A comprehensive study of a 29-capsid AAV library in a non-human primate central nervous systemOleksandr Kondratov - 2021
AbstractNon-human primates (NHPs) are a preferred animal model for
optimizing adeno-associated virus (AAV)-mediated CNS gene
delivery protocols before clinical trials. In spite of its inherent
appeal, it is challenging to compare different serotypes, deliv-
ery routes, and disease indications in a well-powered, compre-
hensive, multigroup NHP experiment. Here, a multiplex
barcode recombinant AAV (rAAV) vector-tracing strategy
has been applied to a systemic analysis of 29 distinct, wild-
type (WT), AAV natural isolates and engineered capsids in
the CNS of eight macaques. The report describes distribution
of each capsid in 15 areas of the macaques’ CNS after intrapar-
enchymal (putamen) injection, or cerebrospinal fluid (CSF)-
mediated administration routes (intracisternal, intrathecal,
or intracerebroventricular). To trace the vector biodistribution
(viral DNA) and targeted tissues transduction (viral mRNA) of
each capsid in each of the analyzed CNS areas, quantitative
next-generation sequencing analysis, assisted by the digital-
droplet PCR technology, was used. The report describes the
most efficient AAV capsid variants targeting specific CNS areas
after each route of administration using the direct side-by-side
comparison of WT AAV isolates and a new generation of ratio-
nally designed capsids. The newly developed bioinformatics
and visualization algorithms, applicable to the comparative
analysis of several mammalian brain models, have been devel-
oped and made available in the public domain.
Transient upregulation of IRF1 during exit from naive pluripotency confers viral protectionMerrit Romeike - 2022
AbstractStem cells intrinsically express a subset of genes which are normally associated with interferon stimulation and the innate immune response. However, the expression of these interferon-stimulated genes (ISG) in stem cells is independent from external stimuli such as viral infection. Here, we show that the interferon regulatory factor 1, Irf1, is directly controlled by the murine formative pluripotency gene regulatory network and transiently upregulated during the transition from naive to formative pluripotency. IRF1 binds to regulatory regions of a conserved set of ISGs and is required for their faithful expression upon exit from naive pluripotency. We show that in the absence of IRF1, cells exiting the naive pluripotent stem cell state are more susceptible to viral infection. Irf1 therefore acts as a link between the formative pluripotency network, regulation of innate immunity genes, and defense against viral infections during formative pluripotency.
Six de novo assemblies from pathogenic and non-pathogenic strains of Fusarium oxysporum f. sp. niveumJames C. Fulton - 2021
AbstractFusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon), is a soilborne disease which significantly limits yield in watermelon (Citrullus lanatus) and occasionally causes the loss of an entire year’s harvest. Reference-quality de novo genomic assemblies of pathogenic and non-pathogenic strains were generated using a combination of next-generation and third-generation sequencing technologies. Chromosomal-level genomes were produced with representatives from all Fon races facilitating comparative genomic analysis and the identification of chromosomal structural variation . Syntenic analysis between isolates allowed differentiation of the core and lineage-specific portions of their genomes. This research will support future efforts to refine the scientific understanding of the molecular and genetic factors underpinning the Fon host range, develop diagnostic assays for each of the four races, and decipher the evolutionary history of race 3.
Six de novo assemblies from pathogenic and non-pathogenic strains of Fusarium oxysporum f. sp. niveumJames C. Fulton - 2021
AbstractFusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon), is a soilborne disease which significantly limits yield in watermelon (Citrullus lanatus) and occasionally causes the loss of an entire year’s harvest. Reference-quality de novo genomic assemblies of pathogenic and non-pathogenic strains were generated using a combination of next-generation and third-generation sequencing technologies. Chromosomal-level genomes were produced with representatives from all Fon races facilitating comparative genomic analysis and the identification of chromosomal structural variation . Syntenic analysis between isolates allowed differentiation of the core and lineage-specific portions of their genomes. This research will support future efforts to refine the scientific understanding of the molecular and genetic factors underpinning the Fon host range, develop diagnostic assays for each of the four races, and decipher the evolutionary history of race 3.
Whole Genome Sequence based Capsular Typing and Antimicrobial Resistance Prediction of Group B Streptococcal Isolates from Colonized Pregnant Women in NigeriaMienye Bob-Manuel - 2018
AbstractBackground: Streptococcus agalactiae (Group B Streptococcus, GBS) is one of the major bacterial
pathogens responsible for neonatal sepsis. Whole genome sequencing has, in recent years, emerged as a
reliable tool for capsular typing and antimicrobial resistance prediction. This study characterized vaginal
and rectal isolates of Group B Streptococcus obtained from pregnant women in Port Harcourt, Nigeria
using a whole-genome sequence-based approach.
Results: Capsular types Ia, Ib, II, III, IV and V were detected among the 43 isolates sequenced. Twelve
sequence types (STs) were identied, with ST19 (n=9, 27.3%) and ST486 (n=5, 15.2%) the most frequent
among non-duplicated isolates. Of the alpha-like proteins (alp) identied, Alp1 was the most prevalent in
11 (33.3%) isolates. Macrolide and lincosamide resistance determinants were present in 15 (45.5%)
isolates; ermB was detected in 1 (3%) and ermTR in 7 (21.2%) isolates. The lnu gene, was detected in 6
(18.2%) and mef was identied in 3 (9.1%) isolates. Resistance of GBS to erythromycin and clindamycin
was found to be 30.3% and 24.2%, respectively. All isolates were resistant to tetracycline with only the
tetM gene identied. Fluoroquinolone-resistance conferring substitutions in gyrA + parC were detected in
9 (27.3%) isolates and chloramphenicol resistance was predicted in 11 (33.3%).
