Microbiology Commons^™

การคัดแยกยีสต์เพื่อผลิตน้ำมันจากไฮโดรไลเสตของใบอ้อย, รัชนา พระนิมิตร

Chulalongkorn University Theses and Dissertations (Chula ETD)

คัดแยกยีสต์จำนวน 106 ไอโซเลตจากจังหวัดระนอง ประเทศไทย คัดกรองยีสต์ที่สะสมน้ำมันภายในเซลล์สูงโดยการย้อมเซลล์ด้วยสีไนล์เรด (Nile red) พบว่ายีสต์จำนวน 24 ไอโซเลต มีหยดน้ำมันภายในเซลล์ มากกว่า 50% ของปริมาตรเซลล์ และเป็นยีสต์ที่สามารถใช้น้ำตาลไซโลสเป็นแหล่งคาร์บอนเพื่อการเจริญได้ 16 ไอโซเลต น้ำตาลไซโลสเป็นองค์ประกอบหลักในไฮโดรไลเสตใบอ้อยเช่นเดียวกับน้ำตาลกลูโคส ผลการวิเคราะห์ปริมาณน้ำมันที่สะสมภายในเซลล์ของยีสต์16 ไอโซเลตที่คัดกรองได้ โดยเลี้ยงในอาหารที่มีปริมาณกลูโคส 5% (น้ำหนัก/ปริมาตร) แต่มีปริมาณไนโตรเจนจำกัด พบว่าเป็นยีสต์โอลิจินัส (ยีสต์ซึ่งสะสมน้ำมันภายในเซลล์มากกว่า 20% น้ำหนัก/น้ำหนัก ของน้ำหนักแห้งเซลล์) จำนวน 5 สายพันธุ์ คือ Cryptococcus humicola NG2, Trichosporon mycotoxinivorans MG11-12.3, Cyberlindnera subsufficiens NG8.2, Rhodotorula mucilaginosa MG11-2.3 และ Yarrowia sp. NG17 ผลการวิจัยนี้นับเป็นการรายงานว่ายีสต์ T. mycotoxinivorans และ C. subsufficiens เป็นยีสต์โอลิจินัสเป็นครั้งแรก แต่เนื่องจากยีสต์ T. mycotoxinivorans เป็นยีสต์ก่อโรคจึงไม่นำมาศึกษาต่อ นำยีสต์ 4 สายพันธุ์ที่คัดกรองได้ มาผลิตน้ำมันโดยเลี้ยงในไฮโดรไลเสตใบอ้อยซึ่งมีปริมาณน้ำตาลกลูโคสและน้ำตาลไซโลสเท่ากับ 18.7 กรัม/ลิตร และ 19.1 กรัม/ลิตร โดยการปรับสภาพด้วยกรดซัลฟูริคเจือจางและย่อยต่อด้วยเอนไซม์เซลลูเลสทางการค้า ผลการเปรียบเทียบปริมาณน้ำมันที่ผลิตได้ในไฮโดรไลเสตใบอ้อยที่ผ่านการปรับด่างเกินเพื่อกำจัดสารยับยั้งการเจริญของยีสต์ และไม่ผ่านการปรับด่างเกิน พบว่ายีสต์ทั้ง 4 สายพันธุ์ผลิตน้ำมันในไฮโดรไลเสตใบอ้อยที่ไม่ผ่านการปรับด่างเกินได้มากกว่า โดย Yarrowia NG17 ผลิตน้ำมันสูงที่สุดเท่ากับ 10.15% น้ำหนัก/น้ำหนักของน้ำหนักเซลล์แห้ง ผลการหาภาวะที่เหมาะสมสำหรับการผลิตน้ำมันของ Yarrowia NG17 โดยแปรผันการเติมและไม่เติม แคลเซียมคลอไรด์ (CaCl2) โพแทสเซียมไดไฮโดรเจนฟอสเฟต (KH2PO4) และแมกนีเซียมซัลเฟต (MgSO4) ในไฮโดรไลเสตใบอ้อย พบว่ายีสต์ Yarrowia NG17 มีอัตราการผลิตน้ำมันสูงที่สุดเท่ากับ 1.52 กรัม/ลิตร/วัน เมื่อเจริญในไฮโดรไลเสตใบอ้อยที่ไม่เติมสารอาหารใดๆที่ทดสอบ ผลการแปรผันค่าพีเอชเริ่มต้นช่วง …

