Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative to azadirachtin to control Dysaphis plantaginea Passerini (Hemiptera: Aphidae) in organic apple production

Abstract The rosy apple aphid, Dysaphis plantaginea Passerini (Hemiptera: Aphidae), is a major pest of apple trees. In organic apple production, this aphid is commonly controlled by spraying azadirachtin, targeted against fundatrices in spring. However, this is the only active ingredient that has proved effective for the management of this pest in organic production, and therefore it would be desirable to provide other alternatives. In this study, several treatments (pyrethrins, garlic extract, kaolin, potassium salts of fatty acids, and defoliation) applied in autumn to prevent or reduce the presence of winged forms and oviparae in the trees were compared. In addition, applications of paraffin oil and lime sulphur in winter against rosy apple aphid eggs were tested. The trials were carried out in Catalonia (NE of Spain) from 2005 to 2010. The results showed that pyrethrins reduced the presence of rosy apple aphid oviparae but they did not have a knockdown effect. The time of application was crucial since the spring infestation was kept under control only when pyrethrins were sprayed throughout the period when oviparae were in the apple trees. It was demonstrated for the first time that pyrethrins sprayed in autumn can prevent outbreaks of rosy apple aphid and can therefore provide an alternative to azadirachtin. As a result, the rosy apple aphid can be successfully managed in countries where azadirachtin is not approved and the likelihood of development of resistance will be reduced since more than one active ingredient will be available for the control of this pest.
Fitness Landscapes Reveal Simple Strategies for Steering Evolution to Minimize Antibiotic Resistance

The evolution of antibiotic resistance presents a practical and theoretical challenge: the design of strategies that limit the risk of evolved resistance while effectively treating current patients. Sequentially cycling antibiotics has been proposed as a way to slow the evolution of resistance by reducing the extent of adaptation to a given drug, and clinical trials have demonstrated its effectiveness in some settings. Empirical fitness landscapes in theory allow the sequence of drugs to be refined to maximize tradeoffs between drugs and thereby slow adaptation even further. Using the measured growth rates of 16 genotypes of Escherichia coli in the presence of β-lactam antibiotics, we test an adaptive strategy, based on a Markov chain transition matrix, to select drug sequences that continuously minimize resistance. Cycling is never selected over the long term. Instead, monotherapy with the antibiotic that permits the least growth in its landscape’s absorbing state is rapidly selected from different starting conditions. Analysis of a synthetic fitness landscape shows that cycling drugs that induce sensitivity to one other could, in theory, outperform monotherapy. These results underscore the importance of considering the specific topologies of fitness landscape in determining whether to cycle drugs and suggest a general computational approach to identify high performing, practical strategies to manage resistance.
Development of legume based complementary food Products

The study was conducted with the aim of development of legume based complimentary food products between age group of 6 to 18 months using drum dryer. The products can be used as a protein and energy complimented combining legumes and cereals. Accordingly, chickpea, maize and millet were selected based on their nutritional value, availability in the local market and affordability. By Applying simplex-centroid design, formulation containing 66.66% chickpea, 16.666% maize and 16.666% millet of flour was selected as the best source of protein and energy. The physical properties (viscosity and bulk density), functional properties (water absorption capacity, oil absorption capacity and Dispersibility) were done, the blend with drum temperature only (130, and 150 C), Drum speed (200 and, 300 rpm) and particle size (0.8 and 1 mm). Sensory characteristics of complementary food products (color, appearance, odor, taste and overall acceptability) were also studied to evaluate the suitability of the product. Using the blend ratio obtained from the design, the product containing 16 % protein, 382.3kcal Energy, 3.07 % of fat and 73.6 % of carbohydrate found in the complimentary food products. The viscosity and bulk density were found highly affected by drum temperature and particle size. As the drum temperature increased from 130C to 150C and the drum speed remain at 200 rpm and particle size 1mm. the product viscosity decrease to (13.5*10-2Pa.s, 7.36*10-2Pa.s) respectively. And lower bulk density (0.3999g/ml) were found. As the Particle size increases from (0.8mm, 1mm) the viscosity of the product decrease to (14.4*10-2Pa.s, 7.36*10-2Pa.s; 6.18; 4.91) respectively. Drum speed effect was seen on the proximate chemical composition of the product and physical properties of the product. When the drum speed increase 200 to 300 rpm viscosity was decrease (7.36*10-, 4.91*10Pa.s) respectively. But bulk density showed an increment (0.399 to 0.457 g/ml). The functional properties, water absorption capacity, oil absorption capacity and Dispersibility of the Product (346.7%, 1.834 ml/g and 31.3%) were found to be higher than that of formulated flour (119.3%, 0.845ml/g and 74%) due to starch gelatinization. Results on the calcium, zinc and iron studies showed that (144.4, 1.926, 1.587 mg/100g) respectively and Antinutrient reduction of 43.2% in phytate and 25% in tannin. The sensory results indicated that the product produced with a temperature of 150C, and drum speed of 300 rpm and particle size of 1mm was perceived as the most accepted product, as compared to the other formulated complementary food products.
Spontaneous nongenetic variation of group size creates cheater-free groups of social microbes

