Differential Retention Research Articles

Expression and functional divergence of a type-A response regulator paralog pair formed by dispersed duplication during Populus deltoides evolution

Gene duplication and divergence are essential to plant evolution. The Arabidopsis type-A response regulator (ARR) family, negative regulators in cytokinin signaling, exemplifies gene expansion and differential retention. Despite extensive research, the understanding of type-A RR homologs in woody plants remains limited. In this study, the evolution history of type-A RR gene families across four rosids and one monocot has been comprehensively investigated. Focusing on Populus deltoides, a unique pair of dispersed duplicates, PdRR8 and PdFERR, is identified, and their duplication is estimated to have occurred in the common ancestor of the four rosids. The duplication remnants corresponding to PdRR8 have been retained in all rosids but the counterpart of PdFERR has been lost. In poplar, PdRR8 shows the highest expression levels in leaves, while PdFERR is specifically expressed in female floral buds. Among various external stimuli, cold strongly represses PdRR8 promoter activity, whereas 6-BA markedly inhibits that of PdFERR. Overexpression of PdRR8 in the Arabidopsis arr16arr17 double-mutant fully complements the reduced hydrotropic response. In contrast, PdFERR fails to rescue the hydrotropic defects of the mutant. Results of evolutionary, expression and functional analyses indicate that PdRR8, rather than PdFERR, is the true ortholog of the ARR16-ARR17 paralogs. Though PdRR8 and PdFERR originate from a common ancestral gene and evolve under strong negative selection, these two dispersed duplicates have exhibited differential expression and some degree of functional divergence.

Comparing occurrence of per- and polyfluoroalkyl substances (PFAS) in municipal biosolids and industrial wastewater sludge: A City of Los Angeles study

Biosolids and sludge are what remain after the liquid fraction of wastewater is separated during wastewater treatment. These high organic content matrices are known to contain organic contaminants, a few of which are the hazardous and environmentally persistent per- and polyfluoroalkyl substances (PFAS). The current study investigates whether sludge from a treatment facility serving mostly industrial establishments and biosolids from a facility serving mostly domestic dwellings retain these ‘forever chemicals’ similarly. Using 31 markers covering different classes of PFAS, the sludge was found to contain higher levels of PFAS (869 ± 791 ng/g; 21 of 31) than biosolids (31 ± 7 ng/g, 11 of 31). The most abundant overall was perfluorooctane sulfonic acid (PFOS), mostly in sludge (range: 71–1300 ng/g versus 0–18 ng/g in biosolids). The large PFAS concentration variability in sludge was seasonal and sinusoidal. Sludge, additionally, contained all long chain PFAS, precursors (mostly surfactant ingredients and their transformation byproducts) and short chain PFAS (perhaps because of higher moisture content). By regression, the sludge is shown to consistently contain twice as much PFAS as biosolids when the same amounts are exposed to increasing levels of PFAS. Factors observed to cause differential PFAS retention between sludge and biosolids were moisture (98.6 % and 72.1 %, respectively), chain length, input quality (industrial versus residential) and functional group. Sulfonic acids for instance are one C atom shorter than carboxylates with similar occurrence in sludge and biosolids. More studies are needed to define the roles that organic carbon of sludge/biosolids, water chemistry, temperature and factors not considered here play in partitioning PFAS between the two matrices with respect to inputs. Existing Koc values could not help in explaining observed trends, but the ratio of biosolids-to-influent concentrations was found to correlate positively with PFAS size. Using influent in the ratio, and not effluent, is novel. SynopsisSludge and biosolids are soil amendments; they contain hazardous and persistent PFAS. Methods of decoupling PFAS from these matrices start with understanding matrix-driven PFAS partitioning as shown here.

Biased Retention of Environment-Responsive Genes Following Genome Fractionation.

The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.

HDAC1 Promotes Mitochondrial Pathway Apoptosis and Inhibits the Endoplasmic Reticulum Stress Response in High Glucose-Treated Schwann Cells via Decreased U4 Spliceosomal RNA.

