Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of myxidium rhodei (Cnidaria, Myxosporea) in the Lake Baikal basin

Distribution and prevalence of a myxosporean parasite, Myxidium rhodei Leger, 1905, infecting two cyprinid fish, a roach Rutilus rutilus and Siberian dace Leuciscus leuciscus baikalensis, have been studied in water bodies of the Lake Baikal basin. Over 15-year period (1998-2013), a total of 246 roaches and 189 daces from 27 stations were surveyed. Plasmodia of M. rhodei were registered in the Bowman’s capsules and interstitials in fish kidneys. M. rhodei was recorded in roach and dace almost in all studied water bodies and rivers of the Lake Baikal basin, except Lake Ugii-Nur and the northern part of Lake Khovsgol. Infection intensity of roaches was significantly higher in Lake Baikal than in rivers and lakes of the basin. Benthophagous roaches displayed significantly higher infection intensity than euryphagous daces.
Carbon Source and Soil Origin Shape Soil Microbiomes and Tomato Soilborne Pathogen Populations During Anaerobic Soil Disinfestation

Soilborne disease complexes are an emerging constraint in protected culture tomato production systems in the Midwestern United States. Diseases in these complexes include Verticillium wilt (Verticillium dahliae), black dot root rot (Colletotrichum coccodes), corky root rot (Pyrenochaeta lycopersici), and root knot (Meloidogyne spp.). Anaerobic soil disinfestation (ASD) may be a viable, environmentally benign strategy for managing these complexes. Soils from two farms in Ohio were used to determine the impacts of ASD, using wheat bran, molasses, or ethanol as carbon sources, on soilborne diseases and soil bacterial communities. ASD with wheat bran or ethanol amendments led to significantly reduced tomato root rot severity, while nematode galling damage was significantly reduced following ASD with any carbon source compared with nontreated controls. When ethanol was used as a carbon source in ASD, the colonization of tomato roots by P. lycopersici and C. coccodes was observed less frequently than in control roots. A high throughput sequencing approach was used to characterize soil bacterial communities following ASD. Carbon source and soil origin influenced the composition of bacterial communities in soils treated with ASD. Bacterial community diversity decreased following ASD with wheat bran in all soils tested and following ASD with ethanol in soils from one farm. The abundance of bacteria in the phylum Firmicutes generally increased significantly following ASD, while the abundance of those in the phyla Acidobacteria, Actinobacteria, Chloroflexi, and Plantomycetes generally decreased following ASD. These findings provide insight into the impacts of ASD on microbial communities and soilborne diseases and will be used to optimize ASD as a tool for Midwestern vegetable growers.
Four new induced pluripotent stem cell lines produced from northern white rhinoceros with non-integrating reprogramming factors

Since we first published methods for generation of induced pluripotent stem cells from endangered species1, we have developed improved non-integrating methods for reprogramming the functionally extinct northern white rhinoceros, and generated iPSCs from four more individuals. Our work is part of a long-term plan for assisted reproduction for conservation of endangered species.
Development of a new bioinsecticde base on a Chrysodeixis chalcites nucleopolyhedrovirus from the Canary Islands

Chrysodeixis chalcites (Lepidoptera: Noctuidae) larvae cause up to 30% production loss in banana crops in the Canary Islands. Larvae of this species are susceptible to a nucleopolyhedrovirus (ChchNPV). This study aimed at evaluating the genetic diversity and bioinsecticidal activity of ChchNPV isolates collected from C. chalcites larvae in the Canary Islands. From a total 97 isolates collected in different banana greenhouses, restriction endonuclease analysis identified five genetic variants that differed slightly from ChchNPV isolates from Netherlands (ChchSNPV-NL) and Almería, Spain (ChchNPV-SP1). Physical maps revealed minimal differences at genome level mostly due to variation in the position/existence of restriction sites. ChchSNPV-TF1 was the most prevalent variant, representing 78% of isolates examined, and was isolated at all Canary Island sampling sites. This isolate was the most pathogenic isolate against C. chalcites second instars in terms of dose-response metrics, compared to homologous variants or two heterologous viruses Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Anagrapha falcifera multiple nucleopolyhedrovirus (AnfaMNPV). ChchSNPV-TF1 was also one of the fastest killing variant although no differences were observed in occlusion body production among the different variants in second instars. We conclude that ChchSNPV-TF1 merits further evaluation as the basis for a biological insecticide for control of C. chalcites in banana crops in the Canary Islands. This chapter has been published in Biological Control as: A. Bernal, A. Carnero, E. HernandezSúarez, T. Williams, P. Caballero and O. Simón, 2013. A native variant of Chrysodeixis chalcites nucleopolyhedrovirus: The basis for a promising bioinsecticide for control of C. chalcites in Canary Islands’ banana crops. Biological Control 67, 101–110. Chapter 2 A native ChchSNPV: The basis for a promising bioinsecticide 68
Intersexual segregation in foraging microhabitat use by Magellanic Woodpeckers (Campephilus magellanicus): Seasonal and habitat effects at the world's southernmost forests

