High-Affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water

We prepared a series of water-soluble aromatic oligoamide sequences all composed of a segment prone to form a single helix and a segment prone to dimerize into a double helix. These sequences exclusively assemble as antiparallel duplexes. The modification of the duplex inner rim by varying the nature of the substituents borne by the aromatic monomers allowed us to identify sequences that can hybridize by combining two chemically different strands, with high affinity and complete selectivity in water. X-ray crystallography confirmed the expected antiparallel configuration of the duplexes whereas NMR spectroscopy and mass spectrometry allowed us to assess precisely the extent of the hybridization. The hybridization kinetics of the aromatic strands was shown to depend on both the nature of the substituents responsible for strand complementarity and the length of the aromatic strand. These results highlight the great potential of aromatic hetero-duplex as a tool to construct non-symmetrical dynamic supramolecular assemblies.

Controlling aromatic helix dimerization in water by tuning charge repulsions

Several helically folded aromatic oligoamides were designed and synthesized. The sequences were all water-soluble thanks to the charged side chains borne by the monomers. Replacing a few, sometimes only two, charged side chains by neutral methoxy groups was shown to trigger the formation of various aggregates which could be tentatively assigned to head-to-head stacked dimers of single helices, double helical duplexes and a quadruplex, none of which would form in organic solvent with organic-soluble analogues. The nature of the aggregates was supported by concentration and solvent dependent NMR studies, 1H DOSY experiments, mass spectrometry, and X-ray crystallography or energy-minimized models, as well as analogies with earlier studies. The hydrophobic effect appears to be the main driving force for aggregation but it can be finely modulated by the presence or absence of a small number of charges to an extent that had no precedent in aromatic foldamer architectures. These results will serve as a benchmark for future foldamer design in water.

Self-assembly of achiral building blocks into chiral cyclophanes using non-directional interactions

The diastereoselective assembly of achiral constituents through a single spontaneous process into complex covalent architectures bearing multiple stereogenic elements still remains a challenge for synthetic chemists. Here, we show that such an extreme level of control can be achieved by implementing stereo-electronic information on synthetic organic building blocks and templates and that non-directional interactions (i.e., electrostatic and steric interactions) can transfer this information to deliver, after self-assembly, high-molecular weight macrocyclic species carrying up to 16 stereogenic elements. Beyond the field of supramolecular chemistry, this proof of concept should stimulate the on-demand production of highly structured polyfunctional architectures.

(Re-)Directing Oligomerization of a Single Building Block into Two Specific Dynamic Covalent Foldamers through pH

Dynamic foldamers are synthetic folded molecules which can change their conformation in response to an external stimulus and are currently at the forefront of foldamer chemistry. However, constitutionally dynamic foldamers, which can change not only their conformation but also their molecular constitution in response to their environment, are without precedent. We now report a size- and shape-switching small dynamic covalent foldamer network which responds to changes in pH. Specifically, acidic conditions direct the oligomerization of a dipeptide-based building block into a 16-subunit macrocycle with well-defined conformation and with high selectivity. At higher pH the same building block yields another cyclic foldamer with a smaller ring size (9mer). The two foldamers readily and repeatedly interconvert upon adjustment of the pH of the solution. We have previously shown that addition of a template can direct oligomerization of the same building block to yet other rings sizes (including a 12mer and a 13mer, accompanied by a minor amount of 14mer). This brings the total number of discrete foldamers that can be accessed from a single building block to five. For a single building block system to exhibit such highly diverse structure space is unique and sets this system of foldamers apart from proteins. Furthermore, the emergence of constitutional dynamicity opens up new avenues to foldamers with adaptive behavior.

Generalizing the Aromatic δ‐Amino Acid Foldamer Helix

A series of aromatic oligoamide foldamer sequences containing different proportions of three δ‐amino acids derived from quinoline, pyridine, and benzene and possessing varying flexibility, for example due to methylene bridges, were synthesized. Crystallographic structures of two key sequences and ¹H NMR data in water concur to show that a canonical aromatic helix fold prevails in almost all cases and that helix stability critically depends on the ratio between rigid and flexible units. Notwithstanding subtle variations of curvature, i. e. the numbers of units per turn, the aromatic δ‐peptide helix is therefore shown to be general and tolerant of a great number of sp³ centers. We also demonstrate canonical helical folding upon alternating two monomers that do not promote folding when taken separately: folding occurs with two methylenes between every other unit, not with one methylene between every unit. These findings highlight that a fine‐tuning of helix handedness inversion kinetics, curvature, and side chain positioning in aromatic δ‐peptidic foldamers can be realized by systematically combining different yet compatible δ‐amino acids.

Racemic crystal structures of A-DNA duplexes

Racemic crystallography benefits the identification of a structural form of a DNA sequence that was not previously observed for the enantiopure equivalent.

