Genetic analysis of photomorphogenic mutants in tomato = [Genetische analyse van fotomorfogenese mutanten in tomaat]

To sense light quality and quantity plants possess different groups of photoreceptors. This thesis describes the isolation and characterization of several photomorphogenic mutants in the model plant tomato. The use of a genetic approach to determine the roles of the different photoreceptors, in photomorphogenesis and to study their mode of action, is one of the most promising approaches used in photomorphogenic research. M 2 populations were screened for aberrant seedling phenotypes in blue and/or red light (R). This resulted in the isolation of two allelic mutants ( fri 1 and fti 2) that resembled the phytochrome A (phyA)-deficient mutants of Arabidopsis in their far-red light (FR) insensitivity. Immunochemically detectable phyA polypeptide is absent as is the bulk of the spectrophotometrically detectable labile phytochrome pool in etiolated fri seedlings. The fri locus mapped to chromosome 10 at a position similar to that of the PhyA locus on the RFLP map. Four allelic mutants, that had longer hypocotyls under continuous R, were isolated. These mutants are only insensitive to R during the first two days upon transition from darkness to R and were designated tri 1 to tri4 (temporarily led light insensitive). Immunochemically detectable phyB1 protein is either absent, reduced or truncated. The tri mutants differ from phyB-deficient mutants found in other species in their relatively normal end-of-day FR and supplementary daytime FR responses. The tri mutant gene and the PhyB1 gene were mapped to the same position on the RFLP map of chromosome 1. The nature of the mutations in au and yg-2 was analysed by crossing both mutants with a transgenic tomato line that overexpresses oat phyA-3. Immunochemically detectable oat PHYA-3 is present in both the au,PhyA-3 and yg-2,PhyA-3 'double mutant'. However, spectrophotometrical analysis revealed that it is non active, as indicated by the long-hypocotyl phenotype of the 'double' mutants. The results were consistent with both mutants being disturbed in the phytochrome chromophore biosynthesis. The three remaining phytochrome genes (PhyB2, E and F ), for which no mutants have been found thus far, have also been mapped to the RFLP map of chromosomes 5, 2 and 7, respectively. In addition, it has been proved that there are two distinct hp loci, each with several alleles. The hp-2 gene has been located on both the genetic and molecular linkage maps of chromosome 1

Transcriptome-Guided Identification of Drugs for Repurposing to Treat Age-Related Hearing Loss

Age-related hearing loss (ARHL) or presbycusis is a prevalent condition associated with social isolation, cognitive impairment, and dementia. Age-related changes in the cochlea, the auditory portion of the inner ear, are the primary cause of ARHL. Unfortunately, there are currently no pharmaceutical approaches to treat ARHL. To examine the biological processes underlying age-related changes in the cochlea and identify candidate drugs for rapid repurposing to treat ARHL, we utilized bulk RNA sequencing to obtain transcriptomes from the functional substructures of the cochlea-the sensorineural structures, including the organ of Corti and spiral ganglion neurons (OC/SGN) and the stria vascularis and spiral ligament (SV/SL)-in young (6-week-old) and old (2-year-old) C57BL/6 mice. Transcriptomic analyses revealed both overlapping and unique patterns of gene expression and gene enrichment between substructures and with ageing. Based on these age-related transcriptional changes, we queried the protein products of genes differentially expressed with ageing in DrugBank and identified 27 FDA/EMA-approved drugs that are suitable to be repurposed to treat ARHL. These drugs target the protein products of genes that are differentially expressed with ageing uniquely in either the OC/SGN or SV/SL and that interrelate diverse biological processes. Further transcriptomic analyses revealed that most genes differentially expressed with ageing in both substructures encode protein products that are promising drug target candidates but are, nevertheless, not yet linked to approved drugs. Thus, with this study, we apply a novel approach to characterize the druggable genetic landscape for ARHL and propose a list of drugs to test in pre-clinical studies as potential treatment options for ARHL.</p

Sodium-activated potassium channels shape peripheral auditory function and activity of the primary auditory neurons in mice

