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Item Impact of salinity on morphology, growth, and pigment profiles of Scenedesmus obliquus HTB1 under ambient air and elevated CO2 (10%) conditions(2024) Jiao, Fanglue; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Certain microalgal species tolerate high CO2 concentrations and proliferate faster with elevated CO2 than with ambient air. This feature makes them attractive for carbon sequestration, a tool for mitigating climate change due to increasing atmospheric CO2. Scenedesmus species are among these microalgae. Scenedesmus obliquus strain HTB1 is a microalgal strain isolated from the Baltimore Inner Harbor (brackish water) and has shown a faster growth with 10% CO2 compared to air. However, how HTB1 grows under different salinity and if the salt response is affected by elevated CO2 remains elusive. Two experiments were set up to address these questions. The first experiment tested the impact of salinity gradient (0, 17.5, 20, 22.5, 25, 27.5, and 30 ppt) on HTB1 under ambient air. With increasing salinity, HTB1 cells became smaller, and the cultures changed color from green to brown, yellowish brown, and then to pale white. The pigment analysis showed that HTB1 reduced several pigments (i.e. zeaxanthin, lutein, chlorophyll b) in response to salt stress. However, HTB1 produced higher concentrations of canthaxanthin under the salt stress. The growth of HTB1 decreased with increasing salinity and was inhibited when the salinity was greater than 22.5 ppt. In the second experiment, we compared the impact of salinity (0, 10, and 20 ppt) on HTB1 under air and 10% CO2, respectively. HTB1 cultures showed little color change with increasing salinity under 10% CO2. In contrast, the change of culture color from dark green to brown was observed with increasing salinity when HTB1 was grown with air. Interestingly, the growth of HTB1 was less inhibited with salt under 10% CO2 than with air, suggesting that elevated CO2 mitigates the salt stress of HTB1. Lutein and canthaxanthin increased with increasing salinity when HTB1 was grown with 10% CO2. Our results indicate that increased salinity affects the growth of Scenedesmus obliquus HTB1 more with air than with 10% CO2. This study provides insight into the impact of salt stress on algal morphology, growth, and pigment composition.Item INVESTIGATION OF A NOVEL O-GLCNAC MODIFICATION OF A VACCINIA VIRUS CORE PROTEIN(2024) Zhang, Yunliang; Scull, Margaret; Moss, Bernard; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Vaccinia virus (VACV) is a large, complex, enveloped virus that is the prototypic member of the genus Orthopoxvirus of the Poxviridae family and is well known as the live-virus vaccine that eradicated smallpox. It has a linear, double-stranded DNA genome of approximately 190 kbp that encodes about 200 proteins some of which undergo various post-translational modifications. These modifications are crucial for regulating protein function and influencing the virus behavior within the vertebrate and insect cells. Among these, O-GlcNAcylation is notable for its reversible modulation of protein function, like phosphorylation. Although over 5,000 human proteins have been documented as O-GlcNAcylated, the prevalence and function of this modification in viral proteins remain underexplored.Early studies from the Moss laboratory demonstrated the presence of a 40-kDa protein that contained N-acetylglucosamine in purified virions. The small size of the pronase-digestion product and the absence of other sugars suggested one or few glucosamines. The current study advances this understanding by pinpointing the novel O-linked β-N-acetylglucosamine (O-GlcNAc)-modified protein in VACV infectious particles. Enzymatic labeling of purified virions was performed using the mutant β-1,4-galactosyltransferase (GalT1 (Y289L)) to specifically transfer azido-modified galactose (GalNAz) from UDP-GalNAz to O-GlcNAc residues. Following copper catalyzed azide-alkyne cycloaddition (CuAAC) of biotin or an infrared dye, the candidate O-GlcNAc proteins were detected by SDS-polyacrylamide gel electrophoresis and identified by mass spectrometry (MS). Then using strain-promoted cycloaddition (SPACC) chemistry to attach a polyethylene glycol mass tag of 10 kDa to the O-GlcNAc protein, a significant shift in the electrophoretic mobility of the VACV A4 protein was documented by western blotting. The presence of O-GlcNAc in A4 was confirmed by MS and by binding to specific antibodies. Multiple modification sites were pinpointed using higher-energy collisional dissociation induced electron-transfer dissociation in MS. Further evidence linking cellular protein O-GlcNAc transferase (OGT) to the modification of A4 was derived from experiments conducted with an A4-expressing cell line. Disruption of OGT activity, either through chemical inhibition or knock-down techniques, reduced A4 O-GlcNAc modification without impairing VACV infectivity. This finding suggests that