Title: De-Novo Genome Assembly of Fusarium Species (F. Proliferatum YN-41 and F. Sacchari CNO-1) and Genome Wide Analysis to Identify Novel Secondary Metabolites

Abstract:

De-Novo Genome Assembly of Fusarium Species (F. Proliferatum YN-41 and F. Sacchari CNO-1) and Genome Wide Analysis to Identify Novel Secondary Metabolite

Pokkah boeng disease (PBD) is a major constraint to sugarcane production globally and is re-emerging as predominant foliar disease in China. PBD is an airborne disease of sugarcane, caused by Fusarium fujikuroi species complex (FFSC). In this study, we present high quality genome sequences, which is the first report of full genome for F. sacchari CNO-1. We performed whole-genome sequencing of Fs. CNO-1 and Fp. YN41 by utilizing a combination of second and third generation sequencing technology. De-novo assembly processes resulted in thirteen pseudo-chromosomes including twelve chromosomes and one mitochondrial genome for Fs. CNO-1 and Fp. YN-41. We estimated that Fs. CNO-1 diverged ~6.16 million years ago (mya), approximately ~4.17 mya earlier than its closely related Fp. YN41 species. Further, we performed combined transcriptome, proteome, and metabolome analysis to identify the potential secondary metabolite biosynthetic gene clusters. We found that despite close association of Fs. CNO-1 and Fp. YN-41 genomic organization, both markedly differ with respect to presence and absence of secondary metabolites gene clusters in their genomes. HPLC-FTMS analysis revealed that fumonisin (FUM), fujikurins (FFUJ) and fusarinine (FSC) secondary metabolites which are encoded by Polyketide synthase gene (PKS) 11, PKS 19 and Non-ribosomal peptide synthetase gene (NRPS) 17 gene clusters, are absent in Fs. CNO-1. While PKS-8, NRPS-25 and DTC2-GA which encode gibberellins, are not found in Fp. YN41. Genome wide comparative analysis revealed higher number of genes encoding transcription factors, transporters, amino acid permeases, Carbohydrate-Active enZYmes (CAZymes), and polysaccharide lyase (PL) in Fp. YN41. Two unique PL families (PL20 and PL22) have been identified in Fp. YN41. Thus, through combined comparative genomics and genome wide analysis, we discovered novel genes and gene clusters that contribute to the host adaptability and pathogenicity of Fp. YN-41 and Fs. CNO-1, as sugarcane pathogen.

Biography:

I am Sehrish Akbar from Pakistan. Currently, I am doing my Post-Doctorate from State Key Laboratory for Conservation and Utilization of Agro bioresources, Guangxi University, China with Professor Mu-Qing Zhang. Major focus of my research is on sugarcane diseases (viral and fungal) and their resistant strategies (through RNAi, CRISPR). I did my PhD from National University of Science and Technology (NUST), Pakistan. During my PhD studies, I targeted one of devastating viral pathogen of sugarcane crop (Sugarcane mosaic virus) using amiNA and RNAi pathways. I have one-year research experience in CSIRO, Australia. Due to my previous academic record and hands-on-experience on various molecular techniques, I got selected for post of Research Associate in USDA-ICARDA project. Our team focused on development of resistant against Begomovirus through the modification of beta-satellite containing cytochrome c and RNAi knockouts.

Title: The use of in vivo confocal microscopy to track treatment success in fungal keratitis and to differentiate between Fusarium and Aspergillus keratitis

Abstract:

The use of in vivo confocal microscopy to track treatment success in fungal keratitis and to differentiate between Fusarium and Aspergillus keratitis

Purpose: To evaluate the usefulness of serial in vivo confocal microscopy (IVCM) examinations to measure hyphal density for monitoring the treatment success among patients with fungal keratitis, and to compare the hyphal diameter as well as branching angle as a way of differentiation between Aspergillus and Fusarium species observed in IVCM.

Study design: Prospective nonrandomized study.

Patients and methods: The study was conducted from February 2015 to September 2016. Hyphal diameter, density and branching angle measurements were performed using IVCM at admission and on a weekly basis for at least 2 weeks after the start of treatment.

Results: During the period of study, 65 patients with culture-confirmed fungal keratitis were recruited. Of them, 40 were culture-positive for Fusarium spp. and 25 patients for Aspergillus spp. Before the start of treatment, the mean branching angle did not differ between the two species and the mean hyphal diameter was statistically higher for Aspergillus spp. (p = 0.029). Two weeks after the start of treatment, the mean hyphal diameter was statistically lower (p < 0.001) in the treatment failure group. Also the hyphal density significantly decreased with successful treatment (p < 0.05).

