Biology subjects

Golberg, A.

Publications and source records attributed to Golberg, A..

7 recordsLinked to original sources

bioRxiv2026

Micro-C-TALE: BAC-based targeted high-resolution measurement of 3D chromatin interactions

Chromosome conformation capture methods have greatly advanced our understanding of genome organization, but obtaining high-resolution interaction maps of selected genomic regions remains costly due to the sequencing requirements. Here, we introduce Micro-C-TALE, a new chromosome conformation capture method that combines Micro-C, which uses micrococcal nuclease to improve the resolution and sensitivity of chromatin interaction measurements, and C-TALE, which uses probes generated from bacterial artificial chromosomes (BACs) for targeted enrichment. This combination enables the generation of high-resolution interaction maps without requiring custom synthesis of capture oligonucleotides. We applied Micro-C-TALE to a 214 kb region in human HAP1 cells, obtaining detailed interaction maps with approximately 5-6 million sequenced read pairs. Compared with published genome-wide Micro-C data, Micro-C-TALE yielded a higher amount of informative interactions within the targeted region despite ~550-fold lower sequencing depth. To evaluate the sensitivity of the method to fine-scale changes in genome organization, we introduced a heterozygous CTCF binding site into the targeted region using CRISPR-Cas9. Comparing Micro-C-TALE to the restriction enzyme-based C-TALE, we found Micro-C-TALE yielded a ~5-fold higher fraction of informative reads and detected novel CTCF-mediated point interactions associated with the inserted CTCF site, which were barely discernible using C-TALE. Our results demonstrate that Micro-C-TALE provides a flexible and cost-effective approach for targeted high-resolution measurement of chromatin interactions, facilitating the investigation of fine-scale genome organization and its response to genetic perturbations.

genomics↗

bioRxiv2026

CTCF-mediated cis-regulatory chromatin insulation enforces a central B-cell tolerance checkpoint

The generation of a diverse and self-tolerant B cell repertoire is essential for adaptive immunity and is achieved through V(D)J recombination. In mice, Ig{kappa} is the dominant light chain, whereas Ig{lambda} rearrangement typically occurs in response to nonproductive or autoreactive Ig{kappa} recombination, a process termed receptor editing. Recombination at the RS element deletes the Ig{kappa} constant exon, silencing the locus and enabling Ig{lambda} expression. However, the epigenetic regulatory framework that orchestrates and governs receptor editing remains poorly defined. Here, we identify a CTCF-binding insulator element (CBE) within the 3' Ig{kappa} super-enhancer (3'-SE{kappa}) that regulates receptor editing and directs the {kappa}-to-{lambda} switch required for Ig{lambda} B-cell development. Mechanistically, loss of this CBE activates an insulated enhancer within the 3'-SE{kappa}, causing aberrant V{kappa} rearrangements and altered chromatin interactions through disrupted loop extrusion dynamics. Notably, loss of this CBE in mice leads to increased autoantibody production by ten weeks of age, demonstrating that CBE-mediated chromatin architecture shapes B cell fate by constraining autoreactive potential. Collectively, our findings define a novel CTCF-dependent cis-regulatory insulation checkpoint that connects chromatin loop extrusion to antigen-driven receptor editing, thereby enforcing B-cell tolerance.

immunology↗

bioRxiv2023

Production of single-cell-protein (SCP)/poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) matrices through fermentation of archaea Haloferax mediterranei

The idea of in-situ integrating poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) sieves in a single-cell protein (SCP) represents a promising approach to enhance the properties of microbial biomass as protein alternatives. Archaea SCP/PHBV matrix was successfully produced with a concentration of 8.0 {+/-} 0.1 g L-1 and a productivity of 11.1 mg L-1 h-1 using Haloferax mediterranei. This was achieved by employing 30 g L-1 of enzymatically hydrolyzed bread waste (BW) and 200 g L-1 of red sea salt at 42 {degrees}C and with shaking at 150 rpm for 3 days. The amino acid profile of the SCP/PHBV matrix revealed a total amino acid content of 358 g kg-1, including 147 g kg-1 of essential amino acids. The protein quality of the H. mediterranei SCP/PHBV matrix was assessed using the in-vitro enzyme digestion method, indicating a high-quality protein with an in-vitro digestibility value of 0.91 and a protein digestibility-corrected amino acid score (PDCAAS) of 0.78. The PHBV component (36.0 {+/-} 6.3% w/w) in the SCP/PHBV matrix consisted of a copolymer of 3-hydroxybutyrate and 3- hydroxyvalerate in a 91:9 mol% ratio, respectively. The simultaneous production of PHBV polymeric sieves within the H. mediterranei SCP/PHBV matrix provides an alternative protein source with enhanced physicochemical and thermal properties. HighlightsO_LISCP/PHBV matrices were produced from wasted bread by archaea H. mediterranei. C_LIO_LIThis is the first report that explored the production and properties of SCP/PHBV. C_LIO_LIThe presence of PHBV in SCP affected its physicochemical and thermal properties. C_LIO_LISCP/PHBV with high-quality protein was achieved with a PDCAAS value of 0.78. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/571855v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@773447org.highwire.dtl.DTLVardef@94a96org.highwire.dtl.DTLVardef@1ffdfb8org.highwire.dtl.DTLVardef@1b8e27a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Cultivation of Ulva sp. offshore the Eastern Mediterranean Sea in experimental bioreactors: seasonal growth dynamics and environmental effects

