Biology subjects

Tripathi, A.

Publications and source records attributed to Tripathi, A..

5 recordsLinked to original sources

bioRxiv2018

The Cuon Enigma: Genome survey and comparative genomics of the endangered Dhole (Cuon alpinus)

The Asiatic wild dog is an endangered monophyletic canid restricted to Asia; facing threats from habitat fragmentation and other anthropogenic factors. Dholes have unique adaptations as compared to other wolf-like canids for large litter size (larger number of mammae) and hypercarnivory making it evolutionarily notable. Over evolutionary time, dhole and the subsequent divergent wild canids have lost coat patterns found in African wild dog. Here we report the first high coverage genome survey of Asiatic wild dog and mapped it with African wild dog, dingo and domestic dog to assess the structural variants. We generated a total of 124.8 Gb data from 416140921 raw read pairs and retained 398659457 reads with 52X coverage and mapped 99.16% of the clean reads to the three reference genomes. We identified ~13553269 SNVs, ~2858184 InDels, ~41000 SVs, ~1854109 SSRs and about 1000 CNVs. We compared the annotated genome of dingo and domestic dog with dhole genome sequence to understand the role of genes responsible in pelage pattern, dentition and mammary glands. Positively selected genes for these phenotypes were looked for SNP variants and top ranked genes for coat pattern, dentition and mammary glands were found to play a role in signalling and developmental pathways. Mitochondrial genome assembly predicted 35 genes, 11 CDS and 24 tRNA. This genome information will help in understanding the divergence of two monophlyletic canids, Cuon and Lycaon, and the evolutionary adaptations of dholes with respect to other canids.

genomics↗

bioRxiv2018

Petrobactin protects against oxidative stress and enhances sporulation efficiency in Bacillus anthracis Sterne

Bacillus anthracis is a gram-positive bacillus that under conditions of environmental stress, such as low nutrients, can convert from a vegetative bacillus to a highly durable spore that enables long-term survival. The sporulation process is regulated by a sequential cascade of dedicated transcription factors but requires key nutrients to complete, one of which is iron. Iron acquisition by the iron-scavenging siderophore petrobactin is the only such system known to be required for vegetative growth of B. anthracis in iron-depleted conditions, e.g., in the host. However, the extent to which petrobactin is involved in spore formation is unknown. This work shows that efficient in vitro sporulation of B. anthracis requires petrobactin, that the petrobactin biosynthesis operon (asbA-F) is induced prior to sporulation, and that petrobactin itself is associated with spores. Petrobactin is also required for both oxidative stress protection during late stage growth and wild-type levels of sporulation in sporulation medium. When considered with the petrobactin-dependent sporulation in bovine blood also described in this work, these effects on in vitro growth and sporulation suggest that petrobactin is required for B. anthracis transmission via the spore during natural infections in addition to its key functions during active anthrax infections.\n\nImportanceBacillus anthracis causes the disease anthrax, which is transmitted via its dormant, spore phase. However, converting from bacilli to spore is a complex, energetically costly process that requires many nutrients including iron. B. anthracis requires the siderophore petrobactin to scavenge iron from host environments. We show that in the Sterne strain, petrobactin is required also for efficient sporulation, even when ample iron is available. The petrobactin biosynthesis operon is expressed during sporulation, and petrobactin is biosynthesized during growth in high iron sporulation medium but instead of being exported, the petrobactin remains intracellular to protect against oxidative stress and improve sporulation. It is also required for full growth and sporulation in blood (bovine), an essential step for anthrax transmission between mammalian hosts.

