Miracle-dz/UniFAR-FTUs huggingface dataset:
Advances in Transgenic Rice Biotechnology

Rice is the most amenable crop plant for genetic manipulation amongst monocots due to its small genome size, enriched genetic map, availability of entire genome sequence, and relative ease of transformation. Improvement in agronomic traits of rice is bound to affect a sizeable population since it is a primary source of sustenance. Recent advances like use of ‘clean gene’ technology or matrix attachment regions would help improve rice transformation. Function of several novel genes and their promoters has been analyzed in transgenic rice. Significant progress has been made in introducing traits like herbicide, biotic stress and abiotic stress tolerance. Attempts also have been made to enhance nutritional characteristics of the grain and yield. Identification of genes controlling growth and development can be used to modify plant architecture and heading period. Transgenic rice can serve as a biofactory for the production of molecules of pharmaceutical and industrial utility. The drive to apply transgenic rice for public good as well as commercial gains has fueled research to an all time high. Successful field trials and biosafety of transgenic rice have been reported. This would act as a catalyst for greater acceptance of genetically modified food crops. The lessons learnt from rice can be extended to other cereals thereby opening new opportunities and possibilities.
Host range and habitats of the aphid parasitoid Diaeretiella rapae (Hymenoptera: Aphidiidae) in Washington State.

Host aphids of the parasitoid Diaeretiella rapae (M’Intosh,) are defined for Washington State, together with a listing of world findings. Specifics are given on host habitats frequented by the parasitoid, comparative population abundance, associated parasitoid species, and host switching. D. rapae is a common parasitoid of Brachycorynella asparagi (Mordvilko), Hayhurstia atriplicis (L.), Brevicoryne brassicae (L.), Diuraphis noxia (Kurdjumov), and sometimes Myzus persicae (Sulzer). In total, 19 species of aphids were positively linked with D. rapae and 6 are reported as hosts for the first time— Acyrthosiphon lactucae (Passerini), Phorodon humuli (Schrank), Dysaphis plantaginea (Passerini), Brachycaudus tragopogonis (Kaltenbach), Uroleucon ivae Robinson, and Braggia sp. D. rapae was shown to switch or alternate successfully between hosts, which suggests that certain host habitats might be used in conjunction with farmlands to enhance host opportunities for the parasitoid and improve its population stability. Two of its primary aphid hosts, B. asparagi and D. noxia, reached pest status shortly after their arrival in Washington but are less problematic today, in part at least because of host switching and acceptance by D. rapae.
Factors influencing fish catch levels on Kenya's coral reefs

The factors influencing fish catches on Kenya's coral reefs were studied. Catch data were collected at the species level by counting the number of fish landed at each landing site of each fishing ground. Live coral cover, topographic complexity, fish and sea urchin density, and the number of fishers and gear units used in each fishing ground were compared with catch data. Fishing grounds included one location where only basket traps were allowed, six locations where all gear types were used except beach seines, and three locations where all types of gear, including beach seines, were used. Catch and effort variables were similar across the fishing grounds whereas live coral cover and sea urchin density differed (P < 0.01). The sites fished by all types of gear including beach seines had the lowest coral cover (8.4 ± 0.9%) and topographic complexity (1.12 ± 0.01). Catch levels were positively correlated with the number of fishers and fish density but not with the number of gear units deployed or sea urchin density. The number of fishers and live coral cover were the strongest factors determining total catch levels. The results suggest that high levels of fishing effort coupled with the use of destructive gear types, exacerbate the effects of overfishing on Kenya's reefs.
Investigation of Fungi Associated with the Spoilage of Chrysophyllum Albidum (G.Don) Fruits.

