Open Access Case Report

Pivotal Role of High Sensitivity Variant Calls and Confirmation Methods for Next-Generation Sequencing Findings: A Case Report

Mario Gorenjak, Gregor Jezernik, Katja Repnik, Natasa Marcun Varda, Uros Potocnik

Annual Research & Review in Biology, Page 1-5
DOI: 10.9734/ARRB/2018/40312

Aims: The aim of this case report is to demonstrate the importance of prioritization of sensitivity over specificity, coupled with additional confirmation by using standard methods. Next-generation sequencing has revolutionized genetic research as it has allowed sequencing of human genomes within days. Generated raw sequencing data are manipulated using bioinformatic approaches for variant detection. Variant discovery should be performed on appropriately pre-processed data with the aforementioned prioritization of sensitivity over specificity.

Presentation of the Case: Here, we report a case of a low quality variant call, emitted due to prioritization of sensitivity over specificity. This call was found to be a causative variant for the patient’s phenotype. DNA extracted from peripheral venous blood of a young female with encephalopathy was sequenced on a MiSeq apparatus. The obtained and analyzed call set emitted a low quality heterozygous insertion with a high probability of a false negative call. Annotation revealed a known pathogenic insertion rs758946412 with a frameshift consequence flagged with “Early infantile epileptic encephalopathy type 9” in ClinVar. The emitted insertion was validated and confirmed by using SANGER sequencing and RFLP.                

Conclusion: In the presented case, the variant could have easily been missed without the prioritization of sensitivity over specificity. Furthermore, the presented case also demonstrates the importance of additional methods for confirmation of NGS calls that do not meet the thresholds.

Open Access Original Research Article

Oxidative Stress and Antioxidant Defenses: With Special Reference to Oral Lesions

Parul Tripathi, Alka Yadu, Aditi Singh

Annual Research & Review in Biology, Page 1-7
DOI: 10.9734/ARRB/2018/39454

Background: Oxidative stress is involved in the pathogenesis of various lifestyle-related diseases, including malignancies. The body naturally produces antioxidants as a means of defending itself against these free radicals which neutralize them, thereby rendering them harmless to other cells. There is a close relation between oxidative stress and all aspects of cancer, from carcinogenesis to the tumor-bearing state, from treatment to its prevention.

Aim: The present study was aimed to estimate the plasma levels of antioxidant enzymes and molecules in cases of oral lesion patients.

Study Design and Methodology: A case control study was designed in Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow campus. A total of fifty histopathologically proven oral lesion cases (leukoplakia, erythroplakia, lichen planus and oral submucous fibrosis patients) were taken for the study. Their blood samples were collected and plasma was subjected to evaluation of oxidative stress markers. Control group consisted of equal number of healthy subjects. The data is expressed as mean±SD. Student -t test was applied for significance of the biochemical parameters.

Results: The results have demonstrated that levels of catalase, myeloperoxidase, reduced glutathione glutathione reductase and glutathione peroxidase are decreased whereas those of malondialdehyde and nitric oxide have increased in the oral lesions patient group as compared to controls.

Conclusion: Oxidative stress has been shown to be an important indicator in case of oral cancer. Similar findings in pre-malignant oral lesions can be correlated in establishing the role of oxidative stress in initiation and conversion of premalignant lesions into malignant ones.

Open Access Original Research Article

Assessment of Tolerance Potential of Cassava (Manihot esculenta Crantz) Genotypes to Whiteflies (Bemisia tabaci) in East Cameroon

