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Tag: Jessica Kissinger

Jessica Kissinger named 2025 University Professor

Donna Huber on March 4, 2025

photo of Jessica KissingerCTEGD faculty member Jessica Kissinger earned the distinction of University Professor, a title bestowed on those who have made a significant impact on the university in addition to fulfilling their regular academic responsibilities.

An integral voice on the university’s 2020 and 2025 strategic planning committees, Kissinger has championed initiatives designed to move UGA into the ranks of the world’s elite research universities. The recommendations developed by Kissinger and her colleagues helped lay the groundwork for strategic faculty hiring initiatives that have attracted leading researchers and scholars to UGA and new programs that have increased graduate student enrollment and support for graduate students.

“In a nutshell, I am a strategist and problem solver with a vision, who has worked hard to make UGA better for all,” she said.

Kissinger’s impact on the university includes her service as a member of the university’s Goldwater Selection Committee since 2015, and as a standing member of the Committee for Fellowships and Awards in the Franklin College of Arts and Sciences. She has also provided valuable guidance to senior leadership as a member of the Provost’s Working Group on Centers and Institutes and the Digital Infrastructure Development Committee.

Kissinger is a founding member of UGA’s Institute of Bioinformatics, a group dedicated to facilitating interdisciplinary research in bioinformatics and computational biology and its applications. Under her leadership as director from 2011-2019, the institute grew to include faculty from four colleges and more than 45 graduate students. The institute unifies the exploration of genomics and bioinformatics on campus and provides graduate training in a setting that melds the two disciplines unlike many bioinformatics programs in the U.S.

The success of the Georgia Advanced Computing Resource Center, a high-performance computing and networking infrastructure for UGA researchers, can also be linked to Kissinger’s leadership. She was part of a team that established UGA’s first centralized high-performance computing cluster, and she was a tireless advocate for expanding these resources for researchers across campus. Additionally, she encouraged the GACRC to provide centralized storage and she supported the early adoption of graphical processing units, or GPUs, the driving computational power behind artificial intelligence computing.

Kissinger has been recognized many times for research and leadership. She is a recipient of the Creative Research Medal, the Lamar Dodd Creative Research Award, the Faculty Excellence in Diversity Leadership Award and the Richard F. Reiff Internationalization Award, all presented by UGA. She is a fellow of the American Association for the Advancement of Science and the American Society for Tropical Medicine and Hygiene. Most recently, she was awarded a Fulbright U.S. Scholar award to teach and conduct research at Makerere University in Uganda.

University Professors receive a permanent salary increase of $10,000 and a yearly academic support of $5,000. Nominations from the deans of UGA’s schools and colleges are reviewed by a committee, which makes a recommendation to the provost.

Full story is available at https://news.uga.edu/carmichael-kissinger-named-2025-university-professors/

Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole-Genome Oxford Nanopore Sequencing

Donna Huber on February 28, 2025

Circos plot illustrating a synteny comparison between the reference S. aureus ATCC-29213 genome sequence and pre- and post-amplification genome assemblies.

Multiple displacement amplification (MDA) outperforms conventional PCR in long fragment and whole-genome amplification, making it attractive to couple MDA with long-read sequencing of samples with limited quantities of DNA to obtain improved genome assemblies. Here, we explore the efficacy and limits of MDA for efficient low-cost genome sequence assembly using Oxford Nanopore Technologies (ONTs) rapid library preparations and minION sequencing. We successfully generated almost complete genome sequences for all organisms examined, including Gram-positive (Staphylococcus aureus, Enterococcus faecium) and Gram-negative (Escherichia coli) prokaryotes and one challenging eukaryotic pathogen (Cryptosporidium spp) representing a broad spectrum of critical infectious disease pathogens. High-quality data from those samples were generated starting with only 0.025 ng of total DNA. Controlled sheared DNA samples exhibited a distinct pattern of size increase after MDA, which may be associated with the amplification of long, low-abundance fragments present in the assay, as well as generating concatemeric sequences during amplification. To address concatemers, we developed a computational pipeline (CADECT: Concatemer Detection Tool) to identify and remove putative concatemeric sequences. This study highlights the efficacy of MDA in generating high-quality genome assemblies from limited amounts of input DNA. Also, the CADECT pipeline effectively mitigated the impact of concatemeric sequences, enabling the assembly of contiguous sequences even in cases where the input genomic DNA was degraded. These results have significant implications for the study of organisms that are challenging to culture in vitro, such as Cryptosporidium, and for expediting critical results in clinical settings with limited quantities of available genomic DNA.

Fiifi Agyabeng-Dadzie, Megan S Beaudry, Alex Deyanov, Haley Slanis, Minh Q Duong, Randi Turner, Asis Khan, Cesar A Arias, Jessica C Kissinger, Travis C Glenn, Rodrigo de Paula Baptista. Mol Ecol Resour. 2025 Feb 28:e14094. doi: 10.1111/1755-0998.14094.

