Strategies to evade false positives in the in situ analysis of peptide antibiotics in SDS-PAGE gels

In situ activity assay is one of the promising techniques for the characterization of peptide antibiotics. This assay was carried out for the peptide purified from a new bacterial isolate Paenibacillus alvei and commercial peptide antibiotic polymixin E. Towards this, the routine and new protocols were tried. Interestingly, the unexpected result of these experiments - the "switch over activity" has led us to have further investigations. Here, we have addressed the potential problem in the methodology of in situ assay and demonstrated a fool proof protocol to evade the false positive results.     

A synergistic effect of suppressive CGG codon in +2 position and downstream CAT repeats for efficient heterologous protein expression in Escherichia coli

The negative effect of NGG codons at +2 position has been well documented for the down regulation of recombinant protein expression in Escherichia coli. But this is not true when certain specific sequences are present in the downstream of NGG codons. This has been proved in our study while expressing human Erythropoietin (EPO) in E. coli GJ1158. Towards this, nine recombinant constructs were made and their expression profile was compared. In our results, we found that the suppressive nature of NGG codon (GGG, CGG) in the +2 position was overcome by imposing a downstream CAT repeat motif. The expression of EPO levels is higher in the constructs having the combination of both CGG codon at 2nd position and CAT repeats than the other constructs having either CGG or CAT repeat alone. In addition, it is also interesting to note that increasing number of CAT repeats shows increased expression levels.     

High intraspecific genetic divergence in the versatile fairy shrimp <Emphasis Type="Italic">Branchinecta lindahli</Emphasis> with a comment on cryptic species in the genus <Emphasis Type="Italic">Branchinecta</Emphasis> (Crustacea: Anostraca)

A new Arctic Ostracode Database-2015 (AOD-2015) provides census data for 96 species of benthic marine Ostracoda from 1340 modern surface sediments from the Arctic Ocean and subarctic seas. Ostracoda is a meiofaunal, Crustacea group that secretes a bivalved calcareous (CaCO₃) shell commonly preserved in sediments. Arctic and subarctic ostracode species have ecological limits controlled by temperature, salinity, oxygen, sea ice, food, and other habitat-related factors. Unique species ecology, shell chemistry (Mg/Ca ratios, stable isotopes), and limited stratigraphic ranges make them a useful tool for paleoceanographic reconstructions and biostratigraphy. The database, described here, will facilitate the investigation of modern ostracode biogeography, regional community structure, and ecology. These data, when compared to downcore faunal data from sediment cores, will provide a better understanding of how the Arctic has been affected by climatic and oceanographic change during the Quaternary. Images of all species and biogeographic distribution maps for selected species are presented, with brief discussion of representative species’ biogeographic and ecological significance. Publication of AOD-2015 is open-sourced and will be available online at several public websites with latitude, longitude, water depth, and bottom water temperature for most samples. It includes material from Arctic abyssal plains and submarine ridges, continental slopes, and shelves of the Kara, Laptev, East Siberian, Chukchi, Beaufort Seas, and several subarctic regions.     

<Emphasis Type="Italic">In vitro</Emphasis> and <Emphasis Type="Italic">in silico</Emphasis> studies on fibrinolytic activity of nattokinase: A clot buster from <Emphasis Type="Italic">Bacillus</Emphasis> sp.

Background

Nattokinase (NK) is a serine protease enzyme of the subtilisin family. It exhibits a strong fibrinolytic activity. The fibrinolytic enzymes from Bacillus sp. have attracted interest as thrombolytic agents because of their efficiency in the fibrinolytic process including plasmin activation.

Methods

In the present study, VIT garden soil was collected and subjected to isolation process in order to screen for the NK production. Screening for NK enzyme was performed by radial caseinolytic assay. The production of NK enzyme was done in two different production medium for comparative studies. The NK enzyme was purified by gel permeation chromatography. The activity of the purified NK was checked by clot lysis and casein digestion assay. To investigate the structural basis of NK and fibrinogen interaction and also to identify the best binding mode, molecular dynamics and docking studies were performed.