microbiology↗

bioRxiv2018

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages

A major aspect of our daily lives is the need to acquire, store and prepare our food. Storage and preparation can have drastic effects on the compositional chemistry of our foods, but we have a limited understanding of the temporal nature of processes such as storage, spoilage, fermentation and brewing on the chemistry of the foods we eat. Here, we performed a temporal analysis of the chemical changes in foods during common household preparations using untargeted mass spectrometry and novel data analysis approaches. Common treatments of foods such as home fermentation of yogurt, brewing of tea, spoilage of meats and ripening of tomatoes altered the chemical makeup through time, through both chemical and biological processes. For example, brewing tea altered its composition by increasing the diversity of molecules, but this change was halted after 4 min of brewing. The results indicate that this is largely due to differential extraction of the material from the tea and not modification of the molecules during the brewing process. This is in contrast to the preparation of yogurt from milk, spoilage of meat and the ripening of tomatoes where biological transformations directly altered the foods molecular composition. Comprehensive assessment of chemical changes using multivariate statistics showed the varied impacts of the different food treatments, while analysis of individual chemical changes show specific alterations of chemical families in the different food types. The methods developed here represent novel approaches to studying the changes in food chemistry that can reveal global alterations in chemical profiles and specific transformations at the chemical level.\n\nO_LSTHighlightsC_LSTO_LIWe created a reference data set for tomato, milk to yogurt, tea, coffee, turkey and beef.\nC_LIO_LIWe show that normal preparation and handling affects the molecular make-up.\nC_LIO_LITea preparation is largely driven by differential extraction.\nC_LIO_LIFormation of yogurt involves chemical transformations.\nC_LIO_LIThe majority of meat molecules are not altered in 5 days at room temperature.\nC_LI

biochemistry↗

bioRxiv2016

A Pilot Study: Development of a Reference Spatiotemporal Gait Data Set for Indian Subjects.

1.Interpretation of pathological gait has, for decades, offered insight into amputee anomalies and diseases such as cerebral palsy. Gait analysis has been actively used at the Bhagwan Mahaveer Viklang Sahatya Samiti for such purposes. The normative gait data used to compare data obtained from amputees, however, has been collected from laboratories under dissimilar conditions, skewing interpretation. Spatiotemporal gait parameters were extractedfrom 43 male Indian subjects using a 7.5m walkway and the BTS Bioengineering GAITLAB setup. Working under the hypothesis that a lack of cross-cultural validity was somewhat responsible for variations in normative gait, we attempted to develop a region-specific data set for use at the headquarters of the Jaipur Foot Organization Bhagwan Mahaveer Viklang Sahatya Samiti (BMVSS). Stratified random sampling was used to recruit subjects and measures were taken to ensure minimal effects of extraneous variables. Statistical analysis was performed on obtained data using one-way analysis of variance (ANOVA) to gauge the effect age and ethnicity had on normative values of the parameters investigated. We found statistically significant p-values for a few spatiotemporal parameters in the analysis of variance for both age and ethnicity. While the results were much less significant than initially hypothesized, the study proved an efficient way to create a normative gait data set exclusively for use at the gait laboratory of the Jaipur Foot Organization, thereby eliminating potential erroneous interpretation of pathological gait when comparing said gait to normative gait data obtained in laboratories under dissimilar conditions.

bioengineering↗

bioRxiv2016

A Probabilistic Approach to the Detection and Diagnosis of Obstructive Sleep Apnea and Its Environmental Factors Using Chest Movement Analysis, Recursive Noise Reduction and Machine Learning Algorithms.

1In a novel approach to diagnose Obstructive Sleep Apnea, electronic components, such as an Arduino Mega, a Bluetooth Transceiver, an accelerometer, and a air-quality sensor, were put together to create a wearable that would detect the frequency of apnea events, detect and diagnose the disorder, and sound an alarm when necessary. A primary consideration was to make the mechanism accessible and affordable, and in doing so, lower the cases of Obstructive Sleep Apnea that go undiagnosed due to the cost and inconvenience associated with the traditional diagnosis method--a Polysomnogram. Bluetooth capability was an additional consideration so that the device would transmit data directly to an android smartphone, eliminating the need for an additional output mechanism. The total cost of the device, quite surprisingly, did not exceed $30, and therein rendered the device an accessible, affordable mechanism for diagnosis. Tests of the device on diagnosed patients yielded data consistent with the diagnosis, with a few false positives as a result of the excessive sensitivity of the sensors.

biophysics↗