Offshore macroalgae production could provide an alternative source of biomass for food, materials and energy. However, the offshore environment in general, and specifically the Eastern Mediterranean Sea (EMS) offshore, is a high energy and low nutrients environment and thus is challenging for macroalgae farming. This study aims to understand the effects of season, depth, and fertilization duration on growth rates and chemical composition in offshore Ulva biomass production and develop a predictive model suitable to offshore conditions. We hypothesize that offshore Ulva growth rates and chemical composition will follow a seasonal trend and that applying rapid onshore fertilization could refill nutrient storages and enable continuous offshore cultivation. We test this hypothesis by measuring Ulva biomass and internal nitrogen in offshore experiments in the nitrogen-poor EMS a few kilometers offshore the Israeli coast. We construct a predictive cultivation model to estimate N concentrations in the sea during experiments. This study demonstrates the feasibility of growing Ulva sp. offshore the EMS with an onshore nutrient supply and develops a better understanding of seasonal growth dynamics and environmental effects (nitrogen, waves, depth, etc.). Furthermore, the study showcases the applicability of the macroalgae cultivation model in the offshore environment and its potential contribution throughout the whole lifecycle of seaweed cultivation.

bioengineering↗

bioRxiv2023

Modeling of growth of Ulva sp. macroalgae in a controlled photobioreactor based on nitrogen accumulation dynamics

Macroalgae biomass production models that capture nutrient dynamics, temperature, light, and salinity are important for the design and operation of large-scale farms. The goal of this study is to understand how the nitrogen fertilizing regime, relating to fertilizing dose (M N week-1), amplitude (M N), and duration (hours), affects the dynamics of nitrogen content and biomass production of the Ulva sp. macroalgae. We hypothesize that the nitrogen fertilizing regime controls the Ulva Nitrogen Use Efficiency (NUE), defined here as the fraction of fertilizer nitrogen that is utilized and allocated to yield N, and, accordingly, also nitrogen assimilation in the biomass and the growth rate. We test this hypothesis by measuring internal nitrogen and biomass weight and by calculating NUE under various fertilization regimes in controlled photobioreactors. Based on this experimental data, we developed a biomass productivity model that predicts nitrogen and biomass dynamics in time over three weeks of cultivation. This study points out efficient fertilizing regimes and enables the development of a comprehensive understanding of the dynamic relationship between external N, internal N, and biomass production of the Ulva sp. macroalgae under varying external N levels, which is important for real-world agricultural applications. This study provides a better understanding of the external N-internal N-biomass triangle followed by an improved dynamic cultivation model, enabling better control of nutrient application and biomass production in macroalgae farming for a sustainable marine bioeconomy.

bioengineering↗

bioRxiv2020

Marine Bacteria Associated with the Green Seaweed Ulva sp. for the Production of Polyhydroxyalkanoates

The biosynthesis of polyhydroxyalkanoate (PHA) biopolymers from certain marine microbes, associated with green macroalgae Ulva sp., has attracted significant attention. The Ulva sp. is abundant biomass in numerous locations around the world and could be easily cultivated by marine farming. The variety of sugars found in Ulva sp. homogenate could be used as a carbon source for microbial growth and PHA production. In this work, we isolated and explored a series of bacterial strains that function as potential producers of P(3HB), utilizing a range of common sugars found in Ulva sp. Analysis of 16S rDNA gene-sequence revealed that the PHA-producing bacteria were phylogenetically related to species of the genus Cobetia, Bacillus, Pseudoaltermonas, and Sulfito-bacter. The highest-yield of P(3HB) was observed in the case of new Cobetia strain, C. amphilecti, with up to 61% (w/w) in the presence of mannitol and 12% (w/w) on Ulva sp. acid hydrolysate as a substrate.

microbiology↗

bioRxiv2020

Multi-Scale Modeling of Intensive Macroalgae Cultivation and Marine Nitrogen Sequestration

Multi-scale macroalgae growth models are required for the efficient design of sustainable, economically viable and environmentally safe farms. Here, we develop a multi-scale model for Ulva sp. macroalgae growth and nitrogen sequestration in an intensive cultivation farm, regulated by temperature, light and nutrients. The model incorporates a range of scales by incorporating spatial effects in two steps: light extinction at the reactor scale (1 m) and nutrient absorption at the farm scale (1 km). The model was validated on real data from an experimental reactor installed in the sea. Biomass production rates, chemical compositions and nitrogen removal were simulated under different seasons, levels of dilution in the environment and water-exchange rate in the reactor. This multi-scale model provides an important tool for environmental authorities and seaweed farmers who desire to upscale to large bioremediation and/or macroalgae biomass production farms, thus promoting the marine sustainable development and the macroalgae-based bioeconomy.

bioengineering↗