The ease with which racemic mixtures crystallize compared with the equivalent chiral systems is routinely taken advantage of to produce crystals of small molecules. However, biological macromolecules such as DNA and proteins are naturally chiral, and thus the limited range of chiral space groups available hampers the crystallization of such molecules. Inspiring work over the past 15 years has shown that racemic mixtures of proteins, which were made possible by impressive advances in protein chemical synthesis, can indeed improve the success rate of protein crystallization experiments. More recently, the racemic crystallization approach was extended to include nucleic acids as a possible aid in the determination of enantiopure DNA crystal structures. Here, findings are reported that suggest that the benefits may extend beyond this. Two racemic crystal structures of the DNA sequence d(CCCGGG) are described which were found to fold into A-form DNA. This form differs from the Z-form DNA conformation adopted by the chiral equivalent in the solid state, suggesting that the use of racemates may also favour the emergence of new conformations. Importantly, the racemic mixture forms interactions in the solid state that differ from the chiral equivalent (including the formation of racemic pseudo-helices), suggesting that the use of racemic DNA mixtures could provide new possibilities for the design of precise self-assembled nanomaterials and nanostructures.

Discrete Stacked Dimers of Aromatic Oligoamide Helices

Tight binding was observed between the C‐terminal cross section of aromatic oligoamide helices in aqueous solution, leading to the formation of discrete head‐to‐head dimers in slow exchange on the NMR timescale with the corresponding monomers. The nature and structure of the dimers was evidenced by 2D NOESY and DOSY spectroscopy, mass spectrometry and X‐ray crystallography. The binding interface involves a large hydrophobic aromatic surface and hydrogen bonding. Dimerization requires that helices have the same handedness and the presence of a C‐terminal carboxy function. The protonation state of the carboxy group plays a crucial role, resulting in pH dependence of the association. Dimerization is also influenced by neighboring side chains and can be programmed to selectively produce heteromeric aggregates.

Conformational interplay in hybrid peptide-helical aromatic foldamer macrocycles

Macrocyclic peptides are an important class of bioactive substances. When inserting an aromatic foldamer segment in a macrocyclic peptide, the strong folding propensity of the former may influence the conformation and alter the properties of the latter. Such an insertion is relevant because some foldamer-peptide hybrids have recently been shown to be tolerated by the ribosome, prior to forming macrocycles, and can thus be produced using an in vitro translation system. We have investigated the interplay of peptide and foldamer conformations in such hybrid macrocycles. We show that foldamer helical folding always prevails and stands as a viable means to stretch, i.e. unfold, peptides in a solvent dependent manner. Conversely, the peptide systematically has a reciprocal influence and gives rise to strong foldamer helix handedness bias as well as foldamer helix stabilisation. The hybrid macrocycles also show resistance towards proteolytic degradation.

Quantitative helix handedness bias through a single H vs. CH3 stereochemical differentiation

A novel chiral aromatic δ-amino acid building block was shown to fully induce handedness in quinoline oligoamide foldamers with the possibility of further increasing the bias by combining multiples of these units in the same sequence. Through its incorporation within the helix, both N- and C-termini are still accessible for further functionalisation.

Aromatic Foldamer Helices as α-Helix Extended Surface Mimetics

Helically folded aromatic oligoamide foldamers have a size and geometrical parameters very distinct from those of α-helices and are not obvious candidates for α-helix mimicry. Nevertheless, they offer multiple sites for attaching side chains. It was found that some arrays of side chains at the surface of an aromatic helix make it possible to mimic extended α-helical surfaces. Synthetic methods were developed to produce quinoline monomers suitably functionalized for solid phase synthesis. A dodecamer was prepared. Its crystal structure validated the initial design and showed helix bundling involving the α-helix-like interface. These results open up new uses of aromatic helices to recognize protein surfaces and to program helix bundling in water.

Hybrid Sequences that Express both Aromatic Amide and α-Peptidic Folding Features

Foldamers combining aliphatic and aromatic main-chain units often produce atypical structures that cannot easily be accessed from purely aromatic or aliphatic sequences. We report solid-state evidence that sequences comprising α-amino acids and quinoline-based monomers adopt conformations that combine the folding propensities of both components. Foldamers 2 and 3 having an XQQ repeat motif (X=α-amino acid, Q=quinoline) were synthesized. Crystals of 2 (X=Phe, Q with an anionic side chain) obtained from water revealed an aromatic helix where amide groups belonging to the α-amino acids created a hydrogen-bond array typical of peptidic helices. Crystals of 3 (X=Ser, Q with a lipophilic side chain) obtained from organic solvents revealed a helix-turn-helix structure in which α-amino acid side chains interfere with main-chain hydrogen bonding. High sequence-dependency of the conformation is typical of peptides but is shown here to include aromatic folding features.

