LINE-1 mRNA 3' end dynamics shape its biology and retrotransposition potential

LINE-1 (L1) retrotransposons are mobile genetic elements that create new genomic insertions by a copy-paste mechanism involving L1 RNA/RNP intermediates. L1 encodes two ORFs, of which L1-ORF2p nicks genomic DNA and reverse transcribes L1 mRNA using the nicked DNA as a primer which base-pairs with poly(A) tail of L1 mRNA. To better understand the importance of non-templated L1 3' ends' dynamics and the interplay between L1 3' and 5' ends, we investigated the effects of genomic knock-outs and temporal knock-downs of XRN1, DCP2, and other factors. We hypothesized that in the absence of XRN1, the major 5'→3' exoribonuclease, there would be more L1 mRNA and retrotransposition. Conversely, we observed that loss of XRN1 decreased L1 retrotransposition. This occurred despite slight stabilization of L1 mRNA, but with decreased L1 RNP formation. Similarly, loss of DCP2, the catalytic subunit of the decapping complex, lowered retrotransposition despite increased steady-state levels of L1 proteins. In both XRN1 and DCP2 depletions we observed shortening of L1 3' poly(A) tails and their increased uridylation by TUT4/7. We explain the observed reduction of L1 retrotransposition by the changed qualities of non-templated L1 mRNA 3' ends demonstrating the important role of L1 3' end dynamics in L1 biology.

From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution

Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.

The Effect of Photodynamic Therapy on Oral-Premalignant Lesions: A Systematic Review

Background

Material and Methods

Results

Conclusions

EP.WE.453Impact of COVID 19 pandemic on colorectal rapid access investigations

Aim

The impact of the COVID-19 pandemic on delays in diagnosis of cancer has been highlighted at a national level. Such a delay represents an ongoing source of mortality and morbidity missing from the COVID-19 statistics. This study examines the delay in investigation of patients referred to the urgent colorectal cancer referral service at a single centre.

Method

Retrospective data was collated from prospective database for all 1,894 referrals to the urgent colorectal cancer referral service for the period 21 January to 24 December 2020. The time to appointment (TTA) was compared by date of referral and outcome type (endoscopy, CT abdomen pelvis (CT-AP), CT colonography (CT-C), clinic appointment).

Results

Across 2020, fewer than 25% of patients met the NICE recommendation of appointment within 14 days (median TTA 30 days, first quartile 19). TTA increased dramatically in the first months of the pandemic (February median: 19; March: 80.5). TTA remained high, not falling below a median wait of 28 days until November. CT-C tests were particularly delayed (median TTA: 86) due to concerns regarding aerosol generation and COVID-19 transmission. Patients were offered CT-AP tests while awaiting their delayed CT-C, as CT-AP had a significantly better wait of 15 days.

Conclusion

COVID-19 was a major disruptor of colorectal cancer diagnosis in 2020, with patients waiting more than twice as long as NICE recommends. This will likely continue into 2021, with further research required to assess the impact of this disruption on mortality and morbidity.

131 Perioperative Management of Warfarin on Surgical Wards at District General Hospital

Introduction

Many patients admitted to surgical wards are on warfarin. Poor knowledge of guidelines regarding reversal and restarting of anticoagulant medications can delay surgery, lead to poor outcomes and delay the discharge of patients. The aim of this audit was to establish whether junior doctors are confident in managing warfarin according to local guidelines and to improve their knowledge and confidence.

Method

A questionnaire was used to assess confidence of junior doctors currently working in general surgical departments. An educational poster was placed in the junior doctors’ office and the questionnaire was repeated. We then conducted a teaching session on the perioperative management of warfarin and repeated the questionnaire again.

Results

Confidence in reversing and restarting warfarin was significantly higher following the teaching session (p = 0.017 and p < 0.001 respectively). No significant difference was seen following the introduction of educational posters. Confidence in applying the guidelines on perioperative warfarin management was significantly higher following the teaching session (p < 0.001). Following the introduction of educational posters and the formal teaching session doctors felt they knew better how to access the guidelines (not statistically significant for either guideline) and referred to them more (p = 0.0178 for warfarin reversing and p = 0.0940 for warfarin restarting guideline).

Conclusions

Having doctors who are confident in managing warfarin is crucial to avoid delays in treatment and discharge. This audit showed that a teaching session indeed improved doctors’ knowledge and confidence. Regular formal teaching is essential, and a repeat audit is planned to be performed during the next rotation.

