Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations

U2AF1 is one of the most recurrently mutated splicing factors in lung adenocarcinoma and has been shown to cause transcriptome-wide pre-mRNA splicing alterations; however, the full-length altered mRNA isoforms associated with the mutation are largely unknown. To better understand the impact U2AF1 has on full-length isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without a U2AF1 S34F mutation. We identified 49,366 multi-exon transcript isoforms, more than half of which did not match GENCODE or short-read-assembled isoforms. We found 198 transcript isoforms with significant expression and usage changes relative to WT, only 68% of which were assembled by short reads. Expression of isoforms from immune-related genes is largely down-regulated in mutant cells and without observed splicing changes. Finally, we reveal that isoforms likely targeted by nonsense-mediated decay are down-regulated in U2AF1 S34F cells, suggesting that isoform changes may alter the translational output of those affected genes. Altogether, our work provides a resource of full-length isoforms associated with U2AF1 S34F in lung cells.

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

Cellular exposure to free fatty acids (FFAs) is implicated in the pathogenesis of obesity-associated diseases. However, there are no scalable approaches to comprehensively assess the diverse FFAs circulating in human plasma. Furthermore, assessing how FFA-mediated processes interact with genetic risk for disease remains elusive. Here, we report the design and implementation of fatty acid library for comprehensive ontologies (FALCON), an unbiased, scalable, and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids associated with decreased membrane fluidity. Furthermore, we prioritized genes that reflect the combined effects of harmful FFA exposure and genetic risk for type 2 diabetes (T2D). We found that c-MAF-inducing protein (CMIP) protects cells from FFA exposure by modulating Akt signaling. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism.

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

Cellular exposure to free fatty acids (FFA) is implicated in the pathogenesis of obesity-associated diseases. However, studies to date have assumed that a few select FFAs are representative of broad structural categories, and there are no scalable approaches to comprehensively assess the biological processes induced by exposure to diverse FFAs circulating in human plasma. Furthermore, assessing how these FFA- mediated processes interact with genetic risk for disease remains elusive. Here we report the design and implementation of FALCON (Fatty Acid Library for Comprehensive ONtologies) as an unbiased, scalable and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids (MUFAs) with a distinct lipidomic profile associated with decreased membrane fluidity. Furthermore, we developed a new approach to prioritize genes that reflect the combined effects of exposure to harmful FFAs and genetic risk for type 2 diabetes (T2D). Importantly, we found that c-MAF inducing protein (CMIP) protects cells from exposure to FFAs by modulating Akt signaling and we validated the role of CMIP in human pancreatic beta cells. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism.

Highlights

FALCON (Fatty Acid Library for Comprehensive ONtologies) enables multimodal profiling of 61 free fatty acids (FFAs) to reveal 5 FFA clusters with distinct biological effectsFALCON is applicable to many and diverse cell typesA subset of monounsaturated FAs (MUFAs) equally or more toxic than canonical lipotoxic saturated FAs (SFAs) leads to decreased membrane fluidityNew approach prioritizes genes that represent the combined effects of environmental (FFA) exposure and genetic risk for diseaseC-Maf inducing protein (CMIP) is identified as a suppressor of FFA-induced lipotoxicity via Akt-mediated signaling.

Solid bioprocess of tarbush (Flourensia cernua) leaves for β-glucosidase production by Aspergillus niger: initial approach to fiber-glycoside interaction for enzyme induction

Commercial cellulase production has increased in recent years and consistent research has been carried out to improve levels of β-glucosidase. Bioprocesses have been successfully adapted to produce this enzyme, with solid-state fermentations as the best-suited technique involving fungi. The aim of this study was to use leaves of tarbush (Flourensia cernua), an abundant shrub of the Chihuahuan Desert, as a carbon source for β-glucosidase production by Aspergillus niger. During the solid bioprocess, this enzyme reached its peak production at 36 h of culture with 3876.6 U/L. There is a particular interest in the substrate composition because of the possibility of phenolic glycosides having an important role in β-glucosidase production. HPLC-MS analyses showed that glycosides were present with the highest accumulation at 36 h of fungal culture. Luteolin and apigenin glycosides [1.8 and 2.4 absorbance units, respectively] were also detected and showed their highest point of detection alongside the highest β-glucosidase activity. No apparent changes in cellulose were observed, while hemicellulose content decreased, which could be related to production and activity of β-glucosidase. This study shows that leaves of F. cernua are an important raw material for β-glucosidase production and give a source of compounds of added value which also may have an important role for β-glucosidase production.

