Life Sciences Commons^™

Mechanical Test Methods For Assessing Porcine Carotid And Uterine Artery Burst Pressure Following Ex Vivo Ultrasonic Ligature Seal And Transection, Carissa M. Krane, Margaret Pinnell, Courtney Gardner, Mercedes Thompson, James Coleman, Robert Wilkens

Robert J. Wilkens

A test method was developed to identify those variables important for assessing the performance of ultrasonic surgical devices in ex vivo ligature sealing of porcine carotid and uterine arteries. Ruggedness testing using a small sample size in pilot experiments was conducted using a newly developed test method in an effort to assess the usefulness of this methodology and to identify test variables that might warrant further testing. The development of this test method included the use of a custom-designed prototypic tension device for load-controlled ex vivo vessel stretching during saline perfusion and subsequent seal and transection of porcine arteries with …

Molecular Evolution Of Dengue Type 2 Virus In Thailand, Rebeca Rico-Hesse, Lisa M. Harrison, Ananda Nisalak, David W. Vaughn, Siripen Kalayanarooj, Sharone Green, Alan L. Rothman, Francis A. Ennis

Sharone Green

Dengue is a mosquito-borne viral infection that in recent years has become a major international public health concern. Dengue hemorrhagic fever (DHF), first recognized in Southeast Asia in the 1950s, is today a leading cause of childhood death in many countries. The pathogenesis of this illness is poorly understood, mainly because there are no laboratory or animal models of disease. We have studied the genetic relationships of dengue viruses of serotype 2, one of four antigenically distinct dengue virus groups, to determine if viruses obtained from cases of less severe dengue fever (DF) have distinct evolutionary origins from those obtained …

Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti

Catherine Putonti

Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with …

Draft Genome For A Urinary Isolate Of Lactobacillus Crispatus, Travis Kyle Price, Majed Shaheen, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe

Catherine Putonti

While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms.

Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, Alan J. Wolfe

Catherine Putonti

A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N50 of 109,831 bp.

Genome Sequences And Annotation Of Two Urinary Isolates Of E. Coli, Travis Kyle Price, Arya Mehtash, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe

Catherine Putonti

The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not …

Freshwater Metaviromics And Bacteriophages: A Current Assessment Of The State Of The Art In Relation To Bioinformatic Challenges, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins, Catherine Putonti

Catherine Putonti

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with …

Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti

Catherine Putonti

Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from …

18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti

Catherine Putonti

Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Catherine Putonti

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …

Suggested Reference Ranges In Clinical Chemistry For Apparently Healthy Males And Females Of Pakistan., Ayesha Molla, Mohammad Khurshid, William T. Manser, Rukhsana Lalani, Anis Alam, Zubaida Mohammad

Mohammad Khurshid

Abstract Seven hundred and eighty six apparently healthy males (418) and females (368) aged 0-69 years were randomly selected for estimation of reference ranges of 24 serum analytes at the clinical chemistry laboratory of The Ago Khon University Hospital (AKUH). Of the total study samples, 56% (439/786) were in the poediatric age group (0-14 years) and 44% (347/786) in the adult (1 5_60 years) group. Beckman Astra Ideal Autoanalyzer was used for all the estimations. Moon and standard deviations (SD) were calculated for each of the age groups. Reference ranges were calculated following standard methods of the International Federation of …

Frequency Of Hereditary Thrombophilia: An Akuh Experience., Safoorah Khalid, Raihan Sajid, Salman Adil, Mohammad Khurshid

Mohammad Khurshid

Abstract Objective: To determine the frequency of various causes of hereditary thrombophilia at a referral laboratory and the age and gender distribution. Methods: This is a descriptive study incorporating a retrospective analysis of requests for thrombophilia screening sent to Clinical laboratory, Aga Khan University Hospital from November 1995 to May 2002.Patients were screened for hereditary causes of thrombophilia including Protein C, Protein S, antithrombin III, Factor V Leiden and homocysteine. Frequency of each disorder; and age and sex distribution was determined. Results: All the patients suspected clinically for thrombophilia were screened. Of the 2825 patients, 70 were diagnosed to have …