Applications of the versatile CRISPR-Cas13 RNA targeting system

CRISPR-Cas are adaptable natural prokaryotic defense systems that act against invading viruses and plasmids. Among the six currently known major CRISPR-Cas types, the type VI CRISPR-Cas13 is the only one known to exclusively bind and cleave foreign RNA. Within the last couple of years, this system has been adapted to serve numerous, and sometimes not obvious, applications, including some that might be developed as effective molecular therapies. Indeed, Cas13 has been adapted to kill antibiotic-resistant bacteria. In a cell-free environment, Cas13 has been used in the development of highly specific, sensitive, multiplexing-capable, and field-adaptable detection tools. Importantly, Cas13 can be reprogrammed and applied to eukaryotes to either combat pathogenic RNA viruses or in the regulation of gene expression, facilitating the knockdown of mRNA, circular RNA, and noncoding RNA. Furthermore, Cas13 has been harnessed for in vivo RNA modifications including programmable regulation of alternative splicing, A-to-I and C to U editing, and m6A modifications. Finally, approaches allowing for the detection and characterization of RNA-interacting proteins have also been demonstrated. Here, we provide a comprehensive overview of the applications utilizing CRISPR-Cas13 that illustrate its versatility. We also discuss the most important limitations of the CRISPR-Cas13-based technologies, and controversies regarding them. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Liming effects of poultry litter derived biochar on soil acidity amelioration and maize growth

Crop production in acid soils is facing enormous challenges due to low soil quality associated with an increase in the acidification rate and aluminum toxicity. Despite comprehensive prior work with biochar application on nutrient availability and crop productivity in acid soils, little information is available about the recommendation or standardization of biochar application rates that are more suitable for soil fertility improvement under different soil environments (physico-chemical properties) for maximizing the benefits of biochar applications and minimizing the potential environmental risk. Thus, the objective of this study was to investigate the effectiveness of poultry litter (PL) and poultry litter biochar (PLB) in ameliorating the fertility of acid soils through incubation and pot experiments. The soil was amended with different materials as follows; lime (1 g kg^-1), PL (5, 10 and 15 g kg^-1) and PLB (5, 10 and 15 g kg^-1) along with control (non-amended). A pot experiment was also conducted using similar treatments to observe the responses of maize crop to the different amendments. The results indicated an increase in the pH and a decrease in exchangeable acidity in lime, PL and PLB amended soils. Lower soil pH, base cations and soil available phosphorus (P), and higher exchangeable acidity were found in control than the amended soils. Compared to PL and lime, PLB achieved greater increase rate in soil pH and reduction rate in soil exchangeable acidity with increased soil exchangeable base cations. An increase in soil available calcium (Ca) was observed in the lime treatment, while in PL and PLB treatments, there was an increase in soil available Ca, magnesium (Mg), potassium (K) and P. Application of the amendments increased availability of nitrogen (N), P, K, Ca and Mg relative to the control for maize in the pot experiment. When PL and PLB amendments were compared, it was found that the PLB was the best choice for the amelioration of acid soils as well as nutrient uptake by maize plants. It is suggested that application of PLB at the rate of 15 g kg^-1 is suitable for maize growth in acid soils.

Role of High-Resolution Dynamic Contrast-Enhanced MRI with Golden-Angle Radial Sparse Parallel Reconstruction to Identify the Normal Pituitary Gland in Patients with Macroadenomas

BACKGROUND AND PURPOSE

Preoperative localization of the pituitary gland with imaging in patients with macroadenomas has been inadequately explored. The pituitary gland enhancing more avidly than a macroadenoma has been described in the literature. Taking advantage of this differential enhancement pattern, our aim was to evaluate the role of high-resolution dynamic MR imaging with golden-angle radial sparse parallel reconstruction in localizing the pituitary gland in patients undergoing trans-sphenoidal resection of a macroadenoma.

MATERIALS AND METHODS

A retrospective study was performed in 17 patients who underwent trans-sphenoidal surgery for pituitary macroadenoma. Radial volumetric interpolated brain examination sequences with golden-angle radial sparse parallel technique were obtained. Using an ROI-based method to obtain signal-time curves and permeability measures, 3 separate readers identified the normal pituitary gland distinct from the macroadenoma. The readers' localizations were then compared with the intraoperative location of the gland. Statistical analyses were performed to assess the interobserver agreement and correlation with operative findings.

RESULTS

The normal pituitary gland was found to have steeper enhancement-time curves as well as higher peak enhancement values compared with the macroadenoma (P < .001). Interobserver agreement was almost perfect in all 3 planes (κ = 0.89). In the 14 cases in which the gland was clearly identified intraoperatively, the correlation between the readers' localization and the true location derived from surgery was also nearly perfect (κ = 0.95).

CONCLUSIONS

This study confirms our ability to consistently and accurately identify the normal pituitary gland in patients with macroadenomas with the golden-angle radial sparse parallel technique with quantitative permeability measurements and enhancement-time curves.

Extensive subclinical sinusitis leading to Moraxella osloensis meningitis

We report a case of a 31 year old male with extensive subclinical sinusitis leading to erosion in the cribriform plate and subsequent meningitis caused by the organism Moraxella osloensis. The patient presented to the emergency department with rapid onset confusion, neck stiffness and headache. Inflammatory markers, renal and liver function, and a chest radiograph were all normal. CT Head showed extensive polyp disease in the paranasal sinuses with expansion of the left frontal sinus and CT Sinuses revealed an area of low attenuation in the cribriform plate consistent with bony erosion. MRI Head showed thick loculated sinus inflammation. Lumbar puncture yielded CSF with a high white cell count of predominantly mononuclear cells, no visible organisms and an elevated protein. CSF microscopy, culture and viral PCR were not diagnostic, and so the CSF was sent for 16S rDNA PCR screening, which identified the rDNA of Moraxella osloensis. Moraxella osloensis is a rare cause of bacterial meningitis, with only a few reported cases. This case illustrates that sinusitis, while a common condition, when severe can predispose to intracranial infection with atypical and low virulence organisms such as Moraxella species, which do not commonly cause invasive CNS disease. This case represents the first case of Moraxella osloensis meningitis reported from the United Kingdom.

