Miracle-dz/UniFAR-FTUs huggingface dataset:
Larval Anuran Stable Isotope Signatures and Stoichiometry Across Multiple Geographically Isolated Wetlands in the Southeastern United States

Abstract Animals live in complex environments that vary spatially and temporally. This heterogeneity strongly influences the availability and quality of food resources and has strong impacts on growth and survival of consumers. Geographically isolated wetlands provide an interesting system to study trophic relationships because they vary spatially and temporally in hydrology and vegetation. Larval anurans play an important role in these wetland systems because they are often the most abundant consumers. Yet, little is known about larval anuran diet. Here we assessed the diet of 3 larval anurans (Acris gryllus [Southern Cricket Frog], Hyla gratiosa [Barking Treefrog], and Lithobates sphenocephalus [Southern Leopard Frog]), across 2 isolated wetland types (marsh and cypress savanna) using a stable isotope mixing model, stable isotope analysis in R (SIAR). Furthermore, we assessed variation in basal resource and anuran tissue stoichiometry (C:N). Our analyses suggested that larvae of these 3 species primarily function as herbivores and detritivores. All fed on a mix of algal resources, detrital particulate organic matter, and litter originating from the wetland canopy. Barking Treefrog had a lower C:N than the other two species, suggesting their dietary N requirements may be greater. Understanding the trophic roles of these animals is essential in determining their ecological significance and contributes to a more complete view of isolated wetlands in the surrounding landscape.
Identification of epigenetic mechanisms involved in transcriptional activation of silent HPV-16 genomes

An important initial step towards cervical cancer is the integration of HPV DNA copies into the host genome. Subsequently, the viral DNA gets targeted by methylation leading to its transcriptional silencing (Jeon et al., 1995; Yu et al., 2005). Later on, demethylation of these inserted HPV genomes correlates with further progression of cervical cancer (Badal et al., 2003). Therefore, characterisation of epigenetic mechanisms involved in oncogene re-expression is required to potentially counteract cancer development. In this study, the contribution of both epigenetic mechanisms, DNA demethylation and incorporation of histone variant H3.3 for the re-activation of the viral DNA transcription was analyzed. The cervical cancer cell line CaSki harbors approximately 600 mostly methylated HPV-16 copies and provides an excellent in vitro model to study epigenetic mechanisms in the context of HPV induced carcinogenesis. DNA demethylation was induced by treatment of these cells with 5-Desoxy-Azacytidine (DAC), which led to demethylation of approximately 50% of the silent HPV-16 copies. In addition, clones stably expressing a Myc-tagged H3.3 were generated and characterized in combination with DAC treatment. On protein level, DAC treatment of CaSki cells was accompanied by an unexpected down-regulation of the oncoprotein E7, where intracellular half life was rescued after exposure to proteosomal and calpain inhibitors. Additionally, for the first time, an interaction of E7 with, the transcription activating histone arginine methyltransferase, CARM1 was detected after E7-IP by Mass Spectrometry and Western blot. On transcriptional level, a slightly down-regulation of the E7 oncogene was detectable after DAC treatment of CaSki cells. Importantly, the same treatment induced E7 transcription in CaSki clones expressing Myc-H3.3, which was verified by both qPCR and Northern blot. In summary, this study demonstrates that DAC treatment induces down-regulation of oncoprotein E7 in CaSki cells. In addition, the data imply that DNA demethylation alone is not sufficient for re-activation of silent HPV genomes, since induction of E7 transcription strictly requires both, DNA demethylation and incorporation of the histone variant H3.3 into the URR of HPV-16.
Hypoxia has lasting effects on fast startle behavior of a tropical fish, (Haemulon plumieri)

