Nondegenerate Solitons in Manakov System

It is known that the Manakov equation which describes wave propagation in two mode optical fibers, photorefractive materials, etc., can admit solitons which allow energy redistribution between the modes on collision that also leads to logical computing. In this Letter, we point out that the Manakov system can admit a more general type of nondegenerate fundamental solitons corresponding to different wave numbers, which undergo collisions without any energy redistribution. The previously known class of solitons which allows energy redistribution among the modes turns out to be a special case corresponding to solitary waves with identical wave numbers in both the modes and traveling with the same velocity. We trace out the reason behind such a possibility and analyze the physical consequences.

Comprehensive subcellular topologies of polypeptides in Streptomyces

Background

Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach.

Results

Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible. We first introduced a uniform, improved nomenclature that re-annotated the names of ~ 4000 proteins based on functional and structural information. Then protein localization was assigned de novo using prediction tools and edited by manual curation for 7494 proteins, including information for 183 proteins that resulted from a recent genome re-annotation and are not available in current databases. The S. lividans proteome was also linked with those of other model bacterial strains including Streptomyces coelicolor A3(2) and Escherichia coli K-12, based on protein homology, and can be accessed through an open web interface. Finally, experimental data derived from proteomics experiments have been incorporated and provide validation for protein existence or topology for 579 proteins. Proteomics also reveals proteins released from vesicles that bleb off the membrane. All export systems known in S. lividans are also presented and exported proteins assigned export routes, where known.

Conclusions

SToPSdb provides an updated and comprehensive protein localization annotation resource for S. lividans and other streptomycetes. It forms the basis for future linking to databases containing experimental data of proteomics, genomics and metabolomics studies for this organism.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0892-0) contains supplementary material, which is available to authorized users.

Aggregating sequences that occur in many proteins constitute weak spots of bacterial proteostasis

Aggregation is a sequence-specific process, nucleated by short aggregation-prone regions (APRs) that can be exploited to induce aggregation of proteins containing the same APR. Here, we find that most APRs are unique within a proteome, but that a small minority of APRs occur in many proteins. When aggregation is nucleated in bacteria by such frequently occurring APRs, it leads to massive and lethal inclusion body formation containing a large number of proteins. Buildup of bacterial resistance against these peptides is slow. In addition, the approach is effective against drug-resistant clinical isolates of Escherichiacoli and Acinetobacterbaumannii, reducing bacterial load in a murine bladder infection model. Our results indicate that redundant APRs are weak points of bacterial protein homeostasis and that targeting these may be an attractive antibacterial strategy.

Aggregation is sequence-specific and nucleated by short aggregating protein segments (APR). Here authors use a multidisciplinary approach to show that in E.coli some frequently occurring APRs lead to protein aggregation and ultimately bacterial cell death, which could serve as antibacterial strategy.

Health-seeking behaviour among patients with faecal incontinence in a Malaysian academic setting

BACKGROUND

Faecal incontinence (FI) is not a common presenting complaint in Malaysia, and little has been published on this topic. Since it is a treatable condition, a greater understanding of factors contributing to healthseeking behaviour is needed in order to plan effective provision of services.

METHODS

A survey of 1000 patients and accompanying relatives, visiting general surgical and obstetrics and gynaecology clinics for matters unrelated to FI, was conducted at University Malaya Medical Centre between January 2009 and February 2010. A follow-up regression analysis of the 83 patients who had FI, to identify factors associated with health-seeking behaviour, was performed. Variables identified through univariate analysis were subjected to multivariate analysis to determine independence. Reasons for not seeking treatment were also analysed.

RESULTS

Only eight patients (9.6%) had sought medical treatment. On univariate analysis, the likelihood of seeking treatment was significantly higher among patients who had more severe symptoms (OR 30.0, p=0.002), had incontinence to liquid stool (OR 3.83, p=0.002) or when there was an alteration to lifestyle (OR: 17.34; p<0.001). Nevertheless, the only independently-associated variable was alteration in lifestyle. Common reasons given for not seeking treatment was that the condition did not affect patients' daily activities (88.0%), "social taboo" (5.3%) and "other" reasons (6.7%).

CONCLUSIONS

Lifestyle alteration is the main driver of healthseeking behaviour in FI. However, the majority do not seek treatment. Greater public and physician-awareness on FI and available treatment options is needed.

