Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat

BACKGROUND: Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult to study AS evolution in mammals and its biomedical implications. RESULTS: Here we describe a cross-species EST-to-genome comparison algorithm (ENACE) that can identify novel exons for EST-scanty species and distinguish conserved and lineage-specific exons. The identified exons represent not only novel exons but also evolutionarily meaningful AS events that are not previously annotated. A genome-wide AS analysis in human, mouse and rat using ENACE reveals a total of 758 novel cassette-on exons and 167 novel retained introns that have no EST evidence from the same species. RT-PCR-sequencing experiments validated ~50 ~80% of the tested exons, indicating high presence of exons predicted by ENACE. ENACE is particularly powerful when applied to closely related species. In addition, our analysis shows that the ENACE-identified AS exons tend not to pass the nonsynonymous-to-synonymous substitution ratio test and not to contain protein domain, implying that such exons may be under positive selection or relaxed negative selection. These AS exons may contribute to considerable inter-species functional divergence. Our analysis further indicates that a large number of exons may have been gained or lost during mammalian evolution. Moreover, a functional analysis shows that inter-species divergence of AS events may be substantial in protein carriers and receptor proteins in mammals. These exons may be of interest to studies of AS evolution. The ENACE programs and sequences of the ENACE-identified AS events are available for download. CONCLUSION: ENACE can identify potential novel cassette exons and retained introns between closely related species using a comparative approach. It can also provide information regarding lineage- or species-specificity in transcript isoforms, which are important for evolutionary and functional studies

INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events

Insertion and deletion (indel) events usually have dramatic effects on genome structure and gene function. Species-specific indels have been demonstrated to be associated with species-unique traits. Currently, indel identifications mainly rely on pair-wise sequence alignments (the ‘pair-wise indels’), which suffer lack of discrimination of species specificity and insertion versus deletion. Also, there is no freely accessible web server for genome-wide identification of indels. Therefore, we develop a web server—INDELSCAN— to identify four types of indels using multiple sequence alignments that include sequences from one target, one subject and ≥1 out-group species. The four types of indels identified encompass target species-specific, subject species-specific, non-species-specific and target-subject pair-wise indels. Insertions and deletions are discriminated with reference to out-group sequences. The genomic locations (5′UTR, intron, CDS, 3′UTR and intergenic region) of these indels are also provided for functional analysis. INDELSCAN provides genomic sequences and gene annotations from a wide spectrum of taxa for users to select from, including nine target species (human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), dog (Canis familiaris), opossum (Monodelphis domestica), chicken (Gallus gallus), zebrafish (Danio rerio), fly (Drosophila melanogaster) and yeast (Saccharomyces cerevisiae) and >35 subject/out-group species, ranging from yeasts to mammals. The server also provides analytic figures and supports indel identification from user-uploaded alignments/annotations. INDELSCAN is freely accessible at http://indelscan.genomics.sinica.edu.tw/IndelScan/

Biodiesel Produced from Catalyzed Transesterification of Triglycerides Using ion-Exchanged Zeolite Beta and MCM-22

AbstractIn this work, biodiesel production from catalyzed transesterification of triglycerides with excess methanol was studied by using ion-exchanged Zeolite Beta and MCM-22 as heterogeneous catalysts. Zeolite Beta and MCM-22 were synthesized with hydrothermal processes and, subsequently, modified by ion-exchanged with alkali ions. These as-obtained zeolite catalysts could yield a high conversion of triglycerides to biodiesel. The conversion efficiency was largely affected by crystallinity and frameworks of zeolite support, pH value of alkali ion-exchange solutions and alkali loadings onto the zeolite support. Furthermore, the effects of the duration of the sodium ion-exchange process on the final conversion efficiency of triolein to biodiesel, both the as-prepared Zeolite MCM-22 and Zeolite Beta catalysts were used. The effect of the duration of the sodium ion-exchange process is insignificant in transesterification using Na-ion-exchanged Zeolite MCM-22 catalysts from 0.5 to 4h. In contrast, the conversion efficiency of triolein to biodiesel reached ca. 95% in 0.5hours of transesterification using Zeolite Beta ion-exchanged with 3 mmol-eq. Na+/g cat for 0.5hours