Crystal structures of disordered Z-type helices

The X-ray crystal structures of a decamer sequence d(CGCGTACGCG)₂ and a tetradecamer sequence d(CGCGCGTACGCGCG)₂ are presented here. Both sequences are alternating pyrimidine-purine repeat sequences and they form disordered, pseudo-continuous left handed Z-type helices. They demonstrate interesting variants of the 'bundles of columns of helices' mode of packing.

Crystal structure of phospholipase A2 in complex with 1-naphthaleneacetic acid

Phospholipase A₂ (PLA₂ ) is one of the rate limiting enzymes involved in the production of arachidonic acid, a potent inflammatory mediator. PLA₂ is widely distributed all over the animal kingdom. It is also seen in inflammatory exudation and venoms of different organisms. The studies demonstrated that PLA₂ inhibitors have broad spectrum activities that they can either be used against inflammation or envenomation. In this study, the inhibitory activity of 1-napthaleneacetic acid (NAA) against porcine pancreatic PLA₂ has been explained through isothermal titration calorimetry and enzyme kinetics studies. The atomic level of interactions of NAA with PLA₂ was also studied using X-ray crystallography. Apart from these findings, the theoretical binding affinities and mode of interactions of two naphthalene-based NSAIDs such as naproxen (NAP) and nabumetone (NAB) were studied through molecular modeling. The studies proved that the selected ligands are binding at the doorway of the active site cleft and hindering the substrate entry to the active site. The study brings out a potential scaffold for the designing of broad spectrum PLA₂ inhibitors which can be used for inflammation or envenomation. © 2018 IUBMB Life, 70(10):995-1001, 2018.

Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids

Translation, the mRNA-templated synthesis of peptides by the ribosome, can be manipulated to incorporate variants of the 20 cognate amino acids. Such approaches for expanding the range of chemical entities that can be produced by the ribosome may accelerate the discovery of molecules that can perform functions for which poorly folded, short peptidic sequences are ill suited. Here, we show that the ribosome tolerates some artificial helical aromatic oligomers, so-called foldamers. Using a flexible tRNA-acylation ribozyme-flexizyme-foldamers were attached to tRNA, and the resulting acylated tRNAs were delivered to the ribosome to initiate the synthesis of non-cyclic and cyclic foldamer-peptide hybrid molecules. Passing through the ribosome exit tunnel requires the foldamers to unfold. Yet foldamers encode sufficient folding information to influence the peptide structure once translation is completed. We also show that in cyclic hybrids, the foldamer portion can fold into a helix and force the peptide segment to adopt a constrained and stretched conformation.

Abstract PD6-06: Understanding the complexity of macrophage and mesenchymal stem cell interactions to improve treatment outcome for IBC patients

Cells within the tumor microenvironment, including but not limited to macrophages and mesenchymal stem cells (MSCs), can promote the phenotype and aggressiveness of inflammatory breast cancer (IBC). For example, co-injection of MSCs with SUM149 IBC cells significantly increased the clinical features of IBC such as skin invasion and metastasis. Our preliminary work showed that MSCs can be educated by co-culture with M1 polarized (anti-tumor) or M2 polarized (pro-tumor) mouse Raw macrophages. Such education of MSCs by M2 Raw macrophages leads to increased IL6 secretion by MSCs, relative to M1-educated or uneducated MSCs. M2-educated MSCs also have increased migration toward IBC cell lines SUM149 and IBC3, effects that can be blocked by an anti-IL6 antibody. Co-culture with M2-educated MSCs also enhances migration and mammosphere formation of IBC cells. Radiation response of IBC cells upon interactions with cells from the tumor microenvironment was also analyzed. Preliminary work shows that co-culture of IBC cells (SUM149 and KPL4) with M2-polarized human THP1 macrophages, prior to ionizing radiation, mediates radiation resistance of IBC cells, and this effect can be decreased by either adding HDL lipoproteins during co-culture period or by STAT6 inhibitors that block IL4/IL13-mediated phosphorylation of STAT6 and M2-polarization in THP1 macrophages. MSCs can also be polarized into either a MSC1 phenotype or a MSC2 phenotype by exposure to toll-like receptor (TLR) ligands TLR4 or TLR3, respectively. Indoleamine-pyrrole 2,3-dioxygenase (IDO) expression in MSCs is a marker of MSC2 polarization that is induced after exposure with TLR3 ligand (PolyIC) relative to MSC1 (TLR4 stimulated; LPS-treated) or parental MSCs. Similar to macrophage polarization, while MSC1 mediates anti-tumor effects, MSC2 are immunosuppressive and thus contribute to tumor growth. Preliminary work also shows that co-culture of IBC cells with MSC2 mediates radioresistance and this can be decreased as well by exposure to HDL during co-culture period prior to radiation. HDL protective effects, in part, can be explained by decreased expression of TLR3-induced IDO mRNA levels in MSC2. In the present work, we extended the above mentioned observations regarding the crosstalk between mouse Raw macrophages and MSCs by analyzing the effect of co-culture of human THP1 macrophages (parental designated as M0, M1- or M2-polarized) with MSCs on the IDO mRNA expression in MSCs, a marker of MSC2 polarization. Surprisingly, co-culture of M1-polarized THP1 with MSCs resulted in a robust increased expression of IDO mRNA in MSC relative to parental MSC (uneducated) or MSCs co-cultured with M2-THP1. Further studies are needed to determine the effects of increased IDO expression in MSC, upon M1-THP1 co-culture, on the aggressive behavior of IBC cells and whether this could be altered with IDO inhibitors. Our results suggest that there could be inter-species differences between mouse and human macrophages on the education of human MSCs. Based on our findings we propose testing a combination of STAT6 inhibitors that reverse M2-polarization of macrophages and IDO inhibitors that can decrease MSC2 phenotype mediated by TLR3 exposure and/or M1-THP1 education.

