1 Molecular Analysis of Honey Bee Foraging Ecology Dissertation
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Studies on Authentication of True Source of Honey Using Pollen DNA
Journal of Entomology and Zoology Studies 2018; 6(3): 255-261 E-ISSN: 2320-7078 P-ISSN: 2349-6800 Studies on authentication of true source of honey JEZS 2018; 6(3): 255-261 © 2018 JEZS using pollen DNA barcoding Received: 09-03-2018 Accepted: 10-04-2018 Praghadeesh Manivanan Praghadeesh Manivanan, Srinivasan Madapuji Rajagopalan and Department of Plant Mohankumar Subbarayalu Biotechnology, Centre for Plant Molecular Biology& Biotechnology, Tamil Nadu Abstract Agricultural University, Plant pollen DNA comprising unique barcode signatures– serve as a highly resilient biomarker to Coimbatore, Tamil Nadu, India establish its true biological origin. Over a decade, DNA barcoding of plants has evolved as an effective tool to identify its origin down to species level that promptedits practical applications in various fields of Srinivasan Madapuji Rajagopalan applied biology. Premium unifloral honey, due to its economic value as a medicinal product is vulnerable Department of Agricultural to intentional mislabelling and adulteration to fetch higher price. Melissopalynological and Entomology, Tamil Nadu physiochemical based approaches to ascertain the true source of honey is not yet available on commercial Agricultural University, scale. DNA barcoding of pollen trapped in honey can be effectively used to identify the true source of Coimbatore, Tamil Nadu, India honey with high feasibility across labs at cheaper price. The current study was carried out to standardise Mohankumar Subbarayalu an efficient pollen DNA isolation protocol and to assess the efficiency of two barcode (rbcL and matK Professor and Head, Department gene) combinations in identifying the botanical origin of pollen and to ascertain its true source. Six honey of Plant Biotechnology, Centre samples with diverse characteristics were used in the study. -
Introduction to Bacteriology and Bacterial Structure/Function
INTRODUCTION TO BACTERIOLOGY AND BACTERIAL STRUCTURE/FUNCTION LEARNING OBJECTIVES To describe historical landmarks of medical microbiology To describe Koch’s Postulates To describe the characteristic structures and chemical nature of cellular constituents that distinguish eukaryotic and prokaryotic cells To describe chemical, structural, and functional components of the bacterial cytoplasmic and outer membranes, cell wall and surface appendages To name the general structures, and polymers that make up bacterial cell walls To explain the differences between gram negative and gram positive cells To describe the chemical composition, function and serological classification as H antigen of bacterial flagella and how they differ from flagella of eucaryotic cells To describe the chemical composition and function of pili To explain the unique chemical composition of bacterial spores To list medically relevant bacteria that form spores To explain the function of spores in terms of chemical and heat resistance To describe characteristics of different types of membrane transport To describe the exact cellular location and serological classification as O antigen of Lipopolysaccharide (LPS) To explain how the structure of LPS confers antigenic specificity and toxicity To describe the exact cellular location of Lipid A To explain the term endotoxin in terms of its chemical composition and location in bacterial cells INTRODUCTION TO BACTERIOLOGY 1. Two main threads in the history of bacteriology: 1) the natural history of bacteria and 2) the contagious nature of infectious diseases, were united in the latter half of the 19th century. During that period many of the bacteria that cause human disease were identified and characterized. 2. Individual bacteria were first observed microscopically by Antony van Leeuwenhoek at the end of the 17th century. -
Using RNA-Seq to Characterize Pollen–Stigma Interactions for Pollination
