Loop-mediated isothermal amplification assay for detection of Mycobacterium tuberculosis complex in infertile women

BACKGROUND

Female genital tuberculosis (FGTB) has a profound impact on the reproductive health of patients including infertility. Conventional diagnostic techniques have low sensitivity and specificity as well as long turnaround time. There is a need of developing newer, rapid and practically adaptable technique, especially in low-income countries.

OBJECTIVE

To standardize and evaluate loop-mediated isothermal amplification (LAMP) technique for diagnosis of FGTB.

METHODS

A total of 300 endometrial biopsy samples from infertile females were subjected to Ziehl-Neelsen (ZN) staining, Lowenstein-Jensen culture, automated culture (BACTEC mycobacterial growth indicator tube), histopathological examination (HPE), nucleic acid amplification by polymerase chain reaction (PCR) and LAMP technique. Composite gold standard (either smear/culture/HPE/PCR positive) was considered for calculation of outcome parameters.

RESULTS

The observed sensitivities of ZN smear, culture, HPE, PCR and LAMP were 2.94%, 10.29%, 8.82%, 95.59% and 66.18%, respectively. Overall concordance between PCR and LAMP was 63%, which shows a good agreement.

CONCLUSION

This study is the first to evaluate LAMP in the diagnosis of FGTB and found it to be a rapid and convenient technique, especially in low resource endemic settings.

Zollinger-Ellison syndrome: an unusual case of chronic diarrhoea in a child

Most cases of Zollinger-Ellison syndrome (ZES) are described in adults. It is a rare disorder in childhood. Most cases present with abdominal pain due to peptic ulceration and chronic diarrhoea not responding to general measures. The symptom complex is initially confused with other more common diseases, which lead to a delay in diagnosis. We present a rare case of a-12-year boy who initially presented with abdominal pain, diarrhoea, vomiting and progressive weight loss for over a two-year period before he was finally diagnosed as a case of ZES with the primary tumour in the pancreatic head and with multiple metastasis in both the liver and lymph nodes.

Image-guided fine-needle aspiration cytology of deep-seated enlarged lymph nodes

Purpose: To evaluate the role of image-guided fine-needle aspiration cytology (FNAC) of deep-seated lymph nodes.

Material and Methods: Image-guided FNACs were performed on 242 patients of deep-seated lymph nodes which included thoracic, retroperitoneal and abdominal nodes. A sterile 3.5/5-MHz micro convex sector probe was used for localisation of the node. The FNAC was performed using a 0.7- to 0.9-mm needle with the stylet removed and attached to a 20-ml syringe and FNAC handle after the needle was visualised in the lesion. For each case a minimum of 4-5 smears were made, and two observers without bias interpreted the smears.

Results: A total of 242 patients were aspirated, of which 216 (90%) aspirations were US-guided and the remaining 26 (10%) were CT-guided. Adequate material for cytologic diagnosis was obtained in 208 (86%) patients with a similar diagnostic accuracy. The aspirate material was non-representative or scanty in 34 (14%) patients. The most common cytological diagnosis was tuberculosis/consistent with tuberculosis seen in 108 (45%) patients followed by metastasis (17%) and reactive hyperplasia (10%). Non-Hodgkin lymphoma was diagnosed in 22 (9%) patients. All patients were briefly followed for a period of 1 1/2 to 2 years (mean 1 year).

Conclusion: Image-guided FNAC has a pivotal role, and is a cost-effective tool for establishing tissue diagnosis as a primary investigative modality. It is also helpful and accurate in follow-up of patients with a known malignant disease, thereby avoiding surgical intervention.

Morphometric analysis of endometrial cells in liquid-based cervical cytology samples

BACKGROUND

Exfoliated endometrial cells can be seen in cervical smears in association with a wide variety of conditions ranging from normal proliferative endometrium to endometrial malignancies. It is often difficult to differentiate between benign, atypical and malignant endometrial cells using cytomorphology alone. This study was conducted to evaluate if morphometric analysis of endometrial nuclei on liquid-based cervical samples could be of help in differentiating between these endometrial cells.

