Miracle-dz/UniFAR-FTUs huggingface dataset:
Alcohol causes lasting differential transcription in Drosophila mushroom body neurons

Repeated alcohol experiences can produce long-lasting memories for sensory cues associated with intoxication. These memories can ultimately trigger relapse in individuals recovering from alcohol use disorder (AUD). The molecular mechanisms by which alcohol changes memories to become long-lasting and inflexible remain unclear. New methods to analyze gene expression within precise neuronal cell-types can provide further insight towards AUD prevention and treatment. Here, we employed genetic tools in Drosophila melanogaster to investigate the lasting consequences of ethanol on transcription in memory-encoding neurons. Drosophila rely on mushroom body (MB) neurons to make associative memories, including memories of ethanol-associated sensory cues. Differential expression analyses found that distinct transcripts, but not genes, in the MB were associated with experiencing ethanol alone compared to forming a memory of an odor cue associated with ethanol. These findings reveal the dynamic and highly context-specific regulation of splicing associated with encoding behavioral experiences. Our data thus demonstrate that alcohol can have lasting effects on transcription and RNA processing during memory formation, and identify new transcript targets for future AUD and addiction investigation.
Habitat selection, parasites and injuries in Amazonian crocodilians

Caíman crocodilus is found most frequently in relatively warm, shallow or grassy areas in the larger rivers, lakes and canals of Amazonia. The habitats that it uses are increasing in area because of human activities. Paleosuchus trigonatus appears to be ¡estricted to small forest st¡eams in dense forest. Water temperatures are relatively low and constant in the streams and opportunities to bask are limited . in the forest. P¿leosuchus pølpebrosus and M. niger æe both found most commonly in the parts of major lakes, rivers and canals which have steep banks and little floating grass. To what extent the present distributions are influenced by intensive hunting of M. niger is unknown, Animals had similar injury rates in all habitats but in the Lago Amanã area individuals in the lake had higher leech, and lower nematode infestation than individuals in the sur¡ounding canals. The giant rctifer Limniøs ceratophylli is reported for the first time as an epizoic on the ventral surfaces ofM. niger.
Observations of Double Brooding and Inbreeding of Piping Plovers on Fire and Westhampton Islands, New York

Abstract In the summer of 2016, we observed a pair of Charadrius melodus (Piping Plover) successfully hatch 2 nests at Fire Island National Seashore and fledge chicks from both broods. Double brooding is rare among Piping Plovers, and fledging chicks from both broods is rarer still. In 2017, we observed male and female siblings, 1 individual hatched from each of the double brood nests, incubating the same clutch of eggs on Westhampton Island. Although double brooding has been noted before in this species, this is the first observation of subsequent inbreeding from such an observation on the Atlantic Coast. This observation is unlikely to be evidence of widespread inbreeding within Piping Plover populations due to little evidence of allelic diversity problems in past genetic studies.
A preliminary study on copper and zinc levels and associated haematological changes in the blood of goats slaughtered at Bodija Abattoir, Nigeria

Copper and zinc are two micro-minerals important for maintenance of health and optimal production. This research sought to establish the levels of copper and zinc in goats to provide data for further studies on micronutrients, their interaction and deficiency states. Health status of sampled goats were clinically evaluated. Blood samples were collected through jugular venu-puncture. One (1) ml of each blood sample was acid digested with concentrated nitric acid, assayed for zinc and copper using atomic absorption spectrophotometer. Haematology was also done using whole blood as a health index. Most of the goats looked apparently healthy, while few goats showed emaciation, crusty skin lesions, varying degrees of achromotrichia (change in coat colour) and rough hair coats. 89.9 % had hypocupraemia, while none of the sampled goats showed zinc deficiency. However, zinc toxicity occurred in 84.4 % of the sampled goats when compared to reference values. Haematology showed varying result, ranging from monocytic hypochromic anaemia to polycytaemia. All anaemic animals were found to be deficient in copper. The study has highlighted the presence of copper deficiency and or zinc toxicity in goats and forms a preliminary data to the study of the fate of small ruminant health in the face of micronutrient imbalance. Keywords: Copper, Zinc, Micronutrient, Haematology, Hypocupraemia, Achromotrichia, Goats
Space Radiation-Induced Hematopoietic Stem Cell Injury

Space radiation is an unavoidable health risk during space activities. Hematopoietic cells are sensitive to radiation including proton and oxygen radiation and so on. Understanding the mechanisms responsible for detrimental effects of space radiation is important to achieve countermeasures protecting hematopoietic stem cells (HSCs), which generates different hematopoietic populations. However, the biological effects of various sources of space radiation on HSCs are not understood well. Induction of cellular apoptosis, reactive oxygen species (ROS), and DNA damage upon space radiation is believed to be critical mediators for HSC damage. In this chapter, we will mainly discuss the biological effectiveness of proton and oxygen radiation on the numbers and function of HSCs. Space radiation-induced apoptosis, ROS, and DNA damage were examined as well, which will provide foundation to develop novel strategies protecting HSCs from space radiation.
Tobacco War: Inside the California Battles

