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1.  Astrocytes Assemble Thalamocortical Synapses by Bridging Nrx1α and NL1 via Hevin 
Cell  2016;164(0):183-196.
SUMMARY
Proper establishment of synapses is critical for constructing functional circuits. Interactions between presynaptic neurexins and postsynaptic neuroligins coordinate the formation of synaptic adhesions. An isoform code determines the direct interactions of neurexins and neuroligins across the synapse. However, whether extracellular linker proteins can expand such a code is unknown. Using a combination of in vitro and in vivo approaches, we found that hevin, an astrocyte-secreted synaptogenic protein, assembles glutamatergic synapses by bridging neurexin-1α and neuroligin-1B, two isoforms that do not interact with each other. Bridging of neurexin-1α and neuroligin-1B via hevin is critical for the formation and plasticity of thalamocortical connections in the developing visual cortex. These results show that astrocytes promote the formation of synapses by modulating neurexin/neuroligin adhesions through hevin secretion. Our findings also provide an important mechanistic insight into how mutations in these genes may lead to circuit dysfunction in diseases such as autism.
doi:10.1016/j.cell.2015.11.034
PMCID: PMC4715262  PMID: 26771491
2.  A childhood acute lymphoblastic leukemia genome-wide association study identifies novel sex-specific risk variants 
Medicine  2016;95(46):e5300.
Supplemental Digital Content is available in the text
Abstract
Childhood acute lymphoblastic leukemia (ALL) occurs more frequently in males. Reasons behind sex differences in childhood ALL risk are unknown. In the present genome-wide association study (GWAS), we explored the genetic basis of sex differences by comparing genotype frequencies between male and female cases in a case-only study to assess effect-modification by sex.
The case-only design included 236 incident cases of childhood ALL consecutively recruited at the Texas Children's Cancer Center in Houston, Texas from 2007 to 2012. All cases were non-Hispanic whites, aged 1 to 10 years, and diagnosed with confirmed B-cell precursor ALL. Genotyping was performed using the Illumina HumanCoreExome BeadChip on the Illumina Infinium platform. Besides the top 100 statistically most significant results, results were also analyzed by the top 100 highest effect size with a nominal statistical significance (P <0.05).
The statistically most significant sex-specific association (P = 4 × 10−6) was with the single nucleotide polymorphism (SNP) rs4813720 (RASSF2), an expression quantitative trait locus (eQTL) for RASSF2 in peripheral blood. rs4813720 is also a strong methylation QTL (meQTL) for a CpG site (cg22485289) within RASSF2 in pregnancy, at birth, childhood, and adolescence. cg22485289 is one of the hypomethylated CpG sites in ALL compared with pre-B cells. Two missense SNPs, rs12722042 and 12722039, in the HLA-DQA1 gene yielded the highest effect sizes (odds ratio [OR] ∼ 14; P <0.01) for sex-specific results. The HLA-DQA1 SNPs belong to DQA1∗01 and confirmed the previously reported male-specific association with DQA1∗01. This finding supports the proposed infection-related etiology in childhood ALL risk for males. Further analyses revealed that most SNPs (either direct effect or through linkage disequilibrium) were within active enhancers or active promoter regions and had regulatory effects on gene expression levels.
Cumulative data suggested that RASSF2 rs4813720, which correlates with increased RASSF2 expression, may counteract the suppressor effect of estrogen-regulated miR-17-92 on RASSF2 resulting in protection in males. Given the amount of sex hormone-related mechanisms suggested by our findings, future studies should examine prenatal or early postnatal programming by sex hormones when hormone levels show a large variation.
doi:10.1097/MD.0000000000005300
PMCID: PMC5120913  PMID: 27861356
acute lymphoblastic leukemia; case-only study; effect modification; expression quantitative trait loci; gene expression regulation; genome-wide association study; sex-specific association
3.  PEPlife: A Repository of the Half-life of Peptides 
Scientific Reports  2016;6:36617.