Laryngeal Granular Cell Tumor

Granular cell tumor (GCT) of the larynx is an uncommon, benign laryngeal neoplasm. Abrikossoff first described the tumor in 1926 as myoblastoma. The origin of this tumor has been debated in the literature. Most of the authors believe that the tumor is of neural origin due to the characteristic immunohistochemical-staining pattern. The authors describe two cases of laryngeal GCTs located in different sites with a review of the histological and clinical features, the differential diagnosis, and the treatment and the prognosis of the tumor.

Effect of prenatal uterine position on male and female rats sexual behavior

It is well known that female rats developing close to a male in utero show a higher frequency of heterotypical or male-like behavior in adulthood, and have longer anogenital distances. The present investigation was designed to evaluate the in utero masculine influence on the homotypical sexual behavior of male and female rats. Also explored was the influence on body weight on Gestation Day 21 (day of cesarean delivery) and 21, 40. and 120 days after birth, testicle weight following the gonadectomy of males on Day 40, and serum testosterone in males and females on the day of delivery. The presence of a contiguous male fetus located caudally with respect to uterine blood flow led to the masculinization of male-like behavior in male rats, the defeminization of female like behavior in females and to increased body weights on Day 21 of gestation in both sexes. No significant differences were detected in the remaining parameters. Findings indicated a gradation in the intensity of expression of male and female sexual behavior in adulthood related to the intrauterine position resulting in interindividual variability. The possible implication of this physiological phenomenon in the structure of rodent populations is discussed.

Comparative study of the use of poly(glycolic acid), calcium alginate and pluronics in the engineering of autologous porcine cartilage

New cartilage formation has been successfully achieved by technology referred to as tissue engineering. Polymers and hydrogels such as poly(glycolic acid), calcium alginate, and poly(ethylene) and poly(propylene) hydrogels have been used as cell carriers to regenerate cartilage in the nude mouse model. The next step toward human applications of engineered cartilage is to demonstrate their potential in immunocompetent animal models. This study compared the suitability of three polymers for generating tissue engineered elastic cartilage using autologous cells in an immuno-competent porcine animal model. Auricular cartilage was obtained from pigs. Chondrocytes were isolated onto fiber based poly(glycolic acid) (PGA) scaffolds or suspended in calcium alginate or pluronic F127 gel at constant concentrations. Chondrocyte-polymer constructs were either implanted (PGA) or injected (calcium alginate and pluronic) as autologous implants subcutaneously into the pigs from which the cells had been isolated. Specimens were harvested and analyzed grossly and historically after 6 weeks in vivo. All explants demonstrated cartilage formation to a variable degree. When using PGA or calcium alginate, the overall histological appearance of the tissue formed is that of fibrocartilage with thick bundles of collagen dispersed in the tissue. When using pluronics as scaffold, histologic features resemble those of native elastic cartilage, showing a more organized arrangement of the cells, which seems to correlate to functional properties as elastin presence in the tissue engineered cartilage. Elastic cartilage engineered in an immunocompetent animal model varies with the type of polymer used. The behavior of the cell-polymer constructs is not fully understood and outcome seems to be related to several factors, including inflammatory reaction. Further studies with similar models are needed to determine the feasibility of engineering tissue generated from different cell-polymer constructs prior to human application.

Isolation from Trypanosoma cruzi-infected mice of CD8+, MHC-restricted cytotoxic T cells that lyse parasite-infected target cells

Recent in vivo depletion studies in mice demonstrated that CD8+ T cells play a critical role in acute resistance to experimental Trypanosoma cruzi infections. As part of efforts to characterize these protective CD8+ T cell effector populations, we report here that splenic lymphocytes from mice chronically infected with T. cruzi can be induced to express high levels of cytolytic activity after stimulation in vitro with irradiated T. cruzi-infected macrophages. Cytolytic activity can either be detected using a nonspecific lectin-dependent 51Cr-release assay or using 51Cr-labeled T. cruzi-infected target cells. Fresh splenocytes from chronically infected mice stimulated with T. cruzi-infected macrophages exhibit relatively "promiscuous" killing activity inasmuch as significant lysis of both T. cruzi-infected and uninfected syngeneic and allogeneic cells is detected. However, subsequent rounds of in vitro stimulation lead to the expression of lytic activity that is T. cruzi Ag-specific and MHC-restricted. Several short term in vitro maintained cytolytic T cell lines were shown to have mixed phenotypes by FACS analysis; approximately 50% to 75% of the cells in these populations were CD4-, CD8+, whereas 20% to 40% were CD4-, CD8-. Experiments in which effector cells were positively selected by adherence to anti-CD8 mAb-treated plates confirmed that CD8+ T cell could exhibit Ag-specific cytolytic activity against T. cruzi-infected target cells. Efforts are under way to clone these CTL to test their in vivo function and to determine their Ag specificity.

