Amit Kumar Subudhi

Amit Kumar Subudhi
King Abdullah University of Science and Technology | KAUST · Department of Environmental Science and Engineering

Ph.D, BITS, Pilani

About

58
Publications
25,523
Reads
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491
Citations
Introduction
Hardworking, Humble, Team player, Target oriented.
Additional affiliations
November 2015 - present
King Abdullah University of Science and Technology
Position
  • PostDoc Position
March 2010 - April 2013
Birla Institute of Technology and Science Pilani
Position
  • CSIR-Senior Research Fellow
August 2007 - February 2010
Birla Institute of Technology and Science Pilani
Position
  • Research Assistant
Education
January 2008 - May 2015
Birla Institute of Technology and Science Pilani
Field of study
  • Molecular Parasitology
July 2004 - June 2006
Alagappa University
Field of study
  • Biotechnology
July 1999 - June 2002
Sambalpur University
Field of study
  • Zoology (Hons), Botany, Chemistry

Publications

Publications (58)
Article
Full-text available
Malaria in humans is caused by six species of . Plasmodium parasites, of which the nuclear genome sequences for the two . Plasmodium ovale spp., . P. ovale curtisi and . P. ovale wallikeri, and . Plasmodium malariae have not yet been analyzed. Here we present an analysis of the nuclear genome sequences of these three parasites, and describe gene fa...
Article
Systems biology approaches that are based on gene expression and bioinformatics analysis have been successful in predicting the functions of many genes in Plasmodium falciparum, a protozoan parasite responsible for most of the deaths due to malaria. However, approaches that can provide information about the biological processes that are active in t...
Article
Full-text available
PP1 is a conserved eukaryotic serine/threonine phosphatase that regulates many aspects of mitosis and meiosis, often working in concert with other phosphatases, such as CDC14 and CDC25. The proliferative stages of the malaria parasite life cycle include sexual development within the mosquito vector, with male gamete formation characterized by an at...
Preprint
Full-text available
Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. The availability of patient hospital records is crucial for linking the genomic sequence information to virus function during the course of infections. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia...
Preprint
Full-text available
PP1 is a conserved eukaryotic serine/threonine phosphatase that regulates many aspects of mitosis and meiosis, often working in concert with other phosphatases, such as CDC14 and CDC25. The proliferative stages of the parasite life cycle include sexual development within the mosquito vector, with male gamete formation characterized by an atypical r...
Article
Full-text available
Cell cycle transitions are generally triggered by variation in the activity of cyclin-dependent kinases (CDKs) bound to cyclins. Malaria-causing parasites have a life cycle with unique cell-division cycles, and a repertoire of divergent CDKs and cyclins of poorly understood function and interdependency. We show that Plasmodium berghei CDK-related k...
Article
Full-text available
Cell cycle transitions are generally triggered by variation in the activity of cyclin-dependent kinases (CDKs) bound to cyclins. Malaria-causing parasites have a life cycle with unique cell-division cycles, and a repertoire of divergent CDKs and cyclins of poorly understood function and interdependency. We show that Plasmodium berghei CDK-related k...
Article
Full-text available
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit daily rhythms...
Preprint
Full-text available
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 hours (depending on the species), suggesting a circadian basis to the asexual cell cycle, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches using rodent and human malaria parasites, we reveal that: (i)...
Article
Full-text available
Background The transcriptional regulation that occurs in malaria parasites during the erythrocytic stages of infection can be studied in vivo with rodent malaria parasites propagated in mice. Time-series transcriptome profiling commonly involves the euthanasia of groups of mice at specific time points followed by the extraction of parasite RNA from...
Article
Full-text available
Background: There are several techniques to analyse copy number variation in both research and clinical settings, such as whole genome amplification (sWGA), SNP arrays and one of the most commonly used techniques, array based comparative genomic hybridization (aCGH). In the latter, copy number comparison is obtained between differentially labelled...
Preprint
Full-text available
The transcriptional regulation occurring in malaria parasites during the clinically important life stages within host erythrocytes can be studied in vivo with rodent malaria parasites propagated in mice. Time-series transcriptome profiling commonly involves the euthanasia of groups of mice at specific time points followed by the extraction of paras...
Article
Due to the rise of drug resistant forms of tuberculosis there is an urgent need for novel antibiotics to effectively combat these cases and shorten treatment regimens. Recently, drug screens using whole cell analyses have been shown to be successful. However, current high-throughput screens focus mostly on stricto sensu life-death screening that gi...
Article
Full-text available
Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for the...
Data
Parasite rhythms are inverted in hosts fed in the day versus night. The proportion of parasites at early trophozoite, mid trophozoite and late trophozoite stages (ring stages are presented in Fig 3B) according to the feeding treatment of their hosts (light fed mice, red, and dark fed mice, blue). White and grey bars indicate lights on and lights of...
Data
Rhythmicity and timing in parasite developmental stages in light and dark fed mice. Results from analyses testing whether each parasite stage displays circadian rhythms (i.e. a rhythm with a period, or duration, of 24 hours) and centre of gravity (CoG) estimates for each rhythm (mean ± SEM), comparisons of CoG for parasites in light (LF) and dark (...
Data
Parasites suffer cost of mismatch to the host’s SCN rhythms. (A) Minimum red blood cell density and (B) parasite density. Sampling occurred on day 9 post infection for red blood cell density and day 6 post infection for parasite density. Means (± SEM, N≥12) is plotted for each treatment group (matched infections, grey; mismatched infections, light...
Data
Parasites remain synchronous during rescheduling. (A) The amplitude of rhythmic parasite stages in light (LF) and dark (DF) fed mice does not vary significantly between feeding treatments, suggesting parasites do not lose synchrony when rescheduling to the phase of host feeding rhythms. Amplitude is calculated as the difference between the minimum...
Data