Does Red Blood Cell Distribution Width (Rdw) Improve Evaluation Of Microcytic Anaemias?, Muhammad Sajjad Baqar, Mohammad Khurshid, A Molla

Mohammad Khurshid

Abstract The red cell distribution width (RDW) is an index of the variation in red cells size (anisocytosis). A study was conducted to examine the validity of using RDW in improving classification of microcytic anaemias. A total of 300 blood samples collected from a patient population aged 3 months to 55 years who were referred for haemoglobin electrophoresis were examined at The Aga Khan University Hospital (AKUH). On complete blood count, initially 200 patients (66.6%) were found to have hypochromic microcytic anaemia. Following haemoglobin electrophoresis 41% (821200) patients were diagnosed to have thalassemia minor and 59% (1181200) had hypochromic microcytic …

Chromosomal Abnormalities In Primary Myelodysplastic Syndrome, Anila Rashid, Mohammad Khurshid, Usman Shaikh, Salman Adil

Mohammad Khurshid

Objective: To determine the frequency of cytogenetic abnormalities in patients diagnosed as primary myelodysplastic syndrome (MDS) using conventional karyotyping. Study Design: Case series. Place and Duration of Study: The Clinical Laboratory, The Aga Khan University Hospital, Karachi, between January 2006 - June 2012. Methodology: Patients of all ages and either gender who fulfilled WHO criteria for MDS were included. Cytogenetic analysis was conducted at the time of diagnosis. Patients who had secondary MDS were excluded from analysis. Chromosome identification and karyotype description was done according to the International System for Chromosome Nomenclature (ISCN, 1995) and described as frequency percentage. Results: …

Dengue Virus Ns2b/Ns3 Protease Inhibitors Exploiting The Prime Side, Kuan-Hung Lin, Akbar Ali, Linah Rusere, Djade I. Soumana, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

The mosquito-transmitted dengue virus (DENV) infects millions of people in tropical and subtropical regions. Maturation of DENV particles requires proper cleavage of the viral polyprotein, including processing of 8 of the 13 substrate cleavage sites by dengue virus NS2B/NS3 protease. With no available direct-acting antiviral targeting DENV, NS2/NS3 protease is a promising target for inhibitor design. Current design efforts focus on the nonprime side of the DENV protease active site, resulting in highly hydrophilic and nonspecific scaffolds. However, the prime side also significantly modulates DENV protease binding affinity, as revealed by engineering the binding loop of aprotinin, a small protein …

Freshwater Fungal Infections, Dennis J. Baumgardner

Dennis J. Baumgardner, MD

Fungal infections as a result of freshwater exposure or trauma are fortunately rare. Etiologic agents are varied, but commonly include filamentous fungi and Candida. This narrative review describes various sources of potential freshwater fungal exposure and the diseases that may result, including fungal keratitis, acute otitis externa and tinea pedis, as well as rare deep soft tissue or bone infections and pulmonary or central nervous system infections following traumatic freshwater exposure during natural disasters or near-drowning episodes. Fungal etiology should be suspected in appropriate scenarios when bacterial cultures or molecular tests are normal or when the infection worsens or fails …

Symptomatic Surgically Treated Non-Neoplastic Cysts Of The Central Nervous System: A Clinicopathological Study From Pakistan, Nasir Ud Din, Huma Arshad, Zubair Ahmad, Sheema H Hasan, Mohammad Ehsan Bar

