Miracle-dz/UniFAR-FTUs huggingface dataset:
1 Introduction to C. elegans Biology

I. GENERAL DESCRIPTION Caenorhabditis elegans is a small, free-living soil nematode found commonly in many parts of the world. It feeds primarily on bacteria and reproduces with a life cycle of about 3 days under optimal conditions. The two sexes, hermaphrodites and males, are each about 1 mm in length but differ in appearance as adults, as shown in Figure 1. Hermaphrodites produce both oocytes and sperm and can reproduce by self-fertilization. Males, which arise spontaneously at low frequency, can fertilize hermaphrodites; hermaphrodites cannot fertilize each other. A hermaphrodite that has not mated lays about 300 eggs during its reproductive life span. Juvenile worms hatch and develop through four stages (commonly referred to as larval stages, although no metamorphosis is involved), punctuated by molts. The mature adult emerging from the fourth molt is fertile for about 4 days and then lives for an additional 10–15 days. C. elegans is a simple organism, both anatomically and genetically. The adult hermaphrodite has only 959 somatic nuclei, and the adult male has only 1031. The haploid genome size is 8 × 10 7 nucleotide pairs, about eight times that of the yeast Saccharomyces or one-half that of the fruit fly Drosophila. C. elegans is easily maintained in the laboratory, where it can be grown on agar plates or in liquid culture with Escherichia coli as a food source (see Methods). It can also be grown axenically in liquid media. Individual animals are conveniently observed and manipulated with the aid of a dissecting microscope,.
Spawning closures: ecological and economic trade-offs in management of mixed demersal flatfish fisheries in the North Sea

In dit rapport wordt een verkennende analyse gepresenteerd naar de effecten van seizoenvisserij in de Noordzee platvisvisserij. De studie analyseert de effecten van een sluiting van de visserij in de paaiperiode van schol en tong. Naast de effecten op de bestandsgrootte van de hoofdsoorten van de platvisvisserij, schol en tong, wordt ook het effect onderzocht op de commercieel belangrijke bijvangst soorten tarbot en griet, en op een aantal ecosysteem indicatoren.The contribution of spawning closures to sustainable management of North Sea flatfish fisheries is explored using a spatial and temporal explicit model of four target species (sole, plaice, turbot and brill) and two bycatch species (cod, rays). Seasonal patterns in fishing effort and partial fishing mortality rates per day at sea by age group and area are estimated to quantify the effect of different spawning closure scenarios for sole and plaice on the exploitation pattern (F-at-age).
Investigation on the Isolation and Identification of the Listeria Species in the White and Civil Cheeses Purchased From Erzurum Region

In this study, 34 white cheeses and 16 civil (local name) cheeses purchased from markets and shops in Erzurum during the period of January 1995-April 1996 were analysed. The samples were streaked directly onto LSA and Palcam Agar media in Petri Plates and incubated at 37C° for 48 hours. After the incubation, the growing colonies on LSA-agar plates were examined by Henry's Modified IIIumination Method while collonies on Palcam agar were examined by naked eye. Typical colonies were selected and used for several biochemical tests. As a result, it was found that only one sample (2.94%) of the white cheeses examined was found to contain three Listeria spp. (2 L. monocytogenes and 1 L. innocua). On the other hand, only one sample (6.25%) of a total of 16 civil cheeses examined was found to contain one Listeria sp ( L. monocytogenes ). The results were discussed in light of the literature.
Contribution à la définition d’idéotypes de miscanthus valorisables pour la production de bioéthanol de 2ème génération et perspectives en sélection

Face a l’epuisement du petrole, l’Europe s’oriente vers la production de bioethanol 2eme generation a partir de biomasse vegetale. L’espece Miscanthus x giganteus est prometteuse de par son fort rendement et ses faibles impacts environnementaux. Cependant, sa diversite genetique est faible et sa composition de biomasse pas forcement optimale pour produire du bioethanol 2eme generation. Cette these explore donc differentes especes de Miscanthus pour definir des ideotypes et des pistes en selection afin d’ameliorer le miscanthus pour ce debouche. Trois approches ont ete menees : une etude bibliographique, une etude experimentale au champ et des tests en pilote industriel. L’etude bibliographique montre une forte variabilite environnementale et genotypique pour les caracteres associes a la production et a la composition de biomasse. L’analyse des donnees experimentales revele des caracteres antagonistes : une forte production de biomasse est associee a de fortes teneurs en cellulose et lignines, mais a de faibles teneurs en hemicelluloses, solubles et cendres. De fortes teneurs en lignines contribuent egalement a reduire l’efficacite de la transformation de la biomasse en bioethanol 2eme generation. Enfin, des outils de phenotypage ont ete definis : la hauteur de vegetation et le volume aerien de la plante permettent de predire la production de biomasse des stades adultes a partir des stades jeunes. La spectroscopie proche infra-rouge permet aussi de predire la composition de la biomasse. Ce travail contribue a la definition d’ideotypes de miscanthus pour une valorisation en bioethanol 2eme generation en proposant des criteres, des outils et des perspectives en selection.
Characterization of the 16S/23S ribosomal RNA intergenic spacer regions of Listeria