"Tobacco War" charts the dramatic and complex history of tobacco politics in California over the past quarter century. Beginning with the activities of a small band of activists who, in the 1970s, put forward the radical notion that people should not have to breathe second-hand tobacco smoke, Stanton Glantz and Edith Balbach follow the movement through the 1980s, when activists created hundreds of city and county ordinances by working through their local officials, to the present - when tobacco is a highly visible issue in American politics and smoke-free restaurants and bars are a reality throughout the state. The authors show how these accomplishments rest on the groundwork laid over the past two decades by tobacco control activists who have worked across the U.S. to change how people view the tobacco industry and its behavior. "Tobacco War" is accessibly written, balanced, and meticulously researched.The California experience provides a graphic demonstration of the successes and failures of both the tobacco industry and public health forces. It shows how public health advocates slowly learned to control the terms of the debate and how they discovered that simply establishing tobacco control programs was not enough, that constant vigilance was necessary to protect programs from a hostile legislature and governor. In the end, the California experience proves that it is possible to dramatically change how people think about tobacco and the tobacco industry and to rapidly reduce tobacco consumption. But California's experience also demonstrates that it is possible to run such programs successfully only as long as the public health community exerts power effectively. With legal settlements bringing big dollars to tobacco control programs in every state, this book is must reading for anyone interested in battling and beating the tobacco industry.
Sex dimorphic phrase combinatorics in the song of the indris (Indri indri)

We used a logic distance to investigate intra and inter-individual variation in the phrase combinatorics of a singing primate, the indri, which inhabits the montane rain forests of Madagascar. Indris combine long notes, short single notes, and phrases consisting of two, three, four, or five units with slightly descending frequency. We calculated the similarity across different individual songs using the Levenshtein distance. We then analyzed the degree of similarity within and between individuals and found that: i) the phrase structure of songs varied between reproductive males and females; ii) male contributions to the song are overall more similar to those of other males; iii) male contributions are more stereotyped than females' ones. The picture emerging from phrase combinatorics in the indris is in agreement with previous findings of rhythmic features and repertoire size, which also suggested that female songs are potentially more distinctive than those of males.
CVRMS: Cross-validated Rank-based Marker Selection for Genome-wide Prediction of Low Heritability

CVRMS is an R package designed to extract marker subsets from repeated rank-based marker datasets generated from genome-wide association studies or marker effects for genome-wide prediction (https://github.com/lovemun/CVRMS). CVRMS provides an optimized genome-wide biomarker set with the best predictability of phenotype by implemented ridge regression using genetic information. Applying our method to human, animal, and plant datasets with wide heritability (zero to one), we selected hundreds to thousands of biomarkers for precise prediction.
Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity

Terpenoids comprise tens of thousands of small molecule natural products that are widely distributed across all domains of life. Plants produce by far the largest array of terpenoids with various roles in development and chemical ecology. Driven by selective pressure to adapt to their specific ecological niche, individual species form only a fraction of the myriad plant terpenoids, typically representing unique metabolite blends. Terpene synthase (TPS) enzymes are the gatekeepers in generating terpenoid diversity by catalyzing complex carbocation-driven cyclization, rearrangement, and elimination reactions that enable the transformation of a few acyclic prenyl diphosphate substrates into a vast chemical library of hydrocarbon and, for a few enzymes, oxygenated terpene scaffolds. The seven currently defined clades (a-h) forming the plant TPS family evolved from ancestral triterpene synthase- and prenyl transferase–type enzymes through repeated events of gene duplication and subsequent loss, gain, or fusion of protein domains and further functional diversification. Lineage-specific expansion of these TPS clades led to variable family sizes that may range from a single TPS gene to families of more than 100 members that may further function as part of modular metabolic networks to maximize the number of possible products. Accompanying gene family expansion, the TPS family shows a profound functional plasticity, where minor active site alterations can dramatically impact product outcome, thus enabling the emergence of new functions with minimal investment in evolving new enzymes. This article reviews current knowledge on the functional diversity and molecular evolution of the plant TPS family that underlies the chemical diversity of bioactive terpenoids across the plant kingdom.
Mapping the S1 and S1’ subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents

The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. A series of 26 new compounds waswere designed, synthesized, and tested against the recombinant cruzain (Cz) to map its S1/S1′ subsites. The same series was evaluated on a panel of four human cysteine proteases (CatB, CatK, CatL, CatS) and Leishmania mexicana CPB, which is a potential target for the treatment of cutaneous leishmaniasis. The synthesized compounds are dipeptidyl nitriles designed based on the most promising combinations of different moieties in P1 (ten), P2 (six), and P3 (four different building blocks). Eight compounds exhibited a Ki smaller than 20.0 nM for Cz, whereas three compounds met these criteria for LmCPB. The three inhibitors had an EC50 value of ca. 4 μM, thus being equipotent to benznidazole according to the anti-trypanosomal effects. Our mapping approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cysteine proteases. Author Summary Despite many achievements in identifying novel agents for the treatment of tropical and neglected diseases, further research continues to be of fundamental importance. Our research groups have been using the cruzipain cysteine protease in its recombinant form, cruzain (Cz), to identify new trypanocidal agents. Considering the possible interchangeability with other cysteine proteases, the same series of dipeptidyl nitriles was tested in Leishmania mexicana LmCPB. Other potential targets for such inhibitors are human cysteine cathepsins, which are involved in different disease states. Thus, the inhibitors were also tested against cathepsins B, L, K, and S. Our results demonstrate that inhibition of these cysteine proteases can be achieved by appropriate structural modifications of dipeptidyl nitriles. It was also possible to identify trypanocidal agents, equipotent to benznidazole, the current drug of choice used for the treatment of Chagas disease.
Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa

The interesting history of Southern Africa has put the region in the spotlight for population medical genetics. Major events including the Bantu expansion and European colonialism have imprinted unique genetic signatures within autochthonous populations of Southern Africa, this resulting in differential allele frequencies across the region. This genetic structure has potential implications on susceptibility and resistance to infectious diseases such as human immunodeficiency virus (HIV) infection. Southern Africa is the region affected worst by HIV. Here, we discuss advances made in genome-wide association studies (GWAS) of HIV-1 in the past 12 years and dissect population diversity within Southern Africa. Our findings accentuate that a plethora of factors such as migration, language and culture, admixture, and natural selection have profiled the genetics of the people of Southern Africa. Genetic structure has been observed among the Khoe-San, among Bantu speakers, and between the Khoe-San, Coloureds, and Bantu speakers. Moreover, Southern African populations have complex admixture scenarios. Few GWAS of HIV-1 have been conducted in Southern Africa, with only one of these identifying two novel variants (HCG22rs2535307 and CCNG1kgp22385164) significantly associated with HIV-1 acquisition and progression. High genetic diversity, multi-wave genetic mixture and low linkage disequilibrium of Southern African populations constitute a challenge in identifying genetic variants with modest risk or protective effect against HIV-1. We therefore posit that it is compelling to assess genome-wide contribution of ancestry to HIV-1 infection. We further suggest robust methods that can pin-point population-specific variants that may contribute to the control of HIV-1 in Southern Africa.
Ribosome pausing, a dangerous necessity for co-translational events

Abstract In recent years translation elongation has emerged as an important contributor to the regulation of gene expression. There are multiple quality control checkpoints along the way of producing mature proteins and targeting them to the right cellular compartment, or associating them correctly with their partners. Ribosomes pause to allow co-translational protein folding, protein targeting or protein interactions, and the pausing is dictated by a combination of the mRNA sequence and structure, the tRNA availability and the nascent peptide. However, ribosome pausing can also lead to ribosome collisions and co-translational degradation of both mRNA and nascent chain. Understanding how the translating ribosome tunes the different maturation steps that nascent proteins must undergo, what the timing of these maturation events is, and how degradation can be avoided when pausing is needed, is now possible by the emergence of methods to follow ribosome dynamics in vivo. This review summarizes some of the recent studies that have advanced our knowledge about co-translational events using the power of ribosome profiling, and some of the questions that have emerged from these studies.
A Preliminary inventory of alien and cryptogenic species in Monastir Bay, Tunisia: spatial distribution, introduction trends and pathways

The Mediterranean Sea is a marine biodiversity hotspot under threat. One of the major impacts on its biological resources and services comes from the invasiveness of non-indigenous species (NIS). Nevertheless, NIS monitoring programs in the south basin of the Mediterranean Sea are in an early implementation stage. This study aims to describe NIS and cryptogenic species distribution in Monastir Bay (Tunisia) and to identify risk areas for the introduction and spread of invasive species, providing a baseline for future monitoring programs. To this end, a series of Rapid Assessment Surveys were carried out to identify NIS and cryptogenic species in one marina, five fishing ports, two aquaculture farms and the Special Conservation Area of the Kuriat islands. 24 species were found, of which 11 constitute new records for Monastir Bay, which represent a 33.3% of the total NIS reported in this Bay. Assemblages differed between substrata types, being NIS more abundant in artificial than in natural substrata. Regarding locations, Cap Monastir Marina was the most invaded site, the most transited by vessels and the only one visited by international sailing. Hence, this marina constitutes the main risk area to be monitored, although the fishing ports and fishing farms in the semi-enclosed coastal lagoon of Monastir Bay can also be considered as risk areas. Nevertheless, more research effort is needed in Monastir Bay in order to update the records of NIS and cryptogenic species and increase insight on the ecological evolution of these species and their related impacts on natural communities and marine resources.
Melliferous potential of Mentha aquatica

