Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase

Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes. Our sequence analysis reveals that archaeal TSs possess all zinc chelating residues to bind a metal ion that are lacking in the structurally characterized homologs. Phylogenetic analysis suggests that TSs with an N-terminal zinc ribbon likely represents the ancestral state of the enzyme while TSs without a zinc ribbon must have diverged later in specific lineages. The zinc ribbon and its N- and C-terminal extensions are important for enzyme stability, activity and regulation. It is likely that the zinc ribbon domain is involved in higher order oligomerization or mediating interactions with other biomolecules leading to formation of larger metabolic complexes.

Inhibition of the Quorum Sensing System (ComDE Pathway) by Aromatic 1,3-di-m-tolylurea (DMTU): Cariostatic Effect with Fluoride in Wistar Rats

Dental caries occurs as a result of dysbiosis among commensal and pathogenic bacteria leading to demineralization of enamel within a dental biofilm (plaque) as a consequence of lower pH in the oral cavity. In our previous study, we have reported 1,3-disubstituted ureas particularly, 1,3-di-m-tolylurea (DMTU) could inhibit the biofilm formation along with lower concentrations of fluoride (31.25 ppm) without affecting bacterial growth. In the present study, RT-qPCR analysis showed the target specific molecular mechanism of DMTU. In vivo treatment with DMTU, alone or in combination with fluoride, resulted in inhibition of caries (biofilm development of Streptococcus mutans) using a Wistar rat model for dental caries. The histopathological analysis reported the development of lesions on dentine in infected subjects whereas the dentines of treated rodents were found to be intact and healthy. Reduction in inflammatory markers in rodents' blood and liver samples was observed when treated with DMTU. Collectively, data speculate that DMTU is an effective anti-biofilm and anti-inflammatory agent, which may improve the cariostatic properties of fluoride.

Abstract 348: Comparison of the response of the NCI60 NSCLC panel with the response of patient-derived NSCLC lines to approved and investigational agents

An 800 compound screen with the NCI60 cell lines and 5 patient-derived NSCLC lines (PD NSCLC), was conducted at 9 concentrations and included the FDA approved oncology agents and an investigational agents library. The screen was conducted using 384-well monolayer cultures, an exposure time of 72 hrs and compound concentrations from 1 nM to 10 uM. CellTiter-Glo was used to measure viability as an endpoint. The NCI60 NSCLC panel consists of 9 cell lines: A549, EKVX, HOP-62, HOP-92, NCI-H226, NCI-H23, NCI-H322M, NCI-H460 and NCI-H522. The response of these lines was compared with the response of 5 PD NSCLC lines and 60 SCLC lines. While both sets of NSCLC lines had similar responses to the majority of compounds, there were some marked differences. Differences in response of the NCI60 NSCLC lines and the PD NSCLC lines were notable upon exposure to tubulin fragmenters, KSP/EG5 inhibitors, GAR transformylase inhibitors, Polo-like kinase-1 inhibitors (PLK1), MEK inhibitors, and IAP inhibitors. The NCI60 NSCLC lines were more sensitive to the tubulin fragmenters than were the PD NSCLC and the SCLC lines. Verubulin had a mean GI50 in NCI60 NSCLC of 0.0037 uM and 0.0042 uM in SCLC versus 0.047uM in the PD NSCLC lines. The NCI60 NSCLC lines were more sensitive to the KSP inhibitor, ARRY-520 (mean GI50 0.0049 uM) than the SCLC lines (0.028 uM) and the PD NSCLC lines (0.26 uM). The NCI60 NSCLC lines (mean GI50 0.019 uM) and the SCLC lines (mean GI50 0.04 uM) were more sensitive to PLK1 inhibitors such as BI-2536 than the PD NSCLC lines (0.13 uM). However, the NCI60 NSCLC lines (mean GI50 0.8 uM) and the SCLC lines (mean GI50 0.134 uM) were less sensitive than the PD NSCLC lines (mean GI50 0.025uM) to GAR transformylase inhibitors such as pelitrexol. The NCI60 NSCLC lines (mean GI50 6.3 uM) and SCLC lines (mean GI50 10 uM) were also less responsive to IAP inhibitors, than were PD NSCLC lines (mean GI50 1.6 uM). A heterogeneous response to the MEK inhibitors such as cobimetinib (GDC-0973) was observed with the SCLC lines (mean GI50 8.9 uM) versus 1.15 uM in the NCI60 NSCLC lines and 0.56 uM in the PD NSCLC lines. PD NSCLC lines exhibit some interesting differences in response from established lung cancer lines upon in vitro exposure to anticancer agents and thus add to our knowledge and understanding of NSCLC and help inform discovery efforts and/or clinical development of therapeutics in this disease. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Beverly A. Teicher, David Evans, Thomas Silvers, Michael Selby, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Joel Morris, Gurmeet Kaur, James Doroshow. Comparison of the response of the NCI60 NSCLC panel with the response of patient-derived NSCLC lines to approved and investigational agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 348. doi:10.1158/1538-7445.AM2017-348

Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts

The HU superfamily of proteins, with a unique DNA-binding mode, has been extensively studied as the primary chromosome-packaging protein of the bacterial superkingdom. Representatives also play a role in DNA-structuring during recombination events and in eukaryotic organellar genome maintenance. However, beyond these well-studied roles, little is understood of the functional diversification of this large superfamily. Using sensitive sequence and structure analysis methods we identify multiple novel clades of the HU superfamily. We present evidence that a novel eukaryotic clade prototyped by the human CCDC81 protein acquired roles beyond DNA-binding, likely in protein-protein interaction in centrosome organization and as a potential cargo-binding protein in conjunction with Dynein-VII. We also show that these eukaryotic versions were acquired via an early lateral transfer from bacteroidetes, where we predict a role in chromosome partition. This likely happened before the last eukaryotic common ancestor, pointing to potential endosymbiont contributions beyond that of the mitochondrial progenitor. Further, we show that the dramatic lineage-specific expansion of this domain in the bacteroidetes lineage primarily is linked to a functional shift related to potential recognition and preemption of genome invasive entities such as mobile elements. Remarkably, the CCDC81 clade has undergone a similar massive lineage-specific expansion within the archosaurian lineage in birds, suggesting a possible use of the HU superfamily in a similar capacity in recognition of non-self molecules even in this case.

Biomacromolecule immobilization: grafting of fish-scale collagen peptides onto aminolyzed P(3HB-co-4HB) scaffolds as a potential wound dressing

Polyhydroxyalkanoate (PHA) is a microbial polymer that has been at the forefront of many attempts at tissue engineering. However, the surface of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB)) is hydrophobic with few recognition sites for cell attachment. Various concentrations of fish-scale collagen peptides (FSCPs) were incorporated into P(3HB-co-4HB) copolymer by aminolysis. Later, FSCPs were introduced onto the aminolyzed P(3HB-co-4HB) scaffolds. Introduction of the FSCP groups was verified using Fourier transform infrared spectroscopy and the ninhydrin method. The effect of the incorporation of FSCPs on hydrophilicity was investigated using the water contact angle. As the concentration of FSCPs increased, the water contact angle decreased. In vitro study demonstrated that P(3HB-co-4HB)/FSCP scaffolds provided better cell attachment and growth of L929 mouse fibroblast cells and better cell proliferation. In vivo study showed that P(3HB-co-4HB)/1.5 wt% FSCPs had a significant effect on wound contractions, with the highest percentage of wound closure (61%) in 7 d.

Small Cell Lung Cancer Screen of Oncology Drugs, Investigational Agents, and Gene and microRNA Expression

BACKGROUND

Small cell lung carcinoma (SCLC) is an aggressive, recalcitrant cancer, often metastatic at diagnosis and unresponsive to chemotherapy upon recurrence, thus it is challenging to treat.

METHODS

Sixty-three human SCLC lines and three NSCLC lines were screened for response to 103 US Food and Drug Administration-approved oncology agents and 423 investigational agents. The investigational agents library was a diverse set of small molecules that included multiple compounds targeting the same molecular entity. The compounds were screened in triplicate at nine concentrations with a 96-hour exposure time using an ATP Lite endpoint. Gene expression was assessed by exon array, and microRNA expression was derived by direct digital detection. Activity across the SCLC lines was associated with molecular characteristics using pair-wise Pearson correlations.

RESULTS

Results are presented for inhibitors of targets: BCL2, PARP1, mTOR, IGF1R, KSP/Eg5, PLK-1, AURK, and FGFR1. A relational map identified compounds with similar patterns of response. Unsupervised microRNA clustering resulted in three distinct SCLC subgroups. Associating drug response with micro-RNA expression indicated that lines most sensitive to etoposide and topotecan expressed high miR-200c-3p and low miR-140-5p and miR-9-5p. The BCL-2/BCL-XL inhibitors produced similar response patterns. Sensitivity to ABT-737 correlated with higher ASCL1 and BCL2. Several classes of compounds targeting nuclear proteins regulating mitosis produced a response pattern distinct from the etoposide response pattern.

CONCLUSIONS

Agents targeting nuclear kinases appear to be effective in SCLC lines. Confirmation of SCLC line findings in xenografts is needed. The drug and compound response, gene expression, and microRNA expression data are publicly available at http://sclccelllines.cancer.gov.

Basic concepts for sample size calculation: Critical step for any clinical trials!