Isolation from Trypanosoma cruzi-infected mice of CD8+, MHC-restricted cytotoxic T cells that lyse parasite-infected target cells

Recent in vivo depletion studies in mice demonstrated that CD8+ T cells play a critical role in acute resistance to experimental Trypanosoma cruzi infections. As part of efforts to characterize these protective CD8+ T cell effector populations, we report here that splenic lymphocytes from mice chronically infected with T. cruzi can be induced to express high levels of cytolytic activity after stimulation in vitro with irradiated T. cruzi-infected macrophages. Cytolytic activity can either be detected using a nonspecific lectin-dependent 51Cr-release assay or using 51Cr-labeled T. cruzi-infected target cells. Fresh splenocytes from chronically infected mice stimulated with T. cruzi-infected macrophages exhibit relatively "promiscuous" killing activity inasmuch as significant lysis of both T. cruzi-infected and uninfected syngeneic and allogeneic cells is detected. However, subsequent rounds of in vitro stimulation lead to the expression of lytic activity that is T. cruzi Ag-specific and MHC-restricted. Several short term in vitro maintained cytolytic T cell lines were shown to have mixed phenotypes by FACS analysis; approximately 50% to 75% of the cells in these populations were CD4-, CD8+, whereas 20% to 40% were CD4-, CD8-. Experiments in which effector cells were positively selected by adherence to anti-CD8 mAb-treated plates confirmed that CD8+ T cell could exhibit Ag-specific cytolytic activity against T. cruzi-infected target cells. Efforts are under way to clone these CTL to test their in vivo function and to determine their Ag specificity.

Antibiotic management of outpatients with endocarditis due to penicillin-susceptible streptococci

Thirty patients with endocarditis caused by penicillin-susceptible streptococci were enrolled in one of two groups in this study. Fifteen patients received ceftriaxone (2 g once daily) for 4 weeks; the other 15 received the same dosage of ceftriaxone for 2 weeks and then received oral amoxicillin (1 g four times a day) for 2 weeks. For the 27 patients treated predominantly as outpatients, 380 days of hospitalization were avoided. Clinical cure was achieved for all patients in both groups. We conclude that ceftriaxone, alone or followed by a course of amoxicillin, is an efficacious mode of treatment for infective endocarditis caused by penicillin-susceptible streptococci. Treatment with these agents can be administered predominantly on an outpatient basis.

[Relationship between various erythrocyte antigens and hematologic disorders]

The antigen pattern pertaining to the ABO (A, B, AB, O (H)), Rh (D, C, c, E, e), Duffy (Fya and b), Kell (K, k) and MNS (M, N) systems were determined in 144 patients between 1 and 74 years of age who had leukemia, lymphoma or myeloma. An association of phenotype Fy (a-b+) with acute lymphatic leukemia and phenotype NN with chronic myeloid leukemia was demonstrated (p less than 0.05, chi sq). Other associations were statistically not significant. Thus, a susceptibility of the aforementioned phenotype patterns to the type of leukemia described is suggested by these findings.

A prospective evaluation of bacteremic patients with chronic liver disease

We prospectively studied 51 consecutive bacteremic patients with chronic liver disease in order to evaluate their clinical presentation and to assess the relationship of various clinical parameters to mortality. Forty-two patients had alcoholic liver disease and 40 were in Class C, by the Pugh modification of Child's criteria. Soft tissue infections were the most common source of bacteremia, followed by pneumonia, spontaneous bacterial peritonitis and urinary tract infection. Gram positive organisms were isolated in 69% of cases, and Gram negative ones in 31%. In nine patients, no source of bacteremia was detected. Leukocytosis occurred in 59% of patients and bandemia in only 41%. Although appropriate antibiotic therapy was begun in all cases on admission, 17 patients (33%) died in the hospital. Of 38 clinical parameters evaluated, multivariate analysis revealed that the three variables contributing the most independent information toward predicting in-hospital mortality were the absence of a history of fever, an elevated serum creatinine and marked leukocytosis. Improved understanding of the pathophysiologic relationship between these parameters and patient outcome may enable us to improve the therapy of bacteremic patients with chronic liver disease.