Chrysophyllum albidum (African star apple) fruit is among the well known indigenous fruit trees in the tropical rainforest zone of the Western region of Africa. The fruits are much cherished by both the young and the old and are of huge commercial interest in Nigeria. The fruits often deteriorate within a very short period and become spoilt as a result of fungi attacks. The study therefore carried out the survey of fungi attacks on C. albidum and investigates the etiology of post harvest deterioration. Fresh fruits were procured from purposively selected markets in Ogun State for microbial analysis. Descriptive and cross tabulation analysis were used to analyze the data and these include: percentages, frequency distribution and cross tabulation. The results of this study showed that five fungal genera were associated with African star apple fruits. The fungi found on the surface of the fruits were Fusarium solani, Aspergillus niger, Aspergillus fumigatus, Penicillium citrinum, Lasiodiplodia theobromae and Rhizopus spp. Fusarium solani was the most abundant and prevalent in almost all the localities. The incidence of the occurrence of fungi found associated with highest percentage of Lasiodiplodia theobromae (40.37%) and Fusarium solani (26.23%) respectively. The least occurrence of all the fungal isolates is Aspergillus flavus. Aspergillus niger, Penicillum citrinum and Aspergillus fumigatus . They all were found to be pathogenic to C.albidum fruits and responsible for their spoilage. Therefore the use of local preservatives (plant extracts) like Afromomum danielli, Afromomum melegueta and chemical disinfectants like paraozone, sodium chloride and sodium benzoate at mild dosages were recommended to reduce the losses due to storage moulds. Early harvesting of the fruits, prevention of over ripening and keeping the fruits dry and cool at all time should be ensured. Keywords : Chrysophyllum albidum , fungi attacks, etiology, microbial analysis, preservatives
Revision of Heliconia sect. Heliconia (Musaceae)

The section Heliconia comprises stout musoid species with erect inflorescences, thick, deeply cymbiform spathes and greenish flowers on untwisted pedicels. Seven species are recognized viz.: (1) H. bihai (L.) L. , (2) H. rodriguensis Aristeg. , (3) H. caribaea Lam. , (4) H. bourgaeana Peters. , (5) H. stricta Huber, (6) H. wagneriana Peters, and (7) H. ortotricha Anderss. sp. nov. The circumscription of the section is discussed, and it appears that closest affinities are with H. latispalha Benth. , H. spatho–circinata Aristeg. and allied species, and also with H. lourteigii Emygdio & Santos and H. tenebrosa Macbr. Two groups can be discerned in the section, one comprising species 1–3 and the other species 5–7, H. bourgaeana occupying a somewhat isolated and more or less intermediate position. A key to species is given and each species is described and illustrated. Particular attention is paid to variation in diagnostically important features.
rbcL gene sequences reveal relationships among north‐east Pacific species of Porphyra (Bangiales, Rhodophyta) and a new species, P. aestivalis

Phylogenetic analyses of the rbcL (chloroplast Rubisco large subunit) gene from 23 newly sequenced species of Porphyra, primarily from the north‐east Pacific, one Bangia and previously published sequences from both genera resolve relationships among most species of Porphyra and reveal five clades of species with Porphyra‐type morphologies among a number of Bangia lineages: (1) P. papenfussii V. Krishnam; (2) P. mumfordii S. C. Lindstrom et K. M. Cole and P. rediviva Stiller et Waaland together with a group of north Atlantic species, including the type of the genus, P. purpurea (Wahl‐enb.) C. Agardh; (3) P. cuneiformis (Setch. et Hus) V. Krishnam. , P. occidentalis Setch. et Hus, P. schizo‐phylla Hollenb. , and P. variegata (Kjellm.) Kjellm. and their Atlantic sibling species, all distromatic; (4) P. aestivalis sp. nov. and its north Atlantic sibling, P. birdiae C. D. Neefus et A. C. Mathieson; and (5) a speciose clade containing both Pacific and Atlantic representatives. Close relationships are confirmed between sibling species previously identified by iso‐zymes, morphology and chromosomal features. The morphologically similar dioecious P. pseudolanceolata V. Krishnam. , P. conwayae (S. C. Lindstrom et K. M. Cole) stat. nov., and P. lanceolata (Setch. et Hus) G. M. Smith occur in a strongly supported subclade in clade 5 together with the monoecious P. fallax S. C. Lindstrom et K. M. Cole. Results presented here highlight the need for intensive taxon sampling and for examination of different parts of the genome to understand more fully relationships among species and higher level taxa in the Bangiales.
Assembly of DNA polymerase 6 and e holoenzymes depends on the geometry of the DNA template

