Investigation of the source‐detector separation in near infrared spectroscopy for healthy and clinical applications

Understanding near infrared light propagation in tissue is vital for designing next generation optical brain imaging devices. Monte Carlo (MC) simulations provide a controlled mechanism to characterize and evaluate contributions of diverse near infrared spectroscopy (NIRS) sensor configurations and parameters. In this study, we developed a multilayer adult digital head model under both healthy and clinical settings and assessed light‐tissue interaction through MC simulations in terms of partial differential pathlength, mean total optical pathlength, diffuse reflectance, detector light intensity and spatial sensitivity profile of optical measurements. The model incorporated four layers: scalp, skull, cerebrospinal‐fluid and cerebral cortex with and without a customizable lesion for modeling hematoma of different sizes and depths. The effect of source‐detector separation (SDS) on optical measurements' sensitivity to brain tissue was investigated. Results from 1330 separate simulations [(4 lesion volumes × 4 lesion depths for clinical +3 healthy settings) × 7 SDS × 10 simulation = 1330)] each with 100 million photons indicated that selection of SDS is critical to acquire optimal measurements from the brain and recommended SDS to be 25 to 35 mm depending on the wavelengths to obtain optical monitoring of the adult brain function. The findings here can guide the design of future NIRS probes for functional neuroimaging and clinical diagnostic systems.      

Major bioactive metabolites from marine fungi: A Review

Biologists and chemists of the world have been attracted towards marine natural products for the last five decades. Approximately 16,000 marine natural products have been isolated from marine organisms which have been reported in approximately 6,800 publications, proving marine microorganisms to be a invaluable source for the production of novel antibiotic, anti tumor, and anti inflammatory agents. The marine fungi particularly those associated with marine alga, sponge, invertebrates, and sediments appear to be a rich source for secondary metabolites, possessing Antibiotic, antiviral, antifungal and antiyeast activities. Besides, a few growth stimulant properties which may be useful in studies on wound healing, carcinogenic properties, and in the study of cancers are reported. Recent investigations on marine filamentous fungi looking for biologically active secondary metabolites indicate the tremendous potential of them as a source of new medicines. The present study reviews about some important bioactive metabolites reported from marine fungal strains which are anti bacterial, anti tumour and anti inflammatory in action. It highlights the chemistry and biological activity of the major bioactive alkaloids, polyketides, terpenoids, isoprenoid and non-isoprenoid compounds, quinones, isolated from marine fungi.     

Screening of mitochondrial mutations and insertion–deletion polymorphism in gestational diabetes mellitus in the Asian Indian population

In this study we scrutinized the association between the A8344G/A3243G mutations and a 9-bp deletion polymorphism with gestational diabetes mellitus (GDM) in an Asian Indian population. The A3243G mutation in the mitochondrial tRNA^Leu(UUR) causes mitochondrial encephalopathy myopathy, lactic acidosis, and stroke-like episodes (MELAS), while the A8344G mutation in tRNA^Lys causes myoclonus epilepsy with ragged red fibers (MERRF). We screened 140 pregnant women diagnosed with GDM and 140 non-GDM participants for these mutations by PCR-RFLP analysis. Both A3243G and A8344G were associated with GDM (A3243: OR-3.667, 95% CI = 1.001–13.43, p = 0.03; A8344G: OR-11.00, 95% CI = 0.6026–200.8, p = 0.04). Mitochondrial DNA mutations contribute to the development of GDM. Our results conclude that mitochondrial mutations are associated with the GDM women in our population. Thus it is important to screen other mitochondrial mutations in the GDM women.     

Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis)

Background

Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon’s range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.

Results

Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma.

Conclusions

Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1437-0) contains supplementary material, which is available to authorized users.     

