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Digital data for quick response (QR) codes of alkalophilic Bacillus pumilus to identify and to compare bacilli isolated from Lonar Crator Lake, India.

ABSTRACT: Microbiologists are routinely engaged isolation, identification and comparison of isolated bacteria for their novelty. 16S rRNA sequences of Bacillus pumilus were retrieved from NCBI repository and generated QR codes for sequences (FASTA format and full Gene Bank information). 16SrRNA were used to generate quick response (QR) codes of Bacillus pumilus isolated from Lonar Crator Lake (19° 58' N; 76° 31' E), India. Bacillus pumilus 16S rRNA gene sequences were used to generate CGR, FCGR and PCA. These can be used for visual comparison and evaluation respectively. The hyperlinked QR codes, CGR, FCGR and PCA of all the isolates are made available to the users on a portal https://sites.google.com/site/bhagwanrekadwad/. This generated digital data helps to evaluate and compare any Bacillus pumilus strain, minimizes laboratory efforts and avoid misinterpretation of the species.

SUBMITTER: Rekadwad BN

PROVIDER: S-EPMC4838933 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Digital data for Quick Response (QR) codes of thermophiles to identify and compare the bacterial species isolated from Unkeshwar hot springs (India).

Project description:16S rRNA sequences of morphologically and biochemically identified 21 thermophilic bacteria isolated from Unkeshwar hot springs (19°85'N and 78°25'E), Dist. Nanded (India) has been deposited in NCBI repository. The 16S rRNA gene sequences were used to generate QR codes for sequences (FASTA format and full Gene Bank information). Diversity among the isolates is compared with known isolates and evaluated using CGR, FCGR and PCA i.e. visual comparison and evaluation respectively. Considerable biodiversity was observed among the identified bacteria isolated from Unkeshwar hot springs. The hyperlinked QR codes, CGR, FCGR and PCA of all the isolates are made available to the users on a portal https://sites.google.com/site/bhagwanrekadwad/.

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Can the implementation of electronic surveys with quick response (QR) codes be useful in the COVID-19 era?

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Utility of QR codes in biological collections.

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Microbiology of Lonar Lake and other soda lakes.

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Bacterial diversity of lonar soda lake of India.

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When quick response codes didn't do the trick.

Project description:Medical education programs in the United States or Canada comply with the Liaison Committee on medical education standards to ensure their graduates provide proficient medical care. One standard includes student development as a lifelong learner. The competency of lifelong learning is developed through self-directed activities such as students evaluating their learning objectives and resources without external help.Quick response (QR) codes were the technological tools introduced in a traditional medical institution to enhance students' self-directed initiative to tap resources. Relevant lecture objectives and other information such as supplemental discipline content, reading assignments and web-based link resources were embedded into codes and 'pasted' onto all pages of their course PDF handouts. It was anticipated that most students had access to smart phones to conveniently scan the codes and retrieve the information.However, an in-class survey conducted showed that only 30% of the students found the QR codes useful. Further questioning revealed that some students just didn't know how to use the codes or didn't think the information embedded was worth the effort to decrypt. Although students were tech-savvy in the social and entertainment realms, they were not adept in the use of technology for educational purposes.QR codes presented several theoretical, pedagogical advantages to enhance experiential and self-directed learning. However, implementation among students, in a traditional classroom, required prior instructions on usage. Student feedback was also imperative when introducing novel, innovative tools like QR codes.

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Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake.

Project description:We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10-20 mg carbon L-1) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2-3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.

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Draft genome sequence of Cecembia lonarensis strain LW9T, isolated from Lonar Lake, a haloalkaline lake in India.

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A SNP panel and online tool for checking genotype concordance through comparing QR codes.

Project description:In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.

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Improving Inpatient Surveys: Web-Based Computer Adaptive Testing Accessed via Mobile Phone QR Codes.

Project description:BackgroundThe National Health Service (NHS) 70-item inpatient questionnaire surveys inpatients on their perceptions of their hospitalization experience. However, it imposes more burden on the patient than other similar surveys. The literature shows that computerized adaptive testing (CAT) based on item response theory can help shorten the item length of a questionnaire without compromising its precision.ObjectiveOur aim was to investigate whether CAT can be (1) efficient with item reduction and (2) used with quick response (QR) codes scanned by mobile phones.MethodsAfter downloading the 2008 inpatient survey data from the Picker Institute Europe website and analyzing the difficulties of this 70-item questionnaire, we used an author-made Excel program using the Rasch partial credit model to simulate 1000 patients' true scores followed by a standard normal distribution. The CAT was compared to two other scenarios of answering all items (AAI) and the randomized selection method (RSM), as we investigated item length (efficiency) and measurement accuracy. The author-made Web-based CAT program for gathering patient feedback was effectively accessed from mobile phones by scanning the QR code.ResultsWe found that the CAT can be more efficient for patients answering questions (ie, fewer items to respond to) than either AAI or RSM without compromising its measurement accuracy. A Web-based CAT inpatient survey accessed by scanning a QR code on a mobile phone was viable for gathering inpatient satisfaction responses.ConclusionsWith advances in technology, patients can now be offered alternatives for providing feedback about hospitalization satisfaction. This Web-based CAT is a possible option in health care settings for reducing the number of survey items, as well as offering an innovative QR code access.

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