Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes

Global spectrum of CNVs is required to catalog variations to provide a high-resolution on the dynamics of genome-organization and human migration. In this study, we performed genome-wide genotyping using high-resolution arrays and identified 44,109 CNVs from 1,715 genomes across 12 populations. The study unraveled the force of independent evolutionary dynamics on genome-organizational plasticity across populations. We demonstrated the use of CNV tool to study human migration and identified a second major settlement establishing new migration routes in addition to existing ones.     

A Gamma-Knife-Enabled Mouse Model of Cerebral Single-Hemisphere Delayed Radiation Necrosis

Purpose

To develop a Gamma Knife-based mouse model of late time-to-onset, cerebral radiation necrosis (RN) with serial evaluation by magnetic resonance imaging (MRI) and histology.

Methods and Materials

Mice were irradiated with the Leksell Gamma Knife^® (GK) Perfexion^TM (Elekta AB; Stockholm, Sweden) with total single-hemispheric radiation doses (TRD) of 45- to 60-Gy, delivered in one to three fractions. RN was measured using T2-weighted MR images, while confirmation of tissue damage was assessed histologically by hematoxylin & eosin, trichrome, and PTAH staining.

Results

MRI measurements demonstrate that TRD is a more important determinant of both time-to-onset and progression of RN than fractionation. The development of RN is significantly slower in mice irradiated with 45-Gy than 50- or 60-Gy, where RN development is similar. Irradiated mouse brains demonstrate all of the pathologic features observed clinically in patients with confirmed RN. A semi-quantitative (0 to 3) histologic grading system, capturing both the extent and severity of injury, is described and illustrated. Tissue damage, as assessed by a histologic score, correlates well with total necrotic volume measured by MRI (correlation coefficient = 0.948, with p<0.0001), and with post-irradiation time (correlation coefficient = 0.508, with p<0.0001).

Conclusions

Following GK irradiation, mice develop late time-to-onset cerebral RN histology mirroring clinical observations. MR imaging provides reliable quantification of the necrotic volume that correlates well with histologic score. This mouse model of RN will provide a platform for mechanism of action studies, the identification of imaging biomarkers of RN, and the development of clinical studies for improved mitigation and neuroprotection.     

Balancing functions of annexin A6 maintain equilibrium between hypertrophy and apoptosis in cardiomyocytes

