Training Manual ICAR Short course on Application of advanced molecular methods in marine fishery resource management, conservation and sustainable mariculture

Molecular Biology and Biotechnology has undergone incredible progress in this decade mainly due to the rapid advancements in DNA sequencing technologies. Marine biology and fishery science also reaped the fruits of these modern inventions improving our understanding regarding complex adaptations in aquatic organisms. Fish Genetics have evolved into genomics incorporating knowledge about neutral and non-neutral markers. A project called Genome 10k was started by the international community of scientists for sequencing the genome of 10000 vertebrates. Whole genomes of many marine organisms are now available which provided insights into the evolution of many important traits. Transcriptome sequencing provides insights into expressed genes and metagenome sequencing provides information regarding the microbes present in environment. All these technologies are rapid and cost effective. Over years, these technologies provided exciting opportunities for understanding ecology and evolution. Genomic information can also be sustainably utilized to enhance productivity of mariculture activities by selective breeding, genetic improvement and manipulation of economically important traits. ICAR-Central Marine Fisheries Research Institute has contributed significantly to marine biotechnology research in the country and played a pivotal role in development of marine fisheries sector. The short course on “Application of advanced molecular methods in marine fisheries resource management, conservation and sustainable mariculture” conducted in ICAR-CMFRI from 24th October, 2018 to 2nd November, 2018 is specially designed to provide exposure to various applications of molecular tools in fisheries resource management, conservation of biodiversity and mariculture. I hope this compendium of lectures and protocols will be extremely useful for the participants to effectively utilize the knowledge in their own area of research. Simultaneously, on behalf of ICAR-CMFRI, I warmly welcome all the participants from various institutions and wish them all success in their future endeavors. I am sure that this training will result in new knowledge, collaborations and friendships

Plants and Environment

Changing environmental condition and global population demands understanding the plant responses to hostile environment. Significant progress has been made over the past few decades through amalgamation of molecular breeding with non-conventional breeding. Understanding the cellular and molecular mechanisms to stress tolerance has received considerable scientific scrutiny because of the uniqueness of such processes to plant biology, and also its importance in the campaign "Freedom From Hunger". The main intention of this publication is to provide a state-of-the-art and up-to-date knowledge of recent developments in understanding of plant responses to major abiotic stresses, limitations and the current status of crop improvement. A better insight will help in taking a multidisciplinary approach to address the issues affecting plant development and performance under adverse conditions. I trust this book will act as a platform to excel in the field of stress biology

Plant cell wall degradation in Coleoptera: investigation of three glycoside hydrolase families implicated in cellulose and hemicellulose digestion in Phytophaga beetles

