A Nonstatistical Approach to the Prediction of Regular Structures in Proteins by the Example of α Helices

A new approach to the analysis of regular structures in proteins that is based on the method of molecular mechanics is proposed. The method uses only the information about the amino acid sequence. The -helical conformation was simulated using the ICM program of molecular mechanics. Energy profiles of the sequences in the -helical conformation, spanning the entire polypeptide chain, were plotted for eight proteins from the Protein Data Bank. The regions of each profile that exhibit energy minima were found to correspond to the -helical regions of the real spatial structure of the protein. Twenty-four out of 25 helices were distinctly pronounced, which indicates a rather high accuracy of the prediction. The energy profiles also help reveal the short regions that correspond to 3/10-helices and the turns that include local -helical conformations. Unlike the known statistical methods of prediction, this method makes it possible to establish the physical principles of the formation of -helical conformations.     

Preparation of an Octadeoxyribonucleoside Heptaphosphorothioate by the Phosphotriester Approach in Solution†

Abstract

The synthesis of the octadeoxyribonucleoside heptaphosphorothioate, d[Tp(s)Tp(s)Gp(s)Gp(s)Gp(s)Gp(s)Tp(s)T] by the phosphotriester approach in solution is described. The phosphorothioate internucleotide linkages are protected by the S-(2-cyanoethyl) group and 1-(mesitylene-2-sulfonyl)-3-nitro-1,2,4-1H-triazole (MSNT) is used as the coupling agent. A block synthesis strategy (2 + 2 → 4 and 4 + 4 → 8) is followed.

     

What are the Evolutionary Origins of Mitochondria? A Complex Network Approach

Mitochondria originated endosymbiotically from an Alphaproteobacteria-like ancestor. However, it is still uncertain which extant group of Alphaproteobacteria is phylogenetically closer to the mitochondrial ancestor. The proposed groups comprise the order Rickettsiales, the family Rhodospirillaceae, and the genus Rickettsia. In this study, we apply a new complex network approach to investigate the evolutionary origins of mitochondria, analyzing protein sequences modules in a critical network obtained through a critical similarity threshold between the studied sequences. The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c). In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor. Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.     

Endoscopic Endonasal Approach in the Management of Rathke’s Cleft Cysts

Objective

Rathke’s cleft cysts (RCCs) are quite uncommon sellar lesions that can extend or even arise in the suprasellar area. The purpose of this study is to evaluate the effectiveness of both standard and extended endoscopic endonasal approaches in the management of different located RCCs.

Methods

We retrospectively analyzed a series of 29 patients (9 males, 20 females) complaining of a RCC, who underwent a standard or an extended endoscopic transsphenoidal approach at the Division of Neurosurgery, Department of Neurosciences and Reproductive and Odontostomatological Sciences, of the Università degli Studi di Napoli "Federico II”. Data regarding patients’ demographics, clinical evaluation, cyst characteristics, surgical treatments, complications and outcomes were extracted from our electronic database (Filemaker Pro 11, File Maker Inc., Santa Clara, California, USA).

Results

A standard transsphenoidal approach was used in 19 cases, while the extended variation of the approach in 10 cases (5 purely suprasellar and 5 intra-suprasellar RCC). Cysts contents was fully drained in all the 29 cases, whilst a gross total removal, that accounts on the complete cyst wall removal, was achieved in an overall 55,1% of patients (16/29), specifically 36,8% (7/19) that received standard approach and 90% (9/10) of those that underwent to extended approach. We reported a 56.2% of recovery from headache, 38.5% of complete recovery and 53.8% of improvement from visual field defect and an overall 46.7% of improvement of the endocrine functions. Postoperative permanent DI rate was 10.3%, overall post-operative CSF leak rate 6.9%; recurrence/regrowth occurred in 4 patients (4/29, 13.8%), but only one required a second surgery.

Conclusion

The endoscopic transsphenoidal approach for the removal of a symptomatic RCC offers several advantages in terms of visualization of the surgical field during both the exposure and removal of the lesion. The “extended” variation of the endoscopic approach provides a direct access to the supradiaphragmatic space, allowing adequate view and room for the safe removal of selected supradiaphragmatic RCCs, regardless of the sellar size (even a not enlarged sella), and provides a higher likelihood of preserving normal pituitary tissue and functions.     