www.nature.com/scientificreports OPEN Using RNA‑seq to characterize pollen–stigma interactions for pollination studies Juan Lobaton1,3*, Rose Andrew1, Jorge Duitama2, Lindsey Kirkland1, Sarina Macfadyen3 & Romina Rader1 Insects are essential for the reproduction of pollinator‑dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world’s food crops. Understanding pollen fow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the feld is complex and laborious. We developed a feld experiment in a pollinator‑dependent crop and used high throughput RNA sequencing (RNA‑seq) to quantify pollen fow by measuring changes in gene expression between pollination treatments across diferent apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with feld data by observing single and multiple visits by honey bees (Apis mellifera) to apple fowers and measured fruit set in a commercial apple orchard. The frst indicator of successful outcrossing was revealed via diferential gene expression in the cross‑pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specifc genes related to pollen tube formation and defense response at three diferent time intervals in the stigma and the style following cross‑pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specifc to donor pollen could be detected in cross‑pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or fve fower visits by honey bees were insufcient and at least 10 honey bee fower visits were required to achieve a 25% probability of fruit set under orchard conditions. -
Fungal Genomes Tell a Story of Ecological Adaptations
Folia Biologica et Oecologica 10: 9–17 (2014) Acta Universitatis Lodziensis Fungal genomes tell a story of ecological adaptations ANNA MUSZEWSKA Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland E-mail: [email protected] ABSTRACT One genome enables a fungus to have various lifestyles and strategies depending on environmental conditions and in the presence of specific counterparts. The nature of their interactions with other living and abiotic elements is a consequence of their osmotrophism. The ability to degrade complex compounds and especially plant biomass makes them a key component of the global carbon circulation cycle. Since the first fungal genomic sequence was published in 1996 mycology has benefited from the technolgical progress. The available data create an unprecedented opportunity to perform massive comparative studies with complex study design variants targeted at all cellular processes. KEY WORDS: fungal genomics, osmotroph, pathogenic fungi, mycorrhiza, symbiotic fungi, HGT Fungal ecology is a consequence of osmotrophy Fungi play a pivotal role both in encountered as leaf endosymbionts industry and human health (Fisher et al. (Spatafora et al. 2007). Since fungi are 2012). They are involved in biomass involved in complex relationships with degradation, plant and animal infections, other organisms, their ecological fermentation and chemical industry etc. repertoire is reflected in their genomes. They can be present in the form of The nature of their interactions with other resting spores, motile spores, amebae (in organisms and environment is defined by Cryptomycota, Blastocladiomycota, their osmotrophic lifestyle. Nutrient Chytrydiomycota), hyphae or fruiting acquisition and communication with bodies. The same fungal species symbionts and hosts are mediated by depending on environmental conditions secreted molecules. -
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
Experimental Quantification of Pollen with DNA Metabarcoding Using
www.nature.com/scientificreports OPEN Experimental quantifcation of pollen with DNA metabarcoding using ITS1 and trnL Sandra Baksay 1*, André Pornon1, Monique Burrus1, Jérôme Mariette2, Christophe Andalo1 & Nathalie Escaravage1 Although the use of metabarcoding to identify taxa in DNA mixtures is widely approved, its reliability in quantifying taxon abundance is still the subject of debate. In this study we investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high- throughput sequence reads and how the relationship was afected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have diferent characteristics. We found a signifcant positive relationship between the number of DNA sequences and the number of pollen grains in the mock solutions. However, better relationships were obtained with light microscopy as a pollen grain counting method compared with fow cytometry, with the chloroplastic trnL marker compared with ribosomal ITS1 and with 30 when compared with 25 or 35 PCR cycles. We provide a list of recommendations to improve pollen quantifcation. Environmental DNA metabarcoding is a molecular method that consists of investigating environmental DNA samples made of complex mixtures of genomes from numerous organisms1. Due to new sequencing technologies and bioinformatics tools, metabarcoding has been increasingly used to identify taxa in environmental samples1 to monitor biodiversity2–4, to investigate ecosystem functioning5 and interaction networks6–8, in both aquatic and terrestrial ecosystems. Nevertheless, its reliability in quantitative approaches, which depend on the match between counts of high-throughput sequence reads and the amount of sampled biological material2, is still the subject of debate9,10. -
