Biology subjects

Baum, C.

Publications and source records attributed to Baum, C..

6 recordsLinked to original sources

bioRxiv2026

Electrical stimulation precisely reproduces naturalistic spiking activity in complete and intermixed neural populations in the primate retina

Neurostimulation technologies have the potential to restore complex brain functions by evoking naturalistic patterns of neural activity. However, faithfully mimicking the brains natural neural code in diverse neuron types remains an unsolved challenge. Here we exploit focal electrical stimulation and recording to reproduce natural visual signals at cellular resolution in two intermixed and oppositely-tuned neural populations in the isolated macaque retina. We calibrated and delivered electrical stimulation sequences to precisely mimic recorded visually-evoked responses to natural images in complete populations of ~50 ON and OFF parasol cells uniformly sampling ~4{degrees} x 4{degrees} of visual angle. Distinct and opposing visually-evoked response patterns in the two intermixed populations were closely replicated spike-by-spike in 5 retinal preparations using electrical stimulation, reproducing spike trains with 51 {+/-} 17% lower variability than repeated presentations of the same visual stimulus. Focal electrical stimulation also replicated traveling waves of neural activity in response to visual motion, and highly structured artificial response patterns. These findings demonstrate for the first time that neurostimulation can match or exceed biological signaling fidelity in large, complete and intermixed neural populations.

bioengineering↗

bioRxiv2025

Altered RNA-processing provides a mechanistic framework delineating human sex reversal associated with pathogenic variants in the RNA-helicase DHX37

Recurrent heterozygous missense variants in the highly conserved RNA-helicase DHX37, which is required for ribosome biogenesis, are a frequent cause of 46,XY sex-reversal or testis regression syndrome. How these missense variants specifically disrupt testis formation is unknown. Here, we demonstrate that mutant DHX37 proteins retain their ATPase activity and are not associated with stabilization of cellular {beta}-catenin. Transfection of DHX37 p.R674Q mutant protein in an in-vitro cellular model recapitulating human Sertoli cell formation, showed a reduced activation of pro-testis genes compared to the WT protein. The expression of a DHX37 mutant protein in in-vitro derived human Sertoli-like cells (iSLCs) was also associated with global changes in gene expression, predicted to impact basic cellular functions. To define RNA transcripts interacting with either the WT or a mutant (p.R674Q) protein, we combined HyperTRIBE and single-cell full-length RNA-sequencing approaches using iSLCs. Gene ontology analysis indicated that transcripts targeted by WT DHX37 were primarily associated with cytoskeleton organization, including cell motility and cell adhesion. However, in contrast transcripts targeted by the mutated DHX37 protein, were not only associated with cytoskeleton organization but also with protein degradation and cell death. These data provide mechanistic framework that may explain how variants in the DHX37 protein can result in 46,XY sex-reversal through altered RNA networks that are required for the formation and maintenance of the supporting cell lineages of the human testis.

cell biology↗

bioRxiv2024

Knock-down of genes essential for homoacetogenic growth using sugar inducible promoters in the thermophile Thermoanaerobacter kivui

