Miracle-dz/UniFAR-FTUs huggingface dataset:
Superantigen responsive T cells are required for nasopharyngeal infection by Streptococcus pyogenes

Streptococcus pyogenes is a human-specific pathogen that is responsible for serious morbidity and mortality worldwide despite being susceptible to common antibiotics. Furthermore, there is currently no licensed vaccine available against this organism. Previous research from our laboratory implicated a critical role for superantigens in a transgenic mouse model of acute nasopharyngeal infection by S. pyogenes. Herein, we are able to detect superantigen production in vivo and establish that anti-superantigen antibodies generated by either passive immunization or active vaccination with a major histocompatibility complex II-binding interface superantigen toxoid reduces S. pyogenes nasopharyngeal burden. We were also able to demonstrate that this organism requires responsive Vβ-specific T cells in order to efficiently infect the upper respiratory tract. These experiments remarkably reveal that S. pyogenes manipulates T cells to promote infection and also supports targeting superantigens as vaccine candidates to prevent nasopharyngeal carrier and subsequent disease caused by this globally important pathogen.
Restriction polymorphism maps of Neurospora crassa: 2000 update

Restriction fragment length polymorphisms (RFLPs) can be used to determine the approximate map location of any cloned piece of DNA. To establish an RFLP mapping system for N. crassa, R.L. Metzenberg and coworkers crossed strains with multiple sequence differences, an Oak Ridge laboratory strain (designated "O") and a Mauriceville-1c wild-collected strain (designated "M"; Metzenberg et al. 1984 Neurospora Newsl. 31:35-39; ibid. 1985 Proc. Natl. Acad. Sci. U.S.A. 82:2067-2071; Metzenberg and Grotelueschen 1995 Fungal Genet. Newsl. 42:82-90). Progeny from two separate crosses have been widely distributed and used for mapping. For the first cross, 38 progeny from 18 ordered asci were analyzed. Because nonsister spores from the same half of the ascus were selected, first-division segregation can be distinguished from second-division. For the second cross 18 random ascospore progeny were analyzed. The first cross is preferred for RFLP mapping, for several reasons: resolution is better because more loci have been scored; distance from the centromere can be estimated regardless of which linkage group is involved; double crossovers within intervals can be recognized, as can putative gene conversions or scoring errors.However, updated maps for both crosses are presented here. Creative Commons License This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. This special paper is available in Fungal Genetics Reports: http://newprairiepress.org/fgr/vol47/iss1/4
Chlamydomonas Reinhardtii:from microscopic swimming to macroscopic rheology

The unicellar green alga Chlamydomonas Reinhardtii has two flagella with which it performs a ’breaststroke’ like movement to propel itself. This alga is currently investigated for industrial purposes on the macroscale, and has recently drawn attention by physical experiments on the microscale of a single organism. This thesis aims to give an insight in both the swimming behaviour of a single alga and the influence of swimming at the macroscopic properties of suspensions of many algae. The simple analytic three-point-force model and a qualitative analysis of the flagellar stroke reproduces the experimentally obtained flow fields of Guasto et al. [23]. Two new derivations are presented for the effective viscosity of a dilute suspension of Chlamydomonas cells. Both are in agreement with previous theoretical results. The effective viscosity depends on the average swimming direction of the algae. A literature study on the ordering of active suspensions leads to the conclusion that swimming results in an increase of the viscosity for small shear rates, for higher shear rates it is undistinguishable compared to a passive suspension.
The Activity of Wungu Leaf ( Graptophyllum pictum (L) Griff) Extract in Reducing Blood Glucose Level of Hyperglycemic Mice

Wungu leaf (Graptophyllum pictum (L.) Griff) is a plant thought to have potential use in alleviating symptoms of diabetes mellitus. The purpose of the present study was to evaluate the activity of wungu leaf extracts in decreasing blood glucose level of alloxan (200 mg/kg BW)-induced hyperglycemic mice. Extracts of wungu leaf were obtained by macerating with ethanol and then partitioning the extract with diethyl ether, ethyl acetate, and butanol. Each extract obtained was used to treat hyperglycemic mice for 28 days. The results showed that wungu leaf extracts have the ability to decrease the blood glucose level of hyperglycemic mice (dose 50 mg/kg BW). The ethyl acetate extract showed the highest activity, bringing about a decrease of blood glucose of 37.6 %. The wungu leaf extract has the potential to be developed as a source of anti-diabetic agents.
Discovery of Pyrimidine-based Heterocycles as Single Agents With Combination Chemotherapy Potential And As Inhibitors Of Purine Nucleotide Biosynthesis For The Treatment of Cancer