Open Thweattetd1.Pdf
The Pennsylvania State University The Graduate School CHARACTERIZATION OF PIGMENT BIOSYNTHESIS AND LIGHT-HARVESTING COMPLEXES OF SELECTED ANOXYGENIC PHOTOTROPHIC BACTERIA A Dissertation in Biochemistry, Microbiology, and Molecular Biology and Astrobiology by Jennifer L. Thweatt 2019 Jennifer L. Thweatt Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2019 ii The dissertation of Jennifer L. Thweatt was reviewed and approved* by the following: Donald A. Bryant Ernest C. Pollard Professor in Biotechnology and Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee Squire J. Booker Howard Hughes Medical Investigator Professor of Chemistry and Professor of Biochemistry and Molecular Biology Eberly Distinguished Chair in Science John H. Golbeck Professor of Biochemistry and Biophysics Professor of Chemistry Jennifer L. Macalady Associate Professor of Geosciences Timothy I. Miyashiro Assistant Professor of Biochemistry and Molecular Biology Wendy Hanna-Rose Professor of Biochemistry and Molecular Biology Department Head, Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT This dissertation describes work on pigment biosynthesis and the light-harvesting apparatus of two classes of anoxygenic phototrophic bacteria, namely the green bacteria and a newly isolated purple sulfur bacterium. Green bacteria are introduced in Chapter 1 and include chlorophototrophic members of the phyla Chlorobi, Chloroflexi, and Acidobacteria. The green bacteria are defined by their use of chlorosomes for light harvesting. Chlorosomes contain thousands of unique chlorin molecules, known as bacteriochlorophyll (BChl) c, d, e, or f, which are arranged in supramolecular aggregates. Additionally, all green bacteria can synthesize BChl a, the and green members of the phyla Chlorobi and Acidobacteria can synthesize chlorophyll (Chl) a. -
Bee Pollen Diet Alters the Bacterial Flora and Antimicrobial Peptides in the Oral Cavities of Mice
foods Article Bee Pollen Diet Alters the Bacterial Flora and Antimicrobial Peptides in the Oral Cavities of Mice Ariuntsetseg Khurelchuluun 1,2,† , Osamu Uehara 3,† , Durga Paudel 1 , Tetsuro Morikawa 1, Yutaka Kawano 4 , Mashu Sakata 5, Hiroshi Shibata 5, Koki Yoshida 1 , Jun Sato 1, Hiroko Miura 3, Hiroki Nagayasu 2 and Yoshihiro Abiko 1,* 1 Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] (A.K.); [email protected] (D.P.); [email protected] (T.M.); [email protected] (K.Y.); [email protected] (J.S.) 2 Division of Oral and Maxillofacial Surgery, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] 3 Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] (O.U.); [email protected] (H.M.) 4 Institute of Preventive Medical Science, Health Sciences University of Hokkaido, Ainosato 2-5, Kita-ku, Sapporo, Hokkaido 002-8072, Japan; [email protected] 5 Belle Coeur Institute, Utsukushigaoka 5-9-10-30, Kiyota-ku, Sapporo, Hokkaido 004-0851, Japan; [email protected] (M.S.); [email protected] (H.S.) * Correspondence: [email protected]; Tel.: +81-133-23-1390 † Both authors contributed equally to this work. -
Effects of Shade Stress on Morphophysiology and Rhizosphere Soil Bacterial Communities of Two Contrasting Shade-Tolerant Turfgrasses
Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses Juanjuan Fu ( [email protected] ) Northwest Agriculture and Forestry University https://orcid.org/0000-0001-8178-6698 Yilan Luo Northwest A&F University Pengyue Sun Northwest A&F University Jinzhu Gao Northwest A&F University Donghao Zhao Northwest A&F University Peizhi Yang Northwest A&F University Tianming Hu Northwest A&F University Research article Keywords: Community structure and diversity, Rhizosphere bacteria, Shade stress, Shade tolerance, 16S rRNA gene sequencing Posted Date: June 13th, 2019 DOI: https://doi.org/10.21203/rs.2.10288/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/14 Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress inuences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade- intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. -
Lecture 6 Gram Posi/Ve & Nega/Ve Bacteria