A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis

Donna Huber on December 18, 2024

DNA synteny plot mapping the contigs of CmUKMEL1 to the eight chromosome-level contigs of CmTU1867. Jupiterplot between the previous CmUKMEL1 genome sequence and the new CmTU1867 genome sequence. Ribbons are colored with respect to the reference CmTU1867 chromosome.

 

Cryptosporidium spp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants, immunosuppressed populations and many animals. Although most human Cryptosporidium infections are caused by C. parvum and C. hominis, there are several other human-infecting species including C. meleagridis, which are commonly observed in developing countries. Here, we annotated a hybrid long-read Oxford Nanopore Technologies and short-read Illumina genome assembly for C. meleagridis (CmTU1867) with DNA generated using multiple displacement amplification. The assembly was then compared to the previous C. meleagridis (CmUKMEL1) assembly and annotation and a recent telomere-to-telomere C. parvum genome assembly. The chromosome-level assembly is 9.2 Mb with a contig N50 of 1.1 Mb. Annotation revealed 3,919 protein-encoding genes. A BUSCO analysis indicates a completeness of 96.6%. The new annotation contains 166 additional protein-encoding genes and reveals high synteny to C. parvum IOWA II (CpBGF). The new C. meleagridis genome assembly is nearly gap-free and provides a valuable new resource for the Cryptosporidium community and future studies on evolution and host-specificity.

Lasya R Penumarthi, Rodrigo P Baptista, Megan S Beaudry, Travis C Glenn, Jessica C Kissinger. Sci Data. 2024 Dec 18;11(1):1388. doi: 10.1038/s41597-024-04235-7.

The first Cryptosporidium meeting: a concerted effort to fight cryptosporidiosis

Donna Huber on June 7, 2024

The first biennial Cryptosporidium meeting was held on 10–12 March 2024 in Philadelphia, PA, USA. The organizers, Dr Boris Striepen and Dr Christopher Hunter, welcomed more than 130 attendees to the University of Pennsylvania School of Veterinary Medicine. The meeting opened with a panel discussion featuring a diverse group of researchers, clinicians, non-profit and industry partners who offered unique insights into the problems of cryptosporidiosis. Seven research themed sessions (‘Impact of cryptosporidiosis’, ‘Population genetics’, ‘Genomics and new tools for research and translation’, ‘Parasite cell and developmental biology’, ‘Host–parasite interaction and immunity’, ‘Cryptosporidium metabolism and emerging targets’, and ‘Immunity to Cryptosporidium and vaccines’), as well as two poster sessions completed the meeting. A farewell dinner in the domed Asia gallery of the Penn Museum was organized for all the attendees. The meeting was graciously supported by the Bill and Melinda Gates Foundation, the Burroughs Wellcome Fund, Novartis, Zoetis, and several centers and departments of the University of Pennsylvania. In this TrendsTalk, we invited the session chairs to highlight the innovative research and discoveries presented during the inaugural Cryptosporidium meeting.

Wes van Voorhis, Joyce Siwila, Jessica C Kissinger, Natalia Bayona Vásquez, Guy Robinson, Rodrigo Baptista, Asis Khan, Amandine Guérin, Yi-Wei Chang, Zannatun Noor, N Bishara Marzook, Sumiti Vinayak, Sam Arnold, Chelsea Marie, Robert K M Choy, Mattie C Pawlowic, Rajiv S Jumani. Trends Parasitol. 2024 Jun;40(6):431-438. doi: 10.1016/j.pt.2024.04.005

Cryptosporidium Genomics – Current Understanding, Advances, and Applications

Donna Huber on May 31, 2024

Genome assembly impacts annotation quality, gene family member estimates, and genetic variation analyses.
Genome assembly impacts annotation quality, gene family member estimates, and genetic variation analyses.

Purpose of review: Here we highlight the significant contribution that genomics-based approaches have had on the field of Cryptosporidium research and the insights these approaches have generated into Cryptosporidium biology and transmission.

Recent findings: There are advances in genomics, genetic manipulation, gene expression, and single-cell technologies. New and better genome sequences have revealed variable sub-telomeric gene families and genes under selection. RNA expression data now include single-cell and post-infection time points. These data have provided insights into the Cryptosporidium life cycle and host-pathogen interactions. Antisense and ncRNA transcripts are abundant. The critical role of the dsRNA virus is becoming apparent.

Summary: The community’s ability to identify genomic targets in the abundant, yet still lacking, collection of genomic data, combined with their increased ability to assess function via gene knock-out, is revolutionizing the field. Advances in the detection of virulence genes, surveillance, population genomics, recombination studies, and epigenetics are upon us.