Discovery And Characterization Of Bile Acid And Steroid Metabolism Pathways In Gut-Associated Microbes, Spencer Harris

Theses and Dissertations

The human gut microbiome is a complex microbial ecosystem residing in the lumen of our gastrointestinal tract. The type and amounts of microbes present in this ecosystem varies based on numerous factors, including host genetics, diet, and environmental factors. The human gut microbiome plays an important role in normal host physiological functions, including providing energy to colonocytes in the form of short-chain fatty acids. However, gut microbial metabolites have also been associated with numerous disease states. Current tools for analyzing the gut microbiome, such as high-throughput sequencing techniques, are limited in their predictive ability. Additionally, “-omic” approaches of studying the …

Hub Proteins, Paralogs, And Unknown Proteins In Bacterial Interaction Networks, Neha Sakhawalkar

Theses and Dissertations

Proteins are the functional units of cells. However, a major portion of the proteome does not have a known functional annotation. This dissertation explores protein -protein interactions, involving these uncharacterized or unknown function proteins. Initially, protein – protein interactions were tested and analyzed for paralogous proteins in Escherichia coli. To expand this concept further and to get an overview, protein – protein interactions were analyzed using ‘comparative interactomics’ for four pathogenic bacterial species including Escherichia coli, Yersinia pestis, Vibrio cholerae and Staphylococcus aureus. This approach was used to study unknown function protein pairs as well as to …

In Search Of A Function For An Uncharacterized Conserved Protein In Streptococcus Sanguinis Sk36, Ayana Scott-Elliston

Theses and Dissertations

With the number of fully sequenced bacterial genomes increasing in the past 7 years, it has been discovered that a large percentage of the putative protein coding genes have no known function. This lack of knowledge leaves scientists with an incomplete understanding of bacteria. In this study, conserved hypothetical protein mutants from Streptococcus sanguinis SK36 were screened on solid media with various environmental conditions. From these screens, the candidate protein, SSA_2372, displayed a sensitivity to acidic conditions. Its homolog in Bacillus subtilis 168, BSU00030, also displayed a sensitivity to pH conditions at its acid tolerance extremes unlike its other homolog …

Frequency Of Colistin And Fosfomycin Resistance In Carbapenem-Resistant Enterobacteriaceae From A Tertiary Care Hospital In Karachi, Salima Qamar, Najma Shaheen, Sadia Shakoor, Joveria Farooqi, Kauser Jabeen, Rumina Hasan

Department of Pathology and Laboratory Medicine

Introduction:
Management of infections with carbapenem-resistant Enterobacteriaceae (CRE) is challenging. In recent times, agents such as colistin and fosfomycin have been used in combination with other antibiotics to treat such infections. In this study, we aim to seek frequency of colistin and fosfomycin resistance in CRE from Pakistan.
Methods:
This study was conducted at clinical laboratories, Aga Khan University Hospital. In total, 251 CRE were included in the study. Colistin minimum inhibitory concentrations (MICs) were performed using broth microdilution (BMD) method and VITEK 2 system, whereas fosfomycin susceptibility was performed using Kirby-Bauer method. MIC50 and MIC90 were calculated for colistin …

Rapid Detection Of In Vitro Antituberculous Drug Resistance Among Smear-Positive Respiratory Samples Using Microcolony Detection-Based Direct Drug Susceptibility Testing Method, Irim Iftikhar, Seema Irfan, Joveria Farooqi, Zahida Azizullah, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background: With the rise in multidrug-resistant tuberculosis, there is a search for newer techniques that will rapidly detect drug-resistant Mycobacterium tuberculosis. Although molecular techniques can detect resistance, culture is still considered gold standard, especially in resource-limited settings where quick, cheap, and easy techniques are needed. The aim of the study was to evaluate microcolony method thin layer agar (TLA) for quick detection of resistance against the first- and second-line antituberculous drugs in clinical isolates. This was a cross-sectional study performed at Aga Khan University Hospital.
Material and Methods: A total of 87 Z-N stain smear-positive pulmonary samples were received and …