Citation Format: Rahal OM, Wolfe AR, Mandal PK, Larson R, Tin S, Reuben JM, McMurray JS, Woodward WA. Understanding the complexity of macrophage and mesenchymal stem cell interactions to improve treatment outcome for IBC patients [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD6-06.

Optimizing side chains for crystal growth from water: a case study of aromatic amide foldamers

The growth of crystals of aromatic compounds from water much depends on the nature of the water solubilizing functions that they carry. Rationalizing crystallization from water, and structure elucidation, of aromatic molecular and supramolecular systems is of general value across various fields of chemistry. Taking helical aromatic foldamers as a test case, we have validated several short polar side chains as efficient substituents to provide both solubility in, and crystal growth ability from, water. New 8-amino-2-quinolinecarboxylic acids bearing charged or neutral aminomethyl, carboxymethyl, sulfonic acid, or bis(hydroxymethyl)-methoxy side chains in position 4 or 5, were prepared on a multi gram scale. Fmoc protection of the main chain amine and suitable protections of the side chains ensured compatibility with solid phase synthesis. One tetrameric and five octameric oligoamides displaying these side chains were synthesized and shown to be soluble in water. In all cases but one, crystals were obtained using the hanging drop method, thus validating the initial design principle to combine polarity and rigidity. The only case that resisted crystallization appeared to be due to exceedingly high water solubility endowed by eight sulfonic acid functions. The neutral side chain did provide crystal growth ability from water but contributed poorly to solubility.

Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 Å resolution

We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)₂ all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P4₁2₁2 to P4₁. The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G₁₃ bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.

Interferon γ is a STAT1-dependent direct inducer of BCL6 expression in imatinib-treated chronic myeloid leukemia cells

B-cell CLL/lymphoma 6 (BCL6) exerts oncogenic effects in several human hematopoietic malignancies including chronic myeloid leukemia (CML), where BCL6 expression was shown to be essential for CML stem cell survival and self-renewal during imatinib mesylate (IM) treatment. As several lines of evidence suggest that interferon γ (IFNγ) production in CML patients might have a central role in the response to tyrosine kinase inhibitor (TKI) therapy, we analyzed if IFNγ modulates BCL6 expression in CML cells. Although separate IFNγ or IM treatment only slightly upregulated BCL6 expression, combined treatment induced remarkable BCL6 upregulation in CML lines and primary human CD34+ CML stem cells. We proved that during combined treatment, inhibition of constitutive signal transducer and activator of transcription (STAT) 5 activation by IM allowed the specific enhancement of the STAT1 dependent, direct upregulation of BCL6 by IFNγ in CML cells. By using colony-forming assay, we found that IFNγ enhanced the ex vivo colony or cluster-forming capacity of human CML stem cells in the absence or presence of IM, respectively. Furthermore, inhibition of the transcriptional repressor function of BCL6 in the presence of IM and IFNγ almost completely blocked the cluster formation of human CML stem cells. On the other hand, by using small interfering RNA knockdown of BCL6, we demonstrated that in an IM-treated CML line the antiapoptotic effect of IFNγ was independent of BCL6 upregulation. We found that IFNγ also upregulated several antiapoptotic members of the BCL2 and BIRC gene families in CML cells, including the long isoform of MCL1, which proved to be essential for the antiapoptotic effect of IFNγ in an IM-treated CML line. Our results suggest that combination of TKIs with BCL6 and MCL1 inhibitors may potentially lead to the complete eradication of CML stem cells.

Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography

It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods-that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence 'TATAAT'. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65-2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence.

Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains

Using commercial screens for crystallization of biomolecules and taking advantage of the use of racemic crystallography allowed the production of X-ray quality single crystals and the elucidation at 1.08 Å resolution of the solid state structure of a difficult target: the complex between glucopyranose and a water soluble macrocyclic receptor equipped with dendritic multianionic solubilizing chains.