Summary statement This study describes for the first time long-lasting behavioral effects of hypoxia on a tropical fish, the white grunt (Haemulon plumieri) from Puerto Rico. Anthropogenic activities and climate change have resulted in an increase in hypoxia in nearshore ecosystems worldwide. The San Juan Bay Estuary System in Puerto Rico is one such ecosystem that has undergone an increase in hypoxic events over the past few years. We collected white grunts (Haemulon plumieri) from one of the estuary lagoons to study the effects of hypoxia on fast startle responses (fast-starts). We hypothesized that exposure to hypoxia would significantly decrease the frequency of fast-starts evoked by an abrupt sound stimulus. After an exposure to an oxygen concentration of 2.5 mg L-1 (40% of air saturation), there is a significant reduction in the frequency of fast-starts that is maintained for at least 24 h after the exposure. Exposure to a random sequence of oxygen levels of 5.0, 4.3 and 3.7 mg L-1 (80, 70, and 60% of air saturation) did not show a significant effect until one hour after exposure. We speculate that the lasting effect of hypoxia on fast-starts, thought to be involved in escape, will result in a greater susceptibility of the white grunt to predation. We have identified the Mauthner cell, known to initiate fast-starts, to allow future studies on how low oxygen levels impact a single cell and its circuit, the behavior it initiates and ultimately how changes in the behavior affect population and ecosystem levels.
CANDIDATUS LIBERIBACTER ASIATICUS CAUSING CITRUS HUANGLONGBING ON CITRUS SINENSIS IN BANGLADESH

Citrus huanglongbing (greening) is one of the important diseases of citrus in Asia (Bove, 2006). The symptoms include blotchy chlorosis and/or mottling of the leaves, stunted growth, poor root growth, small, green, and malformed fruits and decline of the trees. The disease is caused by the phloem-limited unculturable fastidious bacteria Candidatus Liberibacter asiaticus (CLas), Ca. L. africanus (CLaf), and Ca. L. americanus (CLam) (Bove, 2006; Jagoueix et al., 1994). Among them CLas is the most widespread (e.g., Asia, Brazil and North America). In recent years the presence of huanglongbing was suspected in different regions of Bangladesh. To establish whether this is the case, in July, 2016 symptomatic plant samples of Citrus sinensis were collected from four citrus-growing areas of the country: Jaintapur (Sylhet), Akbarpur, (Moulvibazar), Dighinala (Khagrachari) and Hathazari (Chittagong). The samples were analyzed by polymerase PCR using the ‘CLas’ specific primers A2 (5'-TATAAAGGTTGACCTTTCGAGTTT-3') and J5 (5'- ACAAAAGCAGAAATAGCACGAACAA-3') which amplify a partial sequence of the β- operon (rplKAJL-rpoBC operon) of ribosomal protein genes (Hocquellet et al., 1999). A product 703 bp in size specific to Ca. L. asiaticus was amplified, sequenced and deposited in GenBank (accession No. KX826950). The nucleotide sequence of the recoverd CLas shared 100% sequence identity with other Ca. L. asiaticus strains from NCBI database (e.g. KC477384, KT164844, KC133065). To our knowledge this is the first molecular-based detection of Candidatus Liberibacter asiaticus infecting Citrus sinensis in Bangladesh.
Efficacy of mixed adsorbent in ameliorating ochratoxicosis in broilers fed ochratoxin A contaminated diets

Abstract The current study was conducted to evaluate the ability of mixed adsorbent (Na-MMT + YCW) for the preventing effect of Ochratoxin A in broiler productivity, biochemical parameters, histochemical changes and OTA residues. A total of 96 broiler chicks were grouped in three experimental and one control group (24 chicks in each group, 3 replicates each). Birds were fed basal dietary or that with Ochratoxin A and mixed adsorbent (Na-MMT + YCW) to determine the effect of this compound during mycotoxicoses. When compared with the controls, feed: gain (F/G) were significantly higher for broilers fed diets containing OTA alone (p < .05). No differences were found between the F/G of broiler chickens fed diets without OTA and those of chickens fed mixed adsorbent. The diet containing 2 mg OTA/kg without adsorbents added increased relative liver, kidney, spleen weights and decreased relative thymus, bursa weights. Alterations in the levels of serum TP, ALB, GLB, BUN and enzymatic activity of ALT, AST, ALP and GGT were observed for OTA diets, and moderate protection was provided by the sorbent. Supplementing mixed adsorbent group (Na-MMT + YCW) showed intestinal villus height and crypt depth similar to control chicks, and a significant reduction residue in livers and kidney tissue, as well as a significantly higher OTA content in the faeces compared with OTA- group were recorded. These results suggest that effects of OTA treatment were ameliorated when mixed adsorbent was used in the broiler chick diets.
Soil Microbial Ecology Associated with Disease Control of Fusarium oxysporum f. sp.Cucumerinum in Cucumis sativus Cultivation