Feeding mice in the day time does not affect body weight, pre- or post-treatment. Mean ± SEM body weight for N = 10 mice per treatment group. All mice were weighed before feeding time manipulation (pre) and after recovering from infections (post). All mice gained weight over the 4 weeks of the experiment, and weight did not differ significantly at...
Data
Rhythmic cytokines and chemokines during matched and mismatched malaria infections. Median fluorescence intensity (used a proxy for cytokine concentration in pg/mol) for each infection and fitted curves for each treatment group (infections matched to the circadian rhythm of the host, green, and mismatched by 6 hours, orange). Sampling occurred ever...
Data
Body temperature and locomotor activity rhythms are disrupted by feeding mice in the day time. Comparisons of the centre of gravity (CoG) times for each rhythm (body temperature and locomotor activity). All relevant comparisons are indicated as subscript letters (e.g. comparing (a) with (a)). a and b comparisons are non-significant, whereas c-f are...
Data
No significant differences between treatment groups in the densities of parasites and the virulence of infections. (A) Red blood cell density and (B) asexual parasite density for each treatment group (light fed mice, red, and dark fed mice, blue). Sampling occurred twice per day from days 0–5 and 9–16 post infection and 6 hourly during days 6–8 (in...
Data
Ring stage rhythms remain synchronous during rescheduling to the host rhythm. Mean ± SEM (N = 4 per time point) for parasites matched to the SCN rhythms of the host (green, undergo schizogony around ZT 17, indicated by green dashed line) and parasites mismatched by 6 hours to the circadian rhythm of the host (orange, undergo schizogony around ZT 23...
Data
Divergence of parasite rhythms in light and dark fed mice. Parasite stage proportions observed in light (LF) and dark (DF) fed mice diverge as infections progress (significant day by feeding treatment interaction, χ2(9,14) = 235.26, p<0.0001). Rings are presented as the focal phase marker (see Fig 4) and all rhythmic stages are analysed here (mean...
Data
Blood glucose concentration before and after feeding in light and dark fed mice. Fig 6 reveals steep increases in blood glucose concentration before and after the main bout of feeding occurs in each group (i.e. just after lights on in light fed, LF, mice and lights off in dark fed, DF, mice, mean ± SEM). Comparison of glucose concentration at ZT0/Z...
Preprint
Full-text available
Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for the...
Article
Full-text available
High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best op...
Article
Full-text available
Malarial parasite P. falciparum, an apicomplexan protozoan has a 23.3 MB nuclear genome and encodes ~ 5600 transcripts.The genetic diversity of the parasite within and across geographical zones is a challenge to gene expression studies which are essential for understanding of disease process, outcome and developing markers for diagnostics and progn...
Article
Systems biology approaches that are based on gene expression and bioinformatics analysis have been successful in predicting the functions of many genes in Plasmodium falciparum, a protozoan parasite responsible for most of the deaths due to malaria. However, approaches that can provide information about the biological processes that are active in t...
Article
Full-text available
Natural Antisense transcripts (NATs) have been detected in many organisms and shown to regulate gene expression. Similarly, NATs have also been observed in malaria parasites with most studies focused on P. falciparum. There were no reports on presence of NATs in P. vivax, which has also been shown to cause severe malaria like P. falciparum, until a...
Article
Full-text available
Antisense transcription is pervasive among biological systems and one of the products of antisense transcription is natural antisense transcripts (NATs). Emerging evidences suggest that they are key regulators of gene expression. With the discovery of NATs in Plasmodium falciparum, it has been suggested that these might also be playing regulatory r...
Article
Full-text available
Background & objectives: Description of severe vivax malaria and mixed species infection requires good clinical study. The present study was undertaken to evalute the characteristics of severe malaria patients in Bikaner, northwest India. Methods: This prospective study included 539 admitted adult patients of severe malaria (Plasmodium falciparu...
Article
Full-text available
The 28S rRNA gene was amplified and sequenced from P. falciparum and P. vivax isolates collected from northwest India. Based upon the sequence diversity of the Plasmodium 28SrRNA gene in comparison with its human counterpart, various nested polymerase chain reaction (PCR) primers were designed from the 3R region of the 28SrRNA gene and evaluated on...
Article
Full-text available
The 28S rRNA gene was amplified and sequenced from P. falciparum and P. vivax isolates collected from northwest India. Based upon the sequence diversity of the Plasmodium 28SrRNA gene in comparison with its human counterpart, various nested polymerase chain reaction (PCR) primers were designed from the 3R region of the 28SrRNA gene and evaluated on...
Article
Full-text available
To evaluate microscopy, OptiMAL® and multiplex PCR for the identification of Plasmodium falciparumm (P. falciparum) and Plasmodium vivax (P. vivax) from the field isolates of Bikaner, Rajasthan (Northwest India). In this study, a multiplex PCR (P. falciparum and P. vivax) was further developed with the incorporation of Plasmodium malariae (P. malar...
Article
Plasmodium vivax is the predominant species of the human malaria parasite present in the Indian subcontinent. There have been recent reports on Chloroquine (CQ) resistance and severe manifestations shown by P. vivax from different regions of the world including India. This study focuses on Bikaner, India where during the last few years there have b...
Article
The apicomplexan parasite Plasmodium vivax is responsible for causing more than 70% of human malaria cases in Central and South America, Southeastern Asia and the Indian subcontinent. The rising severity of the disease and the increasing incidences of resistance shown by this parasite towards usual therapeutic regimens have necessitated investigati...
Article
Full-text available
The occurrence, relation and magnitude of thrombocytopenia in different species of malaria are not clearly defined. This study included 1,064 patients admitted with malaria to study thrombocytopenia (platelet count <150,000 /cumm) in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) mono infection and mixed infection (Pf + Pv). The species diagn...
Article
Full-text available
Malaria causes a worldwide annual mortality of about a million people. Rapidly evolving drug-resistant species of the parasite have created a pressing need for the identification of new drug targets and vaccine candidates. By developing fractionation protocols to enrich parasites from low-parasitemia patient samples, we have carried out the first e...

