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Biology subjects

Baruch, K.

Publications and source records attributed to Baruch, K..

5 recordsLinked to original sources

A single injection of anti-PD-L1 blocking antibody induces a transient reduction in tau pathology in P301S (PS19) mouse model of tauopathy

Blocking the inhibitory PD-1/PD-L1 immune checkpoint pathway has been shown to arrest cognitive decline and reduce multiple aspects of brain pathology in various mouse models of amyloidosis and tauopathy. In this study, we evaluated whether anti-PD-L1 treatment would be effective in a tauopathy model characterized by rapidly progressing pathology. Using the P301S (PS19) transgenic mouse model, we found that a single injection of anti-PD-L1 antibody significantly attenuated cognitive deficits, with effects detectable 1-month post-treatment, aligned with the kinetics reported in other models. This cognitive benefit was observed irrespective of microglial TREM2 signalling. The effect on brain pathology was transient; phosphorylated tau in the brain, and total tau in the cerebrospinal fluid were significantly reduced 14 days post-treatment but not at 28 days. These findings indicate that PD-L1 blockade is effective across multiple disease models, while emphasizing the importance of carefully monitoring the timing of effect assessments, treatment outcomes, and dosing frequency, especially in models with accelerated disease progression.

immunology↗

Sex-dependent dominance maintains migration supergene in rainbow trout

Traits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.

evolutionary biology↗

High-quality assembly of sweet basil genome

Sweet basil, sometimes called the King of Herbs, is well known for its culinary uses, especially in the Italian sauce Pesto. It is also used in traditional medicine, as a source for essential oils and as an ornamental plant. So far, basil was bred by classical and traditional methods due to lack of a reference genome that will allow optimized application of the most up-to-date sequencing techniques. Here, we report on the first completion of the sweet basil genome of the cultivar Perrie, a fresh-cut Genovese-type basil, using several next generation sequencing platforms followed by genome assembly with NRGENEs DeNovoMAGIC assembly tool. We determined that the genome size of sweet basil is 2.13 Gbp and assembled it into 12,212 scaffolds. The high-quality of the assembly is reflected in that more than 90% of the assembly size is composed of only 107 scaffolds. An independent analysis of single copy orthologues genes showed a 93% completeness which reveal also that 74% of them were duplicated, indicating that the sweet basil is a tetraploid organism. A reference genome of sweet basil will enable to develop precise molecular markers for various agricultural important traits such as disease resistance and tolerance to various environmental conditions. We will gain a better understanding of the underlying mechanisms of various metabolic processes such as aroma production and pigment accumulation. Finally, it will save time and money for basil breeders and scientists and ensure higher throughput and robustness in future studies.

genomics↗

New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing.

High quality genomes are essential to resolve challenges in breeding, comparative biology, medicine and conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies for non-model organisms, moving them toward reference quality genomes. We report on the latest genome assembly of the Atlantic bottlenose dolphin leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs, long insert paired ends and standard paired ends. Data were assembled with the commercial DeNovoMAGICTM assembly software resulting in two assemblies, a traditional \"haploid\" assembly (Tur_tru_Illumina_hap_v1) that is a mosaic of the two parental haplotypes and a phased assembly (Tur_tru_Illumina_phased_v1) where each scaffold has sequence from a single homologous chromosome. We show that Tur_tru_Illumina_hap_v1 is more complete and accurate compared to the current best reference based on the amount and composition of sequence, the consistency of the mate pair alignments to the assembled scaffolds, and on the analysis of conserved single-copy mammalian orthologs. The phased de novo assembly Tur_tru_Illumina_phased_v1 is the first publicly available for this species and provides the community with novel and accurate ways to explore the heterozygous nature of the dolphin genome.

genomics↗

European Flint reference sequences complement the maize pan-genome

The genomic diversity of maize is reflected by a large number of SNPs and substantial structural variation. Here, we report the de novo assembly of two European Flint maize lines to remedy the scarcity of sequence resources for the Flint pool. EP1 and F7 are important founder lines of European hybrid breeding programs. The lines were sequenced on an Illumina platform at 320X and 225X coverage. Using NRGene{acute}s DeNovoMAGIC 2.0 technology, pseudochromosomes were assembled encompassing a total of 2,463 Mb for EP1 and 2,405 Mb for F7. Structural and functional annotation of the two genomes is currently in progress. The two high-quality de novo assemblies complement the existing maize pan-genome and will pave the way for future functional and comparative studies.

genomics↗