Fusarium oxysporum f. sp. Cucumerinum is a pathogen affecting continuous crop monoculture cucumber (Cucumis sativus) production. Soil fumigation and rotation of cucumber with other crops are two methods control the disease. Disease control is when yield is increased and disease incidence is reduce after treatment. Fumigation of soil with anhydrous ammonia and rotation of cucumber with other crops were investigated as disease management methods in continuous crop monoculture cucumber fields with high disease incidence and reduced yield. In 2013 at a continuous crop monoculture cucumber field near Jinhua, Zhejiang, China, three soil samples were collected from seven growing season time points from two soil treatments: 1) fumigated with anhydrous ammonia; or 2) not-fumigated. A total of forty-two samples. In 2014 at the same field above, eight soil samples were collected from one growing season time point from three soil treatments: 1) fumigated with anhydrous ammonia the year prior; 2) cucumber-tomato-celery crop rotation; or 3) not-fumigated in continuous crop monoculture cucumber. A total of 24 samples. Soil was analyzed for chemical properties. Soil microbial communities were profiled using bioinformatics software tools by analyzing sequenced amplicons of bacterial and archaeal 16s and fungal ITS1 rDNA from extracted soil sample DNA. Yield was increased and disease incidence was reduced by soil fumigation with anhydrous ammonia and crop rotation. In 2013, soil fumigation significantly affected 116 unique fungal species and 28
The influence of nitrogen and calcium fertilizers on septoria late blight and yield of celery

Tesfaendrias, M. T. , Trueman, C. L. , Gossen, B. D. , McKeown, A. W. and McDonald, M. R. 2014. The influence of nitrogen and calcium fertilizers on septoria late blight and yield of celery. Can. J. Plant Sci. 94: 1391-1399. Late blight (Septoria apiicola) reduces both yield and quality of fresh market and processing celery. Field trials were conducted over 4 site-years to evaluate the effect of nitrogen (N) rate and foliar calcium (Ca) fertilization on the development of late blight and yield on celery grown on muck soils, which have a high organic matter (OM) content. A treatment with the protectant fungicide chlorothalonil was included to determine if fertilizer could replace fungicide application in celery production. There was a cultivar×site-year interaction for each of the disease and yield variables. Repeated application of chlorothalonil fungicide reduced late blight and generally increased plant height, weight and marketable yield. The rate of N applied had a small effect on late blight, which varied among site-years. Area under the disease progress curve decreased with increasing rate of N at both sites in 2008. Similarly, an increasing rate of N resulted in an increase in yield in one of four site-years. Application of Ca did not affect late blight severity and increased yield in only 1 site-year. There was a negative correlation between late blight severity and yield. Tissue N concentrations varied among the treatments at sites with a relatively low OM content, but not at the high OM sites. The treatments had no effect on Ca tissue concentrations. Application of N and Ca alone did not adequately control late blight, but there was a slight reduction in late blight severity with increasing rates of N. Application of both N and Ca can improve yield and also contribute indirectly to improved late blight management in combination with fungicides and other integrated crop management practices.
SURVEY OF TRUE SPIDERS IN THE EGYPTIAN RIEC FIELDS AT RASHEID REGION BEHEIRA GAVARNARTE

A survey was carried out at farms of Rasheid, Beheira gavernorate during two successive rice seasons,2009 and 2010. Two sowing dates were studied; the first is the normal date of sowing (early May), the second sowing date is the late one (early June) using three traps (sweep net,pit fall and water pan). 10 species of true spiders were belonging to 6 families surveyed from the Egyptian rice fields. The spiders were recorded for the first date 9 species of true spiders were surveyed from rice fields at from Rasheid EL-Behira governorate. 6 spider families were surveyed, with 807 individuals belonging to 9 spider Species. The surveyed spiders and Families and their percentages were as follows: Thomicidae ( Thomisius sp ) with 3.46 % Lycosidae (Lycosa sp., Pardosa spp., Trochosa sp.,) with 9.04 % 25.65 % and 7.89 %, respectively. Tetragnothridae had two species ( Tetragnatha javana, Tetragnatha nitens ) with 40.89 %. Philodromidae ( Thanatus Albini) ) with 4.08% Araneidae ( Singa sp.) with 6.44 % and Pisawridae ( Dolomedes sp. ) with2. 72 % and the second 7 spider families were surveyed, with 719 individuals belonging to 10 spider Species . The surveyed spared and Families and their percentages were as follows: Thomicidae ( Thomisius sp .) with2.78% Lycosidae (Lycosa sp., Pardosa spp., Trochosa sp.,) with 9.59 % 17.52 % and 3.47 %, respectively. Tetragnothridae had if two species ( Tetragnatha javana, Tetragnatha nitens ) with 54.65 % Philodromidae ( Thanatus Albini) ) with 3.33% Araneidae ( Singa sp.) with 5.98 % and Pisawridae ( Dolomedes sp. ) with 2.50 % and Salticidae Mendoza sp with 0.13 %.
Precise and Predictable DNA Fragment Editing Reveals Principles of Cas9-Mediated Nucleotide Insertion