A. Mogo, M. W. C. Tagong, E. L. Ngonkeu Mangaptche, J. N. Fomekong, Fotso ., N. Woin

Annual Research & Review in Biology, Page 1-12
DOI: 10.9734/ARRB/2018/35074

Cassava is a basic staple in Cameroon whose industrialization faces major constraints especially those related to the management of whiteflies (Bemisia tabaci), a vector of the African cassava mosaic virus (ACMV). This work has as main objective to identify the tolerance of some cassava genotypes to whiteflies and to undertake an agro-morphological characterization of infected cultivars to the ACMV. Data were collected from September to November 2015 on six cultivars: Five improved (TMS92/0057, TMS92/0067, TMS92/0326, TMS96/1414 and TME419) and one local (NTOLO), on a young plot (three months old) and mature plot (six months age). Adult whiteflies were counted on the underside of the last leaves of one apex and for nymphs; they were counted randomly between the ninth and fourteenth leaves. Three cultivars (TMS96/1414; TMS92/0057 and TMS92/0067) ramified early with a large number of apices. For the younger plants (three months old), three cultivars (NTOLO, TMS96/1414 and TMS92/0326) harbored the largest number of adult whiteflies, whereas two others (TMS92/0326 and TME 419) were the most attacked by the ACMD. Younger plants (3 Months old) were most vulnerable to ACMV attack (r = 0,307** with whiteflies population), while the older ones (at 6 Months), represent early senescence period for short-cycle genotypes.

Open Access Original Research Article

Management of Eastern Brown and Tiger Snake Envenomation in Domestic Animals in South Australia

Madeleine J. Wright, Suong N. T. Ngo

Annual Research & Review in Biology, Page 1-12
DOI: 10.9734/ARRB/2018/40513

Aims: The aims of this study were to examine the key important clinical features in domestic animals (e.g. dogs and cats) accompanying envenomation by eastern brown or tiger snakes in South Australia, to establish whether routine use of snake venom detection kits (SVDKs) is a useful diagnostic approach for identifying offending snake species and help to improve animal’s condition and survival.

Methodology: Clinical records from 155 dogs and cats, with suspected or confirmed snake envenomation were collected from two veterinary practices in South Australia. Chi-square analysis was used to compare patient outcome with diagnostic method, and descriptive analysis were undertaken to compare features between the envenomation cases.

Results: Brown snakes were responsible for 97% of cases, with the remaining 3% due to tiger snakes. The most common presenting signs were recumbency and hind limb paresis. Patients were 20% less likely to survive when diagnosis of the offending snake species was made by means other than the use of a SVDK. An inconclusive result occurred approximately 14% of the time when using a SVDK. The overall survival rate for cases that were treated was 81% in dogs and 92% in cats.

Conclusion: Species-specific snake diagnosis using a SVDK will lead to improved patient outcome, however care is required when performing and interpreting the test due to a high proportion of contradictory results obtained.

Open Access Original Research Article

Growth, Body Composition and Resistance to Aeromonas hydrophila Challenge in Juvenile African Catfish (Clarias gariepinus) Fed Diets Supplemented with Spirulina (Arthrospira platensis)

Nor Fatihah Mohd Nasir, Mohammad Noor Azmai Amal, Hishamuddin Omar, Ahmad Ismail, Nurul Shaqinah Nasruddin

Annual Research & Review in Biology, Page 1-15
DOI: 10.9734/ARRB/2018/40870

This study evaluates the growth, body composition, and resistance to Aeromonas hydrophila challenge in juvenile African catfish (Clarias gariepinus) fed diets supplemented with spirulina (Arthrospira platensis). Five experimental diets containing different percentages of locally grown dried spirulina (0, 1, 3, 5 and 7%) were fed daily to catfish juveniles at 5% of their body weight. The growth and body composition of the catfish were determined up to 90 days of the study period. At day 91, the catfish were intraperitoneally injected with 10CFU/ml of virulent A. hydrophila. Generally, the growth and body composition of the catfish in spirulina inclusion groups showed no significant difference with the control group. The survival rate following A. hydrophila challenge was significantly low in the control group compared to all of the other treatment groups. After the challenge trial, only the white blood cell count value was significantly higher in all of the groups supplemented with spirulina compared to the control group. We concluded that the locally grown spirulina do not improve growth and body composition, but it increased the catfish resistance towards A. hydrophila infection.