Short half-life is one of the key challenges in the field of therapeutic peptides. Various studies have reported enhancement in the stability of peptides using methods like chemical modifications, D-amino acid substitution, cyclization, replacement of labile aminos acids, etc. In order to study this scattered data, there is a pressing need for a repository dedicated to the half-life of peptides. To fill this lacuna, we have developed PEPlife (http://crdd.osdd.net/raghava/peplife), a manually curated resource of experimentally determined half-life of peptides. PEPlife contains 2229 entries covering 1193 unique peptides. Each entry provides detailed information of the peptide, like its name, sequence, half-life, modifications, the experimental assay for determining half-life, biological nature and activity of the peptide. We also maintain SMILES and structures of peptides. We have incorporated web-based modules to offer user-friendly data searching and browsing in the database. PEPlife integrates numerous tools to perform various types of analysis such as BLAST, Smith-Waterman algorithm, GGSEARCH, Jalview and MUSTANG. PEPlife would augment the understanding of different factors that affect the half-life of peptides like modifications, sequence, length, route of delivery of the peptide, etc. We anticipate that PEPlife will be useful for the researchers working in the area of peptide-based therapeutics.
doi:10.1038/srep36617
PMCID: PMC5098197  PMID: 27819351
4.  HDAC8 Inhibition Specifically Targets Inv(16) Acute Myeloid Leukemic Stem Cells by Restoring p53 Acetylation 
Cell stem cell  2015;17(5):597-610.
Summary
Acute myeloid leukemia (AML) is driven and sustained by leukemia stem cells (LSCs) with unlimited self-renewal capacity and resistance to chemotherapy. Mutation in the TP53 tumor suppressor is relatively rare in de novo AML; however, p53 can be regulated through post-translational mechanisms. Here, we show that p53 activity is inhibited in inv(16)+ AML LSCs via interactions with the CBFβ-SMMHC (CM) fusion protein and histone deacetylase 8 (HDAC8). HDAC8 aberrantly deacetylates p53 and promotes LSC transformation and maintenance. HDAC8 deficiency or inhibition using HDAC8-selective inhibitors (HDAC8i) effectively restores p53 acetylation and activity. Importantly, HDAC8 inhibition induces apoptosis in inv(16)+ AML CD34+ cells while sparing the normal hematopoietic stem cells. Furthermore, in vivo HDAC8i administration profoundly diminishes AML propagation and abrogates leukemia-initiating capacity of both murine and patient-derived LSCs. This study elucidates a HDAC8-mediated p53-inactivating mechanism promoting LSC activity, and highlights HDAC8 inhibition as a promising approach to selectively target inv(16)+ LSCs.
Graphical Abstract
doi:10.1016/j.stem.2015.08.004
PMCID: PMC4636961  PMID: 26387755
5.  Percutaneous management of coronary embolism with prosthetic heart valve thrombosis after Bentall's procedure 
Indian Heart Journal  2015;67(6):589-591.
We describe a young male who had undergone a Bentall's procedure seven years ago presenting with acute severe chest pain. He was diagnosed to have coronary embolism from prosthetic heart valve thrombosis. Multiple treatment strategies for the patient were available and we briefly discuss the merits of each of them. We also describe the encountered difficulties in the percutaneous revascularization procedure.
doi:10.1016/j.ihj.2015.10.372
PMCID: PMC4699981  PMID: 26702693
Acute myocardial infarction; Coronary embolism; Prosthetic valve thrombosis; Percutaneous coronary intervention
6.  In vitro propagation of Rudraksha (Elaeocarpus sphaericus (Gaertn.) K. Schum): a biotechnological approach for conservation 
The species Elaeocarpus sphaericus (Rudraksha) is a religious, medicinally important threatened tree of India. An efficient micropropagation protocol has been developed from nodal explants of this plant species collected from north-east India for large scale production of planting material at favourable sites within the country. Best shoot initiation occurred in MS medium supplemented with 2.2μM BA+2.2μM Kn in combination. Addition of Casein Hydrolysate (CH) (100mg/L) increased the shoot number. Microshoots excised and subcultured in 2.0μM BA further enhanced growth and multiplication. The shoot cultures were maintained in this concentration for 2years with subculturing at 6weeks interval. MS medium containing 5.0μM NAA was most effective for rooting. Successfully acclimatized plants (80%) showed normal growth under suitable habitat conditions.