The 16S/23S ribosomal RNA (rRNA) intergenic spacer (1GS) regions from pathogenic and non-pathogenic species (spp.) of Listeria were characterized by the polymerase chain reaction (PCR) and DNA sequencing. DNA sequencing data for the small rRNA IGS region showed that this 1GS was approximately 244 bp in length and was highly homologous (95 to 99 %) in five of the six Listeria spp examined; i.e., L. monocytogenes, L. innocua, L. seeligeri, L. welshimeri, and L ivancvii. A lower degree of homology (91 to 94 %) was detected in the large rRNA IGS region (ca. 494 bp) of the«e species. The DNA sequence data was used to develop two sets of oligonucleotide primers for PCR-based detection of the members of the genus Listeria. The first set of primers were Listeria genus-specific and, the second set of primers were L. monocytogenes-speciiic.
Receptor-Dependent Phagocytosis of Clostridium sordellii by Human Decidual Macrophages

Clostridium sordellii is an emerging pathogen associated with highly-lethal female reproductive tract (FRT) infections following childbirth, abortion, or cervical instrumentation. Gaps in our understanding of the pathogenesis of C. sordellii infections present major challenges to the development of better preventive and therapeutic strategies against this problem. We sought to determine the mechanisms whereby uterine DMs phagocytose this bacterium and tested the hypothesis that human DMs utilize class A scavenger receptors (CASRs) to internalize unopsonized C. sordellii. In vitro phagocytosis assays with human DMs incubated with pharmacological inhibitors of CASRs (fucoidan, polyinosinic acid, and dextran sulfate) revealed a role for these receptors in C. sordellii phagocytosis. Soluble macrophage receptor with collagenous structure (MARCO) receptor prevented C. sordellii internalization, suggesting that MARCO is an important CASR in DM phagocytosis of this microbe. Peritoneal macrophages from MARCO-deficient mice, but not wild-type or SR-AI/II-deficient mice, showed impaired C. sordellii phagocytosis. MARCOnull mice were more susceptible to death from C. sordellii uterine infection than wild-type mice and exhibited impaired clearance of this bacterium from the infected uterus. Thus, MARCO is an important phagocytic receptor utilized by human and mouse macrophages to clear C. sordellii from the infected uterus.
Investigations on ileal microbial flora in weaning piglets

To characterize ileal microbial flora in weaning piglets a slaughter trial was conducted. 224 German Landrace piglets of both genders were allocated to four different feeding regimes (with or without avilamycin, 3 resp. 8 % crude fibre content). At predefined times pre- and postweaning piglets were sacrificed, the whole intestinal tract was removed and its content collected separately for each section. The microbial community was examined applying classical plate counting (selective agar plates) and molecular techniques (DGGE, 16SrDNA-sequencing). Furthermore a range of microbial metabolites was determined. Changes in ileal microflora ? rather due to age than to diet - were observed pre- and postweaning.
Effects of olive leaf extract on rumen microbial fermentation in in vitro semi-continuous culture system (RUSITEC).

