Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying beneficial traits for heat stress around reproductive phases of growth in wheat

There is a need for heat tolerant traits in wheat to be identified in order to maintain and increase yields in future climates. The aim of this project was to assess genotypic variation in crop response to heat stress by comparing a southern European wheat genotype (Renesansa; Rht-D1a, Rht8, Ppd-D1a) with a UK genotype (Savannah; RhtD1b, Ppd-D1b, 1BL/1RS) and their doubled haploid progeny. This would allow for the identification of traits and alleles that would benefit UK and European wheat production under climate change scenarios through the use of a combination of phenotyping, genotyping and crop modelling. Heat stress experiments were conducted in controlled environments to identify the most susceptible growth stages to heat stress within the population and to identify potentially tolerant traits. An appraisal of the crop model SIRIUS and how it simulates heat stress was undertaken. Finally, a field trial was conducted to identify which traits perform well in UK field conditions. Two periods of susceptibility in Savannah and Renesansa were identified as susceptible to heat stress, through reductions in grain number. The first period was identified around booting, with the second being identified one day before mid anthesis. The period around heading was found to be relatively tolerant. Compensation of reduced grain numbers through increases in grain size was limited and variable. Rht8 was not found to influence heat stress tolerance. The photoperiod insensitivity allele Ppd-D1a was found to increase susceptibility to heat stress, while the semi dwarfing allele Rht-D1b was found to confer tolerance to it. Rht8 was associated with reduced yield in UK field conditions. Simulations from SIRIUS suggest that yield loss due to heat stress could increase by three fold in central Europe by 2090, though it is not expected to be a major issue in the UK.
Biological estimation of water quality of the Bovan Reservoir

Water samples for microbiological analyses, as well as material of the water community to be considered in the assessment of quantitative and qualitative composition of phyto- and zooplankton, and bottom fauna were taken in November 2005 at three profiles. According to presence of heterotrophic bacteria, water was characterized as I-II class KOHL, 1975). Also, four groups of phyto- and four groups of zooplankton were recorded. Relative abundance and qualitative composition values of plankton show that saprobic index ranged from 1.90-1.99 pointing β-mesosaprobic character of the accumulation. Saprobic index when oligochaetes were considered amounted up to 2.64 (β-α-mesosaprobic water).
Resistance status of cultivated potatoes to early blight (Alternaria solani) in Denmark

Field experiments were conducted in 2015 and 2016 to classify the resistance level to early blight of the main potato cultivars in Denmark. A total of 27 and 38 cultivars were used in 2015 and 2016, respectively. The experiment was designed as a randomized complete block design (RCBD) with four replicates. The potatoes were inoculated by spreading barley (Hordeum vulgare L.) kernels infested with A. solani and A. alternata. Disease assessment was done at weekly intervals starting from the onset of the first symptoms. The disease progress curves (DPC) of early blight on the cultivars were compared to that of Bintje. A multivariate analysis was performed with the apparent infection rate, the relative area under the disease progress curve, the time to reach 50% severity, the daily defoliation, the disease severity in the middle of the epidemic and the duration of the epidemic to classify the resistance level of the cultivars. The analysis of the DPC of the cultivars showed that none of the cultivars was completely resistant to early blight. However, the epidemic development differed between the different cultivars. The resistance levels of the cultivars were thus classified into Class I, Class II, Class III and Class IV interpreted as “very susceptible”, “susceptible”, “moderately slow blighting” and “slow blighting”, respectively. All the late maturity cultivars were classified as Class IV, and the earlier maturing cultivars were either Class I or Class II. This article is protected by copyright. All rights reserved.
Inheritance of Male Sterility in

Pollen fertility and inheritance patterns of male sterility were analyzed in various cultivars and selections of Japanese apricot (Prunus mume Sieb. et Zucc.). Male sterility segregated differently in two types of crosses. In pairings of male-sterile and male-fertile parents, progenies were either all male-fertile, all male-sterile, or mixed. Crossing two male-fertile plants resulted in offspring that were either all male-fertile or mixed. Male sterility in Japanese apricot appears to be of the gene-cytoplasmic type. The genotypes of 10 cultivars and three selections are determined.
The Role of H-NS in Bacterial Evolution and Factors that Modulate its Silencing Activity