Pathological cardiac hypertrophy is a major risk factor associated with heart failure, a state concomitant with increased cell death. However, the mechanism governing progression of hypertrophy to apoptosis at the single-cell level remains elusive. Here, we demonstrate annexin A6 (Anxa6), a calcium (Ca²⁺)-dependent phospholipid-binding protein critically regulates the transition of chronic hypertrophied cardiomyocytes to apoptosis. Treatment of the H9c2(2-1) cardiomyocytes with hypertrophic agonists upregulates and relocalizes Anxa6 with increased cytosolic punctate appearance. Live cell imaging revealed that chronic exposure to hypertrophic agonists such as phenylephrine (PE) compromises the mitochondrial membrane potential (ΔΨ_m) and morphological dynamics. Such chronic hypertrophic induction also activated the caspases 9 and 3 and induced cleavage of the poly-(ADP-ribose) polymerase 1 (Parp1), which are the typical downstream events in the mitochondrial pathways of apoptosis. An increased rate of apoptosis was evident in the hypertrophied cardiomyocytes after 48–72 h of treatment with the hypertrophic agonists. Anxa6 was progressively associated with the mitochondrial fraction under chronic hypertrophic stimulation, and Anxa6 knockdown severely abrogated mitochondrial network and dynamics. Ectopically expressed Anxa6 protected the mitochondrial morphology and dynamics under PE treatment, and also increased the cellular susceptibility to apoptosis. Biochemical analysis showed that Anxa6 interacts with Parp1 and its 89 kDa cleaved product in a Ca²⁺-dependent manner through the N-terminal residues (1–28). Furthermore, expression of Anxa6^S13E, a mutant dominant negative with respect to Parp1 binding, served as an enhancer of mitochondrial dynamics, even under chronic PE treatment. Chemical inhibition of Parp1 activity released the cellular vulnerability to apoptosis in Anxa6-expressing stable cell lines, thereby shifting the equilibrium away from cell death. Taken together, the present study depicts a dual regulatory function of Anxa6 that is crucial for balancing hypertrophy with apoptosis in cardiomyocytes.Complex machineries govern the life and death decisions in mammalian cells through a dynamic equilibrium, which is essential for physiological homeostasis.¹ Such equilibrium is critical for cardiac myocytes because of their terminally differentiated states and low proliferative capacities. Stress response in cardiomyocytes often involves a switch between survival and cell death pathways.^{2, 3, 4} Cardiomyocyte hypertrophy is an adaptive response to stress, which may turn maladaptive and fatal,⁵ as evident in cardiovascular disorders that leads to heart failure.⁶ Hypertrophied phenotypes are also associated with a balance between cell growth and programmed cell death.⁷ These processes are aided by several patrolling proteins, which sense and operate to ameliorate the anomalies.^{8, 9} Understanding the dynamics of such signaling events is vital for the development of novel therapeutic strategies.Anxa6 belongs to the annexin family of calcium (Ca²⁺)/phospholipid-binding proteins.¹⁰ A major cardiac annexin,¹¹ Anxa6 has diverse functions ranging from handling intracellular Ca²⁺ signaling, cholesterol transport,¹² Ras inactivation¹³ and vesicular traffic.¹⁴ Anxa6 mostly functions as an intracellular scaffold.¹⁵ Although mice with targeted depletion of the Anxa6 gene remain viable,¹⁶ functional redundancies within the annexin family have been proposed to compensate for the loss of Anxa6 function.^{17, 18} A 10-fold overexpression of Anxa6 targeted to the heart developed cardiomyopathies in mice, whereas cardiomyocytes from Anxa6-knockout mice exhibited increased contractility and altered Ca²⁺ turnover.^{19, 20} Such contradictory findings may indicate participation of Anxa6 in counterbalancing signaling mechanisms. Moreover, end-stage heart failures have been reported to be associated with downregulation of Anxa6, and, in general, Anxa6 has compensatory roles in chronic pathological conditions.^{20, 21, 22} However, the function of differential Anxa6 expression or dynamics in chronic cardiomyocyte hypertrophy is poorly understood.We have reported the interactions of Anxa6 with the sarcomeric α-actinin and its role in cardiomyocyte contractility.²³ Recently, we have characterized a role of Anxa6 in the antihypertrophic signaling via the regulation of atrial natriuretic peptide (ANP) secretion.²⁴ The mechanistic spectrum of Anxa6 in the earlier study was limited to a short-term (24 h) exposure of H9c2 cardiomyocytes to the α1-adrenergic receptor agonist phenylephrine (PE). The dynamics of Anxa6 within this small window yielded valuable insight into the spatiotemporal regulation of hypertrophic signaling. Here, we extended the study to understand the dynamics of Anxa6 under chronic hypertrophic conditions. The mechanodeficient H9c2(2-1) cardiomyocyte line has been instrumental in our study to rule out the contributions of Anxa6 towards contractility,²³ owing to its multidimensional scaffold activity and functional compensations.^{17, 18} The H9c2 cardiomyocytes have been extensively characterized and ARE an established animal origin-free model for studying signal-transduction pathways in cardiomyocytes, including hypertrophy.^{25, 26}Adrenergic stimulation is crucial in compensatory and pathological cardiac hypertrophy, an early state that may proceed towards heart failure.²⁷ Cardiac hypertrophy at advanced stages (chronic) is associated with mitochondrial dysfunction, which also contributes to cardiac decompensation.²⁸ To explore the temporal events under chronic hypertrophy, we analyzed the effects of adrenergic induction on mitochondrial membrane potential (ΔΨm) and morphological dynamics, parameters that are directly correlated with mitochondrial dysfunction and programmed cell death.^{29, 30, 31} Anxa6 has been reported to be associated with mitochondria in some cell types.^{17, 32, 33} In the present study, we aim to understand the functions of Anxa6 under chronic hypertrophic conditions that may progress towards apoptosis.     

Association and impact of <Emphasis Type="Italic">XPG Asp</Emphasis> 1104 <Emphasis Type="Italic">His</Emphasis> gene polymorphism in HIV 1 disease progression to AIDS among north Indian HIV seropositive individuals

Various efforts made to stop the deadly epidemic of HIV since its discovery in 1983 remain unsuccessful and this virus still continues to claim the lives of millions of individuals every year. The viral effect in the cell is complicated and the overall disease outcome is the result of interaction between a few viral proteins and complex host immune response. Because it has been reported that XPG (Xeroderma pigementesum group G) gene does play a role in reducing UV induced apoptosis and participate in Nucleotide Excision Repair (NER) process of DNA damage, it was hypothesized that polymorphism in this gene may have a role in HIV 1 disease progression to AIDS. The aim of the present study, therefore, was to find out the association between XPG gene polymorphism and its effect on the rate of HIV 1 disease progression to AIDS. 300 HIV seropositive cases and an equal number of age and sex matched controls were recruited for the study from north Indian population. The PCR-RFLP method was utilized to genotype 600 study subject for the XPG Asp ¹¹⁰⁴ His gene polymorphism. There was significant difference in the frequency of the His/His variant genotype (OR 1.95, 95% CI = 1.93–3.63, P = 0.04) between cases and controls indicating a probable role of this gene in host viral interactions.     