doi:10.1007/s12298-015-0316-0
PMCID: PMC4646877  PMID: 26600688
Rudraksha; Elaeocarpus sphaericus; Nodal explants; Cytokinins; Shoot proliferation; Rooting of microshoots; Acclimatization
7.  Development of macaronic Hindi-English ‘Hinglish’ text message content for a coronary heart disease secondary prevention programme 
Heart Asia  2016;8(2):32-38.
Background
Coronary heart disease (CHD) is a leading cause of morbidity and mortality in India. Text message based prevention programs have demonstrated reduction in cardiovascular risk factors among patients with CHD in selected populations. Customisation is important as behaviour change is influenced by culture and linguistic context.
Objectives
To customise a mobile phone text message program supporting behaviour and treatment adherence in CHD for delivery in North India.
Methods
We used an iterative process with mixed methods involving three phases: (1) Initial translation, (2) Review and incorporation of feedback including review by cardiologists in India to assess alignment with local guidelines and by consumers on perceived utility and clarity and (3) Pilot testing of message management software.
Results
Messages were translated in three ways: symmetrical translation, asymmetrical translation and substitution. Feedback from cardiologists and 25 patients was incorporated to develop the final bank. Patients reported Hinglish messages were easy to understand (93%) and useful (78%). The software located in Australia successfully delivered messages to participants based in Delhi-surrounds (India).
Conclusions
Our process for customisation of a text message program considered cultural, linguistic and the medical context of potential participants. This is important in optimising intervention fidelity across populations enabling examination of the generalisability of text message programs across populations. We also demonstrated the customised program was acceptable to patients in India and that a centralised cross-country delivery model was feasible. This process could be used as a guide for other groups seeking to customise their programs.
Trial registration number
TEXTMEDS Australia (Parent study)—ACTRN 12613000793718.
doi:10.1136/heartasia-2016-010789
PMCID: PMC5051379  PMID: 27752288
CORONARY ARTERY DISEASE
8.  ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis 
Scientific Reports  2016;6:32713.
Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates.
doi:10.1038/srep32713
PMCID: PMC5025660  PMID: 27633273
9.  YAP1 REGULATES OCT4 ACTIVITY AND SOX2 EXPRESSION TO FACILITATE SELF-RENEWAL AND VASCULAR MIMICRY OF STEM-LIKE CELLS 
Stem cells (Dayton, Ohio)  2015;33(6):1705-1718.
Non-small cell lung cancer (NSCLC) is highly correlated with smoking and has very low survival rates. Multiple studies have shown that stem-like cells contribute to the genesis and progression of NSCLC. Our results show that the transcriptional co-activator YAP1, which is the oncogenic component of the Hippo signaling pathway, is elevated in the stem-like cells from NSCLC and contributes to their self-renewal and ability to form angiogenic tubules. Inhibition of YAP1 by a small molecule or depletion of YAP1 by siRNAs suppressed self-renewal and vascular mimicry of stem-like cells. These effects of YAP1 were mediated through the embryonic stem cell transcription factor, Sox2. YAP1 could transcriptionally induce Sox2 through a physical interaction with Oct4; Sox2 induction occurred independent of TEAD2 transcription factor, which is the predominant mediator of YAP1 functions. The binding of Oct4 to YAP1 could be detected in cell lines as well as tumor tissues; the interaction was elevated in NSCLC samples compared to normal tissue as seen by proximity ligation assays. YAP1 bound to Oct4 through the WW domain, and a peptide corresponding to this region could disrupt the interaction. Delivery of the WW domain peptide to stem-like cells disrupted the interaction and abrogated Sox2 expression, self-renewal and vascular mimicry. Depleting YAP1 reduced the expression of multiple EMT genes and prevented the growth and metastasis of tumor xenografts in mice; overexpression of Sox2 in YAP1 null cells rescued these functions. These results demonstrate a novel regulation of stem-like functions by YAP1, through the modulation of Sox2 expression.