Dysfunction of Schwann cells, including cell apoptosis, autophagy inhibition, dedifferentiation, and pyroptosis, is a pivotal pathogenic factor in induced diabetic peripheral neuropathy (DPN). Histone deacetylases (HDACs) are an important family of proteins that epigenetically regulate gene transcription by affecting chromatin dynamics. Here, we explored the effect of HDAC1 on high glucose-cultured Schwann cells. HDAC1 expression was increased in diabetic mice and high glucose-cultured RSC96 cells, accompanied by cell apoptosis. High glucose also increased the mitochondrial pathway apoptosis-related Bax/Bcl-2 and cleaved caspase-9/caspase-9 ratios and decreased endoplasmic reticulum response-related GRP78, CHOP, and ATF4 expression in RSC96 cells (P < 0.05). Furthermore, overexpression of HDAC1 increased the ratios of Bax/Bcl-2, cleaved caspase-9/caspase-9, and cleaved caspase-3 and reduced the levels of GRP78, CHOP, and ATF4 in RSC96 cells (P < 0.05). In contrast, knockdown of HDAC1 inhibited high glucose-promoted mitochondrial pathway apoptosis and suppressed the endoplasmic reticulum response. Moreover, RNA sequencing revealed that U4 spliceosomal RNA was significantly reduced in HDAC1-overexpressing RSC96 cells. Silencing of U4 spliceosomal RNA led to an increase in Bax/Bcl-2 and cleaved caspase-9 and a decrease in CHOP and ATF4. Conversely, overexpression of U4 spliceosomal RNA blocked HDAC1-promoted mitochondrial pathway apoptosis and inhibited the endoplasmic reticulum response. In addition, alternative splicing analysis of HDAC1-overexpressing RSC96 cells showed that significantly differential intron retention (IR) of Rpl21, Cdc34, and Mtmr11 might be dominant downstream targets that mediate U4 deficiency-induced Schwann cell dysfunction. Taken together, these findings indicate that HDAC1 promotes mitochondrial pathway-mediated apoptosis and inhibits the endoplasmic reticulum stress response in high glucose-cultured Schwann cells by decreasing the U4 spliceosomal RNA/IR of Rpl21, Cdc34, and Mtmr11.

Deep Transcriptomics Reveals Cell-Specific Isoforms of Pan-Neuronal Genes.

Profiling gene expression in single neurons using single-cell RNA-Seq is a powerful method for understanding the molecular diversity of the nervous system. Profiling alternative splicing in single neurons using these methods is more challenging, however, due to low capture efficiency and sensitivity. As a result, we know much less about splicing patterns and regulation across neurons than we do about gene expression. Here we leverage unique attributes of the C. elegans nervous system to investigate deep cell-specific transcriptomes complete with biological replicates generated by the CeNGEN consortium, enabling high-confidence assessment of splicing across neuron types even for lowly-expressed genes. Global splicing maps reveal several striking observations, including pan-neuronal genes that harbor cell-specific splice variants, abundant differential intron retention across neuron types, and a single neuron highly enriched for upstream alternative 3' splice sites. We develop an algorithm to identify unique cell-specific expression patterns and use it to discover both cell-specific isoforms and potential regulatory RNA binding proteins that establish these isoforms. Genetic interrogation of these RNA binding proteins in vivo identifies three distinct regulatory factors employed to establish unique splicing patterns in a single neuron. Finally, we develop a user-friendly platform for spatial transcriptomic visualization of these splicing patterns with single-neuron resolution.

Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages

Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.