Results

Based on the morphological and biochemical characterization, the isolate was identified as Bacillus sp. The overall purification fold of NK was about 3 with the specific activity of 664U/mg and 9.9% yield. Homogeneity of the purified enzyme was analyzed and confirmed by the single band obtained in SDS-PAGE. Molecular weight of the purified protease was estimated as 25 kDa. Purified NK enzyme exhibited 97% of effective clot lysis activity. The NK was docked in to the knob region of the fibrinogen at its binding site using Dock server. A total of 26 residues of fibrinogen and 29 residues of NK constitute the interface region. However, 9 residues of fibrinogen (THR238, MET264, LYS266, ARG275, THR277, ALA279, ASN308, MET310, and LYS321) and 8 residues of NK (GLY61, SER63, THR99, PHE189, LEU209, TYR217, ASN218, and MET222) are involved in intact binding.

Conclusions

A significant amount of NK enzyme was obtained from Bacillus sp. The docking analysis revealed that the NK and fibrinogen adopt an extended binding pattern and interacts with the crucial residues to exhibit their activity.

     

Microbial fuel cell characterisation and evaluation of <Emphasis Type="Italic">Lysinibacillus macroides</Emphasis> MFC02 electrigenic capability

Microbial fuel cell (MFC) is the most prominent research field due to its capability to generate electricity by utilizing the renewable sources. In the present study, Two MFC designs namely, H type-Microbial fuel cell (HT-MFC) and U type-Microbial fuel cell (UT-MFC) were constructed based on standardized H shaped anode and cathode compartment as well as U shaped anode and cathode compartments, respectively. In order to lower the cost for MFC construction, Pencil graphite lead was used as electrode and salt agar as Proton exchange membrane. Results inferred that newly constructed UT-MFC showed high electron production when compared to the HT-MFC. UT-MFC displayed an output of about 377?±?18.85 mV (millivolts); whereas HT-MFC rendered only 237?±?11.85 mV (millivolts) of power generation, which might be due to the low internal resistance. By increasing the number of cathode in UT-MFC, power production was increased upto 313?±?15.65 mV in Open circuit voltage (OCV). Electrogenic bacteria namely, Lysinibacillus macroides (Acc. No. KX011879) rendered enriched power generation. The attachment of bacteria as a biofilm on pencil graphite lead was analyzed using fluorescent microscope and Scanning Electron Microscope (SEM). Based on our findings, it was observed that UT-MFC has a tendency to produce high electron generation using pencil graphite lead as the electrode material.     

Additive interaction of <Emphasis Type="Italic">Helicoverpa armigera</Emphasis> Nucleopolyhedrovirus and Azadirachtin

Mortality of Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) was higher in the combined treatment of Nucleopolyhedrovirus (NPV) and Azadirachtin (AZA) and mortality was increased when AZA concentration was doubled. Larval mortality decreased as the age of the larvae increased in all the treatments. The time for 100% kill of third instar larvae was significantly reduced to 72 h when AZA (0.1 ppm) was combined with NPV (10³ PIB/ml) when compared to 168 and 120 h for the same dose NPV and AZA individual treatments, respectively. The average leaf disc consumption, consumption index (CI), relative growth rate (RGR), the efficiency of conversion of ingested (ECI) and digested (ECD) food values were drastically reduced in the combined treatment of NPV and AZA than in the individual treatments. Larval as well as pupal durations were significantly extended and the adult longevity and fecundity were significantly reduced in the combined treatment of NPV and AZA. Weight of 14 day old control larvae was 420 mg and it was reduced to 299 and 248 mg after NPV (5 × 10² PIB/ml) and AZA (0.025 ppm) treatments, respectively. The larval weight was drastically decreased to 99 mg after the combined treatment at the same dose. The additive interaction between both the treatments, AZA and NPV, was found to be in a dose dependent manner and were highly compatible in disrupting the survival, feeding and biology of H. armigera.     

