Miracle-dz/UniFAR-FTUs huggingface dataset:
HRM-facilitated rapid identification and genotyping of mutations induced by CRISPR/Cas9 mutagenesis in rice

The clustered regularly interspaced short palindromic repeat (CRISPR)/ CRISPR-associated (Cas) technology has recently emerged as a powerful genomic editing tool with great potential for crop breeding. However, commonly used protocols for screening of CRISPR/Cas9-induced mutations are laborious, timeconsuming, and costly. In the present study we examined the applicability of high resolution melting (HRM) analysis fast screening CRISPR/Cas9-induced mutations in T0 plants and subsequent genotyping of T1 populations. Comparative analysis demonstrated that HRM analysis could identify mutant T0 plants carrying various types of mutation, including single nucleotide substitutions and short insertion/deletions, with false positive/negative rates of 0-2.78%. Furthermore, T1 plants derived from single T0 plants could be correctly genotyped by HRM analysis using WT parents and T0 plants as controls. We hence recommend the adoption of HRM analysis in CRISPR/Cas9 mediated genetic studies and breeding in rice and other crop species.
FLI1 Expression Levels during Megakaryopoiesis Affect Thrombopoiesis and Platelet Biology

Friend Leukemia Virus Integration 1 (FLI1) is a critical transcription factor (TF) in terminal megakaryocyte differentiation. It is amongst the genes missing from an inherited hemizygous deletion on chromosome 11q termed Jacobsen syndrome and often results in a dysmegakaryopoiesis and macrothrombocytopenia termed Paris Trousseau syndrome (PTSx) described as being due to FLI1 allelic exclusion. It has also been reported that heterozygote FLI1 mutations in its DNA-binding domain region cause thrombocytopenia in patients suspected to have inherited platelet defects. To date, there are no reports containing comprehensive in vitro or in vivo characterization of platelet defects due to heterozygous FLI1 deletion or mutations, or that of platelets expressing increased levels of FLI1. We used induced pluripotent stem cell (iPSC)derived megakaryocytes (iMegs) to determine if the platelet disorder observed in PTSx could be replicated, either with iPSCs generated from a PTSx patient or from a targeted heterozygous knockout of FLI1 (FLI1+/-) in control iPSCs. These studies indicate that PTSx and FLI1+/iMegs replicate many of the clinical features described in PTSx and showed more in vitro injury to the resulting iMegs with fewer platelets released in vivo. These platelets had shortened half-lives and were functionally defective. We then examined whether increased levels of FLI1 would affect megakaryopoiesis and thrombopoiesis, and found an increased number of iMegs with less in vitro injury compared to control iMegs. FLI1-overexpressing iMegs also released more platelets in recipient mice with increased half-life and functionality. These studies confirm FLI1 heterozygosity results in defects in megakaryopoiesis and thrombopoiesis similar to that noted with other megakaryocyte-specific TFs, but unlike those TFs, FLI1 overexpression is not associated with quality or quantitative platelet deficiencies, but improved yield and functionality that may have clinical applicability. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Pharmacology First Advisor Mortimer Poncz
Regulation of checkpoint kinase signalling and tumorigenesis by the NF-κB regulated gene, CLSPN

Inhibition of the tumour promoting activities of NF-κB by cell signalling pathways has been proposed as a natural mechanism to limit the development of cancer. However, there has been a lack of evidence for these effects in vivo. Here we report that RelAT505A mice, where a CHK1 targeted Thr505 phosphosite is mutated to alanine, display earlier onset of MYC driven lymphoma than wild type littermates. We describe a positive feedback loop in which the NF-κB subunits RelA and c-Rel, in a manner dependent upon RelA Thr505 phosphorylation, drive the expression of the ATR checkpoint kinase regulator Claspin in response to DNA replication stress in cancer cells. This in turn is required for maintenance of CHK1 activity. Loss of a single allele of the Clspn gene in mice is sufficient to drive earlier tumorigenesis and low levels of CLSPN mRNA expression are associated with worse survival in some forms of human cancer. We propose that loss of this pathway early in tumorigenesis promotes cancer development through increased genomic instability. However, in malignant cancer cells it can help promote their addiction to the checkpoint kinase signalling required for the maintenance of genomic integrity. Importantly, disruption of this pathway leads to resistance of cells to treatment with CHK1 inhibitors. Claspin expression could therefore act as a biomarker for responsiveness of patients to CHK1 inhibitors and provide a potential pathway for the development of tumour resistance.
Preliminary Habitat Models of Foraging and Roosting Sites Used By Two Rehabilitated Adult Male Andean Condors (Vultur gryphus) In Peru