CEREBRAL PALSY—An Approach to the Problem

A program for the cerebral palsied child has been developed in California which has been made possible through the cooperation of the state and local departments of education, the state and local departments of health, the Children''s Hospital and Orthopedic Hospital at Los Angeles and the University of California School of Medicine in San Francisco. An attempt is being made to deal with not only the medical and educational needs of the cerebral palsied but also the social and emotional aspects.     

Predicting Therapeutic Template by Evaluating the Structural Stability of Anti-Cancer Peptides—A Computational Approach

Clinically significant antibiotic resistance has evolved against virtually every antibiotic deployed. Yet the development of new classes of antibiotics has lagged far behind our growing need for such drugs. Antimicrobial peptides (AMPs) have emerged as novel therapeutics hailed for their bactericidal and immunomodulatory properties. However, the process of optimizing antimicrobial peptide stability, using large peptide libraries is both tedious and expensive. The intent of this study is to analyze computationally the stability of anti-cancer peptides (ACPs) and to discover a potential template from a pool of ACPs for therapeutic use. Consequently we highlighted that ACP, NK-Lysin appears advantageous over the other ACPs with respect to stability, and may provide a convenient platform for the development of anticancer therapeutic peptide.     

Three-Dimensional Organization of Polyribosomes–A Modern Approach

Polyribosomes in cells usually have a certain structural organization whose significance has not yet been elucidated. The development of cryo electron tomography has provided a new approach to study polyribosome structure. New data confirm or correct observations made earlier by classical techniques of electron microscopy. The existence of circular and linear (zigzag) topology of polyribosomes was confirmed, and their relationship with the frequently observed tworow forms was clarified. Contacts between ribosomes have been identified in densely packed three-dimensional helical polyribosomes. At the same time, modern cell-free translation systems have opened the possibility of investigating polyribosomes on mRNA of a given structure to elucidate the mechanism of polyribosome structure formation, especially of circular polyribosomes. There is an increasing amount of data supporting the idea of interdependence between polyribosome structure and their translational activity. Moreover, participation of polyribosomes in mRNA transport and localization of protein synthesis in the cell has been shown. Improvement of the resolution and the development of the cryo electron tomography technique for the analysis of polyribosomes in situ will enable further progress in understanding the process of protein synthesis in cells.     

Synthesis of Oligoribonucleotides by the H-Phosphonate Approach Using Base Labile 2′-O-Protecting Groups. V. Recent Progress in Development of the Method

Abstract

A simple and inexpensive method for the preparation of oligoribonucleotides using N-isopropoxyacety(phenoxyacetyl)-2′-O-(2-chlorobenzoyl)-5′-O-dimethoxytritylnucleoside H-phosphonate building blocks has been developed.     

Validation of ‘Variable Number of Tandem Repeat’-Based Approach for Examination of ‘Candidatus Liberibacter asiaticus’ Diversity and Its Applications for the Analysis of the Pathogen Populations in the Areas of Recent Introduction

Citrus greening (Huanglongbing, HLB) is one of the most destructive diseases of citrus worldwide. In South Asia HLB has been known for more than a century, while in Americas the disease was found relatively recently. HLB is associated with three species of ‘Candidatus Liberibacter’ among which ‘Ca. Liberibacter asiaticus’ (CLas) has most wide distribution. Recently, a number of studies identified different regions in the CLas genome with variable number of tandem repeats (VNTRs) that could be used for examination of CLas diversity. One of the objectives of the work presented here was to further validate the VNTR analysis-based approach by assessing the stability of these repeats upon multiplication of the pathogen in a host over an extended period of time and upon its passaging from a host to a host using CLas populations from Florida. Our results showed that the numbers of tandem repeats in the four loci tested display very distinguishable “signature profiles” for the two Florida-type CLas haplotype groups. Remarkably, the profiles do not change upon passage of the pathogen in citrus and psyllid hosts as well as after its presence within a host over a period of five years, suggesting that VNTR analysis-based approach represents a valid methodology for examination of the pathogen populations in various geographical regions. Interestingly, an extended analysis of CLas populations in different locations throughout Florida and in several countries in the Caribbean and Central America regions and in Mexico where the pathogen has been introduced recently demonstrated the dispersion of the same haplotypes of CLas. On the other hand, these CLas populations appeared to differ significantly from those obtained from locations where the disease has been present for a much longer time.     

