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Supplementary Figures 1-3 from Retinoblastoma Tumor Suppressor Status Is a Critical Determinant of Therapeutic Response in Prostate Cancer Cells

The retinoblastoma tumor suppressor protein (RB), a critical mediator of cell cycle progression, is functionally inactivated in the majority of human cancers, including prostatic adenocarcinoma. The importance of RB tumor suppressor function in this disease is evident because 25% to 50% of prostatic adenocarcinomas harbor aberrations in RB pathway. However, no previous studies challenged the consequence of RB inactivation on tumor cell proliferation or therapeutic response. Here, we show that RB depletion facilitates deregulation of specific E2F target genes, but does not confer a significant proliferative advantage in the presence of androgen. However, RB-deficient cells failed to elicit a cytostatic response (compared with RB proficient isogenic controls) when challenged with androgen ablation, AR antagonist, or combined androgen blockade. These data indicate that RB deficiency can facilitate bypass of first-line hormonal therapies used to treat prostate cancer. Given the established effect of RB on DNA damage checkpoints, these studies were then extended to determine the impact of RB depletion on the response to cytotoxic agents used to treat advanced disease. In this context, RB-deficient prostate cancer cells showed enhanced susceptibility to cell death induced by only a selected subset of cytotoxic agents (antimicrotubule agents and a topoisomerase inhibitor). Combined, these data indicate that RB depletion dramatically alters the cellular response to therapeutic intervention in prostate cancer cells and suggest that RB status could potentially be developed as a marker for effectively directing therapy. [Cancer Res 2007;67(13):6192–203]

Supplementary Legends 1-3 from Retinoblastoma Tumor Suppressor Status Is a Critical Determinant of Therapeutic Response in Prostate Cancer Cells

Thiamine is a vital co-factor for several anti-inflammatory and antioxidant processes that are critical for mitigation of sepsis-associated inflammation, but pharmacokinetic (PK) analysis has not been reported in horses. We hypothesized that IV thiamine hydrochloride (TH) at increasing dosages would result in corresponding increases in plasma thiamine concentrations without causing adverse effects. A randomized cross-over study was performed in 9 healthy horses that each received TH at 5, 10, and 20 mg/kg IV. Blood was collected immediately prior to drug administration and at several time points thereafter. High-performance liquid chromatography with mass spectrometry was used to quantify thiamine concentrations at each time point. Non-compartmental PK methods showed that IV TH resulted in supraphysiologic plasma concentrations with a short half-life (0.77-1.12 h) and no adverse clinical signs were observed. The terminal rate constant decreased as the dosage increased (p < .0001) and clearance significantly decreased at the 20 mg/kg dosage (p = .0011). The area under the curve (AUC) increased in a non-linear fashion. These findings suggest that thiamine follows non-linear elimination kinetics in horses, which is likely due to saturation of renal elimination. Future studies are needed to identify therapeutic plasma concentrations and develop thiamine dosing recommendations for horses.

Background Producing animal protein while reducing the animal’s impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. Results Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets. Conclusions Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual’s future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.

Background In metabolically stable horses, alpha‐2‐agonists suppress insulin secretion with transient hyperglycemia and rebound hyperinsulinemia. In horses with insulin dysregulation (ID), the effect of alpha‐2‐agonists has not been investigated; however, both the alpha‐2‐agonist‐induced suppression of insulin secretion and rebound hyperinsulinemia could have clinical relevance. Hypothesis/Objectives In horses with ID, alpha‐2‐agonists will alter insulin and glucose dynamics. Animals Seven horses with ID and 7 control horses. Methods In this randomized crossover study, xylazine hydrochloride (1.1 mg/kg) or detomidine hydrochloride (30 μg/kg) were administered IV, and blood was collected for glucose and insulin concentrations at 0, 15, 30, 45, 60, 90, 120, 150, 180, and 300 minutes after administration. Horses received each drug in a random order with a 24‐hour washout period between drugs. Percent change in glucose and insulin concentrations was compared between groups, drugs, and over time with P

