96 research outputs found
Development of phoA transposon construct for studies on the molecular pathogenesis of Mycoplasma gallisepticum
No full text© 2014 Dr. Indu Somasundara PanickerMycoplasma gallisepticum is a major poultry pathogen and causes severe economic loss to the poultry industry. Many of the pathogenic avian mycoplasmas have been sequenced but the role of many genes in pathogenesis, the mechanisms of regulation of transcription, translation and gene expression are not fully understood in mycoplasmas. Hence development of molecular tools for genetic analysis, improved reporter gene systems and cloning vectors are necessary for advances in molecular studies of mycoplasmas.
This thesis describes the use of the alkaline phosphatase gene (phoA) from Escherichia coli as a reporter in mycoplasmas. The promoter region of the gene of elongation factor Tu (ltuf) and leader sequence from vlhA1.1 gene from M. gallisepticum with phoA gene were introduced into a transposon to generate the pISM2062.2ltufacyphoA plasmid (pTAP). The plasmid was used to transform M. gallisepticum to enable expression of functional PhoA as a lipoprotein on the cell surface. The pTAP vector will be a valuable and versatile tool for studies analysing regulatory effects of promoter regions, gene expression using different translational start codons and leader sequences and also for optimising expression of foreign antigens.
The translational start codon usage in Mycoplasma spp. was analysed from their annotated genomes, and the predominant translational initiation codon in Mycoplasma spp. was found to be the AUG codon. The study then assessed the effect of an alternate translational start codon on expression of a reporter protein in M. gallisepticum using the pTAP vector. The relative efficiency of translation was significantly higher with the GUG codon than with the AUG codon, suggesting that it was a more efficient translational initiation codon.
This result prompted a similar approach to investigate if there is any preference for specific residues and any targeting role attributable to different residues following the cysteine at amino terminus in lipoproteins of M. gallisepticum. Threonine is the most prevalent +2 amino acid in lipoproteins in M. gallisepticum. Replacement of the threonine at the +2 position in the PhoA lipoprotein with the hydrophobic amino acids resulted in higher levels of expression of alkaline phosphatase whereas hydrophilic amino acids at the +2 position resulted in lower levels of expression of alkaline phosphatase. This is the first study to examine the role of the +2 amino acid in mycoplasma lipoproteins and establish a difference in M. gallisepticum compared to Gram-positive and Gram-negative bacteria. These studies will also have value in optimising the design of recombinant lipopeptides and lipoprotein genes in mycoplasmas to ensure maximal levels of expression and stability on the cell surface.
Thus this study has demonstrated the utility of phoA as a reporter gene in M. gallisepticum, developed a phoA vector that could be used to study gene regulation and facilitate optimisation of expression of heterologous antigens on the mycoplasma cell surface
The Tale of a Choreographer, Her student, River and an endangered Heritage: Indu Mitha’s Qaseeda-i-Ilm of Jamal/ “An Ode to Wisdom and Beauty”
No full textChoreographing in Pakistan since the 50’s, the country’s senior most 90+ years young classical dance maestro Indu Mitha has made trailblazing contributions within the Kalakshtera Bharata Natyam using North Indian music, interesting and contemporary content, while also producing more tableau forms of dance.
In one of her recent solo pieces in the later style, titled “Qaseeda-i-Ilm of Jamal” or “An Ode to Wisdom and Beauty” Indu engages with symbolisms of a Hindu goddess of knowledge and Aesthetics_Saraswati and pays tribute to a forgotten dried up river of the same name. Indu Mitha allows the author, for whom and on whose body the dance is made, to bring in the forgotten river in her engagement with people’s histories of the land of present-day Pakistan and eventually facilitates her accessing of and embodying a pluralistic space of inter faith harmony which was occluded
Toxocara seroprevalence in Canada—Climate, environment and culture
No full textHuman infection with larvae of canine and feline roundworms belonging to the genus Toxocara can lead to devastating visceral, neural or ocular larvae migrans disease. However, such overt disease represents a fraction of cases. Far more common is covert toxocariasis, a less severe, but clinically symptomatic form of disease, and those who are exposed to infective larvae and seroconvert, but appear to be asymptomatic. Canada represents a unique epidemiological environment for Toxocara infection and exposure. Although the freezing conditions of the vast Arctic Tundra region of the North are thought unlikely to support the lifecycle of Toxocara spp., exposure and seroconversion does occur in people belonging to Inuit communities of this region. Further south, in the sub-Arctic of northern Quebec and Saskatchewan, there is a higher seroprevalence in many Canadian First Nations communities. The epidemiology of these infections is different to that seen in the non-Indigenous communities of the Humid Continental region. Poverty and climate play a major part in the risk of Toxocara seropositive status in Canada, but other factors such as unique cultural practices, population density of humans and reservoir hosts, and contact with wildlife are also factors in exposure and subsequent seroconversion in Canadian communities.