Antifungal Genome Mining And Genetics In Filamentous Actinomycete Bacteria Isolated From Local Soils, Jacob Alex, Kevin Lou, Bilal Makhdoom

Undergraduate Research Symposium Posters

Actinomycetes are gram positive, filamentous bacteria that produce useful antibiotics, antitumor agents, and agricultural products. A series of enrichments were undertaken to isolate actinomycetes from local soils, varying enrichment media, antibacterials, and soil treatments (including heat and CaCO3). Isolates were characterized by 16S rDNA sequencing, phenotypic and morphological observations, and antibiotic production. The genetic tractability of select isolates was analyzed using a panel of integrating vectors derived from ɸC31, ɸBT1, and OzzyJ phage using intergeneric conjugation. Further, a semi-degenerate multiplex PCR assay to detect ɸBT1 genomic integrants was designed and tested for the first time. Finally, PCR screens were used …

Eukaryotic Microbes, Principally Fungi And Labyrinthulomycetes, Dominate Biomass On Bathypelagic Marine Snow, Alexander B. Bochdansky, Melissa A. Clouse, Gerhard J. Herndl

OES Faculty Publications

In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto μm filters from similar to 1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant …

Season, But Not Symbiont State, Drives Microbiome Structure In The Temperate Coral Astrangia Poculata., Koty H. Sharp, Zoe A. Pratte, Allison H. Kerwin

Arts & Sciences Faculty Publications

BACKGROUND: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome …

Using Rainbow Trout Cell Lines As A Model For Understanding The Innate Anti-Fv3 Immune Response, Graeme Robert Jones Lisser

Theses and Dissertations (Comprehensive)

Ranavirus infections are on the rise and have been implicated in numerous species die-offs across the globe. Frog virus 3 (FV3) is the type-species of the genus, yet the immune mechanisms governing susceptibility remain poorly understood. Arguably the most important immune response to infection is the type I interferon (IFN) response. Type I IFNs trigger an “antiviral state” in host cells via the production of numerous interferon-stimulated genes (ISGs) that act to inhibit virus replication in various way, including the induction of apoptosis. Apoptosis is an important antiviral defense mechanism to limit virus replication within infected cells. This study employed …

Controlling Brochothrix Thermosphacta As A Spoilage Risk Using In Package Atmospheric Cold Plasma, Apurva Patange, Daniela Boehm, Carmen Bueno-Ferrer, Patrick J. Cullen, Paula Bourke

Articles

Brochothrix thermosphacta is a predominant spoilage microorganism in meat and its control in processing environments is important to maintain meat product quality. Atmospheric cold plasma is of interest for control of pathogenic and spoilage microorganisms in foods. This study ascertained the potential of dielectric barrier discharge atmospheric cold plasma (DBD-ACP) for control of B. thermosphacta in response to key parameters such as treatment time, voltage level, interactions with media composition and post treatment storage conditions. Challenge populations were evaluated as suspensions in PBS, as biofilms in meat model medium and surface attached on raw lamb chops under MAP.

ACP treatment …

Navigating Human Cytomegalovirus (Hcmv) Envelopment And Egress, William Longeway Close

Wayne State University Dissertations

Human cytomegalovirus (HCMV) is a ubiquitous viral pathogen. In individuals with fully functioning and mature immune systems, HCMV is associated with mild symptoms prior to establishing latency. In individuals with naïve or compromised immune systems, HCMV is capable of causing severe organ damage. HCMV is the leading infectious cause of congenital birth defects and a major non-genetic cause of hearing loss. Unfortunately, antiviral treatment options lack diversity due to limited knowledge of virion replication. If HCMV replication were better understood, new antiviral treatments could be developed.