iv LIST OF TABLES viii LIST OF FIGURES ix LIST OF SCHEMES xi LIST OF ABBREVIATIONS xiv I. BIOLOGICAL REVIEW 1 II. CHEMICAL REVIEW 43 III. STATEMENT OF THE PROBLEM 67 IV. CHEMICAL DISCUSSION 123 V. EXPERIMENTAL 177 VI. SUMMARY 218 VII. BIBLIOGRAPHY 225 VIII. APPENDIX 243
Pharmacophore Modelling of Phytochemicals from Clinacanthus Nutans for Antimicrobial Activity

Pharmacophore modelling is incorporated as a part of approach in computer-aided drug design (CADD) which assists high-throughput virtual screening and drug design. It offers information on protein-ligand interaction as well as pharmacophore features responsible for interaction with the protein target. Current studies of phytochemicals isolated from Clinacanthus nutans Lindau locally known as belalai gajah are rich of flavonoids and phenolic compounds which able to induce antimicrobial activity. However, essential information of compounds activity against target protein is still inadequate. Hexane, ethyl acetate and methanol fractions of C. nutans showed no inhibition zone against Gram-negative bacterial strain namely Escherichia coli and Gram-positive bacterial strains namely Staphylococcus aureus and Salmonella typhimurium. Pharmacophore model generated from selected broad-spectrum antibiotics (cefixime, ampicillin, amoxicillin and ciprofloxacin) revealed features of hydrogen bond donor and acceptor, hydrophobic and aromatic ring. Six C-glycosyl flavones reported from literature have more similar features and higher fit-value to generated pharmacophore model. We recommend further study to determine minimum inhibitory concentration of C. nutans using various solvent extracts to justify claim of antimicrobial activity of this plant. Synergic effect and concentration of bioactive flavonoids against antimicrobial activity also need to be considered in future studies.
Rational development of in vitro propagation conservation of worm killer plant (Aristolochia bracteolata)

Aristolochia bracteolata Linn. (familyAristolochiaceae) commonly called as Hukka-Bel and worm killer in English). It is used in traditional medicines as a gastric stimulant and in the treatment of cancer, lung inflammation, dysentery and snakebites. In the indigenous system of medicine, the plant was antipyretic & anti-inflammatory agents. The plant contain Aristolochic acid, has many medicinal properties in various disease condition. The Phytochemical showing revealed the presence of alkaloids, triterpenoids, steroids and sterols, flavonoids, tannins and phenolic compounds and cardio glycosides. Maximum bud break of the explant was obtained on MS medium supplemented with 2.0 mg l-1 of benzyl adenine (BA) + additives. Multiple shoots produced from MS+0.25 mgl-1 each of BAP, Kinetin and IAA. After 10-15 days of cultures. Amplified shoots from meristematic explants. In vitro multiplied shoots pulse treated with root hormone the rooted plantlets were hardened in green house with relieve and transplanted into black polybags containing a 1:1:1 (v/v/v) ratio of garden soil, organic manure and sand.
Design of Z-Shape Compact Antenna for Next Generation Wireless Network

The wireless communication technology is developing day by day so that various generations are taken birth. The fifth generation is considered as the next generation network and awaiting for implementation. Considering this scenario, compact antenna plays a vital role to make this dream to be realized. In this research work authors have taken a strive to design such required antenna where the bandwidth has been enhanced. The two different frequencies range covers up to fourth generation networks and beyond. Similarly, the bandwidth has been enhanced up to 75 MHz and 112.5 MHz which is approximately doubles the value of the current bandwidth. The antenna has to be pasted in the mobile circuit to maintain the data transfer in seamless mode. For suitability of the space Z-shape micro strip antenna has been developed. The result shows the achievement in terms of bandwidth, return loss, VSWR, directivity and gain. It is of Cband/ S-band satellite communication for application in wireless communication. Keywords—Next generation Network, Micro strip antenna, dual band antenna, broadband antenna, wireless communication
Calcium-dependent protein kinases in Physcomitrella patens