The abundance and diversity of flowers have declined and bees are chronically exposed to numerous pressures such as cocktails of agrochemicals, parasites and predators, climate change, and lack of floral resources. Chronic exposure to multiple interacting stressors is driving honey bee colony losses and declines of wild pollinators, that may lead to “pollination crisis” in which crop yields begin to fall. Effective monitoring of pollinator populations is urgently needed to inform management strategies into the future. Additionally, strategies to reinforce the health and well-being of bees are needed. Based on the literature data gathered, we propose to use Mentha aquatica as an additional melliferous plant to support bees’ nutritional needs and develop diverse and nutritionally balanced plant communities. Here, we review the literature data concerning the implantation of the genus Mentha to complete the foraging schedule of Apis mellifera with special emphasis on its use as valuable nutritionally resource and source of nutritional diversity. Additionally, we discuss the aspects of attractiveness of genus Mentha to honey bees. Our list of facts thus far reported in the literature on the use of M. aquatica will help in implementation of this specimen in helping the bees that are in difficult situation.
Effects of clear-cutting and selective felling in Swedish Boreal coniferous forest: response of invertebrate taxa eaten by birds

Our aim was to analyse the short-term effects (0-4 years) of selective felling and clear-cutting on the food resources of insectivorous birds. Literature data on bird diets showed that herbivorous larvae (Lepidoptera and Hymenoptera: Symphyta) and spiders (Araneae) were used by 81 and 50%, respectively, of 16 bird species breeding in the Swedish boreal coniferous forest. A field study comparing selective fellings, clear-cuttings and uncut controls showed con siderable effects of clear-cutting on both terricolous and field layer inverte brates.
IN VITRO AND IN VIVO EFFICIENCY OF FENNEL ESSENTIAL OIL AGAINST TOMATO FUSARIUM WILT AND ITS PROMOTION EFFECT ON PLANT GROWTH

In the present study, the potential biocontrol ability of fennel seeds essential oil against Fusarium oxysporum f. sp. lycopersici (FOL), in vitro and in vivo conditions was evaluated. Chemical composition of the essential oil was determined by GC-MS analysis and major components identified were trans-anethole, L-Fenchone, Estragole and Limonene. The different essential oils concentrations revealed to be efficient to inhibit the FOL growth with IC50 values =300.37 μl/l. Under greenhouse conditions using susceptible tomato plants, the use fennel essential oil as a curative treatment, resulted in a good protection against Fusarium wilt. In fact, the essential oil displayed a significant decrease (42.85%) in disease severity on tomato in comparison to control. Treatment with fennel essential oil significantly exhibited a growth promotion of infected or non-infected tomato plants. Moreover, the resistance induction was associated with several physiological changes in tomato plants. After 3 weeks post infection, physiological parameters such as, relative water content, total chlorophyll and carotenoid contents were altered by FOL and interestingly increased in fennel essential oil treated plants. This study demonstrated that fennel seeds essential oil was a promising biocontrol compound and could be considered in formulation of biofungicide used against Fusarium wilt.
Developing novel approaches to treat trauma-associated fungal infections

Traumatic injuries often result in infections leading to high morbidity and mortality. Fungal spores, the point of interest of this research, of species such as Mucormycetes, Scedosporium, Lomentospora, Fusarium and Candida, are ubiquitous in the environment. Here, we have taken a dual approach to investigate: 1) how two, novel treatments - acetic acid and blue light - are effective against those fungal species, and 2) how highly pathogenic and antifungal resistant species of Scedosporium and Lomentospora interact with innate immune cells. Firstly, I have demonstrated that low concentrations of acetic acid can inhibit spore germination as well as prevent growth of all fungal species tested. Therefore, acetic acid can be used as a potential preventative measure and/or treatment on infected wounds. Secondly, I have shown that blue light irradiation is effective against some, but not all fungal species, and should therefore be used with caution in a healthcare setting. In the latter part of this thesis I characterize the Scedosporium and Lomentospora interaction with macrophages. Using this system, I show for the first time that vomocytosis and lateral transfer are two distinct events and that these neglected fungal pathogens may hold interesting promise as a tool for understanding the fungal/host interaction. Lastly, I report on our preliminary attempts to establish a novel ex-vivo skin model and show that Langerhans cells within the epidermis do not mature nor release TNFα cytokine following infection with R. microsporus and S. apiospermum.