A review on host-pathogen interactions: classification and prediction

The research on host-pathogen interactions is an ever-emerging and evolving field. Every other day a new pathogen gets discovered, along with comes the challenge of its prevention and cure. As the intelligent human always vies for prevention, which is better than cure, understanding the mechanisms of host-pathogen interactions gets prior importance. There are many mechanisms involved from the pathogen as well as the host sides while an interaction happens. It is a vis-a-vis fight of the counter genes and proteins from both sides. Who wins depends on whether a host gets an infection or not. Moreover, a higher level of complexity arises when the pathogens evolve and become resistant to a host's defense mechanisms. Such pathogens pose serious challenges for treatment. The entire human population is in danger of such long-lasting persistent infections. Some of these infections even increase the rate of mortality. Hence there is an immediate emergency to understand how the pathogens interact with their host for successful invasion. It may lead to discovery of appropriate preventive measures, and the development of rational therapeutic measures and medication against such infections and diseases. This review, a state-of-the-art updated scenario of host-pathogen interaction research, has been done by keeping in mind this urgency. It covers the biological and computational aspects of host-pathogen interactions, classification of the methods by which the pathogens interact with their hosts, different machine learning techniques for prediction of host-pathogen interactions, and future scopes of this research field.

Rationally designed donor-acceptor scheme based molecules for applications in opto-electronic devices

Several donor (D)-acceptor (A) based molecules are rationally designed by adopting three different schemes in which the conjugation length, strength of the donor and acceptor moieties, and planarity of the molecules are varied. These variations are made by introducing a π-conjugated linkage unit, terminating the ends of the moieties by different electron donating and accepting functional groups, and fusing the donor and acceptor moieties, respectively. Our DFT and TDDFT based calculations reveal that using the above-mentioned design schemes, the electronic and optical properties of the D-A based molecules can be largely tuned. While introduction of a linkage and fusing of moieties enhance the π-π interaction, addition of electron donating groups (-CH3, -OH, and -NH2) and electron accepting groups (-CF3, -CN, -NO2, and -NH3(+)) varies the strength of the donor and acceptor moieties. These factors lead to modulation of the HOMO and LUMO energy levels and facilitate the engineering of the HOMO-LUMO gap and the optical gap over a wide range of ∼0.7-3.7 eV. Moreover, on the basis of calculated ionization potential and reorganization energy, most of the investigated molecules are predicted to be air stable and to exhibit high electron mobility, with the possibility of the presence of ambipolar characteristics in a few of them. The results of our calculations not only demonstrate the examined molecules to be the potential materials for organic opto-electronic devices, but also establish an understanding of the composition-structure-property correlation, which will provide guidelines for designing and synthesizing new materials of choice.

Physico-chemical and biological characteristics of compost from decentralised composting programmes

Composts that originated from small-scale composting programmes including home, community and canteen waste composters were studied. Heavy metals concentration indicated compliance with current regulations for conventional and organic agriculture. Compost from canteen waste showed high organic matter content (74% VS), while community (44 ± 20% VS) and home composts (31 ± 16% VS) had moderate levels. N content increased from home compost (1.3 ± 0.9% dm) to community (2.0 ± 0.9%) and canteen compost (2.5-3.0%) while P content ranged from 0.4% to 0.6% dm. C/N, absorbance E4/E6 and N-NH4(+)/N-NO3(-) ratios as well as respiration index indicated well-stabilized final products. Culturable bacterial and fungal cfu linkage to composting dynamics were identified and higher diversity of invertebrates was found in the smaller scale static systems. With similar process evolution indicators to industrial systems, overall results support the sustainability of these small-scale, self-managed composting systems.

Diacerein-mediated inhibition of IL-6/IL-6R signaling induces apoptotic effects on breast cancer

Interleukin-6 (IL-6) signaling network has been implicated in oncogenic transformations making it attractive target for the discovery of novel cancer therapeutics. In this study, potent antiproliferative and apoptotic effect of diacerein were observed against breast cancer. In vitro apoptosis was induced by this drug in breast cancer cells as verified by increased sub-G1 population, LIVE/DEAD assay, cell cytotoxicity and presence of terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells, as well as downregulation of antiapoptotic proteins Bcl-2 and Bcl-xL and upregulation of apoptotic protein Bax. In addition, apoptosis induction was found to be caspase dependent. Further molecular investigations indicated that diacerein instigated apoptosis was associated with inhibition of IL-6/IL-6R autocrine signaling axis. Suppression of STAT3, MAPK and Akt pathways were also observed as a consequence of diacerein-mediated upstream inhibition of IL-6/IL-6R. Fluorescence study and western blot analysis revealed cytosolic accumulation of STAT3 in diacerein-treated cells. The docking study showed diacerein/IL-6R interaction that was further validated by competitive binding assay and isothermal titration calorimetry. Most interestingly, it was found that diacerein considerably suppressed tumor growth in MDA-MB-231 xenograft model. The in vivo antitumor effect was correlated with decreased proliferation (Ki-67), increased apoptosis (TUNEL) and inhibition of IL-6/IL-6R-mediated STAT3, MAPK and Akt pathway in tumor remnants. Taken together, diacerein offered a novel blueprint for cancer therapy by hampering IL-6/IL-6R/STAT3/MAPK/Akt network.