Consequence of neo-adjuvant chemotherapy on morphology of breast carcinoma: A systematic evaluation

BACKGROUND

Neo-adjuvant chemotherapy (NAC) in locally advanced breast cancer is the present trend. Following NAC, a considerable alteration of morphology occurs in the tumor.

AIMS

To study effects of NAC on morphology of breast carcinoma and to evaluate the pathologic response (PR).

MATERIALS AND METHODS

A total of 39 surgically resected mastectomy specimens of patients of invasive locally advanced breast carcinoma who received NAC were evaluated for macroscopic and microscopic (by routine stains and immunohistochemistry) alteration of morphology.

RESULTS

Macroscopically well-defined tumor noted in 25 cases (64.1%) and in the rest (14 cases, 35.9%), only fibrotic areas identified. Microscopic examination identified malignant cells in 29 (74.4%), significant chronic inflammation in 24 (61.5%), hyalinized fibrosed stroma in 25 (64.1%) and necrosis in 11 (28.2%) cases. Immunohistochemistry assisted in differentiating malignant cells from histiocytes. In 15 cases (38.5%), axillary lymph nodes isolated where fibrosis seen in 12 (30.8%) and malignant cell in 8 (20.5%) cases. In 34 cases where the pre-treatment biopsy were available, complete pathologic response (pCR) and partial pathologic response (pPR) were achieved in 7 (20.6%) and 23 (67.4%) cases respectively.

DISCUSSION

Protocol of systematic evaluation of morphological changes is different in cases of a patient treated by NAC. Nature of malignancy was difficult to categorize as morphology of typical breast carcinomas were altered. Sometimes, immunohistochemistry is advantageous as routine H and E stains are not sufficient to isolate malignant cells in fibrotic and necrotic areas. Appropriate morphological evaluation of the mastectomy specimen is absolutely crucial for assessment of PR and subsequent management.

Parkinson's disease detection using olfactory loss and REM sleep disorder features

In Parkinson's disease, there exists a prodromal or a premotor phase characterized by symptoms like olfactory loss and sleep disorders, which may last for years or even decades before the onset of motor clinical symptoms. Diagnostic tools based on machine learning using these features can be very useful as they have the potential in early diagnosis of the disease. In the paper, we use olfactory loss feature from 40-item University of Pennsylvania Smell Identification Test (UPSIT) and Sleep behavior disorder feature from Rapid eye movement sleep Behavior Disorder Screening Questionnaire (RBDSQ), obtained from the Parkinson's Progression Marker's Initiative (PPMI) database, to develop automated diagnostic models using Support Vector Machine (SVM) and classification tree methods. The advantage of using UPSIT and RBDSQ is that they are quick, cheap, and can be self-administered. Results show that the models performed with high accuracy and sensitivity, and that they have the potential to aid in early diagnosis of Parkinson's disease.

Nitrate Starvation Induced Changes in Root System Architecture, Carbon:Nitrogen Metabolism, and miRNA Expression in Nitrogen-Responsive Wheat Genotypes

Improvement of nutrient use efficiency in cereal crops is highly essential not only to reduce the cost of cultivation but also to save the environmental pollution, reduce energy consumption for production of these chemical fertilizers, improve soil health, and ultimately help in mitigating climate change. In the present investigation, we have studied the morphological (with special emphasis on root system architecture) and biochemical responses (in terms of assay of the key enzymes involved in N assimilation) of two N-responsive wheat genotypes, at the seedling stage, under nitrate-optimum and nitrate-starved conditions grown in hydroponics. Expression profile of a few known wheat micro RNAs (miRNAs) was also studied in the root tissue. Total root size, primary root length, and first- and second-order lateral root numbers responded significantly under nitrate-starved condition. Morphological parameters in terms of root and shoot length and fresh and dry weight of roots and shoots have also been observed to be significant between N-optimum and N-starved condition for each genotypes. Nitrate reductase (NR), glutamine synthatase (GS), and glutamate dehydrogenase (GDH) activity significantly decreased under N-starved condition. Glutamine oxoglutarate amino transferase (GOGAT) and pyruvate kinase (PK) activity was found to be genotype dependent. Most of the selected miRNAs were expressed in root tissues, and some of them showed their differential N-responsive expression. Our studies indicate that one of the N-responsive genotype (NP-890) did not get affected significantly under nitrogen starvation at seedling stage.