Abstract Satellite telemetry is widely used to generate information on species' use of space, which contributes to meeting conservation goals. Between June 2015 and September 2016, we obtained approximately 11,000 GPS points from two adult male Andean Condors (Vultur gryphus) that had been fitted with satellite transmitters and released in the central Andes of Peru. We used GPS coordinates and associated data to produce habitat distribution models (binomial Generalized Linear Models) from presence and pseudo-absence data of roosting sites and foraging areas visited by these individuals. The best potential habitats for Andean Condors in Peru were west of the Andes, from the border with Ecuador, south to Bolivia and Chile. Foraging areas of both individuals were at higher elevations than roosting sites (means: 3934 masl and 3356 masl, respectively). Roosting sites were in areas dominated by grasslands and agriculture, whereas foraging areas were dominated by puna grassland and brush. Conservation strategies for Andean Condors in Peru should be informed by data derived from satellite telemetry and should focus on preserving natural short vegetation above 3000 m west of the Andes for foraging and, for roosting sites, on maintaining areas free from the disturbances of road construction.
Effect of energy and protein supplementation on growth and nutrient requirement estimation in crossbred bull calf

This study was carried out to investigate the effects of supplying different levels of energy and protein on the growth performance and nutrient requirements estimation in crossbred bull calves. Feeding trial was conducted for 60 days with 12 numbers of crossbred bull calves. The animals were divided into four groups i.e. T 0 , T 1 , T 2 and T 3 . Four levels of metabolizable energy (ME) and digestible crude protein (DCP) were supplied respectively in four dietary groups, T 0 =17.4 MJ/d and 85 g/d as maintenance ration, T 1 =19.22 MJ/d and 188 g/d for 200 g/d targeted BWG, T 2 =21.29 MJ/d and 243 g/d for 400g/d targeted BWG, T 3 =23.37 MJ/d and 255 g/d for 600g/d targeted BWG. A positively correlation of BWG with uptake of nutrients (energy and protein) and feed conversion efficiency of different dietary groups was observed. Results revealed that the average daily body weight gain (BWG) in T 1 (200 g/d) fulfills against the targeted BWG 200 g/d, T 2 maintaining BWG 327 g/d against the targeted BWG 400 g/d and T 3 maintaining BWG 422 g/d against the targeted BWG 600 g/d. Considering the growth response of crossbred bull calves it is evident that T 1 is better than other dietary groups. Again, estimated ME requirement for maintenance was 16.14 MJ/d and for each kg BWG/d requires ME was 14.69 MJ for 100 kg body weight of crossbred bull calves. The maintenance requirement of DCP was 60.65 g/d and for each kg BWG/d requires DCP was 0.56 g for 100 kg body weight of crossbred bull calves. Bang. J. Anim. Sci. 2017. 46 (3): 179-187
Analysis of molecular genetic diversity of endangered Punjab urial (Ovis vignei punjabiensis) based on interleukin 2 gene sequences

T. HUSSAIN, M. M. MUSTHAFA, M. E. BABAR, W. A. KHAN, Z. ULLAH, M. AQEEL, A. YAQUB & F. M. M. T. MARIKAR Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan; Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan; Pet Center, University of Veterinary and Animal Sciences, Lahore, Pakistan; Bioinformatics Lab, National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, Pakistan; Department of Zoology, Government College University, Lahore, Pakistan; Pakistan Wildlife Foundation, Islamabad, Pakistan; General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
Updates on animal models of systemic sclerosis

Systemic sclerosis (SSc) is a connective tissue disease of unknown etiology that is characterized by fibrosis of the skin and several internal organs, vasculopathy, inflammation and autoimmunity. Animal models have improved our understanding of the pathogenesis of SSc. Many inducible and genetic animal models of SSc have been developed and characterized in the last years. All of these models have different strengths and limitations and mimic different aspects of the pathogenesis of SSc. The purpose of this review is to summarize the characteristics of the various animal models of SSc and to provide an outline of how to use these models to study certain aspects in the pathogenesis of SSc and to test the effects of potential therapeutic approaches.
An efficient CAPS marker for bacterial-blight resistance gene xa25 in rice