Questions

Questions (5)
Question
Hi all,
I have list of genes with their phase of expression. Frequency of phase distributions shows two distinct phase clusters. I would like to calculate the mean of each phase clusters (circular phase) What I understand is simple averaging is not right for this type of directional data.
It would be great if someone can help me to calculate the mean circular phase of phase clusters. what I have with me is phase of expression of each gene and frequency of each phase.
Question
I am analyzing a set of 203 intra-population sequences of a gene using DnaSP and getting the Tajima's D and Fu and Li's D and F statistic values in negative with P values being significant P< 0.02. Can any one help me in interpreting the biological significance of this? 
Question
I am using Affymetrix GeneChip Human Genome U133 Plus 2.0 Array for human PBMCs transcription profiling. I am a new user of this array platform. According to my knowledge the probe sets have been classified into 4 types i.e probe set with _at, _s_at, _a_at and _x_at.
Should I consider only the probe sets with ID ending in _at, or can I consider the other group of probe sets too? The other question is if a gene is represented by multiple probe sets, then should I average the expression values of the multiple probe sets representing the same gene?
Question
I am planning to detect antisense transcripts for some of the selected genes for which antisense transcripts have been detected by the strand specific microarray experiments conducted by me. Can anyone suggest the best protocols to use to conduct strand specific realtime/RT pcr to validate my findings. The experiment is focused on detecting antisense transcripts from the protozoan parasite Plamsodium falciparum.

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