doi:10.1002/stem.1993
PMCID: PMC4441573  PMID: 25754111
self-renewal; vascular mimicry; side-population cells; non-small cell lung cancer; transcriptional regulation
10.  Insulin-Like Growth Factor Binding Protein-4 as a Marker of Chronic Lupus Nephritis 
PLoS ONE  2016;11(3):e0151491.
Kidney biopsy remains the mainstay of Lupus Nephritis (LN) diagnosis and prognostication. The objective of this study is to identify non-invasive biomarkers that closely parallel renal pathology in LN. Previous reports have demonstrated that serum Insulin-like growth factor binding protein 4 (IGFBP-4) was increased in diabetic nephropathy in both animal models and patients. We proceeded to assess if IGFBP4 could be associated with LN. We performed ELISA using the serum of 86 patients with LN. Normal healthy adults (N = 23) and patients with other glomerular diseases (N = 20) served as controls. Compared to the healthy controls or other glomerular disease controls, serum IGFBP-4 levels were significantly higher in the patients with LN. Serum IGFBP-4 did not correlate well with systemic lupus erythematosus disease activity index (SLEDAI), renal SLEDAI or proteinuria, but it did correlate with estimated glomerular filtration rate (R = 0.609, P < 0.0001). Interestingly, in 18 patients with proliferative LN whose blood samples were obtained at the time of renal biopsy, serum IGFBP-4 levels correlated strongly with the chronicity index of renal pathology (R = 0.713, P < 0.001). IGFBP-4 emerges a potential marker of lupus nephritis, reflective of renal pathology chronicity changes.
doi:10.1371/journal.pone.0151491
PMCID: PMC4809566  PMID: 27019456
11.  RelB/p50 complexes regulate cytokine-induced YKL-40 expression1 
The secreted protein, YKL-40, has been proposed as a biomarker of a variety of human diseases characterized by ongoing inflammation, including chronic neurological pathologies such as multiple sclerosis (MS)2 and Alzheimer’s disease. However, inflammatory mediators and the molecular mechanism responsible for enhanced expression of YKL-40 remained elusive. Using several mouse models of inflammation, we now show that YKL-40 expression correlated with increased expression of both IL-1 and IL-6. Furthermore, IL-1 together with IL-6 or the IL-6 family cytokine, oncostatin M (OSM), synergistically upregulated YKL-40 expression in both primary human and mouse astrocytes in vitro. The robust cytokine-driven expression of YKL-40 in astrocytes required both STAT3 and NF-κB binding elements of the YKL-40 promoter. Additionally, YKL-40 expression was enhanced by constitutively active STAT3 and inhibited by dominant-negative IκBα. Surprisingly, cytokine-driven expression of YKL-40 in astrocytes was independent of the p65 subunit of NF-κB and instead required subunits RelB and p50. Mechanistically, we show that IL-1-induced RelB/p50 complex formation was further promoted by OSM and that these complexes directly bound to the YKL-40 promoter. Moreover, we found that expression of RelB was strongly upregulated during inflammation in vivo and by IL-1 in astrocytes in vitro. We propose that IL-1 and the IL-6 family of cytokines regulate YKL-40 expression during sterile inflammation via both STAT3 and RelB/p50 complexes. These results suggest that IL-1 may regulate the expression of specific anti-inflammatory genes in non-lymphoid tissues via the canonical activation of the RelB/p50 complexes.
doi:10.4049/jimmunol.1400874
PMCID: PMC4355396  PMID: 25681350
12.  β-arrestin-1 mediates nicotine-induced metastasis through E2F1 target genes that modulate epithelial-mesenchymal transition 
Cancer research  2015;75(6):1009-1020.