Interpretation of spin wave modes in Co/Ag nanodot arrays probed by broadband ferromagnetic resonance

Ferromagnetic resonance (FMR) and the measurement of magnetization dynamics in general have become sophisticated tools for the study of magnetic systems at the nanoscale. Nanosystems, such as the nanodots of this study, are technologically important structures, which find applications in a number of devices, such as magnetic storage and spintronic systems. In this work, we describe the detailed investigation of cobalt nanodots with a 200 nm diameter arranged in a square pitch array with a periodicity of 400 nm. Due to their size, such structures can support standing spin-wave modes, which can have complex spectral responses. To interpret the experimentally measured broadband FMR, we are comparing the spectra of the nanoarray structure with the unpatterned film of identical thickness. This allows us to obtain the general magnetic properties of the system, such as the magnetization, g-factor and magnetic anisotropy. We then use state-of-the-art simulations of the dynamic response to identify the nature of the excitation modes. This allows us to assess the boundary conditions for the system. We then proceed to calculate the spectral response of our system, for which we obtained good agreement. Indeed, our procedure provides a high degree of confidence, since we have interpreted all the experimental data to a good degree of accuracy. In presenting this work, we provide a full description of the theoretical framework and its application to our system, and we also describe in detail the novel simulation method used.Comment: 20 pages, 14 figure

Association of clinical symptomatic hypoglycemia with cardiovascular events and total mortality in type 2 diabetes a nationwide population-based study

OBJECTIVE Hypoglycemia is associated with serious health outcomes for patients treated for diabetes. However, the outcome of outpatients with type 2 diabetes who have experienced hypoglycemia episodes is largely unknown. RESEARCH DESIGN AND METHODS The study population, derived from the National Health Insurance Research Database released by the Taiwan National Health Research Institutes during 1998–2009, comprised 77,611 patients with newly diagnosed type 2 diabetes. We designed a prospective study consisting of randomly selected hypoglycemic type 2 diabetic patients and matched type 2 diabetic patients without hypoglycemia. We investigated the relationships of hypoglycemia with total mortality and cardiovascular events, including stroke, coronary heart disease, cardiovascular diseases, and all-cause hospitalization. RESULTS There were 1,844 hypoglycemic events (500 inpatients and 1,344 outpatients) among the 77,611 patients. Both mild (outpatient) and severe (inpatient) hypoglycemia cases had a higher percentage of comorbidities, including hypertension, renal diseases, cancer, stroke, and heart disease. In multivariate Cox regression models, including diabetes treatment adjustment, diabetic patients with hypoglycemia had a significantly higher risk of cardiovascular events during clinical treatment periods. After constructing a model adjusted with propensity scores, mild and severe hypoglycemia still demonstrated higher hazard ratios (HRs) for cardiovascular diseases (HR 2.09 [95% CI 1.63–2.67]), all-cause hospitalization (2.51 [2.00–3.16]), and total mortality (2.48 [1.41–4.38]). CONCLUSIONS Symptomatic hypoglycemia, whether clinically mild or severe, is associated with an increased risk of cardiovascular events, all-cause hospitalization, and all-cause mortality. More attention may be needed for diabetic patients with hypoglycemic episodes.Pai-Feng Hsu, Shih-Hsien Sung, Hao-Min Cheng, Jong-Shiuan Yeh, Wen-Ling Liu, Wan-Leong Chan, Chen-Huan Chen, Pesus Chou, Shao-Yuan Chuan

Cancer stem cells, not bulk tumor cells, determine mechanisms of resistance to SMO inhibitors.