Profiling of Brevibacillus borstelensis transcriptome exposed to high temperature shock

To understand the molecular mechanisms underlying the ability of the bacteria to survive at high temperature, gene expression profile of Brevibacillusborstelensis at 55°C during 5 and 10min heat shock period was carried out by high-throughput sequencing technology. A total of 2555 non-redundant transcripts were annotated. A total of 575 genes at 5min and 400 genes at 10min exhibited significant differential expression in response to temperature upshift from 50 to 55°C. Genes up-regulated under heat shock were associated with metabolism (mtnE), membrane transport, signal transduction, transcriptional regulation (ycxD, codY) and folding and sorting (hsp90). A larger number of genes encoding hypothetical proteins were identified. RT-PCR experimental results carried out on genes expressed under heat shock were found to be consistent with transcriptome data. The results enhance our understanding of adaptation strategy of thermophilic bacteria thereby providing a strong background for in depth research in thermophiles.

Assessment of genetic diversity of Bacillus spp. isolated from eutrophic fish culture pond

The genus Bacillus comprises of a diverse group with a wide range of nutritional requirements and physiological and metabolic diversity. Their role in nutrient cycle is well documented. 16S rDNA sequences do not always allow the species to be discriminated. In this study 40 Bacillus spp. obtained from fish culture pond and 10 culture type strains were analysed for their genomic diversity by PCR-RFLP of intergenic spacer region of 16S-23S and HSP60 genes. TaqI digestion of PCR products amplified by ITS PCR did not render distinctive RFLP patterns. Numerical analysis of ITS PCR-RFLP pattern differentiated the isolates into 11 clusters. Same species were found to be grouped in different clusters. But PstI digested PCR products amplified from HSP60 gene of the isolates showed distinctive RFLP patterns. The dendrogram constructed from HSP60 PCR-RFLP delineated the isolates into 11 clusters also. All the clusters, except cluster I grouped only one type of species. The results showed that Bacillus spp. could be clearly distinguished by PCR-RFLP of HSP60 gene. Therefore, the HSP60 gene is proposed as an additional molecular marker for discrimination of Bacillus group.

Immunohistochemical detection of axillary lymph node micrometastases in breast cancer patients: Increasing the accuracy of detection and decreasing labor intensive serial sectioning

Background: The histological detection of axillary lymph node tumor metastases in cases of breast carcinoma is of major prognostic significance, but may be difficult when metastases are of microscopic size. The micrometastases can be detected either by immunohistochemistry (IHC) or serial sectioning. Aims: We investigated whether immunohistochemical techniques and serial sectioning can increase the accuracy of metastatic detection and compared the efficacy of both. Materials and Methods: Thirty cases of breast carcinoma were studied in all of whom the axillary lymph nodes had been reported as free of metastases. Blocks from these cases were serially sectioned and stained with hematoxylin and eosin and a single section was stained with monoclonal antibody to cytokeratin AE1/AE3 and epithelial membrane antigen. The positivity for micrometastases was correlated with size, number, grade and histological type of primary tumor, lymph node size and number. Results and Conclusion: In 5/30 previously unsuspected cases, micrometastases were revealed by IHC and in 1/30 by serial sectioning. These findings suggested that serial sectioning is a labor intensive, time consuming and impractical procedure. Micrometastases were more frequently detected with age of patient >50 years, Grade 2/3 tumor, tumor size >5 cm and more than one primary tumor. Immunohistochemical analysis can be recommended as a routine procedure or an adjunct to routine histological procedures for the correct staging of breast carcinoma and use of adjuvant chemotherapy, especially in the high risk group.

Specific oligonucleotide primers for detection of endoglucanase positive Bacillus subtilis by PCR

A polymerase chain reaction (PCR) assay was developed for discrimination of Bacillus subtilis from other members of B. subtilis group as well as rapid identification from environmental samples. Primers ENIF and EN1R from endoglucanase gene were used to amplify a1311 bp DNA fragment. The specificity of the primers was tested with seven reference strains and 28 locally isolated strains of endoglucanase positive Bacillus species. The PCR product was only produced from B. subtilis. The results demonstrated high specificity of two oligonucleotides for B. subtilis. This species-specific PCR method provides a quick, simple, powerful and reliable alternative to conventional methods in the detection and identification of B. subtilis. To our knowledge this is the first report of a B. subtilis specific primer set.