Horizontal gene transfer (HGT) is the primary source of genetic variability among freeliving bacteria. Genes acquired by HGT typically display a lower AT content than the host genome average, but the reason for this bias is unknown. H-NS is a pleiotropic regulatory protein that is thought to facilitate HGT by silencing the expression of foreign genes with a lower AT-content than the host genome. In Salmonella enterica serovar Typhimurium H-NS represses 12% of the genome and loss of H-NS function imposes severe growth penalties on hns mutant cells. Here I applied an experimental evolution approach to examine the underlying basis for the hns mutant fitness defects. Genetic adaptions that improved hns mutant growth included deletion of the horizontally acquired Salmonella pathogenicity island 1 (SPI-1) and missense mutations that enhanced the gene silencing properties of the H-NS paralogue protein StpA. My findings support a role for H-NS in maintaining genomic integrity and suggest that the determinants responsible for the functional distinctions between StpA and H-NS reside in their self-association domains.
Assessment of Vitamin E and Vitamin C against silica intoxication

A B S T R A C T The aim of the present study was to observe the alteration of blood and also to show whether therapeutic agents used in study may provide recovery against exposure to silica. In this study, silica was administered as silicon dioxide at a dose of 40 mg/kg for 28 days to produce toxic effect. Recovery pattern was evaluated by vitamin E + vitamin C (50 mg/kg, ip & 100 mg/kg, po). Toxicological consequences were evident by the increased activities of AST, ALT, and ALP in serum after silica administration. Level of blood sugar, blood urea, serum protein, serum cholesterol and creatinine was also increased. 5 days therapy with vitamin E + vitamin C was effective and showing preventive aspect in recouping all biochemical parameters. Our findings suggest that vitamin E + vitamin C possess protective efficacy against silica -related diseases such as silicosis.
Did crocodiles become secondarily ectothermic ? : a paleohistological approach

Archosaurs are a clade of vertebrates that includes birds, crocodiles, and numerous fossil groups. This clade has been a matter of debate among paleontologists for decades concerning the evolution of thermometabolism in its different lineages. The classical hypothesis considers that only modern birds are true endotherms, whereas all other archosaurs are ectotherms. Bone histology allows to study several traits linked to bone growth rate and thermometabolism, otherwise impossible to estimate on fossil specimens; for this reason, we used characters measured on long bone histological sections.In the first section, we extensively reviewed the measure of phylogenetic signal for osteohistological features in two clades of vertebrates, which was then used to define the methodology for building our predictive models.After a preliminary study during which we built a predictive model for bone growth rate, we built a global model to predict the metabolic rate of our fossil specimens, using both histological features and phylogenetic information for each specimen. Our results show that a majority of archosaurs in our sample were endotherms. This implies that the last common ancestor of archosaurs was likely an endotherm, and that modern crocodiles became secondarily ectothermic, probably in response to their aquatic environment. More specific studies on pseudosuchians should allow to precisely identify the level of the phylogenetic tree at which the ectothermic state was acquired, as well as adaptive constraints behind this acquisition.
Evidence of compensation in the brain networks of Lewy body dementia and Alzheimer’s disease patients

Dementia with Lewy bodies (DLB) and Alzheimer’s disease (AD) require differential management despite presenting with symptomatic overlap. A human electrophysiological difference is a decrease of dominant frequency (DF) −the highest power frequency between 4-15Hz– in DLB; a characteristic of Parkinsonian diseases. We analysed electroencephalographic (EEG) recordings from old adults: healthy controls (HCs), AD, DLB and Parkinson’s disease dementia (PDD) patients. Brain networks were assessed with the minimum spanning tree (MST) within six EEG bands: delta, theta, high-theta, alpha, beta and DF. Patients showed lower alpha band connectivity and lower DF than HCs. Lewy body dementias showed a randomised MST compared with HCs and AD in high-theta and alpha but not within the DF. The MST randomisation in DLB and PDD reflects decreased brain efficiency as well as impaired neural synchronisation. However, the lack of network topology differences at the DF indicates a compensatory response of the brain to the neuropathology.
Modifiable risk factors moderate the relationship between amyloid and cognition in midlife