Research on water blocking and residue damage mechanism of fracturing fluid in Yongjin tight reservoirs

The existing reservoir in the Yongjin block exhibits an extremely low matrix permeability, posing challenges in precisely evaluating the damage caused by fracturing fluid using traditional core flow experimental methods. Currently, there is no established quantitative method for characterizing the degree of damage. In this study, we integrated online nuclear magnetic resonance, microscopic computed tomography, and core displacement experimental techniques, pioneering a novel approach to evaluate damage in deep tight oil reservoirs subjected to hydraulic fracturing. We analyzed the influence patterns of key factors such as backflow pressure differential, shut-in time, invasion volume, and residual retention on rock matrix damage in the operational area. The study unveiled the mechanisms behind water sensitivity, water block, and fracturing fluid retention damage among oil, water, and rock. The results indicate that water sensitivity damage is less than 20%, primarily occurring within large pores. Water block damage can significantly reduce the residual oil permeability. Experimental findings suggest that optimizing liquid backflow with a pressure differential and well shut-in time set at 5 MPa and 9 days can markedly reduce the intrusion volume of gel-breaking fluid, restoring the residual oil permeability. Under high-pressure differential conditions, residual fracturing fluid can infiltrate the rock matrix, resulting in pore damage. Additionally, it can accumulate on the fracture surfaces, thereby reducing the permeability of microfractures.

Genome organization and botanical diversity.

The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.

Is Percentage Improvement in Anteroposterior Pelvic Diameter a Valuable Marker for Successful Drainage Postpyeloplasty in Isolated Pediatric Pelvi-ureteric Junction Obstruction.

Pelvic-ureteric junction obstruction (PUJO) causes urine stasis in the renal pelvis and progressive kidney damage. Postpyeloplasty improvement of renal function and urinary drainage is assessed by diuretic isotope renogram and ultrasonography. Renograms are expensive and have radiation exposure. This study explores whether ultrasound parameters such as percentage improvement in anteroposterior pelvic diameter (PI-APD) is a valuable markers for successful pediatric pyeloplasties. The aim of this study was to identify patients who would benefit from ultrasound monitoring of PI-APD alone instead of diuretic isotope renal scan for postoperative follow-up of pyeloplasty. This was a retrospective descriptive study. We analyzed 127 pediatric pyeloplasties performed and under follow-up between June 2016 and May 2021. We recorded the postoperative ultrasound and isotope renogram parameters. PI-APD (preoperative AP diameter - postoperative AP diameter)/preoperative AP diameter × 100) was compared with improvement in renogram parameters (differential renal function, Tmax, curve pattern, and retention) to look for a correlation between them. SPSS version 20.5, Chi-square and paired t-test were used for statistical analysis. About 73.2% of patients were males, with most cases detected antenatally (76.4%). The majority was left-sided PUJO (67.7%). The mean age at surgery was 30.8 months. We identified a statistically significant correlation between the ultrasound parameter PI-APD and the renogram parameter Tmax. There is no significant correlation between PI-APD and other renogram parameters. In patients whose ultrasound parameter PI-APD is >40% and renal parenchymal thickness has increased, isotope renograms can be avoided for follow-up of postpyeloplasty patients.

Differential expansion and retention patterns of LRR-RLK genes across plant evolution.

To maximize overall fitness, plants must accurately respond to a host of growth, developmental, and environmental signals throughout their life. Many of these internal and external signals are perceived by the leucine-rich repeat receptor-like kinases, which play roles in regulating growth, development, and immunity. This largest family of receptor kinases in plants can be divided into subfamilies based on the conservation of the kinase domain, which demonstrates that shared evolutionary history often indicates shared molecular function. Here we investigate the evolutionary history of this family across the evolution of 112 plant species. We identify lineage-specific expansions of the malectin-domain containing subfamily LRR subfamily I primarily in the Brassicales and bryophytes. Most other plant lineages instead show a large expansion in LRR subfamily XII, which in Arabidopsis is known to contain key receptors in pathogen perception. This striking asymmetric expansion may reveal a dichotomy in the evolutionary history and adaptation strategies employed by plants. A greater understanding of the evolutionary pressures and adaptation strategies acting on members of this receptor family offers a way to improve functional predictions for orphan receptors and simplify the identification of novel stress-related receptors.

Differential sperm histone retention in normozoospermic ejaculates of infertile men negatively affects sperm functional competence and embryo quality.