This review discusses previous Toxocara seroprevalence studies performed in Canada, summarizes the data for domestic and wild animal reservoir hosts of Toxocara canis, Toxocara cati, Toxocara vitulorum and the closely related helminth, Toxascaris leonina. It also discusses how the unique and varied aspects of climate, culture and environment impacts human Toxocara exposure in Canada
A novel load balanced energy conservation approach in WSN using biogeography based optimization
No full textClustering sensor nodes is an effective technique to reduce energy consumption of the sensor nodes and maximize the lifetime of Wireless sensor networks. Balancing load of the cluster head is an important factor in long run operation of WSNs. In this paper we propose a novel load balancing approach using biogeography based optimization (LB-BBO). LB-BBO uses two separate fitness functions to perform load balancing of equal and unequal load respectively. The proposed method is simulated using matlab and compared with existing methods. The proposed method shows better performance than all the previous works implemented for energy conservation in WSN
A short note on Chinae Hans Muscuovy ducks in Bengal, India
No full textSummaryMuscuovy ducks (Cairina moschata) are popular as a source of poultry meat. Reports on availability of Muscovies (in the free range system of management) in the eastern region of Indu is lacking. In the West Bengal state of Indu two strains of Muscovies have been identified, the strains resemble Black Muscuovy L 303 and White Muscuovy ducks. Ironically they are known as Chinae haras (Chinese duck). Presently a detailed study is being conducted by the author and is being used to develop a strain of broader duck (mule duck) in the region. Reports on availability of Muscovies in this part of the subcontinent are lacking.</jats:p
Determining epitope specificity of T-cell receptors with Transformers
No full textTransformers have dominated the field of natural language processing due to their competency in learning complex relationships within a sequence. Reusing a pre-trained transformer for a downstream task is known as Trans-fer learning. Transfer learning restricts the transformer to a fixed vocabulary; modification in transformer implementation will extend the utility of the transformer. Implementing transformers for complex biological problems can be beneficial in addressing the complexities in the biological sequences. One such biological problem is to capture the specificity of diverse T-cell repertoire to the unique antigens (i.e., immunogenic pathogenic elements). Using transformers to assess the relationship between T-cell receptors and antigen at the sequence level can provide us with better insights into the processes involved in these precise and complex immune responses in humans and murine. In this work, we determined the specificity of multiple TCR to unique antigens by classifying the CDR3 re-gions of TCR sequences to a particular antigen. For this problem, we used three pre-trained auto-encoder (ProtBERT, ProtALBERT, ProtELECTRA) and one pre-trained auto-regressive (ProtXLNet) transformer model wherein, to adapt to the challenges of the complex biological problem at hand, we implemented modifications in the transformers chosen here. We used the VDJdb to obtain the biological data for training and testing the selected transformers. After pre-processing data, we predicted the TCR specificity for 25 antigens (classes) in a multi-class setting. Transformers could predict the specificity of TCRs to an antigen with just the CDR3 sequences from the TCRB chain (weighted F1 score 0.48), the data that was unseen by the transformers. With additional features incorpo-rated, i.e., gene names for TCRs, the weighted F1 improved to 0.55 in the best performing transformer. We demon-strated that different modifications in transformers recognized out-of-vocabulary features with these results. When com-paring the AUC from the transformer model to other previously developed methods for the same biological problem such as TCRGP, TCRDist and DeepTCR, we observed that the transformers outperformed the previously available methods. To exemplify, the MCMV epitope family that suffered from restricted performance in TCRGP due to fewer training samples (~100 samples) showed 10% improvement in AUC with transformers under similar training samples. Transformer's proficiency in learning from fewer data combined with holistic modifications in transformers implementations proves that we can extend its capabilities to explore other biological settings. Further ingenuity in utiliz-ing the full potential of transformers either through attention head visualization or introducing additional features can fur-ther extend T-cell research avenues.Computer Science | Data Science and Technolog
Synthesis of non-hydrazine solution processed Cu2(ZnSn)S4 thin films for solar cells applications
No full textDoes History Matter Only When it Matters Little? The Case of City-Indu try Location
No full textWhen will an industry subject to agglomeration economies move from an old, high-cost site to a new, low-cost site? It is argued that history, in the form of sunk costs resulting from the operation of many firms at a site, creates a first-mover disadvantage that can prevent relocation. It is demonstrated that developers of industrial parks can partly overcome this inertia through discriminatory pricing of land over time, and empirical evidence is provided that they actually engage in such behavior. It is also shown that other aspects of developer land-sale strategy can be a source of information on the nature of interfirm externalities.
The Effect of an Alternate Start Codon on Heterologous Expression of a PhoA Fusion Protein in Mycoplasma gallisepticum.
No full textWhile the genomes of many Mycoplasma species have been sequenced, there are no collated data on translational start codon usage, and the effects of alternate start codons on gene expression have not been studied. Analysis of the annotated genomes found that ATG was the most prevalent translational start codon among Mycoplasma spp. However in Mycoplasma gallisepticum a GTG start codon is commonly used in the vlhA multigene family, which encodes a highly abundant, phase variable lipoprotein adhesin. Therefore, the effect of this alternate start codon on expression of a reporter PhoA lipoprotein was examined in M. gallisepticum. Mutation of the start codon from ATG to GTG resulted in a 2.5 fold reduction in the level of transcription of the phoA reporter, but the level of PhoA activity in the transformants containing phoA with a GTG start codon was only 63% of that of the transformants with a phoA with an ATG start codon, suggesting that GTG was a more efficient translational initiation codon. The effect of swapping the translational start codon in phoA reporter gene expression was less in M. gallisepticum than has been seen previously in Escherichia coli or Bacillus subtilis, suggesting the process of translational initiation in mycoplasmas may have some significant differences from those used in other bacteria. This is the first study of translational start codon usage in mycoplasmas and the impact of the use of an alternate start codon on expression in these bacteria
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