Interleukin 4 induces apoptosis of acute myeloid leukemia cells in a Stat6-dependent manner

Cytokines provide signals that regulate immature normal and acute myeloid leukemia (AML) cells in the bone marrow microenvironment. We here identify interleukin 4 (IL4) as a selective inhibitor of AML cell growth and survival in a cytokine screen using fluorescently labeled AML cells. RNA-sequencing of the AML cells revealed an IL4-induced upregulation of Stat6 target genes and enrichment of apoptosis-related gene expression signatures. Consistent with these findings, we found that IL4 stimulation of AML cells induced Stat6 phosphorylation and that disruption of Stat6 using CRISPR/Cas9-genetic engineering rendered cells partially resistant to IL4-induced apoptosis. To evaluate whether IL4 inhibits AML cells in vivo, we expressed IL4 ectopically in AML cells transplanted into mice and also injected IL4 into leukemic mice; both strategies resulted in the suppression of the leukemia cell burden and increased survival. Notably, IL4 exposure caused reduced growth and survival of primary AML CD34⁺CD38^- patient cells from several genetic subtypes of AML, whereas normal stem and progenitor cells were less affected. The IL4-induced apoptosis of AML cells was linked to Caspase-3 activation. Our results demonstrate that IL4 selectively induces apoptosis of AML cells in a Stat6-dependent manner-findings that may translate into new therapeutic opportunities in AML.

Prevalence and antibacterial resistance patterns of extended-spectrum beta-lactamase producing Gram-negative bacteria isolated from ocular infections

Purpose:

Extended-spectrum beta-lactamases (ESBLs) mediated resistance is more prevalent worldwide, especially among Gram-negative bacterial isolates, conferring resistance to the expanded spectrum cephalosporins. As limited data were available on the prevalence of ESBLs in this area, the current study was undertaken to determine the prevalence, antibacterial resistance patterns, and molecular detection and characterization of ESBL encoding resistance genes among ocular Gram-negative bacterial isolates from ocular infections.

Materials and Methods:

A prospective study was done on 252 ocular Gram-negative bacterial isolates recovered from ocular infections during a study period from February 2011 to January 2014. All isolates were subjected to detection of ESBLs by cephalosporin/clavulanate combination disc test and their antibacterial resistance pattern was studied. Molecular detection and characterization of ESBL encoding bla_TEM-, bla_SHV, bla_OXA-, and bla_CTX-M (phylogenetic groups 1, 2, 9, and 8/25) resistance genes by multiplex polymerase chain reaction and DNA sequence analysis.

Results:

Of all Gram-negative bacteria, Pseudomonas aeruginosa (44%) was the most common strain, followed by Enterobacter agglomerans and Klebsiella pneumoniae each (10%). Among the 252, 42 (17%) were ESBL producers. The major source of ESBL producers were corneal scraping specimens, highest ESBL production was observed in P. aeruginosa 16 (38%) and Escherichia coli 7 (16.6%). Among ESBL-producing genes, the prevalence of bla_TEM-gene was the highest (83%) followed by bla_OXA-gene (35%), bla_SHV-gene (18.5%), and bla_CTX-M-1-gene (18.5%) alone or together.

Conclusion:

The higher rate of prevalence of ESBLs-encoding genes among ocular Gram-negative bacteria is of great concern, as it causes limitation to therapeutic options. This regional knowledge will help in guiding appropriate antibiotic use which is highly warranted.

Clinical and genetic characterization of a large primary open angle glaucoma pedigree

PURPOSE

To both characterize the clinical features of large primary open angle glaucoma (POAG) pedigree from a village in southern India and to investigate the genetic basis of their disease.

MATERIALS AND METHODS

Eighty-four members of a large pedigree received complete eye examinations including slit lamp examination, tonometry, gonioscopy, and ophthalmoscopy. Some were further studied with perimetry. Those diagnosed with POAG were tested for disease-causing mutations in the myocilin and optineurin genes with Sanger sequencing.

RESULTS

Fourteen of 84 family members were diagnosed with POAG, while eight were clinically judged to be POAG-suspects. The family structure and the pattern of glaucoma in the pedigree are complex. Features of glaucoma in this pedigree include relatively early age at diagnosis (mean 50 ± 14 years) and maximum intraocular pressures ranging from 14 to 36 mm Hg with a mean of 23 mm Hg ± 6.5 mm Hg. Patients had an average central corneal thickness (mean 529 ± 37.8 microns) and moderate cup-to-disc ratios (0.74 ± 0.14). No mutations were detected in myocilin, optineurin, or TANK binding kinase 1 (TBK1).

