Biology subjects

Sloan, D.

Publications and source records attributed to Sloan, D..

6 recordsLinked to original sources

bioRxiv2026

Uracil/guanine mismatches trigger MutS HOMOLOG1-dependent mitochondrial DNA double-strand breaks in Arabidopsis

Angiosperm mitochondrial genomes exhibit exceptionally low nucleotide substitution rates, likely supported by active homologous recombination-mediated repair, while maintaining genome integrity by suppressing illegitimate recombination between imperfectly matched sequences that could otherwise cause deleterious structural rearrangements. The nuclear-encoded MutS HOMOLOG1 (MSH1) protein has been proposed to help resolve this paradox by recognizing mismatches and promoting DNA double-strand break-associated repair responses that suppress both point mutations and illegitimate recombination. However, direct experimental evidence for this proposed activity of MSH1 has been lacking. Here, we demonstrate that targeted base editing using a mitochondrial TALE-cytidine deaminase fusion (mitoTALECD) in Arabidopsis mitochondria induces deletions at the redundant gene atp6-2. These deletions phenocopy those generated by mitochondria-targeted TALEN (mitoTALEN) cleavage at the same locus. Notably, deletion events that encompass the base-editing target site were markedly reduced in msh1 mutant backgrounds, indicating that functional MSH1 promotes their formation. In vitro assays further demonstrated that recombinantly expressed MSH1 efficiently recognizes U:G mismatches derived from deoxycytidine-to-deoxyuridine deamination events and performs coordinated double incisions, thereby generating staggered dsDNA breaks with short 3' overhangs. Together, these findings provide direct experimental support for the long-postulated role of MSH1: the induction of mismatch-triggered DNA double-strand breaks. This MSH1 activity likely promotes the repair of mismatched bases and prevents illegitimate recombination by rejecting annealing between imperfect repeat sequences, thereby helping maintain the characteristic mutational stasis and recombinational dynamics of angiosperm mitochondrial genomes.

Plant Biology↗

bioRxiv2023

Securin Regulates the Spatiotemporal Dynamics of Separase

Separase is a key regulator of the metaphase to anaphase transition with multiple functions. Separase cleaves cohesin to allow chromosome segregation and localizes to vesicles to promote exocytosis in mid-anaphase. The anaphase promoting complex/cyclosome (APC/C) activates separase by ubiquitinating its inhibitory chaperone, securin, triggering its degradation. How this pathway controls the exocytic function of separase has not been investigated. During meiosis I, securin is degraded over several minutes, while separase rapidly relocalizes from kinetochore structures at the spindle and cortex to sites of action on chromosomes and vesicles at anaphase onset. The loss of cohesin coincides with the relocalization of separase to the chromosome midbivalent at anaphase onset. APC/C depletion prevents separase relocalization, while securin depletion causes precocious separase relocalization. Expression of non-degradable securin inhibits chromosome segregation, exocytosis, and separase localization to vesicles but not to the anaphase spindle. We conclude that APC/C mediated securin degradation controls separase localization. This spatiotemporal regulation will impact the effective local concentration of separase for more precise targeting of substrates in anaphase.

cell biology↗

bioRxiv2023

Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events in Gossypium Allopolyploids

A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). This latter process was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly account for autapomorphic SNPs that may lead to similar patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events. Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid Gossypium species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange. Using this new method, we find little evidence for homoeologous gene conversion in allopolyploid cottons and that only two of the forty best-supported events are shared by more than one species. We do, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species. Overall, our analyses demonstrate that homoeologous gene conversion and homoeologous exchanges are uncommon in Gossypium, affecting between zero and 24 genes per subgenome (0.0 - 0.065%) across the seven species. More generally, we highlight the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids. SIGNIFICANCE STATEMENTAllopolyploidy is a prominent process in plant diversification, involving the union of two divergent genomes in a single nucleus via interspecific hybridization and genome doubling. The merger of genomes sets in motion a variety of inter-genomic and epigenomic interactions that are thought to lead to the origin of new phenotypes. Among these is recombinational exchange between duplicated chromosomes, which can involve sequence lengths ranging from several bases to entire chromosome arms, and which can be either reciprocal or unidirectional in their effects. Here we present a new analytical framework for detecting these inter-genomic recombinational processes in allopolyploids, and demonstrate that they have been rare in a group of allopolyploid species in the cotton genus.

evolutionary biology↗

bioRxiv2020

Therapeutic activity of an inhaled potent SARS-CoV-2 neutralizing human monoclonal antibody in hamsters