CALCIUM-DEPENDENT PROTEIN KINASES IN PHYSCOMITRELLA PATENS by Kathryn Chervincky University of New Hampshire, December, 2006 Calcium-dependent protein kinases (CDPKs) are a group of plant serine-threonine kinases that are stimulated in response to increases in intracellular calcium concentrations. Physcomitrella patens is a moss and a member of the bryophyte family. Physcomitrella has gained popularity as a model research organism due to the simple morphology of the plant as well as many other desirable characteristics. My research utilized Physcomitrella to accomplish four goals. The first goal was to identify and obtain sequence for as many CDPKs as possible in Physcomitrella. The second goal was to confirm the calcium-activated protein kinase activity of the identified CDPKs. The third goal consisted of two parts: first, to determine the expression pattern of a specific CDPK (CPK6) and second, to determine the role of a 5’ UTR intron in CPK6 expression. The fourth goal was to silence expression of CPK6, and possibly other closely related CDPKs, by RNA interference (RNAi) in order to screen for a phenotype. My results showed that there are at least 16 CDPKs in Physcomitrella patens. Two of those CDPKs were tested and displayed calcium-activated protein kinase activity. Expression analysis of CPK6 showed strongest expression in protonemal tip cells, immature phyllids, base of the gametophore at the site of protonemal attachment, and
The effect of temperature on the duration of spawning markers—migratory-nucleus and hydrated oocytes and postovulatory follicles—in the multiple-batch spawner Japanese flounder(Paralichthys olivaceus)

The duration of spawning markers (e.g. signs of previous or imminent spawnings) is essential information for estimating spawning frequency of fish. In this study, the effect of temperature on the duration of spawning markers (i.e., oocytes at early migratory nucleus, late migratory nucleus, and hydrated stages, as well as new postovulatory follicles) of an indeterminate multiple-batch spawner, Japanese f lounder (Paralichthys olivaceus), was evaluated. Cannulation was performed to remove samples of oocytes, eggs, and postovulatory follicles in individual females at 2–4 hour intervals over 27–48 hours. The duration of spawning markers was successfully evaluated in 14 trials ranging between 9.2° and 22.6°C for six females (total length 484–730 mm). The durations of spawning markers decreased exponentially with temperature and were seen to decrease by a factor of 0.16, 0.36, 0.30, and 0.31 as temperature increased by 10°C for oocytes at early migratory nucleus, late migratory nucleus, and hydrated stages, and new postovulatory follicles, respectively. Thus, temperature should be considered when estimating spawning frequency from these spawning markers, especially for those fish that do not spawn synchronously in the population.
Development of transgenic Brassica napus with an optimized cry1C* gene for resistance to diamondback moth (Plutella xylostella)

Wang, Y. , Zhang, Y. , Wang, F. , Liu, C. and Liu, K. 2014. Development of transgenic Brassica napus with an optimized cry1C* gene for resistance to diamondback moth (Plutella xylostella). Can. J. Plant Sci. 94: 1501-1506. Bacillus thuringiensis (Bt) cry1Ac gene has been transformed into rapeseed to control diamondback moth (DBM, Plutella xylostella), which is one of the major lepidopteran pests of rapeseed (Brassica napus). However, Cry1A-resistant DBM populations have already developed in the field. Cry1C* is a new synthetic Bt gene based on the original cry1Ca5 sequence through optimizing its codons as well as removing AT-rich sequences and inverted repeats. In our present study, the cry1C* gene was introduced into rapeseed via Agrobacterium-mediated transformation, and a total of 42 transgenic lines were recovered. The results of polymerase chain reaction (PCR) and Southern blot both confirmed the expression of the cry1C* gene in the genomes of the transformants. We also assessed the expression of this foreign gene at the mRNA level in some selected transgenic lines by real-time reverse transcription (RT) PCR analysis. Enzyme-linked immunosorbent assay (ELISA) showed that the Cry1C* expression at the protein level greatly varied among individual transgenic plants, and transgenic line 1C-8 had the highest protein level of 799.32 ng g-1. The transgenic rapeseed plants expressing cry1C* gene showed a high efficacy against DBM. Taken together, the cry1C*-transgenic rapeseed could be employed as a useful germplasm in pest management and in the broad bioinsecticidal spectrum to prevent and postpone the development of pest resistance.
Agri-Environment Scheme Habitat Preferences of Yellowhammer Emberiza citrinella on English Farmland

