A noninvasive molecular approach: exploiting species-locus-specific PCR primers in defeating numts and DNA cross-contamination of cercopithecidae

The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts)

A review on environmental DNA (eDNA) metabarcoding markers for wildlife monitoring research

Environmental DNA or eDNA utilizes traceable genetic materials in the environment for monitoring the presence of organisms in a given area and it is now gaining popularity as an alternative for traditional monitoring methods. Thus, the selection of genetic markers is crucial for identification of species in wildlife monitoring. This paper aims to review several DNA markers which are appropriate and reliable for detection of organisms from the environmental samples. We performed systematic literature search from SCOPUS database to review all molecular markers of eDNA. This study focuses on the importance of markers selection which can be utilized by next-generation sequencing (NGS) for biodiversity monitoring. Cytochrome C oxidase Subunit I (COI) are noted as the most widely used marker in metabarcoding research for detection of targeted species

Enhancement and reproducibility of high quality factor, one-dimensional photonic crystal/photonic wire (1D PhC/PhW) microcavities

Background: The production of compact and multi-functional photonic devices has become a topic of major research activity in recent years. Devices have emerged that can be used for functional requirements in high speed optical data processing, filtering, nonlinear optical functions such as all-optical switching - and many other applications. The combination of photonic crystal (PhC) structures consisting of a single row of holes embedded in a narrow photonic wire (PhW) waveguide realised in high index-contrast materials is a possible contender for provision of a range of compact devices on a single chip. This trend has been motivated by the availability of a silicon technology that can support monolithic integration to form fully functional devices on CMOS chips. Results: We have successfully demonstrated experimentally an enhancement of the quality factor of a one-dimensional (1D) photonic crystal/photonic wire (PhC/PhW) microcavity that can exhibit resonance quality factor (Q-factor) values as high as 800,000 - together with a low modal volume of approximately 0.5 (λ/n)3. These results are based on the use of a mode matching approach previously used for device design - through the engineering of tapered hole sections within and outside the cavity - and were achieved without removing the silica cladding layer below the silicon waveguide core. The simulation results obtained in this case also agree with the experimental results obtained. Conclusions: In this work we have demonstrated that the mode matching, as light enters the photonic crystal structure, can be further enhanced through the use of careful fine tuning of the third hole, t3 of the tapered hole region outside the cavity. The Q-factor value obtained was approximately four times greater than that achieved in our previous work on a similar structure

The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers

Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality

Observation and study of baryonic B decays: B -> D(*) p pbar, D(*) p pbar pi, and D(*) p pbar pi pi

We present a study of ten B-meson decays to a D(*), a proton-antiproton pair, and a system of up to two pions using BaBar's data set of 455x10^6 BBbar pairs. Four of the modes (B0bar -> D0 p anti-p, B0bar -> D*0 p anti-p, B0bar -> D+ p anti-p pi-, B0bar -> D*+ p anti-p pi-) are studied with improved statistics compared to previous measurements; six of the modes (B- -> D0 p anti-p pi-, B- -> D*0 p anti-p pi-, B0bar -> D0 p anti-p pi- pi+, B0bar -> D*0 p anti-p pi- pi+, B- -> D+ p anti-p pi- pi-, B- -> D*+ p anti-p pi- pi-) are first observations. The branching fractions for 3- and 5-body decays are suppressed compared to 4-body decays. Kinematic distributions for 3-body decays show non-overlapping threshold enhancements in m(p anti-p) and m(D(*)0 p) in the Dalitz plots. For 4-body decays, m(p pi-) mass projections show a narrow peak with mass and full width of (1497.4 +- 3.0 +- 0.9) MeV/c2, and (47 +- 12 +- 4) MeV/c2, respectively, where the first (second) errors are statistical (systematic). For 5-body decays, mass projections are similar to phase space expectations. All results are preliminary.Comment: 28 pages, 90 postscript figures, submitted to LP0

Search for rare quark-annihilation decays, B --> Ds(*) Phi

We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context of the Standard Model, these decays are expected to be highly suppressed since they proceed through annihilation of the b and u-bar quarks in the B- meson. Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected with the BABAR detector at SLAC. We find no evidence for these decays, and we set Bayesian 90% confidence level upper limits on the branching fractions BF(B- --> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid Communications