Background Risk factors for the prediction of late-onset tumor recurrence in meningioma patients are sparse but needed to estimate duration and control intervals during long-term follow-up in meningioma patients. In this study, we therefore analyzed the value of established risk factors for postoperative meningioma recurrence for the prediction of long-term prognosis in a large, single-center series. Material and methods Correlations of established clinical (age, sex, tumor location, extent of resection), radiological (postoperative tumor volume) and histopathological variables (WHO grade, brain invasion) with tumor relapse were analyzed separately after 3, 5, and 10 years following microsurgery for primary diagnosed intracranial meningioma between 1991 and 2021 in uni- and multivariate analyses. The prognostic value was compared to findings in the entire cohort. Results Within a median follow-up of 29 months (range: 0-307 months), recurrence was observed in 141 patients (12%) after a median PFS of 36 months. PFS among the entire cohort (n=1218) at 3, 5, 10 and 15 years postoperatively were 90%, 84%, 74% and 70%, respectively. Among all patients included, skull base location (HR: 1.51, 95%CI 1.05-2.16; p=.026), Simpson ≥IV resections (HR: 2.41, 95%CI 1.52-3.84; p.05). In 147 patients with a follow-up of ≥ ten years, ten recurrences occurred, and no correlation was found with any of the analyzed variables. Conclusion Skull base tumor location and high-grade histology but not the extent of resection should be considered when planning follow-up duration and intervals following ≥5 years after meningioma surgery. Tumor relapses following more than ten years after surgery are very rare, and corresponding predictors are lacking.

As technological advancements enhance our ability to study population genetics, we must understand how the intrinsic properties of our datasets influence the decisions we make when designing experiments. Filtering parameter thresholds, such as call rate and minimum minor allele frequency (MAF), are known to affect inferences of population structure in reduced representation sequencing (RRS) studies. However, it is unclear to what extent the impacts of these parameter choices vary across datasets. Here, we reviewed literature on filtering choices and levels of genetic differentiation across RRS studies on wild populations to highlight the diverse approaches that have been used. Next, we hypothesized that choices in filtering thresholds would have the greatest impact when analyzing datasets with low levels of genetic differentiation between populations. To test this hypothesis, we produced seven simulated RRS datasets with varying levels of population structure, and analyzed them using four different combinations of call rate and MAF. We performed the same analysis on two empirical RRS datasets (low or high population structure). Our simulated and empirical results suggest that the effects of filtering choices indeed vary based on inherent levels of differentiation: specifically, choosing stringent filtering choices was important to detect distinct populations that were slightly differentiated, but not those that were highly differentiated. As a result, experimental design and analysis choices need to consider attributes of each specific dataset. Based on our literature review and analyses, we recommend testing a range of filtering parameter choices, and presenting all results with clear justification for ultimate filtering decisions used in downstream analyses.

Fatty acids from microalgae are attractive compounds for catalytic upgrading to chemicals, but their extraction often requires multi-step procedures and the use of various organic solvents. To relieve this bottleneck, we propose a straightforward approach of combined extraction and catalytic functionalization via olefin cross-metathesis (ethenolysis and butenolysis) in supercritical CO2 (scCO2). This is demonstrated for Phaeodactylum tricornutum microalgae biomass. ScCO2 at optimum conditions (90 °C, 620 atm, ρ(CO2) = 0.90 g mL−1) extracted the lipids selectively and quantitatively from previously disrupted cells, while organic solvent extraction for comparison additionally extracted polar diacylglycerides and chlorophylls. In a one-pot approach, olefin cross-metathesis of the unsaturated fatty acids (FA16:1, FA18:1 and FA20:5) by alkenolysis yielded the desirable mid-chain olefin and unsaturated ester products. The product spectrum compares to alkenolysis of individual model compounds in scCO2 as well as of separately scCO2 extracted microalgae oil. Both these ethenolysis and butenolysis proceed with conversions of more than 81% and high selectivities to the desired products. This biorefinery approach was further illustrated by the simultaneous extraction and catalytic isomerizing alkoxycarbonylation in scCO2. published