MATERIALS AND METHODS

Three groups of cervical samples with histopathological correlation were selected: Group A: showing benign endometrial cells; Group B: showing atypical endometrial cells and Group C: showing malignant endometrial cells. There were 30 cases each in Group A and B and 39 cases in Group C. Image J, NIH, USA was used for selecting the endometrial nuclei and performing the morphometric measurements. MANOVA was used for statistical analysis.

RESULTS

The mean nuclear area and nuclear perimeter were significantly different between the three groups of endometrial cells with a P-value <0.05. However, the mean standard deviation of the nuclear area (SDNA) was not significantly different between atypical and malignant endometrial cells (P = 0.765) and the mean nuclear diameter was not statistically different between benign and atypical cells (P = 0.112). Also, the difference in the mean integrated gray density amongst all three groups was not statistically significant (P = 0.397, 0.844, 0.732).

CONCLUSION

We conclude that the morphometric parameters of the nuclear area and nuclear perimeter are helpful in differentiating between benign, atypical and malignant endometrial nuclei even in liquid-based cervical cytology samples.

Significance of epithelial cell clusters in pseudomyxoma peritonei

BACKGROUND

Pseudomyxoma peritonei (PMP) is a rare clinical syndrome characterised by distension of the peritoneum by jelly-like ascites. Cytological evaluation of peritoneal fluid is often an initial diagnostic test for possible ovarian and/or appendiceal primary tumours.

AIMS AND OBJECTIVES

The present work was conducted to study the usefulness of peritoneal fluid cytomorphology in the early diagnosis of PMP and to evaluate the significance of the presence of epithelial cell (EC) clusters and their prognostic implications.

MATERIALS AND METHODS

We evaluated the detailed cytological features of 21 cases of PMP retrospectively. Both conventional and liquid-based cytology smears of peritoneal fluid were reviewed, cytological features were compared with histological findings and cases were classified into disseminated peritoneal adenomucinosis (DPAM) and peritoneal mucinous carcinomatosis (PMCA).

RESULTS

In our study, the common causes of PMP were primary gastrointestinal malignancies (appendix and colorectal, 57.14%), followed by primary ovarian mucinous neoplasms (28.57%) and synchronous ovarian and appendicular tumours (14.28%). Thick mucinous material was present in all cases (100%). ECs were present in 18 of 21 (85.17%) patients, with mild nuclear atypia in the majority of cases. Histiocytes, mesothelial cells and fibroblast-like, spindle-shaped cells with entrapped mucin were also noted in the background. The cases of PMCA showed greater numbers of EC clusters in cytology smears and these patients had recurrent episodes of PMP.

CONCLUSION

On cytomorphology, high-grade tumours were more cellular and frequently showed EC clusters with moderate to severe atypia, prominent nucleoli and mitosis, and were more prone to PMCA.

Strong Quantum Coherence between Fermi Liquid Mahan Excitons

In modulation doped quantum wells, the excitons are formed as a result of the interactions of the charged holes with the electrons at the Fermi edge in the conduction band, leading to the so-called "Mahan excitons." The binding energy of Mahan excitons is expected to be greatly reduced and any quantum coherence destroyed as a result of the screening and electron-electron interactions. Surprisingly, we observe strong quantum coherence between the heavy hole and light hole excitons. Such correlations are revealed by the dominating cross-diagonal peaks in both one-quantum and two-quantum two-dimensional Fourier transform spectra. Theoretical simulations based on the optical Bloch equations where many-body effects are included phenomenologically reproduce well the experimental spectra. Time-dependent density functional theory calculations provide insight into the underlying physics and attribute the observed strong quantum coherence to a significantly reduced screening length and collective excitations of the many-electron system.

Efficacy of modified rapid economic acetic acid-based Papanicolaou stain

BACKGROUND

Papanicolaou (Pap) staining is used with various modifications for the staining of cervical smears. It gives a good contrast with sharp nuclear features which aid in accurate interpretation. However, it utilises ethyl alcohol, which is expensive and difficult to purchase. We have attempted to devise a rapid Pap technique which uses acetic acid instead of ethyl alcohol, and yet provides good staining for correct diagnosis.

