Pengaruh Retardan Paklobutrazol Terhadap Pertumbuhan Dan Pemulihan Dua Aksesi Ubi Kayu

Normal growth medium is not effective for in vitro conservation due to the risk of somaclonal variation that may increase dueto short interval between subculture. Two experiments involving growth retardant paclobutrazol (PBZ) were conducted toreduce explants growth and extend subculture interval. In order to develop medium-term conservation of cassava, therecovery of plantlets after in vitro storage was also observed. Accession 433 and 450 were used in two independentexperiments. Completely Randomized Design was used with three replications. PBZ at 0, 3.4, 6.8, and 10.2 μM weresupplemented onto MS medium + arginin 100 ppm. Observation was done on shoot length, number of nodes and leaves, andnumber of white and senescence leaves. The results showed that after nine months without subculture, both cassavaaccessions showed different results in in vitro growth and their recovery. PBZ 3.4 μM performed as the best treatment inaccession 433 and 450 to reduce in vitro growth and their recovery after storage

Pengaruh Retardan Paklobutrazol terhadap Pertumbuhan dan Pemulihan Dua Aksesi Ubi Kayu

Normal growth medium is not effective for in vitro conservation due to the risk of somaclonal variation that may increase dueto short interval between subculture. Two experiments involving growth retardant paclobutrazol (PBZ) were conducted toreduce explants growth and extend subculture interval. In order to develop medium-term conservation of cassava, therecovery of plantlets after in vitro storage was also observed. Accession 433 and 450 were used in two independentexperiments. Completely Randomized Design was used with three replications. PBZ at 0, 3.4, 6.8, and 10.2 μM weresupplemented onto MS medium + arginin 100 ppm. Observation was done on shoot length, number of nodes and leaves, andnumber of white and senescence leaves. The results showed that after nine months without subculture, both cassavaaccessions showed different results in in vitro growth and their recovery. PBZ 3.4 μM performed as the best treatment inaccession 433 and 450 to reduce in vitro growth and their recovery after storage

The Role of OsWRKY71 and Its Interacting Proteins in Seed Germination and Early Growth of Cereal Grains

During seed germination and early seedling growth, complex molecular and physiological events occur in rice (Oryza sativa) and other cereal grains. As the seed transitions to vegetative tissue, it responds to both favorable and unfavorable environmental conditions and is vulnerable to attack by predation and disease. Although seeds are relatively small and tender in size, extensive and sophisticated molecular networks enables the immobile seed to grow, survive and adapt in its environment. One of the networks I am interested in is in the crosstalk between the gibberellin (GA) and abscisic acid (ABA) signaling pathways. These pathways are interesting because they are largely antagonistic. GA is a hormone that generally promotes germination and growth- related processes while ABA, also a hormone, promotes seed dormancy and represses growth. Although a great deal of research has been dedicated towards understanding these two pathways, the actual mechanism of crosstalk during seed germination is less understood. Any deficiencies in GA and ABA regulation and response may result in altered interpretation of environmental signals and aberrations in seed development and germination, leading to lower grain yields. My research is dedicated towards deciphering the specific role of Oryza sativa WRKY71 (OsWRKY71; amino acid W-R-K-Y) and harpin-induced1-like (HIL) members in the crosstalk between GA and ABA in rice, with the goal that this research will be used to improve cereal grain yield in areas of the world with limited plant productivity. The crosstalk between GA and ABA directs the synthesis of α-amylase, which is an enzyme that breaks down starch in seeds to provide energy for germination. OsWRKY71 was shown to be a transcriptional regulator of α-amylase and was regulated by both GA and ABA in barley. In this study, I have provided a model of the regulation of OsWRKY71 in seed germination in rice. Although it was previously determined that OsWRKY71 negatively regulated α-amylase, I show that it positively regulated not only germination but also root growth. To support this, I performed seed germination and root elongation assays using knockout mutants of OsWRKY71. Mutant analysis determined that germination in oswrky71 was delayed for approximately 1 day and was able to recover from the delay. Additionally, after 4 days, oswrky71 seedling roots were nearly 2 cm shorter than wildtype (wt), suggesting that OsWRKY71 may regulate other aspects of plant development. This is further supported by analysis of β-Glucuronidase (GUS) reporter expression of OsWRKY71p-GUS, which indicated that OsWRKY71 was localized to the third node of rice culms. Thus, the function of OsWRKY71 appears to be more complex and versatile than predicted. To further understand the mechanism of OsWRKY71 regulation in rice seed germination, I investigated the role of one of its interacting partners, Oryza sativa harpin-induced1-like 58 (OsHIL58). Using rice aleurone RNA-sequencing data, I found that OsHIL58 was induced upon ABA treatment. Thus, the two proteins may interact during ABA induction. I also annotated the HIL family using in silico methods and identified several other HIL members that were differentially and significantly expressed in the aleurone. One member, OsHIL16, was highly expressed and also coexpressed with an ABA receptor, regulatory component of ABA receptor 9 (RCAR9). Surprisingly, both were repressed by ABA, suggesting that they be involved in the same pathway in the aleurone aside from OsWRKY71 regulation. From this annotation, I also identified and compiled a large family of 104 unique HIL members expressed in various rice tissues. A classification system was designed based on the presence of several conserved amino acid motifs: NPN, RPP, and YQYF. Most HIL members, including OsHIL16 and -58, were Group I members with all three motifs present. These and further analyses suggest that HILs may have multiple roles in plant development, including in seed germination

METABOLIC MODELING AND OMICS-INTEGRATIVE ANALYSIS OF SINGLE AND MULTI-ORGANISM SYSTEMS: DISCOVERY AND REDESIGN

Computations and modeling have emerged as indispensable tools that drive the process of understanding, discovery, and redesign of biological systems. With the accelerating pace of genome sequencing and annotation information generation, the development of computational pipelines for the rapid reconstruction of high-quality genome-scale metabolic networks has received significant attention. These models provide a rich tapestry for computational tools to quantitatively assess the metabolic phenotypes for various systems-level studies and to develop engineering interventions at the DNA, RNA, or enzymatic level by careful tuning in the biophysical modeling frameworks. in silico genome-scale metabolic modeling algorithms based on the concept of optimization, along with the incorporation of multi-level omics information, provides a diverse array of toolboxes for new discovery in the metabolism of living organisms (which includes single-cell microbes, plants, animals, and microbial ecosystems) and allows for the reprogramming of metabolism for desired output(s). Throughout my doctoral research, I used genome-scale metabolic models and omics-integrative analysis tools to study how microbes, plants, animal, and microbial ecosystems respond or adapt to diverse environmental cues, and how to leverage the knowledge gleaned from that to answer important biological questions. Each chapter in this dissertation will provide a detailed description of the methodology, results, and conclusions from one specific research project. The research works presented in this dissertation represent important foundational advance in Systems Biology and are crucial for sustainable development in food, pharmaceuticals and bioproduction of the future. Advisor: Rajib Sah