Quality of clinical trials has improved steadily over last two decades, but certain areas in trial methodology still require special attention like in sample size calculation. The sample size is one of the basic steps in planning any clinical trial and any negligence in its calculation may lead to rejection of true findings and false results may get approval. Although statisticians play a major role in sample size estimation basic knowledge regarding sample size calculation is very sparse among most of the anesthesiologists related to research including under trainee doctors. In this review, we will discuss how important sample size calculation is for research studies and the effects of underestimation or overestimation of sample size on project's results. We have highlighted the basic concepts regarding various parameters needed to calculate the sample size along with examples.

Prevalence of Psychiatric Morbidity in Females amongst Infertile Couples- A Hospital Based Report

INTRODUCTION

Infertility leads to significant stress among couple and the reaction to infertility differs among males and females.

AIM

To know the prevalence of psychiatric morbidity in infertile couples and compare the prevalence of various psychiatric disorders among husband and wife.

MATERIALS AND METHODS

A cross-sectional study was conducted on 50 couples diagnosed with infertility from outdoor clinics. Both male and female partner of couple were interviewed for detailed history and clinical examination was done. General Health Questionnaire (GHQ-12) was applied to detect any psychological strain in couples and in those with illness, final diagnosis were made on the basis of DSM -IV (TR). The data thus generated was subjected to appropriate Statistical Analysis.

RESULTS

Out of the 50 couples, 54% of females had psychiatric morbidity. The most common diagnosis amongst the female participants was MDD (Major Depressive Disorder) (18%), whereas the second most common diagnosis was GAD (Generalized Anxiety Disorder) (16%). Psychiatric morbidity was found in only 26% of males suffering with Adjustment Disorder being most common diagnosis (8%) and Dysthymia and MDD as the second most common diagnosis (6% each). Majority of patients having psychiatric morbidity were from age group 20-29 years. The difference between females and male counterparts was statistically significant.

CONCLUSION

Psychiatric morbidity was higher among female partners than male partners. The difference was statistically significant and the situation needs further workup.

Phylogenetic analysis of VP2 gene of canine parvovirus and comparison with Indian and world isolates

Canine parvovirus (CPV) causes hemorrhagic enteritis, especially in young dogs, leading to high morbidity and mortality. It has four main antigenic types CPV-2, CPV-2a, CPV-2b and CPV-2c. Virus protein 2 (VP2) is the main capsid protein and mutations affecting VP2 gene are responsible for the evolution of various antigenic types of CPV. Full length VP2 gene from field isolates was amplified and cloned for sequence analysis. The sequences were submitted to the GenBank and were assigned Acc. Nos., viz. KP406928.1 for P12, KP406927.1 for P15, KP406930.1 for P32, KP406926.1 for Megavac-6 and KP406929.1 for NobivacDHPPi. Phylogenetic analysis indicated that the samples were forming a separate clad with vaccine strains. When the samples were compared with the world and Indian isolates, it was observed that samples formed a separate node indicating regional genetic variation in CPV.

Combinatorial Effects of Aromatic 1,3-Disubstituted Ureas and Fluoride on In vitro Inhibition of Streptococcus mutans Biofilm Formation

Dental caries occur as a result of disequilibrium between acid producing pathogenic bacteria and alkali generating commensal bacteria within a dental biofilm (dental plaque). Streptococcus mutans has been reported as a primary cariogenic pathogen associated with dental caries. Emergence of multidrug resistant as well as fluoride resistant strains of S. mutans due to over use of various antibiotics are a rising problem and prompted the researchers worldwide to search for alternative therapies. In this perspective, the present study was aimed to screen selective inhibitors against ComA, a bacteriocin associated ABC transporter, involved in the quorum sensing of S. mutans. In light of our present in silico findings, 1,3-disubstituted urea derivatives which had better affinity to ComA were chemically synthesized in the present study for in vitro evaluation of S. mutans biofilm inhibition. The results revealed that 1,3-disubstituted urea derivatives showed good biofilm inhibition. In addition, synthesized compounds exhibited potent synergy with a very low concentration of fluoride (31.25-62.5 ppm) in inhibiting the biofilm formation of S. mutans without affecting the bacterial growth. Further, the results were supported by confocal laser scanning microscopy. On the whole, from our experimental results we conclude that the combinatorial application of fluoride and disubstituted ureas has a potential synergistic effect which has a promising approach in combating multidrug resistant and fluoride resistant S. mutans in dental caries management.

Evolutionary relationships between heme-binding ferredoxin α + β barrels

BACKGROUND

The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. Several members of this superfamily bind heme in order to carry out their functions.

RESULTS

We analyze the heme-binding sites in these proteins as well as their barrel topologies. Our comparative structural analysis of these heme-binding barrels reveals two distinct modes of packing of the ferredoxin-like domains to constitute the α + β barrel, which is typified by the Type-1/IsdG-like and Type-2/OxdA-like proteins, respectively. We examine the heme-binding pockets and explore the versatility of the α + β barrels ability to accommodate heme or heme-related moieties, such as siroheme, in at least three different sites, namely, the mode seen in IsdG/OxdA, Cld/DyP/EfeB/HemQ and siroheme decarboxylase barrels.

