Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on the Effect of Various Seed Surface Sterilization and Growing Media on the In-vitro Germination of Lemon Balm (Melissa officinalis L.)

Objectives: Lemon balm (Melissa officinalis) is a perennial herb belongs to Lamiaceae, which is native to South Europe, Middle East and North America. Lemon balm is used for anti-cancer, digestive problems, anxiety, gastrointestinal disorders, thyroid, chronic fatigue syndrome and Alzheimer’s disease. A successful and efficient system for in vitro seed sterilization and germination has been established in the present study. Methods/ Statistical Analysis: The seeds were soaked in distilled water for 10 hours and exposed with various concentrations of different surface sterilization agent for various intervals of time. Surface sterilized seeds were inoculated on different culture media such as Murashige and Skoog (MS) basal, half strength MS and B5 media with different sucrose concentrations. Findings: By comparison of measured characteristics results (ANOVA) we found that the best sterilizing agent for seed surface sterilization and uniform growth of seedling in M. officinalis was 2.5% Sodium Hypochlorite for 3 min. Maximum germination rate, shoot length and root length were recorded in half strength MS medium with 1% (W/V) sucrose. The analysis of data revealed the correlation between GP, GR, shoot length and root length were significant and positive. Application/Improvement: We optimized seed surface sterilization protocol and culture condition that may be useful quick regenerative, transformation and conservation method for Melissa officinalis, an important medicinal plant.
Design, Synthesis and Preliminary Antimicrobial Evaluation of New Derivatives of Cephalexin

There is a continuous and massive need for newer cephalosporins that should have resistance against Î²-lactamases and can be used orally. An approach of using cephalexin, as a well-studied and potent antibacterial compound is considered to prepare new designed derivatives. These derivatives include the incorporation of amino acid moiety linked through an amide bond with the Î±-amino group of cephalexin. Certain aliphatic amino acids were used, such as glycine, alanine, valine and proline. The chemical structures of these derivatives were confirmed by IR spectroscopy and elemental analyses. All the synthesized compounds were subjected for preliminary evaluation of antimicrobial activity using well diffusion method, against certain microbes. Most of the synthesized compounds were found to possess significant antibacterial activities. Compound 1 (125 Î¼g and 250Î¼g) showed significant activity against P. aeruginosa. Compound 2 (125 and 250Î¼g) exhibited significant activity against P. aeruginosa and Bacillus cereus. Compound 3 (125 and 250Î¼g) demonstrated very significant activity against E. coli, P. aeruginosa and Bacillus cereus and slight activity towards S. aureus. Compound 4 (250Î¼g) showed significant activity against P. aeruginosa and no antibacterial activities against E. coli, S. aureus and Bacillus cereus, as compared with cephalexin as the standard compound. Keywords: Cephalosporins, Cephalexin, Glycine, Alanine, Valine, Proline.
Metal(loid)-Contaminated Soils as a Source of Culturable Heterotrophic Aerobic Bacteria for Remediation Applications

ABSTRACT Heavy metal–contaminated soils are a serious environmental problem. Herein, the culturable heterotrophic bacterial community present on two metal(loid)-contaminated sites in the Northern Portugal was investigated. The bacterial counts ranged from 5.96 to 7.69 and 7.04 to 7.51 (log CFU g−1 soil) in Sites 1 and 3, respectively. The bacterial population was predominantly composed of Firmicutes, Proteobacteria, and Actinobacteria on both sites. The most represented genera in Site 1 were Bacillus (41%) and Pseudomonas (27%), whereas Arthrobacter (21%) and Pseudomonas (13%) were the most represented genera in Site 3. Several bacterial isolates showed tolerance to high concentrations of metal(loid)s, suggesting that both contaminated sites are a valuable source of metal(loid)-tolerant bacteria, which may be further used in bioremediation and/or phytoremediation processes.
Problems with bioclimatic definitions of vegetation types

Problems with bioclimatic definitions of vegetation types Peter J. Grubb, Frida I. Piper and Peter J. Bellingham Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK; Centro de Investigación en Ecosistemas de la Patagonia, Alto Baguales s/n, Coyhaique, Chile; Instituto de Ecología y Biodiversidad–IEB, Las Palmeras 3425, Ñuñoa, Santiago, Chile; Landcare Research, P.O. Box 69040, Lincoln, 7640, New Zealand
Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions

The synthetic biology firstly refers to the design and fabrication of biological components and systems that do not already exist in the natural world and to the redesign and fabrication of existing biological systems. The link of computational tools to cell-free systems, converts to synthetic biology is an emerging field expert to build artificial biological systems through the combination of molecular biology and engineering approaches. Herein, most findings describing the differences between in vivo and in vitro reactions and systems have been extensively described. The specific applications of computational tools to the design of an in vitro gene expression platform known as the artificial cell, its components and the strategies developed to predict activities of processor modules and to control the expression of genes have been discussed in detail. Potential applications of artificial cells in drug delivery, in biosynthesis, among others, have been described. Two sources of models for the possible developing of the computational toolbox for cell-free synthetic biology include: i) Physical models of single cellular components able to be created from original principles, guiding to focus on tools to predict structure and dynamics of particular components; ii) A wide-range of mathematical models for predicting system dynamics of natural cells. Regarding modeling algorithms, there is a broad kind of models available for synthetic biologists and some areas of potential growth identified for researchers interested in developing tools for cell-free systems. Among them, deterministic, exploratory, molecular dynamic, stochastic, all atom models, among others, have been described and discussed. By using computational models to set up quantitative differences between in vitro reactions and in vivo systems, could identify specific mechanisms in living organisms to be further used in in vitro reactions in order to facilitate their processes. Thus, computational modeling would bridge the gap between in vitro and in vivo reactions.
Effects of Simultaneous Melatonin Administration on the Testis of the Experimentally Induced Hyper- and Hypothyroidism in the Adult Male Albino Rat

Background: The most common disorders of the thyroid gland are hyperthyroidism and hypothyroidism. Both have been linked to cell damage.Aim of Work: This study was designed to evaluate the effect of melatonin administration on the testis of both hyperthyroidic and hypothyroidic adult male albino rats models.Materials and Methods: Fifty adult male albino rats were used in this study and divided into five groups; ten rats each. Control group (G1) was given distilled water. Hyperthyroidic group (G2) was given thyroxin (0.2 mg/kg b.w). Hyperthyroidic+melatonin group (G3) was given thyroxin (0.2 mg/kg b.w) and melatonin (2.5 mg / kg b.w). Hypothyroidic group (G4) was given carbimazole (1.35 mg/kg b.w). Hypothyroidic+melatonin group (G5) was given carbimazole (1.35 mg/kg b.w) and melatonin (2.5 mg / kg b.w). All the treatments were given orally for 15 days. At the end of the study, the animals of all groups were sacrificed and their testes were rapidly dissected out. The testicular mass was calculated. Testicular specimens of each group were processed for light and electron microscopic studies.Results: The testicular mass was significantly decreased in both hyperthyroidic group (G2) and hypothyroidic group (G4) when compared with the control. Light and electron microscopy of the hyperthyroidic group (G2) and hypothyroidic group (G4) showed seminiferous tubular germ cells disorganization with increased intercellular spaces, necrosis and cellular damage. Melatonin supplementation to rats given Thyroxin (G3) improved the testicular mass and the cell damage. On the contrary, melatonin supplementation to rats given carbimazole (G5) did not show any improvement on both morphometrical and histological levels.Conclusion: It was concluded that simultaneous melatonin administration effectively depresses the negative effects of hyperthyroidism but not hypothyroidism on the adult male rat testis.
In Vitro Production of Cormels in Gladiolus hybridus through Gamma Rays

Gladiolus (Gladiolus hybridus L.) is an important bulbous ornamental plant, is one of the most important and popular herbaceous cut flowers. The major gladiolus growing countries are Holland, Germany, and the United State of America. In India, the total area under gladiolus cultivation is around 1,270 hectares covering West Bengal, Sikkim, Himachal Pradesh, Jammu and Kashmir, Punjab, Karnataka, Tamil Nadu and Maharashtra. In Punjab, gladiolus is grown in an area of about 150 ha during September to April (NHB 2014). It is grown worldwide for cut flower trade and garden displays. It occupies a pristine place in the garden for its magnificent inflorescence, wide array of colours, and fascinating varieties of shapes and sizes (Singh et al., 2010). Gladiolus is propagated mainly through vegetative reproduction of corms and cormels. Although, seeds are an effective means of propagation in gladiolus but plants raised from seed may not produce true to type plants (Hussain et al., 2001). Moreover, it takes more time for blooming. However, the multiplication rate of corms and cormels is slow and the conventional methods are insufficient to meet the demand of planting material. However, one of the major constrains in commercial cultivation is non-availability of large International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 10 (2017) pp. 1308-1318 Journal homepage: http://www.ijcmas. com
Extractive fermentation for fumaric acid production by Rhizopus oryzae

ABSTRACT Low product concentration and high cost of recovery process have motivated the study of in situ removal of fumaric acid from fermentation broth. After a series of screenings, an integrated process with fumaric acid fermentation and extraction was developed. Under this integrated process, fumaric acid production and productivity increased from 18.06 g/L to 34.23 g/L, and from 0.27 g/L/h to 0.57 g/L/h, respectively. Neutralizing agent utilization decreased by 58.75%, and 140.7 g/L ammonium fumarate was obtained after back extraction, which could be directed used to produce related derivatives without concentration. Thus, the integrated process was more economic and environmental friendly.
Studies of rhizobial competitiveness for nodulation in soybean using a non-destructive split-root system