Abstract To study in details the assembly of DNA polymerases delta and epsilon holoenzymes a circular double-stranded DNA template containing a gap of 45 nucleotides was constructed. Both replication factor C and proliferating cell nuclear antigen were absolutely required and sufficient for assembly of DNA polymerase delta holoenzyme complex on DNA. On such a circular DNA substrate replication protein A (or E. coli single-strand DNA binding protein) was neither required for assembly of DNA polymerase delta holoenzyme complex nor for the gap-filling reaction. A circular structure of the DNA substrate was found to be absolutely critical for the ability of auxiliary proteins to interact with DNA polymerases. The linearization of the circular DNA template resulted in three dramatic effects: (i) DNA synthesis by DNA polymerase delta holoenzyme was abolished, (ii) the inhibition effect of replication factor C and proliferating cell nuclear antigen on DNA polymerase alpha was relieved and (iii) DNA polymerase epsilon could not form any longer a holoenzyme with replication factor C and proliferating cell nuclear antigen. The comparison of the effect of replication factor C and proliferating cell nuclear antigen on DNA polymerases alpha, delta and epsilon indicated that the auxiliary proteins appear to form a mobile clamp, which can easily slide along double-stranded DNA.
Classification of atrial electrograms in atrial fibrillation using Information Theory-based measures

Classification of complex fractionated atrial electrograms (CFAE) is crucial for the study of atrial fibrillation and for the development of treatment strategies, because these electrophysiological phenomena represent a common target for radiofrequency ablation. Since the description of CFAEs in 2004, the scientific community have been focused their efforts into its characterization and automatic classification considering the degree of fractionation, a clinical scale used in ablation procedures. Endocardial sites associated to CFAEs are usual targets in ablation therapy, as is though that they play a role in maintenance of the arrhythmia.
Heparan Sulfate Proteoglycans Are Ligands for Receptor Protein Tyrosine Phosphatase σ

ABSTRACT RPTPσ is a cell adhesion molecule-like receptor protein tyrosine phosphatase involved in nervous system development. Its avian orthologue, known as cPTPσ or CRYPα, promotes intraretinal axon growth and controls the morphology of growth cones. The molecular mechanisms underlying the functions of cPTPσ are still to be determined, since neither its physiological ligand(s) nor its substrates have been described. Nevertheless, a major class of ligand(s) is present in the retinal basal lamina and glial endfeet, the potent native growth substrate for retinal axons. We demonstrate here that cPTPσ is a heparin-binding protein and that its basal lamina ligands include the heparan sulfate proteoglycans (HSPGs) agrin and collagen XVIII. These molecules interact with high affinity with cPTPσ in vitro, and this binding is totally dependent upon their heparan sulfate chains. Using molecular modelling and site-directed mutagenesis, a binding site for heparin and heparan sulfate was identified in the first immunoglobulin-like domain of cPTPσ. HSPGs are therefore a novel class of heterotypic ligand for cPTPσ, suggesting that cPTPσ signaling in axons and growth cones is directly responsive to matrix-associated cues.
Genetic and antigenic analysis of Babesia bigemina isolates from five geographical regions of Brazil

A molecular epidemiological study was performed with Babesia bigemina isolates from five geographical regions of Brazil. The genetic analysis was done with random amplification of polymorphic DNA (RAPD), repetitive extragenic palindromic elements-polymerase chain reaction (REP-PCR) and enterobacterial repetitive intergenic consensus sequences-polymerase chain reaction (ERIC-PCR) that showed genetic polymorphism between these isolates and generated fingerprinting. In RAPD, ILO872 and ILO876 primers were able to detect at least one fingerprinting for each B. bigemina isolate. The amplification of B. bigemina DNA fragments by REP-PCR and ERIC-PCR gave evidence for the presence in this haemoprotozoan of the sequences described previously in microorganisms of the bacterial kingdom. For the first time it was demonstrated that both techniques can be used for genetic analysis of a protozoan parasite, although the ERIC-PCR was more discriminatory than REP-PCR. The dendogram with similarity coefficient among isolates showed two clusters and one subcluster. The Northeastern and Mid-Western isolates showed the greatest genetic diversity, while the Southeastern and Southern isolates were the closest. The antigenic analysis was done through indirect fluorescent antibody technique and Western blotting using a panel of monoclonal antibodies directed against epitopes on the merozoite membrane surface, rhoptries and membrane of infected erythrocytes. As expected, the merozoite variable surface antigens, major surface antigen (MSA)-1 and MSA-2 showed antigenic diversity. However, B cell epitopes on rhoptries and infected erythrocytes were conserved among all isolates studied. In this study it was possible to identify variable and conserved antigens, which had already been described as potential immunogens. Considering that an attenuated Babesia clone used as immunogen selected populations capable of evading the immunity induced by this vaccine, it is necessary to evaluate more deeply the cross-protection conferred by genetically more distant Brazilian B. bigemina isolates and make an evaluation of the polymorphism degree of variable antigens such as MSA-1 and MSA-2.
Microsatellite DNA markers for a grasshopper: Prionotropis hystrix rhodanica (Orthoptera, Pamphagidae)