Although evidence suggests a relationship between elevated beta-amyloid and cognitive decline, approximately 30% of older adults with positive markers of amyloid remain cognitively healthy. Our objective was to test if the presence of modifiable risk factors (i.e., central obesity, hypertension, and depressive symptoms) moderated the relationship between amyloid and longitudinal cognitive performance. Data were from 207 adults (140 females; age range=40-70) enriched for Alzheimer’s disease risk (73% parental history of Alzheimer’s disease) enrolled in the Wisconsin Registry for Alzheimer’s Prevention study. Participants completed at least two neuropsychological evaluations and one biomarker visit ([C11] Pittsburgh Compound B PET scan or lumbar puncture). Participants were characterized as high or low on amyloid using cutoffs developed for [C11] Pittsburgh Compound B-PET distribution volume ratio or CSF amyloid beta 1-42 values. Participants were also coded as high or low risk on obesity, hypertension, and depressive symptoms. Linear mixed effects regression models examined three-way interactions between modifiable risk factor status x amyloid group x age at each study visit on longitudinal Verbal Learning & Memory and Speed & Flexibility factor scores. Results indicated that the relationship between beta-amyloid and Verbal Learning & Memory decline was associated with hypertension status (Likelihood ratio test for significance of hypertension status age x amyloid status x visit age interaction term; χ2 (1) = 5.28, p = . 02). The relationship between beta-amyloid and Speed & Flexibility decline was associated with depression status (Likelihood ratio test for significance of amyloid status x depression status x visit age interaction term; χ2 (1) = 7.10, p = . 03). The presence of obesity did not significantly moderate the relationship between beta-amyloid status and cognitive performance, although the direction of relationship was similar to above relationships (Likelihood ratio test for significance of obesity status x amyloid status x visit age interaction term; χ2 (1) = 1.52, p = . 21). In this at-risk for Alzheimer’s disease cohort, the modifiable risk factors of hypertension and depression significantly moderated the relationship between beta-amyloid and cognitive decline. Identification and modification of these risk factors in late middle age may slow the effect of amyloid on the progression of cognitive symptoms.
Wing base structure supports Coleorrhyncha + Auchenorrhyncha (Insecta: Hemiptera)

The phylogenetic placement of the moss bugs (Insecta: Hemiptera: Coleorrhyncha) has been highly controversial. Many apparent morphological apomorphies support the close relationship between Coleorrhyncha and Heteroptera (=true bugs). However, a recent phylogenomic study strongly supported a sister group relationship between Coleorrhyncha and Auchenorrhyncha (planthoppers, leafhoppers, treehoppers, spittlebugs, and cicadas). To test these two alternative hypotheses, we examined the fore- and hindwing base structure of the only known extant macropterous species of Coleorrhyncha using binocular and confocal laser scanning microscopes and analyzed the data selected from the wing base phylogenetically. When full morphological data including the wing base characters were analyzed, the sister group relationship between Coleorrhyncha + Heteroptera was supported, agreeing with previous consensus based on morphology. In contrast, when only wing base characters were analyzed separately, the clade Coleorrhyncha + Auchenorrhyncha was recovered, in agreement with the result from the phylogenomic study. The membranous condition of the proximal median plate in the forewing was identified as a potential synapomorphy of the latter grouping, and the absence of the tegula was excluded as a potential synapomorphy of Coleorrhyncha and Heteroptera.
Anaesthetic efficacy and biochemical effects of 1,8‐cineole in rainbow trout (Oncorhynchus mykiss, Walbaum, 1792)