Upregulation of transcripts for metabolism in diverse environments is a shared response associated with survival and adaptation of Klebsiella pneumoniae in response to temperature extremes

Klebsiella pneumoniae being ubiquitous in nature encounters wide differences in environmental condition. The organism's abundance in natural water reservoirs exposed to temperature variation forms the basis of its persistence and spread in the soil and other farm produce. In order to investigate the effect of temperature changes on the survival and adaptation of the bacteria, the transcriptional response of K. pneumoniae subjected to low (20 °C) and high (50 °C) temperature shock were executed using Applied Biosystems SOLiD platform. Approximately, 33 and 34% of protein coding genes expressed in response to 20 and 50 °C, respectively, displayed significant up- or downregulation (p < 0.01). Most of the significantly expressed transcripts mapped to metabolism, membrane transport, and cell motility were downregulated at 50 °C, except for protein folding, sorting, and degradation, suggesting that heat stress causes general downregulation of gene expression together with induction of heat shock proteins. While at 20 °C, the transcripts of carbohydrate, lipid, and amino acid metabolism were highly upregulated. Hypothetical proteins as well as canonical heat and cold shock proteins, viz. grpE, clpX, recA, and deaD were upregulated commonly in response to 20 and 50 °C. Significant upregulation of genes encoding ribosomal proteins at 20 and 50 °C possibly suggest their role in the survival of K. pneumoniae cells under low- and high-temperature stress.

Histopathologic changes following neoadjuvant chemotherapy in locally advanced breast cancer

AIMS

To compare the clinical and pathologic assessment of response to neoadjuvant chemotherapy and describe the various histopathologic changes observed.

MATERIALS AND METHODS

We studied a group of 40 patients with locally advanced breast cancer who had their initial workup in the form of clinico-imaging assessment of the size and pretreatment biopsy from the lesion. All the patients received two to six cycles of neoadjuvant chemotherapy, either cyclophosphamide 50 to 60 mg/m 2 IV, doxorubicin 40 to 50 mg/m 2 IV and 5-fluorouracil 500 to 800 mg/m 2 IV (CAF) or cyclophosphamide, epirubicin, and 5-fluorouracil (CEF). Clinical and pathologic assessment of response to chemotherapy was done based on the UICC guidelines.

RESULT

Complete clinical response (cCR) was seen in 10% cases (4/40), thirty percent patients had (12/40) partial response and 60% (24/40) had stable disease after neoadjuvant chemotherapy. Pathologic complete response (pCR) with no evidence of viable tumor was observed in 20% patients (8/40). Fifteen patients (37.5%) showed partial response and 42.5% patients (17/40) had a stable disease. No patient progressed during the course of chemotherapy. Changes in the tumor type were observed following chemotherapy, most common being the mucinous change. Histologic changes like dyscohesion, shrinkage of tumor cells, elastosis, collagenization, necrosis, lymphocytic reaction, giant cell response are some of the common observations seen following treatment with neoadjuvant chemotherapy.

CONCLUSION

Pathologic assessment of response to neoadjuvant chemotherapy is a better predictor than the clinical response. The chemotherapy drugs can be modified based on the response observed after 1-2 cycles of neoadjuvant, the response being based on both tumor and patient's responsiveness.

Enhanced 2 μm broad-band emission and NIR to visible frequency up-conversion from Ho3+/Yb3+ co-doped Bi2O3-GeO2-ZnO glasses

In this work, a new and non-conventional oxide glass composition based on Bi2O3-GeO2-ZnO system has been formulated with an aim to realize low phonon oxide glass and elucidate its performance when co-doped with Ho(3+)/Yb(3+) for the energy transfer based NIR emission at 2 μm from Ho(3+) ions under Yb(3+) excitation. The glass with 1.0 mol% Ho2O3 and 0.5 mol% Yb2O3 has exhibited maximum energy transfer rate (3602 s(-1)) and energy transfer efficiency (65.92%). Important radiative properties have been predicted for emission transitions of Ho(3+) ions using intensity parameters derived from measured absorption spectra using standard Judd-Ofelt theory. At lower acceptor ion concentration (0.1 mol%), an efficient NIR to visible up-conversion emission has been observed based on two photon absorption process which has found to be reduced significantly at higher Ho(3+) concentrations with simultaneous enhancement in 2 μm emission. Hence, this newly developed glass codoped with Yb(3+)/Ho(3+) is promising glass for sensitized 2 μm emission applications as broad band tunable lasers because of the combination of low phonon energy (707 cm(-1)), high energy transfer efficiency, moderately high emission cross-section (5.33×10(-21) cm(2)) and larger effective half-width of the emission band value of 169 nm.

Sensitive detection of CO2 implementing tunable thulium-doped all-fiber laser

In this paper a compact, yet sensitive gas detection system based on a modulated, tunable thulium-doped fiber laser in the 2 μm wavelength region is reported. The laser operating wavelength range centered at a wavelength of 1.995 μm has been selected to access the R(50) transition (ν1+2ν2+ν3) of CO2 based on its line strength and to achieve isolation from interfering high-temperature water absorption features. The laser linewidth and tuning range are optimized accordingly. The modulation of the fiber laser, achieved through pump source modulation and a locking detection mechanism, has been utilized to stabilize the laser system and therefore to create a compact gas sensor with high sensitivity. The absorption spectrum, as well as the line strength and the concentration level of CO2, have been monitored through absorption spectroscopy techniques. The measured minimum detectable concentration of CO2 obtained using the system shows that it is quite capable of detecting trace gas at the ppm (parts in 10(6)) level. The stable laser performance achieved in the sensor system illustrates its potential for the development of practical, compact, yet sensitive fiber-laser-based gas sensor systems.