METHODS

Liquid-based cytology samples were collected from 102 patients as a part of routine screening. Two smears were prepared from each sample, which were stained with conventional as well as rapid Pap. In the rapid Pap method, the smears were fixed in methanol and dehydration was performed before and after OG6 with 0.5% acetic acid. The final dehydration was performed with methanol. Smears from both techniques were compared by two independent observers for staining quality.

RESULTS

With the rapid Pap stain, nuclear staining was comparable with that of conventional Pap (P < 0.05). Cytoplasmic staining was optimal in 69.6% of cases; however, the suboptimal staining in the rest of the smears did not pose any diagnostic problem.

CONCLUSION

The rapid Pap technique is a cost-effective alternative to conventional Pap which also saves time and provides good staining quality without compromising the diagnostic interpretation.

Optical Coherence in Atomic-Monolayer Transition-Metal Dichalcogenides Limited by Electron-Phonon Interactions

We systematically investigate the excitonic dephasing of three representative transition-metal dichalcogenides, namely, MoS_{2}, MoSe_{2}, and WSe_{2} atomic monolayer thick and bulk crystals, in order to gain a proper understanding of the factors that determine the optical coherence in these materials. Coherent nonlinear optical spectroscopy and temperature dependent absorption, combined with theoretical calculations of the phonon spectra, indicate electron-phonon interactions, to be the limiting factor. Surprisingly, the excitonic dephasing, differs only slightly between atomic monolayers and high quality bulk crystals, which indicates that material imperfections are not the limiting factor in atomically thin monolayer samples. The temperature dependence of the electronic band gap and the excitonic linewidth combined with "ab initio" calculations of the phonon energies and the phonon density of states reveal a strong interaction with the E' and E" phonon modes.

Abstract P3-04-04: Estrogen receptor β5 increases aggressiveness of the triple negative breast cancer cell line SUM159

Recent clinical studies are indicating that the estrogen receptor β variant β5 (ERβ5) expression correlates to worse prognosis. We wanted to know if expression of ERβ5 is changing the growth behavior of the triple negative cell line SUM159. Estrogen receptor β5 is highly similar to estrogen receptor β1 except for a truncated C-terminus making the remaining ligand binding domain incapable of binding to estrogen. In addition a 4 amino acid unique peptide is added to the C-terminal end. Stably expressing ERβ5 using a transposon integrated tetracycline regulated expression system we find that expression of ERβ5 increases proliferation of the triple negative SUM159 cells especially in reduced serum condition compared to control cells. Since SUM159 have been shown to depend on autocrine stimulation for growth we are suggesting that expression of ERβ5 is affecting the production of autocrine growth factors.

Citation Format: Faria M, Tin-U C, Dey P, Gustafsson J-A, Strom AM. Estrogen receptor β5 increases aggressiveness of the triple negative breast cancer cell line SUM159. [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 P3-04-04.

Biexciton formation and exciton coherent coupling in layered GaSe

Nonlinear two-dimensional Fourier transform (2DFT) and linear absorption spectroscopy are used to study the electronic structure and optical properties of excitons in the layered semiconductor GaSe. At the 1s exciton resonance, two peaks are identified in the absorption spectra, which are assigned to splitting of the exciton ground state into the triplet and singlet states. 2DFT spectra acquired for co-linear polarization of the excitation pulses feature an additional peak originating from coherent energy transfer between the singlet and triplet. At cross-linear polarization of the excitation pulses, the 2DFT spectra expose a new peak likely originating from bound biexcitons. The polarization dependent 2DFT spectra are well reproduced by simulations using the optical Bloch equations for a four level system, where many-body effects are included phenomenologically. Although biexciton effects are thought to be strong in this material, only moderate contributions from bound biexciton creation can be observed. The biexciton binding energy of ∼2 meV was estimated from the separation of the peaks in the 2DFT spectra. Temperature dependent absorption and 2DFT measurements, combined with "ab initio" theoretical calculations of the phonon spectra, indicate strong interaction with the A1 (') phonon mode. Excitation density dependent 2DFT measurements reveal excitation induced dephasing and provide a lower limit for the homogeneous linewidth of the excitons in the present GaSe crystal.