Split-root systems (SRS) constitute an appropriate methodology for studying the relevance of both local and systemic mechanisms that participate in the control of rhizobia-legume symbioses. In fact, this kind of approach allowed to demonstrate the autoregulation of nodulation (AON) systemic response in soybean in the 1980s. In SRS, the plant main root is cut and two lateral roots that emerge from the seedlings after root-tip removal are confined into separate compartments. After several days of growth, these plants have two separate roots that can be inoculated with the same or with different bacteria, at the same or at different times. In this work, we have used a non-destructive SRS to study two different competitiveness relations between rhizobial strains in soybean roots. One of them is the competition for nodulation between two soybean-nodulating rhizobia: the slow-grower Bradyrhizobium japonicum USDA110 and the fast-grower Sinorhizobium fredii HH103. The second is the competitive blocking of S. fredii 257DH4 nodulation in the American soybean Osumi by Sinorhizobium fredii USDA257, which is unable to nodulate American soybeans. Our results showed that the competitiveness relationships studied in this work are mitigated or even avoided when the competitive strains are spatially separated in different compartments containing half-roots from the same plant, suggesting that competitive relations are more related to local plant responses. In our opinion, split-root systems are an appropriate approach to further study competitive relations among rhizobial strains.
Assessing the impact of marine seismic surveys on southeast Australian scallop and lobster fisheries

The present study, undertaken by University of Tasmania’s Institute for Marine and Antarctic Studies in conjunction with Curtin University’s Centre for Marine Science and Technology, was developed to investigate the potential impact of seismic surveys on economically important fishery species. Substantial overlap exists between important fishing grounds and areas of interest for oil and gas exploration within southeast Australian waters. The fishing industry is now very concerned about the potential of intense low frequency acoustic signals produced during these surveys to disturb, harm or even kill fisheries species. Studies conducted to date generally report that fish can demonstrate behavioural responses to seismic activities, including startle and flight responses, displacement, dispersal, and disruption of feeding or breeding activity. These behavioural responses could in turn result in changes in commercial catch rates. There have been very few dedicated studies of the effects of marine seismic surveys on invertebrates, and the limited information on invertebrates suggests that they may be relatively resilient to seismic sound, however, further research is required before the impacts of seismic activity on commercially important invertebrates can be dismissed. In the light of a general lack of well-designed and scientifically rigorous studies examining the effect of marine seismic surveys on invertebrates and in the absence of any detailed specific studies on commercial scallops ( Pecten fumatus ) and southern rock lobster ( Jasus edwardsii ), fishers in Victoria and Tasmania have lobbied for dedicated research targeting these valuable resources. This study aimed to use a field and laboratory experimental approach to determine the impact of marine seismic surveys on these important fisheries species. The results obtained are broadly applicable to scallop and spiny lobster fisheries throughout the world, and bivalve and crustacean fisheries in general.
Bioactivities of bacterial endophytes isolated from leaf tissues of Hyptis suaveolens against some clinically significant pathogens

Objectives: This study examined antimicrobial potentials of endophytic bacteria isolated from leaf tissues of Hyptis suaveolens against some clinically significant pathogens. Methods: Endophytic bacteria were isolated from surface sterilized leaf fragments of Hyptis suaveolens. The isolates were grown in Nutrient Broth (NB) medium and medium amended with host plant extract. Antimicrobial activity was determined by spot inoculation and disc diffusion methods. Results: The result indicated that 60% of the isolates showed antimicrobial activity inhibiting at least one of the test pathogens in preliminary screening. Amongst the isolates, two bacterial isolates showed considerable antimicrobial activity against the test pathogens. The isolates were identified as Bacillus and Pseudomonas species by morphological and biochemical characterization. Phylogenetic analysis of 16S rDNA sequences of the isolates showed closest homolog to endophytic Bacillus and Pseudomonas species. The crude extracts exhibited moderate antibacterial and anti-candidal activity both by BLIS and agar diffusion assays. Enhanced antimicrobial activity was observed in nutrient broth medium amended with host plant extract. Spectrophotometric analyses of the crude metabolites of the isolates indicate presence of bioactive component. The metabolite obtained from Bacillus sp. showed a λ-max of 1.541 at 254 nm and that of Pseudomonas sp. was 0.155 at 250 nm. Conclusion: The study indicated that endophytic bacteria harbouring medicinal plants could be a potential source of antimicrobial agents.
speB Genosensor for Rapid Detection of Streptococcus pyogenes CausingDamage of Heart Valves in Human

speB Genosensor for early detection of Streptococcus pyogenes in human throat swab samples were fabricated using screen printed modified gold electrode. The electrochemical changes before and after hybridization was measured using cyclic voltammetry (CV) in the presence of redox indicator. The sensitivity of the genosensor was 80(μA/cm2)/ng and lower limit of detection (LOD) was 0.10 ng/6μl with the regression coefficient (R2) of 0.921 using CV. The sensor is highly specific, simple and takes only 30 min for detection of S. pyogenes infection. The sensor was further characterized by atomic force microscopy (AFM). Genosensor was found stable upto 6 months with only 10% loss in initial peak current in CV analysis on storage at 4°C. The speB gene based sensor can be used to prevent the damage of mitral and aortic heart valves by early diagnosis and treatment of the disease.
Advanced Diamond Microfabrication for Microoptics and Photonics