Animals facing seasonal food shortage and habitat degradation may adjust their foraging behaviour to reduce intraspecific competition. In the harsh environment of the world's southernmost forests in the Magellanic sub-Antarctic ecoregion in Chile, we studied intersexual foraging differences in the largest South American woodpecker species, the Magellanic Woodpecker (Campephilus magellanicus). We assessed whether niche overlap between males and females decrease when food resources are less abundant or accessible, that is, during winter and in secondary forests, compared to summer and in old-growth forests, respectively. We analysed 421 foraging microhabitat observations from six males and six females during 2011 and 2012. As predicted, the amount of niche overlap between males and females decreased during winter, when provisioning is more difficult. During winter, males and females (i) used trees with different diameter at breast height (DBH); (ii) fed in trunk sections with different diameters; and (iii) fed at different heights on tree trunks or branches. Vertical niche partitioning between sexes was found in both old-growth and secondary forests. Such a niche partitioning during winter may be a seasonal strategy to avoid competition between sexes when prey resources are less abundant or accessible. Our results suggest that the conservation of this forest specialist, dimorphic and charismatic woodpecker species requires considering differences in habitat use between males and females.
Efficacy of different advanced fungicides against late blight of potato incited by Phytophthora infestans in southern Karnataka

Late blight caused by oomycete Phytophthora infestans (Mont.) de Bary has historically been an important dreaded disease of potato across the world. The late blight disease caused widespread crop failures throughout southern Karnataka including Hassan, Chikamagalore, Kolar, Chickaballapura and Bengaluru rural districts. The epidemics of late blight in southern Karnataka have been associated with the emergence of new strain of Phytophthora infestans and in which Metalaxyl resistance was found. With an objective of identification of suitable fungicide formulation, concentration and its interval to manage late blight of potato in southern Karnataka. An experiment was conducted during Kharif season for three consecutive years from 2014 to 2016 at Horticulture Research and Extension Station, Somanahallikaval, Hassan, Karnataka. The pooled data of three years indicated that among nine different fungicidal treatments, least per cent disease intensity of 19.44 was observed in the treatment of Femoxidone + Cymoxanil @ 0.1 per cent, which resulted in highest marketable tuber yield of 17.77 t/ha with lowest blighted tubers of 0.42 t/ha followed by treatment with Ametoctradin + Dimethomorph @ 0.1 per cent, wherein 21.32 per cent disease intensity with marketable tuber yield of 14.27 t/ha and 0.57 t/ha of blighted tubers were documented and it was found on par with treatment of Fenamidone + Mancozeb @ 0.3 per cent with 22.85 per cent disease intensity and marketable tuber yield of 13.78 t/ha with 0.65 t/ha of late blight affected tubers were documented. Further in control highest disease intensity of 57.66 per cent with lowest marketable tuber yield of 6.79 t/ha and highest blighted tubers of 1.22 t/ha were recorded.
FISH COMMUNITY STRUCTURE IN A NATURAL RAINFOREST LAKE, NIGERIA

Studies on fish community of Agulu Lake were conducted from April to July 2015. Fish samples were bought from fishermen who caught them using gillnets and traps. A total of 159 fish samples belonging to 3 orders, 7 families, 8 genera and 10 species were obtained during the study. Station I had the highest fish abundance of 50.9 %, while station III had the lowest fish abundance of 23.5 %. Fishes belonging to the order Perciformes were the most abundant (66.04 %) of the total catch. This was followed by Siluriformes (31.43 %). The least order Osteoglossiformes was represented by 1.26 % of the total fish caught. Cichlidae, the most abundant family, has the highest number (103, 64.78%) of fish caught from the lake. The monospecific families encountered in the study were Channidae (Parachanna obscura), Bagridae (Chrysichthys nigrodigitatus), Mochokidae (Synodontis ocellifer), Malapteruridae (Malapterurus electricus) and Notopteridae (Papyrocranus afer). The highest number of fish was caught in May (52, 32.7 %) and the lowest number of fish was caught in July (28, 17.6 %). The general diversity index (H) was highest (0.741) in station I and lowest (0.605) in station II. Evenness (E) followed the same trend being highest (0.741) in station I and lowest (0.670) in station II. Dominance was maximum (0.342) in station II and minimum (0.270) in station 1. The same trend was observed in Simpson’s index which was highest (0.324) in station III and lowest (0.258) in station I.
The Quaternary plant fossil record from the volcanic Azores Archipelago (Portugal, North Atlantic Ocean): a review