هذا العمل ل يغني عن الرجع الساسي للمذاكرة Lecture 6 Gram Posi0ve & Negave Bacteria • Important • Term • Extra explanaon • Addi0onal notes Objectives • Know the general basic characteristics of bacteria. • Differentiate between gram positive and gram negative bacteria characteristics. • Know the classes and groups of gram positive bacteria and gram negative, cocci and bacilli (rods). • Know the common identification characteristic of these groups. • Know the common infections and diseases caused by these organisms and the antibiotics used for their treatment. Gram Stain • Developed in 1884 by the Danish physician Hans Christian Gram • An important tool in bacterial taxonomy (the branch of science concerned with classification), distinguishing so-called Gram-positive bacteria, which remain colored after the staining procedure, from Gram- negative bacteria, which do not retain dye and need to be counter- stained. • Can be applied to pure cultures of bacteria or to clinical specimens. Type Gram positive cell wall Gram negative cell wall • Thick, homogenous sheath of • Outer membrane containing peptidoglycan 20-80 nm thick lipopolysaccharide (LPS) • Tightly bound acidic • Thin shell of peptidoglycan Consist of polysaccharides, including • Periplasmic space (between the teichoic acid and lipoteichoic cell wall & plasma membrane) acid • Inner membrane • Cell membrane Retain crystal violet and stain Lose crystal violet and stain PINK stain PURPLE or BLUE or RED from safranin counterstain counterstain Safraninٍ تتفظ هذه البكتيريا بلونها بعد أن حتى ل تنسى تذكر أن: تصبغت بصبغة جرام مهما تعرضت الزعفران لونه أحمر و نوع هذه لي مادة كيميائية، فهي كالكرستال البكتيريا تتصبغ باللون الحمر قوية وصلبة Gram Stain لحظ كيف اختفى اللون البنفسجي وأصبحت بل لون (Decolorization) Or acetone Gram Stain Gram Negative Baciili(rods) E.Coli ( Pure culture ) Gram Negative Cocci With Pus Cells Neisseria gonorrhoeae (Smear of urethral pus) - Clinical specimen Gram Positive Bacteria Occurring optionally in response to circumstances rather than by nature. -
Pollen DNA Barcoding: Current Applications and Future Prospects
Page 1 of 43 Pollen DNA barcoding: current applications and future prospects Authors: Karen L. Bell 1, Natasha de Vere 2, Alexander Keller 3, Rodney T. Richardson 4, Annemarie Gous 5,6 , Kevin S. Burgess 7, Berry J. Brosi 1 1Emory University, School of Environmental Sciences, Atlanta, GA, USA 2National Botanic Garden of Wales, Llanarthne, United Kingdom 3Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany 4Department of Entomology, The Ohio State University, Columbus, OH, USA 5Biotechnology Platform , Agricultural Research Council , Pretoria, South Africa 6School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa 7Columbus State University, Columbus, GA, USA Keywords (3-6): DNA metabarcoding; metagenomics; pollen; palynology; high-throughput sequencing; next-generation sequencing Genome Downloaded from www.nrcresearchpress.com by MICHIGAN STATE UNIV on 04/18/16 1 For personal use only. This Just-IN manuscript is the accepted prior to copy editing and page composition. It may differ from final official version of record. Page 2 of 43 ABSTRACT (<200 words) Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. -
Applying Pollen DNA Metabarcoding to the Study of Plant-Pollinator Interactions Karen L
Applying Pollen DNA Metabarcoding to the Study of Plant-Pollinator Interactions Karen L. Bell, Emory University Julie Fowler, Emory University Kevin S. Burgess, The University of Western Australia Emily K. Dobbs, Emory University David Gruenewald, Emory University Brice Lawley, Emory University Connor Morozumi, Emory University Berry Brosi, Emory University Journal Title: Applications in Plant Sciences Volume: Volume 5, Number 6 Publisher: Botanical Society of America: APPS | 2017-06-01 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.3732/apps.1600124 Permanent URL: https://pid.emory.edu/ark:/25593/s3w2z Final published version: http://dx.doi.org/10.3732/apps.1600124 Copyright information: © 2017 Bell et al. Published by the Botanical Society of America This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (http://creativecommons.org/licenses/by-nc-sa/4.0/). Accessed September 26, 2021 6:17 AM EDT Applying Pollen DNA Metabarcoding to the Study of Plant–Pollinator Interactions Author(s): Karen L. Bell, Julie Fowler, Kevin S. Burgess, Emily K. Dobbs, David Gruenewald, Brice Lawley, Connor Morozumi, and Berry J. Brosi Source: Applications in Plant Sciences, 5(6) Published By: Botanical Society of America https://doi.org/10.3732/apps.1600124 URL: http://www.bioone.org/doi/full/10.3732/apps.1600124 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use.