First Report of Potato leaf roll virus (PLRV) Naturally Occurring on Jute (Corchorus olitorius) in India

Jute (Corchorus olitorius L.) is an important bast fiber crop that is mainly grown in the Southeast Asian countries like India, Bangladesh, Nepal, China, Indonesia, Thailand, Myanmar, and a few South American countries. In June 2013, symptoms suggestive of a viral disease were noticed on jute (cv. JRO524) in an experimental field of the CRIJAF research farm, Barrackpore, India, and the incidence of the disease was less than 2%. The infected plants showed stunted growth and short height. Mostly the upper leaves elongated with curling and coiling of lamina. Puckering and shoe string effect were also noticed. Petioles and stipules of the affected leaves were exceptionally longer. Although initially the incidence was low, it may spread to larger areas in subsequent years. Because the jute fiber is extracted from the stem, stunted growth and short height would badly affect the fiber yield and quality. Ten symptomatic and ten asymptomatic healthy looking samples were collected from the field. Corchorus golden mosaic begomovirus is common in jute; therefore, all the samples were tested by PCR using JMFL-AF/JMFL-AR, DNA-A component specific primer pair and JMFL-BF/JMFL-BR, DNA-B component specific primer pairs (1). However, there was no amplification. Because the aphid Aphis gossypii was often noticed in the jute field, all the samples were tested by double-antibody sandwich (DAS)-ELISA for common aphid transmitted viruses, e.g., Cucumber mosaic virus, Bean common mosaic virus, Cowpea mosaic virus, Papaya ring spot virus, Potato leaf roll virus (PLRV), Potato virus Y, and Watermelon mosaic virus using commercial diagnostic kits (Agdia). The symptomatic samples showed positive reaction only for PLRV. Five ELISA-positive samples and five asymptomatic healthy samples were used for RNA extraction. Total RNA was extracted by using QIAGEN RNeasy mini kit. RT-PCR was carried out with PLRV CP gene specific primer pair (3) which generated a cDNA amplicon of 627 bp in all ELISA-positive symptomatic samples. PLRV was not detected in symptomless samples. The five purified cDNA products were cloned in a pGEM-T Easy vector (Promega) and were sequenced. One of the five identical sequences was deposited in GenBank (Accession No. KF233880). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the coat protein sequence of PLRV reference strain (S77421). Nucleotide span and ORF finder (NCBI) analysis indicated the 627-bp PCR amplicon coded part of a coat protein gene that had 100% identity with translated gene product (Protein ID AAB33483). PLRV is a small isometric RNA virus with worldwide distribution belonging to the family Luteoviridae whose natural host range is mainly restricted to solanaceous plants and few plants of other families (2,4). To the best of our knowledge, this is the first report of PLRV naturally occurring on jute (C. olitorius). References: (1) R. Ghosh et al. J. Virol. Methods 159:34, 2009. (2) S. Guyader and D. G. Ducray. J. Gen. Virol. 83:1799, 2002. (3) M. A. Mayo et al. J. Gen. Virol. 70:1037, 1989. (4) K. Mukherjee et al. Virus Genes 26:247, 2003.

Exploring two-dimensional electron gases with two-dimensional Fourier transform spectroscopy

The dephasing of the Fermi edge singularity excitations in two modulation doped single quantum wells of 12 nm and 18 nm thickness and in-well carrier concentration of ∼4 × 10(11) cm(-2) was carefully measured using spectrally resolved four-wave mixing (FWM) and two-dimensional Fourier transform (2DFT) spectroscopy. Although the absorption at the Fermi edge is broad at this doping level, the spectrally resolved FWM shows narrow resonances. Two peaks are observed separated by the heavy hole/light hole energy splitting. Temperature dependent "rephasing" (S1) 2DFT spectra show a rapid linear increase of the homogeneous linewidth with temperature. The dephasing rate increases faster with temperature in the narrower 12 nm quantum well, likely due to an increased carrier-phonon scattering rate. The S1 2DFT spectra were measured using co-linear, cross-linear, and co-circular polarizations. Distinct 2DFT lineshapes were observed for co-linear and cross-linear polarizations, suggesting the existence of polarization dependent contributions. The "two-quantum coherence" (S3) 2DFT spectra for the 12 nm quantum well show a single peak for both co-linear and co-circular polarizations.