Comparative metatranscriptomic signatures of wood and paper feeding in the gut of the termite Reticulitermes flavipes (Isoptera: Rhinotermitidae)

Termites are highly eusocial insects that thrive on recalcitrant materials like wood and soil and thus play important roles in global carbon recycling and also in damaging wooden structures. Termites, such as Reticulitermes flavipes (Rhinotermitidae), owe their success to their ability to extract nutrients from lignocellulose (a major component of wood) with the help of gut-dwelling symbionts. With the aim to gain new insights into this enzymatic process we provided R. flavipes with a complex lignocellulose (wood) or pure cellulose (paper) diet and followed the resulting differential gene expression on a custom oligonucleotide-microarray platform. We identified a set of expressed sequence tags (ESTs) with differential abundance between the two diet treatments and demonstrated the source (host/symbiont) of these genes, providing novel information on termite nutritional symbiosis. Our results reveal: (1) the majority of responsive wood- and paper-abundant ESTs are from host and symbionts, respectively; (2) distinct pathways are associated with lignocellulose and cellulose feeding in both host and symbionts; and (3) sets of diet-responsive ESTs encode putative digestive and wood-related detoxification enzymes. Thus, this study illuminates the dynamics of termite nutritional symbiosis and reveals a pool of genes as potential targets for termite control and functional studies of termite-symbiont interactions.

Heterotopic pancreas presenting as ileoileal intussusception

Heterotopic, aberrant or ectopic pancreas is defined as the presence of pancreatic tissue in topographic anomaly, with no anatomical, neural or vascular connection to the normal pancreas. It is a rare condition found mainly in stomach, duodenum and jejunum. Ileal heterotopic pancreas is an uncommon condition and has been rarely reported in children so far. Hereby we report a case of heterotopic pancreas presenting as ileal poyp leading to ileoileal intussusception in a 12 year child.

Aspiration cytology of adenomatoid tumor of epididymis: An important diagnostic tool

Adenomatoid tumor is a benign mesothelial neoplasm of the paratesticular region in males but can also occur in female genital tracts. The epididymis is the most common site of involvement and constitutes 32% of paratesticular neoplasms.

We diagnosed a case of adenomatoid tumor on cytopathology in 24 years old male, who presented with mass lesion right epididymis since 2 months. The diagnosis was confirmed on histopathology and immunohistochemistry after surgical excision of the nodule.

FNAC is a rapid, reliable and cost effective diagnostic tool for preoperative diagnosis to take appropriate surgical decisions. Pathologists should be aware of the cytological features of such lesions so as to differentiate it from other paratesticular lesions.

Teratoma of the tongue

Teratomas are the benign tumours, which may occur anywhere in the body. Development of these lesions in the oral cavity is extremely rare. In the oral cavity, they usually arise in the midline, in the floor of mouth. Infrequently, they may be seen in the tongue proper. We hereby, present a case of swelling tongue in 56 years female diagnosed as teratoma.

Composition analysis and material characterization of an emulsifying extracellular polysaccharide (EPS) produced by Bacillus megaterium RB-05: a hydrodynamic sediment-attached isolate of freshwater origin

AIMS

This work was aimed to isolate, purify and characterize an extracellular polysaccharide (EPS) produced by a freshwater dynamic sediment-attached micro-organism, Bacillus megaterium RB-05, and study its emulsifying potential in different hydrocarbon media.

METHODS AND RESULTS

Bacillus megaterium RB-05 was found to produce EPSs in glucose mineral salts medium, and maximum yield (0.864 g l(-1) ) was achieved after 24-h incubation. The recovery rates of the polysaccharide material by ion-exchange and gel filtration chromatography were around 67 and 93%, respectively. As evident from HPLC and FT-IR analyses, the polysaccharide was found to be a heteropolymer-containing glucose, galactose, mannose, arabinose, fucose and N-acetyl glucosamine. Different oligosaccharide combinations namely hexose(3), hexose(4), hexose(5) deoxyhexose(1) and hexose(5) deoxyhexose(1) pentose(3) were obtained after partial hydrolysis of the polymer using MALDI-ToF-MS. The polysaccharide with an average molecular weight of 170 kDa and thermal stability up to 180°C showed pseudoplastic rheology and significant emulsifying activity in hydrocarbon media.

CONCLUSIONS

Isolated polysaccharide was found to be of high molecular weight and thermally stable. The purified EPS fraction was composed of hexose, pentose and deoxyhexose sugar residues, which is a rare combination for bacterial polysaccharides. Emulsifying property was either better or comparable to that of other commercially available natural gums and polysaccharides.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is probably one of the few reports about characterizing an emulsifying EPS produced by a freshwater sediment-attached bacterium. The results of this study contribute to understand the influence of chemical composition and material properties of a new microbial polysaccharide on its application in industrial biotechnology. Furthermore, this work reconfirms freshwater dynamic sediment as a potential habitat for bioprospecting extracellular polymer-producing bacteria. This study will improve our knowledge on the exploitation of a nonconventional renewable resource, which also seems to be ecologically significant.