The unique epigenetic architecture that sperm cells acquire during spermiogenesis by retaining <15% of either canonical or variant histone proteins in their genome is essential for normal embryogenesis. Whilst heterogeneous levels of retained histones are found in morphologically normal spermatozoa, their effect on reproductive outcomes is not fully understood. Processed spermatozoa (n=62) were tested for DNA integrity by sperm chromatin dispersion assay, and retained histones were extracted and subjected to dot-blot analysis. The impact of retained histone modifications in normozoospermic patients on sperm functional characteristics, embryo quality, metabolic signature in embryo spent culture medium and pregnancy outcome was studied. Dot-blot analysis showed heterogeneous levels of retained histones in the genome of normozoospermic ejaculates. Post-wash sperm yield was affected by an increase in H3K27Me3 and H4K20Me3 levels in the sperm chromatin (p<0.05). Also, spermatozoa with higher histone H3 retention had increased DNA damage (p<0.05). Spermatozoa from these cohorts, when injected into donor oocytes, correlated to a significant decrease in the fertilisation rate with an increase in sperm histone H3 (p<0.05) and H3K27Me3 (p<0.01). An increase in histone H3 negatively affected embryo quality (p<0.01) and clinical pregnancy outcome post-embryo transfer (p<0.05). On the other hand, spent culture medium metabolites assessed by high-resolution (800MHz) nuclear magnetic resonance showed an increased intensity of the amino acid methionine in the non-pregnant group than in the pregnant group (p<0.05) and a negative correlation with sperm histone H3 in the pregnant group (p<0.05). Histone retention in spermatozoa can be one of the factors behind the development of idiopathic male infertility. Such spermatozoa may influence embryonic behaviour and thereby affect the success rate of assisted reproductive technology procedures. These results, although descriptive in nature, warrant further research to address the underlying mechanisms behind these clinically important observations.

Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes.

Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.

#2989 SELECTIVE RENAL DISPOSITION OF THE CALCINEURIN INHIBITORS VOCLSOPORIN, CYCLOSPORINE, AND TACROLIMUS

Abstract Background and Aims The calcineurin inhibitors (CNI) cyclosporine (CSA) and tacrolimus (TAC) were revolutionary immunosuppressants when first introduced for solid organ transplantation in the 1980s. Voclosporin (VCS), a novel CNI, recently became the first oral therapy approved in the United States, Great Britain, and Europe for the treatment of active lupus nephritis based on positive results from Phase 2 and 3 clinical trials. Unlike CSA and TAC, VCS has demonstrated a consistent pharmacokinetic and pharmacodynamic profile, eliminating the need for therapeutic drug monitoring. Further, VCS is associated with a more favorable metabolic profile and has not been associated with electrolyte disturbances. Emerging evidence indicates small molecule therapeutics may display differential disposition within organ tissues. This suggests that CNIs may be differentially distributed and retained in the kidney, potentially explaining the difference in their efficacy and safety profiles. To evaluate renal disposition of CSA, TAC, and VCS, we assessed in mice and humans the disposition of each CNI in the kidney relative to its systemic drug exposure. Method Single 30 mg/kg doses of CSA, TAC and VCS were administered intravenously to mice. Following intravenous administration, kidneys were collected at 15 minutes, 30 minutes, 1 hour and 2 hours, flash frozen in liquid nitrogen, and stored at −20 °C until sectioning. Sections of 10 μm kidney tissue were mounted on indium tin oxide coated glass slides. Matrix of 10 mg/mL α-Cyano-4-hydroxycinnamic acid in 85% acetonitrile/13% ethanol + 2% water + 0.1% trifluoroacetic acid was sprayed on the tissue using an HTX tissue sprayer, dried for 10 minutes in the vacuum, and subjected to Matrix-assisted Laser Desorption and Ionization Mass Spectrometry Imaging (MALDI-MSI). The systemic and renal clearance in humans of CSA and TAC were obtained from the literature; pharmacokinetic data on VCS was obtained from data on file. Renal secretion of each drug was compared to its expected passive filtration based on glomerular filtration rate (GFR), fraction unbound in plasma (fu), and respective systemic drug exposure. Results MALDI-MSI demonstrated significantly higher concentrations of drug and more diffuse tissue disposition of CSA in mouse kidney compared to VCS (Figure 1). CSA was retained in all kidney tissues up to 2 hours post-administration. Higher concentrations and more diffuse disposition of TAC was also noted compared to VCS at 15 and 30 minutes; TAC was distinctively retained in the cortex and medulla. VCS had moderate distribution in the cortex and was rapidly excreted with low levels of drug present in the kidney after 1 hour. According to published data, CSA has a measured renal clearance of 1.48 mL/min in healthy human subjects, representing approximately 10% of expected passive filtration of 12.5 mL/min (Table 1). TAC has a renal clearance of 0.014 mL/min representing &amp;lt;2% of expected passive filtration of 1.25 mL/min. VCS has a renal clearance of 7.82 mL/min representing approximately 200% of its expected passive filtration rate of 3.75 mL/min. Conclusion MALDI-MSI revealed differential retention and distribution of CSA, TAC and VCS in mice, consistent with their respective renal clearances in humans. Higher drug exposure and &amp;gt;90% renal reabsorption was observed for both CSA and TAC in this study, whereas the renal handling of VCS suggested a significant component of tubular secretion. The higher rate of secretion and lower overall exposure of kidney tissue to VCS may be associated with an improved safety profile when compared to the more diffuse distribution and greater renal retention of CSA and TAC.