Conclusion: Decreasing hyphal density in serial IVCMs might be used as an indicator to predict the successful response of fungal ulcers to treatment. Branching angle is not different between Aspergillus and Fusarium keratitis. The mean hyphal diameter is significantly lower in the treatment failure group.

Biography:

Mohammad Soleimani MD, FICO is an associate professor in Farabi Eye Hospital ,Tehran University of Medical Sciences. He received his anterior segment fellowship in 2012; he is especially working on ocular trauma, ocular surface and keratitis

Title: Managing Fungal and Bacterial Risks

Abstract:

   Managing Fungal and Bacterial Risks

In the last two years there have been several high-profile illnesses in cannabis users, notably the e-cigarette, or vaping, product-use associated lung injury (EVALI), and heavy metal poisoning in California and Michigan. While these are undeniably deserving of attention, they have led to a focus on chemical contaminants and causes of illness, rather than microbial ones. With an estimated combined market of over $10B in retail sales this year, it’s not a matter of if, but when will the cannabis industry have its first major microbial or food-borne outbreak and product recall. This can be mitigated by implementing proper quality control measures, but what does that mean? Presented within is a general overview of quality control in 2 aspects of the cannabis industry particularly focusing on bacterial and fungal contamination and steps to mitigate it.

Learning Objectives:

1. Introduce the audience to a general overview of bacterial and fungal contamination

2. Identify areas in the growing and manufacturing industries to monitor for bacterial and fungal contamination

3. Present general steps forward to monitor and mitigate contamination.

Biography:

Josh Smith has spent the last decade researching alternative anti-microbial therapies in the pharmaceutical industry. In particular, he has spent most of his career developing molecular diagnostic methods and genetically modifying E. coli to prevent or kill off infections. Most recently, he worked on developing treatments for catheterized patients to guard against UTIs as well as clearing wound and skin graft sites prior to treatment. This work led to developing a patent pending new diagnostic test for identifying bacterial infections within 4 hours of receipt by the lab. His graduate degree is in clinical microbiology but, during the course of his education, he spent a large amount of time in microbial genetics, biochemistry, x-ray crystallography, and protein kinetics, particularly with the hemolysin hpmA of P. mirabilis. In 2018, Josh was approached to found Premium CBD Labs, a hemp testing laboratory located in Madison, WI. His focus is bringing the standards and ethical accountability of clinical labs to the cannabis testing industry.

Title: OneTest PathoGenome: A Target Hybridization-Based Next-Generation Sequencing Assay to Tackle Undiagnosed Infections

Abstract:

OneTest PathoGenome: A Target Hybridization-Based Next-Generation Sequencing Assay to Tackle Undiagnosed Infections

Every year, approximately 800,000 critically ill patients are hospitals in the USA with undiagnosed infections. The only option is to treat these patients with broad-spectrum antimicrobial therapy and hope for the best outcome. The inability to obtain specific actionable information in a clinically relevant time-frame, combined with ineffective treatment, contributes to increased disease burden, mortality, hospitalizations, and drug resistance. The consequence is direct hospitalization costs of more than $27 billion, with another $26 billion lost due to antimicrobial resistance. What is urgently needed is precise and comprehensive targeted pathogen identification, including the capacity to detect drug-resistant mutations, for routine diagnosis to support effective treatment and control measures.
Fusion Genomics Corp.’s mission is to address this need and enable precision medicine for infectious diseases by developing a pan-pathogen test - the ONETest™ PathoGenome - that identifies all human pathogens (~1,400) and provides the genomic information necessary to guide treatment, including drug resistance and human genetic susceptibility markers in a timely fashion. The assay uses next-generation DNA sequencing (NGS) along with Fusion’s novel DNA hybridization technology, QuantumProbes, to enrich bacterial/viral/fungal genomes prior to sequencing. The assay will be functionally equivalent, yet clinically superior, to whole metagenome sequencing, but at 1/10th the cost, 1/3rd the time, and several times the sensitivity.

Learning Objectives: 

1. learn how NGS will impact undiagnosed infections  
2. learn about the advantages of using targeted sequencing versus whole metagenome sequencing

Biography:

Dr Qadir's training is in genetics and molecular biology. Dr Qadir has over 17 years of research experience. The last ten were at the British Columbia Cancer Agency where he worked with world-renowned experts in genomics and drug development. Dr Qadir is the co-inventor of the CHILDSeq-Sarcoma assay and CHILDDecode (part of FUSIONCloud™). Dr Qadir oversees all the scientific aspects of research and development efforts at FUSION GENOMICS and also serves as the interface for all collaborators.