Conclusion: The data available from the whole genome sequencing of these isolates offers a small but
insightful description of common serotypes and resistance features within colonizing GBS in Nigeria
A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated EnvironmentNatalia Carrillo Gaeto - 2020
AbstractThe use of heavy metals in economic and social development can create an accumulation of toxic waste in the environment. High concentrations of heavy metals can damage human and animal health, lead to the development of antibiotic resistance, and possibly change in bovine microbiota. It is important to investigate the influence of heavy metals in food systems to determine potential harmful effects environmental heavy metal contamination on human health. Because of a mining dam rupture, 43 million cubic meters of iron ore waste flowed into the Doce river basin surrounding Mariana City, Brazil, in 2015. Following this environmental disaster, we investigated the consequences of long-term exposure to contaminated drinking water on the microbiome and resistome of dairy cattle. We identified bacterial antimicrobial resistance (AMR) genes in the feces, rumen fluid, and nasopharynx of 16 dairy cattle 4 years after the environmental disaster. Cattle had been continuously exposed to heavy metal contaminated water until sample collection (A) and compared them to analogous samples from 16 dairy cattle in an unaffected farm, 356 km away (B). The microbiome and resistome of farm A and farm B differed in many aspects. The distribution of genes present in the cattle’s nasopharynx, rumen, and feces conferring AMR was highly heterogeneous, and most genes were present in only a few samples. The relative abundance and prevalence (presence/absence) of AMR genes were higher in farm A than in farm B. Samples from farm A had a higher prevalence (presence) of genes conferring resistance to multiple drugs, metals, biocides, and multi-compound resistance. Fecal samples had a higher relative abundance of AMR genes, followed by rumen fluid samples, and the nasopharynx had the lowest relative abundance of AMR genes detected. Metagenome functional annotation suggested that selective pressures of heavy metal exposure potentially skewed pathway diversity toward fewer, more specialized functions. This is the first study that evaluates the consequences of a Brazilian environmental accident with mining ore dam failure in the microbiome of dairy cows. Our findings suggest that the long-term persistence of heavy metals in the environment may result in differences in the microbiota and enrichment of antimicrobial-resistant bacteria. Our results also suggest that AMR genes are most readily detected in fecal samples compared to rumen and nasopharyngeal samples which had relatively lower bacterial read counts. Since heavy metal contamination has an effect on the animal microbiome, environmental management is warranted to protect the food system from hazardous consequences.
Genomic Insights and Ecological Adaptations of Deep-Subsurface and Near Subsurface Thermococcus IsolatesLilja Caitlin Strang - 2020
AbstractMembers of the Archaeal genus Thermococcus are sulfur-dependent hyperthermophiles found in hydrothermal vents throughout the world. Previous analysis of a Thermococcus culture collection containing isolates from the Juan de Fuca Ridge, Gorda Ridge, and South East Pacific Rise using amplified fragment length polymorphism analysis and multilocus sequence typing revealed a distinct clade of Thermococcus isolated from the 1996 megaplume event at Gorda
Ridge, indicating that they originated from a deep-subsurface habitat. The aim of this study was to elucidate the functional adaptations that allow for the survival of the Gorda Ridge clade in a deepsubsurface habitat as compared to representative Thermococcus isolates from shallow subsurface environments. This was accomplished through a pangenomic analysis of representative isolates in this clade and others from this culture collection. The Gorda Ridge megaplume group was enriched for genes relating to DNA repair and stabilization including a predicted endonuclease distantly related to Archaeal Holliday junction resolvase, DNA mismatch repair ATPase mutS, CRISPR/Cas elements, and dnaK (hsp70). The group was also enriched for ABC-type branched-chain amino acid (BCAA) transport system, enzymes for the Shikimate pathway for aromatic amino acid
synthesis, as well as TupA for tungstate transport. These findings suggest that Thermococcus inhabiting deep-subsurface fluid reservoir require the added ability to prevent and repair damage to their DNA, presumably due to the energy demands of DNA replication. The enrichment in BCAA and tungstate transporters may indicate the use of an amino acid catabolism pathway followed by fermentation catalyzed by the tungstopterin containing enzymes aldehyde ferredoxin oxidoreductase and alcohol dehydrogenase, suggesting a preference for peptides over carbohydrates as an energy source in the deep-subsurface.
Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elementsHenry Thomas - 2020
AbstractMany genes are regulated by multiple enhancers that often simultaneously activate their target gene. Yet, how individual enhancers collaborate to activate transcription is not well understood. Here, we dissect the functions and interdependencies of five enhancer elements that form a previously identified enhancer cluster and activate the Fgf5 locus during exit from naïve murine pluripotency. Four elements are located downstream of the Fgf5 gene and form a super-enhancer. Each of these elements contributes to Fgf5 induction at a distinct time point of differentiation. The fifth element is located in the first intron of the Fgf5 gene and contributes to Fgf5 expression at every time point by amplifying overall Fgf5 expression levels. This amplifier element strongly accumulates paused RNA Polymerase II but does not give rise to a mature Fgf5 mRNA. By transplanting the amplifier to a different genomic position, we demonstrate that it enriches for high levels of paused RNA Polymerase II autonomously. Based on our data, we propose a model for a mechanism by which RNA Polymerase II accumulation at a novel type of enhancer element, the amplifier, contributes to enhancer collaboration.