Abstract The recessive Xanthomonas oryzae pv. oryzae (Xoo) resistance gene, xa25, which mediates race-specific resistance to the Xoo isolate PXO339, has previously been characterized in rice (Oryza sativa L.). Its dominant allele, Xa25, is transcriptionally induced by Xoo infection, which in turn results in susceptibility to PXO339. Utilizing a base substitution (−40, G to T) in the xa25/Xa25 promoters, a cleaved amplified polymorphic sequence (CAPS) marker was designed for effective identification of the xa25 gene. This marker co-segregated with the xa25 gene and explicitly distinguished the genotypes of xa25/Xa25 gene in rice. The marker was further tested on nine Chinese rice landraces, revealing the association of xa25/Xa25 genotypes with resistance/susceptibility to PXO339, respectively. Therefore, this marker is reliable and cost-effective for marker-assisted selection of the xa25 gene in rice.
New expression system

PURPOSE: To obtain a new baculovirus transfer vector useful for obtaining a number of recombinants of baculovirus. CONSTITUTION: This baculovirus transfer vector contains a restriction site for insertion of a DNA sequence encoding a heterologous polypeptide, regulatory elements to provide for expression of the DNA sequence, when inserted into the restriction site, and a loxP DNA sequence acting as a substrate for the Cre recombinase protein. The loxP DNA sequence is identical, for example, to the sequence of the formula. This transfer vector can be constructed by adequately manipulating a known or available transfer vector with standard techniques in this field. COPYRIGHT: (C)1993,JPO
Plant ecophysiological responses to drought, nocturnal warming and variable climate in the Pannonian sand forest-steppe: results of a six-year climate manipulation experiment

Abstract The impacts of year-round nocturnal warming or late spring rain exclusion on three plant functional types were studied in a plot-scale climate simulation experiment in a semiarid sand forest-steppe of Central Hungary. Ecophysiological traits were followed through six years for the C3 bunch grass Festuca vaginata, the spreading C4 grass Cynodon dactylon and shrub-sized root suckers of Populus alba. In general, experimental treatments had slighter effects than weather fluctuations yielding extremities did. Populus alba responded to nocturnal warming with developing slenderer leaves. Rain exclusion reduced leaf physiological activity or growth, but only during or just after the treatment, and in certain years. When assessing treatment and background climatic variation effects together, in spring, leaf area growth was consistently stimulated by increasing temperature, but decreased with longer rainless periods for P. alba and F. vaginata. Physiological responses in spring indicated low temperature limitation for C. dactylon, and both low and high temperature control for P. alba. Longer summer droughts reduced leaf gas exchange, particularly for F. vaginata with substantial drop in photochemical activity and chlorophyll content. These results suggest that shallow rooted C3 bunch grasses can be the most susceptible to climatic variation, thus their abundance is expected to decline in the Pannonian forest-steppe. In contrast, plants having deeper roots and clonal integration will probably be less affected by the projected warming and drying climate. C4 photosynthesis or southern geographical distribution may also be beneficial, thus, the abundance of such species is expected to diminish less or even increase.
The impact of the kelp (Laminaria hyperborea) forest on the organic matter content in sediment of the west coast of Norway

ABSTRACT Sediment cores were collected from an area off the west coast of Norway, where a well-established kelp community made up mainly of Laminaria hyperborea is found. Chemical analyses of the sectioned sediment cores were made, which included organic carbon, carbohydrates and phenols. These were used to collate the sediments in order to establish whether the different sites had a common origin and if this was kelp-related. The organic matter content in the surface sediments appears to be related to the water depth, which determines the degree of perturbation at the sediment-water boundary and hence the sedimentation of the organic matter. The relation between carbohydrates and phenols in the sediment appears to indicate a common origin. However, the carbohydrate and phenol content in the sediment organic fraction appears to closely resemble (to be analogous) to that of the kelp Laminaria hyperborea. Although there are some diagenetic and decomposition changes in the subsurface (historical) organic matter (that may alter its findings), this study provides good evidence that the deposits were supplied by the kelp forest in the region. The sedimentation and export of kelp-derived material is of particular significance in terms of benthic ecology and production and may also play a significant role in the global carbon budget.
Validation of yellow nutsedge (Cyperus esculentus) control strategies in maize in an on-farm, large-scale field trial