IgA Determines Bacterial Composition in the Gut.

Classically, IgA in the gut prevents the invasion of microorganisms to systemic organs through the process of neutralization and immune exclusion. Interestingly, recent reports suggest that IgA might help in biofilm formation and promote bacterial growth inside the intestine. In this study, we used flow cytometry, ELISA, and chemical models of colitis to test whether the quality and quantity of IgA can select for bacterial persistence in the gut. We found that members of Proteobacteria, such as γ-Proteobacteria and SFB, are preferentially coated by IgA in WT mice. In the partial absence of either T-dependent or -independent IgA responses, there are no significant differences in the frequency of bacteria coated with IgA in mice. However, Rag-/- mice that lack all antibodies had a severe reduction in Proteobacteria and were resistant to DSS-induced colitis, suggesting that secretory IgA might be essential for differential retention of these taxa in the mouse gut. Rag-/- littermates in the F2 generation generated from (B6 × Rag-/-) F1 mice acquired the underrepresented bacteria taxa such as γ-Proteobacteria through vertical transmission of flora. They died soon after weaning, possibly due to the acquired flora. Additionally, continued exposure of Rag-/- mice to B6 flora by cohousing mice led to the acquisition of γ-Proteobacteria and mortality. Together, our results indicate that host survival in the complete absence of an IgA response necessitates the exclusion of specific bacterial taxa from the gut microbiome.

Retention of Cenobamate in the Real World (P4-1.005)