Bu arastirmada rumen simulasyon teknigi (RUSITEC) kullanilarak zeytin yapragi ekstraktinin % 50 kaba yem % 50 konsantre yemden olusan bir rasyonun in vitro fermantasyonu uzerine etkilerinin arastirilmasi ve bu etkilerin monensinin etkileri ile karsilastirilmasi amaclandi. Rusitec sistemde 8 fermenter kullanildi: Bunlardan ilk ikisine gunluk 150 mg (OLE-H), diger ikisine ise gunluk 15 mg (OLE-L) zeytin yapragi ekstrakti ilave edildi. Kalan 4 fermenterden ikisine gunluk 5 mg monensin (MON, pozitif kontrol) ilavesi yapilirken, son iki fermentere hicbir ilave yapilmayip kontrol (CTR) olarak kullanildi. Yedi gunluk adaptasyon fazindan sonra, 7 gun boyunca temel fermantasyon parametreleri belirlendi. Deneme gruplari arasinda pH ve organik madde sindirilebilirligi acisindan istatistiksel bir farklilik bulunmadi. MON propiyonat uretimini istatistiksel olarak belirgin bir sekilde artirirken (p < 0,05), asetat ve butirat uretimleri, asetatin propiyonata orani, protozoon sayisi ve NH3-N konsantrasyonunu belirgin bir sekilde azaltti (p < 0,05). CTR ile karsilastirildiginda, OLE’nin her iki konsantrasyonu da toplam ucucu yag asidi (UYA) ve propiyonat uretimlerini istatistiksel olarak anlamli bir sekilde arttirdi (p < 0,05). Ancak OLE-H butirat uretimi ve toplam protozoon sayisini azaltti (p < 0,05). Bu arastirmanin sonuclarina dayanarak zeytin yapragi ekstraktinin yari-surekli rumen simulasyon kultur sisteminde bazi fermantasyon parametreleri uzerinde olumlu etkiler olusturdugunu, dolayisiyla rumendeki fermantasyon verimliligini artirabilecegini soyleyebiliriz
Genetics in Sustainable Fisheries Management

Contributors . Preface . Introduction . Biological units in fishery management . Marine genetic resources and sustainable fisheries . Framework for conservation and management of genetic resources of marine fish . Freshwater fish genetic resources and conservation approaches . Genome manipulation in fishery management . Gene transfer in fisheries . Genetic factors in production . Introgressive hybridization of introduced peled with the native whitefish . Microsatellite DNA markers for monitoring genetic change in hatchery stock for release and net--cage culture of red sea bream . Index
Autoregulatory and Paracrine Control of Synaptic and Behavioral Plasticity by Dual Modes of Octopaminergic Signaling: A Dissertation

Synaptic plasticity – the ability of a synapse to change – is fundamental to basic brain function and behavioral adaptation. Studying the mechanisms of synaptic plasticity benefits our understanding of the formation of neuronal connections and circuitry, which has great implications in the field of learning and memory and the studies of numerous human diseases. The Drosophila larval neuromuscular junction (NMJ) system is a powerful system for studying synaptic plasticity. The NMJ consists of at least two different types of motorneurons innervating the body wall muscles. Type I motorneurons controls muscle contraction using glutamate as the neurotransmitter, while type II are modulatory neurons that contain octopamine. Octopamine is a potent modulator of behavior in invertebrates. Nevertheless, its function at the synapse is poorly understood. In my thesis research, I investigated the role of octopamine in synaptic plasticity using the Drosophila NMJ system. Preliminary observations indicate that increased larval locomotion during starvation results in an increase of filopodia-like structures at type II terminals. These structures, which we termed as “synaptopods” in our previous studies, contain synaptic proteins and can mature into type II synapses. I demonstrated that this outgrowth of type II terminals is dependent on activity and octopamine. Mutations and genetic manipulations affecting the production of octopamine decrease synaptopods, whereas increase of type II activity or exogenous application of octopamine increase synaptopods. Interestingly, I found that the type II octopaminergic neurons have an absolute dependence on activity for their innervation of the muscles.
Drosophila piRNA Function in Genome Maintenance, Telomere Protection and Genome Evolution: A Dissertation