Social microbes are exposed to cheaters that exploit the advantages of cooperative actions without paying their fair share. Upon starvation, myxobacterial cells cooperatively aggregate into discrete fruiting bodies containing stress-resistant spores. Fruiting bodies formed from a genetically identical population can vary greatly in the number of spores that they carry. We show that such variation allows the exclusion of cheaters from some fruiting bodies and can be a mechanism to maintain cooperation.
The complete mitochondrial genome of Sardinella lemuru (Clupeinae, Clupeidae, Clupeoidei) and phylogenetic studies of Clupeoidei

Abstract The complete mitochondrial genome of Sardinella lemuru was sequenced using PCR amplification and primer walking sequence method. The complete mitochondrial genome of S. lemuru was 16,616 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). The overall base composition was A 25.04%, C 29.36%, G 20.40%, T 25.20%. In this study, the gene arrangement was consistent with other Sardinella mitochondrial genomes. Additionally, the phylogenetic relationships of 23 Clupeoidei species based on the complete genome was analyzed, and the result showed that S. lemuru firstly clustered with other two Sardinella species, S. albella and S. maderensis. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Clupeoidei.
Relationship between Maternal Aging and Risk of Chromosome 21 Nondisjucntion: Where We Are and Where We Have To Go?

Several lines of researches have revealed that the women having Down Syndrome (DS) child are usually biologically older than the women of same chronological age with euploid baby. On other hand, Women having DS child often suffer from early onset of Alzheimer disease (AD). Frequent association between AD and DS in some families intuitively suggests sharing of some common genetic risk factors between maternal precocious aging and chromosomal nondisjunction. Subsequent molecular analyses have revealed polymorphisms of certain genes simultaneously associated with AD and DS birth. In this regard polymorphic alleles of APOE, Presinilin-1 and BubR1 are of particular interest. So, understanding the molecular relation between accelerated maternal aging and increased risk of DS conception will provide basis of future research that may have large medical applicability.
Verbenone Decreases Whitebark Pine Mortality Throughout a Mountain Pine Beetle Outbreak

Mountain pine beetles (Dendroctonus ponderosae Hopkins) have been killing pines on millions of ha throughout the western United States since 2000. One species being affected is whitebark pine (Pinus albicaulis Engelm.), a five-needle pine already experiencing a number of other threats. Whitebark pine is a keystone species providing a variety of values including watershed protection and food and habitat for wildlife. An increasingly used method of protecting pines from mountain pine beetles involves the antiaggregation pheromone verbenone, but no studies have evaluated the ability of verbenone applied annually to protect whitebark pines throughout mountain pine beetle outbreaks. We applied verbenone pouches annually for 7 years until an outbreak ended. Probabilities that whitebark pines survived through the end of the outbreak were 0.34 0.15 for control trees and 0.68 0.17 for trees treated with verbenone once per year. Evidence from a second verbenone treatment that was discontinued before the end of the outbreak suggested that applying verbenone twice, as opposed to once, per year may more effectively protect trees. Increased survival did not appear to vary with tree size (i.e., dbh). We believe increased survival of the magnitude we observed could reduce risks to threatened whitebark pine populations.
Environmental drivers of taxonomic, functional and phylogenetic diversity (alpha, beta and gamma components) in estuarine fish communities

We applied a diversity partitioning approach to identify the influence of multiple environmental factors on taxonomic, functional and phylogenetic diversity of estuarine fish assemblages at different spatial scales. Our aim was to determine (1) how variation in γ‐diversity (estuary scale) is supported by changes in α‐ (local scale) and β‐components (dissimilarity between these two scales) for the three diversity facets and (2) how these diversity measures are related to biogeographic, hydroclimatic, marine, estuarine and land cover conditions.
The Y rescued by the X ? : evolution of dosage compensation in humans and other questions on sex chromosome evolution in eukaryotes