In this work, we describe the development and implementation of new tools to study …

Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands …

Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He

Computer Science Faculty Publications

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …

Phenotypic Low-Level Isoniazid Resistance As A Marker To Predict Ethionamide Resistance In Mycobacterium Tuberculosis, Salima Qamar, Joveria Q. Farooqi, Kausar Jabeen, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background: Tuberculosis is one of the most prevalent diseases in Pakistan. Pakistan has the highest burden of MDR-TB in the Eastern Mediterranean region. Ethionamide is an anti-tuberculous drug frequently used to treat MDR-TB. Its drug susceptibility testing is not easily available in resource limited settings. Since it acts on the same target protein as isoniazid (inhA protein encoded by inhA gene), we sought to find out if phenotypic isoniazid resistance can be a marker of ethionamide resistance.
Materials and Methods: This was a retrospective observational study conducted at the Aga Khan University hospital section of microbiology. Data was retrieved between …

Utility Of Peripheral Film Findings And Its Correlation With Automated Analyzer - An Audit From Tertiary Care Hospital, Sidra Asad, Imran Ahmed, Natasha Ali

Department of Pathology and Laboratory Medicine

Background and Objective: With the advent of automated hematology analyzer, the use of traditional microscopy of blood film has become limited. The objective of our study was to determine the percentage of peripheral blood smear review in our institution in the era of automation and to identify reasons of manual review.
Materials and Methods: This was a prospective audit from January 1, 2015, to January 15, 2015. Consecutive complete blood count (CBC) samples and peripheral smear requests made up the sample size. All age groups and genders were included. CBCs were performed on Sysmex XE-5000. The variables to be analyzed …

Papillary Craniopharyngioma: A Clinicopathologic Study Of A Rare Entity From A Major Tertiary Care Center In Pakistan, Muhammad Usman Tariq, Nasir Ud Din, Zubair Ahmad, Wasim Memon

Department of Pathology and Laboratory Medicine

Background: Papillary craniopharyngioma (PCP) are uncommon variants of craniopharyngiomas (CP), which are benign epithelial neoplasms of the sellar and suprasellar region. Histologically, PCPs are typically composed of well-differentiated stratified squamous epithelium; however, focal variations are not uncommon. A distinction from other lesions of the region, despite being difficult to achieve due to the overlapping radiological and clinical features, is important for adequate treatment to be administered.
Objective: Our aim was to study the clinical and histological features of PCP with emphasis on features that are helpful in its distinction from other lesions that are similar in appearance.
Materials and Methods: …

Hplc-Uv Quantitation Of Folate Synthesized By Rickettsia Endosymbiot Ixodes Pacificus (Reip), Junyan Chen

Cal Poly Humboldt theses and projects

Ticks are the most important vector of many infectious diseases in the United States. Understanding the nature of the relationship between Rickettsia endosymbiont Ixodes pacificus (REIP) and Exudes pacificus will help develop strategies for the control of tick-borne diseases, such as Lyme disease, and Rocky Mountain spotted fever. Folate, also known as vitamin B9, is a necessary vitamin for tick survival, and plays a central role in one-carbon metabolism in cells. Folate exist as a large family of structurally related forms that transfer one-carbon groups among biomolecules that are important to cell growth, differentiation, and survival. In Dr. Zheng’s lab, …

Readiness For Antimicrobial Resistance (Amr) Surveillance In Pakistan; A Model For Laboratory Strengthening, Dania Khalid Saeed, Rumina Hasan, Mahwish Naim, Afia Zafar, Erum Khan, Kauser Jabeen, Seema Irfan, Imran Ahmed Haq, Mohammad Zeeshan, Zabin Wajidali, Joveria Farooqi, Sadia Shakoor, Abdul Chagla, Jason Roy

Department of Pathology and Laboratory Medicine

Background: Limited capacity of laboratories for antimicrobial susceptibility testing (AST) presents a critical diagnostic bottleneck in resource limited countries. This paper aims to identify such gaps and to explore whether laboratory networks could contribute towards improving AST in low resource settings.
Methods: A self-assessment tool to assess antimicrobial susceptibility testing capacity was administered as a pre-workshop activity to participants from 30 microbiology laboratories in 3 cities in Pakistan. Data from public and private laboratories was analyzed and capacity of each scored in percentage terms. Laboratories from Karachi were invited to join a support network. A cohort of five laboratories that …

A Rare Case Of Erythema Elevatum Diutinum Presenting As Diffuse Neuropathy, G H. Nguyen, E L. Guo, D Norris

Faculty, Staff and Students Publications

No abstract provided.

