Solution structure and dynamics of glia maturation factor from Caenorhabditis elegans

BACKGROUND

The GMF class of the ADF-H domain family proteins regulate actin dynamics by binding to the Arp2/3 complex and F-actin through their Site-1 and Site-2, respectively. CeGMF of C. elegans is analogous to GMFγ of human and mouse and is 138 amino acids in length.

METHODS

We have characterized the solution structure and dynamics of CeGMF by solution NMR spectroscopy and its thermal stability by DSC.

RESULTS

The solution structure of CeGMF shows canonical ADF-H fold with two additional β-strands in the β4-β5 loop region. The Site-1 of CeGMF is well formed and residues of all three regions of Site-1 show dynamic flexibility. However, the β4-β5 loop of Site-2 is less inclined towards the C-terminal, as the latter is truncated by four residues in comparison to GMF isoforms of human and mouse. Regions of Site-2 show motions on ns-ps timescale, but dynamic flexibility of β4-β5 loop is low in comparison to corresponding F-loop region of ADF/cofilin UNC-60B. A general difference in packing of α3 and α1 between GMF and ADF/cofilins was noticed. Additionally, thermal stability of CeGMF was significantly higher than its ADF/cofilin homologs.

CONCLUSION

We have presented the first solution structure of GMF from C. elegans, which highlights the structural differences between the Site-2 of CeGMF and mammalian GMF isoforms. Further, we have seen the differences in structure, dynamics, and thermal stability of GMF and ADF/cofilin.

GENERAL SIGNIFICANCE

This study provides a useful insight to structural and dynamics factors that define the specificity of GMF towards Arp2/3 complex.

Clinical and molecular characterization of patients with cancer of unknown primary in the modern era

Background

On the basis of historical data, patients with cancer of unknown primary (CUP) are generally assumed to have a dismal prognosis with overall survival of less than 1 year. Treatment is typically cytotoxic chemotherapy guided by histologic features and the pattern of metastatic spread. The purpose of this study was to provide a clinical and pathologic description of patients with CUP in the modern era, to define the frequency of clinically actionable molecular alterations in this population, to determine how molecular testing can alter therapeutic decisions, and to investigate novel uses of next-generation sequencing in the evaluation and treatment of patients with CUP.

Patients and methods

Under Institutional Review Board approval, we identified all CUP patients evaluated at our institution over a recent 2-year period. We documented demographic information, clinical outcomes, pathologic evaluations, next-generation sequencing of available tumor tissue, use of targeted therapies, and clinical trial enrollment.

Results

We identified 333 patients with a diagnosis of CUP evaluated at our institution from 1 January 2014 through 30 June 2016. Of these patients, 150 had targeted next-generation sequencing carried out on available tissue. Median overall survival in this cohort was 13 months. Forty-five of 150 (30%) patients had potentially targetable genomic alterations identified by tumor molecular profiling, and 15 of 150 (10%) received targeted therapies. Dominant mutation signatures were identified in 21 of 150 (14%), largely implicating exogenous mutagen exposures such as ultraviolet radiation and tobacco.

Conclusions

Patients with CUP represent a heterogeneous population, harboring a variety of potentially targetable alterations. Next-generation sequencing may provide an opportunity for CUP patients to benefit from novel personalized therapies.

High xylan recovery using two stage alkali pre-treatment process from high lignin biomass and its valorisation to xylooligosaccharides of low degree of polymerisation