the O-GlcNAc modification of A4 does not play an essential role in VACV infectivity, which is not correlated with the A4 deletion phenotype. Therefore, the specific effects of O-GlcNAc modification on the VACV lifecycle remain elusive, indicating further studies are required to determine the potentially subtle effects of O-GlcNAcylated A4 on the VACV life cycle.Item AN INVESTIGATION ON THE MOLECULAR BASIS FOR DIMER FORMATION OF A BACTERIOPHAGE ENDOLYSIN POSSESSING ANTIMICROBIAL ACTIVITY AGAINST STREPTOCOCCUS PNEUMONIAE(2023) Alreja, Adit Bipin; Nelson, Daniel C; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The global rise of antibiotic resistance casts a shadow on treating infectious disease. An alternative to the use of antibiotics is bacteriophage-derived peptidoglycan hydrolases called endolysins. Endolysins, produced at the end of a bacteriophage replication cycle, cause bacterial cell lysis and virion release. When applied exogenously as recombinant proteins, they are also capable of cleaving the Gram-positive bacterial peptidoglycan. Various studies conducted in vitro and in vivo showcase the therapeutic potential of endolysins as the next generation of antimicrobials. Streptococcus pneumoniae is the most common cause of a variety of infections ranging from otitis media to invasive bloodstream infection (bacteremia) and meningitis (brain infection). While pneumococcal vaccination programs have proven to be effective, the high rates of antibiotic resistance reported for S. pneumoniae has led to the CDC classifying it as a “serious” threat. One of the most studied endolysins targeting S. pneumoniae is Cpl-1. This thesis represents an investigation into the molecular basis for dimer formation of the Cpl-1 endolysin which displays antibacterial activity against S. pneumoniae. In addition to disproving a long-accepted mechanism of dimerization of Cpl-1 in the presence of choline, we have conclusively identified the residue involved in the formation of the Cpl-1 dimer. Our findings led to the discovery of a novel C-terminal consensus sequence shared by all pneumococcal endolysins that informs their propensity to form dimers in the presence of choline. Next, through a bioinformatics approach we identified a new endolysin containing this C-terminal consensus sequence, produced it, named it SP-CHAP, and showed that it forms a dimer in the presence of choline, indicative of the widespread dimerization phenomenon associated with pneumococcal endolysins. Of interest, SP-CHAP is the first endolysin with antimicrobial activity against S. pneumoniae that possesses a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain. SP-CHAP was subsequently characterized for its biochemical and antimicrobial properties and benchmarked against Cpl-1. SP-CHAP is active in all physiologically relevant conditions (pH, temperature) against various S. pneumoniae strains and displays no activity towards oral/nasal commensal organisms. This enzyme also displays pneumococcal biofilm eradication ability to a greater extent than Cpl-1, as visualized by confocal microscopy. To further translate the antimicrobial potential of this enzyme, the antimicrobial efficacy of SP-CHAP was validated in a S. pneumoniae mouse nasopharyngeal colonization model. Our results demonstrate the therapeutic potential of SP-CHAP as an attractive endolysin to treat S. pneumoniae infections and warrant further translational development of this enzyme.Item Climate Change and Vibrio species: Investigation of Environmental Parameters Associated with Occurrence and Transmission(2023) Brumfield, Kyle David; Colwell, Rita R.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Climate change, associated with shifts in the geographical range of biological species, has become increasingly important in emergence and re-emergence of disease. Vibrio spp., native to aquatic ecosystems, are commonly associated with aquatic invertebrates, notably crustaceans and zooplankton. Some species of the genus Vibrio cause infection in humans, of which Vibrio cholerae, the etiological agent of pandemic cholera, is the most documented. Pathogenic non-cholera Vibrio spp., namely Vibrio parahaemolyticus and Vibrio vulnificus, cause gastroenteritis and also septicemia and extra-intestinal infections. They are responsible for a large number of public health emergencies in developed countries, including the United States. As sea temperatures rise and salinity profiles are altered, a pattern of poleward spreading of non-cholera Vibrio spp. has been observed globally, demonstrating significant geographic expansion of these bacterial populations, corroborated by an associated increase in the number of reported vibriosis cases. Since Vibrio spp., including pathogenic vibrios, play an important role in the degradation of polymeric substances, such as chitin, and in biogeochemical processes, they cannot be eradicated. Hence, routine monitoring and an early warning system are needed for public health