Potassium (K+) channels shape the response properties of neurons. Although enormous progress has been made to characterize K+ channels in the primary auditory neurons, the molecular identities of many of these channels and their contributions to hearing in vivo remain unknown. Using a combination of RNA sequencing and single molecule fluorescent in situ hybridization, we localized expression of transcripts encoding the sodium-activated potassium channels K(Na)1.1(SLO2.2/Slack) and K(Na)1.2 (SLO2.1/Slick) to the primary auditory neurons (spiral ganglion neurons, SGNs). To examine the contribution of these channels to function of the SGNs in vivo, we measured auditory brainstem responses in K(Na)1.1/1.2 double knockout (DKO) mice. Although auditory brainstem response (wave I) thresholds were not altered, the amplitudes of suprathreshold responses were reduced in DKO mice. This reduction in amplitude occurred despite normal numbers and molecular architecture of the SGNs and their synapses with the inner hair cells. Patch clamp electrophysiology of SGNs isolated from DKO mice displayed altered membrane properties, including reduced action potential thresholds and amplitudes. These findings show that K(Na)1 channel activity is essential for normal cochlear function and suggest that early forms of hearing loss may result from physiological changes in the activity of the primary auditory neurons

Photomorphogenic mutants of tomato

Photomorphogenesis of tomato is being studied with the aid of mutants which are either modified in their photore- ceptor composition or in their signal transduction chain(s) . Several mutants affecting the phytochrome family of photoreceptors, some of which appear deficient for specific genes encoding phytochrome apoproteins have been isolated . In addition, other mutants, including transgenic lines overexpressing phytochrome A, exhibit exaggerated photomorphogenesis during de-etiolation . Anthocyanin biosynthesis and plastid development are being used as model systems for the dissection of the complex interactions among photomorphogenic photoreceptors and to elucidate the nature of their transduction chains

Evaluation of Dosing Guidelines for Gentamicin in Neonates and Children

Although aminoglycosides are frequently prescribed to neonates and children, the ability to reach effective and safe target concentrations with the currently used dosing regimens remains unclear. This study aims to evaluate the target attainment of the currently used dosing regimens for gentamicin in neonates and children. We conducted a retrospective single-center cohort study in neonates and children receiving gentamicin between January 2019 and July 2022, in the Beatrix Children’s Hospital. The first gentamicin concentration used for therapeutic drug monitoring was collected for each patient, in conjunction with information on dosing and clinical status. Target trough concentrations were ≤1 mg/L for neonates and ≤0.5 mg/L for children. Target peak concentrations were 8–12 mg/L for neonates and 15–20 mg/L for children. In total, 658 patients were included (335 neonates and 323 children). Trough concentrations were outside the target range in 46.2% and 9.9% of neonates and children, respectively. Peak concentrations were outside the target range in 46.0% and 68.7% of neonates and children, respectively. In children, higher creatinine concentrations were associated with higher gentamicin trough concentrations. This study corroborates earlier observational studies showing that, with a standard dose, drug concentration targets were met in only approximately 50% of the cases. Our findings show that additional parameters are needed to improve target attainment

Whole genome resequencing reveals signatures of selection and timing of duck domestication

Background The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual. Results Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggest that genes affecting brain and neuronal development have undergone strong positive selection during domestication. Our FST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis associated transcription factor locus. Conclusions Our results advance the understanding of animal domestication and selection for complex phenotypic traits

Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats

Naked mole-rats are highly vocal, eusocial, subterranean rodents with, counterintuitively, poor hearing. The causes underlying their altered hearing are unknown. Moreover, whether altered hearing is degenerate or adaptive to their unique lifestyles is controversial. We used various methods to identify the factors contributing to altered hearing in naked and the related Damaraland mole-rats and to examine whether these alterations result from relaxed or adaptive selection. Remarkably, we found that cochlear amplification was absent from both species despite normal prestin function in outer hair cells isolated from naked mole-rats. Instead, loss of cochlear amplification appears to result from abnormal hair bundle morphologies observed in both species. By exploiting a well-curated deafness phenotype-genotype database, we identified amino acid substitutions consistent with abnormal hair bundle morphology and reduced hearing sensitivity. Amino acid substitutions were found in unique groups of six hair bundle link proteins. Molecular evolutionary analyses revealed shifts in selection pressure at both the gene and the codon level for five of these six hair bundle link proteins. Substitutions in three of these proteins are associated exclusively with altered hearing. Altogether, our findings identify the likely mechanism of altered hearing in African mole-rats, making them the only identified mammals naturally lacking cochlear amplification. Moreover, our findings suggest that altered hearing in African mole-rats is adaptive, perhaps tailoring hearing to eusocial and subterranean lifestyles. Finally, our work reveals multiple, unique evolutionary trajectories in African mole-rat hearing and establishes species members as naturally occurring disease models to investigate human hearing loss