Geochemistry and Bacterial Recovery from Hindu Kush Range Glacier and Their Potential for Metal Resistance and Antibiotic Production

In this study, we isolated and characterized bacteria and analyzed the geochemistry of unexplored non-polar Tirich Mir glacier, Chitral, Pakistan. The glacier is located in the Hindu Kush mountains range with the highest peak of 7708 m. Three types of samples, i.e. glacial ice, sediment, and melt water were collected. The geochemical analysis demonstrated a higher concentration of heavy metals Fe⁺², Mn⁺², and Cr⁺², cations Na⁺², Ca⁺², and Mg⁺², anions SO₄^?2 and Cl^?1. While among the dissolved free amino acids, tyrosine was detected in high concentration. A total of 43 strains were isolated based on colony morphology. Molecular identification revealed these isolates belong to four phyla, i.e. Proteobacteria 23(54%), Bacteroidetes 4(9%), Actinobacteria 7(16%), and Firmicutes 9(21). Gram-negative bacteria were enrich relative to Gram-positive bacteria. The bacterial communities were more abundant in sediment (21) than in water (12) and ice (10) samples. The isolates also exhibited potent activity against both ATCC and multidrug-resistant clinical isolates. The increased level of tolerance against heavy metals (Cd⁺², Cr⁺³, Hg⁺², Fe⁺³, Ar⁺³, and Ni⁺²) and NaCl was observed. Tirich Mir glacier was found to have a diverse bacterial community structure, with potential candidates having ability to produce bioactive metabolites with possible industrial applications.     

Floral resources to enhance the potential of the parasitoid Aphidius colemani for biological control of the aphid Myzus persicae

Flowering plants have been widely used to enhance biological control. However, this approach has been limited to some extent by the lack of suitable flowering plant species of wide applicability, particularly for global pests. A key example is the green peach aphid, Myzus persicae (GPA). It is commonly attacked by the polyphagous koinobiont aphidiidae, Aphidius colemani, which is also of global occurrence. Here, eight flowering plants were evaluated for the potential enhancement of GPA biological control using A. colemani under laboratory conditions. These included buckwheat (Fagopyrum esculentum), alyssum (Lobularia maritima), white rocket (Diplotaxis erucoides.), wild mustard (Sinapis arvensis), lavender (Lavandula angustifolia), wild marjoram (Origanum vulgare), thyme (Origanum marjorana) and pepper mint (Mentha piperita). The effects of access to these flowers on the longevity (days), potential fecundity (number of dissected eggs) and parasitism rate for A. colemani compared with the control treatment (water) were studied. Longevity of A. colemani which had access to buckwheat was 4–5 times longer than the control and 2–3 times longer than it was in the other plant treatments; the latter did not differ significantly between each other. Potential fecundity of A. colemani was the highest when it had been provided with buckwheat flowers. Exposing A. colemani to flowering plants for longer time intervals (12 hr and 24 hr) increased the number of eggs produced compared with 6 hr. The number of parasitized aphids/female A. colemani with buckwheat flowers was the highest of all treatments; it ranged from 14 in the control to 219 with buckwheat. Further studies should be carried out under field conditions to determine the effect of a range of flowering plants on A. colemani. For example, although buckwheat was highly effective, in many climates it may be a useful component in mixtures comprising other, more robust species.     

Synthesis and biological evaluation of novel analogues of Gly-l-Pro-l-Glu (GPE) as neuroprotective agents

This study investigated the anti-inflammatory effects of novel pseudotripeptides (GPE 1–3) as potential candidates to counteract neuroinflammation processes in Alzheimer’s disease.GPE 1–3 pseudotripeptides are synthetic derivatives of Gly-l-Pro-l-Glu (GPE), the N-terminal tripeptide of IGF-1, obtained through the introduction of isosteres of the amidic bond (aminomethylene unit) to increase the metabolic stability of the native tripeptide. The results showed that all synthetic derivatives possessed higher half-lives (t_1/2?>?4?h) than GPE (t_1/2?=?30?min) in human plasma and had good water solubility. The biological results demonstrated that GPE 1–3 had protective properties in several experimental models of treated THP-1 cells. Notably, the novel pseudotripeptides influenced inflammatory cytokine expression (IL-1β, IL-18, and TNF-α) in Aβ_25–35-, PMA-, and LPS-treated THP-1 cells. In PMA-differentiated THP-1 macrophages, both GPE 1 and GPE 3 reduced the expression levels of all selected cyto-chemokines, even though GPE 3 showed the best neuroprotective properties.     