preparedness. Since the 1960’s, ongoing research has focused on environmental factors linked with occurrence and distribution of clinically relevant Vibrio spp. and their role in disease transmission. We have reported that lack of, or damage to, water, sanitation, and hygiene (WASH) infrastructure, coupled with elevated air temperatures, and followed by above average rainfall promotes exposure of a population to contaminated water, hence increases the risk of an outbreak of cholera. Global predictive intelligence models applicable to diseases caused by non-cholera Vibrio spp. are in development. The research reported here describes results of intensive sampling to detect and characterize Vibrio spp. in the Chesapeake Bay, Maryland, and the Florida Gulf Coast, the latter an area significantly impacted by Hurricane Ian, September 2022, with a spike in confirmed vibriosis cases and deaths during weeks following the storm. Results of this study provide confirmation of environmental predictors for Vibrio spp. and document long-term increase and extended seasonality of Vibrio populations in the Chesapeake Bay. Using satellite remote sensing data, we demonstrate the impact of extreme heat, precipitation, and other key environmental and geophysical factors (e.g., temperature, salinity, and chlorophyll) on prevalence of pathogenic Vibrio spp. in aquatic systems. This study lays the groundwork for a predictive intelligence system for Vibrio spp. and other pathogens under varying climatic scenarios.Item Development and characterization of Epstein-Barr virus (EBV) antibodies and testing their efficacy in a humanized mouse model(2022) Kim, JungHyun Rachel; Zhu, Xiaoping; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Epstein-Barr virus (EBV) is one of the most prevalent human viruses with more than 90% of the adult population infected with EBV. EBV is well-known to cause infectious mononucleosis, but also is associated with several B cell lymphomas and epithelial cell carcinomas. In bone marrow or solid organ transplant patients and individuals with X-linked lymphoproliferative disease, primary EBV infection can lead to life-threatening complications. There is no licensed vaccine and even if one is available, these immunocompromised individuals might not respond well to the vaccine. Thus, an effective vaccine and therapeutic are both needed. Here, I have evaluated the efficacy of (a) EBV hyperimmune globulin isolated from healthy plasma donors with high EBV gp350 antibody and EBV B cell neutralizing titers, (b) several EBV gp350, gH/gL and gp42 monoclonal antibodies (mAbs) isolated from human plasma or vaccinated monkeys, (c) a bispecific antibody targeting both gH/gL and gp42, and (d) gH/gL and gH/gL/gp42 nanoparticle vaccines in a humanized mouse model. Animals that received hyperimmune globulin showed protection from EBV infection at a similar level as that seen in animals receiving intravenous immunoglobulin. However, humanized mice that received gH/gL mAb B10 or gp42 mAb A10 showed increased survival and reduced viremia compared to animals that received other gH/gL or gp42 mAbs. These two mAbs also demonstrated protection from development of EBV B cell lymphomas in animals. Humanized mice that received bispecific antibody derived from gH/gL mAb B10 and gp42 mAb A10 showed similar protection against EBV as animals that received the combination of the two antibodies. Passive transfer of IgG isolated from mice immunized with a gH/gL or gH/gL/gp42 nanoparticle vaccine showed reduction in viremia and no development of EBV lymphomas compared to mice that received IgG from naïve mice. These findings suggest that development of vaccines or therapeutics targeting gH/gL and/or gp42 may provide protection in healthy individuals and severely immunocompromised individuals from EBV infection and B cell lymphoma.Item MECHANISMS OF SEXUAL MODE EVOLUTION IN CAENORHABDITIS ELEGANS(2022) Skelly, Lauren E; Haag, Eric S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)ABSTRACT Title of dissertation: MECHANISMS OF SEXUAL MODE EVOLUTION IN CAENORHABDITIS ELEGANS Lauren Skelly, Doctor of Philosophy, 2022 Dissertation directed by: Professor Eric S. Haag, Department of Biology The evolution of phenotypic novelties is a broad biological phenomenon, and how organisms evolve new traits is dependent on the molecular mechanisms that underlie those traits. Transcriptional regulation is often the focus of phenotype evolution, but post-transcriptional mechanisms such as mRNA splicing, stability, and translational control are also important components. Germ cells are particularly influenced by post-transcriptional mechanisms and are therefore a good system to study how these mechanisms lead to phenotypic novelties. This topic can be studied especially well in model systems that contain closely related species with recently evolved traits, such as self-fertility in Caenorhabditis elegans hermaphrodites. C. elegans hermaphrodites are essentially XX females that evolved