Abstract. Agri-Environment Schemes (AES) have been implemented across Europe in an attempt to address biodiversity losses associated with agricultural intensification. For many declining farmland bird species, the reduced availability and suitability of nesting and foraging habitats are thought to play a major role in population declines and some AES have hoped to counteract this by encouraging the provision of such habitats. This study aimed to determine the relative importance of AES on the territory selection of a widespread but declining farmland bird, the Yellowhammer Emberiza citrinella. Yellowhammers were more likely to locate territories in areas containing ‘enhanced margins’; i.e. where field margin habitats were sown with wild flowers and/or agricultural legumes. An average of 0.033 ± 0.008 ha of this ‘enhanced margin’ habitat was present within 100 m of Yellowhammer territories compared to 0.020 ± 0.008 ha within 100 m of random points. This preference may reflect the higher invertebrate chick food abundance associated with this habitat as they contained, on average 46.3% and 36.8% more invertebrate food items than cereal and floral crops respectively. Alternatively, given that chick food abundance was similar between grass and enhanced field margins, this observed preference may be the result of a more open sward structure which increases prey accessibility and improves predator avoidance. Yellowhammers selected territories containing early succession hedgerows, as these constitute the most suitable nesting sites, and preferred territories containing a suitable songpost. Our results suggest that management strategies aiming to conserve breeding Yellowhammers should focus on increasing the coverage of invertebrate rich AES habitats such as floristically-enhanced margins and pollen and nectar plots, and ensure that they are located within typical foraging ranges of cut hedges with elevated songposts.
Future breeding and foraging sites of a southern edge population of the locally endangered Black Guillemot Cepphus grylle

ABSTRACT Capsule: One of the southernmost populations of the Black Guillemot Cepphus grylle is currently endangered, and the risk may be exacerbated by climate change. Aims: We evaluated the future vulnerability of the Black Guillemot by predicting the impact of climate change on the geographic distribution of its breeding and foraging range in the Baltic Sea. Methods: We used MaxEnt, a species distribution modelling technique, to predict the current and future breeding grounds and foraging sites. Results: We found that although the foraging range is expected to increase in the southern Baltic Sea in future, these areas will no longer be suitable as breeding grounds due to a changing climate, creating a spatial mismatch. Conclusion: Our predictions indicate where threats to the species may be most severe and can be used to guide conservation planning. We advocate conservation measures which integrate potential future threats and focus on breeding sites across the current and future potential geographic range of the Black Guillemot.
Taking the short- or long-chain route: conversion efficiency of alpha linolenic acid to long-chain omega-3 fatty acids in aerial insectivore chicks

Food availability and quality are both critical for growing young animals. In nature, swallows (Tachycineta bicolor) and other aerial insectivores feed on both aquatic insects, which are rich in omega-3 long-chain polyunsaturated fatty acid (LCPUFA) and terrestrial insects, which contain considerably less LCPUFA. Carnivorous mammals and fishes must obtain LCPUFA from diet, as they have lost the capacity to convert the precursor omega-3 ALA into LCPUFA. Thus, the relative value of aquatic versus terrestrial insects depends not only on the fatty acid composition of the prey, but also upon the capacity of consumers to convert ALA into LCPUFA. We used a combination of stable-isotope-labeled fatty acid tracers to ask if, and how efficiently, Tree Swallows can deposit newly synthesized LCPUFA into tissue. Our data show for the first time that Tree Swallows can convert ALA into LCPUFA deposited in liver and skeletal muscle. However, high Tree Swallow demand for LCPUFA combined with low ALA availability in natural terrestrial foods may strain their modest conversion ability. This suggests that while Tree Swallows can synthesize LCPUFA de novo, LCPUFA are ecologically essential nutrients in natural systems. Our findings thus provide mechanistic support for our previous findings and the importance of LCPUFA-rich aquatic insects for Tree Swallows and most likely other aerial insectivores with similar niches. Summary Statement A stable-isotope-labeled tracer reveals the mechanism for omega-3 long-chain polyunsaturated fatty acid (LCPUFA) limitation in a wild avian insectivore, showing that LCPUFA are an ecologically essential nutrient.
Evolutionary trends in dental morphology of the genus Prolagus (Ochotonidae, Lagomorpha) in the Mediterranean islands

