Biology subjects

Berg, P.

Publications and source records attributed to Berg, P..

7 recordsLinked to original sources

bioRxiv2026

Impaired renal base excretion in secretin receptor knock-out mice during prolonged base-loading

AimSecretin was recently found to play a pivotal role in the renal adaptation to acute base excess. Here, secretin increases pendrin-dependent HCO3- secretion from the beta-intercalated cells in the cortical collecting ducts. Whether secretin and its receptor play a role during prolonged base-loading remains unknown. MethodsUrine and blood acid-base analyses were carried out in secretin receptor (SCTR) KO and WT mice at baseline and after 1 and up to 8 days of base-loading with NaHCO3-enriched drinking water. Changes in pendrin protein abundance and function were assessed by immunoblotting and isolated tubule perfusion experiments. Plasma secretin levels and renal SCTR expression were assessed after 24 hours of acid/base-loading by radioimmunoassay and qPCR, respectively. ResultsSCTR KO mice responded with diminished urine alkalization and a lesser reduction of urinary acid excretion when base-loaded for 48 hours. Concordantly, SCTR KO mice presented with increased blood base retention compared with WTs. Base-loaded SCTR WT and KO mice showed comparable total pendrin protein abundance. Despite this, pendrin function was markedly lower in SCTR KO mice. Base-loaded mice had higher plasma secretin and renal SCTR levels compared with acid-loaded mice. Higher arterial HCO - associated with higher renal SCTR mRNA expression. ConclusionLoss of the SCTR diminishes renal base excretion capacity and exacerbates systemic base accumulation during prolonged base-loading. Further, plasma secretin and renal SCTR mRNA levels are modulated by acid-base intake. These findings further support a central role of secretin and its receptor in the regulation of both acute and prolonged base excess. Key pointsO_LIIn mice, the receptor of the gut hormone secretin is required for the kidney to adequately handle a sustained base load. In mice with secretin receptor knockout, renal base excretion is impaired and metabolic alkalosis is aggravated and slower to resolve. C_LIO_LIBase-loaded knockout mice up-regulate pendrin protein abundance normally, the bicarbonate-secreting Cl-/HCO3-exchanger in collecting-duct {beta}-intercalated cells, but exhibit lower pendrin function. This suggests that the defect lies in the activation of pendrin, rather than in the regulation of its abundance. C_LIO_LIRenal secretin-receptor expression increases with higher arterial bicarbonate and plasma secretin, and renal secretin receptor expression, levels are lower in acid-loaded mice compared to base-loaded mice. This indicates that the secretin/secretin receptor system is itself affected by acid-base status/acid-base intake. C_LI

physiology↗

bioRxiv2024

The turbulent soundscape of intertidal oyster reefs

Turbulence and sound are important cues for oyster reef larval recruitment. Numerous studies have found a relationship between turbulence intensity and swimming behaviors of marine larvae, while others have documented the importance of sounds in enhancing larval recruitment to oyster reefs. However, the relationship between turbulence and the reef soundscape is not well understood. In this study we made side-by-side acoustic Doppler velocimeter turbulence measurements and hydrophone soundscape recordings over 2 intertidal oyster reefs (1 natural and 1 restored) and 1 adjacent bare mudflat as a reference. Sound pressure levels (SPL) were similar across all three sites, although SPL > 2000 Hz was highest at the restored reef, likely due to its larger area that contained a greater number of sound-producing organisms. Flow noise (FN), defined as the mean of pressure fluctuations recorded by the hydrophone at f < 100 Hz, was significantly related to mean flow speed, turbulent kinetic energy, and turbulence dissipation rate ({varepsilon}), agreeing with theoretical calculations for turbulence. Our results also show a similar relationship between {varepsilon} and FN to what has been previously reported for {varepsilon} vs. downward larval swimming velocity (wb), with both FN and wb demonstrating rapid growth at {varepsilon} > 0.1 cm2 s-3. These results suggest that reef turbulence and sounds may attract oyster larvae in complementary and synergistic ways.

biophysics↗

bioRxiv2024

Individual variation in meiotic crossover positioning, rate and interference are driven by distinct genetic processes in domestic pigs.

Meiotic crossovers are essential for proper chromosome segregation, and provide an important mechanism for adaptation through linking beneficial alleles and purging deleterious mutations. However, crossovers can also break apart beneficial alleles and are themselves a source of new mutations within the genome. The rate and distribution of crossovers shows huge variation both within and between chromosomes, individuals and species, yet the molecular and evolutionary causes and consequences of this variation remain poorly understood. A key step in understanding this variation is to understand the genetic architecture of how many crossovers occur, where they occur, and how they interfere, as this allows us to identify the degree to which these factors are governed by common or distinct genetic processes. Here, we investigate individual variation in crossover count, crossover interference ({nu}), and crossover positioning measured as both intra-chromosomal allelic shuffling and distance to telomere (Mb), in a large genotyped breeding population of domestic pigs. Using measures from 82,474 gametes from 4,704 mothers and 271 fathers, we show that crossover traits are heritable within each sex (h2 = 0.03 - 0.11), with the exception of male crossover interference. Crossover count and interference have a strongly shared genetic architecture in females, mostly driven by variants at RNF212. Female crossover positioning is mediated by variants at MEI4, PRDM9, and SYCP2. We also identify tentative associations at genomic regions corresponding to CTCF and REC114/REC8/CCNB1IP1 (crossover count), and ZCWPW1 and ZCWPW2 (crossover positioning). Our results show that crossover count and crossover positioning in female pigs have the capacity to evolve somewhat independently in our dataset.

genomics↗

bioRxiv2023

Genetic architecture of individual meiotic crossover rate and distribution in a large Atlantic Salmon (Salmo salar) breeding population.