Zubair Ahmad

Objective: To report clinicopathologic features of symptomatic surgically removed non-neoplastic cysts of the central nervous system (CNS). Study Design: Case series. Place and Duration of Study: The Aga Khan University Hospital, Karachi, from 2003 to 2012. Methodology: All non-neoplastic CNS cysts reported during the study period were retrieved and reviewed. Age, gender, location, histologic type and clinical features were noted. Results: A total of 124 cysts were diagnosed in the study period. These included 44 epidermoid cysts (mean age 30.5 ± 13.8 years), 35 colloid cysts (mean age 31 ± 13.2 years), 32 arachnoid cysts (mean age 24.8 ± 20.2 …

In-House Daily Consensus Conference: An Important Quality Control/Quality Assurance Activity--Experience At A Major Referral Center., Amna Khurshid, Zubair Ahmad, Asim Qureshi

Zubair Ahmad

Background:For every practicing histopathologist, improvement of diagnostic accuracy is an important objective. Personal consults are an important component of quality control (QC)/quality assurance (QA) in our Section of Histopathology. In addition, the College of American Pathologists recommends a daily in-house consensus conference, which is a prospective system by which all difficult and problematic cases are reviewed and discussed and signed out by consensus. Design: In-house consensus conference is held daily using a multi-headed microscope. This collegial session is run by the seniormost consultant in the section and is attended by all histopathology consultants and residents. The consultants and residents …

Histological Pattern Of Ovarian Neoplasma., Zubair Ahmad, Naila Kayani, Sheema H. Hasan, Suhail Muzaffar, Muhammad Shafiq Gill

Zubair Ahmad

Abstract Objective: To see the morphological pattern of benign and malignant ovarian neoplasms. Method: Retrospective study of all consecutive cases of ovarian neoplasms diagnosed at Aga Khan University Hospital between 1st January 1993 and 30th September 1998. Setting: The Section of Histopathology, AKUH, Karachi. Observation: Of 855 ovarian tumours 506 (59.18%) were benign and 349(40.81%) malignant. Surface epithelial - stromal tumours comprised 63.50% of all tumours. Benign cystic teratoma was the commonest benign tumour (35.17% of all benign tumours) and serous cystadenocarcinoma was the commonest malignant tumour (33.33% of all malignant tumours). Mucinous cystadenocarcinomas are more common in our population …

Frequency Of Hereditary Thrombophilia: An Akuh Experience., Safoorah Khalid, Raihan Sajid, Salman Adil, Mohammad Khurshid

Salman Naseem Adil

Abstract Objective: To determine the frequency of various causes of hereditary thrombophilia at a referral laboratory and the age and gender distribution. Methods: This is a descriptive study incorporating a retrospective analysis of requests for thrombophilia screening sent to Clinical laboratory, Aga Khan University Hospital from November 1995 to May 2002.Patients were screened for hereditary causes of thrombophilia including Protein C, Protein S, antithrombin III, Factor V Leiden and homocysteine. Frequency of each disorder; and age and sex distribution was determined. Results: All the patients suspected clinically for thrombophilia were screened. Of the 2825 patients, 70 were diagnosed to have …

Emergence Of Carbapenem Resistant Gram Negative And Vancomycin Resistant Gram Positive Organisms In Bacteremic Isolates Of Febrile Neutropenic Patients: A Descriptive Study., Seema Irfan, Faiza Idrees, Vikram Mehraj, Faizah Habib, Salman Adil, Rumina Hasan

Salman Naseem Adil

Background:This study was conducted to evaluate drug resistance amongst bacteremic isolates of febrile neutropenic Patients with particular emphasis on emergence of carbapenem resistant Gram negative bacteria and vancomycin resistant Enterococcus species. Methods: A descriptive study was performed by reviewing the blood culture reports from febrile neutropenic Patients during the two study periods i.e., 1999-00 and 2001-06. Blood cultures were performed using BACTEC 9240 automated system. Isolates were identified and antibiotic sensitivities were done using standard microbiological procedures. Results: Seven twenty six febrile neutropenic Patients were admitted during the study period. A total of 5840 blood cultures were received, off these …