catala[gual que altres taxa de vertebrats, el genere Prolagusva sofrir modificacions morfo-funcionals importants als ambients insulars mediterranis. El mes evident es un increment al-Iometric de la mida general, seguit per altres canvis notables a nivell dentari: increment de la hipsodoncia i del nivell de complexitat de plegament de l'esmalt, i modificacions de les proporcions de diversos trets dentaris. Aquests canvis peculiars es podrien explicar com a adaptacions paral-leles a ambients oberts secs, amb una vegetacio molt dura i amb pressions de depredacio baixes. Esdevenen a totes les especies endemiques de Prolagus diferenciades a ambients insulars mediterranis, fins i tot encara que no tinguin un ancestre directe comu. Algunes formes europees continentals poden mostrar algunes de les caracteristiques esmentades (per exemple, nomes gegantisme o nomes presencia d'esmalt dentari molt plegat) degut a adaptacions locals alimentaries o ambientals. Nomes la presencia conjunta dels trets dalt esmentats identifica les especies de Prolagus insulars. EnglishAs other vertebrate taxa, genus Prolagus undergoes major morpho-dimensional modifications in Mediterranean insular environments. The most evident is an allometric general size increase, followed by other remarkable changes at the dental level: increase of hypsodonty and of enamel folding complexity, modification of relative proportions of some dental features. Such peculiar changes could be explained by a parallel adaptation to dry, open environments with harder vegetation and by a minor predatory pressure. They occur in all the Prolagus endemic species differentiated in insular Mediterranean environments, even if they do not share a common direct ancestor. Some continental European forms, actually, can show some of the listed features (e.g.: giantism only, or highly folded dental enamel only) due to particular dietary/environmental local adaptations. Only the coincident occurrence of the above mentioned characters identifies an insular endemic Prolagus species.
PARENTAGE VERIFICATION USING IMPUTED MICROSATELLITE AND SNP DATA IN SLOVENIAN BROWN SWISS POPULATION

Parentage verification for cattle in Slovenia is routinely done using microsatellite markers (MS). With the incoming SNP da ta the re is currently a discordance bet ween genotypic data available for different animals, which is not suitable for parentage verification. To overcome this problem imputation of MS from SNP data was implemented for Slovenian Brown-Swiss animals. The imputation was performed adopting McClure et al. (2013) methodology and haplotype reference. MS imputation was performed utilising Beagle software. The overall microsatellite imputation accuracy was 91.7 % . Additionally, already confirmed parentages were re-tested using imputed MS. Out of 65 cases of two-parents testing 15.4 % and 44.6 % had 0 and 1 MS misconcordances, respectively, and the parentage was confirmed. For 40.0 % cases with ≥ 2 MS misconcordances parentage was rejected. Next, pa rentage verification using 800 SNPs was implemented. Out of 43 cases of one-parent testing 90.7 % and 9.3 % had 0 and 1 SNP misconcordances, respectively, therefore verifying all tested parentages. When replacing the real parent with a half-sibling or grandparent, the number of SNP misconcordances was >25 in all cases. The results suggest that MS imputation needs additional optimisation to reach required accuracies, possibly by using a haplotype reference consisting of animals that are genetically more similar to the studied Brown-Swiss population. On the other hand, verification using SNPs has proven as a reliable tool for routine use.
RNA FROM FRESH FROZEN CRYOSECTIONS OF OIL PALM INFLORESCENCES IS SUPERIOR TO FFPE SECTIONS

Formalin-fixed, paraffin-embedded (FFPE) and fresh frozen (FF) tissue sections are valuable sources for histology and molecular studies. However, FFPE tissue sections usually provide poor quality RNA that is unsuitable for most downstream molecular applications. In this study, tissue preparation for cryosectioning and RNA extraction protocols were optimised for FF oil palm inflorescences. FF tissue treated with sucrose offered good cellular image resolution and more importantly, good RNA quality. Higher RNA quality with good RIN values (>6) was obtained from FF sections compared to the fragmented RNA from FFPE tissue sections. However, FFPE sections provided better resolution in terms of cellular morphology. The quality of cellular morphology of the FF sections was moderate, but was sufficient to distinguish the different cell types. Hence, FF oil palm inflorescences is a better choice for downstream transcriptomics studies that require tissue sections without compromising the cytological details.