Cigarette smoking is a major risk factor in the development of non-small cell lung cancer (NSCLC), which accounts for 80% of all lung cancers. Nicotine, the major addictive component of tobacco smoke, can induce proliferation, invasion and epithelial-mesenchymal transition (EMT) in NSCLC cell lines and promote metastasis of NSCLC in mice. Here we demonstrate that the scaffolding protein β-arrestin-1 is necessary for nicotine-mediated induction of mesenchymal genes vimentin and fibronectin as well as EMT regulators ZEB1 and ZEB2. Nicotine induced changes in cell morphology and ablate tight junctions consistent with EMT; β-arrestin-1, but not β-arrestin-2, was required for these changes. β-arrestin-1 promoted the expression of the mesenchymal genes as well as ZEB1 and ZEB2 through the mediation of the E2F1 transcription factor; this required Src kinase activity. Stimulation of multiple NSCLC cell lines with nicotine led to enhanced recruitment of β-arrestin-1 and E2F1 on vimentin, fibronectin, ZEB1 and ZEB2 promoters. Further, there was significantly more β-arrestin-1 and E2F1 associated with these promoters in human NSCLC tumors and β-arrestin-1 levels correlated with vimentin and fibronectin levels in human NSCLC samples. A549-luciferase cells lacking β-arrestin-1 showed a significantly reduced capacity for tumor growth and metastasis when orthotopically implanted into the lungs of SCID-beige mice. Taken together, these studies reveal a novel role for β-arrestin-1 in the growth and metastasis of NSCLC.
doi:10.1158/0008-5472.CAN-14-0681
PMCID: PMC4359962  PMID: 25600647
Rb; E2F1; Zeb1; Zeb2; fibronectin; vimentin
13.  A Web Server and Mobile App for Computing Hemolytic Potency of Peptides 
Scientific Reports  2016;6:22843.
Numerous therapeutic peptides do not enter the clinical trials just because of their high hemolytic activity. Recently, we developed a database, Hemolytik, for maintaining experimentally validated hemolytic and non-hemolytic peptides. The present study describes a web server and mobile app developed for predicting, and screening of peptides having hemolytic potency. Firstly, we generated a dataset HemoPI-1 that contains 552 hemolytic peptides extracted from Hemolytik database and 552 random non-hemolytic peptides (from Swiss-Prot). The sequence analysis of these peptides revealed that certain residues (e.g., L, K, F, W) and motifs (e.g., “FKK”, “LKL”, “KKLL”, “KWK”, “VLK”, “CYCR”, “CRR”, “RFC”, “RRR”, “LKKL”) are more abundant in hemolytic peptides. Therefore, we developed models for discriminating hemolytic and non-hemolytic peptides using various machine learning techniques and achieved more than 95% accuracy. We also developed models for discriminating peptides having high and low hemolytic potential on different datasets called HemoPI-2 and HemoPI-3. In order to serve the scientific community, we developed a web server, mobile app and JAVA-based standalone software (http://crdd.osdd.net/raghava/hemopi/).
doi:10.1038/srep22843
PMCID: PMC4782144  PMID: 26953092
14.  Feasibility study of a novel intraosseous device in adult human cadavers 
Background & objectives:
Intraosseous (IO) access is an alternative to difficult intravenous (iv) access during emergency clinical situations. Existing IO solutions are expensive, require power supply and trained manpower; limiting their use in resource constrained settings. To address these limitations, a novel IO device has been developed. The objectives of this study were to evaluate functionality and safety of this device in adult human cadavers.
Methods:
The ability of the IO device to penetrate the proximal and/or distal tibia was evaluated in three adult cadavers. Subjective parameters of loss of resistance, stable needle hold, easy needle withdrawal and any damage to the device were evaluated during the study. The insertion time was the objective parameter measured. Four sets of radiographs per insertion confirmed the position of the needle and identified complications.
