovery from only five pairs of samples before and after tumor resection in glioma patients

Biomarkers are measurable changes associated with the disease. Without the control of homeostatic mechanisms, urine accumulates systemic body changes and thus serves as an excellent early biomarker source. However, urine is affected by many factors other than disease. Although many candidate biomarkers have been identified in animal models, a large number of clinical samples might still be required for the disease related changes. A self-controlled study should be able to avoid the interferences of individual differences among patients. Gliomas are the most common primary malignant brain tumors and have a very poor prognosis. Early diagnosis of gliomas and the monitoring of tumor recurrence are crucial to improve glioma patient outcomes. Here we set to try if biomarker candidates can be identified by comparing urine samples from five glioma patients collected at the time of tumor diagnosis and after surgical removal of the tumor. Using label-free liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) quantification, twenty-seven urinary proteins were significantly changed after tumor resection (fold change ≥ 1.5, P-value < 0.05, and similar changes in all 5 patients), many of which have been previously associated with gliomas, such as CEACAM1, ANXA7, CALR, CRYAB, CD276, pIgR and cathepsin D. Functions of these proteins were significantly enriched in the regulation of tissue remodeling, autophagy, the inhibition of gene expression, the positive regulation of natural killer cell-mediated cytotoxicity and angiogenesis, which are associated with glioma development. Our results suggested that using the self-control of before and after tumor resection is an effective method to identify differential proteins associated with the disease, even with a small number of patients.
Remodelling of the cardiac caveolar domain in heart failure and its putative influence on beta adrenergic signalling

Over 500,000 people in the UK have heart failure (HF). After an initial insult to the heart, sympathetic drive increases which leads to detrimental remodelling of cardiac β-adrenergic receptors (βAR) and further cardiac dysfunction. The main βAR expressed in the heart are the β1AR and β2AR. In heart failure, remodelling is characterised by reduced β1AR density, desensitisation of the remaining β1AR and aberrations of normal βAR signal compartmentalisation. Caveolae, flask-shaped lipid rafts, are present in most cells including cardiac myocytes and are characterised by the presence of caveolin and cavin proteins. Caveolar proteins create distinct micro-domains within the membrane and play a key role in compartmentalisation of signalling from both the β1AR and β2AR. Isolated reports of changes in caveolar structure and proteins in HF have implications for β-AR signalling, however the full array of caveolar protein changes in HF has not previously been assessed. Here we establish how the expression and membrane location of β-AR cascade and caveolar proteins changes in rat models of right ventricular (RV) and left ventricular (LV) failure induced by monocrotaline and aortic banding, respectively. For the RV model, we examined changes in β-AR responsiveness, and tested the potential for reversing functional and caveolar remodelling using a common LV therapy (the β-blocker metoprolol). Quantitative analyses of caveolar protein expression in myocyte and myocardial samples was also carried out using custom-designed calibrating peptides (CavCATs). Both HF models showed a reduction in caveolar protein expression, with protein redistribution also found in the RV model. Decreased expression of β-AR signalling proteins (β1AR, adenylyl cyclase) accompanied by increased expression of inhibitory proteins (Gαi, GRK2) was also observed in both models, with some remodelling of membrane distribution. β-blocker treatment in RV failure partially recovered expression of caveolar and β-AR cascade proteins. Cardiac β1AR responsiveness was reduced in RV failure and again, this was partially recovered by β-blocker treatment. Quantitative work highlights the importance of studying non muscle-specific caveolar protein isoforms in the cardiac myocyte given e.g. similar expression of Cav 3 and Cav 1 in these cells. Caveolae are dynamic membrane compartments which change in HF. This work suggests that caveolar changes affect β-AR signalling protein membrane location, which contributes to aberrations of signalling which (in the case of RV failure) can be reversed by β blockers.