In the present work, xylan from arecanut husk was extracted using 2 stage alkaline pretreatment process. In first step, biomass was incubated in alkali at different temperatures (25 °C, 50 °C and 65 °C), alkali concentrations (5%, 10%, 15% and 20% w/v), and incubation periods (8 h, 16 h and 24 h) and evaluated for xylan recovery. It was observed that 40-52% of available xylan could be recovered using 10% alkali when incubated for 8-24 h at 65 °C. Subsequently, the alkali pretreatment operating conditions which provided good xylan recovery were processed further using hydrothermal treatment to extract more xylan. For maximum xylan recovery (>90%), best operating conditions were identified when biomass was treated under hydrothermal treatment (1, 1.5 and 2 h) with varying incubation periods (8, 16, 24 h) and alkali concentrations (5%, 10%) using full factorial design. Incubating arecanut husk with 10% w/v NaOH, at 65 °C for a period of 8 h, followed by hydrothermal treatment at 121 °C for 1 h helped recover >94% xylan. In the next step, enzymatic hydrolysis process was optimized to recover maximum XOS (Optimized condition: 50 °C, pH 4 and 10 U enzyme dose). The hydrolysate comprised of xylobiose: 25.0 ± 1.2 g/100 g xylan (∼71% of XOS), xylotriose: 9.2 ± 0.65 g/100 g xylan (26.2% of XOS) and xylotetrose: 0.9 ± 0.04 g/100 g xylan (2% of XOS). The developed process enables to reduce alkali consumption for high recovery of xylan from biomass with relatively higher lignin content for its valorisation into a potential prebiotic oligosaccharide.

NMR elucidation of monomer-dimer transition and conformational heterogeneity in histone-like DNA binding protein of Helicobacter pylori

Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is histone-like DNA binding protein (Hup), which in its homo-dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation. Legitimately, if the binding of Hup to DNA is suppressed, it will directly impact on the survival of the bacterium, thus making Hup a potential therapeutic target for developing new anti-H. pylori agents. However, to inhibit the binding of Hup to DNA, it is necessary to gain detailed insights into the molecular and structural basis of Hup-dimerization and its binding mechanism to DNA. As a first step in this direction, we report here the nuclear magnetic resonance (NMR) assignments and structural features of Hup at pH 6.0. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations. The dynamic equilibrium was found to shifting towards dimer both at low temperature and low pH; whereas DNA binding studies evidenced that the protein binds to DNA in its dimeric form. These preliminary investigations correlate very well with the diverse functionality of protein and will form the basis for future studies aiming to develop novel anti-H. pylori agents employing structure-based-rational drug discovery approach.

Patients' preferences and existential perspective: what to consider and how should patient's expectations be guided?

With an ageing population, surgical procedures in older patients are becoming increasingly more common. This can pose clinical and ethical dilemmas, during which clinicians need to make complex decisions. In this paper we discuss the importance of assessing mental capacity to assess if the older patient can make his or her own decisions relating to surgery. We also discuss the importance of understanding ethical principles, in order that clinicians can better guide patient's decision-making. In addition, we look at ageism, frailty, and co-morbidities, and their influence on clinician's decisions regarding surgery in older patients. Further to this, we look at the influence of evidence-based medicine on treatment options, and the under representation of older people in clinical trials and the importance of this. Finally, we consider the importance of considered decisions regarding resuscitation, when considering surgical intervention in older patients. We conclude that patient-centred individualised care, considering patients expectations, wishes, and priorities is vital, whilst aiming to improve or maintain quality of life, and minimise risks when able.

Differential accumulation of β-carotene and tissue specific expression of phytoene synthase (MaPsy) gene in banana (Musa sp) cultivars

An experiment was conducted with twelve major Indian banana cultivars to investigate the molecular relationship between the differential accumulation of β-carotene in peel and pulp of the banana fruit and carotenoid biosynthetic pathway genes. The high performance liquid chromatography showed that all banana cultivars accumulated two-three fold more β-carotene in non-edible portion of the banana fruit. However, Nendran, a famous orange fleshed cultivar of South India, had high β-carotene content (1362 µg/100 g) in edible pulp. The gene encoding Musa accuminata phytoene synthase (MaPsy) was successfully amplified using a pair of degenerate primers designed from Oncidium orchid. The deduced amino acid sequences shared a high level of identity to phytoene synthase gene from other plants. Gene expression analysis confirmed the presence of two isoforms (MaPsy1 and MaPsy2) of MaPsy gene in banana fruits. Presence of two isoforms of MaPsy gene in peel and one in pulp confirmed the differential accumulation of β-carotene in banana fruits. However, Nendran accumulated more β-carotene in edible pulp due to presence of both the isoforms of MaPsy gene. Thus, carotenoid accumulation is a tissue specific process strongly dependent on differential expression pattern of two isoforms of MaPsy gene in banana.

