The Environment Shapes the Inner Vestibule of LeuT

Human neurotransmitter transporters are found in the nervous system terminating synaptic signals by rapid removal of neurotransmitter molecules from the synaptic cleft. The homologous transporter LeuT, found in Aquifex aeolicus, was crystallized in different conformations. Here, we investigated the inward-open state of LeuT. We compared LeuT in membranes and micelles using molecular dynamics simulations and lanthanide-based resonance energy transfer (LRET). Simulations of micelle-solubilized LeuT revealed a stable and widely open inward-facing conformation. However, this conformation was unstable in a membrane environment. The helix dipole and the charged amino acid of the first transmembrane helix (TM1A) partitioned out of the hydrophobic membrane core. Free energy calculations showed that movement of TM1A by 0.30 nm was driven by a free energy difference of similar to 15 kJ/mol. Distance measurements by LRET showed TM1A movements, consistent with the simulations, confirming a substantially different inward-open conformation in lipid bilayer from that inferred from the crystal structure

INDIAN RESEARCH CONTRIBUTIONS IN THE AQUACULTURE JOURNAL DURING 1972 – 2011: A SCIENTOMETRIC STUDY

The total number of publications contributed by the Indian authors in the Aquaculture journal was 374 during the study period 1972 – 2011. The highest numbers of papers were published during 2002 – 2006 with 103 contributions; especially in 2006 there were 47 contributions. The least number of papers was recorded during 1972 – 1976 with 9 contributions. The percentage of Indian contribution was 2.74. Overall, 1373 authors contributed 374 publications in the Aquaculture journal. Among these, two authored publications were 114 (30.48%), more than that of any other authorship pattern. The degree of collaborations was 0.98. A total of 1373 authors contributed 374 publications with an average of 3.67 authors per paper. 600 (43.70%) authors contributed one publication each. Among the Indian authors, A. S. Sahul Hameed scored first rank with 27 publications. Central Institute of Freshwater Aquaculture (ICAR), Bhubaneswar, Odisha scored first rank with 40 publications among Indian Institutions. Tamil Nadu secured first position with 133 contributions. Original articles were predominant in the Aquaculture journal. The publication of I. Karunasagar et al. (1994) has highest citation both in SCOPUS database (240) and Google Scholar database (380). More research was carried out in the Penaeus monodon with 39 publications

SOS independent survival against mitomycin C induced lethality in a rifampicin-nalidixic acid-resistant mutant of Escherichia coli

A combination of specific rifampicin-resistant (rpoB87) and nalidixic acid-resistant (gyrA87) mutations results in a marked increase in the survival of Escherichia coli against mitomycin C-induced lethality in mutants defective for SOS induction and excision repair. Although the response does not seem to be obligatorily dependent upon the RecA protein, the efficiency is markedly increased in its presence, even in a conventionally inactive form. This response is not elicited against lethality due to ultraviolet radiation or N-methyl-N' -nitro-N-nitrosoguanidine exposure. The combination of rpoB87 and gyrA87 mutations also greatly alleviates post-mitomycin C degradation of DNA under SOS non-inducible conditions. It is proposed that the rpoB subunit of RNA polymerase and gyrA subunit of DNA gyrase could participate in the repair of certain types of DNA damage, such as cross-links, in a mode independent of SOS-regulated excision repair and post-replication repair

The sir locus of Escherichia coli: a gene involved in SOS-independent repair of mitomycin C-induced DNA damage

A Mud1 (lac Apr) insertion has been isolated in a delta (lac)recA+ lexA3(Ind-)rpoB87 gyrA87 mutant of Escherichia coli resulting in a decrease in mitomycin C tolerance and an increase in post-mitomycin C DNA degradation. The mitomycin C sensitivity of the insertion mutant is not further increased by substituting either the rpoB87 or the gyrA mutation by the respective wild-type alleles. However, when both rpoB87 and gyrA87 mutations are replaced by rpoB+ and gyrA+ the strain becomes hypersensitive to mitomycin C. Inactivation of recA in the insertion mutant has no effect on its mitomycin C sensitivity provided both rpoB87 and gyrA87 are present. When either or both of the mutations is/are replaced by the wild-type allele inactivation of recA renders the strain hypersensitive to mitomycin C. The locus of Mud1 (lac Apr) insertion, designated sir (SOS-independent repair), has been mapped between 57 and 61 min on the E. coli linkage map. Expression of the sir gene seems to be constitutive and not enhanced by mitomycin C. These results are discussed in relation to the SOS-independent repair of mitomycin C-induced DNA damage reported earlier

Protein engineering for feedback resistance in 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase

The shikimate pathway delivers aromatic amino acids (AAAs) in prokaryotes, fungi, and plants and is highly utilized in the industrial synthesis of bioactive compounds. Carbon flow into this pathway is controlled by the initial enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS). AAAs produced further downstream, phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), regulate DAHPS by feedback inhibition. Corynebacterium glutamicum, the industrial workhorse for amino acid production, has two isoenzymes of DAHPS, AroF (Tyr sensitive) and AroG (Phe and Tyr sensitive). Here, we introduce feedback resistance against Tyr in the class I DAHPS AroF (AroFcg). We pursued a consensus approach by drawing on structural modeling, sequence and structural comparisons, knowledge of feedback-resistant variants in E. coli homologs, and computed folding free energy changes. Two types of variants were predicted: Those where substitutions putatively either destabilize the inhibitor binding site or directly interfere with inhibitor binding. The recombinant variants were purified and assessed in enzyme activity assays in the presence or absence of Tyr. Of eight AroFcg variants, two yielded > 80% (E154N) and > 50% (P155L) residual activity at 5 mM Tyr and showed > 50% specific activity of the wt AroFcg in the absence of Tyr. Evaluation of two and four further variants at positions 154 and 155 yielded E154S, completely resistant to 5 mM Tyr, and P155I, which behaves similarly to P155L. Hence, feedback-resistant variants were found that are unlikely to evolve by point mutations from the parental gene and, thus, would be missed by classical strain engineering

Influence of thermophilic bacteria on corrosion of carbon steel in hyper chloride environment

The present study evaluates, the oxidation behaviour of thermophilic bacteria Geobacillus thermoparaffinivorans IR2, Geobacillus stearothermophillus IR4 and Bacillus licheniformis MN6 on carbon steel API 5 LX by weight loss, electrochemical studies (impedance and polarization analysis) and surface analysis (X-ray diffraction spectroscopy). The presence of IR2, IR4 and MN6 showed highest corrosion rate (CR) of 2.51, 2.82 and 2.41 mm/year, respectively, than the abiotic control (0.95 mm/year). Whereas in the presence of biocide tetrakis (hydroxymethyl) phosphonium sulphate (THPS) inhibition of the biofilm formation was noticed on the carbon steel and thus reduced the CR of about 0.36, 0.46 and 0.42 mm/year. The electrochemical studies also revealed that higher charge transfer resistance (105 Ω cm 2 ) and solution resistance (6.99 Ω cm 2 ) in the presence of THPS due to the intact protective film on carbon steel surface. Thus, THPS is found to act as an effective candidate towards control microbial influenced corrosion by thermophilic bacteria on carbon steel API5LX in a 36% chloride environment

Confirmation of acute nitrate poisoning differentiating from anthrax in three Indian indigenous cattle

This article reports cases of nitrate poisoning in Indian indigenous cattle breeds comprising two Gir cows aging 4 years each, and one Barugur cow at 1.5 years of age. The cattle with case history of sudden death and oozing of partially clotted blood from the anal opening were brought to the Central University Laboratory (CUL), Center for Animal Health Studies (CAHS), Tamil Nadu Veterinary and Animal Sciences University (TANUVAS) for diagnostic investigation with a suspicion of anthrax. According to anamnesis, all the animals were clinically normal and did not reveal any abnormality on the previous day. The animals were fed with recently harvested sorghum leaves and stalks. Smears examined for anthrax were found negative. Biological test (mice inoculation) for anthrax was also negative. Gross lesions on necropsy examination of the carcases were suggestive of nitrate intoxication. Finally, nitrate intoxication of these cattle was confirmed by chemical and toxicological analysis of fodder, rumen content, aqueous humor, liver, kidney and urine

Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain

<div><p>The human dopamine transporter (hDAT) is located on presynaptic neurons, where it plays an essential role in limiting dopaminergic signaling by temporarily curtailing high neurotransmitter concentration through rapid re-uptake. Transport by hDAT is energized by transmembrane ionic gradients. Dysfunction of this transporter leads to disease states, such as Parkinson’s disease, bipolar disorder or depression. It has been shown that hDAT and other members of the monoamine transporter family exist in oligomeric forms at the plasma membrane. Several residues are known to be involved in oligomerization, but interaction interfaces, oligomer orientation and the quarternary arrangement in the plasma membrane remain poorly understood. Here we examine oligomeric forms of hDAT using a direct approach, by following dimerization of two randomly-oriented hDAT transporters in 512 independent simulations, each being 2 μs in length. We employed the DAFT (docking assay for transmembrane components) approach, which is an unbiased molecular dynamics simulation method to identify oligomers, their conformations and populations. The overall ensemble of a total of >1 ms simulation time revealed a limited number of symmetric and asymmetric dimers. The identified dimer interfaces include all residues known to be involved in dimerization. Importantly, we find that the surface of the bundle domain is largely excluded from engaging in dimeric interfaces. Such an interaction would typically lead to inhibition by stabilization of one conformation, while substrate transport relies on a large scale rotation between the inward-facing and the outward-facing state.</p></div