DNA fragment editing (DFE) or chromosomal engineering including inversions, deletions, and duplications by Cas9 with paired sgRNAs are important to investigate structural genome variations and developmental gene regulation, but little is known about the underlying mechanisms. Here we report that debilitating CtIP, which is thought to function in NHEJ, enhances precise DNA fragment deletion. By analyzing the inserted nucleotides at the junctions of DNA fragment inversions, deletions, and duplications, we find that Cas9 cleaves the noncomplementary strand with a flexible profile upstream of the PAM site and rationally-designed Cas9 nucleases have distinct cleavage profiles. Finally, Cas9-mediated nucleotide insertions of DFE are nonrandom and are equal to the combined sequences upstream of both PAM sites with predicted frequencies. Thus, precise and predictable DFEs could be achieved by perturbing DNA repair genes and using appropriate PAM configurations. These findings have important applications regarding 3D chromatin folding and enhancer insulation during gene regulation.
Rapid evolution in a crop-weed complex ( Raphanus spp.)

The development and adoption of transgenic crops with novel traits has raised awareness of the potential for weed populations to evolve increased weediness after hybridization with cultivated relatives. I explored the evolutionary and ecological consequences of gene flow between crop radish (Raphanus sativus) and its weedy relative (wild radish, R. raphanistrum). Hybridization may generate the genetic and phenotypic variation necessary for an evolutionary response by weeds. First, I imposed artificial selection on wild and hybrid lineages for four generations for early flowering a potentially advantageous trait for weeds. Hybrid lineages evolved more rapidly under selection for early flowering and rapidly recovered a wild-type phenology and fertility. Second, I established replicated wild and hybrid populations in agricultural landscape and measured their evolutionary response to natural conditions after three generations. Natural conditions favoured larger plants in both wild and hybrid populations. However, because an advantageous trait, large size, had been transferred to hybrid populations, hybridization resulted in significantly larger hybrid than wild weeds and accelerated weed evolution. Further, I asked whether environmental context affected the success of hybrid relative to wild radish. Using a response surface competition experiment, I examined the consequences of competition on life history and lifetime fecundity of hybrid and wild
Spatiotemporal dynamics of bacterial community composition in large shallow eutrophic Lake Taihu: High overlap between free‐living and particle‐attached assemblages

In eutrophic lakes, heterotrophic bacteria are closely associated with algal detritus and play a crucial role in nutrient cycling. However, the seasonal and spatial dynamics of free‐living (FL) and particle‐attached (PA) bacteria and the environmental factors shaping this relationship remain poorly understood. To address this issue, we explored the spatiotemporal patterns of bacterial community composition (BCC) in Lake Taihu, China, using terminal restriction fragment length polymorphism (T‐RFLP) and 454‐tag pyrosequencing of 16S rRNA gene. We generated a total of 218,027 high quality non‐cyanobacterial sequence reads that resulted in 4940 OTUs (97% cutoff), with Actinobacteria, β‐ and α‐proteobacteria being the predominant taxa. Although PA communities contained significantly higher alpha‐diversity than FL ones, we found that 59% of OTUs, that accounted for 96% of the total reads, were shared by both communities. The high degree of overlap between FL and PA communities indicates a high rate of dispersal potential, highlighting an underestimated connectivity and potentially similar ecological role for these two components. Distinct seasonal trends were recorded in both FL and PA communities, while spatial differences in BCC were small. In addition, both FL and PA bacterial communities exhibited similar patterns and synchrony, correlated to water temperature, nitrate and total suspended solids (TSS). Accordingly, the effects of eutrophication and hydrodynamics on the phylogenetic overlap and diversity between FL and PA communities were discussed.
Causes and Consequences of Straying into Small Populations of Pacific Salmon

