Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

CRISPR-Cas system epitomizes prokaryote-specific quintessential adaptive defense machinery that limits the genome invasion of mobile genetic elements. It confers adaptive immunity to bacteria by capturing a protospacer fragment from invading foreign DNA, which is later inserted into the leader proximal end of CRIPSR array and serves as immunological memory to recognize recurrent invasions. The universally conserved Cas1 and Cas2 form an integration complex that is known to mediate the protospacer invasion into the CRISPR array. However, the mechanism by which this protospacer fragment gets integrated in a directional fashion into the leader proximal end is elusive. Here, we employ CRISPR/dCas9 mediated immunoprecipitation and genetic analysis to identify Integration Host Factor (IHF) as an indispensable accessory factor for spacer acquisition in Escherichia coli Further, we show that the leader region abutting the first CRISPR repeat localizes IHF and Cas1-2 complex. IHF binding to the leader region induces bending by about 120° that in turn engenders the regeneration of the cognate binding site for protospacer bound Cas1-2 complex and brings it in proximity with the first CRISPR repeat. This appears to guide Cas1-2 complex to orient the protospacer invasion towards the leader-repeat junction thus driving the integration in a polarized fashion.

Virtual fracture clinic delivers British Orthopaedic Association compliance

INTRODUCTION The British Orthopaedic Association recommends that patients referred to fracture clinic are thereafter reviewed within 72 hours. With the aim of improving care by seeking to meet this target, waiting times for fracture clinic appointments in a district general hospital were audited prospectively against this national guideline, with the intervening implementation of a virtual fracture clinic. MATERIALS AND METHODS The study was conducted as a prospective closed-loop audit in which the second cycle took place several months after a change in the clinical pathway for all referrals from the emergency department to fracture clinic. Data were gathered in real-time via a pro forma during fracture clinic consultations. RESULTS The first cycle demonstrated a non-compliant mean waiting time of 10.7 days, with 6% of patients being seen within the 72-hour target. Following the implementation of the virtual fracture clinic, the second cycle found that all patients were reviewed within the 72-hour target (mean 1.3 days). DISCUSSION The improvement in performance was delivered with no increase in clinic capacity. The cost of implementation was negligible. CONCLUSION A simple virtual fracture clinic model delivered a significant reduction in waiting times and achieved compliance with the British Orthopaedic Association guideline. Similar results could be achieved in subsequent deployment elsewhere in the NHS.

Squamous cell carcinoma and dental implants: A systematic review of case reports

Cancer is one of the leading causes of death world-wide. Apart from the most common etiopathological factors related to cancer, at times very rare causes such as irritant or foreign body induced carcinogenesis is not to be overlooked. To systematically review case reports concerned with the association between dental implants and oral squamous cell carcinoma. A Medline (PubMed), Cochrane database, and Google Scholar search was conducted of dental article published in English related to case reports concerned with oral squamous cell carcinoma occurring around dental implants from 2000 to 2014. Twenty articles were retrieved, which included 20 rare case reports which were systematically reviewed and the results were obtained pertaining to age, clinical symptoms, habits, previous history of cancer, potentially malignant disorders, systemic illness, and local factors. It is imperative to identify promptly persisting inflammation associated with implants. Since malignancy may disguise as periimplantitis, especially in patients who are at risk with contributing prominent predisposing factors.

Robotics and medicine: A scientific rainbow in hospital

The journey of robotics is a real wonder and astonishingly can be considered as a scientific rainbow showering surprising priceless power in the era of future technologies. The astonishing seven technologies discussed in this paper are da Vinci Robotic surgical system and sperm sorters for infertility, Veebot for blood investigation, Hanako the robotic dental patient for simulating the dental patient and helping a trainee dentist, RP-7 robot who is around-the-clock physician connecting the physician and patient, Robot for Interactive Body Assistance (RIBA) who is a RIBA serving as a nurse, Bushbot serving as a brilliant surgeon, and Virtibot helping in virtual autopsy. Thus, robotics in medicine is a budding field contributing a great lot to human life from before birth to afterlife in seven forms thus gracefully portraying a scientific rainbow in hospital environment.

Theranostics: A treasured tailor for tomorrow

Emerging as a targeted, safe, and efficient pharmacotherapy is the approach of theranostics, which focuses on patient-centered care. It is a combination of diagnosis and therapeutics. It provides a transition from conventional medicine to personalized medicine. It deals with the custom made treatment plan based on uniqueness of every individual thus resulting in right drug for the right patient at the right time. Genetics plays a significant role in theranostics. Theranostics provides a cost-effective specific successful treatment protocol. Pharmacogenetics, proteomics and biomarker profiling forms the backbone of theranostics. The role of theranostics is interestingly appreciated at multi levels with special consideration in oncology wherein nano formulations in the form of liposomes, dendrimers, polymeric nanoparticles, metallic nanoparticles, quantum dots and carbon nanotubes play a very important role. Thus, theranostics is a holistic transition from trial and error medicine to predictive, preventive and personalized medicine leading to improved quality care of pharmacotherapy.

Analysis of association of TaqI VDR gene polymorphism with the chronic periodontitis in Dravidian ethnicity

AIM

The aim of this study is to analyze the association of TaqI vitamin D receptor (VDR) gene polymorphism with the chronic periodontitis (CP) in Dravidian ethnicity.

MATERIALS AND METHODS

A total of 120 subjects were recruited for this study, which included 60 CP and 60 healthy controls. TaqI VDR gene polymorphism was analyzed using specific primers and amplified by polymerase chain reaction (PCR) and visualized under 2% agarose gel.

RESULTS

Our study results showed that Tt and tt genotype had a higher frequency of occurrence in CP compared with controls. Similarly, t allele was found to be associated with CP.