CONCLUSIONS

We report a five-generation pedigree with a complex pattern of POAG inheritance that includes 22 POAG patients and glaucoma suspects. Although the familial clustering of POAG in this pedigree is consistent with dominant inheritance of a glaucoma-causing gene, mutations were not detected in genes previously associated with autosomal dominant glaucoma, suggesting the involvement of a novel disease-causing gene in this pedigree.

An Experimental Analysis of the Catecholamines in Hyperglycemia and Acidosis-Induced Rat Brain

Hyperglycemia and acidosis are the hallmarks of diabetes. Since these factors play an important role in diabetic complications, we have studied the brain catecholamine levels in hyperglycemic and acidotic conditions per se. Experimentally induced hyperglycemia and acidosis are accompanied by significant alterations in the catecholamine levels in discrete areas of the brain. We and others have shown that chronic or acute diabetes in animals, as well as in humans results in altered neurotransmitter levels. In the present study, hyperglycemia maintained by daily external administration of glucose for thirty days showed increased level of dopamine in striatum and hippocampus, elevation of norepinephrine in hippocampus, and increased level of epinephrine in hypothalamus, midbrain and pons medulla. The ammonium chloride induced acidosis demonstrated significant elevation of dopamine in midbrain and significant increase of norepinephrine in hypothalamus and midbrain, and increased level of epinephrine in hypothalamus, pons medulla and cerebral cortex. On the other hand, sodium acetoacetate induced acidosis did not show any significant change in the level of catecholamines in any of the areas studied. In conclusion, the changes in catecholamine levels observed in experimentally induced hyperglycemic as well as in acidotic conditions are closely related to the changes observed in spontaneous or alloxan or streptozotocin diabetic animals, thereby suggesting that these conditions may be responsible for the changes observed in diabetic animals.

Abstract P2-12-20: Rapid evaporative ionisation mass spectrometry towards real time intraoperative oncological margin status determination in breast conserving surgery

Introduction: Positive tumour margins following attempted breast conserving surgery (BCS) is an important risk factor for local recurrence. Nationally in the United Kingdom on average approximately 25% of patients undergoing BCS require additional surgery for positive margins. Traditional techniques such as specimen xray, frozen section & imprint cytology to optimise margin clearance have significant limitations. Various research methods under investigation include optical spectroscopy, high resolution imaging and radiofrequency spectroscopy. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) is a new method that uses mass spectrometric analysis of the tissue specific ionic content of the surgical diathermy smoke plume for the rapid identification of dissected breast tissues as an intelligent knife (iKnife). We investigate the ability of the "iKnife" to analyze heterogeneous breast tissue intraoperatively using mass spectrometric techniques.

Method: The study involved three stages that comprised: method development, tissue specific ex-vivo database construction and intraoperative analysis. Smoke aerosol produced as a result of electrosurgical diathermy from a variety of frozen, fresh and in-vivo breast samples were aspirated into a mass spectrometer via a modified surgical handpiece. Tissue diagnosis was confirmed by subsequent histopathological validation. The data underwent computational analysis using multivariate statistics –predominantly Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), along with leave one patient out cross-validation. A total of 128 patients (n=40 method development, n=66 ex-vivo database, n=22 intraoperative analysis) undergoing breast surgery were enrolled in this study. Ethical approval was obtained from the Research Ethics Committee.

Results: 40 patients contributed breast samples (normal and cancerous) for method optimisation to enable analysis of high intensity spectra from heterogeneous breast tissue. Following optimisation an ex-vivo database was constructed from 89 excised fresh breast tissue samples from 66 patients using 330 spectra (246 Normal, 60 Tumour – IDC, ILC, IMC and 24 Benign - fibroadenoma). Multivariate statistical analysis of data revealed classification of tumour compared to normal tissue with sensitivities of 93.0% and specificity of 91.9%. The iKnife was used intraoperatively during the entire operation of 25 surgeries. Spectral data was obtained within 1-2 seconds. Specific margin analysis correctly identified negative margins in 10 cases.

Conclusions: The iKnife has been successfully developed for analysis of intraoperative heterogeneous breast tissue. Preliminary data suggests that this technique is suitable with high accuracy for the separation of normal, benign (fibroadenoma) and cancerous (invasive ductal and invasive lobular carcinoma) breast tissues. In comparison to the normal breast, cancerous tissues exhibit statistically different spectral profiles. Further work is aimed at the development of a real time algorithm able to match intraoperative data with the pre-existing database for the rapid interpretation and real time feedback of intraoperative data towards detecting positive margins intraoperatively.