The first line of defense against biotic and abiotic stresses in plants consists of a diverse set of sugar-based compounds forming the plant cell wall. The major component of the plant cell wall is cellulose, a polysaccharide consisting of β-1,4-linked glucose moieties. Any organism being able to degrade cellulose would benefit from a huge source of energy as well as gaining access to nutrient-rich cell contents. Cellulose-degrading enzymes (cellulases) are well described in a wide range of microbes but were thought to be absent in animals. Recently, it became clear that some animals encode endogenous plant cell wall degrading enzymes (PCWDEs) belonging to several glycoside hydrolase families (GH), including putative cellulases of family 45 (GH45) and putative mannanases of family 5 subfamily 10 (GH5_10). In Arthropoda, GH45s and GH5_10s are most prominently encoded by insects including the Phytophaga clade of beetles (leaf beetles, longhorned beetles, bark beetles and weevils). Nonetheless, the distribution of both GH families in insects is erratic and it is assumed that they are not of ancestral origin but were acquired separately, likely through horizontal gene transfer (HGT) events from microbe to animal. Despite the intricate evolution of GH45s and GH5_10s and an emerging role of PCWDEs in biofuel industries both GH families in Phytophaga beetles remain largely unexplored. Therefore, the major aim of this thesis was to investigate beetle-derived members of GH5_10 and GH45 with focus on their enzymatic activity, physiological importance and evolutionary history. In conclusion, this thesis has greatly contributed to our understanding of PCWDEs encoded by Phytophaga beetles. In particular, our knowledge on GH45 and GH5_10 members encoded by Chrysomelidae and Curculionidae has greatly increased, demonstrating that not a vertical but a horizontal gene transfer was likely responsible for GH45 (and possibly for GH5_10) inheritance in these beetles. The following species-specific, independent gene duplications allowed for functional diversification and likely adaptation to their food source. These results provide fundamental insights into the evolution of PCWDEs and the molecular mechanisms of acquiring novel enzymatic functions. Furthermore, based on a variety of industrial applications of PCWDEs, beetle-derived GH45 and GH5_10 enzymes may contribute greatly to Society by being introduced into several industrial applications (e.g. biofuel production) and ultimately reducing a progressing greenhouse effect.Die erste Abwehr von Pflanzen gegen biotische und abiotische Stressfaktoren bildet die pflanzliche Zellwand, einem Polymer zusammengesetzt aus diversen Zuckerderivaten. Der Hauptbestandteil der Pflanzenzellwand besteht aus Zellulose - einem Polysaccharid aufgebaut aus β-1,4-verbundenen Glucoseeinheiten. Ein Organismus, der die Fähigkeit besitzt Zellulose abzubauen, würde sich damit nicht nur eine große Energiequelle erschließen, sondern sich auch Zugang zu einem nähstoffreichen Zellinhalt verschaffen. Zelluloseverdauende Enzyme (Zellulasen) waren lange Zeit dafür bekannt Bestandteil einiger Mikroorganismen zu sein, galten aber gleichzeitig als nicht von Tieren selbst zu kodierend. In den vergangenen zwei Jahrzehnten wurde jedoch bekannt, dass Pflanzenzellwand-verdauende Enzyme (PZVE) auch von einigen Tierarten endogen kodiert werden. Zu diesen PZVE gehören u.a. Vertreter der Glycosidhydrolasefamilie (GH) und schließen auch putative Zellulasen der Familie 45 (GH45) und potentielle Mannanasen der Familie 5 Unterfamilie 10 (GH5_10) mit ein. In Arthropoden sind GH45 und GH5_10 hauptsächlich innerhalb der Insekten vertreten, zu denen auch Käfer der Klade Phytophaga (Blatt-, Bock-, Borken- und Rüsselkäfer) zählen. Dennoch ist die Verteilung beider Genfamilien in Insekten unregelmäßig und es wird angenommen, dass ihre Herkunft nicht auf einen anzestralen Ursprung zurückzuführen ist. Wahrscheinlicher ist es, dass sie separat erworben wurden - womöglich durch einen horizontalen Gentransfer (HGT) zwischen Mikroorganismus und Tier. Trotz der komplexen Evolution von GH45 und GH5_10 und der aufstrebenden Rolle von PZVE in der Biokraftstoffindustrie, sind beide Genfamilien in Phytophaga Käfern nur wenig untersucht. Das Hauptziel dieser These ist es daher PZVE der GH45 und GH5_10 aus Phytophagen Käfern -- mit Fokus auf enzymatischer Aktivität, physiologischer Bedeutung und Evolutionsgeschichte -- näher zu untersuchen. Diese Doktorarbeit hat wesentlich zum Verständnis der Funktion von Phytophaga Käfern kodierenden PZVE beigetragen. Dabei konnte unser Wissen über Käfer GH45 und GH5_10 maßgeblich vertieft werden. Die vorliegenden Ergebnisse zeigen, dass nicht ein vertikaler sondern ein horizontaler Gentransfer die mögliche Ursache der ursprünglichen Vererbung von GH45 (und wahrscheinlich GH5_10) in Käfern war. Die anschließenden spezies-spezifischen, unabhängigen Genduplikationen erlaubten eine funktionelle Diversifizierung und mögliche Adaption an die Nahrungsquelle der Käfer. Diese Untersuchungen geben einen fundamentalen Einblick in die Evolution von PZVE und der molekularen Mechanismen notwendig für den Erwerb neuer enzymatische Funktionen. Die Fähigkeit von GH45 und GH5_10 Pflanzenzellwandmaterial abzubauen, macht sie zu interessanten Kandidaten für die Anwendung in diversen Industriezweigen wie z.B. in Wein- und Bierbrauereien oder Textil- und Nahrungsmittelindustrie. Insbesondere können GH45 Zellulasen Anwendung in der Biokraftstoffproduktion finden und damit einem fortschreitenden Treibhauseffekt entgegenwirken

Diseases in Asian Aquaculture VII

Proceedings of the Seventh Symposium on Diseases in Asian Aquaculture 20-26 June 2008 Taipei, Taiwan

Training Manual In the frame work of the project: DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals 2015-18

This is a limited edition of the CMFRI Training Manual provided to participants of the “DBT sponsored Three Months National Training in Molecular Biology and Biotechnology for Fisheries Professionals” organized by the Marine Biotechnology Division of Central Marine Fisheries Research Institute (CMFRI), from 2nd February 2015 - 31st March 2018

Winter School on Vistas in Marine Biotechnology

Winter School on Vistas in Marine Biotechnology, 5th to 26th October, 2010 at Marine Biotechnology Division CMFRI, Koch