Results:
A single physician performed 12 IO access procedures using the same device. Penetration of proximal and/or distal tibia was achieved in all instances. It was successful in the first attempt in eight (66.7%) and during second attempt in the remaining. The mean time to insertion was 4.1 ± 3.1 sec. Appropriate insertion of needle in the intra-medullary space of bone was confirmed with radiological examination in 10 (83.3%) insertions. In two occasions after penetrating the cortical layer of bone, the device overshot the intra-medullary space, as detected by radiological examination. Device got bent during insertion in one instance. There was no evidence of needle breakage or bone fracture. The needle could be withdrawn effortlessly in all instances.
Interpretation & conclusions:
The novel IO device could successfully penetrate the adult cadaver bones in most cases. Further studies are needed to confirm these results on a large sample.
doi:10.4103/0971-5916.182616
PMCID: PMC4892072  PMID: 27241639
Difficult intravenous access; emergency medicine; intraosseous access; intraosseous device; resuscitation; vascular access
15.  Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell lines 
BMC Cancer  2016;16:77.
Background
In past, numerous quantitative structure-activity relationship (QSAR) based models have been developed for predicting anticancer activity for a specific class of molecules against different cancer drug targets. In contrast, limited attempt have been made to predict the anticancer activity of a diverse class of chemicals against a wide variety of cancer cell lines. In this study, we described a hybrid method developed on thousands of anticancer and non-anticancer molecules tested against National Cancer Institute (NCI) 60 cancer cell lines.
Results
Our analysis of anticancer molecules revealed that majority of anticancer molecules contains 18–24 carbon atoms and are dominated by functional groups like R2NH, R3N, ROH, RCOR, and ROR. It was also observed that certain substructures (e.g., 1-methoxy-4-methylbenzene, 1-methoxy benzene, Nitrobenzene, Indole, Propenyl benzene) are more abundant in anticancer molecules. Next, we developed anticancer molecule prediction models using various machine-learning techniques and achieved maximum matthews correlation coefficient (MCC) of 0.81 with 90.40 % accuracy using support vector machine (SVM) based models. In another approach, a novel similarity or potency score based method has been developed using selected fragments/fingerprints and achieved maximum MCC of 0.82 with 90.65 % accuracy. Finally, we combined the strength of above methods and developed a hybrid method with maximum MCC of 0.85 with 92.47 % accuracy.
Conclusions
We developed a hybrid method utilizing the best of machine learning and potency score based method. The highly accurate hybrid method can be used for classification of anticancer and non-anticancer molecules. In order to facilitate scientific community working in the field of anticancer drug discovery, we integrate hybrid and potency method in a web server CancerIN. This server provides various facilities that includes; virtual screening of anticancer molecules, analog based drug design, and similarity with known anticancer molecules (http://crdd.osdd.net/oscadd/cancerin).
Electronic supplementary material
The online version of this article (doi:10.1186/s12885-016-2082-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12885-016-2082-y
PMCID: PMC4748564  PMID: 26860193
Cancer inhibitors; Classification of cancer inhibitors and non-inhibitors; Active substructure; Active functional groups; Fingerprints; QSAR; Potency score; SVM light
16.  Ultrasensitive interplay between ferromagnetism and superconductivity in NbGd composite thin films 
Scientific Reports  2016;6:18689.
A model binary hybrid system composed of a randomly distributed rare-earth ferromagnetic (Gd) part embedded in an s-wave superconducting (Nb) matrix is being manufactured to study the interplay between competing superconducting and ferromagnetic order parameters. The normal metallic to superconducting phase transition appears to be very sensitive to the magnetic counterpart and the modulation of the superconducing properties follow closely to the Abrikosov-Gor’kov (AG) theory of magnetic impurity induced pair breaking mechanism. A critical concentration of Gd is obtained for the studied NbGd based composite films (CFs) above which superconductivity disappears. Besides, a magnetic ordering resembling the paramagnetic Meissner effect (PME) appears in DC magnetization measurements at temperatures close to the superconducting transition temperature. The positive magnetization related to the PME emerges upon doping Nb with Gd. The temperature dependent resistance measurements evolve in a similar fashion with the concentration of Gd as that with an external magnetic field and in both the cases, the transition curves accompany several intermediate features indicating the traces of magnetism originated either from Gd or from the external field. Finally, the signatures of magnetism appear evidently in the magnetization and transport measurements for the CFs with very low (<1 at.%) doping of Gd.