Phonon Sidebands in Monolayer Transition Metal Dichalcogenides

Excitons dominate the optical properties of monolayer transition metal dichalcogenides (TMDs). Besides optically accessible bright exciton states, TMDs exhibit also a multitude of optically forbidden dark excitons. Here, we show that efficient exciton-phonon scattering couples bright and dark states and gives rise to an asymmetric excitonic line shape. The observed asymmetry can be traced back to phonon-induced sidebands that are accompanied by a polaron redshift. We present a joint theory-experiment study investigating the microscopic origin of these sidebands in different TMD materials taking into account intra- and intervalley scattering channels opened by optical and acoustic phonons. The gained insights contribute to a better understanding of the optical fingerprint of these technologically promising nanomaterials.

Recombinant Calponin of human filariid Brugia malayi: Secondary structure and immunoprophylactic potential

In the search for potential vaccine candidates for the control of human lymphatic filariasis, we recently identified calponin-like protein, that regulates actin/myosin interactions, in a proinflammatory fraction F8 (45.24-48.64kDa) of Brugia malayi adult worms. In the present study, the gene was cloned, expressed, and the recombinant Calponin of B. malayi (r-ClpBm) was prepared and characterized. r-ClpBm bears homology with OV9M of Onchocerca volvulus, a non-lymphatic filariid that causes loss of vision and cutaneous pathology. r-ClpBm was found to be a ∼45kDa protein that folds into a predominantly α-helix conformation. The protective efficacy of r-ClpBm against B. malayi infection in Mastomys coucha was investigated by assessing the course of microfilaraemia and adult worm burden in the host immunized with r-ClpBm and subsequently infected with infective third stage larvae (L3). Expression of the Calponin was detected in all life stages (microfilariae, L3, L4, L5 and adults) of the parasite and immunization with r-ClpBm partially protected M. coucha against establishment of infection as inferred by ∼42% inhibition in parasite burden. Upregulated cellular proliferation, TNF-α, IFN-γ, IL-1β, IL-4, nitric oxide (NO) release, expression of iNOS, and specific IgG, IgG1 and IgG2b in immunized animals correlated with parasitological findings. r-ClpBm immunization caused degranulation in majority of mast cells indicating possible involvement of mast cell products in reducing the parasite survival. It appears that complex mechanisms including Th1, Th2, NO and mast cells are involved in the clearance of infection. To the best of our knowledge this is the first report on cloning, expression of the gene and purification of r-ClpBm, determination of its secondary structure and its ability to partially prevent establishment of B. malayi infection. Thus, r-ClpBm may further be studied and developed in combination with other protective molecules of B. malayi as a component of potential filarial cocktail vaccine candidate.

Fatty acid synthase as a potential therapeutic target in feline oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is an aggressive and treatment-resistant malignancy in both feline and human patients. Recent work has demonstrated aberrant expression of fatty acid synthase (FASN) and an increased capacity for lipogenesis in human OSCC and other cancers. In human OSCC, inhibition of FASN decreased cell viability and growth in vitro, and diminished tumour growth and metastasis in murine preclinical models. This study aimed to characterize FASN as a therapeutic target in feline OSCC. Immunohistochemistry revealed high FASN expression in primary feline OSCC tumours, and FASN expression was detected in OSCC cell lines (3 feline and 3 human) by immunoblotting and quantitative real-time-polymerase chain reaction (qRT-PCR). Orlistat, a FASN inhibitor, substantially reduced cell viability in both feline and human OSCC lines, although feline cell lines consistently displayed higher sensitivity to the drug. FASN mRNA expression among cell lines mirrored sensitivity to orlistat, with feline cell lines expressing higher levels of FASN. Consistent with this observation, diminished sensitivity to orlistat treatment and decreased FASN mRNA expression were observed in feline OSCC cells following incubation under hypoxic conditions. Treatment with orlistat did not potentiate sensitivity to carboplatin in the cell lines investigated; instead, combinations of the 2 drugs resulted in additive to antagonistic effects. Our results suggest that FASN inhibition is a viable therapeutic target for feline OSCC. Furthermore, cats may serve as a spontaneous large animal model for human oral cancer, although differences in the regulation of lipogenesis between these 2 species require further investigation.