The minimal structural requirement of concanavalin A that retains its functional aspects

A systematic investigation of the effects of several commonly used detergents on the conformation and function of concanavalin A at pH 7 in solution form was made by using circular dichroism (CD), intrinsic fluorescence, 1-anilino 8-sulphonic acid (ANS) binding, dynamic light scattering (DLS) and sugar inhibition assay. In the presence of 6.0 mM sodium dodecyl sulphate (SDS), an anionic detergent, and 0.8 mM cetyl tri methyl ammonium bromide (CTAB), a cationic detergent, intermediate states of concanavalin A were obtained having a negative CD peaks at 222 and 208 nm respectively, a characteristic of alpha-helix. These states also retained tertiary contacts with altered tryptophan environment and high ANS binding (exposed hydrophobic area) which can be characterized as molten globule states. Concanavalin A in the presence of 5.0 mM 3-[(3-cholamidopropyl) dimethyl-ammonio]-1-propanesulphonate (CHAPS), a zwitterionic detergent, and 0.07 mM brij-35, a non-ionic detergent, also exists in intermediate states. These intermediates (molten globules) had high ANS binding with native-like secondary (inherent beta-sheet) and tertiary structure. The intermediate states were characterized further by means of dynamic light-scattering measurements and kinetic data. To study the possible functional requirement of the minimum structure, the intermediate states characterized in the presence of detergents were shown to retain the activity with polysaccharide (dextran). The pattern of activity observed was brij-35 > CHAPS > CTAB > SDS. The specific binding and activity of concanavalin A with ovalbumin was investigated as a function of time by turbidity measurements. Cationic and anionic detergents showed significant effects on the structure of concanavalin A as compared with zwitterionic and non-ionic detergents.     

Different molten globule-like folding intermediates of hen egg white lysozyme induced by high pH and tertiary butanol

We have provided evidence that hen egg white lysozyme (HEWL) existed in alpha helical and beta structure dominated molten globule (MG) states at high pH and in the presence of tertiary butanol, respectively. Circular dichroism (CD), intrinsic fluorescence, ANS binding and acrylamide-induced fluorescence quenching techniques have been used to investigate alkali-induced unfolding of HEWL and the effect of tertiary butanol on the alkaline-induced state. At pH 12.75, HEWL existed as molten globule like intermediate. The observed MG-like intermediate was characterized by (i) retention of 77% of the native secondary structure, (ii) enhanced binding of ANS (approximately 5 times) compared to native and completely unfolded state, (iii) loss of the tertiary structure as indicated by the tertiary structural probes (near-UV, CD and Intrinsic fluorescence) and (iv) acrylamide quenching studies showed that MG state has compactness intermediate between native and completely unfolded states. Moreover, structural properties of the protein at isoelectric point (pI) and denatured states have also been described. We have also shown that in the presence of 45% tertiary butanol (t-butanol), HEWL at pH 7.0 and 11.0 (pI 11.0) existed in helical structure without much affecting tertiary structure. Interestingly, MG state of HEWL at pH 12.7 transformed into another MG state (MG2) at 20% t-butanol (v/v), in which secondary structure is mainly beta sheets. On further increasing the t-butanol concentration alpha helix was found to reform. We have proposed that formation of both alpha helical and beta sheet dominated intermediate may be possible in the folding pathway of alpha + beta protein.     

Purification and characterization of a mesophilic lipase from Bacillus subtilis FH5 stable at high temperature and pH

Lipases are a class of enzymes which catalyze the hydrolysis of long-chain triglycerides. Microbial lipases are currently receiving much attention with the rapid development of enzyme technology. Bacillus subtilis FH5, isolated from tannery wastes, produced a thermostable alkalophilic lipase and was purified to homogeneity as judged by SDS-PAGE. The purification steps included acetone fractionation and sequential column chromatography on DEAE-cellulose, Sephadex G-75 and adsorption chromatography on Hydroxylapatite. The results of chromatographies showed that two types of lipases were present having molecular weights approximately 62 kDa and 24 kDa, respectively. The purified enzyme was found to be 100% stable at pH 10 and about 80% residual activity was present at 60 degrees C. The enzyme was found to be stable in the presence of Mg2+, Mn2+ and Ca2+ ions. Km value was calculated as 5.05 mM and Vmax as 0.416 micromol/ml/min. Bacillus subtilis FH5 was isolated from tannery waste, therefore, enzyme is environmentally compatible for application in leather degreasing process.