Spectrum of bacterial pathogens and their antibiogram from cases of urinary tract infection among renal disorder patients

Urinary tract infection (UTI) is the commonest bacterial infection occurring in renal disorder patients and is associated with significant morbidity. Resistance to antibiotics is highly prevalent in bacterial isolates and is an emerging problem in UTI. A hospital based cross sectional study was conducted from April 2011 to September 2011 to determine the frequency and bacterial profile of urinary tract infections in the patients with renal disorders visiting KIST Hospital along with their antimicrobial susceptibility pattern. Urine samples were collected from 300 clinically-suspected cases of UTI among renal disorder patients and investigated by conventional semi-quantitative culture technique, microscopy and antibiotic susceptibility test. Significant bacteriuria were detected in 34% of the total subjects, mostly from patients with Chronic Kidney Disease. Incidence of bacteriuria was found higher in females (40.40%) than in males (27.52%) and mostly occurred in elderly patients. Escherichia coli (62.75%) was the predominant isolate followed by Klebsiella pneumoniae (10.78%), Staphylococcus aureus (9.80%), Coagulase negative Staphylococcus aureus (CoNS) (5.88%), Enterococcus spp (3.92%), Klebsiella oxytoca (2.00%), Pseudomonas aeruginosa (2.00%), Proteus mirabilis (2.00%) and Proteus vulgaris (1.00%). Multidrug resistance was observed in 68.82% of the total bacterial isolates.

Hashimoto's Thyroiditis and Medullary Carcinoma of Thyroid

Hashimoto's thyroiditis (HT) has been found to be associated with lymphoma, papillary carcinoma and Hürthle cell neoplasms of thyroid. In contrast, there are only a few reports of co-existence of HT with medullary carcinoma of thyroid. An overall prevalence of medullary carcinoma of only 0.35% has been reported in HT patients. Such a rare combination is being presented here. A 33 year old female presented with history of goiter for one year. Fine needle aspiration cytology (FNAC) of the swelling revealed cytological features suggestive of medullary carcinoma of thyroid. Histopathological examination of total thyroidectomy specimen revealed Hashimoto's thyroiditis along with medullary carcinoma of thyroid. Although Hashimoto's thyroiditis can uncommonly co-exist with thyroid neoplasm, its association with medullary carcinoma is extremely rare and hence being presented.

Efficacy of leaves (drumstick, mint and curry leaves) powder as natural preservatives in restructured chicken block

The use of natural preservatives to increase the shelf-life of meat products is promising as they possess antioxidant and antimicrobial properties. Earlier, a highly acceptable restructured chicken slice without the addition of extra fat was developed in the same laboratory which was acceptable up to 10th day of storage under refrigeration and spoilage was mainly due to oxidation. Hence, the present study was planned to determine the efficacy of certain plant leaves' (drumstick, mint and curry leaves) powder at 1 % level as natural preservatives to enhance the shelf life of restructured chicken slices under refrigerated storage. The quality attributes of the products containing different natural preservativs were compared with the control and reference products. The control product contained no preservative and the reference product contained BHT (200 ppm) only. Incorporation of the leaf powders at 1 % level did not show any significant differences for both cooking yield (99.5-99.6 %) and proximate composition (moisture 72.2-72.3 %, protein 19.2-19.4 %, fat 4.2-4.3 % and total ash 2.3-2.4 %) of the restructured chicken slices compared to both control and reference products during storage. All products containing leaf powders showed significantly (P < 0.01) lower microbial counts (2.9-3.7 log10 CFU/g) compared to both control and BHT added products. Yeast and mould were not detected in any of the products throughout the storage period. Sensory evaluation scores showed that the restructured chicken slices incorporated with the leaf powders were as acceptable as the reference product and rated good to very good for appearance, flavor, juiciness and overall acceptability. Restructured chicken slices with the leaf powders could be safely stored without much loss in quality up to 20 days under refrigeration.

Urinary tract infection in vaginitis: a condition often overlooked

Despite the differences between the organisms that cause vaginitis and urinary tract infections (UTI), it is possible that women with vaginitis develop UTI. The main objective of the study was to find the association of the common types of infectious vaginitis with UTI. Cross sectional study was conducted for six months in a referral hospital at Lalitpur, Nepal. Three hundred and sixmid-stream urine samples and high vaginal swabs (HVS) collected from non pregnant women were investigated by standard microbiological techniques. Among the women with bacterial vaginosis (BV), 75% also had UTI. Similarly, 46% and 13% of those with vaginal candidiasis and trichomoniasis respectively had concurrent UTI. Considering this strong association of UTI and vaginitis, women with either of these conditions should be tested for the other.

Anti-inflammatory property of n-hexadecanoic acid: structural evidence and kinetic assessment

Ester bond hydrolysis of membrane phospholipids by Phospholipase A(2) and consequent release of fatty acids are the initiating steps of inflammation. It is proposed in this study that the inhibition of phospholipase A(2) is one of the ways to control inflammation. Investigations are carried out to identify the mode of inhibition of phospholipase A(2) by the n-hexadecanoic acid. It may help in designing of specific inhibitors of phospholipase A(2) as anti-inflammatory agents. The enzyme kinetics study proved that n-hexadecanoic acid inhibits phospholipase A(2) in a competitive manner. It was identified from the crystal structure at 2.5 Å resolution that the position of n-hexadecanoic acid is in the active site of the phospholipase A(2). The binding constant and binding energy have also been calculated using Isothermal Titration Calorimetry. Also, the binding energy of n-hexadecanoic acid to phospholipase A(2) was calculated by in silico method and compared with known inhibitors. It may be concluded from the structural and kinetics studies that the fatty acid, n-hexadecanoic acid, is an inhibitor of phospholipase A(2), hence, an anti-inflammatory compound. The inferences from the present study validate the rigorous use of medicated oils rich in n-hexadecanoic acid for the treatment of rheumatic symptoms in the traditional medical system of India, Ayurveda.