Diamond is an exceptional material – hard, stiff, transparent, which makes it ideal for the fabrication of optical and mechanical systems that take advantage of these properties. Diamond is not only "better", but it offers the possibility of integrating bright colour centres. These optically active defects can be exploited for a variety of applications, including the study of fundamental science, magnetometry, biosensing and new types of lasers. Despite the attractive properties of diamond for optics, no standard platform exists to create photonic circuits and devices. This thesis shows the realisation of a diamond-on-insulator photonics platform, that aims to combine the versatility of the silicon-on-insulator photonics with the capability of performing diamond science in single crystal guided-wave devices. The diamond-on-insulator substrate is achieved via ion implantation-based cut of a single crystal membrane and bonding of the membrane to an insulator layer. This approach provides a monolithic fabrication process that scales to commercial exploitation, bringing convenient access to the study of diamond light-matter interactions without requiring custom substrate fabrication. Furthermore, the possibility of releasing the diamond devices adds access to freestanding structures, opening the way to diamond micro-opto-electro-mechanical systems and optomechanics. Diamond also makes an excellent microoptics substrate, due to its high laser damage threshold, transparency and high refractive index, which is an attractive combination for high-power, compact optical systems operating in the UV, visible and near-infrared. Different diamond etching techniques are developed and investigated in this thesis, that enable the realisation of unique features. These techniques are employed to create diamond diffractive microoptical components, which are then characterised, showing high-quality surfaces that closely match the designed features, indicating reliable fabrication and resulting in excellent optical performance. These devices have applications in high power beamsplitters, beam shapers and compact spectrometers.
High diversity of powdery mildew resistance in the ICARDA wild barley collection

Abstract. Powdery mildew caused by the fungus Blumeria graminis f. sp. hordei (Bgh) is a global disease of barley, and the wild subspecies Hordeum vulgare subsp. spontaneum (Hvs) is the closest relative of cultivated barley (H. vulgare subsp. vulgare). The responses to the pathogen of 363 Hvs accessions maintained by the International Center for Agricultural Research in the Dry Areas (ICARDA) gene bank were assessed. Thirty non-Israeli pathogen isolates representing the global pathogenic diversity were used for testing. Because of genetic heterogeneity within 146 accessions, the results from only 217 accessions are presented and discussed. Additional tests on 152 accessions with homogeneous responses in earlier tests were made by using six Israeli pathogen isolates. There were 154 resistance phenotypes among the set, 141 of which involved single accessions. The six most frequent phenotypes were recorded for 62 accessions, with the most frequent phenotype in 26 accessions that were resistant to all 30 non-Israeli Bgh isolates. The second most frequent phenotype, found in 16 accessions, was susceptible to all 30 non-Israeli isolates. The occurrence of specific resistance was high. The occurrence of specific resistance was high and for breeding barley cultivars the effective resistances can be combined with the resistance gene mlo. In such combinations, the mlo gene prevents rapid increase in the pathogen population from overcoming the given specific resistance, whereas the resistance gene will simultaneously prevent erosion of mlo resistance. A more effective method for achieving durable resistance is accumulation minor resistance genes that are also widely distributed in wild barley.
Paenibacillus terrae AY-38 resistance against Botrytis cinerea in Solanum lycopersicum L. plants through defence hormones regulation

ABSTRACT This study aims to investigate the role of Paenibacillus terrae AY-38 to produce bioactive metabolites and to counteract pathogenic infections caused by B. cinerea. The pure culture of P. terrae (AY-38) showed the secretion of significant amount of IAA (indole-3-acetic acid) (109.57 ± 3.2 µg mL−1). The AY-38 strain also produced siderophore and glucanase, while in the in vitro test, it showed significant antagonism to Botrytis cinerea. In the in vivo plant experiment, the sole application of AY-38 significantly improved plant growth (plant height and leaf area), while in B. cinerea infected plants, AY-38 inoculation not only decreased the disease incidence on leaves and fruits but also reprogramed the plants for higher growth. AY-38 treatments promoted and rescued plant growth by modulating the defence responses of endogenous hormones, such as jasmonic and salicylic acids. Our findings concluded that P. terrae possesses great potential as a possible biocontrol agent against B. cinerea-induced pathogenic infections.