Purification and partial elucidation of the structure of an antioxidant carbohydrate biopolymer from the probiotic bacterium Bacillus coagulans RK-02

An exopolysaccharide (EPS) was isolated from Bacillus coagulans RK-02 and purified by size exclusion chromatography. The purified, homogeneous EPS had an average molecular weight of ∼3 × 10⁴ Da by comparison with FITC-labeled dextran standards. In vivo evaluations showed that, like other reported polysaccharides, this EPS displayed significant antioxidant activity. FTIR spectroscopy analysis showed the presence of hydroxy, carboxy, and α-glycosidic linkages and a mannose residue. GC analysis indicated that the EPS was a heteropolymer composed of glucose, mannose, galactose, glucosamine, and fucose as monomeric constituent units. Partial elucidation of the structure of the carbohydrate biopolymer based on GC-MS and NMR analysis showed the presence of two unique sets of tetrasaccharide repeating units that have 1→3 and 1→6 glycosidic linkages. This is also the first report of a Gram-positive bacterial polysaccharide with both fucose as a sugar monomer and 1→3 and 1→6 glycosidic linkages in the molecular backbone.

Fibrous dysplasia & McCune-Albright syndrome: an experience from a tertiary care centre in north India

BACKGROUND & OBJECTIVES

Fibrous dysplasia (FD) is a rare metabolic bone disease and information available from India is limited to only anecdotal case reports. We describe the clinical profile and therapeutic outcome of 25 patients with FD observed over a period of 14 yr in a tertiary care centre from north India.

METHODS

In this retrospective study patients (n = 25) with diagnosis of fibrous dysplasia based on either classical radiological features and/or histological evidence on bone biopsy, were analyzed. Associated endocrinopathies if any, were evaluated. The diagnosis of McCune Albright syndrome (MAS) was considered when fibrous dysplasia was accompanied by either café-au-lait macules and/or endocrinopathies. The clinical presentation, biochemical parameters and imaging were analysed. Seven patients received bisphosphonate therapy. The final outcome and side effects were noted.

RESULTS

Age of the patients ranged from 7 to 48 yr (mean ± SD, 24.2 ± 11.4 yr) with a lag time between onset of symptoms and presentation ranging from 1 to 20 yr (mean ± SD, 6.6 ± 6.2 yr). The mean duration of follow up was 3.5 ± 2.1 yr. Eighteen (72%) patients had polyostotic disease while the remaining had monostotic FD. Eight patients had endocrinopathies: five had acromegaly, one each had gonadotropin independent precocious puberty (GIPP), hyperthyroidism and hypophosphatemic rickets. One child with GIPP later developed hyperthyroidism. McCune Albright syndrome was observed in 10 (40%) patients. A majority of the patients underwent various minor or major surgical procedures and seven patients received bisphosphonates for recurrent pathological fractures. Bone pain was reduced in all bisphosphonate treated patients with a decrease in subsequent fractures.

INTERPRETATION & CONCLUSIONS

This series of FD patients from north India shows the varying presentations of this rare disease. Medical treatment with bisphosphonates appears to be potentially rewarding.

Benign vs malignant soft tissue neoplasms: limitations of magnetic resonance imaging

AIMS

Various features have been described in the literature to differentiate benign from malignant lesions. The aim of the present study was to study the accuracy of each of these features and that of magnetic resonance imaging (MRI) in diagnosing malignant lesions.

MATERIALS AND METHODS

Fifty-five consecutive patients presenting with neoplastic (both benign and malignant) lesions diagnosed clinically and on ultrasound were studied and their MRI features were compared with the findings on surgical exploration and histopathologic examination.

RESULTS

There were 32 (58%) benign and 23 (42%) malignant masses. Malignant masses were more common in patients older than 20 years (83%), and these had symptoms of less than 6 months duration (75%), as against benign lesions. The swelling was painful in 8 malignant masses and these were more common in the upper limbs (61%). Various features of malignant lesions were size more than 5 cm in 83%, change in signal intensity from homogenous on T1-weighted images to heterogenous on T2-weighted images in 74%, irregular margins in 74%, and heterogenous contrast enhancement in 91%. The accuracy of these features was 76%, 58%, 78%, and 60%, respectively. Most benign and malignant lesions were intramuscular in location. A significant number (38%) of benign lesions were located in the intermuscular facial plane. Definitive diagnosis was made in 42% of the lesions.

CONCLUSIONS

MRI is an excellent modality for evaluating soft tissue neoplasms; however, prediction of a specific diagnosis and differentiation of malignant and benign lesions is not always possible.

Role of granulocyte colony stimulating factor (G-CSF) in chemotherapy induced neutropenia

BACKGROUND

In the past decade, there have been many clinical trials investigating the potential benefits of adjunctive therapy with colony stimulating factors (CSFs) both to ameliorate or prevent profound neutropenia and its potentially life threatening consequences. Neutropenia is the most common dose limiting side effects of cytotoxic chemotherapy. We decided to study the effect of same in our patients coming to haematology clinic.

AIMS AND OBJECTIVES

To see the effect of G-CSF on severity of neutropenia following chemotherapy in patients of haematological malignancies and to see the effect of G-CSF on duration of hospitalization, documented infections and duration of fever as compared to control group in patients with neutropenia following chemotherapy in haematological malignancies.