CONCLUSIONS

Our study offers insights into the plausible evolutionary relationships between the two distinct barrel packing topologies and relate the observed heme-binding sites to these topologies.

Simultaneous dual syringe electrospinning system using benign solvent to fabricate nanofibrous P(3HB-co-4HB)/collagen peptides construct as potential leave-on wound dressing

The main focus of this study is the incorporation of collagen peptides to fabricate P(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] nano-fiber construct to further enhance surface wettability and support cell growth while harbouring desired properties for biodegradable wound dressing. Simultaneous electrospinning of nanofiber P(3HB-co-4HB)/collagen peptides construct was carried out using dual syringe system. The wettability of the constructs increased with the increase in 4HB molar fraction from 20mol% 4HB [53.2°], P(3HB-co-35mol%4HB)[48.9°], P(3HB-co-50mol%4HB)[44.5°] and P(3HB-co-82mol%4HB) [37.7°]. In vitro study carried out using mouse fibroblast cells (L929) grown on nanofiber P(3HB-co-4HB)/collagen peptides construct showed an increase in cell proliferation. In vivo study using animal model (Sprague Dawley rats) showed that nanofibrous P(3HB-co-4HB)/collagen peptides construct had a significant effect on wound contractions with the highest percentage of wound closure of 79%. Hence, P(3HB-co-4HB)/collagen peptides construct suitable for wound dressing have been developed using nano-fabrication technique.

Effectiveness of 3% hypertonic saline nebulization in acute bronchiolitis among Indian children: A quasi-experimental study

OBJECTIVE

To compare the effects of 3% hypertonic saline (HS) and 0.9% normal saline with nebulized 0.9% normal saline with salbutamol in patients of acute viral bronchiolitis.

MATERIALS AND METHODS

Participants were divided into three groups, that is, 3% HS group, 0.9% normal saline group and 0.9% saline with salbutamol group. Four doses at interval of 6 h were given daily until discharge. Average CS score and length of hospital stay were compared. One-way analysis of variance paired t-test and Chi-square test were utilized for statistical analysis.

RESULTS

The mean ages of the patients in three groups were 6.03 ± 3.71, 5.69 ± 3.34 and 5.48 ± 3.35 respectively. The 3(rd) day CS scores for all the groups were 1.0 ± 1.1, 1.9 ± 1.1 and 3.3 ± 0.5 respectively (P = 0.000). The average length of hospital stay was 3.4 ± 1.7, 3.7 ± 1.9 and 4.9 ± 1.4 days respectively (P = 0.001).

CONCLUSION

The present study concludes that 3% HS nebulization (without additional bronchodilators) is an effective and safe treatment for nonasthmatic, moderately ill patients of acute bronchiolitis. The economic benefit of this comparably priced modality of treatment can be enormous in terms of hospital costs with parents returning to work sooner.

Bromodomain and hedgehog pathway targets in small cell lung cancer

Small cell lung cancer (SCLC) is an extremely aggressive cancer that frequently recurs. Twenty-three human SCLC lines were selected representing varied Myc status. Gene expression of lung cancer, stem-like, hedgehog pathway, and notch pathway genes were determined by RT(2)-PCR array and Exon 1.0 ST array. Etoposide and topotecan concentration response was examined. The IC50's for etoposide and topotecan ranged over nearly 3 logs upon 96 hrs exposure to the drugs. Myc status, TOP2A, TOP2B and TOP1 mRNA expression or topoisomerase 1 and topoisomerase 2 protein did not account for the range in the sensitivity to the drugs. γ-secretase inhibitors, RO429097 and PF-03084014, had little activity in the SCLC lines over ranges covering the clinical Cmax concentrations. MYC amplified lines tended to be more sensitive to the bromodomain inhibitor JQ1. The Smo antagonists, erismodegib and vismodegib and the Gli antagonists, HPI1 and SEN-450 had a trend toward greater sensitivity of the MYC amplified line. Recurrent SCLC is among the most recalcitrant cancers and drug development efforts in this cancer are a high priority.

A novel RING finger in the C-terminal domain of the coatomer protein α-COP

The C-terminal domain of α-COP, an essential subunit of the COPI coatomer complex, is composed of an all α-helical region and a small β-sheet domain. We show that this β-sheet domain is a Really Interesting New Gene (RING)-like treble clef zinc finger. The zinc-binding residues are substituted by other aminoacids in many homologs including the structurally-characterized proteins from Saccharomyces cerevisiae and Bos taurus. This RING-like domain is possibly related to those of other vesicle membrane-associated complexes, such as CORVET, HOPS and SEA, and likely mediates interactions with Dsl1p and assist in coat oligomerization.