Correspondence Ali Taheri Mirghaed, Department of Aquatic Animal Health, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran. Email: mirghaed@ut.ac. ir Abstract The aim of the present study was to investigate the anaesthetic efficacy and biochemical effects of 1,8-cineole (cineole) in rainbow trout (Oncorhynchus mykiss). The fish were exposed to 200, 300, 400, 500, 600 and 800 ll/L cineole and time of induction of anaesthesia and recovery from anaesthesia were recorded. Thereafter, the fish haematological and biochemical responses to anaesthesia with different concentrations of cineole were studies. Moreover, the haematological and biochemical response of fish anaesthetized for 300 s with either cineole (283 ll/L) or eugenol (25 ll/L) were compared. Cineole at the concentrations of 200–800 ll/L induced stages 2, 3 and 4 anaesthesia within 109-29.3, 226-59 and 418-117 s respectively. Increase in anaesthesia induction time led to higher stress responses and enzymes’ activity characterized by elevation in red blood cell (RBC), white blood cell (WBC), blood haematocrit and haemoglobin, and plasma cortisol, glucose and lactate levels, and aspartate aminotransferase (AST), alkaline phosphatase (ALP), lactate dehydrogenase and creatine phosphokinase (CPK) activities. However, cineole concentrations had no significant effects on plasma alanine aminotransferase (ALT) activity and ions levels. Comparison of cineole with eugenol showed that cineole showed less change in blood RBC and plasma AST, ALP, CPK, cortisol and glucose levels compared to eugenol. In conclusion, cineole is efficient to anaesthetize trout at concentrations of 200–800 ll/L. Increase in cineole concentration shortens anaesthesia induction time, stress response and probably tissue damage. The concentrations of 600–800 ll/L cineol is recommended for rapid sampling as it causes the least stress and enzymatic responses. The present results suggest that cineole causes slightly lower side effects in trout compared to eugenol.
Mutational Analysis of FLT3 Internal Tandem Duplication and D835 in De novo Adult Acute Myeloid Leukemia

Aims: Acute myeloid leukemia is a clonal hematopoietic malignant disease, resulting from genetic alterations in normal hematopoietic stem cells. Advances in the genomics of acute myeloid leukemia have identified several recurrent gene mutations such as FLT3 that its mutations confer poor outcome to patients. The aim of the present study was to investigate the frequency of FLT3-ITD and FLT3-D835 mutations in Iranian de novo adult AML patients. Study Design: Cohort study. Methodology: We performed mutational analysis in order to detect FLT3-ITD and FLT3-D835 mutations in a group of 91 de novo adult AML patients by using the conventional PCR and PCR-RFLP methods, respectively. Results: The results of the mutation analysis showed that in total 30.76 percent of patients had activating mutations of FLT3-ITD (27.47%) and FLT3-D835 (3.29%). Furthermore, a significant correlation was observed between with white blood cell (WBC) and blast cell count and the detected mutations ( P-value <0.001). Except for the M6, FLT3 mutations were identified in other FAB type groups. In addition, FLT3-ITD and FLT3-D835 mutations were observed in all three cytogenetic risk groups, However, a significant correlation was detected between FLT3-ITD mutation and normal karyotype ( P-value =0.032). Conclusion: Activating mutations in the FLT3 are recurrent in Iranian de novo adult AML patients. The mutational analysis of genes such as FLT3 in acute myeloid leukemia may be helpful in categorizing of the patients, determining prognosis and improving the treatment.
Canis aureus (Carnivore: Canidae)

Abstract: Canis aureus (Linnaeus, 1758), the golden jackal, is a medium-sized, wide spread, terrestrial carnivore. It is 1 of 7 species found in the genus Canis. It ranges from Africa to Europe, the Middle East, Central Asia, and Southeast Asia. Due to its tolerance of dry habitats and its omnivorous diet, C. aureus can live in a wide variety of habitats. It normally lives in open grassland habitat but also occurs in deserts, woodlands, mangroves, and agricultural and rural habitats in India and Bangladesh. It ranges from sea level in Eritrea to 3,500 m in the Bale Mountains of Ethiopia and 2,000 m in India. C. aureus is listed as “Least Concern” by the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species version 2016.1.
Detection and growth of endophytic entomopathogenic fungi in dicot crop plants