Title: A Neo-Virus lifestyle exhibited by a (+)ssRNA virus hosted in an unrelated dsRNA virus: Taxonomic and Evolutionary Considerations

Abstract:

A Neo-Virus lifestyle exhibited by a (+)ssRNA virus hosted in an unrelated dsRNA virus: Taxonomic and Evolutionary Considerations

A rapidly growing number of viruses of lower eukaryotes have been reported in the past few decades. These have enhanced our understanding of virus evolution and diversity. Simultaneously, some unusual viruses have challenged or broken the “common rules” of viruses in sizes and concepts. One such virus group includes the so called dsDNA megaviruses isolated from amoebae that exceed some bacterial parasites in coding capacity and particle size. Other unusual viruses have been found in fungi that include “naked” or “capsidless” RNA viruses unable to form virus particles, exemplified by hypoviruses and narnaviruses. Also among them are fungal multi-segmented dsRNA viruses that are infectious viruses as naked dsRNA. My laboratory also had an opportunity to discover such a virus from an important plant pathogenic fungus, Rosellinia necatrix.

The fungus is a filamentous ascomycete that causes white root rot in diverse perennial crops. A mixed viral infection was found in a hypovirulent strain of R. necatrix. Co-infecting viruses were termed Yado-kari virus 1 (YkV1) with a positive strand (+) RNA genome of approximately 6 kb and Yado-nushi virus 1 (YnV1) with a double-stranded (ds) RNA genome of approximately 9 kb. “Yado” in Japanese literally means home or house, while “kari” and “nushi” refer to “borrower” and “owner,” respectively. Herewith, we show unique mutualistic interactions representing a new virus lifestyle: a capsidless (+) RNA virus, YkV1, hosted by a dsRNA virus YnV1. According to our proposed model (Zhang et al., Nat Microbiol, 2016), YnV1 is an independent virus able to complete its replication cycle like other dsRNA viruses, while YkV1 diverts YnV1 CP as the replication sites where trans-encased YkV1 RdRp synthesizes its own RNA as if it were a dsRNA virus. Furthermore, YkV1 was shown to enhance YnV1 accumulation. Some data with site-directed mutagenesis of available infectious YkV1 cDNA supported the model. This model still needs to be further validated by biochemical analysis with purified heterocapsids. There may be similar mutualistic interactions in other fungi such as Aspergillus foetidus (Kozlakidis et al., 2013; Nerva et al., 2016; Osaki et al., 2016). We propose the family Yadokariviridae that accommodates YkV1 and these related viruses. Their evolutionary implication and comparisons with subviral molecules similar to YkV1 will be discussed in this presentation. 

Biography:

Nobuhiro SUZUKI serves as a full professor of the Institute of Plant Stress and Resources, formerly Research Institute for Bioresouces at Okayama University and Editors for the plant and fungal virus section of Virus Research, Frontiers in Virology and the Journal of General Plant Pathology. He has been Guest Editors to PLoS Pathogens, PNAS, and mBio, and Board Members of Virology and Journal of Virology. Currently he is working on virus/host interactions using several different pathosystems involving fungal and plant viruses. Prior to coming to Kurashiki, Okayama Prefecture, he was a visiting fellow of the Center for Agricultural Biotechnology at the University of Maryland Biotechnology Institute for four years (1997-2001) to study molecular biology of hypoviruses in the laboratory of Professor Donald L. Nuss. Before visiting UMBI, he served as an assistant professor and a lecturer of the Biotechnology Institute at the Akita Prefectural College of Agriculture for 11 years (1988-1998) where he conducted a project on molecular characterization of rice dwarf phytoreovirus, a member of the family Reoviridae. He received awards from the Japanese Phytopathological Society of Japan and Japanese Society for Virology for his outstanding achievements in plant virology. Dr Suzuki received his M. S. (1985) in phytopathology and Ph. D (1989) in virology from Tohoku University in Sendai, Japan.