Given recent interest in hydrogen (H2) as a medium for storing and transporting renewable energy, the ability of acetogenic bacteria to use H2 to directly fix carbon dioxide (CO2) shows great promise. Thermophilic bacteria have long been of interest as industrial strains due to their resistance to contamination. Thermoanaerobacter kivui is among the most thermophilic acetogens. It can be genetically manipulated, but as yet only in an all-or-nothing manner, either complete gene knockouts or very strong constitutive promoters leading to protein overexpression. The sugar inducible promoters characterized here provide the finer control necessary to close remaining gaps in understanding of T. kivuis energy metabolism and for controlled expression of recombinant genes of industrial relevance. Acetogenic bacteria are capable of growing on mixtures of the gasses H2, CO2, and CO using the Wood-Ljungdahl pathway, the most energy efficient CO2 fixation pathway. T. kivui is a thermophilic (Topt = 66{degrees}C) acetogen also capable of growth on sugars including glucose, mannitol, and fructose. RNA-sequencing indicated an operon of phosphotransferase import genes up-regulated on mannitol, and growth on a mixture of glucose and mannitol was diauxic. Given this evidence for sugar responsive transcriptional regulation, the promoter region from the mannitol operon, and a similar operon involved in fructose uptake were used to control expression of a thermostable {beta}-galactosidase reporter gene. Both promoters resulted in higher reporter gene activity when grown on their inducing sugar relative to glucose. The inducible promoters were used to create "knock-down" mutants of the proton-pumping Ech1 hydrogenase. Ech1 is believed to be essential because repeated attempts to knock-out the gene operon have failed. The resulting sugar-inducible Ech1 expression strains grew better on their inducing sugar than on glucose. The mannitol inducible promoter was also used to control expression of an essential gene of the Wood-Ljungdahl pathway, formyl-THF synthetase (fhs), involved in consuming the metabolic intermediate formate. When fhs repressed by growth on glucose significantly more formate accumulated in the culture medium than during growth on mannitol, clear evidence of a metabolic bottleneck under the knock-down condition. The promoters characterized here provide finer control of recombinant or native gene expression in T. kivui, while the thermostable reporter gene allows for rapid characterization of new promoters.

microbiology↗

bioRxiv2024

Random adversarial threshold search enables automated DNA screening

Custom DNA synthesis underpins modern biology, but controlled genes in the wrong hands could threaten many lives and public trust in science. In .1992, a virology-trained mass murderer tried and failed to obtain physical samples of Ebola; today, viruses can be assembled from synthetic DNA fragments. Screening orders for controlled sequences is unreliable and expensive because current similarity search algorithms yield false alarms requiring expert human review. Exact-match search can achieve perfect specificity among short known sequences by detecting subsequences unique to controlled genes, but can be trivially evaded by incorporating mutations. Here we rescue exact-match search by additionally screening for predicted functional variants of pseudo-randomly chosen subsequences that arent found in known unregulated genes. To experimentally assess robustness, we protected nine windows from the M13 bacteriophage virus, then invited a "red team" to launch up to 21,000 attacks at each window and measure the fitness of their designed mutants. We identified defensible windows from regulated pathogens, built a test database that our experiments indicate will block 99.999% of functional attacks, and verified its sensitivity against redesigned enzymes. Exact-match search with functional variant prediction offers a promising way to safeguard biotechnology by automating DNA synthesis screening. SummarySearching for exact matches to pre-computed functional variants unique to controlled genes enables sensitive, secure, and automated DNA synthesis screening.

synthetic biology↗

bioRxiv2021

Reassembling a cannon in the DNA defense arsenal: genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX systems, RM-like activities that employ host protection by DNA modification but replication arrest without evident nuclease action on unmodified phage DNA. We show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a BREX homolog. The stySA29 allele of the hybrid strain LB5000 carries a mutated version of the ancestral LT2 BREX system. Surprisingly, both a restriction and a methylation defect are observed for this lineage despite lack of mutations in brxX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations () in C-terminal domains. To avoid plasmid artifacts and potential stoichiometric interference, we chose to investigate this system in situ, replacing the mutated pglZ and brxC genes with wild type (WT). PglZ-WT supports methylation in the presence of either BrxC or BrxC-WT but not in the presence of a deletion/insertion allele, {Delta}brxC::cat. Restriction of phage L requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. Disruption of four other CDS with cat cassettes still permitted modification, suggesting that BrxC, PglZ and BrxX are principal components of the modification activity. BrxL is required for restriction only. A partial disruption of brxL disrupts transcription globally.

genetics↗

bioRxiv2021

Rapid Identification of Methylase Specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and Single Molecule, Real-Time (SMRT) Sequencing usually misses m5C. Here, we present a new method called RIMS-seq (Rapid Identification of Methylase Specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.

genomics↗