Meiotic recombination through chromosomal crossovers ensures proper segregation of homologous chromosomes in meiosis, while also breaking down linkage disequilibrium and shuffling alleles at loci located on the same chromosome. Rates of recombination can vary between species, but also between and within individuals, sex and chromosomes within species. Indeed, the Atlantic salmon genome is known to have clear sex differences in recombination with female biased heterochiasmy and markedly different landscapes of crossovers between males and females. In male meiosis, crossovers occur strictly in the telomeric regions, whereas in female meiosis crossovers tend to occur closer to the centromeres. However, little is known about the genetic control of these patterns and how this differs at the individual level. Here, we investigate genetic variation in individual measures of recombination in >5000 large full-sib families of a Norwegian Atlantic salmon breeding population with high-density SNP genotypes. We show that females had 1.6x higher crossover counts (CC) than males, with autosomal linkage maps spanning a total of 2174 cM in females and 1483 cM in males. However, because of the extreme telomeric bias of male crossovers, female recombination is much more important for generation of new haplotypes with 8x higher intra-chromosomal genetic shuffling than males. CC was heritable in females (h2 = 0.11) and males (h2 = 0.10), and shuffling was also heritable in both sex but with a lower heritability in females (h2 = 0.06) than in males (h2 = 0.11). Inter-sex genetic correlations for both traits were close to zero, suggesting that rates and distribution of crossovers are genetically distinct traits in males and females, and that there is a potential for independent genetic change in both sexes in the Atlantic Salmon. Together, these findings give novel insights into the genetic architecture of recombination in salmonids and contribute to a better understanding of how rates and distribution of recombination may evolve in eukaryotes more broadly.

genetics↗

bioRxiv2023

Baldur: Bayesian hierarchical modeling for label-free proteomics exploiting gamma dependent mean-variance trends

Due to its simplicity in sample preparation, label-free quantification has become de facto in proteomics research at the expense of precision. We propose a Bayesian hierarchical decision model to test for differences in means between conditions for proteins, peptides, and post-translation modifications. We introduce a novel Bayesian regression model to characterize local mean-variance trends in the data to describe measurement uncertainty and to estimate the decision model hyperparameters. Our model vastly improves over state-of-the-art methods (Limma-Trend and t-test) in several spike-in datasets by having competitive performance in detecting true positives while showing superiority by greatly reducing false positives.

bioinformatics↗

bioRxiv2022

High throughput peptidomics elucidates immunoregulatory functions of plant thimet oligopeptidase-directed proteostasis

Targeted proteolysis activities activated during the plant immune response catalyze the synthesis of stable endogenous peptides. Little is known about their biogenesis and biological roles. Herein, we characterize an Arabidopsis thaliana mutant top1top2 in which targeted proteolysis of immune-active peptides is drastically impaired during effector-triggered immunity (ETI). For effective ETI, the redox-sensitive thimet oligopeptidases TOP1 and TOP2 are required. Quantitative mass spectrometry-based peptidomics allowed differential peptidome profiling of wild type (WT) and top1top2 mutant at the early ETI stages. Biological processes of energy-producing and redox homeostasis were enriched, and TOPs were necessary to maintain the dynamics of ATP and NADP(H) accumulation in the plant during ETI. Subsequently, a set of novel TOPs substrates validated in vitro enabled the definition of the TOP-specific cleavage motif and informed an in-silico model of TOP proteolysis to generate bioactive peptide candidates. Several candidates, including those derived from proteins associated with redox metabolism, were confirmed in planta. The top1top2 background rescued WTs ETI deficiency caused by treatment with peptides derived from targeted proteolysis of the negative immune regulator FBR12, the reductive enzyme APX1, the isoprenoid pathway enzyme DXR, and ATP-subunit {beta}. These results demonstrate TOPs role in orchestrating the production and degradation of phytocytokines.

plant biology↗

bioRxiv2018

Candidate SNP analyses integrated with mRNA expression and hormone levels reveal influence on mammographic density and breast cancer risk

Introduction Introduction Materials and methods Results Discussion Globaltest Conclusion Competing interests Authors contributions Reference List Mammographic density (MD) is a well-documented risk factor for breast cancer[1-9], and thus a promising target for early detection of the disease. Based on mammographic results, the breast is given a percent density (PDEN) score ranging from 0-100% with 0 being the least dense (primarily adipose tissue). It is estimated that the risk of developing breast cancer is four to six times higher in women with an MD score of at least 75% [2,9] and that one-third of breast cancers occur in patients with PDEN scores of at least 50% [2]. MD is ...

genomics↗