DNA-based Eye Color Prediction of Pakhtun Population Living in District Swat KP Pakistan

Background: Forensic DNA Phenotyping (FDP) or the prediction of Externally Visible Characteristics (EVCs) from a DNA sample has gained importance in the last decade or so in the forensic community. If and when the traditional forensic DNA typing via Short Tandem Repeats (STR) fails due to the absence of a reference sample, an individual can be traced by a DNA sample using FDP. Amongst the many available EVCs, eye color is one such character that can be predicted by employing previously developed IrisPlex system using Single Nucleotide Polymorphism (SNP) assay. In this study, we applied the IrisPlex system to samples collected from population of District Swat for prediction of eye colours from DNA.Method: Eye colour digital photographs and buccal swab samples were collected from 267 Pakhtun individuals of District Swat. Any person with eye disease was excluded from the study. Genomic DNA was extracted through Phenol-Chloroform extraction method. The amplified SNPs were typed using Multiplexed Single Base Extension (SBE). The genotypes were checked for eye color phenotypes through IrisPlex online tool and correlation were checked between SNPs, Gender, pie score and eye color.Result: Brown eye color was found prevalent as compared to intermediate and blue. Females have highly brown eye color compared to males while males have intermediate and blue. Three SNPs rs12913832 (in the HERC2), rs1393350 (TYR gene), rs1800407 (OCA2 gene) were strongly significant to eye color. Pie score was also significant to eye color and rs12913832 SNP. IrisPlex analysis in 20 individuals of District Swat was performed. The prediction accuracy of IrisPlex for blue or brown was 100% in the studied individuals. However, the IrisPlex tool predicted the intermediate phenotype incorrectly as brown or blue.Conclusion: It is concluded from the data that intermediate eye colour was not predicted accurately, therefore, inclusion of more SNPs in the IrisPlex system is needed to predict intermediate eye colour accurately.Keywords: Eye colour, IrisPlex, SNPs, Multiplex genotyping, DNA, District Swa

Molecular Analysis of Cold Responsive (COR) Genes in Selected Sugarcane and Saccharum spontaneum L.

Background: Sugarcane (Saccharum derived) is an important commercially harvested crop in all parts of the world including tropical and subtropical areas. Saccharum hybrid is the tall perennial true grasses with sweet stalk rich in sucrose and it is the main source of sugar.Methods: Initially, 23 genes differentially expressed during cold stress in other Andropogoneae tribe members were retrieved from NCBI GenBank and were investigated in the genome of selected sugarcane and Saccharum spontaneum L. Samples. Their presence in our samples was analyzed and confirmed through PCR and Agarose Gel Electrophoresis (AGE).Results: Most of these (COR) genes (21/23) were confirmed in cold tolerant cultivars namely, SPSG-394, CP-851491 and Saccharum spontaneum L. while the least number of genes was observed in cold sensitive cultivar namely, CP-77400. Moreover 10 cold responsive genes, namely CBF1, CBF2, CBF3, COR 6.6, COR 78, COR 47, WCOR 80, WCOR14, C17 and 85KDA were sent for sequencing. Nucleotide sequences analysis of selected genes revealed the homology to stress responsive protein. Furthermore, during a conserved domain search, three conserved domains had been detected, namely gypsy transposon, zinc binding for reverse transcriptase and pepsin like aspartate proteases.Conclusion: The analysis of cold responsive genes in sugarcane could help breeders to select cold tolerant sugarcane cultivars through PCR amplification.Keywords:  NCBI; Sugarcane; COR genes; Conserved domain      