Citation Format: St John ER, Al-Khudairi R, Balog J, Rossi M, Gildea L, Speller A, Ramakrishnan R, Shousha S, Takats Z, Leff DR, Darzi A. Rapid evaporative ionisation mass spectrometry towards real time intraoperative oncological margin status determination in breast conserving surgery. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-12-20.

Biological evaluation of nanosilver incorporated cellulose pulp for hygiene products

Cellulose pulp has a visible market share in personal hygiene products such as sanitary napkins and baby diapers. However it offers good surface for growth of microorganisms. Huge amount of research is going on in developing hygiene products that do not initiate microbial growth. The objective of the present work is to produce antibacterial cellulose pulp by depositing silver nanopowder on the cellulose fiber. The silver nanoparticles used were of less than 100 nm in size and were characterised using transmission electron microscopy and X-ray powder diffraction studies. Antibacterial activity of the functionalized cellulose pulp was proved by JIS L 1902 method. The in-vitro cytotoxicity, in-vivo vaginal irritation and intracutaneous reactivity studies were done with silver nanopowder incorporated cellulose pulp for introducing a new value added product to the market. Cytotoxicity evaluation suggested that the silver nanoparticle incorporated cellulose pulp is non-cytotoxic. No irritation and skin sensitization were identified in animals tested with specific extracts prepared from the test material in the in-vivo experiments. The results indicated that the silver nanopowder incorporated cellulose pulp meets the requirements of the standard practices recommended for evaluating the biological reactivity and has good biocompatibility, hence can be classified as a safe hygiene product.

Controlled release of copper from an intrauterine device using a biodegradable polymer

BACKGROUND

The adverse effects of copper intrauterine devices (IUDs) such as abnormal bleeding, pain and cramps may be due in part to the burst release of copper ions during the first few months of usage. This study focuses on controlling the initial burst release of copper ions.

STUDY DESIGN

This study evaluated in vitro release rates of copper for a period of 1 year from standard CuT380 IUDs (n=6) and from CuT380 IUDs coated with poly(dl-lactide-co-glycolide) (PLGA) films (n=6). This study characterized the coated device for its morphological changes during degradation of film by scanning electron microscopy (SEM).

RESULTS

CuT380 IUDs coated with PLGA film with a thickness of 0.10±0.02 mm showed a reduced initial copper release (40-80 mcg/day) compared with uncoated CuT380 IUDs (150-200 mcg/day). Statistically significant (p<.05) results were obtained at different time intervals during the overall study period of 1 year. SEM images showed degradation of coating.

CONCLUSION

Coating a CuT380 IUD with biodegradable polymer reduced the initial copper release without affecting release at 1 year. Clinical trials are required to determine whether this could reduce side effects such as bleeding and pain associated with copper containing IUDs.

Open angle glaucoma in a case of Type IV Ehler Danlos syndrome: a rarely reported association

A 26-year-old male presented to us with defective vision in the left eye. He had best corrected visual acuity (BCVA) of hand movement (HM) in right eye and 6/9 in left eye. He had ptosis with ectropion in both eyes and relative afferent pupillary defect (RAPD) in right eye. Intraocular pressure (IOP) was 46 and 44 mmHg in right and left eye, respectively. Fundus showed glaucomatous optic atrophy (GOA) in right eye and cup disc ratio (CDR) of 0.75 with bipolar rim thinning in left eye. Systemic examination showed hyperextensible skin and joints, acrogeria, hypodontia, high arched palate, and varicose veins. He gave history of easy bruising and tendency to fall and history of intestinal rupture 5 years ago for which he had undergone surgery. He was diagnosed as a case of Type IV Ehler-Danlos syndrome (EDS) with open angle glaucoma. He underwent trabeculectomy in both eyes. This is a rare case that shows glaucoma in a patient of EDS Type IV. Very few such cases have been reported in literature.

Anterior segment optical coherence tomography documentation of a case of topiramate induced acute angle closure

We present a case report of a 31-year-old female patient who presented to us with a 1 day history of acute bilateral eye pain, blurred vision and headache. She was found to have a myopic shift, raised intraocular pressure (IOP) and shallow anterior chambers in both eyes. She had been commenced on oral topiramate 1 week previously. A number of investigations, including anterior segment optical coherence tomography (AS-OCT) were done and a diagnosis of topiramate induced bilateral acute angle closure (TiAAC) was made. Topiramate was discontinued and she was managed with topical and oral antiglaucoma medications, topical steroids and cyclopegics. Her symptoms subsided dramatically at the next follow-up. The AS-OCT documentation revealed lucidly the improvement in her anterior chamber depth and anterior chamber angle parameters. Her IOP decreased, her myopic shift showed reversal and her AS-OCT findings revealed gross improvement in all the parameters angle opening distance, trabecular iris space area and scleral spur angle. This case report clearly shows with AS OCT documentation the changes which occur in the anterior segment in a case of TiAAC.