Upon fertilization, the early embryo sustains most of the cellular processes using the maternally deposited reserves in the egg itself until the zygotic gene expression takes charge. Among the plethora of essential components provided by the mother are small non-coding RNAs called PIWI-interacting RNAs (piRNAs), which provide immunity to the zygote against transposon challenge. In this thesis, I have presented three different functions of piRNAs in Drosophila melanogaster - in maintenance of genomic integrity, telomere protection and their role as an adaptive immune system against genomic parasites. In Chapter 2, I have described the phenotypic effects of the loss of piRNA function in early embryos. The mutations affecting the piRNA pathway are known to cause embryonic lethality. To describe this lethality in detail, I have shown that all the characterized piRNA mutants show compromised zygotic genomic integrity during early embryogenesis. In addition, two piRNA pathway components, Aubergine (Aub) and Armitage (Armi) are also required for telomere resolution during early embryogenesis. Aub and Armi recruit telomeric protection complex proteins, HOAP and HP1, to the telomeric ends and thus avoid activation of the Non-homologous end joining (NHEJ) DNA repair pathway at the telomeres. There are about 120 transposon families in Drosophila melanogaster and piRNA pathway mutations cause activation of many of the resident transposons in the genome. In Chapter 3, I have described the effects of infection by a single transposon, P-element , in naive strains by introduction through the zygote. Activation of the P-element leads to desilencing of unrelated transposons, causing accumulation of germline DNA damage which is linked to severely reduced fertility in the hybrid females. However, there is partial restoration of fertility as the hybrid progeny age, which correlates with P-element piRNA production and thus P-element silencing. Additionally, a number of transposons mobilize into piRNA generating heterochromatic clusters in the genome, and these insertions are stably inherited in the progeny. Collectively our data shows that piRNA production can be triggered in the adults in an absence of maternal contribution and that piRNAs serve as an adaptive immune system which helps resolve an internal genetic conflict between the host and the parasite. In an effort to understand the phenotypic effects of piRNA dysfunction in Drosophila , we have uncovered new exciting roles for piRNAs in development and presented evidence how transposons can act as architects in restructuring the host genome.
Disruption of actin filaments induces mitochondrial Ca 2+ release to the cytoplasm

Background: Mitochondria are dynamic organelles that move along actin filaments, and serve as calcium stores in plant cells. The positioning and dynamics of mitochondria depend on membrane-cytoskeleton interactions, but it is not clear whether microfilament cytoskeleton has a direct effect on mitochondrial function and Ca 2+ storage. Therefore, we designed a series of experiments to clarify the effects of actin filaments on mitochondrial Ca 2+ storage, cytoplasmic Ca 2+ concentration ([Ca 2+ ]c), and the interaction between mitochondrial Ca 2+ and cytoplasmic Ca 2+ in Arabidopsis root hairs. Results: In this study, we found that treatments with latrunculin B (Lat-B) and jasplakinolide (Jas), which depolymerize and polymerize actin filaments respectively, decreased membrane potential and Ca 2+ stores in the mitochondria of Arabidopsis root hairs. Simultaneously, these treatments induced an instantaneous increase of cytoplasmic Ca 2+ , followed by a continuous decrease. All of these effects were inhibited by pretreatment with cyclosporin A (Cs A), a representative blocker of the mitochondrial permeability transition pore (mPTP). Moreover, we found there was a Ca 2+ concentration gradient in mitochondria from the tip to the base of the root hair, and this gradient could be disrupted by actin-acting drugs. Conclusions: Based on these results, we concluded that the disruption of actin filaments caused by Lat-B or Jas promoted irreversible opening of the mPTP, resulting in mitochondrial Ca 2+ release into the cytoplasm, and consequent changes in [Ca 2+ ]c. We suggest that normal polymerization and depolymerization of actin filaments are essential for mitochondrial Ca 2+ storage in root hairs.
INFLUENCE OF REDUCING IRRIGATION RATE AND ADDITION OF SUPER ABSORBENT POLYMER ON PEACH TREES GROWTH UNDER NORTH SINAI CONDITIONS

Peach trees (Prunus persica L.) about 6 -yearsold planted in sandy soil were used and spaced at 4 × 5 m and received nearly the same cultural care under drip irrigation system during 2013/2014 and 2014/2015 seasons in private Farm "Sleem Elbalwy" orchard at "ElMasmy" farms area in El-Arish district, North Sinai Governorate, Egypt to study the effect of regulated deficit irrigation and super absorbent polymer on vegetative growth of peach trees under North-Sinai Conditions. Three irrigation treatments were applied: a control (100 % of ETc) and two regulated deficit irrigation at 75 % and 50 % of ETc treatments using modified Penman and Monteith's modified equation and three polymer additions: No addition (control), 25 g/tree and 50 g/tree. The results showed that treated with 100% ETc achieved the highest value of each of number of new shoot, new shoots length, new shoots diameter, number of leaves per new shoots, leaf area and tree circumference followed by 75% in both seasons while irrigated with 50% ETc gave the lowest values. Also, the results showed that addition 50g/tree of super absorbent polymer increased all vegetative growth parameters followed by trees treated with 25g/tree compared with no addition treatment in both seasons. All treatments were applied on December 20 in both seasons. Results indicate that regulated deficit irrigation at 75% of ETc, addition 50g absorbent polymer/tree showed the highest increase in vegetative growth compared with 50% of ETc treatment.
Negotiating Identity and Social Existence; Narratives of HIV+ve Trans-Women in Nagaland