The greatest source of global anthropogenic methane (CH4) emissions is from ruminant livestock. Multiple mitigation strategies in livestock are currently being explored. Of these breeding for lower CH4 emitting ruminants has the advantage of being permanent and cumulative and universally applicable to all classes of livestock. Here, we show that methane emissions can be predicted by the complex community of microbiota sampled from rumens enabling evaluation of systems and individuals. Furthermore, there is evidence that the microbial community is controlled not only be the feed substrate but also by the host itself and that selecting hosts that favour a microbial fermentation with lowered methane emissions changes the energy source to the animal, and in turn both rumen physiology and body composition. Current methods for obtaining microbial DNA and subsequent sequencing of an animal’s microbiome, however, are too expensive to implement in commercial selection programs. A methodology that offers fast, low-cost, high throughput profiling of rumen microbiomes using Genotyping-by-sequencing (GBS) has been developed using an unbiased reference free approach to group microbiota. To date, this has been applied to over 4000 sheep samples and validated in cattle. Results show that microbial profiles are heritable and correlated with methane emissions and feed intake. This research is part of a flagship program funded by the global research alliance to disseminate global access to technologies that lower greenhouse gas emissions in ruminant livestock.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important global swine diseases from both an economic and animal welfare standpoint. PRRS has plagued the US swine industry for over 25 yr, and containment of PRRS virus (PRRSV) has been unsuccessful to date. The primary phase of PRRS, tracked by serum viremia, typically clears between 21 and 42 d postinfection (dpi) but tonsils are a main site of PRRSV persistence and PRRSV can be detected in tonsils in excess of 150 dpi. Measuring tonsil virus (TV) levels at late stages of infection (6 to 7 wk postinfection) can be used to assess tonsil persistence, as levels of virus in tonsil at this time likely influence how long the virus will remain in the tissue. TV levels were measured on pigs experimentally infected with either the NVSL-97-7895 (NVSL; n = 524) or KS-2006-72109 (KS06; n = 328) PRRSV type 2 isolates across five trials. The objectives of this study were to (i) estimate the heritability of TV levels at 35 or 42 dpi; (ii) identify factors the affect TV level, including serum viremia; (iii) identify genomic regions associated with TV level; and (iv) compare results for the two PRRSV isolates. TV level was lowly heritable for both isolates (NVSL: 0.05 ± 0.06; KS06: 0.11 ± 0.10). Level of TV was phenotypically associated with traits related to viral clearance from serum: pigs with low TV levels had an earlier and faster rate of maximal serum viral clearance, lower total serum viral load, and lower viremia level at 35 or 42 dpi. Although no genomic regions with major effects on TV level were identified, several showed some association (>0.1% of total genetic variance in the NVSL-infected dataset, the KS06-infected dataset, and the combined dataset). These regions contained the genes CCL1, CCL2, CCL8, HS3ST3B1, GALNT10, TCF7, C1QA/B/C, HPSE, G0S2, and CD34, which are involved in viral infiltration or replication, immune cell migration, and viral clearance from tissue. Results were similar between the two PRRSV isolates. In conclusion, selection for viral clearance traits in serum may reduce PRRSV persistence in the tonsil across PRRSV isolates. However, genetic correlations need to be estimated to determine whether this will be successful.

Genetic and antigenic variability between Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) isolates has encumbered vaccine development. Here, the genetic basis of PRRSV antibody response was assessed using data from experimental infection trials of commercial crossbred weaner pigs across with one of two distinct PRRSV isolates, NVSL-97-7895 (~750 pigs) and KS-2006-72109 (~450 pigs). Objectives were to estimate the genetic parameters of antibody response, measured as the sample to positive ratio (S:P) of PRRSV N-protein specific IgG in serum at 42 d post infection (dpi); assess the relationship of S:P at 42 dpi with serum viremia and growth under infection; and identify genomic regions associated with S:P at 42 dpi. Estimates of heritability of S:P at 42 dpi for NVSL and KS06 were 0.31 ± 0.09 and 0.40 ± 0.10 and appeared to be under similar genetic control (genetic correlation 0.73 ± 0.39). Estimates of genetic correlations of S:P were generally weak with viral load (NVSL: -0.20 ± 0.18; KS06: -0.69 ± 0.20), measured as area under the curve of log10 serum viremia from 0 to 21 dpi, and with weight gain (WG) from 0 to 42 dpi (NVSL: -0.38 ± 0.19; KS06: -0.08 ± 0.25). However, genetic correlations of S:P at 42 dpi with daily serum viremia and with 3-d WG revealed dynamic relationships, with S:P at 42 dpi having the strongest negative genetic correlations with daily viremia when IgG production starts (10-20 dpi), and negative genetic correlations with WG early after infection but positive later on. This suggests that animals that placed more emphasis on immune response early in infection reaped benefits of that later in infection by more effectively clearing the virus. The WUR10000125 SNP on SSC4, previously associated with response to PRRSV, did not have a significant effect on S:P at 42 dpi (P > 0.05) but genotype-specific genetic correlations of S:P with daily viremia and 3-d WG suggested that the lower WG of pigs with the unfavorable AA WUR10000125 genotype may be due to their utilization of a more energetically costly host response compared to pigs with the favorable genotype. Genome-wide association studies identified three SNPs in the Major Histocompatibility Complex associated with S:P that explained ~10 (NVSL) and 45% (KS06) of the genetic variance but were not associated with viremia or WG. In conclusion, antibody response to PRRSV infection is a possible biomarker for improved host response to PRRSV infection.