An Alternative Approach in Gateway® Cloning when the Bacterial Antibiotic Selection Cassettes of the Entry Clone and Destination Vector are the Same

The Gateway^® recombination technology has revolutionized the method of gene cloning for functional analyses and high-throughput ORFeome projects. In general, Gateway cloning is highly efficient because after LR recombination and bacterial transformation, only cells containing the recombinant destination clone are selected on an antibiotic selection plate. However, when the antibiotic resistance gene for bacterial selection is the same in the entry and destination vectors, the direct selection of recombinant destination clones on an antibiotic plate is difficult. Here, we demonstrate an efficient and comprehensive approach to obtain positive destination clones directly on an antibiotic selection plate in this situation. The strategy involves polymerase chain reaction (PCR)-mediated amplification of the entry clone using entry vector-specific primers that bind outside the attL sequences and the subsequent use of this purified PCR product for LR recombination with the destination vector. Our results suggest that cloning of linear DNA fragments into circular destination vectors through LR recombination is an efficient method for inserts up to 7 kb in size. Using this approach, the yield of colony PCR positive destination clones was 100 % for genes of various sizes tested in our experiments.     

A Computational Approach to Characterizing the Impact of Social Influence on Individuals’ Vaccination Decision Making

In modeling individuals vaccination decision making, existing studies have typically used the payoff-based (e.g., game-theoretical) approaches that evaluate the risks and benefits of vaccination. In reality, whether an individual takes vaccine or not is also influenced by the decisions of others, i.e., due to the impact of social influence. In this regard, we present a dual-perspective view on individuals decision making that incorporates both the cost analysis of vaccination and the impact of social influence. In doing so, we consider a group of individuals making their vaccination decisions by both minimizing the associated costs and evaluating the decisions of others. We apply social impact theory (SIT) to characterize the impact of social influence with respect to individuals interaction relationships. By doing so, we propose a novel modeling framework that integrates an extended SIT-based characterization of social influence with a game-theoretical analysis of cost minimization. We consider the scenario of voluntary vaccination against an influenza-like disease through a series of simulations. We investigate the steady state of individuals’ decision making, and thus, assess the impact of social influence by evaluating the coverage of vaccination for infectious diseases control. Our simulation results suggest that individuals high conformity to social influence will increase the vaccination coverage if the cost of vaccination is low, and conversely, will decrease it if the cost is high. Interestingly, if individuals are social followers, the resulting vaccination coverage would converge to a certain level, depending on individuals’ initial level of vaccination willingness rather than the associated costs. We conclude that social influence will have an impact on the control of an infectious disease as they can affect the vaccination coverage. In this respect, our work can provide a means for modeling the impact of social influence as well as for estimating the effectiveness of a voluntary vaccination program.     

Finite Element Analysis of the Cingulata Jaw: An Ecomorphological Approach to Armadillo’s Diets

Finite element analyses (FEA) were applied to assess the lower jaw biomechanics of cingulate xenarthrans: 14 species of armadillos as well as one Pleistocene pampathere (11 extant taxa and the extinct forms Vassallia, Eutatus and Macroeuphractus). The principal goal of this work is to comparatively assess the biomechanical capabilities of the mandible based on FEA and to relate the obtained stress patterns with diet preferences and variability, in extant and extinct species through an ecomorphology approach. The results of FEA showed that omnivorous species have stronger mandibles than insectivorous species. Moreover, this latter group of species showed high variability, including some similar biomechanical features of the insectivorous Tolypeutes matacus and Chlamyphorus truncatus to those of omnivorous species, in agreement with reported diets that include items other than insects. It remains unclear the reasons behind the stronger than expected lower jaw of Dasypus kappleri. On the other hand, the very strong mandible of the fossil taxon Vassallia maxima agrees well with the proposed herbivorous diet. Moreover, Eutatus seguini yielded a stress pattern similar to Vassalia in the posterior part of the lower jaw, but resembling that of the stoutly built Macroeuphractus outesi in the anterior part. The results highlight the need for more detailed studies on the natural history of extant armadillos. FEA proved a powerful tool for biomechanical studies in a comparative framework.     