<h3>Objective:</h3> This retrospective, observational analysis evaluated cenobamate retention in a nationally representative administrative claims database. <h3>Background:</h3> Real-world experience with cenobamate has yet to be reported in a nationally representative sample. <h3>Design/Methods:</h3> We utilized a sample of patients from HealthVerity Marketplace, which includes more than 150 US commercial, Medicare, and Medicaid payers, to identify a cohort of adults (age ≥18 years) with prevalent epilepsy and at least 1 script for cenobamate (initiated at dosages of 12.5–50 mg) or any of the branded ASMs (brivaracetam, eslicarbazepine, lacosamide, perampanel). Outcomes were blended for branded ASMs. Follow-up began May 2020 and extended until December 31, 2021, with only adjudicated medical and pharmacy claims from patients with complete enrollment history included. The index date for the analysis was Day 1 of cenobamate or branded ASM initiation. Patients had to have at least a year’s worth of follow-up before and after the index date for inclusion in the analysis. Using Kaplan-Meier methods, patients were followed until an incident event occurred (cessation of cenobamate or branded ASM) or end of data collection. <h3>Results:</h3> Data were available from 1943 and 18,954 patients on cenobamate and branded ASMs, respectively, with 195 patients (mean age=38.2 years; % female=46.7%) and 4046 patients (mean age=42.4 years; % female=55.6%) meeting the inclusion/exclusion criteria. Median time to discontinuation was not reached in 12 months of follow-up for cenobamate and was 7.8 months for the branded ASMs. Retention at Months 3, 6, 9, and 12 was 72%, 62%, 58%, and 50%, respectively, for cenobamate, and 66%, 55%, 48%, and 40%, respectively, for branded ASMs (<i>P</i>=0.045). <h3>Conclusions:</h3> Cenobamate was associated with significantly better retention vs 4 pooled branded ASMs in this analysis of real-world use. Unmeasured differences across the 2 groups that impact differential retention outcomes (eg, patient severity, drug load, and use of monotherapy) are potential limitations of this analysis. <b>Disclosure:</b> Dr. Weingarten has received personal compensation for serving as an employee of SK Life Science. Mr. Wade has nothing to disclose. Mr. Mandapati has nothing to disclose. Dr. Schabert has nothing to disclose. Mr. Stern has received personal compensation for serving as an employee of SK Life Science.

Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.

Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.

Atomistic Details of Peptide Reversed-Phase Liquid Chromatography from Molecular Dynamics Simulations

Peptide separations by reversed-phase liquid chromatography (RPLC) are an integral part of bottom-up proteomics. These separations typically employ C18 columns with water/acetonitrile gradient elution in the presence of formic acid. Despite the widespread use of such workflows, the exact nature of peptide interactions with the stationary and mobile phases is poorly understood. Here, we employ microsecond molecular dynamics (MD) simulations to uncover details of peptide RPLC. We examined two tryptic peptides, a hydrophobic and a hydrophilic species, in a slit pore lined with C18 chains that were grafted onto SiO2 support. Our simulations explored peptide trapping, followed by desorption and elution. Trapping in an aqueous mobile phase was initiated by C18 contacts with Lys butyl moieties. This was followed by extensive anchoring of nonpolar side chains (Leu/Ile/Val) in the C18 layer. Exposure to water/acetonitrile triggered peptide desorption in a stepwise fashion; charged sites close to the termini were the first to lift off, followed by the other residues. During water/acetonitrile elution, both peptides preferentially resided close to the pore center. The hydrophilic peptide exhibited no contacts with the stationary phase under these conditions. In contrast, the hydrophobic species underwent multiple transient Leu/Ile/Val binding interactions with C18 chains. These nonpolar interactions represent the foundation of differential peptide retention, in agreement with the experimental elution behavior of the two peptides. Extensive peptide/formate ion pairing was observed in water/acetonitrile, particularly at N-terminal sites. Overall, this work uncovers an unprecedented level of RPLC molecular details, paving the way for MD simulations as a future tool for improving retention prediction algorithms and for the design of novel column materials.

Multifaceted Analysis of Cerebrospinal Fluid and Serum from Progressive Multiple Sclerosis Patients: Potential Role of Vitamin C and Metal Ion Imbalance in the Divergence of Primary Progressive Multiple Sclerosis and Secondary Progressive Multiple Sclerosis.

The progressive forms of multiple sclerosis (MS) primary progressive MS (PPMS) and secondary progressive MS (SPMS) are clinically distinguished by the rate at which symptoms worsen. Little is however known about the pathological mechanisms underlying the differential rate of accumulation of pathological changes. In this study, 1H NMR spectroscopy was used to measure low-molecular-weight metabolites in paired cerebrospinal fluid (CSF) and serum of PPMS, SPMS, and control patients, as well as to determine lipoproteins and glycoproteins in serum samples. Additionally, neurodegenerative and inflammatory markers, neurofilament light (NFL) and chitinase-3-like protein 1 (CHI3L1), and the concentration of seven metal elements, Mg, Mn, Cu, Fe, Pb, Zn, and Ca, were also determined in both CSF and serum. The results indicate that the pathological changes associated with progressive MS are mainly localized in the central nervous system (CNS). More so, PPMS and SPMS patients with comparable disability status are pathologically similar in relation to neurodegeneration, neuroinflammation, and some metabolites that distinguish them from controls. However, the rapid progression of PPMS from the onset may be driven by a combination of neurotoxicity induced by heavy metals coupled with diminished CNS antioxidative capacity associated with differential intrathecal ascorbate retention and imbalance of Mg and Cu.