First Report of a 16Sr I-B Phytoplasma Associated with Phyllody and Stem Fasciation of Flax (Linum usitatissimum) in India

Flax or linseed is grown as a fiber or oilseed crop in tropical and temperate regions. It is commercially cultivated in many countries of the world including Canada, China, India, the United States, Ethiopia, Pakistan, Russia, Poland, and Argentina (1). In December 2013, symptoms suggestive of phytoplasma infection were noticed on flax in different experimental fields of Central Research Institute for Jute and Allied Fibres (CRIJAF) research farm, Barrackpore, India, and the incidence was less than 2%. Because incidence of phytoplasma diseases are increasing worldwide, occurrence of a phytoplasma in a new geographical area poses an imminent threat. The infected plants showed floral virescence, phyllody, and stem fasciation (flattened stem). Floral malformation was very conspicuous with abnormal structures replacing normal flowers. All the floral parts, including petals, turned into green leaves. Total DNA was extracted from leaf mid veins of three symptomatic and three asymptomatic plants using a DNeasy Plant Mini Kit (Qiagen). PCR was carried out with the phytoplasma-specific universal P1/P7 primer set followed by nested primer pair R16F2n/R16R2 (2), resulting in DNA amplicons that were 1.8 kb and 1.2 kb, respectively, in all symptomatic samples tested. No amplification was observed with DNA from symptomless samples. This suggested association of a phytoplasma with the disease. The five purified nested PCR products were cloned in a pGEM-T Easy vector (Promega) and sequenced. One of the sequences that proved to be identical to the others was deposited in GenBank (Accession No. KJ417660). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the 16Sr DNA sequence of the 'Candidatus Phytoplasma asteris' reference strain (GenBank HQ828108), which belongs to 16SrI group. The phylogenetic tree based on 16SrDNA sequence of phytoplasmas belonging to group 16SrI and other distinct phytoplasma groups also showed that the phytoplasma clustered with members of group 16SrI (3). The nested PCR product of R16F2n/R16R2 was digested using restriction enzymes AluI, BfaI, BstU, HhaI, HpaI, KpnI, MseI, and RsaI. The RFLP patterns were compared with those of known phytoplasma strains (2) and they matched the patterns for aster yellows subgroup B (16Sr I-B). Subsequently, the iPhyClassifier 16Sr group/subgroup classification based on similarity (4) analyses showed that the studied strain had 16SrDNA sequences in the 16SrI-B group with a similarity coefficient of 1.00. To the best of our knowledge, this is the first report of 16SrI-B phytoplasma associated with flax in India. References: (1) K. P. Akhtar et al. Phytoparasitica 41:383, 2013. (2) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (3) N. Saitou and M. Nei. Mol. Biol. Evol. 4:406, 1987. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

Novel role of pancreatic differentiation 2 in facilitating self-renewal and drug resistance of pancreatic cancer stem cells

BACKGROUND

Cancer stem cells (CSCs) contribute towards disease aggressiveness and drug resistance. Specific identification of CSC maintenance genes and targeting can improve the efficiency of currently available treatment modalities. Pancreatic differentiation 2 (PD2) has a major role in the self-renewal of mouse embryonic stem cells. In the present study, we investigated the role of PD2 in pancreatic CSCs.

METHODS

Characterisation of CSCs and non-CSCs from mouse models, pancreatic cancer cells and human tissues by CSC and self-renewal marker analysis using confocal assay. Effect of PD2 knockdown in CSCs (after gemcitabine treatment) was studied by immunoblot and apoptosis assays.

RESULTS

A subpopulation of cells displayed PD2 overexpression in mouse (Kras(G12D); Pdx1-Cre and Kras(G12D); Trp53(R172H/+); Pdx1-Cre) and human pancreatic tumours, which co-express CSC markers. Cancer stem cells exhibited elevated expression of PD2 and self-renewal markers, such as Oct3/4, Shh and β-catenin. Gemcitabine treatment maintained the CSC population with simultaneous maintenance of PD2 and CSC marker expression. Knockdown of PD2 in CSCs resulted in reduced viability of cells and enhanced apoptosis along with abrogated expression of CD133 and MDR2.