The Important Role of Active Site Water in the Catalytic Mechanism of Human Carbonic Anhydrase II – A Semiempirical MO Approach to the Hydration of CO2 †

The approach of CO₂ to a series of active site model complexes of human carbonic anhydrase II (HCAII) and its catalytic hydration to bicarbonate anion have been investigated using semiempirical MO theory (AM1). The results show that direct nucleophilic attack of zinc-bound hydroxide to the substrate carbon occurs in each model system. Further rearrangement of the bicarbonate complex thus formed via a rotation-like movement of the bicarbonate ligand can only be found in active site model systems that include at least one additional water molecule. Further refinement of the model complex by adding a methanol molecule to mimic Thr-199 makes this process almost activationless. The formation of the final bicarbonate complex by an internal (intramolecular) proton transfer is only possible in the simplest of all model systems, namely {[Im₃Zn(OH)]⁺·CO₂}. The energy of activation for this process, however, is 36.8 kcal·mol^–1 and thus too high for enzymatic catalysis. Therefore, we conclude that within the limitations of the model systems presented and the level of theory employed, the overall mechanism for the formation of the bicarbonate complex comprises an initial direct nucleophilic attack of zinc-bound hydroxide to carbon dioxide followed by a rotation-like rearrangement of the bicarbonate ligand via a penta-coordinate Zn²⁺ transition state structure, including the participation of an extra active site water molecule.Electronic Supplementary Material available.     

Long-term Sonographic and Serological Follow-up of Inactive Echinococcal Cysts of the Liver: Hints for a “Watch-and-Wait” Approach

Human cystic echinococcosis is a chronic, complex and neglected infection. Its clinical management has evolved over decades without adequate evaluation of efficacy. Recent expert opinion recommends that uncomplicated inactive cysts of the liver should be left untreated and solely monitored over time (“watch-and-wait” approach). However, clinical data supporting this approach are still scant and published mostly as conference proceedings. In this study, we report our experience with long-term sonographic and serological follow-up of inactive cysts of the liver. From March 1994 to October 2013, 38 patients with 47 liver cysts, diagnosed as inactive without any previous treatment history, were followed with ultrasound and serology at 6–12 months intervals for a period of at least 24 months (median follow-up 51.95 months) in our outpatient clinic. In 97.4% of patients, the cysts remained inactive over time and in only one case was reactivation of the cyst detected. No complications occurred during the time of monitoring. During follow-up, serology tests for CE were negative at diagnosis or became negative in 74.1% and were positive or became positive in 25.9% of cases. Patients with inactive cysts on ultrasound but positive serological tests were also investigated by CT scan (chest and abdomen) to rule out extra-hepatic cyst localization. This study confirms the importance of a stage-specific approach to the management of cystic echinococcosis and supports the use of a monitoring-only approach to inactive, uncomplicated cysts of the liver. It also confirms that serology plays only an ancillary role in the clinical management of these patients, compared to ultrasound and other imaging techniques. The implications of these findings for clinical management and natural history of cystic echinococcosis are discussed.     

New Approach to the Synthesis of 2′,3′-dideoxyadenosine and 2′,3′-Dideoxyinosine

Abstract

A new approach to the synthesis of 2′,3′-dideoxyadenosine and 2′,3′-dideoxyinosine based on deoxygenation of 2′,3′-di-O-mesylnucleosides was developed.     

Study of Different Copper (I) Catalysts for the “Click Chemistry” Approach to Carbanucleosides

We compare herein the scope of three copper (I) catalysts on the synthesis of various 1,4-disubstitued-1,2,3-triazolo-carbanucleosides through a microwave (and thermic) assisted Huisgen 1,3-dipolar cycloaddition. The tetrakis(acetonitrile)copper hexafluorophosphate ([Cu(CH ₃ CN)₄]PF ₆ ), the imidazoline(mesythyl)copper bromide (Imes)CuBr, and the copper/copper sulfate Cu(0)/CuSO ₄ (II) mixture have been chosen for this study. Their influence in a catalytic amount will be analyzed according to the substituent of the alkyne, the solvent, or the heating method.     

Mangroves of Godavari – Analysis Through Remote Sensing Approach

The expansion of agriculture and aquaculture farms in the coastal areas has led to conversion of mangroves in the recent past. The extent of mangroves has also changed due to the erosion of mangroves along the coast and accretion near river mouths, leading to the formation of new mangrove areas. This study has been undertaken in the mangroves of the Godavari estuary, Andhra Pradesh, India to understand the changes in the extent of mangroves, namely accreted mangroves, erosion due to wave action and river water flow during floods, and changes due to forest restoration between 1986 and 2001, through remote sensing. The geomorphological changes due to river water flow in and around the mangroves have also been analysed. The changes in the vegetation due to forest restoration and natural regeneration are appreciable, while the changes in the area due to erosion and accretion are more or less equal. An analysis of the remote sensing images of 1986 and 2001 reveal that the mangroves outside the forest boundary have been converted to aquaculture. The sand spit of Hope Island has changed with time and has grown nearly 2.6 km between 1937 and 2001.