Crystallographic and spectroscopic studies of d(CCGGTACCGG)

The decanucleotide sequence d(CCGGTACCGG) crystallizes as a four-way junction at low cobalt ion concentrations (i.e., 1 mM). When the cobalt concentration in the crystallization solution is increased to 5 mM, the sequence crystallizes as resolved B-DNA duplexes. Gel retardation studies of the decamer show both a faint slow-moving band and a much thicker fast-moving band at low cobalt ion concentrations, and only the intense fast-moving band at higher ion concentration. Circular dichroism (CD) spectroscopy of the decamer indicates a structural transition as the cobalt ion concentration in the solution is increased, probably from B-type to A-type DNA. These studies revealed that the oligomer sequence has several conformations and structures accessible to it, in a manner dependent on sequence, ion concentration, and DNA concentration. [Supplementary materials are available for this article. Go to the publisher's online edition of Nucleosides, Nucleotides & Nucleic Acids for the following free supplemental resources(s): Supplementary Figures 1, 2, and 3.].

Isolated chondrosarcoma of frontal sinus

An uncommon case of chondrosarcoma involving frontal sinus is presented. Pertinent literature is reviewed to emphasize the management of this tumor at unusual site.DOI: http://dx.doi.org/10.3329/bjo.v18i1.10425  Bangladesh J Otorhinolaryngol 2012; 18(1): 81-83

Structure of d(CGGGTACCCG)4 as a four-way Holliday junction

The crystal structure of the decamer sequence d(CGGGTACCCG)(4) as a four-way Holliday junction has been determined at 2.35 Å resolution. The sequence was designed in order to understand the principles that govern the relationship between sequence and branching structure. It crystallized as a four-way junction structure with an overall geometry similar to those of previously determined Holliday junction structures.

Functional Disability and Associated Chronic Conditions among Geriatric Populations in a Rural Community of India

BACKGROUND

Geriatric population and chronic diseases are increasing throughout the world especially in developing countries like India. Because of social change and urbanization, disability is also a problem in India. As the major reasons for geriatric disabilities are chronic diseases, a study was undertaken.

OBJECTIVES

To find out the prevalence of different chronic diseases and disability among the geriatric population in a rural community of India and to determine the association between chronic diseases and disability of the geriatric population.

METHOD

A cross-sectional, observational community based study was conducted in a rural area of West Bengal, India through house to house visit for Clinical examination, observation and interview with a predesigned pre-tested proforma

RESULTS

Out of 495 study population, 80 (16.16%) were found to be functionally disabled as per ADL scale and more than half (56.2%) of them had 3 or more chronic conditions. 92.5% of study populations had one or more chronic conditions

CONCLUSION

Association between different risk factors and disability was found with age, sex, anaemia, Chronic Obstructive Pulmonary Diseases(C.O.P.D), scabies, hypertrophy of prostate, ischaemic heart disease, osteoporosis, osteoarthritis and acid peptic disorder were the risk factors of disability. These data suggest the significant chronic conditions and risk factors associated with disability. Measures to reduce such chronic conditions and impairment would be the useful approach for the prevention of disability.

The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice

We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind to each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5Å. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.

The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)₂

We report the 2.6Å resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4₃. This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours.

Assessing cold chain status in a metro city of India: an intervention study

BACKGROUND

Cold chain maintenance is an essential activity to maintain the potency of vaccines and to prevent adverse events following immunization. One baseline study highlighted the unsatisfactory cold chain status in city of Kolkata in India.

OBJECTIVES

To assess the changes which occurred in the cold chain status after the intervention undertaken to improve the status and also to assess the awareness of the cold chain handlers regarding cold chain maintenance.

METHODS

Intervention consisted of reorganization of cold chain points and training of health manpower in Kolkata Municipal area regarding immunization and cold chain following the guidelines as laid by Govt of India. Reevaluation of cold chain status was done at 20 institutions selected by stratified systematic random sampling after the intervention. The results were compared with baseline survey.

RESULTS

Significant improvement had been observed in correct placing of cold chain equipment, maintenance of stock security, orderly placing of ice packs, diluents and vaccines inside the equipment, temperature recording and maintenance. But awareness and skill of cold chain handlers regarding basics of cold chain maintenance was not satisfactory.