A dual catalysis approach enables selective functionalization of unconventional feedstocks composed of complex fatty acid mixtures with highly unsaturated portions like eicosapentaenoate (20:5) along with monounsaturated compounds. The degree of unsaturation is unified by selective heterogeneous hydrogenation on Pd/γ-Al2O3, complemented by effective activation to a homogeneous carbonylation catalyst [(dtbpx)PdH(L)]+ by addition of diprotonated diphosphine (dtbpxH2)(OTf)2. By this one-pot approach, neat 20:5 as a model substrate is hydrogenated to up to 80% to the monounsaturated analogue (20:1), this is functionalized to the desired C21 α,ω-diester building block with a linear selectivity of over 90%. This catalytic approach is demonstrated to be suitable for crude microalgae oil from Phaeodactylum tricornutum genetically engineered for this purpose, as well as tall oil, an abundant waste material. Both substrates were fully converted with an overall selectivity to the linear α,ω-diester of up to 75%.

Microbial community profiles have been associated with a variety of traits, including methane emissions in livestock. These profiles can be difficult and expensive to obtain for thousands of samples (e.g. for accurate association of microbial profiles with traits), therefore the objective of this work was to develop a low-cost, high-throughput approach to capture the diversity of the rumen microbiome. Restriction enzyme reduced representation sequencing (RE-RRS) using ApeKI or PstI, and two bioinformatic pipelines (reference-based and reference-free) were compared to bacterial 16S rRNA gene sequencing using repeated samples collected two weeks apart from 118 sheep that were phenotypically extreme (60 high and 58 low) for methane emitted per kg dry matter intake (n = 236). DNA was extracted from freeze-dried rumen samples using a phenol chloroform and bead-beating protocol prior to RE-RRS. The resulting sequences were used to investigate the repeatability of the rumen microbial community profiles, the effect of laboratory and analytical method, and the relationship with methane production. The results suggested that the best method was PstI RE-RRS analyzed with the reference-free approach, which accounted for 53.3±5.9% of reads, and had repeatabilities of 0.49±0.07 and 0.50±0.07 for the first two principal components (PC1 and PC2), phenotypic correlations with methane yield of 0.43±0.06 and 0.46±0.06 for PC1 and PC2, and explained 41±8% of the variation in methane yield. These results were significantly better than for bacterial 16S rRNA gene sequencing of the same samples (p

The use of topical interferon alpha-2b is a well-established treatment for ocular surface squamous neoplasia. There have been numerous reports on its efficacy and high safety profile. Benign reactive lymphoid hyperplasia in ocular tissues has not been previously documented by histopathology after interferon treatment. This case report describes a 55-year-old man who had successful resolution of his ocular surface squamous neoplasia after topical treatment, but developed forniceal tissue deposits. The appearance of the lesions was unexpected and alerted the clinician to the possibility of further neoplastic extension. Excisional biopsy of the lesions confirmed benign reactive lymphoid hyperplasia and resolved with no recurrence.

Microbial community profiles have been associated with a variety of traits, including methane emissions in livestock, however, these profiles can be difficult and expensive to obtain for thousands of samples. The objective of this work was to develop a low-cost, high-throughput approach to capture the diversity of the rumen microbiome. Restriction enzyme reduced representation sequencing (RE-RRS) using ApeKI or PstI, and two bioinformatic pipelines (reference-based and reference-free) were compared to 16S rRNA gene sequencing using repeated samples collected two weeks apart from 118 sheep that were phenotypically extreme (60 high and 58 low) for methane emitted per kg dry matter intake (n=236). DNA was extracted from freeze-dried rumen samples using a phenol chloroform and bead-beating protocol prior to sequencing. The resulting sequences were used to investigate the repeatability of the rumen microbial community profiles, the effect of host genetics, laboratory and analytical method, and the genetic and phenotypic correlations with methane production. The results suggested that the best method was PstI RE-RRS analyzed with the reference-free approach via a correspondence analysis, with estimates for repeatability of 0.62±0.06, heritability 0.31±0.29, and genetic and phenotypic correlation with methane emissions of 0.88±0.25 and 0.64±0.05 respectively for the first component of correspondence analysis. The reference-free approach assigned 62.0±5.7% of reads to common 65 bp tags, much higher than the reference-based approach of 6.8±1.8% of reads assigned. Sensitivity studies suggested approximately 2000 samples could be sequenced in a single lane on an Illumina HiSeq 2500, therefore the current work of 118 samples/lane and future proposed 384 samples/lane are well within that threshold. Our approach is now being used to investigate host factors affecting the rumen and its association with a variety of production and environmental traits. With minor adaptations, our approach could be used to obtain microbial profiles from other metagenomic samples.

Coprinopsis cinerea is an environmental fungus which can cause disseminated infections in immunocompromised patients, often leading to death. Here we report the case of a paediatric patient with an invasive wound infection due to C. cinerea, which was successfully treated with surgical debridement and oral posaconazole. Keywords: Coprinopsis, hormographiella, immunosuppression, posaconazole, skin, wound infection