The emergence of treatment resistance significantly reduces the clinical utility of many effective targeted therapies. Although both genetic and epigenetic mechanisms of drug resistance have been reported, whether these mechanisms are stochastically selected in individual tumors or governed by a predictable underlying principle is unknown. Here, we report that the dependence of cancer stem cells (CSCs), not bulk tumor cells, on the targeted pathway determines the molecular mechanism of resistance in individual tumors. Using both spontaneous and transplantable mouse models of sonic hedgehog (SHH) medulloblastoma (MB) treated with an SHH/Smoothened inhibitor, sonidegib/LDE225, we show that genetic-based resistance occurs only in tumors that contain SHH-dependent CSCs (SD-CSCs). In contrast, SHH MBs containing SHH-dependent bulk tumor cells but SHH-independent CSCs (SI-CSCs) acquire resistance through epigenetic reprogramming. Mechanistically, elevated proteasome activity in SMOi-resistant SI-CSC MBs alters the tumor cell maturation trajectory through enhanced degradation of specific epigenetic regulators, including histone acetylation machinery components, resulting in global reductions in H3K9Ac, H3K14Ac, H3K56Ac, H4K5Ac, and H4K8Ac marks and gene expression changes. These results provide new insights into how selective pressure on distinct tumor cell populations contributes to different mechanisms of resistance to targeted therapies. This insight provides a new conceptual framework to understand responses and resistance to SMOis and other targeted therapies

Observation of Andreev reflection in the c-axis transport of Bi_2Sr_2CaCu_2O_{8+x} single crystals near T_c and search for the preformed-pair state

We observed an enhancement of the $c$-axis differential conductance around the zero-bias in Au$/$Bi$_2$Sr$_2$CaCu$_2$O$_{8+x}$ (Bi2212) junctions near the superconducting transition temperature $T_c$. We attribute the conductance enhancement to the Andreev reflection between the surface Cu-O bilayer with suppressed superconductivity and the neighboring superconducting inner bilayer. The continuous evolution from depression to an enhancement of the zero-bias differential conductance, as the temperature approaches $T_c$ from below, points to weakening of the barrier strength of the non-superconducting layer between adjacent Cu-O bilayers. We observed that the conductance enhancement persisted up to a few degrees above $T_c$ in junctions prepared on slightly overdoped Bi2212 crystals. However, no conductance enhancement was observed above $T_c$ in underdoped crystals, although recently proposed theoretical consideration suggests an even wider temperature range of enhanced zero-bias conductance. This seems to provide negative perspective to the existence of the phase-incoherent preformed pairs in the pseudogap state.Comment: 17 pages including 4 figure

A Simplified Technique of Percutaneous Hepatic Artery Port-Catheter Insertion for the Treatment of Advanced Hepatocellular Carcinoma with Portal Vein Invasion

OBJECTIVE: We assessed the outcomes of a simplified technique for the percutaneous placement of a hepatic artery port-catheter system for chemotherapy infusion in advanced hepatocellular carcinoma with portal vein invasion. MATERIALS AND METHODS: From February 2003 to February 2008, percutaneous hepatic artery port-catheter insertion was performed in 122 patients who had hepatocellular carcinoma with portal vein invasion. The arterial access route was the common femoral artery. The tip of the catheter was wedged into the right gastroepiploic artery without an additional fixation device. A side hole was positioned at the distal common hepatic artery to allow the delivery of chemotherapeutic agents into the hepatic arteries. Coil embolization was performed only to redistribute to the hepatic arteries or to prevent the inadvertent delivery of chemotherapeutic agents into extrahepatic arteries. The port chamber was created at either the supra-inguinal or infra-inguinal region. RESULTS: Technical success was achieved in all patients. Proper positioning of the side hole was checked before each scheduled chemotherapy session by port angiography. Catheter-related complications occurred in 19 patients (16%). Revision was achieved in 15 of 18 patients (83%). CONCLUSION: This simplified method demonstrates excellent technical feasibility, an acceptable range of complications, and is hence recommended for the management of advanced hepatocellular carcinoma with portal vein thrombosis.ope