CONCLUSIONS

The success of intervention included significant improvement of cold chain status including creation of a designated cold chain handler. The gaps lay in non-availability of non-electrical cold chain equipment and separate cold chain room, policy makers should stress. Cold chain handlers need reorientation training regarding heat & cold sensitive vaccines, preventive maintenance and correct contingency plan.

Numerical simulation of unsteady generalized Newtonian blood flow through differently shaped distensible arterial stenoses

An updated numerical simulation of unsteady generalized Newtonian blood flow through differently shaped distensible arterial stenoses is developed. A shear-thinning fluid modelling the deformation dependent viscosity of blood is considered for the characterization of generalized Newtonian behaviour of blood. The arterial model is treated as two-dimensional and axisymmetric with an outline of the stenosis obtained from a three-dimensional casting of a mildly stenosed artery. The full Navier-Stokes equations governing blood flow are written in the dimensionless form and the solution is accomplished by finite time-step advancement through their finite difference staggered grid representations. The marker and cell (MAC) method comprising the use of a set of marker particles moving with the fluid is used for the purpose. Results are obtained for three differently shaped stenoses - irregular, smooth and cosine curve representations. The present results do agree well with those of existing investigations in the steady state, but contrary to their conclusions the present findings demonstrate that the excess pressure drop across the cosine and the smooth stenoses is caused by neither their smoothness nor their higher degree of symmetry relative to the irregular stenosis, but is rather an effect of area cover with respect to the irregular stenosis. This effect clearly prevails throughout the entire physiological range of Reynolds numbers. Further the in-depth study in flow patterns reveals the development of flow separation zones in the diverging part of the stenosis towards the arterial wall, and they are influenced by non-Newtonian blood rheology, distensibility of the wall and flow unsteadiness in order to validate the applicability of the present model.

The structure of d(CACACG).d(CGTGTG)

The crystal structure of d(CACACG).d(CGTGTG) was solved to a resolution of 2.05 A in space group P2(1). The duplex assumes the left-handed Z-DNA structure. The presence of two A.T base pairs in the hexamer does not greatly affect the conformation. The most significant changes compared with the regular structure of Z-DNA are in the values of twist in the central portion of the helix. This variation, as well as others in the values of roll, inclination etc., follow the pattern observed previously in the structure of d(CGCACG).d(CGTGCG).

Cloning of sarco-endoplasmic reticulum Ca2+ -ATPase (SERCA) from Caribbean spiny lobster Panulirus argus

We have previously reported on calcium transport mechanisms in American lobster, Homarus americanus, using (45)Ca(2+) coupled with vesicle preparations of hepatopancreatic endoplasmic reticulum. The active transport of calcium across membranes bordering calcium-sequestering stores such as sarcoplasmic or endoplasmic reticulum is catalyzed by membrane-spanning proteins, the sarco-endoplasmic Ca(2+)-ATPases (SERCAs). In the study described here we used advanced bioinformatics and molecular techniques to clone SERCA from the economically important Caribbean spiny lobster, Panulirus argus. We report the complete cloning of a full-length SERCA from P. argus antenna cDNA (GenBank accession number AY702617). This cDNA has a 1020-amino acid residue open reading frame which is 90% identical to published sequences of other crustacean SERCA proteins. Our data support the hypothesis that one crustacean and three vertebrate genes controlling calcium transport were derived from a common ancestral gene.

Changing profile of Vibrio cholerae O1, O139 in Delhi & its periphery (2003-2005)

BACKGROUND & OBJECTIVE

Cholera caused by either Vibrio cholerae O1 or O139 is endemic in Delhi and its peripheral areas. The present study was carried out to understand the changing epidemiology of V. cholerae in terms of prevalence of serotypes, antibiogram pattern and phage types.

METHODS

A total of 9858 stool samples from the admitted diarrhoea patients were used for the isolation of V. cholerae O1 and O139. Subsets of isolates were tested against thirteen antimicrobials and phage typed.

RESULTS

Among 4251 (43.1%) confirmed cases, 41.6 per cent were V. cholerae O1 and rest (1.5 %) V. cholerae O139. Detection of V. cholerae O1 serotype Inaba was 87.7 per cent during 2005 and rest were serotype Ogawa. Majority of cases (93.1%) were from Delhi. Male:Female ratio remained 1.5:1.0. Children below 5 yr age group constituted 32.7 per cent cases. Shift in the age groups and seasonal incidence were recorded. All 226 strains of V. cholerae O1 and O139 were resistant to nalidixic acid; 96 per cent V. cholerae O1 isolates were multidrug resistant (FX NA SXT). Phage type 27 (98.7%) was the most prevalent and the new phage types were 4, 16 and 25 in this area.

INTERPRETATION & CONCLUSION

Enhanced surveillance helped in bringing down cases from 47.7 per cent in 2003 to 36.8 per cent in 2005. Additionally, the changing epidemiology of V. cholerae O1 and O139 infections and drug resistance need regular monitoring.