The first part of my thesis concerns two different mechanisms of the Y being rescued by the X. Firstly, I contributed to a controversy on mammalian dosage compensation. During the 60s Susumo Ohno hypothesized a two-step dosage compensation mechanism. In males, the high loss of Y-linked genes led to a dosage imbalance: these genes were previously present in two allelic copies and became unicopy, meaning that their expression has been halved. According to Ohno’s hypothesis, in response to this imbalance the mammalian X would have doubled its expression in the two sexes, resulting in a to high expression in females. This second dosage imbalance would have been resolved by the random inactivation of one of the two Xs in females. Whereas the second part of Ohno’s hypothesis, the X-chromosome inactivation, has been well studied, the first part remained speculative until the 2000s. I studied human X-linked expression data and was able to show, concomitantly with other authors, that the first part of Ohno’s hypothesis is not totally true as only some of the X-linked genes are hyperexpressed. I later participated in the writing of a review aiming to give an alternative hypothesis for the evolution of X-chromosome inactivation in mammalian females than dosage compensation. Secondly, I studied signatures of X-Y gene conversion in several genes within numerous primate species. Myresults led me to discuss if these events were indeed selected for. I hypothesize that these gene conversion events occurred in a neutral manner. These two different studies suggest that the X chromosome may not be as much a help for the Y as has been suggested. Lastly, moving away from model species, I studied the peculiar sex chromosomes of a brown alga: Ectocarpus siliculosus. This work allowed me to test if the current hypotheses on sex chromosome evolution still hold in a eukaryotic group that diverged from animals more than one billion years ago
Parkinson’s Disease-associated proteins: studying their role in mitophagy with cellular and Drosophila models

Parkinson’s Disease (PD) is the second most common neurodegenerative disease, for which there is no effective treatment or biomarker. In about 10% of the cases PD is caused by mutations in PD-associated genes. Amongst these genes, the E3 ubiquitin-ligase Parkin and the Ser/Thr kinase PINK1 have been reported to act in a common pathway as key regulators of mitophagy, a selective type of autophagy where mitochondria are engulfed and degraded in the lysosomes. However, the molecular mechanisms leading to PD and the involvement of distinct PD-associated genes in mitophagy is unclear. Here, I studied basal and Parkin-dependent mitophagy in several cellular and Drosophila models, and employed these systems to check the involvement of selected PD-associated proteins in mitophagy. I report that USP30 regulates both, basal and Parkin-dependent mitophagy, showing that USP30 is a druggable target to modulate mitophagy. In addition, I studied the role of Parkin in Drosophila neurons and showed that Parkin activity affects locomotion and survival. Moreover, I have sought in vivo Parkin substrates by performing a mass spectrometry proteomic study employing a fly model that constitutively expresses biotinylated ubiquitin. This led to the identification of both established and novel Parkin substrates, amongst which I found the PDassociated protein VPS35. Finally, I generated a mitophagy reporter fly by introducing mt-Keima and briefly studied mitophagy in vivo. All together, the work performed during this thesis will set the basis for further studies to identify physiologically relevant Parkin substrates and to analyse mitophagy in vivo employing the mt-Keima flies.
Weeds density and late sown maize productivity influenced by compost application and seed rates under temperate environment.

Weeds reduces huge amount of yield of the economic crop ranging from 30 to 70 % of the total production. In upland environment weeds are usually found abundant in field as compared in low land environment due to the dissemination of weeds by animals, winds and due to spring water. Spring water brings weeds seeds to field by passing of water through grassy and Soddy channels in brushy congested herbaceous hilly area and some time by grazing of animals. Weeds spread in to farmer fields in this way. Therefore current field experiment was conducted to evaluate the influence of seed rate and compost on weeds density and late sown of maize productivity. At high elevations in Swat-Pakistan optimum time for maize sowing started from May 15 and continued till to June 15 whereas the experimental plots were sown on July 15 2013. Experiment was comprised on four compost levels (5, 10, 15 and 20 Mg ha) and four seed rate (10, 20, 30 and 40 kg ha) with a test cultivar (cv. Baber). Subplot size was kept 3 m in length and 4.5 m in width (13.5 m). Weeds density significantly influenced all the agronomic traits of the maize plant. Seed rate and compost application significantly affected weeds population per unit area. Minimum weeds per unit area in all growth stages were observed with the application highest seed rate. It was observed from the results that seed rate @ 40 kg ha and compost application at the rate of 5 Mg ha reduced weeds population in all the investigated intervals (25, 50 and 75 DAS). Application of compost @ 20 Mg ha produced optimum cob length (19 cm), plant height (179.19 cm), thousand grain weight (192.83 g) and grain yield (2712 kg ha). While the optimum grain cob 1 were noted in seed sown at the rate of 30 kg ha with the application of compost at the rate of 20 Mg ha (375 grain cob). On the basis of the above results it was concluded that to reduced weeds population per unit area and to enhanced productivity of maize crop seeds should be sown at the rate of 40 kg hawith the application of Compost at the rate of 20 Mg ha for late sowing under the agro ecological condition of Swat
Effects of hatchery supplementation on abundance and productivity of natural-origin Chinook salmon: two decades of evaluation and implications for conservation programs