Fiifi Agyabeng-Dadzie, Rui Xiao, Jessica C Kissinger. Curr Trop Med Rep. 2024;11(2):92-103. doi: 10.1007/s40475-024-00318-y.

 

Temporal gene expression during asexual development of the apicomplexan Sarcocystis neurona

Donna Huber on May 29, 2024

Fig 1 Progression of the schizont stages during the intracellular development of Sarcocystis neurona expressing yellow fluorescent protein. Post-invasion, the merozoites convert into schizonts that progressively develop into early-, mid-, and late-schizonts while undergoing a form of asexual reproduction called endopolygeny. In the final step in endopolygeny, the mature schizont forms 64 haploid merozoites fully equipped to egress and invade new host cells. S. neurona, Sn; DAPI-stained host cell nuclei, HCN.
Fig 1 Progression of the schizont stages during the intracellular development of Sarcocystis neurona expressing yellow fluorescent protein. Post-invasion, the merozoites convert into schizonts that progressively develop into early-, mid-, and late-schizonts while undergoing a form of asexual reproduction called endopolygeny. In the final step in endopolygeny, the mature schizont forms 64 haploid merozoites fully equipped to egress and invade new host cells. S. neurona, Sn; DAPI-stained host cell nuclei, HCN.

Asexual replication in the apicomplexan Sarcocystis neurona involves two main developmental stages: the motile extracellular merozoite and the sessile intracellular schizont. Merozoites invade host cells and transform into schizonts that undergo replication via endopolygeny to form multiple (64) daughter merozoites that are invasive to new host cells. Given that the capabilities of the merozoite vary significantly from the schizont, the patterns of transcript levels throughout the asexual lifecycle were determined and compared in this study. RNA-Seq data were generated from extracellular merozoites and four intracellular schizont development time points. Of the 6,938 genes annotated in the S. neurona genome, 6,784 were identified in the transcriptome. Of these, 4,111 genes exhibited significant differential expression between the merozoite and at least one schizont development time point. Transcript levels were significantly higher for 2,338 genes in the merozoite and 1,773 genes in the schizont stages. Included in this list were genes encoding the secretory pathogenesis determinants (SPDs), which encompass the surface antigen and SAG-related sequence (SAG/SRS) and the secretory organelle proteins of the invasive zoite stage (micronemes, rhoptries, and dense granules). As anticipated, many of the S. neurona SPD gene transcripts were abundant in merozoites. However, several SPD transcripts were elevated in intracellular schizonts, suggesting roles unrelated to host cell invasion and the initial establishment of the intracellular niche. The hypothetical genes that are potentially unique to the genus Sarcocystis are of particular interest. Their conserved expression patterns are instructive for future investigations into the possible functions of these putative Sarcocystis-unique genes.

Importance: The genus Sarcocystis is an expansive clade within the Apicomplexa, with the species S. neurona being an important cause of neurological disease in horses. Research to decipher the biology of S. neurona and its host-pathogen interactions can be enhanced by gene expression data. This study has identified conserved apicomplexan orthologs in S. neurona, putative Sarcocystis-unique genes, and gene transcripts abundant in the merozoite and schizont stages. Importantly, we have identified distinct clusters of genes with transcript levels peaking during different intracellular schizont development time points, reflecting active gene expression changes across endopolygeny. Each cluster also has subsets of transcripts with unknown functions, and investigation of these seemingly Sarcocystis-unique transcripts will provide insights into the interesting biology of this parasite genus.

Sriveny Dangoudoubiyam, Jamie K Norris, Sivaranjani Namasivayam, Rodrigo de Paula Baptista, Naila Cannes do Nascimento, Joseph Camp, Christopher L Schardl, Jessica C Kissinger, Daniel K Howe. mSphere. 2024 May 29:e0011124. doi: 10.1128/msphere.00111-24.

Two CTEGD faculty members receive Creative Research Awards

Donna Huber on April 4, 2024

Jessica Kissinger and Dennis Kyle received the Lamar Dodd Creative Research Award during UGA’s Honors Week. The award recognizes established investigators whose overall scholarly body of work has had a major impact on the field of study and has established the investigator’s international reputation as a leader in the field.

Jessica Kissinger, Distinguished Research Professor in the Franklin College of Arts and Sciences’ genetics department and former director of the UGA Institute of Bioinformatics, has focused her interdisciplinary career on the question of how parasites evolve. She has been a driving force behind the groundbreaking effort to create and maintain novel bioinformatics databases covering omics data for hundreds of dangerous pathogens. The Eukaryotic Pathogen, Vector, and Host Informatics Resources knowledgebase (VEuPathDB.org) is an integrated, centralized resource for data mining on more than 500 organisms. Databases searches are free, permitting researchers to gain insights into and test hypotheses that may pave the way for new approaches to treating or preventing diseases such as malaria and Cryptosporidium (a waterborne parasite). Kissinger has used the databases and other bioinformatics tools to make remarkable discoveries.