Controlled Delivery of Vancomycin from Collagen-tethered Peptide Vehicles for the Treatment of Wound Infections.

Despite the great promise of antibiotic therapy in wound infections, antibiotic resistance stemming from frequent dosing diminishes drug efficacy and contributes to recurrent infection. To identify improvements in antibiotic therapies, new antibiotic delivery systems that maximize pharmacological activity and minimize side effects are needed. In this study, we developed elastin-like peptide and collagen-like peptide nanovesicles (ECnVs) tethered to collagen-containing matrices to control vancomycin delivery and provide extended antibacterial effects against methicillin-resistant Staphylococcus aureus (MRSA). We observed that ECnVs showed enhanced entrapment efficacy of vancomycin by 3-fold as compared to liposome formulations. Additionally, ECnVs enabled the controlled release of vancomycin at a constant rate with zero-order kinetics, whereas liposomes exhibited first-order release kinetics. Moreover, ECnVs could be retained on both collagen-fibrin (co-gel) matrices and collagen-only matrices, with differential retention on the two biomaterials resulting in different local concentrations of released vancomycin. Overall, the biphasic release profiles of vancomycin from ECnVs/co-gel and ECnVs/collagen more effectively inhibited the growth of MRSA for 18 and 24 h, respectively, even after repeated bacterial inoculation, as compared to matrices containing free vancomycin, which just delayed the growth of MRSA. Thus, this newly developed antibiotic delivery system exhibited distinct advantages for controlled vancomycin delivery and prolonged antibacterial activity relevant to the treatment of wound infections.

Is there a difference in ruminal fermentation control between cattle and sheep? A meta-analytical test of a hypothesis on differential particle and fluid retention

Ruminant species differ in digestive physiology. The species-specific ratio of mean retention time of particles and fluid (MRTparticle/MRTfluid) in the reticulorumen has been interpreted as controlling ruminal fermentation: a higher ratio indicates of a more distinct ‘washing’ of particulate digesta by liquid. This should increase the harvest of microbes from the reticulorumen, and keep the microbiome in a state of more intense growth; at the same time, this should increase the metabolic losses of faecal nitrogen of microbial origin, leading to lower values for the apparent digestibility of crude protein (aD CP). A systematic difference has been hypothesized between cattle (higher ratio) and sheep (lower ratio), with a lower MRTfluid in cattle due to a higher saliva production. Here, we test these hypotheses in a meta-analysis, using only studies that investigated cattle and sheep simultaneously. The datasets included 12 studies on MRT (of which 11 contained information on feed intake), yielding 102 (or 89) individual data; and 26 studies on protein digestibility (of which 18 contained information on intake), yielding 349 individual data. Cattle had a higher MRTparticle/MRTfluid (2.1) than sheep (1.7), mainly due to longer MRTparticle; only if body mass was included in the model, MRTfluid was significantly shorter in cattle in the larger MRT dataset (and tended to be shorter in the slightly smaller dataset). Cattle had a significantly lower aD CP than sheep, while there was no such difference in overall (dry or organic matter) digestibility. The dataset confirms a shift in fermentation strategy towards microbial production in cattle. While this has been suggested for ruminants in general, cattle appear particularly far on an evolutionary trajectory of maximizing microbial yield from the forestomach. The application of more specific digestive physiology data (like endogenous losses) gained from sheep to cattle should be done bearing these differences in mind.