Hatchery supplementation has been developed to conserve salmonid populations and provide fisheries. We evaluated supplemented and reference Chinook salmon (Oncorhynchus tshawytscha) populations prior to, during, and after supplementation ceased for 22 years in two major drainages in Idaho, USA. Basin-level analyses showed supplementation increased abundance at some life stages, but effects did not persist into the postsupplementation phase and had no apparent influence on productivity. Natural-origin juvenile abundance increased during supplementation but results for adults were ambiguous. After supplementation ceased, abundance and productivity in supplemented and reference populations returned to their presupplementation relationships. Intensive analyses of supplemented populations with weirs showed abundance increased at some life stages with the addition of female spawners. However, the rate of increase varied with female origin (natural > supplementation ≥ nontreatment hatchery), and effects diminished through the life cycle. Based on these findings, we provide guidance for conservation programs. Supplementation alone is not a panacea because it does not correct limiting factors, which must be addressed to achieve population levels capable of sustaining ecological function and harvest.
Meiosis leads to pervasive segregation distortion and copy-number variation in accessory chromosomes of the wheat pathogen Zymoseptoria tritici

Meiosis is one of the most conserved molecular processes in eukaryotes. The fidelity of pairing and segregation of homologous chromosomes has a major impact on the proper transmission of genetic information. Aberrant chromosomal transmission can have major phenotypic consequences, yet the mechanisms are poorly understood. Fungi are excellent models to investigate processes of chromosomal transmission, because many species have highly polymorphic genomes that include accessory chromosomes. Inheritance of accessory chromosomes is often unstable and chromosomal losses have little impact on fitness. We analyzed chromosomal inheritance in 477 progeny coming from two crosses of the fungal wheat pathogen Zymoseptoria tritici. For this, we developed a high-throughput screening method based on restriction site associated DNA sequencing (RAD-seq) that generated dense coverage of genetic markers along each chromosome. We identified rare instances of chromosomal duplications (disomy) in core chromosomes. Accessory chromosomes showed high overall frequencies of disomy. Chromosomal rearrangements were found exclusively on accessory chromosomes and were more frequent than disomy. Accessory chromosomes present in only one of the parents in an analyzed cross were inherited at significantly higher rates than the expected 1:1 segregation ratio. Both the chromosome and the parental background had significant impacts on the rates of disomy, losses, rearrangements and segregation distortion. We found that chromosomes with higher sequence similarity and lower repeat content were inherited more faithfully. The large number of rearranged progeny chromosomes identified in this species will enable detailed analyses of the mechanisms underlying chromosomal rearrangement.
TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer

Clustering approaches that rely on a large number of variables, such as expression levels of thousands of genes, are often not well adapted to address the complexity and heterogeneity of tumors where small sets of genes may drive multiple cellular processes associated with carcinogenesis. Biclustering algorithms that perform local clustering on subsets of genes and conditions help address this problem. We propose a Tunable Biclustering Algorithm (TuBA) based on a novel pairwise proximity measure among gene pairs, which examines the relationship of samples at the extremes of genes’ expression profiles to identify similarly altered signatures. The identified pairwise associations are illustrated graphically with nodes and edges representing the genes and the shared samples, respectively. Robust biclusters are then identified in these graphs iteratively. The consistency of TuBA’s predictions was tested by comparing biclusters in 3,940 Breast Invasive Carcinoma (BRCA) samples from three independent sources, which employed different technologies for gene expression analysis (RNAseq and Microarray). Over 60% of the biclusters identified independently in each dataset had significant agreement among associated genes as well as similar clinical implications. About 50% of the biclusters were enriched in the ER-/HER2‐ (or basal-like) subtype, while more than 50% were associated with transcriptionally active copy number changes. Biclusters associated with gene expression patterns in non-malignant tissue were also found in tumor specimens. Overall, our method identifies a multitude of altered transcriptional profiles associated with the tremendous heterogeneity of diseased states in breast cancer, both within and across tumor subtypes, which is an important advance in understanding disease heterogeneity, and a necessary first step in individualized therapy.
Polymorphism and the analgesic activity of N-(3-pyridylmethyl)-4-hydroxy-2-oxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide

The advanced study of the analgesic activity of N-(3-pyridylmethyl)-4-hydroxy-2-oxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide selected by the results of the primary pharmacological screening as the leading structure has revealed a significant change in anesthetic properties in different samples of this compound. Since the substance under study was not soluble in water, and animals received it orally as a thin aqueous suspension, the most likely cause of the effect observed was thought to be the changes in the crystalline structure of N-(3pyridylmethyl)-4-hydroxy-2-oxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide occurring in it under the influence of external factors. This assumption has been fully confirmed by the thorough microscopic investigation of high – and low-active samples, as well as more objective data, the methods of powder and single crystal X-ray diffraction analysis. Thus, in particular, it has been found that with all the variety of crystalline and amorphous forms included in the samples studied their qualitative composition appeared to be quite similar. At the same time the quantitative content of some of the phases varies greatly, and obviously, it was the factor determining the size of the analgesic effect.