Highly Anisotropic in-Plane Excitons in Atomically Thin and Bulklike 1T'-ReSe2

Atomically thin materials such as graphene or MoS₂ are of high in-plane symmetry. Crystals with reduced symmetry hold the promise for novel optoelectronic devices based on their anisotropy in current flow or light polarization. Here, we present polarization-resolved optical transmission and photoluminescence spectroscopy of excitons in 1T'-ReSe₂. On reducing the crystal thickness from bulk to a monolayer, we observe a strong blue shift of the optical band gap from 1.37 to 1.50 eV. The excitons are strongly polarized with dipole vectors along different crystal directions, which persist from bulk down to monolayer thickness. The experimental results are well reproduced by ab initio calculations based on the GW-BSE approach within LDA+GdW approximation. The excitons have high binding energies of 860 meV for the monolayer and 120 meV for bulk. They are strongly confined within a single layer even for the bulk crystal. In addition, we find in our calculations a direct band gap in 1T'-ReSe₂ regardless of crystal thickness, indicating weak interlayer coupling effects on the band gap characteristics. Our results pave the way for polarization-sensitive applications, such as optical logic circuits operating in the infrared spectral region.

Laser-driven formation of transient local ferromagnetism in FeRh thin films

The antiferromagnetic to ferromagnetic phase transition in FeRh can be induced globally by either heating the material above its phase transition temperature or applying a combination of external stimuli (such as mechanical strain, electric/magnetic fields) on the material preheated close to its transition temperature. On the other hand, to locally induce this phase transition is more desirable for applications and requires a confined source of energy such as a focused laser beam. Here we combine laser excitation with X-ray magnetic imaging to determine the effect of laser heating on the local and transient magnetization of FeRh using time-resolved photoelectron emission microscopy. Excitation by an ultrashort laser pulse generates a local ferromagnetic state within 0.6ns which recovers its initial antiferromagnetic state after a further 2ns. The form of the domains during the growth and diminution of ferromagnetic ordering suggests an intrinsic speed limit for magnetic and structural changes.

Antibody response against PhoP efficiently discriminates among healthy individuals, tuberculosis patients and their contacts

Tuberculosis continues to be one of the most devastating global health problem. Its diagnosis will benefit in timely initiation of the treatment, cure and therefore reduction in the transmission of the disease. Tests are available, but none can be comprehensively relied on for its diagnosis; especially in TB-endemic zones. PhoP is a key player in Mycobacterium tuberculosis virulence but nothing has been known about its role in the diagnosis of TB. We monitored the presence of anti-PhoP antibodies in the healthy, patients and their contacts. In addition, we also measured antibodies against early secretory antigens ESAT-6 and CFP-10, and latency associated antigen Acr-1 to include proteins that are associated with the different stages of disease progression. Healthy subjects showed high antibody titer against PhoP than patients and their contacts. In addition, a distinct pattern in the ratio of Acr-1/PhoP was observed among all cohorts. This study for the first time demonstrates a novel role of anti-PhoP antibodies, as a possible marker for the diagnosis of TB and therefore will contribute in the appropriate action and management of the disease.

Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase

Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix α3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme.

Substance abuse amongst the medical graduate students in a developing country

Background & objectives:

Substance abuse is found worldwide including among students. We carried out this study to estimate the prevalence of substance abuse among medical student studying in a medical college in north India.

Methods:

Using a validated questionnaire a cross-sectional survey was conducted among 230 undergraduate and postgraduate medical students in a private medical college.

Results:

The prevalence of substance abuse was 20.43 per cent (47/230) among medical students. An increase in substance abuse was observed in the latter years of medical education. A total of 43 of 47 (91.7%) students using these substances were aware of the ill effects. The most common reasons for substance use were relief from psychological stress (34/47, 72.4%) and occasional celebration (34/47, 72.4%). Of the 47 substance users, 28 (59.6%) made past attempts to quit the substance abuse.

Interpretation & conclusions:

Nearly one-fifth of medical students abuse at least one substance despite knowing the ill effects with the main predisposing factor being the psychological stress.