CONCLUSIONS

Our results suggest that PD2 is a novel CSC maintenance protein, loss of which renders the CSCs more susceptible to drug-induced cell death.

Experiences of women referred for urgent assessment of postmenopausal bleeding (PMB)

Women with postmenopausal bleeding (PMB) are referred for specialist assessment within 2 weeks of presentation to their GP. No research has previously examined women's experiences of expedited referral. This was investigated in the present study using questionnaires (6-item State Anxiety Inventory (6-STAI)) and focus groups. A total of 55 women completed questionnaires. Results showed high levels of anxiety at first hospital visit (mean 47.0 (SD 14.27); 95% CI 43.14-50.93). Scores declined by 90 days, but were higher in those not undergoing hysteroscopy. Fifteen women who underwent hysteroscopy attended focus groups. Women recalled fear of cancer from symptom onset until receipt of results. Anxiety was exacerbated by poor knowledge of PMB and lack of awareness of expedited referral. Post-discharge, those with unexplained or recurrent symptoms expressed frustration and upset. Effective strategies to raise awareness of PMB and its causes are needed, including reasons for expedited referral. Women without cancer may also need more support.

First Report of a 16SrV-C Phytoplasma Causing Little Leaf and Bunchy Top of Tossa Jute (Corchorus olitorius) in India

Jute is the most important phloem fiber crop of the world, and is mainly grown in the South East Asian countries of India, Bangladesh, Nepal, China, Indonesia, Thailand, and Myanmar, and few South American countries. The fiber is used in making sacks, ropes, bags, carpets, shoes, geo-textiles, and home decorations. There are two kinds of jute: tossa jute (Corchorus olitorius L.) and white jute (C. capsularis). In June 2012, symptoms suggestive of phytoplasma infection (little leaf and bunchy top) were noticed on tossa jute in different experimental fields of the CRIJAF research farm, Barrackpore, India, and the incidence of the disease varied from 5 to 20%. The infected plants showed profuse lateral branching with a bushy appearance. In many plants, branching at the apical portion developed a bunchy top symptom with tufts of smaller leaves. Leafy stem was also common in many plants with main stems covered with numerous little leaves. Total DNA was extracted from leaf midveins of 15 symptomatic and 5 asymptomatic plants by using an improved salt concentration and simple sodium acetate CTAB method (1). PCR was carried out with universal P1/P7 primer set followed by nested primer pair R16F2n/R16R2 (3), resulting in DNA amplicons that were 1.8 kb and 1.2 kb, respectively, in all symptomatic samples tested. Phytoplasma was not detected in symptomless samples. The five purified nested products were cloned in a pGEM-T Easy vector (Promega) and sequenced. One of the sequences that proved to be identical was deposited in GenBank (Accession No. KF501045). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the 16Sr DNA sequence of the alder yellows phytoplasma reference strain (GenBank Accession No. AY028789), which belongs to the 16SrV group. The phylogenetic tree based on the 16SrDNA sequence of phytoplasmas belonging to group 16SrV and other distinct phytoplasma groups also showed that the phytoplasma clustered with members of subgroup 16SrV (4). Subsequently, in silico RFLP analysis of the nested PCR product with the pDRAW32 program using AluI and TruI restriction site used for 16SrV subgroups A, B, C, D, and E indicated that the 16SrV Corchorus strain belonged to subgroup C. RFLP patterns from all symptomatic C. olitorius samples were identical to the 16SrV-C pattern (2). The vector species transmitting the concerned phytoplasma in C. olitorius still needs to be identified. The leaf hopper, Amrasca biguttula biguttula, may be a potential vector as it is often noticed in jute fields. To the best of our knowledge, this is the first report of 16SrV-C phytoplasma associated with tossa jute (C. olitorius) in India. Initiative has to be taken to manage this disease; otherwise, branching of the main stems would badly affect the fiber quality as well as yield. References: (1) C. Biswas et al. Lett. Appl. Microbiol. 56:105, 2012. (2) B. Duduk et al. J. Phytopathology 152:575, 2004. (3) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (4) N. Saitou and M. Nei. Mol. Biol. Evol. 4:406, 1987.