the ability to produce sperm in an ovary. There are many known components necessary for sperm development, including a protein-protein-mRNA complex consisting of GLD-1, FOG-2 and tra-2. GLD-1 and FOG-2 dimerize and bind the 3’ UTR of tra-2 mRNA to repress its activity during spermatogenesis. In this work, I show FOG-2 directly interacts with TRA-2 protein, leading to the model that FOG-2 targets TRA-2 protein for degradation during its translation allowing sperm to form. I also show the expression pattern of tra-2 mRNA in the germline, and that GLD-1 binding on the 3’ UTR does not influence its localization. Another method for the study of novel traits is through hybridization of closely related species. In this work, I attempt to hybridize two closely related species of Caenorhabditis, another self-fertile species C. briggsae and an outcrossing species C. nigoni, to map the genetic loci underlying self-fertility. These hybrid crosses are unable to map genetic loci because males are inviable. These results agree with previous studies. This work contributes to the study of phenotypic evolution by adding an underlying molecular mechanism to Caenorhabditis sex determination.Item Viromics and biogeography of estuarine virioplankton(2021) Sun, Mengqi; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Viruses are the most abundant biological entity in the ocean, and they can influence microbial mortality, evolution and biogeochemical cycles in marine ecosystems. Virioplankton communities in oceans have been studied extensively using viral metagenomics (viromics), but the estuarine viromes remain relatively unexplored. Estuaries are a complex and dynamic ecosystem. My dissertation is dedicated to understanding the composition and distribution of the virioplankton community in the Delaware Bay and Chesapeake Bay by investigating 16 viromes collected from these two bays. A total of 26,487 viral populations (contigs > 5kb) were identified in the two bays, establishing a high quality viromic dataset. The vast majority of the dominant viral populations are unclassified viruses. Viral sequences obtained from marine single cell genomes or long read single molecule sequencing comprised 13 of the top 20 most abundant viral populations, suggesting that we are still far from understanding the diversity of viruses in estuaries. Abundant viral populations (top 5,000) are significantly different between the Delaware Bay and Chesapeake Bay, indicating a strong niche adaptation of the viral community to each estuary. Surprisingly, no clear spatiotemporal patterns were observed for the viral community based on water temperature and salinity. The composition of known viruses (i.e. phages infecting Acinetobacter, Puniceispirillum, Pelagibacter, Synechococcus, Prochlorococcus, etc.) appeared to be relatively consistent across a wide range of salinity gradients and different seasons. Overall, the estuarine viral community is distinct from that in the ocean according to the composition of known viruses. N4-like viruses belong to a newly established viral family and have been isolated from diverse bacterial groups. Marine N4-like viruses were first found in the Chesapeake Bay, but little is known about their biogeographic pattern in the estuarine environment. N4-like viruses were confirmed to be rare in the estuary, and relatively more abundant in the samples from lower water temperature. Viruses which infect SAR11 bacteria (pelagiphage) are one of most abundant viral groups in the open ocean. We found that the abundance and community profile of pelagiphage in the estuaries is similar to that in the open ocean, and has no correlation with environmental factors.Item TOXIN-ANTITOXIN SYSTEMS AND OTHER STRESS RESPONSE ELEMENTS IN PICOCYANOBACTERIA AND THEIR ECOLOGICAL IMPLICATIONS.(2020) Fucich, Daniel Christopher Ehlers; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Picocyanobacteria (mainly Synechococcus and Prochlorococcus) contribute significantly to oceanic primary production. Unlike Prochlorococcus, which is mainly constrained to the warm and oligotrophic ocean, Synechococcus has a ubiquitous distribution. Synechococcus is present in freshwater, estuarine, coastal, and open ocean habitats. They have also been found in polar regions and hot springs. Endemic to the hot and the cold, the saline and the fresh, and every condition in between, Synechococcus appears to have the capability to adapt and tolerate nearly any environment and climate. This ability to adapt to any aquatic environment is possible through their genome plasticity, a character that is not present in the Prochlorococcus.Due to the differential distribution of the genera, Synechococcus is considered a generalist and Prochlorococcus is considered a specialist in ecological theory. More than 400 picocyanobacterial genomes have now been sequenced, and this large genomic resource enables comprehensive genome mining and comparison. One possibility is to study the prevalence of Toxin-Antitoxin (TA) systems in picocyanobacterial genomes. TA systems are present in nearly all bacteria and archaea and are involved in cell growth regulation in response to environmental stresses. However, little is known about the presence and complexity of TA systems in picocyanobacteria. By querying 77 complete genomes of freshwater, estuarine, coastal and ocean picocyanobacteria, Type II TA systems (the most well studied TA family) were predicted in 27 of 33 (81%) Synechococcus strains, but no type II TA genes were predicted in any of the 38 Prochlorococcus strains. The number of TA pairs varies from 0 to 80 in Synechococcus strains, with a trend for more type II TA systems being predicted in larger genomes. A linear correlation between the genome size and the number of putative TA systems in both coastal and freshwater Synechococcus was established. In general, open ocean Synechococcus contain no or few TA systems, while coastal and freshwater Synechococcus contain more TA systems. The type II TA systems inhibit microbial translation via ribonucleases and allow cells to enter the “dormant” stage in adverse environments. Inheritance of more TA genes in freshwater and coastal Synechococcus could confer a recoverable persister state which would be an important mechanism to survive in variable environments. Different genotypes of Synechococcus are present in the Chesapeake Bay in winter and summer. Winter isolates of Synechococcus have shown high tolerance to cold conditions and other stressors. To explore their potential genetic capability, complete genomes of five representative winter Synechococcus strains CBW1002, CBW1004, CBW1006, CBW1107, and CBW1108 were fully sequenced. These five winter strains share many homologs that are unique to them and not shared with pelagic Synechococcus. Winter Synechococcus genomes are enriched with particular desaturases, chaperones, and transposases. Similar amino acid sequences and annotated features were not found in distantly related Synechococcus from Subcluster 5.1. These shared genomic features between the winter strains imply that maintaining membrane fluidity, protein stability, and genomic plasticity are important to cold adaption of Synechococcus. The winter strains also contain genes that are not traditionally considered with the canonical bacterial cold shock response. They contain a particularly high abundance of Type II TA pairs with complex association networks. They feature promiscuous toxins, like VapC, that pair with multiple antitoxins, which support the mix and match hypothesis. Winter strains also contain more monogamous toxins, such as BrnT, which tend to pair with their traditionally named antitoxin, BrnA. Expression of certain TA transcripts in response to environmental stress has been observed in the model strain CB0101, and the activity of one TA pair in CB0101 for growth arrest has been experimentally confirmed via heterologous expression in E. coli. My thesis work has identified interesting genetic systems related to niche partitioning of picocyanobacteria, particularly among the Chesapeake Bay Synechococcus. Future studies are paramount to understand the functional role of TA systems, desaturases, chaperons, and transposases of picocyanobacteria under various environmental stressors.Item Diet and Stomach Microbiota of Gulf Menhaden, a key forage filter feeding fish species(2020) Hanif, Ammar Wali; Jagus, Rosemary; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Menhaden represent a family of important filter feeding forage fish that serves as a trophic link between plankton and piscivorous predators in the marine environment. Dietary analysis is difficult because diet items are small and >80 % of the stomach content is amorphous material. DNA metabarcoding combines mass-amplification of short DNA sequences (barcodes) with high-throughput sequencing. This application allows the simultaneous identification of many taxa within the same environmental sample, as well as the analysis of many samples simultaneously, providing a comprehensive assessment of diet items and gut microbiota. Here we present a methodological approach using DNA metabarcoding suitable for a small filter feeding fish to identify the stomach contents of juvenile Gulf menhaden (Brevoortia patronus), collected within Apalachicola Bay, Florida. I describe the optimization of DNA extraction, comparison of two primers and sequencing protocols, estimation of menhaden DNA contamination, quality filtering of sequences, post-sequence processing and taxonomic identification of recovered sequences. I characterized the prokaryotic community using 16S universal ribosomal RNA (rRNA) gene sequencing primers in the V3-V4 hypervariable regions. Using two different sequencing protocols employing different “universal” 16S rRNA gene sequencing primers. Although no difference in overall operational taxonomic units (OTUs) was found, the two sequencing protocols gave differences in the relative abundancies of several