Microsatellite loci were isolated from Prionotropis hystrix rhodanica , an endangered grasshopper species, endemic to a steppic area southeast of France. Six polymorphic loci were obtained from an enriched partial genomic libray. A high genetic diversity was observed at all loci, with an observed number of alleles ranging from seven to 29, and an observed heterozygosity between 0.71 and 0.90. Test of cross-amplifications on two closely related taxa are presented.
Physics Models of Pronuclear Movements in Eggs

Based on published experimental data, Newton's laws, and Coulomb's law, we investigate natural and normal pronuclear movements in wild types of eggs and develop physics models to fit the experimental data quantitatively. The difference between our modeling calculated results and the experimental data is less than 20%. Our models explain why and how pronuclei move in even or in variant velocities. We hypothesize: During the migration, positively charged asters (or self assembled microtubules) drive two negatively charged sperm and egg pronuclei to move towards each other. The driving force comes from a spontaneous and strong Electromagnetic Field (EMF). Hamilton's principle determines the path of these movements. A natural and normal EMF inside or around the pronuclei can be alternated environmentally. An abnormal EMF could induce aberrant embryos that cause life disease. We believe our models are helpful to further understand the mechanism of fertilization and have potential clinical value to prevent aberrant embryos that induce human life disease.
Recurrent Selection in Soybeans. III. Selection for Increased Percent Oil in Seeds1

Three cycles of recurrent selection to increase seed oil percentage were conducted in a soybean [Glycine max (L.) Merr. ] population segregating for male sterility (ms1ms1). The base population was planted single plant hills to allow for natural cross pollination of male-sterile plants by male-fertile plants. At maturity, male-sterile plants with the highest seed oil percentages were selected from this crossing block. The halfsib families from the selected plants w.ere grown to maturity in the greenhouse, and the individual within each half-sib family with the highest seed oil percentage was selected. A new cycle was begun by a natural intermating of the progeny of theselected individuals in the field. The selected progenies from each cycle of selection were evaluated in composite populations and singly as lines. The combined composite and lines tests showed cycles of selection, at an average rate of 0.35 ± 0.03/cycle. There was a nonsignificant increase in total oil from 444 to 460 kg/ha. Protein percentage decreased at a rate of −0.52 ± 0.08/cycle. Changes in yield and total protein were not statistically significant.
Lack of change in CA1 dendritic spine density or clustering in rats following training on a radial-arm maze task

Background: Neuronal plasticity is thought to underlie learning and memory formation. The density of dendritic spines in the CA1 region of the hippocampus has been repeatedly linked to mnemonic processes. Both the number and spatial location of the spines, in terms of proximity to nearest neighbour, have been implicated in memory formation. To examine how spatial training impacts synaptic structure in the hippocampus, Lister-Hooded rats were trained on a hippocampal-dependent spatial task in the radial-arm maze. Methods: One group of rats were trained on a hippocampal-dependent spatial task in the radial arm maze. Two further control groups were included: a yoked group which received the same sensorimotor stimulation in the radial-maze but without a memory load, and home-cage controls. At the end of behavioural training, the brains underwent Golgi staining. Spines on CA1 pyramidal neuron dendrites were imaged and quantitatively assessed to provide measures of density and distance from nearest neighbour. Results: There was no difference across behavioural groups either in terms of spine density or in the clustering of dendritic spines. Conclusions: Spatial learning is not always accompanied by changes in either the density or clustering of dendritic spines on the basal arbour of CA1 pyramidal neurons when assessed using Golgi imaging.
Prediction of posttreatment spermatogenesis in patients with testicular cancer by flow cytometric sperm chromatin structure assay