A large on-farm field trial was carried out between 2013 and 2015 to investigate the effect of repetitive maize cropping on Cyperus esculentus infestation over time. Intensive control strategies, developed and investigated in small-scale trials, were validated. Four C. esculentus treatment strategies were installed. Soil samples were taken each year put in the greenhouse and the number of C. esculentus sprouts was assessed. Initial infestation was patchy. Field areas were flooded several times due to heavy rainfall. Despite the inherent variability and the adverse weather conditions following conclusions can be drawn: Growing maize combined with intensive weed control (2-4 passes), reduced infestation on average by 80%. Principal components for Cyperus esculentus control strategies are hoeing, the active substances S-metolachlor, mesotrione, terbuthylazine, rimsulfuron, bentazone, and a herbicide containing foramsulfuron, thiencarbazone and iodosulfuron. Growing maize combined with high intensity weed control is an effective approach to manage and reduce C. esculentus infestation. Yield depressions due to this highly intensive weed control cannot be rule out. Nevertheless, farmers in the affected region have adopted these approaches.
Identification of new biomarkers for cisplatin-resistance in A549 human lung adenocarcinoma cells by an integrated bioinformatical analysis

Background: Drug resistance plays an important role in the failure of clinical therapy. This study aimed to identify the key genes related to cisplatin resistance in A549 human lung adenocarcinoma cells. Methods: The mRNA microarray dataset E-MEXP-3123 and miRNA dataset GSE43249 were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) and miRNAs (DEMs) between parental and cisplatin-resistance A549 lung cancer cells were identified. Functional enrichment analysis and pathway analysis were performed by using the DAVID database. Protein-protein interactions of DEGs, microRNAs (miRNAs) network and their potential gene targets were formed by Cytoscape. Real-time quantitative polymerase chain reaction (qRT-PCR) was used to validate the identified candidate genes in cisplatin-resistant A549 cells. Results: Firstly, a total of 499 DEGs were identified from E-MEXP-3123. In gene ontology (GO) term analysis, DEGs were significantly involved in signal transduction, oxidation-reduction process, multicellular organism development, cell adhesion and inflammatory response. Pathway analysis showed that the most significant pathways were neuroactive ligand-receptor interaction, endocytosis and hippo signaling pathway. PPI network showed that the top five hub genes were CDH1 (cadherin 1), BDKRB2 (bradykinin receptor B2), FPR2 (formyl peptide receptor 2), CCR5 (C-C chemokine receptor type 5) and YWHAE (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon). Secondly, 12 DEMs were identified from GSE43249, and the top six DEMs were miR-194, miR-192, miR-574-3p, miR-106b, miR-146a and miR-182. In subsequent qRT-PCR experiments, low expression levels of miR-192, miR-106b, miR-182 and high expression level of miR-574-3p were confirmed in cisplatin-resistant group compared with control group. Meanwhile as predicted, the overexpression of NCALD, SPIN1 that are miR-182 potential targets and the weak expression of PSMA4 that is miR-574-3p potential target were also experimentally validated in cisplatin-resistant lung cancer cells. Conclusions: These key genes identified in our study might provide new clues for developing effective strategies against cisplatin resistance during lung adenocarcinoma treatment.
Study of Tissue Orientation and Parasite Load in Various Tissues and Blood in an Experimental Mouse Model of Acute Toxoplasmosis