MATERIAL AND METHODS

Thirty patients of acute leukemia were prospectively studied. Patients were given G-CSF 24.hours following chemotherapy induced neutropenia and following parameters were observed. (a) median time to ANC recovery (b) incidence and duration of fever (c) duration of hospitalization following chemotherapy (d) incidence of documented infections. The patients were given G-CSF until the neutrophil count was >1000/ml for 3 days or maximum of 7 days.

RESULTS

Mean age was 29.33 +/- 14 years in G-CSF group and 27.53 +/- 13.75 in control group. Mean duration of neutropenia was 11.4 days (p < 0.05) in G-CSF group and 15.8 days in control group. Mean duration of fever was 8.2 days in G-CSF group and 13.53 days in control group (p < 0.05). Mean duration of hospital stay was 21.33 days in G-CSF group and 25 days in control group (p > 0.05).

CONCLUSIONS

The study demonstrates that G-CSF administration is efficacious in chemotherapy induced neutropenia by decreasing the duration of neutropenia and duration of fever.

Isolated accessory limb of lower eyelid with multiple dermal appendages

We report the first case in the English literature of an isolated occurrence of accessory limb with multiple dermal appendages in a ten-month-old boy. This condition presented at birth as a limb bud below the left eyelid, multiple dermal appendages in the adjacent part of the face below the left orbit and on the upper part of the face. No anomalies of the ocular structures or central nervous system were identified. Accessory limb with multiple dermal appendages, in the absence of a congenital cystic eye, is an extremely rare condition representing a benign aberration in the developing musculoskeletal system. We present the first of such a case and endeavour to explain the embryological basis behind it.

Antimicrobial potential of a lipopeptide biosurfactant derived from a marine Bacillus circulans

AIMS

To isolate the biologically active fraction of the lipopeptide biosurfactant produced by a marine Bacillus circulans and study its antimicrobial potentials.

METHODS AND RESULTS

The marine isolate B. circulans was cultivated in glucose mineral salts medium and the crude biosurfactant was isolated by chemical isolation method. The crude biosurfactants were solvent extracted with methanol and the methanol extract was subjected to reverse phase high-performance liquid chromatography (HPLC). The crude biosurfactants resolved into six major fractions in HPLC. The sixth HPLC fraction eluting at a retention time of 27.3 min showed the maximum surface tension-reducing property and reduced the surface tension of water from 72 mNm(-1) to 28 mNm(-1). Only this fraction was found to posses bioactivity and showed a pronounced antimicrobial action against a panel of Gram-positive and Gram-negative pathogenic and semi-pathogenic micro-organisms including a few multidrug-resistant (MDR) pathogenic clinical isolates. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of this antimicrobial fraction of the biosurfactant were determined for these test organisms. The biosurfactant was found to be active against Gram-negative bacteria such as Proteus vulgaris and Alcaligens faecalis at a concentration as low as 10 microg ml(-1). The biosurfactant was also active against methicillin-resistant Staphylococcus aureus (MRSA) and other MDR pathogenic strains. The chemical identity of this bioactive biosurfactant fraction was determined by post chromatographic detection using thin layer chromatography (TLC) and also by Fourier transform infrared (FTIR) spectroscopy. The antimicrobial HPLC fraction resolved as a single spot on TLC and showed positive reaction with ninhydrin, iodine and rhodamine-B reagents, indicating its lipopeptide nature. IR absorption by this fraction also showed similar and overlapping patterns with that of other lipopeptide biosurfactants such as surfactin and lichenysin, proving this biosurfactant fraction to be a lipopeptide. The biosurfactant did not show any haemolytic activity when tested on blood agar plates, unlike the lipopeptide biosurfactant surfactin produced by Bacillus subtilis.

CONCLUSIONS

The biosurfactant produced by marine B. circulans had a potent antimicrobial activity against Gram-positive and Gram-negative pathogenic and semi-pathogenic microbial strains including MDR strains. Only one of the HPLC fractions of the crude biosurfactants was responsible for its antimicrobial action. The antimicrobial lipopeptide biosurfactant fraction was also found to be nonhaemolytic in nature.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work presents a nonhaemolytic lipopeptide biosurfactant produced by a marine micro-organism possessing a pronounced antimicrobial action against a wide range of bacteria. There is a high demand for new antimicrobial agents because of the increased resistance shown by pathogenic micro-organisms against the existing antimicrobial drugs. This study provides an insight into the search of new bioactive molecules from marine micro-organisms.

Extraskeletal osteochondroma in the nape of the neck: a case report

Extraskeletal osteochondroma in the nape of the neck is rare and its pathological diagnosis is based on radiological and histopathological examination. It is vital that such a diagnosis be considered when a discrete, ossified mass is localised in soft tissues, even at atypical sites. Differential diagnoses include myositis ossificans, a lipomatous lesion, a pseudomalignant osseous tumour, an ossifying fibromyxoid tumour, an extraskeletal chondroma with endochondral ossification, synovial (osteo) chondromatosis, tumoural calcinosis, a synovial sarcoma, and an extraskeletal osteosarcoma. Clinical awareness of this benign entity is important as no malignant transformation or metastasis has been reported. Marginal excision with histopathological identification is the treatment of choice.