The hypothesis to be tested was that abnormal sperm chromatin structure is related to disturbed spermatogenesis in patients with testicular cancer. After orchiectomy but before further treatment ("pretreatment"), semen samples from 39 patients with testicular cancer were analyzed for sperm concentration by light microscopy and by the sperm chromatin structure assay (SCSA). In 28 patients assessment of sperm concentration was repeated 12-26 months after orchiectomy ("posttreatment"). The pretreatment SCSA results for the patients were compared to those from 18 healthy semen donors and assessed for correlation with the patients' posttreatment sperm concentration. Twenty-three patients displayed an abnormal chromatin structure in their pretreatment sample. For the nine evaluable patients on the surveillance program, the pretreatment SCSA results were not correlated with the posttreatment concentration. The results from 19 evaluable patients undergoing cytotoxic treatment (radiotherapy, 13; chemotherapy, 6) indicate that posttreatment recovery of spermatogenesis (recovery in 4 of 5 patients) is observed more often in patients with a normal pretreatment chromatin structure than in those with abnormal SCSA values before treatment (recovery in 2 of 14 patients; P = 0.02). The results of SCSA display sperm characteristics beyond those of light microscopically assessed sperm concentration. Pretreatment SCSA results might help clinicians to identify those testicular cancer patients with a high risk of long-lasting posttreatment disturbance of spermatogenesis.
Can juvenile Fucus (Phaeophyta) really deter grazing by Littorina littorea (Mollusca)?

G.W. Scott and S. Marsham. 2006. Can juvenile Fucus (Phaeophyta) really deter grazing by Littorina littorea (Mollusca)? Phycologia 45: 158–160. DOI: 10.2216/04-102.1 Grazing by herbivores has been shown to induce chemical defences in algae. To investigate the possibilities that these chemical defences are a property of the plant or of the water surrounding the plant we assigned Littorina littorea to one of four experimental treatments and measured the amount of alga consumed. We also used the results to determine if juvenile Fucus sp. can deter grazing by snails. Our results show that previously grazed plants are just as palatable as ungrazed plants and chemical deterrents do not seem to accumulate in the seawater surrounding the plant. We suggest that juvenile Fucus sp. plants do not produce chemicals that effectively deter the herbivore.
PTH-045 Biliary aspirates in suspected pancreatic cancer. a useful adjunct to brushings at ERCP?

Introduction NICE guidelines advocate the use of biliary brushings to obtain a tissue diagnosis in patients suspected of having pancreatic cancer when endoscopic retrograde cholangiopancreatography (ERCP) is used to relieve biliary obstruction. This retrospective audit evaluated whether biliary aspiration in addition to biliary brushings increased diagnostic yields at ERCP at a district general hospital, reducing the need for tertiary referral for endoscopic ultrasound (EUS) and fine needle aspiration (FNA). Methods Retrospective analysis of the local endoscopy database identified all patients undergoing ERCP with biliary brushings and aspirates between July 2012 and December 2018. Histological diagnoses from biliary aspirates/brushings were compared with subsequent FNA, surgical resection or hepatobiliary multi-disciplinary team diagnosis. Results 124 patients underwent ERCP with biliary brushings during the study period. 28 of these patients had biliary aspirates in addition to biliary brushings. Sensitivity for biliary brushings in the whole population was 47.5% (95% CI 37.3–57.8) (table 1). Specificity was 96% (95% CI 79.7–99.9). In the cohort undergoing biliary brushings and aspirate, sensitivity for biliary brushings alone was 23.8% (CI 8.2–47.2), whilst combination of brushings and aspirates was 28.6% (95% CI 11.3–52.5). Abstract PTH-045 Table 1 Cytological diagnosis (aspirate and brushings) at ERCP compared with final diagnosis Conclusions Biliary cytology has modest sensitivity with high specificity in the detection of malignancy at ERCP. Biliary aspirate cytology increases the positive yield by 5% compared to brushings alone and is a quick and easy technique at ERCP. Further data is required to evaluate whether biliary aspirates reliably increase the modest yield at ERCP, but this study shows a improvement from 23.8% to 28.6% in the subgroup who underwent both modalities to identify malignant cells at ERCP.