bacterial classes. The dominant OTUs resulting from 16S rRNA gene sequencing at the phylum level were assigned to Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi and included oil eating bacteria consistent with the Gulf of Mexico location. Stomach microbiota and diet were compared in juvenile Gulf menhaden, Brevoortia patronus, caught at two locations, Two Mile Channel and St. Vincent Sound, in Apalachicola Bay, FL in May and July of 2013. The stomach microbiota of samples from both locations showed a predominance of Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria and Actinobacteria, although significant differences in composition at the class level were seen. The stomach microbiota from fish from Two-Mile Channel showed a higher level of taxonomic richness and there was a strong association between the microbiota and sampling location, correlating with differences in salinity. Approximately 1050 diet items were identified, although significant differences in the species represented were found in samples from the two locations. Members of the Stramenopile/ Alveolate/Rhizaria (SAR) clade accounted for 66 % representation in samples from Two Mile Channel, dominated by the diatoms Cyclotella and Skeletonema, as well as the ciliate Oligotrichia. In contrast, Metazoa (zooplankton) dominated in samples from St. Vincent Sound, accounting for over 80 % of the reads. These are mainly Acartia copepods. Since ciliates are considered to be microzooplankton, this means there is just over 60 % representation of phytoplankton in samples from Two Mile Channel and over 90 % representation of zooplankton in samples from St. Vincent Sound. Overall, I demonstrate the diversity of juvenile menhaden stomach contents that supports a characterization of menhaden as environmental samplers.Item INVESTIGATING THE REGULATION OF GROWTH MECHANISMS IN TWO DISTINCT BRANCHES OF PHOTOSYNTHETIC LIFE(2019) Sittmann, John; Liu, Zhongchi; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Photosynthetic organisms often have limited mobility and rely on a variety of environmental, physiological, and chemical signals to regulate aspects of growth and development. In this thesis, I investigated how two such organisms, one a flowering plant and the other a heterokont alga, incorporate external signaling cues to make decisions regarding reproduction. My dissertation research is focused on 1) investigating molecular mechanisms of crosstalk between photoperiod and shade in regulating asexual reproduction in the wild strawberry Fragaria vesca, and 2) elucidating the mechanism of a bacterium-derived agent in the stimulation of cell division in the marine diatom Phaeodactylum tricornutum. First, strawberry, including woodland strawberry Fragaria vesca, is capable of a form of asexual reproduction by producing horizontal stems with daughter plants at the nodes. These horizontal stems, referred to as stolon, are derived from axillary meristems at the base of the leaves. Depending on the signals the axillary meristem receives, it will give rise to either a branch crown (a flowering shoot) or a stolon. Stolon allows for asexual reproduction to maintain the superior hybrid genotype and hence is of great significance agriculturally. Daughter plants derived from stolon are sold and propagated in strawberry farming. In this work, I have shown that a key regulatory protein FveRGA1 in GA signaling pathway functions as a repressor of stolon development. I further expanded this work by showing that the light quality (shade) signaling pathway interacts with the GA signaling to regulate stolon development. I identified and demonstrated FvePIF3 as a key transcription factor that positively regulates stolon initiation under far-red light (shade). Understanding the mechanisms underlying axillary meristem cell fate determination could advance biotechnology to increase strawberry production. Second, I have discovered and characterized a bacterium-based growth stimulation of the diatom Phaeodactylum tricornutum. Specifically, I noticed that a culture of P. tricornutum that had been accidentally contaminated with bacteria exhibited faster growth. I subsequently identified the responsible bacterium as Bacillus sp, which stimulated rapid Phaeodactylum cell division when added to the Phaeodactylum culture. I experimentally determined that the growth stimulating agent was heat labile and proteinase K-resistant. Further, I showed that the mother cell lysate of Bacillus sp. under sporulation was just as effective in promoting Phaeodactylum. In collaboration with Dr. Jon Clardy lab, we identified the growth-stimulating compounds as two distinct peptide-signaling molecules. The work revealed that the peptides may be previously under-reported signaling molecules for cross-kingdom communications. In addition to the fundamental discovery of novel signaling mechanisms between bacterium and algae, this work may facilitate large-scale diatom culture in biomass production for biofuel and biopharma.