Identification of different species of Bacillus isolated from Nisargruna Biogas Plant by FTIR, UV-Vis and NIR spectroscopy

Definitive identification of microorganisms, including pathogenic and non-pathogenic bacteria, is extremely important for a wide variety of applications including food safety, environmental studies, bio-terrorism threats, microbial forensics, criminal investigations and above all disease diagnosis. Although extremely powerful techniques such as those based on PCR and microarrays exist, they require sophisticated laboratory facilities along with elaborate sample preparation by trained researchers. Among different spectroscopic techniques, FTIR was used in the 1980s and 90s for bacterial identification. In the present study five species of Bacillus were isolated from the aerobic predigester chamber of Nisargruna Biogas Plant (NBP) and were identified to the species level by biochemical and molecular biological (16S ribosomal DNA sequence) methods. Those organisms were further checked by solid state spectroscopic absorbance measurements using a wide range of electromagnetic radiation (wavelength 200 nm to 25,000 nm) encompassing UV, visible, near Infrared and Infrared regions. UV-Vis and NIR spectroscopy was performed on dried bacterial cell suspension on silicon wafer in specular mode while FTIR was performed on KBr pellets containing the bacterial cells. Consistent and reproducible species specific spectra were obtained and sensitivity up to a level of 1000 cells was observed in FTIR with a DTGS detector. This clearly shows the potential of solid state spectroscopic techniques for simple, easy to implement, reliable and sensitive detection of bacteria from environmental samples.

Using a Systems Pharmacology Model of the Blood Coagulation Network to Predict the Effects of Various Therapies on Biomarkers

A number of therapeutics have been developed or are under development aiming to modulate the coagulation network to treat various diseases. We used a systems model to better understand the effect of modulating various components on blood coagulation. A computational model of the coagulation network was built to match in-house in vitro thrombin generation and activated Partial Thromboplastin Time (aPTT) data with various concentrations of recombinant factor VIIa (FVIIa) or factor Xa added to normal human plasma or factor VIII-deficient plasma. Sensitivity analysis applied to the model revealed that lag time, peak thrombin concentration, area under the curve (AUC) of the thrombin generation profile, and aPTT show different sensitivity to changes in coagulation factors' concentrations and type of plasma used (normal or factor VIII-deficient). We also used the model to explore how variability in concentrations of the proteins in coagulation network can impact the response to FVIIa treatment.

Systematic review and meta-analysis of the performance of clinical risk assessment instruments for screening for osteoporosis or low bone density

We performed a systematic review and meta-analysis of the performance of clinical risk assessment instruments for screening for DXA-determined osteoporosis or low bone density. Commonly evaluated risk instruments showed high sensitivity approaching or exceeding 90% at particular thresholds within various populations but low specificity at thresholds required for high sensitivity. Simpler instruments, such as OST, generally performed as well as or better than more complex instruments.

INTRODUCTION

The purpose of the study is to systematically review the performance of clinical risk assessment instruments for screening for dual-energy X-ray absorptiometry (DXA)-determined osteoporosis or low bone density.

METHODS

Systematic review and meta-analysis were performed. Multiple literature sources were searched, and data extracted and analyzed from included references.

RESULTS

One hundred eight references met inclusion criteria. Studies assessed many instruments in 34 countries, most commonly the Osteoporosis Self-Assessment Tool (OST), the Simple Calculated Osteoporosis Risk Estimation (SCORE) instrument, the Osteoporosis Self-Assessment Tool for Asians (OSTA), the Osteoporosis Risk Assessment Instrument (ORAI), and body weight criteria. Meta-analyses of studies evaluating OST using a cutoff threshold of <1 to identify US postmenopausal women with osteoporosis at the femoral neck provided summary sensitivity and specificity estimates of 89% (95%CI 82-96%) and 41% (95%CI 23-59%), respectively. Meta-analyses of studies evaluating OST using a cutoff threshold of 3 to identify US men with osteoporosis at the femoral neck, total hip, or lumbar spine provided summary sensitivity and specificity estimates of 88% (95%CI 79-97%) and 55% (95%CI 42-68%), respectively. Frequently evaluated instruments each had thresholds and populations for which sensitivity for osteoporosis or low bone mass detection approached or exceeded 90% but always with a trade-off of relatively low specificity.

CONCLUSIONS

Commonly evaluated clinical risk assessment instruments each showed high sensitivity approaching or exceeding 90% for identifying individuals with DXA-determined osteoporosis or low BMD at certain thresholds in different populations but low specificity at thresholds required for high sensitivity. Simpler instruments, such as OST, generally performed as well as or better than more complex instruments.