Domestic animals’ identification using PCR-RFLP analysis of cytochrome b gene

Background: Species identification is an important process to identify the origin of meat, adulteration and for  cooked and processed meat. The present study was conducted to identify cattle (Bos taurus) and buffalo (Bubalus bubalis) by using mitochondrial cytochrome-b (Cyt-b) gene. Size of the gene is 1140 bp, but we amplified 359 bp that is cleaved by specific restriction endonucleases. The aim of this study was species identification through Cyt-b gene by using PCR-RFLP analysis.Methods: For this study, 55 blood samples were collected from different species of domestic animals. The DNA was extracted from the whole blood through blood extraction kit. The DNA of these samples were amplified through PCR using universal Cyt-b primers. The amplified product was treated with restriction enzymes Alu I. The resultant fragments were viewed on 3.0 % agarose gel.Results: Cyt-b gene was amplified of all included animals. Different bands were observed as compared with 50 bp DNA ladder. Animals were identified on the base RFLP mediated by Alu1 restriction enzyme.Conclusion: We identified domestic animals on the basis of Mitochondrial Cyt-b gene by the process of PCR-RFLP. To identify specific animals through RFLP, a larger sample size and confirmation by gene sequence analysis may be helpful.Keywords: Domestic Animal Identification; Cytochrome b gene; AluI restriction enzyme; PCR-RFLP Analysi

Molecular Profiling of Pakistani Selected Advance Lines of Rice for Amylose Content

Background: Pakistani rice is well-known for its quality. Its consumption increases with the increase in population. The gel consistency (GC) amylose content (AC) and gelatinization temperature (GT) are the most important rice characters, which are associated directly to eating and cooking attributes. But for its good taste and eating quality depends on its endosperm starch quality and quantity. Amylose, a chief determinant of rice attribute, is principally synthesized and controlled by a major gene (Waxy gene) encoding an enzyme called granule bound starch synthase (GBBS).Methods: Current investigation was carried out to characterize advance lines of rice by both conventional and molecular approaches. In present study Waxy gene was identified in advance lines of rice.Results: Show that out of 17 advanced lines, 9 lines were waxy or low amylose, and 1 line was non waxy or high amylose rice because of the presence of 425 bp fragment and 225 bp fragment of Wx gene respectively. For morphological data 14 morphological quantitative traits were studied.Conclusion: Advance lines of rice analyzed during the present investigation showed better grain quality. A number of advance lines contain extra-long and medium slender grains which have intermediate to high gelatinization temperatures. Thus these advance lines are appropriate for the improvement of saline rice. Except one advance line 19 that showed Hard gel consistency and the majority of advance lines fall in the category of soft gel consistency and thus are of excellent quality.Keywords: Rice; Amylose;  Gelatinization; Wx genes      

Monozygotic and Dizygotic Twins Differences in Fingerprint Patterns of Swat District

Background: The identification of individual is important for both legal and humanitarian reasons. It is of great importance because every individual exists as an entity in a society and is dealt with as such by the legal system. The most commonly used method for identification is fingerprinting which relies on the uniqueness of ridges present on thumbs and fingers. These are unique in arrangements and remain constant throughout an individual’s life. Fingerprints of no two individuals are same even if they are twins. The power of discrimination of the basis of fingerprinting is about one in 64 billion. The study was designed to carry out analysis of fingerprints from mono and dizygotic twins and to differentiate them on the basis of fingerprinting.Methods: This was a prospective cross-sectional study carried out among 30 pairs of twins including 17 pair of monozygotic twins and 13 pair of dizygotic twins. After taking an informed expressed consent, the participants were asked to press their individual fingers on the stamp pad. They were asked to then put and roll the stamped finger onto an A4 size paper on which blocks for each finger were already made. Both left and right hands were fingerprinted and with the help of magnifying glass, different types were identified including Arches, Composite type, Loops and Whorls. SPSS software was used for data analysis.Results: There was 7.6% of Arch type, 6.1% of tented arches, 1.5% of plain arches, 62.32% of loops, 6.66% of double loop, and 3.83% of central pocket loop, 44.83% of ulnar loop, 7% of radial loop, 0.83% of accidental loop, 29.93% of whorls, 9% of plain whorl and 20.1% of central the pocket whorl.Conclusion: When the left and right thumbs are compared with each other using eight (8) points, there are matches on the first six (6) points, matching percentage for each of these pairs of fingers is 75%. But when the both fingers were rotated on 180° and compared, the matching percentage was 87.5%. These 8 points fingerprinting can be used to distinguish twins.Keywords: Fingerprint; Identification; Twin; Monozygotic; Dizygotic