Title: Azole resistance in Aspergillus fumigatus - clinical isolate screening, culture selection, and genetics

Abstract:

Azole resistance in Aspergillus fumigatus - clinical isolate screening, culture selection, and genetics

In the United States, invasive aspergillosis (IA), an invasive fungal infection of the upper respiratory tract of immune compromised patients, is usually caused by Aspergilus fumigatus, while Aspergillus flavus represents only a small fraction of IA cases. In some countries A. flavus is the most frequent IA pathogen. Recently, we described a novel, highly virulent, aggressively invasive, and drug resistant IA pathogen, Aspergillus tanneri. In mouse models of IA and in a non-vertebrate insect model we observed distinct virulence profiles for the three Aspergillus species. Comparative genomics showed that A. tanneri had a larger genome than the other Aspergilli, encoding nearly 1900 more genes than A. fumigatus. A. tanneri genes had numerous orthologs in the other two genomes, however an abundance of genes are unique to A. tanneri. Among the unique genes were multiple gene clusters that encode biosynthetic genes for the synthesis of secondary metabolites, suggesting that A. tanneri produces novel secondary metabolites that may play a role in its high level of pathogenicity. Analysis of genes commonly associated with drug resistance showed that A. tanneri carried CYP51A mutations resulting in or contributing to azole resistance. An important issue featured in the A. tanneri fatal cases and in clinical management of IA is the general limitation in treatment options - only four classes of drugs are available in the context of ever-increasing drug resistance. Drugs used to treat fungal infections target only two differences between human and fungal cells: the presence of ergosterol in fungal cell membranes and of glucans in their cell walls. There remains an urgent need to understand the broad range of genes encoded in the genomes of fungal pathogens that participate in the resistance to the clinically therapeutic antifungals employed in treating infections. To identify novel mechanisms that mediate azole resistance in A. fumigatus, we used whole genome sequencing of in vitro selected azole-resistant strains. To further refine the most significant mechanisms required for resistance, we developed a genetic-sexual system that enables the analysis of complex traits in A. fumigatus and revealed that at least 6 mechanisms for azole resistance exist in this organism. These include mutations in the target protein, CYP51A, and in an additional co-target HMG CoA reductase. The results from this study identify novel drug targets in A. fumigatus and also show that next-generation sequencing coupled with classical genetics experiments is a powerful way to identify genes involved in complex traits.

Biography:

Dr. William Nierman is the Director of the Infectious Disease Program at the J. Craig Venter Institute (JCVI). He is also a Professor the George Washington University School of Medicine and has taught Human Genetics at The Johns Hopkins University. He received his BS degree from the US Naval Academy and his PhD degree from the University of California, Berkeley. Dr. Nierman has broad experience in microbial pathogen genomics. His research focus is the genomic and functional analysis of two the levels of pathogen interaction with the human host, that caused by severe acute disease-causing bacterial pathogens, and that caused by fungi that can cause disease only in an immune-system-compromised host. Burkholderia mallei and Burkholderia pseudomallei are severe bacterial pathogens that cause difficult to diagnose but very life threatening diseases, glanders and melioidosis. At the other end of the pathogenicity scale are Aspergillus and Penicillium fungal pathogens which cause invasive or systemic disease in immune compromised or immune suppressed human hosts. Management of the disease in both classes of infections is becoming increasingly compromised by the rapid evolution of drug resistance in the pathogens. Both groups of organisms pose serious public health issues in both developed and in developing countries.

Title: Next-Generation Sequencing for Diagnosis and Surveillance of Emerging Infections

Abstract:

Next-Generation Sequencing for Diagnosis and Surveillance of Emerging Infections

Next-generation sequencing (NGS) technologies are powerful approaches for diagnosis and surveillance of emerging infections. Unbiased metagenomic NGS can detect the full spectrum of pathogens - viral, bacterial, fungal, or parasite - in clinical samples without the use of targeted primers or probes. Gene expression (transcriptome) profiling using NGS can facilitate the identification for host response biomarkers that may have diagnostic and prognostic utility. New technologies such as nanopore sequencing on a USB-sized platform can enable real-time sequencing analysis in field settings for management and diagnosis of outbreaks, such as Ebola outbreaks in Africa. Here we will discuss development and implementation of NGS approaches to addressing emerging infections in the United States and globally, including Lyme disease, enterovirus D68, chikungunya virus, and Ebola virus. Learning Objectives • To understand the principles and approach of metagenomics next-generation sequencing for unbiased detection of emerging pathogens • To understand how gene expression profiling of infectious diseases can facilitate the identification of diagnostic biomarkers • To understand clinical and public applications of NGS for emerging infections, including Lyme disease, enterovirus D68, chikungunya virus, Ebola virus.