In contemporary usage, 'transgender' is used as an umbrella term for individuals whose gender expression runs against societal binary construction of gender, including transsexuals, cross -dressers, drag-kings, drag-queens, gender queer individuals and those who do not identify themselves with either of the two sexes currently defined. In other words, trans gender may also used as a broad term to refer to people who do not conform to the traditional gender norms and boundaries or whose 'concept of self' appear to conflict with the assigned gender at birth. Generally, those individuals who identify themselves as 'trans genders' defy rigid, binary gender construction, and tend to break away from the prevalent stereotypical gender roles or conventional concept of masculinity and feminity.
The Role Of Intraspecies And Interspecies Communication Of Pseudomonas Aeruginosa Pa14 Towards Phenazine Production And Virulence

Here, we show that quorum sensing (QS) modulates current generation by the anode-respiring bacterium P. aeruginosa by controlling the production of the electron-mediating phenazines. The current generation by a wildtype (WT) strain of P. aeruginosa PA14, two QS signal-negative mutants ∆lasI and ∆rhlI, and a GacS/GacA protein-regulatory mutant retS::TN was investigated under different environmental conditions. The QS signal-negative mutants exhibited significant increases in current production (∆lasI: 5.8-fold; ∆rhlI: 17.6-fold) when the growth medium was exogenously supplemented with the appropriate QS inducing lactone compared to growth medium devoid of the lactones. The retS::TN mutant generated significantly higher current (45fold) than the WT under anaerobic conditions. Interestingly, anaerobic current generation by the WT was 28-fold higher with exogenously supplied lactones. Compared to anaerobic conditions, the WT with some oxygen (microaerobic conditions) exhibited enhanced phenazine production (39-fold) and current levels (48-fold). Iron-rich medium and microaerobic conditions had a negative impact on current generation by retS::TN. All these results are directly linked to QS activity in P. aeruginosa, thus, demonstrating the importance of this bacterial communication
Trade flows analysis in textile sector between China, EU-28 and selected group of countries (2008-2014). A gravity model

In an increasingly globalized world, political and economic relations between countries are of great importance. This article shows the existing business relationship between China and the European Union from 2008 to 2014. Thus focusing on the textile sector, we want to analyze the impact that have exports and Chinese trade flows on the countries of the European Union during the period of economic crisis that has affected the world economy. It is analyzed by a gravitational econometric analysis, which variables are the most important and which ones have more value in the field of study we refer. Furthermore, subsequently, and in order to make a more accurate estimate, another econometric model will be estimated including, apart from the 28 countries of the European Union, the United States, Canada, Brazil, South Africa, Australia, Argentina, Mexico, Morocco and New Zealand, thereby increasing the number of observations. Classification JEL: F10, F13, F14
Control of Harmful Algal Blooms by Clay via Photochemical Reactions

In an attempt to improve the removal efficiency of natural clay to red tide dinoflagellates, Cochlodinium polykrikoides and Prorocentrum micans, the synergistic effect of clay plus light was investigated. The removal capacity of dinoflagellates by clay via photochemical reactions was increased to about 20% of the dark control values. Lightinduced effect began to be occurred when the light intensities above about 2,300 μ㏖·m^(-2)·s^(-1). The capacity of clay plus light to removal the C. polykrikoides was related to the concentration of TiO₂ in caly: the higher the content of TiO₂, the higher the removal rates. Particularly, when the C. polykrikoides treated with TiO₂ or rose bengal were subjected to UV-A (600 μ㏖·m^(-2)·s^(-1)) or white light (λ$gt;320 ㎚; 1,400 μ㏖·m^(-2)·s^(-1)) for 10 min under aerobic conditions, the algal cell was severely damaged with the membrane lysis. The suspension of clay, when exposed to white light, generate reactive oxygen species (ROS) such as singlet oxygen (¹O₂), as measured by the imidazole plus RNO method. These data show that the ROS, photogenerated from clay, -mediated oxidative damages are enhanced the original effect of clay to algal species. These results suggest that the removal efficiency of red tide dinoflagellates by clay under bright sunlight is higher than that of a cloudy day.