On the nature of magnetic state in the spinel Co₂SnO₄

In the spinel Co2SnO4, coexistence of ferrimagnetic ordering below T(N) ≃ 41 K followed by a spin glass state below T(SG) ≃ 39 K was proposed recently based on the temperature dependence of magnetization M(T) data. Here new measurements of the temperature dependence of the specific heat C(P)(T), ac-susceptibilities χ'(T) and χ″(T) measured at frequencies between 0.51 and 1.2 kHz, and the hysteresis loop parameters (coercivity H(C)(T) and remanence M(R)(T)) in two differently prepared samples of Co2SnO4 are reported. The presence of the Co(2+) and Sn(4+) states is confirmed by x-ray photoelectron spectroscopy (XPS) yielding the structure: Co2SnO4 = [Co(2+)][Co(2+)Sn(4+)]O4. The data of C(P) versus T shows only an inflection near 39 K characteristic of spin-glass ordering. The analysis of the frequency dependence of ac-magnetic susceptibility data near 39 K using the Vogel-Fulcher law and the power-law of the critical slowing-down suggests the presence of spin clusters in the system which is close to a spin-glass state. With a decrease in temperature below 39 K, the temperature dependence of the coercivity H(C) and remanence M(R) for the zero-field cooled samples show both H(C) and M(R) reaching their peak magnitudes near 25 K, then decreasing with decreasing T and becoming negligible below 15 K. The plot of C(P)/T versus T also yields a weak inflection near 15 K. This temperature dependence of H(C) and remanence M(R) is likely associated with the different magnitudes of the magnetic moments of Co(2+) ions on the 'A' and 'B' sites and their different temperature dependence.

Androgen receptor as a regulator of ZEB2 expression and its implications in epithelial-to-mesenchymal transition in prostate cancer

Zinc finger E-box-binding protein 2 (ZEB2) is known to help mediate the epithelial-to-mesenchymal transition, and thereby it facilitates cancer metastasis. This study was initiated to explore whether ZEB2 expression differs in prostate cancer (PCa, n=7) and benign prostatic hyperplasia (BPH, n=7) tissues. In PCa tissues, the levels of both immunoreactive ZEB2 and androgen receptor (AR) were found to be significantly higher (P<0.05) when compared with BPH tissues. Co-regulation of AR and ZEB2 prompted us to investigate the role of androgenic stimuli in ZEB2 expression. ZEB2 expression was found to be significantly (P<0.05) upregulated after androgen stimulation and downregulated following AR silencing in LNCaP cells, an androgen-dependent PCa cell line. This finding suggested AR as a positive regulator of ZEB2 expression in androgen-dependent cells. Paradoxically, androgen-independent (AI) cell lines PC3 and DU145, known to possess low AR levels, showed significantly (P<0.05) higher expression of ZEB2 compared with LNCaP cells. Furthermore, forced expression of AR in PC3 (PC3-AR) and DU145 (DU-AR) cells led to reductions in ZEB2 expression, invasiveness, and migration. These cells also exhibited an increase in the levels of E-cadherin (a transcriptional target of ZEB2). Co-transfection of AR and ZEB2 cDNA constructs prevented the decline in invasiveness and migration to a significant extent. Additionally, ZEB2 downregulation was associated with an increase in miR200a/miR200b levels in PC3-AR cells and with a decrease in miR200a/miR200b levels in AR-silenced LNCaP cells. Thus, AR acts as a positive regulator of ZEB2 expression in androgen-dependent cells and as a negative regulator in AI PCa cells.

Full-length cloning and phylogenetic analyses of translationally controlled tumour protein and ferritin genes from the Indian white prawn, Fenneropenaeus indicus (H. Milne Edwards)

Elucidation, through molecular analyses, of bacterial afflictions in commercially important aquaculture-reared shrimps is pivotal for the prevention and/or control of disease outbreaks. In this study, we examined the phylogenetic relatedness and compared the possible immune-related functional roles of both translationally controlled tumour protein (TCTP) and ferritin genes with previous studies. Both TCTP and ferritin genes were substantially upregulated in the Indian white prawn, Fenneropenaeus indicus (H. Milne Edwards), post-larvae following bath challenge with the virulent strain of bacteria, Vibrio harveyi D3. Full-length cloning of these genes by rapid amplification of complementary DNA ends -polymerase chain reaction (RACE-PCR) yielded 727-base pair (bp)-long TCTP and 1212-bp-long ferritin gene sequences. Their open reading frames (ORFs) were 507 and 510 bp, respectively. The TCTP-ORF coded for 168 amino acids with three substitutions at positions 37, 141, 155, and the ferritin ORF coded for 170 amino acids with no species-specific substitutions. Phylogenetic analysis suggested the closest relatedness of both TCTP and ferritin from F. indicus to Chinese white prawn, Fenneropenaeus chinensis (Osbeck). In addition to reporting the full-length sequences of these immune-relevant genes, this study highlighted their conserved natures, which perhaps make them important defence-related proteins in the innate immune system of F. indicus.

Performance of risk assessment instruments for predicting osteoporotic fracture risk: a systematic review

We systematically reviewed the literature on the performance of osteoporosis absolute fracture risk assessment instruments. Relatively few studies have evaluated the calibration of instruments in populations separate from their development cohorts, and findings are mixed. Many studies had methodological limitations making susceptibility to bias a concern.