Biography:

Dr. Charles Chiu, M.D./Ph.D., is an Assistant Professor in Laboratory Medicine and Medicine, Infectious Diseases at the University of California, San Francisco. He is also the Director of UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC) at China Basin and Associate Director of the UCSF Clinical Microbiology Laboratory. Charles is an expert in the emerging field of viral metagenomics, and his research is focused on the development of microarray and deep sequencing technologies for viral pathogen discovery and clinical diagnostics. He is also the principal investigator on an R01 grant from the NIH on blood bank pathogen screening, California Discovery, UC-MEXUS, and National Research Fund for Tickborne Diseases (NRFTD) grants on the microbial epidemiology of encephalitis, diarrhea, and Lyme disease, a QB3 Rogers Family Foundation Award in translational diagnostics, and a UCSF-Abbott Viral Discovery Award. Charles has more than 30 patents and peer-reviewed publications in scientific journals and ongoing collaborations with research groups and public health agencies worldwide, including Abbott Diagnostics, Inc., Global Viral Forecasting, the United States CDC, the American Red Cross, and the Texas Biomedical Research Institute.

Title: Reduction of acrylamide levels in cooked food by using asparaginase extracted from thermophilic fungi

Abstract:

Reduction of acrylamide levels in cooked food by using asparaginase extracted from thermophilic fungi

It is presently more than a long time about ten years since the Swedish Food Authority and the University of Stockholm affirmed the presence of the suspected cancer causing agent acrylamide in a variety of heated foods. Especially foods containing amino acid and sugar. It has adverse effects on human health and is proven to be neurotoxic, genotoxic, carcinogenic, and toxic to reproductive system. Acrylamide is formed from the reaction between asparagine and reducing sugars this process called Maillard reaction. The use of asparaginase extracted from thermophilic fungi to convert asparagine to aspartic acid may provide a means to reduce acrylamide formation, while keeping up sensory quality and Physical properties as texture, flavor and color.  Asparaginase has become a powerful tool for acrylamide mitigation in the food industry. With the success of commercial products, it is likely that asparaginase will be used more and more.

Biography:

Mohamed soud researcher at enzymology and fungal biotechnology lab. Official Spokesman for the international scientific conference at Zagazig University. Member of the American society of microbiology. Master study at faculty of Science at Zagazig University creative writer for (elm3ml) on social media.

Title: Screening for anticancer-compounds producing endophytes inhabiting Egyptian medicinal plants, and metabolic engineering of their biosynthetic machineries

Abstract:

Screening for anticancer-compounds producing endophytes inhabiting Egyptian medicinal plants, and metabolic engineering of their biosynthetic machineries.

Unfortunately, the lower yield of bioactive metabolites is the challenge for its higher accessibility, thus, searching for alternative sources with promising producing potency is the prospective. Endophytic fungi are the potential repertoire for bioactive metabolites, thus exploring the bioactive compounds with anticancer activity was objective. 48 fungal isolates were recovered from the tested medicinal plants in Egypt, at the Enzymology and Fungal Biotechnology Lab, Zagazig University, and their potency to produce compounds with anticancer activity has been assessed using the TLC, HPLC and PCR genome mining. The chemical identity of the compounds was verified by HPLC, NMR, FTIR and LC–MS analyses as alkaloid EFBL with potential activity towards various tumor cell lines. Aspergillus fumigatus was the potent alkaloid EFBL producer as revealed from the chromatographic analyses and PCR of molecular markers. Alkaloid EFBL from A. fumigatus displayed a strong antiproliferative activity against HepG-2 and MCF-7 as revealed from the IC50 values 94.88 and 165.94 μg/ml, respectively. The productivity of Alkaloid EFBL from A. fumigatus was optimized by surface response methodology with Plackett-Burman and Faced Centered Central Composite. With the Plackett-Burman design, the yield of Alkaloid EFBL by its original media (potato dextrose broth) was higher than the Nutrition factorial design one. This is the first report exploring the feasibility of endophytic fungi for Alkaloid EFBL producing potency that could be a novel platform for industrial production.

Biography:

I have completed BSc from Zagazig University. And an advanced diploma from Suez Canal University.  I am working on a master thesis in Enzymology and Fungal Biotechnology lab (EFBL) at Zagazig University. The objective of my work is screening for the presence of an anticancer compound in endophytic fungi isolated from some Egyptians medical plants and evaluate its productivity. My first paper is in the reference step. I hope to get the acceptance as soon as possible, the second is in progress. I am the team leader of EFBL which is a promising lab, we  interested in studying cancer research. We are focusing on extracting compounds and enzymes with a powerful antiproliferative activity against cancer. Many researches have been done in this field under the supervision of Prof. Dr. Ashraf Sabry.