Forensic DNA Phenotyping

The basis for DNA analysis used in forensic research is the concept that everyone, excluding monozygotic twins, shares a genetic makeup. By directly comparing the genetic profile of short tandem repeats obtained from biological samples of unknown origin to a reference sample profile, DNA collected from biological samples can individually identify this material. The requirement for a reference sample for comparison is one of the main drawbacks of this method. Studies looking at the connection between specific polymorphisms and specific phenotypic traits are multiplying, and the results are encouraging for forensic sciences. Externally visible characteristics (EVCs), such as skin color, eye color, hair color, height, facial features, and male baldness pattern, can be inferred from biological samples for forensic purposes. This technique is called “forensic DNA phenotyping” (FDP). Therefore, without the necessity for a reference sample for comparative analysis, FDP offers additional information about the subject to which a specific biological sample belongs. So that this new technology does not encourage segregation or ethnic persecution of certain population groups, several ethical and legal considerations need to be made. Despite this, using these techniques to guide investigations and identify both suspects and victims has helped in a number of actual incidents

Sibling and non-sibling fingerprints comparison of Pakhtun population of Swat district, KP, Pakistan

Background: Fingerprint and other ridges are considered to be the best forensic science tool for identification of humans, alive or dead, and even for decomposed bodies. These fingerprint ridges exhibit various static features throughout life which reflect the person biology. This branch gained immense importance since the past few decades in congenital abnormality. This study was to carry out fingerprints analysis of sibling and non-sibling for differentiation and gender identification.Methods: A total of 80 pairs of fingerprints (1600 prints) were collected from persons aged 15 to 30 years using rolling method. Out of which 20 pairs were brother-brother, 20 were sister-sister, 20 were brother-sister and 20 Pairs were random. Each fingerprint was analyzed for the gender identification on the basis of minutiae, ridge density and types. All the fingerprints were analysed using ACE-V method. After comparison SPSS software was used for further analysis.Results: Our result showed that the types of fingerprints identified was whorl (50%) followed by loop (45.25%), arch (4.5%) and 0.25% of the accidental type. The dominant type was whorl while accidental was the least common type of fingerprints. Statistical analysis showed that between the groups, brother-brother and sister-sister was significant while rest of the groups was not significant. Moreover, greater ridge density was observed in female as compared to male.Conclusion: It is concluded that the sibling fingerprints had greater similarity as compared to non-sibling, however both male and female fingerprints were significantly different in term of ridges density. This study may be useful in crime scene investigation.Keywords: Forensics; Fingerprint ridge density; Fingerprint type; Gender identification

Unveiling <i>Lathyrus aphaca</i> L. as a Newly Identified Host for Begomovirus Infection: A Comprehensive Study

The Begomovirus genus of the family Geminiviridae comprises the largest group of geminiviruses. Begomoviruses are transmitted by the whitefly complex (Bemisia tabaci) and infect dicotyledonous plants in tropical and subtropical regions. The list of begomoviruses is continuously increasing as a result of improvements in the methods for identification, especially from weed plants, which are considered a source of new viruses and reservoirs of economically important viruses but are often neglected during diversity studies. Lathyrus aphaca L. weed plants (yellow-flowered pea) with varicose veins and discoloration of the leaves were found. Amplified genomic DNA through rolling circular amplification was subjected to PCR analysis for the detection of the viral genome and associated DNA-satellites (alphasatellites and betasatellites). A full-length sequence (2.8 kb) of a monopartite begomovirus clone was determined; however, we could not find any associated DNA satellites. The amplified full-length clone of Rose leaf curl virus (RoLCuV) reserved all the characteristics and features of an Old World (OW) monopartite begomovirus. Furthermore, it is the first time it has been reported from a new weed host, yellow-flowered pea. Rolling circle amplification and polymerase chain reaction analysis of associated DNA satellites, alphasatellite, and betasatellite, were frequently accomplished but unable to amplify from the begomovirus-infected samples, indicating the presence of only monopartite Old World begomovirus. It is observed that RoLCuV has the capability to infect different hosts individually without the assistance of any DNA satellite component. Recombination in viruses is also a source of begomovirus infection in different hosts