doi:10.1038/srep18689
PMCID: PMC4698659  PMID: 26725684
17.  Overview of Alzheimer's Disease and Some Therapeutic Approaches Targeting Aβ by Using Several Synthetic and Herbal Compounds 
Alzheimer's disease (AD) is a complex age-related neurodegenerative disease. In this review, we carefully detail amyloid-β metabolism and its role in AD. We also consider the various genetic animal models used to evaluate therapeutics. Finally, we consider the role of synthetic and plant-based compounds in therapeutics.
doi:10.1155/2016/7361613
PMCID: PMC4807045  PMID: 27034741
18.  PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues 
Biology Direct  2015;10:73.
Background
In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natural and non-natural/modified residues.
Results
PEPstrMOD integrates Forcefield_NCAA and Forcefield_PTM force field libraries to handle 147 non-natural residues and 32 types of post-translational modifications respectively by performing molecular dynamics using AMBER. AMBER was also used to handle other modifications like peptide cyclization, use of D-amino acids and capping of terminal residues. In addition, GROMACS was used to implement 210 non-natural side-chains in peptides using SwissSideChain force field library. We evaluated the performance of PEPstrMOD on three datasets generated from Protein Data Bank; i) ModPep dataset contains 501 non-natural peptides, ii) ModPep16, a subset of ModPep, and iii) CyclicPep contains 34 cyclic peptides. We achieved backbone Root Mean Square Deviation between the actual and predicted structure of peptides in the range of 3.81–4.05 Å.
Conclusions
In summary, the method PEPstrMOD has been developed that predicts the structure of modified peptide from the sequence/structure given as input. We validated the PEPstrMOD application using a dataset of peptides having non-natural/modified residues. PEPstrMOD offers unique advantages that allow the users to predict the structures of peptides having i) natural residues, ii) non-naturally modified residues, iii) terminal modifications, iv) post-translational modifications, v) D-amino acids, and also allows extended simulation of predicted peptides. This will help the researchers to have prior structural information of modified peptides to further design the peptides for desired therapeutic property. PEPstrMOD is freely available at http://osddlinux.osdd.net/raghava/pepstrmod/.
Reviewers
This article was reviewed by Prof Michael Gromiha, Dr. Bojan Zagrovic and Dr. Zoltan Gaspari.
Electronic supplementary material
The online version of this article (doi:10.1186/s13062-015-0103-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s13062-015-0103-4
PMCID: PMC4687368  PMID: 26690490
Peptide tertiary structure prediction; Peptide structure of non-natural residues; Peptide modeling peptide prediction
19.  CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides 
Nucleic Acids Research  2015;44(Database issue):D1098-D1103.
CPPsite 2.0 (http://crdd.osdd.net/raghava/cppsite/) is an updated version of manually curated database (CPPsite) of cell-penetrating peptides (CPPs). The current version holds around 1850 peptide entries, which is nearly two times than the entries in the previous version. The updated data were curated from research papers and patents published in last three years. It was observed that most of the CPPs discovered/ tested, in last three years, have diverse chemical modifications (e.g. non-natural residues, linkers, lipid moieties, etc.). We have compiled this information on chemical modifications systematically in the updated version of the database. In order to understand the structure-function relationship of these peptides, we predicted tertiary structure of CPPs, possessing both modified and natural residues, using state-of-the-art techniques. CPPsite 2.0 also maintains information about model systems (in vitro/in vivo) used for CPP evaluation and different type of cargoes (e.g. nucleic acid, protein, nanoparticles, etc.) delivered by these peptides. In order to assist a wide range of users, we developed a user-friendly responsive website, with various tools, suitable for smartphone, tablet and desktop users. In conclusion, CPPsite 2.0 provides significant improvements over the previous version in terms of data content.
doi:10.1093/nar/gkv1266
PMCID: PMC4702894  PMID: 26586798
20.  SATPdb: a database of structurally annotated therapeutic peptides 
Nucleic Acids Research  2015;44(Database issue):D1119-D1126.