SARS-CoV-2 infection results in viral burden in the upper and lower respiratory tract, enabling transmission and often leading to substantial lung pathology. Delivering the antiviral treatment directly to the lungs has the potential to improve lung bioavailability and dosing efficiency. As the SARS-CoV-2 Receptor Binding Domain (RBD) of the Spike (S) is increasingly deemed to be a clinically validated target, RBD-specific B cells were isolated from patients following SARS-CoV-2 infection to derive a panel of fully human monoclonal antibodies (hmAbs) that potently neutralize SARS-CoV-2. The most potent hmAb, 1212C2 was derived from an IgM memory B cell, has high affinity for SARS-CoV-2 RBD which enables its direct inhibition of RBD binding to ACE2. The 1212C2 hmAb exhibits in vivo prophylactic and therapeutic activity against SARS-CoV-2 in hamsters when delivered intraperitoneally, achieving a meaningful reduction in upper and lower respiratory viral burden and lung pathology. Furthermore, liquid nebulized inhale treatment of SARS-CoV-2 infected hamsters with as low as 0.6 mg/kg of inhaled dose, corresponding to approximately 0.03 mg/kg of lung deposited dose, mediated a reduction in respiratory viral burden that is below the detection limit, and mitigated lung pathology. The therapeutic efficacy achieved at an exceedingly low-dose of inhaled 1212C2 supports the rationale for local lung delivery and achieving dose-sparing benefits as compared to the conventional parenteral route of administration. Taken together, these results warrant an accelerated clinical development of 1212C2 hmAb formulated and delivered via inhalation for the prevention and treatment of SARS-CoV-2 infection.

immunology↗

bioRxiv2018

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

Genomic datasets sometimes support unconventional or conflicting phylogenetic relationships when different tree-building methods are applied. Coherent interpretations of such results are enabled by partitioning support for controversial relationships among the constituent genes of a phylogenomic dataset. For the supermatrix (= concatenation) approach, several simple methods that measure the distribution of support and conflict among loci were introduced over 15 years ago. More recently, partitioned coalescence support (PCS) was developed for phylogenetic coalescence methods that account for incomplete lineage sorting and use the summed fits of gene trees to estimate the species tree. Here, we automate computation of PCS to permit application of this index to genome-scale matrices that include hundreds of loci. Reanalyses of four phylogenomic datasets for amniotes, land plants, skinks, and angiosperms demonstrate how PCS scores can be used to: 1) compare conflicting results favored by alternative coalescence methods, 2) identify outlier gene trees that have a disproportionate influence on the resolution of contentious relationships, 3) assess the effects of missing data in species-trees analysis, and 4) clarify biases in commonly-implemented coalescence methods and support indices. We show that key phylogenomic conclusions from these analyses often hinge on just a few gene trees and that results can be driven by specific biases of a particular coalescence method and/or the extreme weight placed on gene trees with high taxon sampling. Attributing exceptionally high weight to some gene trees and very low weight to other gene trees counters the basic logic of phylogenomic coalescence analysis; even clades in species trees with high support according to commonly used indices (likelihood-ratio test, bootstrap, Bayesian local posterior probability) can be unstable to the removal of only one or two gene trees with high PCS. Computer simulations cannot adequately describe all of the contingencies and complexities of empirical genetic data. PCS scores complement simulation work by providing specific insights into a particular dataset given the assumptions of the phylogenetic coalescence method that is applied. In combination with standard measures of nodal support, PCS provides a more complete understanding of the overall genomic evidence for contested evolutionary relationships in species trees.

evolutionary biology↗

bioRxiv2017

Hepatitis B Virus Infection as a Neglected Tropical Disease

BACKGROUND BACKGROUND CURRENT STRATEGIES FOR HBV... APPLICATION OF NTD CRITERIA... RECOMMENDATIONS BASED ON NTD... CONCLUSIONS SUPPORTING INFORMATION LEGEND REFERENCES The Global Hepatitis Health Sector Strategy is aiming for elimination of viral hepatitis as a public health threat by 2030 [1], while enhanced elimination efforts for hepatitis are also promoted under the broader remit of global Sustainable Development Goals (SDGs) [2]. This is an enormous challenge for hepatitis B virus (HBV) given the estimated global burden of 260 million chronic carriers, of whom the majority are unaware of their infection [3] (Figure 1).\n\nWe here present HBV within the framework for ...

microbiology↗