Abstract Plant fossils are known from the Azores Islands, yet poorly studied. We present a comprehensive bibliographical review for the archipelago. A first pre-scientific reference dates from late fifteenth century, while the first scientific description was reported in 1821, accounting for trunks in pyroclastic units and silicified plants within hydrothermal deposits. Throughout the second-half of the nineteenth century and the first-half of the twentieth century, prospection by naturalists and geological mapping work, led to the discovery and description of plant fossils in most islands. From the 1970s onwards, the taxonomic interest ceased, and plant fossils were used mainly for 14C dating. Recently, sediment cores from lakes and peatlands were used for palaeoecological reconstructions and to measure anthropogenic impacts. Generally, plant fossils are younger than 50 ka, although older fossils may exist. Azorean plant fossils include somatofossils of leaves, stems, logs and seeds preserved as impressions, compressions, adpressions, permineralizations, lava tree casts and mummifications. The taphonomy of macrofloral elements is usually related to explosive volcanic activity, while palynological record is associated with lake sediments and peat bogs. The persistence in palaeobotanical and palaeopalynological studies will decisively contribute to disentangle the paleodiversity, palaeoecology, and add crucial information on insular plant phylogeny and biogeography.
Molecular characterization of field strains of Mycoplasma gallisepticum in Malaysia through pMGA and pVPA genes sequencing

Abstract To characterize field strains of Mycoplasma gallisepticum (MG) in Malaysia, selected gene target-specific sequences to MG, hemagglutinin protein A (pMGA) and phase variable putative adhesion protein A (pvpA) genes, were amplified from positive MG samples using conventional polymerase chain reaction (PCR). A total of 25 MG-positive samples out of 94 field samples were sequenced with primer targeting pMGA and pvpA genes. Sequencing and phylogenetic analysis were conducted using bioinformatics softwares (Bioedit and MEGA 5) and genetic variation patterns were evaluated based on partial nucleotide sequencing of pMGA and pvpA genes. In case of pMGA, all 25 field strains showed similar gene size patterns with strains of pathogenic reference (MGS6) and vaccine (MG F), which were different from the PCR product size of less pathogenic vaccine strain (TS 11). However, pvpA partial nucleotide sequences of MG local strains showed that 20 out of 25 strains possessed similar gene size pattern with MG F, which were different from MGS6 and TS 11. In conclusion, based on the molecular characterization from phylogenetic analysis of pMGA and pvpA partial nucleotide sequences, it was found that Malaysian MG strains were different from strains reported in other countries.
SEEDS OF ELEPHANT APPLE (DILLENIA INDICA L.) RESPONSE TO SOME PRE-GERMINATION TREATMENTS