Chromosomal Abnormalities In Primary Myelodysplastic Syndrome, Anila Rashid, Mohammad Khurshid, Usman Shaikh, Salman Adil

Salman Naseem Adil

Objective: To determine the frequency of cytogenetic abnormalities in patients diagnosed as primary myelodysplastic syndrome (MDS) using conventional karyotyping. Study Design: Case series. Place and Duration of Study: The Clinical Laboratory, The Aga Khan University Hospital, Karachi, between January 2006 - June 2012. Methodology: Patients of all ages and either gender who fulfilled WHO criteria for MDS were included. Cytogenetic analysis was conducted at the time of diagnosis. Patients who had secondary MDS were excluded from analysis. Chromosome identification and karyotype description was done according to the International System for Chromosome Nomenclature (ISCN, 1995) and described as frequency percentage. Results: …

Complete Genome Sequence Of Spiroplasma Citri Strain R8-A2 T , Causal Agent Of Stubborn Disease In Citrus Species, Robert E. Davis, Jonathan Shao, Yan Zhao, Gail E. Gasparich, Brady J. Gaynor, Nicole Donofrio

Gail Gasparich

In Vitro Studies On Metabolism Of Salvinorin A, Lukasz M. Kutrzeba, Vardan T. Karamyan, Robert C. Speth, John S. Williamson, Jordan K. Zjawiony

John S. Williamson

Microbial transformation of natural products is a well established model for mammalian metabolism. Salvinorin A, a diterpenoid isolated from the hallucinogenic mint Salvia divinorum Epling & Játiva-M (Lamiaceae), is a potent non-nitrogenous κ-opioid receptor agonist. The metabolism of salvinorin A has still not yet been well established. Thirty fungal species were screened for the ability to metabolize salvinorin A. We observed that salvinorin A undergoes fast hydrolysis of the acetate group at carbon atom C2, resulting in formation of the pharmacologically inactive product, salvinorin B. Ex vivo experiments were also performed using organelle fractions isolated from rat liver and brain. …

Flagellar Formation In C-Ring-Defective Mutants By Overproduction Of Flii, The Atpase Specific For Flagellar Type Iii Secretion, Manabu Konishi, Masaomi Kanbe, Jonathan L. Mcmurry, Shin-Ichi Aizawa

Jonathan McMurry

The flagellar cytoplasmic ring (C ring), which consists of three proteins, FliG, FliM, and FliN, is located on the cytoplasmic side of the flagellum. The C ring is a multifunctional structure necessary for flagellar protein secretion, torque generation, and switching of the rotational direction of the motor. The deletion of any one of the fliG, fliM, and fliN genes results in a Fla - phenotype. Here, we show that the overproduction of the flagellum-specific ATPase FliI overcomes the inability of basal bodies with partial C-ring structures to produce complete flagella. Flagella made upon FliI overproduction were paralyzed, indicating that an …

Environmental Implications Of Francisella Tularensis Biofilms, Jeffrey J. Margolis '00

Jeffrey Margolis

Francisella tularensis survives in one of the widest environmental ranges of any pathogen. Numerous mammals and arthropod vectors are infected by this highly virulent organism. How this zoonotic pathogen persists outside of its many hosts remains unexplored. We aimed to examine how F. tularensis interacts with environmental surfaces, and hypothesized that biofilm formation may enable survival of this organism in nature. By understanding the role these surface-attached bacterial communities play in F. tularensis ecology, we hope to gain insight into the mechanisms of environmental persistence and transmission of this pathogen.

We identify chitin as a potential non-host niche for F. …

Genomic Plasticity And Rapid Host Switching Can Promote The Evolution Of Generalism: A Case Study In The Zoonotic Pathogen Campylobacter, Dan J. Woodcock, Peter Krusche, Norval J. C. Strachan, Ken J. Forbes, Frederick M. Cohan, Guillaume Meric, Samuel K. Sheppard

Frederick M. Cohan