ILCD Handbook Public Consultation Workshop

Introduction

The European Commission is supporting the development of the International Reference Life Cycle Data System (ILCD). This consists primarily of the ILCD Handbook and the ILCD Data Network. This paper gives an insight into the scientific positions of business, governments, consultants, academics, and others that were expressed at this public consultation workshop.

Workshop focus

The workshop focused on four of the topics of the main guidance documents of the ILCD Handbook: (1) general guidance on life cycle assessment (LCA); (2) guidance for generic and average life cycle inventory (LCI) data sets; (3) requirements for environmental impact assessment methods, models and indicators for LCA; and (4) review schemes for LCA.

Workshop participation

This consultation workshop was attended by more than 120 participants during the 4 days of the workshop. Representatives came from 23 countries, from both within and outside the European Union.

Workshop structure

Approximately half of the participants were from business associations or individual companies. Another 20% were governmental representatives. Others came predominantly from consultancies and academia.

Results

This public consultation workshop provided valuable inputs into the overall ILCD Handbook developments as well as for further development. This paper focuses on some of the main scientific issues that were raised.     

4-deoxy-4-fluoro-xyloside derivatives as inhibitors of glycosaminoglycan biosynthesis

Various 4-deoxy-4-fluoro-xylosides were prepared using click chemistry for evaluating their potential utility as inhibitors of glycosaminoglycan biosynthesis. 2,3-Di-O-benzoyl-4-deoxy-4-fluoro-β-D-xylopyranosylazide, obtained from L-arabinopyranose by six steps, was treated with a wide variety of azide-reactive triple bond-containing hydrophobic agents in the presence of Cu(2+) salt/ascorbic acid, a step known as click chemistry. After click chemistry, benzoylated derivatives were deprotected under Zemplén conditions to obtain 4-deoxy-4-fluoro-xyloside derivatives. A mixture of α:β-isomers of twelve derivatives were then separated on a reverse phase C18 column using HPLC and the resulting twenty four 4-deoxy-4-fluoro-xylosides were evaluated for their ability to inhibit glycosaminoglycan biosynthesis in endothelial cells. We identified two xyloside derivatives that selectively inhibit heparan sulfate and chondroitin sulfate/derman sulfate biosynthesis without affecting cell viability. These novel derivatives can potentially be used to define the biological actions of proteoglycans in model organisms and also as therapeutic agents to combat various human diseases in which glycosaminoglycans participate.     

Quantitative determination of formononetin and its metabolite in rat plasma after intravenous bolus administration by HPLC coupled with tandem mass spectrometry

A new simple, rapid, sensitive and accurate quantitative detection method using liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) for the measurement of formononetin (FMN) and daidzein (DZN) levels in rat plasma is described. Analytes were separated on a Supelco Discovery C18 (4.6 × 50 mm, 5.0 μm) column with acetonitrile: methanol (50:50, v/v) and 0.1% acetic acid in the ratio of 90:10 (v/v) as a mobile phase. The method was proved to be accurate and precise at linearity range of 5–100 ng/mL with a correlation coefficient (r) of ≥0.996. The intra- and inter-day assay precision ranged from 1.66–6.82% and 1.87–6.75%, respectively; and intra- and inter-day assay accuracy was between 89.98–107.56% and 90.54–105.63%, respectively for both the analytes. The lowest quantitation limit for FMN and DZN was 5.0 ng/mL in 0.1 mL of rat plasma. Practical utility of this new LC–MS/MS method was demonstrated in a pharmacokinetic study in rats following intravenous administration of FMN.     

Variation of Trace Elements Contents in Asparagus racemosus (Willd)

The present study was carried out to determine the accumulation and variation of trace elements in roots and leaves of Asparagus racemosus collected from four different altitudes in Uttarakhand, India, by atomic absorption spectroscopy. The metals investigated were Zn, Cu, Mn, Fe, Co, Na, K, Ca, and Li. The concentration level of Fe was found to be highest at an altitude of 2,250 m, whereas the level of Cu was lowest. The maximum concentrations of Zn, Cu, Mn, Fe, Co, Na, K, Ca, and Li were found to be 165.0?±?3.2, 34.0?±?0.5, 84.0?±?0.7, 2,040.0?±?0.3, 122.0?±?1.5, 745.0?±?0.3, 13,260.0?±?3.5, 6,153.0?±?1.6, and 58.0?±?3.8 mg/kg, respectively.     

Study on the Variations of Mineral Elements in Swertia speciosa (G. Don)

Variations of micro- and macrominerals concentration in Swertia speciosa were determined by atomic absorption spectroscopy. The mineral elements showed significant changes in roots and leaves collected from different altitudes. Among all the elements, highest concentration (more than 2,000 mg/kg) of Ca and K were recorded in S. speciosa and the concentration of other elements analyzed in the study decreased in the order Fe>Na>Zn>Co>Li>Cu>Mn.