Prof. Dr. M.M. Farahat, Agric. & Biol. Res. Div. , NRC. ABSTRACT: This experiment was consummated under shade at the nursery of Hort. Res. Inst. , ARC, Giza, Egypt during 2013 and 2014 seasons to explore the effect of some pre-sowing treatments, viz. control (untreated seeds), seeds without mucilage, soaking in tap water for 24, 48, 72 h under ambient conditions, soaking in hot water (6070C) for 24h, soaking in absolute ethanol (97%) for either 12 or 24 h and soaking in concentrated sulfuric acid (98.5%) for 3 min on germination measurements of Elephant apple (Dillenia indica L.) seeds and growth of the produced seedlings. The obtained results have shown that seeds of control and those soaked in either hot water or ethanol for 24 h failed to germinate, while seeds without mucilage and those soaked in ethanol for 12 h gave the least germination percentage in the two seasons. The other treatments, however significantly improved germination %, with the superiority of soaking in concentrated H2SO4 for 3 min treatment, which elevated such parameter to 100% in both seasons. Besides, germination % was found to progressively increase with elongating soaking period in tap water to reach 100% in the first season and 83.33% in the second one by the longest soaking period (72 h). The germination velocity and mean germination rate were accelerated and the indices of germination rate and vigour, seeds viability and plumule length were significantly improved by some treatments used in this trial, but the prevalence was also for acid treatment which followed by soaking in tap water for 72 h treatment. Similarly, were those result of seedling growth traits and leaf content of chlorophyll a, b, carotenoids, total soluble sugars, indoles and phenols, as the soaking in concentrated H2SO4 for 3 min treatment scored the best growth of the seedling and the highest content of the various constituents which was accompanied with the least content of total phenols. Also, soaking in tap water for 72 h occupied second rank. So, it advised to soak Elephant apple (Dillenia indica L.) tree seeds either in concentrated sulfuric acid (98.5%) for 3 min or in tap water for 72 h to obtain the best germination and quality of seedlings.
Mecanismos de ação de isolados de leveduras envolvidos no biocontrole de Penicillium digitatum, agente causal do bolor verde em frutos cítricos

1 Programa de Pós-graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista – UNESP, Jaboticabal, SP, Brasil 2 Centro de Citricultura Sylvio Moreira, Instituto Agronômico, Cordeirópolis, SP, Brasil Autor correspondente: Katia Cristina Kupper, Centro de Citricultura Sylvio Moreira, Instituto Agronômico, Rodovia Anhanguera, Km 158, CEP 13490-970, Cordeirópolis, SP, Brasil. E-mail: katia@centrodecitricultura.br RESUMO
Role of climate change awareness in sustainable soil nutrient management by smallholder farms in Burkina Faso

Climate change effects are threats to the livelihood of Sub-Saharan smallholder farms. Farmers’ response and readiness to take adaptive measures depend on how they perceive (perception) and moreover understand and recognize the causes (awareness) of climate change. Most studies used interchangeably perception and awareness to climate change. Taking the example of soil nutrient management, this study demonstrated the importance of distinguishing awareness from perception in climate change adaptation studies and for policy design. The study was conducted in South-western Burkina Faso. Using a semi-structured questionnaire, 360 households were surveyed. Rainfall variation and onset of the cropping season were used as climate change evidences to assess climate change perception and awareness. Descriptive statistics and Z-test were run. Results showed that beyond climate change perception, farmers largely took adaptive measures when they understand and can explain causes of climate change. Therefore, climate change adaptation studies and policy interventions should distinguish awareness from perception, and policy design should stress on raising climate change awareness of smallholder farmers. Key words: Climate change perception, climate change awareness, sustainable soil nutrient management, smallholder farms, Burkina Faso.
Iron availability modulates the effects of future CO2 levels within the marine planktonic food web

Ocean acidification (OA) due to increased anthropogenic CO2 emissions is affecting marine ecosystems at an unprecedented rate altering biogeochemical cycles. Direct empirical studies on natural communities are required to analyse the interactive effects of multiple stressors while spanning multiple trophic levels. We investigated the interactive effects of changes in CO2 and iron availability on functional plankton groups. We used mesocosms manipulating the carbonate system from the start to achieve present (LC) and predicted future pCO2 levels (HC). To manipulate dissolved iron (dFe), half of the mesocosms were amended with 70 nM (final concentration) of the siderophore desferoxamine B (DFB) on day 7 (+DFB and –DFB treatments). Manipulation of both CO2 and DFB increased dFe compared to the control. During the 22 experimental days, the plankton community structure showed two distinct phases. In phase 1 (days 1-10), only bacterioplankton abundances increased at elevated pCO2. In contrast, a strong community response was evident in phase 2 (days 11-22) due to DFB addition. The coccolithophore Emiliania huxleyi biomass increased massively at LC+DFB. HC negatively affected E. huxleyi and Synechococcus and high dFe (+DFB) had a positive effect in both. The rest of the plankton community was unaffected by the treatments. Increased dFe partially mitigated the negative effect of HC imposed on the coccolithophores, indicating that E. huxleyi was able to acclimate better to OA. This physiological Fe-mediated acclimation can diminish the deleterious effects of OA on carbon export and the rain ratio, thus affecting food web dynamics and future ecosystem functioning.
The Role Of Pparγ In Placental Development And Disease