Background: Toxoplasma gondii is an obligate intracellular parasite, which can be found in diﬀerent cells of humans and animals and infect many tissues. The virulence of T. gondii strains is commonly detected, based on the outcomes of infection in mice. The present study was performed to determine the parasite distribution and tissue tropism of tachyzoites of T. gondii RH strain in an experimental mouse model of infection, using quantitative polymerase chain reaction (qPCR). Methods: In this experiment, male and female BALB/c mice were infected through intraperitoneal injection of 103 tachyzoites of T. gondii RHstrain. Theassessmentswereperformedat1,2,3,4,and5dayspostinoculation(dpi),aswellasthetimeof death;themice were monitored 3 times a day. After the animals were sacriﬁced in each group, diﬀerent tissues were collected from the heart, liver, lung, muscle, kidneys, genitals, spleen, brain, eyes, and blood and maintained at -20°C. Then, DNA samples were extracted using kits, and DNA copy number was measured via qPCR, targeting B1 gene. Results: The parasite was distributed in various tissues on the ﬁrst day after infection and exhibited the ability to cross the blood-brain barrier within the brain. Twenty-four hours after tachyzoite inoculation, the highest parasite load was observed in the liver tissues of both groups. Conclusions: Consideringthebloodﬂowtoalltissuesandtransmissionof parasitetoothertissues,thehighestparasitecountwas reported in the present study. These ﬁndings are invaluable for assessing the impact of new drugs on these parasites. There is also the possibility of sexual transmission, causing a signiﬁcant parasite load in the genitals.
Comparative study of physical, chemical, microbiological and sensory aspects of some sun dried fishes in Bangladesh

An investigation was carried out to compare the physical, chemical, microbiological and sensory properties of three freshwater dried fish products of Wallago attu Bloch & Schneider, 1801 (Siluriformes: Siluridae), Channa striatus (Bloch, 1793) (Perciformes: Channidae) and Glossogobius giuris (F. Hamilton, 1822) (Perciformes: Gobiidae). The traditionally sun dried fishes were collected from Kawran Bazar Fish Market, Dhaka, Bangladesh. Results showed that the water reconstitution properties varied among the dried fishes where maximum rehydration was observed in the C. striatus at room temperature, 40 oC and 60 oC. Moisture content of W. attu, C. striatus and G. giuris were 22.70% ± 0.45%, 18.75% ± 0.58% and 21.93% ± 0.54%, respectively; the protein content were 61.85% ± 0.99%, 66.44% ± 1.02% and 62.83% ± 0.87%, respectively; the lipid content were 6.21% ± 0.93%, 6.81% ± 0.72% and 5.98% ± 0.55%, respectively, and the ash content were 6.79% ± 1.11%, 6.49% ± 1.29% and 7.83% ± 0.98%, respectively. Peroxide value, acid value, pH, TVB-N value and aerobic plate count were found to be highest in W. attu followed by G. giuris and C. striatus. Results of this study revealed that traditionally sun dried fish products were acceptable quality in terms of physico-chemical, microbiological and sensory aspects.
Response of greenhouse-grown bell pepper (Capsicum annuum L.) to variable irrigation

Aladenola, O. and Madramootoo, C. 2014. Response of greenhouse-grown bell pepper (Capsicum annuum L.) to variable irrigation. Can. J. Plant Sci. 94: 303-310. In order to optimize water use in bell pepper production information about the appropriate irrigation water applications and agronomic and physiological response to mild and severe water stress is necessary. Different water applications were tested on yield, quality and water stress threshold of greenhouse-grown bell pepper (Capsicum annuum L.) cultivar Red Knight in 2011 and 2012 on the Macdonald Campus of McGill University, Ste Anne De Bellevue, QC. The study was carried out on a soil substrate in the greenhouse. Irrigation was scheduled with four treatments:120% (T1), 100% (T2), 80% (T3), and 40% (T4) replenishment of crop evapotranspiration in a completely randomized design. The highest marketable yield, water use efficiency and irrigation water use efficiency were obtained with T1 in both years. T1 received 20% more water than T2 to produce 23% more marketable yield than T2. Fruit total soluble solids content was highest in T4, and smallest in T1. The mean crop water stress index (CWSI) of the irrigation treatments ranged between 0.08 and 1.18. Leaf stomatal conductance of bell pepper was 75 to 80% lower in T4 than in T1. Regression obtained between stomatal conductance and CWSI resulted in a polynomial curve with coefficients of determination of 0.88 and 0.97 in 2011 and 2012, respectively. The result from this study indicate that the yield derived justifies the use of an extra quantity of water. Information from this study will help water regulators to make appropriate decision about water to be allocated for greenhouse production of bell pepper.