The shift from public to private health care providers and malaria deaths in Jalpaiguri district, West Bengal, India, 2006

We investigated an increase in malaria deaths in order to formulate control measures. A search of records in health care facilities for cases of death following fever, with a blood smear or rapid antigen test positive for Plasmodium falciparum, identified 77 fatalities. Of these, 72 (93%) occurred in hospitals (78% of which in the 24 hours following admission). Of 60 family members of the patients who died interviewed, 70% reported that the patient had received care from unqualified rural private practitioners available round the clock. Among 100 of these rural practitioners assessed, 21% knew anti-malarial dosage and 7% knew malaria severity criteria. There were 65% and 42% vacancies among 240 community health worker and 12 microscopist positions, respectively, in the public sector in the area. As a result, the mean interval between active case search rounds in the community was 35 days (standard: 14) and the median time between blood slide collection and radical treatment was 12 days (standard < 2 days). Deficiencies in the public health system may have led to a shift towards rural practitioners. Poor management of malaria may have contributed to deaths. We posted microscopists and community health workers in the area to restore appropriate malaria management in the public sector.

Vittaforma corneae keratitis in southern India: role of a novel duplex PCR

Microsporidia are obligate intracellular parasites that infect eukaryotic cells and have emerged as major opportunistic human pathogens. Due to the difficulties in definitive laboratory diagnosis and insufficient knowledge, ocular microsporidiosis is infrequently reported in India. To improve diagnostic facilities, we have developed a novel duplex PCR (dPCR) for the simultaneous identification of both genera and species of isolates with microsporidian aetiology that cause keratitis. The material scraped from the corneas of 12 clinically diagnosed microsporidial keratitis patients was subjected to routine microbiological examinations and molecular diagnosis using a novel dPCR that targeted the small-subunit rRNA gene (SSU-rRNA) of microsporidia and Vittaforma corneae using genus- and species-specific primers. Of the 12 corneal scrapes, 6 showed positive results in smears, while dPCR provided positive amplification with both pan-microsporidial and V. corneae species-specific primers for 9 corneal scrapes. The results were validated by sequencing and blast analysis. The sensitivity of this novel dPCR method was higher than that of conventional microscopy in the diagnosis of corneal microsporidial infection. dPCR with specific primers is potentially more sensitive, specific and depends less on more complicated methods for exact identification of the aetiology of microsporidial keratitis.

A study of initial therapy for glaucoma in southern India: India Glaucoma Outcomes and Treatment (INGOT) Study

PURPOSE

To compare initial glaucoma therapy with medications and trabeculectomy in southern India.

METHODS

Patients aged ≥ 30 years newly diagnosed with glaucoma were randomized to trabeculectomy with 5-fluorouracil or medical therapy. Subjects with best-corrected vision <6/18 due to cataract underwent phacoemulsification (phaco/intraocular lens, IOL). Intraocular pressure (IOP), vision and visual function were assessed at 12 months.

RESULTS

Patients assigned to medications and surgery received the expected therapy in 86% (172/199) and 64% (126/199) of cases, respectively. Forty patients (20%) assigned to surgery refused any treatment and 33 (17%) received medications. Among 199 patients randomized to medications, 52 (26.1%) underwent phaco/IOL, as did 89/199 (43.7%) of patients randomized to trabeculectomy. Baseline parameters of the two groups did not differ, nor did 1-year follow-up rates (medication 65%, trabeculectomy 58%, P = 0.15). Final IOP was lower with randomization to trabeculectomy (16.3 ± 5.1 mmHg) than medication (18.8 ± 6.7 mmHg, P < 0.0001). In regression models, randomization to trabeculectomy (P < 0.0001) was associated with lower IOP, and simultaneous trabeculectomy and cataract surgery was associated with higher IOP (P = 0.008) than trabeculectomy alone. Subjects receiving Phaco/IOL had significantly better final acuity (P < 0.0001) and visual function (P = 0.035), despite concurrent glaucoma treatment. Final visual acuity was worse in those receiving trabeculectomy in addition to cataract surgery, but this was of borderline significance (P = 0.06).

CONCLUSIONS

Trabeculectomy lowered IOP significantly more than medical treatment, but with slightly greater loss of visual acuity. Combined phaco/IOL and trabeculectomy improved visual acuity with substantial IOP lowering.