CONCLUSION

Our study concludes that TaqI VDR gene polymorphism is associated with CP in Dravidian ethnicity.

Weight gain with pizotifen therapy

OBJECTIVE

To describe the characteristics of weight gain occurring in children treated for migranous conditions with pizotifen

DESIGN

Retrospective case note review

SETTING

West Suffolk Hospital between 1999 and 2003 PATIENTS: 405 clinic attendances of 121 children receiving pizotifen treatment

MAIN OUTCOME MEASURES

Rates of change in weight for age z score between successive outpatient appointments were used to detect excessive weight gain.

RESULTS

The mean rate of weight z score increase for 105 patients receiving a constant dosage in 181 intervals between appointments was 0.79 standard deviations per year compared with 0.11 standard deviations per year for height z score increases. The rate of weight z score increase was not correlated with pizotifen dose per kg (r = -0.08), per m(2) (r = -0.05) or initial body mass index (r = -0.04). Mean rates of z score increase were similar in patients with a satisfactory and unsatisfactory therapeutic responses.

CONCLUSIONS

Excess weight gain in pizotifen therapy is not predicted by drug dosage or therapeutic response within the range of doses used in clinical practice.

FT-IR, FT-Raman spectra and ab initio HF, DFT vibrational analysis of p-chlorobenzoic acid

The infrared, the Fourier transform infrared and Fourier transform Raman spectra of p-chlorobenzoic acid (p-CBA) has been recorded in the region 4000-600 cm(-1), 4000-400 cm(-1) and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of p-CBA were obtained by the ab initio HF and DFT (B3LYP) methods with complete relaxation in the potential energy surface using 6-311+G(d,p) basis set. The harmonic-vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

Vibrational spectra and assignments of 3-aminobenzyl alcohol by ab initio Hartree-Fock and density functional method

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of 3-aminobenzyl alcohol. The FT-Raman and FT-IR spectra of 3-aminobenzyl alcohol were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by ab initio HF and density functional B3LYP method with 6-311+G(d,p) basis sets. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. A detailed interpretation of the infrared and Raman spectra of 3-aminobenzyl alcohol is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.

FT-IR, FT-Raman spectra and ab initio HF, DFT vibrational analysis of 2,3-difluoro phenol

The FT-IR and FT-Raman spectra of 2,3-difluoro phenol (2,3-DFP) has been recorded in the region 4000-400 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2,3-DFP were obtained by the ab initio HF and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-311+G(d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

Vibrational spectra and assignments of 2-amino-5-iodopyridine by ab initio Hartree-Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra of 2-amino-5-iodopyridine were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) methods with the 6-31G(d,p) basis set for C, N, H and LANL2DZ pseudopotential for I. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of 2-amino-5-iodopyridine is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 2-amino-5-methylphenol

The laser Raman and Fourier transform infrared spectra of 2-amino-5-methylphenol were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by HF and density functional B3LYP methods by using 6-311+G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31G(d,p)/6-311+G(d,p) and B3LYP/6-31G(d,p)/6-311+G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of 2-amino-5-methylphenol is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.

FT-IR, FT-Raman spectra and ab initio DFT vibrational analysis of p-bromophenoxyacetic acid

The Fourier transform Raman and Fourier transform infrared spectra of p-bromophenoxyacetic acid were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) method with the 6-31G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of p-bromophenoxyacetic acid is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2,4-dichloro-6-nitrophenol

The FTIR and FT-Raman spectra of 2,4-dichloro-6-nitrophenol (2,4-DC6NP) has been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of (2,4-DC6NP) were obtained by the ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311+G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2-amino-5-chloropyridine

The FTIR and FT-Raman spectra of 2-amino-5-chloropyridine (ACP) has been recorded in the region 4000-400 and 3500-100 cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of ACP were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311+G(2df,2p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

The culture of articular chondrocytes in hydrogel constructs within a bioreactor enhances cell proliferation and matrix synthesis

Bovine and human articular chondrocytes were seeded in 2% alginate constructs and cultured for up to 19 days in a rotating-wall-vessel (RWV) and under static conditions. Culture within the RWV enhanced DNA levels for bovine chondrocyte-seeded constructs when compared with static conditions but did not produce enhancement for human cells. There was a significant enhancement of glycosaminoglycans and hydroxyproline synthesis for both bovine and human chondrocytes. In all cases, histological analysis revealed enhanced Safranin-O staining in the peripheral regions of the constructs compared with the central region. There was an overall increase in staining intensity after culture within the RWV compared with static conditions. Type-II collagen was produced by both bovine and human chondrocytes in the peripheral and central regions of the constructs and the staining intensity was enhanced by culture within the RWV. A capsule of flattened cells containing type-I collagen developed around the constructs maintained under static conditions when seeded with either bovine or human chondrocytes, but not when cultured within the RWV bioreactor.

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues

MOTIVATION

Position specific scoring matrices (PSSMs) corresponding to aligned sequences of homologous proteins are commonly used in homology detection. A PSSM is generated on the basis of one of the homologues as a reference sequence, which is the query in the case of PSI-BLAST searches. The reference sequence is chosen arbitrarily while generating PSSMs for reverse BLAST searches. In this work we demonstrate that the use of multiple PSSMs corresponding to a given alignment and variable reference sequences is more effective than using traditional single PSSMs and hidden Markov models.

RESULTS

Searches for proteins with known 3-D structures have been made against three databases of protein family profiles corresponding to known structures: (1) One PSSM per family; (2) multiple PSSMs corresponding to an alignment and variable reference sequences for every family; and (3) hidden Markov models. A comparison of the performances of these three approaches suggests that the use of multiple PSSMs is most effective.

CONTACT

ns@mbu.iisc.ernet.in.