The presence and distribution of fungal endophytes in plants is commonly assessed by re-isolation on agar media or detection by PCR-techniques. Histological studies on the process of colonization of the host plant have only scarcely been performed. In the present study, the development of entomopathogenic fungi on the plant surface and inside the tissue was examined by light and fluorescence microscopy of leaf samples treated with various dyes or, to guarantee the specificity of injected endophytes, with primary polyclonal and secondary FITC-conjugated antibodies; diaminobenzidine-tetrahydrochloride (DAB) was applied as stress test for the detection of hydrogen peroxide. Four species of entomopathogenic fungi were studied and compared with three phytopathogenic fungal species. The host plants were oilseed rape (Brassica napus), faba bean (Vicia faba), and cucumber (Cucumis sativus). When blastospores of selected four fungal species were infiltrated into B. napus leaves they appeared to germinate only on the leaf surface, but not within the mesophyll. Successful re-isolation from B. napus inoculated with B. bassiana, Isaria fumosorosea or Metarhizium anisopliae showed that these entomopathogens were able to persist in the tissue for at least two weeks. Formation of brown precipitates after leaf treatment with DAB in the presence of B. bassiana indicated the production of hydrogen peroxide by B. napus but not by V. faba. Overall, the results indicate a lower endophytic colonization than could have been expected from the literature, suggesting nutrient availability in the plant intercellular space and absence of cell wall and cell membrane degrading fungal enzymes as fungal growth-limiting factors. It is concluded that data on endophytic colonization should generally be supported by histological evidence of the kind and amount of fungal growth in the host tissue.
Novel interaction partners of cutaneous HPV types and their role in skin cancer

Ultraviolet (UV) irradiation and UVB in particular, is the major environmental risk factor for the development of skin cancer. Furthermore, an increasing body of evidence supports a role for cutaneous human papillomaviruses (HPVs) in combination with UV irradiation in the development of cutaneous squamous cell carcinoma. Moreover, cutaneous HPV E6 proteins have been described to indirectly influence pathways controlled by p53, to inhibit UV-induced apoptosis and to prolong the life span of keratinocytes, the natural host of all HPVs. The present study identified the LIM protein Ajuba as a novel interaction partner of the E6 protein of the beta2 HPV23, the gamma1 HPV4 and the gamma11 HPV148. These E6 proteins were shown to directly interact with Ajuba both in vitro and in vivo as well as to co-localise with Ajuba in the cytoplasm. Furthermore, the E6 proteins of HPV23 and HPV148 showed a coincidental decrease in protein expression together with their interaction partner Ajuba upon DNA damage induction and siRNA-mediated Ajuba knockdown. This knockdown also revealed that the p53 protein was involved in the regulation of Ajuba and HPV E6 protein levels. On the other hand, Ajuba co-accumulated following overexpression of the cutaneous E6 proteins, further pointing to a close interaction of both proteins in vivo. A trimeric complex formation between p53, Ajuba and HPV148 E6 was additionally discovered, which did not take place with HPV23 E6. Moreover, p53 was shown to co-localise and to interact directly with HPV148 E6 in vitro and in vivo, even in the absence of Ajuba. A functional luciferase reporter assay revealed a strong repression of p53 activity in the presence of HPV148 E6, demonstrating an impairment of the transactivation activity of p53. This observation could however not be reported for HPV23 E6. In summary, the present study identified the LIM protein Ajuba as a novel interaction partner of cutaneous E6 proteins. Additionally, it demonstrated for the first time that the p53 protein not only binds to cutaneous HPV E6 proteins in vitro, but also interacts and co-localises with HPV148 E6 in vivo, subsequently repressing p53 activity. These findings suggest a novel regulatory mechanism elicited by cutaneous E6 proteins and further strengthen the hypothesis that cutaneous HPVs can act as co-factors in the development of skin cancer.