SATPdb (http://crdd.osdd.net/raghava/satpdb/) is a database of structurally annotated therapeutic peptides, curated from 22 public domain peptide databases/datasets including 9 of our own. The current version holds 19192 unique experimentally validated therapeutic peptide sequences having length between 2 and 50 amino acids. It covers peptides having natural, non-natural and modified residues. These peptides were systematically grouped into 10 categories based on their major function or therapeutic property like 1099 anticancer, 10585 antimicrobial, 1642 drug delivery and 1698 antihypertensive peptides. We assigned or annotated structure of these therapeutic peptides using structural databases (Protein Data Bank) and state-of-the-art structure prediction methods like I-TASSER, HHsearch and PEPstrMOD. In addition, SATPdb facilitates users in performing various tasks that include: (i) structure and sequence similarity search, (ii) peptide browsing based on their function and properties, (iii) identification of moonlighting peptides and (iv) searching of peptides having desired structure and therapeutic activities. We hope this database will be useful for researchers working in the field of peptide-based therapeutics.
doi:10.1093/nar/gkv1114
PMCID: PMC4702810  PMID: 26527728
22.  Lung Cancer Stem Cells: Molecular features and Therapeutic Targets 
Lung cancers are highly heterogeneous and resistant to available therapeutic agents, with a five year survival rate of less than 15%. Despite significant advances in our knowledge of the genetic alterations and aberrations in signaling pathways, it has been difficult to determine the basis of lung cancer heterogeneity and drug ressitance. Cancer stem cell model has attracted a significant amount of attention in recent years as a viable explanation for the heterogeneity, drug resistance, dormancy and recurrence and metastasis of various tumors. At the same time, cancer stem cells have been relatively less characetrized in lung cancers. This review summarizes the current understanding of lung cancer stem cells, including their molecular features and signaling pathways that drive their stemness. This review also discusses the potential startegies to inhibit the signaling pathways driving stemness, in an effort to eradicate these cells to combat lung cancer.
doi:10.1016/j.mam.2013.08.003
PMCID: PMC3949216  PMID: 24016594
23.  AntiAngioPred: A Server for Prediction of Anti-Angiogenic Peptides 
PLoS ONE  2015;10(9):e0136990.
The process of angiogenesis is a vital step towards the formation of malignant tumors. Anti-angiogenic peptides are therefore promising candidates in the treatment of cancer. In this study, we have collected anti-angiogenic peptides from the literature and analyzed the residue preference in these peptides. Residues like Cys, Pro, Ser, Arg, Trp, Thr and Gly are preferred while Ala, Asp, Ile, Leu, Val and Phe are not preferred in these peptides. There is a positional preference of Ser, Pro, Trp and Cys in the N terminal region and Cys, Gly and Arg in the C terminal region of anti-angiogenic peptides. Motif analysis suggests the motifs “CG-G”, “TC”, “SC”, “SP-S”, etc., which are highly prominent in anti-angiogenic peptides. Based on the primary analysis, we developed prediction models using different machine learning based methods. The maximum accuracy and MCC for amino acid composition based model is 80.9% and 0.62 respectively. The performance of the models on independent dataset is also reasonable. Based on the above study, we have developed a user-friendly web server named “AntiAngioPred” for the prediction of anti-angiogenic peptides. AntiAngioPred web server is freely accessible at http://clri.res.in/subramanian/tools/antiangiopred/index.html (mirror site: http://crdd.osdd.net/raghava/antiangiopred/).
doi:10.1371/journal.pone.0136990
PMCID: PMC4559406  PMID: 26335203
24.  Stem cell therapy in spinal trauma: Does it have scientific validity? 
doi:10.4103/0019-5413.159683
PMCID: PMC4510807  PMID: 26229174

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