INTRODUCTION

The aim of this study was to systematically review the literature on the performance of osteoporosis clinical fracture risk assessment instruments for predicting absolute fracture risk, or calibration, in populations other than their derivation cohorts.

METHODS

We performed a systematic review, and MEDLINE, Embase, Cochrane Library, and multiple other literature sources were searched. Inclusion and exclusion criteria were applied and data extracted, including information about study participants, study design, potential sources of bias, and predicted and observed fracture probabilities.

RESULTS

A total of 19,949 unique records were identified for review. Fourteen studies met inclusion criteria. There was substantial heterogeneity among included studies. Six studies assessed the WHO's Fracture Risk Assessment (FRAX) instrument in five separate cohorts, and a variety of risk assessment instruments were evaluated in the remainder of the studies. Approximately half found good instrument calibration, with observed fracture probabilities being close to predicted probabilities for different risk categories. Studies that assessed the calibration of FRAX found mixed performance in different populations. A similar proportion of studies that evaluated simple risk assessment instruments (≤5 variables) found good calibration when compared with studies that assessed complex instruments (>5 variables). Many studies had methodological features making them susceptible to bias.

CONCLUSIONS

Few studies have evaluated the performance or calibration of osteoporosis fracture risk assessment instruments in populations separate from their development cohorts. Findings are mixed, and many studies had methodological limitations making susceptibility to bias a possibility, raising concerns about use of these tools outside of the original derivation cohorts. Further studies are needed to assess the calibration of instruments in different populations prior to widespread use.

Free-flap cover of complex defects around the knee using the descending genicular artery as the recipient pedicle

BACKGROUND

Selection of ideal recipient vessels is one of the most important factors determining success in free-flap reconstruction of the lower limb. At the knee, the choice of vessels has traditionally been either the common femoral or the popliteal vessels and their branches but these are often difficult to use or cannot be used.

METHODS

A series of 32 free flaps for cover of complex injuries of the knee involving the distal femur, the knee joint and the upper tibia were reconstructed using the descending genicular branch of the femoral artery in the adductor canal and its muscular branches to the vastus medialis as the recipient vessels.

RESULT

All but one flap survived with no major complications.

CONCLUSION

The use of the descending genicular artery as the recipient vessel for reconstruction with free flaps around the knee has various advantages including: (i) it is mostly remote from the zone of trauma, (ii) it is constant in location, (iii) the recipient vessels are an excellent size match for end-to-end anastomosis, (iv) there is no need for changes of position of the patient when using most free flaps commonly used for knee reconstruction, (v) it is easy to harvest these simultaneously, (vi) secondary exposure of the underlying skeleton from all quadrants is unlikely to divide the flap pedicle as it is superior and (vii), perhaps most important of all, it obviates the need for exploration of the popliteal fossa.

Acute interstitial nephritis and drug rash with secondary to Linezolid

Linezolid, a member of oxazolidinone antibiotic class, is a relatively well-tolerated drug with few side effects. It is active against gram-positive cocci, including multidrug resistant staphylococci and enterococci. We report a case of a 54-year-old diabetic male with alcoholic cirrhosis admitted in intensive care unit with altered sensorium. He was diagnosed as a case of hepatic failure secondary to hepatitis E infection and enterococcal urosepsis. He was started on linezolid based on the urine culture sensitivity report. On day three of linezolid treatment, he developed severe pruritus, macular rash, eosinophilia, and renal dysfunction. Renal biopsy showed acute tubulointerstitial nephritis. Renal functions improved on discontinuation of linezolid and short course of steroid therapy.

Endovascular treatment of A1 aneurysms. A series of five cases with a brief literature review

Aneurysms of the A1 segment of the anterior cerebral artery are rare and represent less than 1% of intracranial aneurysms. There are few reports available in the literature describing the role of endovascular management of these rare aneurysms. In the present series we describe five patients with A1 aneurysms presenting at our institution with various clinical presentations, treated successfully by endovascular method with a good clinical outcome. From January 2008 to July 2011, five patients (two males and three females) with A1 aneurysms were treated by endovascular means. Four of the patients presented with subarachnoid hemorrhage due to rupture of the A1 aneurysm and one patient presented with symptoms of mass effect in the form of headache and ophthalmoplegia. The age group ranges from eight to 52 years with a mean age of 34.2 years. Four of the patients were treated by coiling without any assisted technique whereas one patient who had a dissecting fusiform aneurysm was treated with stent-assisted coiling. Technical success was achieved in all the patients.We did not encounter any procedure-related complications in any of our cases. All the patients had an uneventful course with good clinical outcome. Angiographic follow-up was available in four patients (80%). Endovascular treatment of this rare group of aneurysms is an effective and safe treatment modality, however large series are required to support our findings.