Dennis E. Kyle, professor of cellular biology and infectious diseases in the Franklin College of Arts and Sciences and the College of Veterinary Medicine, is one of the top parasitologists in the world. Kyle serves as director of the Center for Tropical and Emerging Global Diseases, and some of his most recent work focuses on discovery of new drugs that eliminate dormant vivax malaria that can linger in the liver. His group has discovered new drug series that target the dormant liver stages and is moving these novel therapeutics through preclinical studies. He also works on Naegleria fowleri, a rare but deadly parasite known as “brain-eating amoebae.” More than 97% of people infected with these amoebae die within two weeks. Kyle has conducted research into that pathogen, leading to effective repurposed drugs and the first rapid, sensitive diagnostic method.

 

First appeared in 2024 Research Awards

What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species

Donna Huber on March 26, 2024

New data in FungiDB since FungiDB Release 37.
New data in FungiDB since FungiDB Release 37.

 

FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.

Evelina Y Basenko, Achchuthan Shanmugasundram, Ulrike Böhme, David Starns, Paul A Wilkinson, Helen R Davison, Kathryn Crouch, Gareth Maslen, Omar S Harb, Beatrice Amos, Mary Ann McDowell, Jessica C Kissinger, David S Roos, Andrew Jones. Genetics. 2024 Mar 26:iyae035. doi: 10.1093/genetics/iyae035

Genomic and virulence analysis of in vitro cultured Cryptosporidium parvum

Donna Huber on February 28, 2024

Fig 1. Diagramatic section through the hollow fiber bioreactor.
Fig 1. Diagramatic section through the hollow fiber bioreactor.

 

Recent advances in the in vitro cultivation of Cryptosporidium parvum using hollow fiber bioreactor technology (HFB) have permitted continuous growth of parasites that complete all life cycle stages. The method provides access to all stages of the parasite and provides a method for non-animal production of oocysts for use in clinical trials. Here we examined the effect of long-term (>20 months) in vitro culture on virulence-factors, genome conservation, and in vivo pathogenicity of the host by in vitro cultured parasites. We find low-level sequence variation that is consistent with that observed in calf-passaged parasites. Further using a calf model infection, oocysts obtained from the HFB caused diarrhea of the same volume, duration and oocyst shedding intensity as in vivo passaged parasites.

Nigel Yarlett, Mary Morada, Deborah A Schaefer, Kevin Ackman, Elizabeth Carranza, Rodrigo de Paula Baptista, Michael W Riggs, Jessica Kissinger. PLoS Pathog. 2024 Feb 28;20(2):e1011992. doi: 10.1371/journal.ppat.1011992.

Genetic crosses within and between species of Cryptosporidium

Donna Huber on January 2, 2024

Figure 1 PheRS can be used as a selection marker for stable transgenesis.
PheRS can be used as a selection marker for stable transgenesis.

Parasites and their hosts are engaged in reciprocal coevolution that balances competing mechanisms of virulence, resistance, and evasion. This often leads to host specificity, but genomic reassortment between different strains can enable parasites to jump host barriers and conquer new niches. In the apicomplexan parasite Cryptosporidium, genetic exchange has been hypothesized to play a prominent role in adaptation to humans. The sexual lifecycle of the parasite provides a potential mechanism for such exchange; however, the boundaries of Cryptosporidium sex are currently undefined. To explore this experimentally, we established a model for genetic crosses. Drug resistance was engineered using a mutated phenylalanyl tRNA synthetase gene and marking strains with this and the previously used Neo transgene enabled selection of recombinant progeny. This is highly efficient, and genomic recombination is evident and can be continuously monitored in real time by drug resistance, flow cytometry, and PCR mapping. Using this approach, multiple loci can now be modified with ease. We demonstrate that essential genes can be ablated by crossing a Cre recombinase driver strain with floxed strains. We further find that genetic crosses are also feasible between species. Crossing Cryptosporidium parvum, a parasite of cattle and humans, and Cryptosporidium tyzzeri a mouse parasite resulted in progeny with a recombinant genome derived from both species that continues to vigorously replicate sexually. These experiments have important fundamental and translational implications for the evolution of Cryptosporidium and open the door to reverse- and forward-genetic analysis of parasite biology and host specificity.

Sebastian Shaw, Ian S Cohn, Rodrigo P Baptista, Guoqin Xia, Bruno Melillo, Fiifi Agyabeng-Dadzie, Jessica C Kissinger, Boris Striepen. Proc Natl Acad Sci USA. 2024 Jan 2;121(1):e2313210120. doi: 10.1073/pnas.2313210120.