THE ROLE OF PPARΓ IN PLACENTAL DEVELOPMENT AND DISEASE by LEENA KADAM August 2017 Advisor: Dr. Sascha Drewlo Major: Physiology (Reproductive Sciences Concentration) Degree: Doctor of Philosophy The placenta in mammals forms the maternal fetal interface serving as the source of nutrition for the fetus throughout gestation. It comprises of two major trophoblast lineages: (i) the decidua invading extra-villous trophoblast (EVT) and (ii) the placenta residing villous trophoblast (VT). The EVT’s invade the maternal endometrium to establish pregnancy and secure blood-flow to the implantation site. The VT villous trophoblast forms the main maternalfetal exchange surface and ensures nutrient and gas exchange to facilitate growth throughout pregnancy. Additionally, both lineages are involved in immunological functions such as maintaining allogenic tolerance and regulation of immune cell activation at the maternal fetal interface. They also express pattern recognition receptors like TLR (toll-like receptors) and NLR (Nod-like receptors) involved in pathogen recognition. Activation of these receptors leads to an inflammatory cascade aimed at elimination of the pathogen which in severe conditions can lead to preterm birth (PTB) and even fetal death. Proper development of trophoblast cells is thus crucial for placental function and hence for a successful pregnancy. Indeed, pregnancy disorders like pre-eclampsia (PE), intra – uterine growth disorders (IUGR) and preterm birth (PTB) have all been associated with abnormal trophoblast differentiation. Interestingly, elevated levels of
Nontypeable Haemophilus influenzae-induced inflammation, corticosteroids unresponsiveness and functional polarisation in COPD alveolar macrophages

COPD is a chronic inflammatory disease of the airways where many patients have recurrent lower airway bacterial infection, most commonly nontypeable Haemophilus influenzae (NTHi). Corticosteroids are commonly used antiinflammatory drugs in COPD with limited clinical benefit. Previous studies focused on corticosteroid responsiveness in COPD did not consider the role of airway NTHi infection. Alveolar macrophages are the main inflammatory cells in COPD pathogenesis, a shift in their phenotype was highlighted in COPD patients. Some bacteria can modify alveolar macrophage phenotype to persist in the lower airways. I have optimised a clinically relevant in vitro model of NTHi infection; human alveolar macrophages were stimulated with an increasing load of live NTHi clinical isolate (R2846). NTHi provoked time-dependent release of TNF-α, IL-6, CXCL8 and IL-10 from alveolar macrophages, which was correlated with bacterial growth, lysis and phagocytosis in the model. Furthermore, NTHi load was inversely correlated with IL-10 release. These findings suggest that NTHi infection is a dynamic inflammatory process in human alveolar macrophages and pointed to the possible role of IL-10 in the NTHi persistence in the lower airways. NTHi-induced cytokines in alveolar macrophages showed reduced corticosteroid responsiveness, CXCL8 was particularly corticosteroid unresponsive cytokine. NTHi-induced glucocorticoid receptor (GR) phosphorylation at ser 226 residue, which would encourage GR nuclear exportation. This might be one possible mechanism of reduced corticosteroid response in the model. In line with the latter finding, NTHi impaired the corticosteroid-induced GR nuclear localisation, which was partially reversed by p38 MAPK inhibitor (BIRB-796). These results suggest the role of NTHi in corticosteroid unresponsiveness in COPD alveolar macrophages. NTHi-induced cytokine release in alveolar macrophages was mediated by NF-κB, p38 and ERK MAPK pathways. Combination of corticosteroid (dexamethasone) with p38 and ERK MAPK inhibitors (BIRB-796 and AZD6244 respectively) showed a potential synergistic anti-inflammatory effect in the model. Therefore, inhibitors of MAPK pathways might serve as future anti-inflammatory therapies in NTHi-infected COPD patients. NTHi in vitro infection caused upregulation of the pro-inflammatory (TNF-α, CXCL8, CD38) and the anti-inflammatory (IL-10) markers’ mRNA levels in COPD alveolar macrophages. Meanwhile, NTHi downregulated the antigen-presentation molecule (HLA-DR) and the scavenger receptors (CD14, CD36, CD163 and CD206) mRNA levels in COPD alveolar macrophages. Moreover, sputum macrophages from NTHiinfected stable COPD patients showed lower mRNA levels of CD36 and HLA-DR. These findings suggest that the NTHi modification of alveolar macrophage functions, especially antigen presentation and efferocytosis, might be a possible mechanism of NTHi chronic infection and COPD disease progression.