Synthesis and antimycobacterial activity of 4-[5-(substituted phenyl)-4, 5-dihydro-3-isoxazolyl]-2-methylphenols

Compounds based on the isoxazoline moiety were screened for their antimycobacterial activity in vitro against Mycobacterium tuberculosis H37R (MTB), and INH (isoniazid) resistant Mycobacterium tuberculosis (INHR-MTB) using the agar dilution method and bactec 460. Among the synthesized compounds, 4-[5-(4-bromophenyl)-4,5-dihydro-3-isoxazolyl]-2-methylphenol (4l) was found to be the most active agent against MTB and INHR-MTB with minimum inhibitory concentration of 0.62 microM. When compared to INH, compound (4l) was 1.12 fold and 3.0 fold more active against MTB and INHR-MTB, respectively.     

SWAP-70 is important for invasive phenotypes of mouse embryo fibroblasts transformed by v-Src

SWAP-70 is a protein involved in actin rearrangement, especially in membrane ruffling. Mouse embryo fibroblasts (MEFs) deficient in SWAP-70 show impaired membrane ruffling and fail to grow in soft agar after transformation by v-Src. Here, we show that v-Src transformed MEFs expressing SWAP-70 are highly invasive. MEFs expressing SWAP-70 or v-Src alone were far less invasive, suggesting that both proteins were required for the cells to be invasive. Expression of both SWAP-70 and v-Src induced constant membrane ruffling, which may cause vigorous cell movement, probably required for invasiveness of the cells. Expression of v-Src alone morphologically transformed MEFs but formed lamellipodia rather than membrane ruffles, suggesting less aggressive nature of the cells compared with those expressing both SWAP-70 and v-Src. These results suggest that v-Src and SWAP-70 act synergistically in the invasion activity of MEFs.     

Epoxyeicosatrienoic acids are part of the VEGF-activated signaling cascade leading to angiogenesis

Cytochrome P-450 (CYP) epoxygenases metabolize arachidonic acid to epoxyeicosatrienoic acid (EET) regioisomers, which activate several signaling pathways to promote endothelial cell proliferation, migration, and angiogenesis. Since vascular endothelial growth factor (VEGF) plays a key role in angiogenesis, we assessed a possible role of EETs in the VEGF-activated signal transduction cascade. Stimulation with VEGF increased CYP2C promoter activity in endothelial cells and enhanced CYP2C8 mRNA and protein expression resulting in increased intracellular EET levels. VEGF-induced endothelial cell tube formation was inhibited by the EET antagonist 14,15-epoxyeicosa-5(Z)-enoicacid (14,15-EEZE), which did not affect the VEGF-induced phosphorylation of its receptor or basic fibroblast growth factor (bFGF)-stimulated tube formation. Moreover, VEGF-stimulated endothelial cell sprouting in a modified spheroid assay was reduced by CYP2C antisense oligonucleotides. Mechanistically, VEGF stimulated the phosphorylation of the AMP-activated protein kinase (AMPK), which has also been linked to CYP induction, and the overexpression of a constitutively active AMPK mutant increased CYP2C expression. On the other hand, a dominant-negative AMPK mutant prevented the VEGF-induced increase in CYP2C RNA and protein expression in human endothelial cells. In vivo (Matrigel plug assay) in mice, endothelial cells were recruited into VEGF-impregnated plugs; an effect that was sensitive to 14,15-EEZE and the inclusion of small interfering RNA directed against the AMPK. The EET antagonist did not affect responses observed in plugs containing bFGF. Taken together, our data indicate that CYP2C-derived EETs participate as second messengers in the angiogenic response initiated by VEGF and that preventing the increase in CYP expression curtails the angiogenic response to VEGF.