Media Optimization, Scale-Up And Repeated Fed-Batch Operations For The Production Of 1,3-Propanediol From Glycerol By Halanaerobium Hydrogeniformans, Shivani Kalia

Masters Theses

"The development of renewable energy sources, such as biofuels, is of great interest in today's world due to depletion of fossil fuels and concerns about climate change. The production of the main by-product, crude glycerol, in biodiesel production presents an opportunity for the production of industrially relevant commodities. Crude glycerol in biodiesel waste is highly impure and possesses high salt concentrations and alkalinity, making it infeasible for direct industrial utilization. Moreover, current glycerol purification methods are highly cost-intensive, necessitating a search for cost-effective approaches that are feasible to employ. Genome data analysis of Halanaerobium hydrogeniformans, revealed the metabolic capability …

Investigating The Sources And Dynamics Of Escherichia Coli In A Missouri Ozarks Watershed, Kaleb Bassett

Masters Theses

"Escherichia coli, an intestinal bacterium, can serve as an indication of the presence of pathogenic microorganisms in water systems used by humans for recreation, agriculture, or drinking water. Many aquatic systems in the United States exceed the E. coli standard, set by the Environmental Protection Agency, for safe drinking water and recreational use. During 2016, a water sampling program was established in the Mill Creek watershed, a rural watershed located near the city of Newburg in Phelps County, Missouri. Water samples were collected before, during, and after storms throughout the year to examine the relationship between E. coli …

A Systems Biology Approach For Predicting Essential Genes And Deciphering Their Dynamics Under Stress In Streptococcus Sanguinis, Fadi El-Rami

Theses and Dissertations

Infectious diseases are the top leading cause of death worldwide. Identifying essential genes, genes indispensable for survival, has been proven indispensable in defining new therapeutic targets against pathogens, major elements of the minimal set genome to be harnessed in synthetic biology, and determinants of evolutionary relationships of phylogenetically distant species. Thus, essentiality studies promise valuable revenues that can decipher much of biological complexities.

Taking advantage of the available microbial sequences and the essentiality studies conducted in various microbial models, we proposed a framework for the prediction of essential genes based on our experimentally verified knowledge of the pathways involved in …

Contribution Of A Class Ii Ribonucleotide Reductase To The Manganese Dependence Of Streptococcus Sanguinis, John L. Smith

Theses and Dissertations

Manganese-deficient Streptococcus sanguinis mutants exhibit a dramatic decrease in virulence for infective endocarditis and in aerobic growth in manganese-limited media. Loss of activity of a manganese-dependent, oxygen-dependent ribonucleotide reductase (RNR) could explain the decrease in virulence. When the genes encoding this RNR are deleted, there is no growth of the mutant in aerobic broth culture or in an animal model. Testing the contribution of the aerobic RNR to the phenotype of a manganese transporter mutant, a heterologous class II RNR from Lactobacillus leichmannii called NrdJ that requires B₁₂ rather than manganese as a cofactor was previously introduced into an …

Effects Of Fertilizer And Shade Management On Nitrogen Mineralization, Nitrifying Microbial Abundance And Nitrogen-Fixing Capacity Of Erythrina Poeppigiana In Coffee (Coffea Arabica) Agroforestry Systems In Costa Rica, Stuart E. Barker Iii

College of Graduate Studies: Theses & Dissertations

Worldwide chemical fertilizer use has increased by four times during the last 50 years. Conventional agricultural systems have a high nitrifying nature, resulting in a loss of nearly 70% of overall nitrogen (N) fertilizer inputs, an estimated economic loss of $81 billion. Over application of fertilizer is rampant in tropical developing nations in Central America, where coffee is major crop. Agroforestry offers ecologically sustainable land management strategies that promote the provision of ecosystem services such as, protection of biodiversity, climate change mitigation, and water and soil regulation. When legume trees are incorporated as the shade tree in coffee production, direct …