Most Pacific salmon Oncorhynchus spp. migrate to their natal sites to spawn. Some, however, stray into nonnatal habitats and interact (e.g., reproduce) with individuals from other populations. Pacific salmon straying has been heavily studied for several decades, particularly from the perspective of the populations that donate the stray migrants. Conservation consequences are experienced primarily by the populations that receive strays, though, and there is recent evidence of significant levels of genetic introgression in small recipient populations, which could contribute to the loss of local adaptations. Straying may also provide the benefit of a demographic rescue effect that could save declining recipient populations from extirpation. We highlight the influence of population abundances on the magnitude of straying into recipient populations and demonstrate this using evidence we collected from a small population of Sockeye Salmon O. nerka in British Columbia, Canada. We also review potential factors th.
Rose gall wasps and their associated fauna (hymenoptera) in Iran

Over a four year period, the rose gall wasps (Diplolepis spp.) and their associated fauna were studied in the northern regions of Iran. Seventeen species of parasitic wasps were collected and identified, eleven of them are recorded for the first time from Iran. They belong to two superfamilies: Chalcidoidea (16 species belonging to 5 families) and Ichneumonoidea (one ichneumonid species). Eurytoma collina Zerova, 1977 is newly transferred to the genus Aximopsis (comb. n.). A brief biological review of the parasitoids associated with cynipids wasps is given. This complex was compared to those reported in some others countries. A review (Table) of the previous citations of parasitoids associated with Diplolepis species on Rosa sp. in the West-Palearctic is given. A key to the species occurring in Iran is given and illustrated to enable ecologists to better identify the wasps associated with Diplolepis galls. (Resume d'auteur)
Ventriculite parasitária por Libyostrongylus sp em avestruz (Struthio camelus) e identificação de ovos do parasita em amostras de fezes de ratitas de diferentes criatórios do Estado do Rio Grande do Sul

The ventriculus of a bird found dead was sent to the Histopathology Laboratory and processed by routine techniques for histopathological examination. Microscopically, several parasites embedded in the mucosal surface were observed, and the lining of the gizzard presented thickening, erosions and hemorrhagic areas. After this finding, parasitological examinations were carried out in fecal samples from ostriches of rearing farms in which important losses had occurred. All fecal samples, including feces previously collected from the ostrich diagnosed with parasitary ventriculitis were processed by the Parasitology laboratory in order to identify and to count eggs of parasites. The results indicated that the epg values display large amplitude, varying from 50 to 7600. Coprocultures allowed identifying infecting larvae of Lybiostrongylus sp. , confirming the presence of this parasite in ostriches, in Rio Grande do Sul State.
Development of SCAR marker for Thai fragrant rice (Oryza sativa L. var.indica cv. Pathumthani 1) mutants induced by low energy ion beam

Seeds of Thai fragrant rice (Oryza sativa L.var. indica cv. Pathumthani 1) were bombarded by nitrogen ions at a 60 keV energy level with ion fluences of 6 and 8×10 16 ion/cm 2 for induction mutation. After the 5 th generation, a number of mutants were obtained including EPOS1, EPOS2, EPOS3, TPOS1, TPOS2, EBPOS1 and EBPOS3. These mutants showed several improved characteristics including a tall variety and an early flowering variety. Moreover, the seed shape and pericarp color of the mutants were different from the control. In order to determine the scope of genetic variation for these mutants, a HAT-RAPD (High Annealing Temperature-RAPD) analysis was used to investigate the genome of these mutants. From a total of 110 arbitrary primers, one primer named OPAA14 produced a unique candidate fragment at a molecular size of 700 bp and presented only in the EBPOS3 mutant. This fragment was selected for sequencing and conversion to the more reproducible and robust Sequence Characterized Amplified Region (SCAR) marker. PCR amplification using the SCAR marker revealed a 300 bp fragment only in the EBPOS3 mutant. Since new lines or varieties of fragrant rice with modified phenotypes are often developed from their progenitors, the use of SCAR marker is a useful tool for identification purposes for right protection. This technique is a cost-effective and morphologically independent way to identify such mutants.
Infection-mediated Modulation of Drug Transporters in Pregnancy; Implications for Fetal Drug Exposure

Inflammation-mediated changes in the expression and activity of ABC drug-efflux transporters have been shown to alter disposition of their substrates. While ABC transporters play an important role in placenta by limiting transplacental transfer of xenobiotics, little is known about the impact of inflammatory stimuli on these transporters