Saturnina C. Halos

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito’ groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups.

Philippine population database at nine microsatellite loci for forensic and paternity applications

Allele frequency distributions for a Filipino population from the National Capital Region (NCR) were determined for eight STR loci: HUMF13A01, HUMFES/FPS, HUMvWA, HUMFOLP23, HUMD8S306, HUMCSFIPO, HUMTPOX and HUMTHO1; and a VNTR locus: D1S80. Statistical analysis showed that the nine loci showed no deviations from Hardy-Weinberg and linkage equilibrium rules. The average power of paternity exclusion for the nine loci is 0.9962 and the discriminating power is 1-2 x 10(-9). The data obtained from this study will be used as reference data for forensic DNA typing in the Philippines.

Evaluating DNA tests of motherless cases using a Philippine genetic database

BACKGROUND: In 5 percent of paternity determination cases, only DNA samples from the alleged father and child pairs are tested. The absence of the mothers DNA increases the probability of false paternity inclusions, which affects laboratories that use a limited number of DNA markers. The effect of coincidental matches between unrelated individuals on DNA tests of motherless cases was determined using the Philippine population genetic database of the National Capital Region (NCR).

Micropropagation of Pinus caribaea Morelet

Adventitious shoot formation was induced in excised mature embryos of Pinus caribaea using a modified Murashige and Skoog medium (MSM) supplemented with 6-benzyladenine. The highest frequency (96%) of adventitious bud production was observed when embryos were exposed to 8.9 μM BA for one week prior to transfer to a growth regulator-free medium. Increased BA concentration and longer exposure to BA significantly reduced survival rates of explants. Dilution of the basal medium to 1/4× and 1/8× decreased shoot formation but 1/2× was just as effective as full-strength. Addition of auxins, glyphosate and coconut water to the rooting medium did not improve rooting success beyond that of spontaneous rooting. Sucrose at 1.5% significantly increased rooting of shoots. Plantlets were successfully transferred to the soil after preincubation in liquid medium.

Allele frequencies of eight short tandem repeat loci in three Visayas regional populations of the Philippines.

The Philippine Archipelago, composed of 7,100 islands and more than 70 ethno-linguistic groups, is divided into 15 regions on the basis of geographical, cultural, and political variations. Each region is classified under three major island groups: Luzon, Visayas, and Mindanao. The National Capital Region (NCR) is situated south of Luzon, and its population genetic database has been reported (1). However, because the NCR is geographically separated by sea from the rest of the island groups, and because each island group has its own distinct cultural identity, there is a need to study and compare the genetic composition of other regional populations to that of NCR. The present study reports population data at eight short tandem repeat (STR) loci, namely HUMvWA, HUMCSF1PO, HUMTH01, HUMTPOX, HUMF13A01, HUMFES/ FPS, HUMFOLP23, and D8S306 for the Visayas. Visayas refers to the central group of islands in the Philippine Archipelago, where the major language spoken is the Visaya or Bisaya, instead of the more common Filipino (Tagalog) language. It is composed of three political regions, namely, Region VI, VII, and VIII. Blood samples were collected in Region VI (Aklan, Iloilo, n = 114), Region VII (Cebu, n = 140), and Region VIII (Leyte, n = 92) and blotted on FITZCO FTA™ cards. Genomic DNA was purified according to manufacturers instructions (Flinders Technology, Massachusetts). PCR amplification was performed as described previously (1). Amplified products were detected with the ALFExpress sequencer and using ALFwin and Allelelinks software (Pharmacia Biotech) using automated flourescence technology. Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE) were checked by the Exact Test using the DNA View software (2). Homogeneity tests were performed using Popgene ver 1.32 (3).

Allele frequency distributions of the polymorphic STR loci HUMVWA, HUMFES, HUMF13A01 and the VNTR D1S80 in a Filipino population from Metro Manila

Allele frequency distributions at the short tandem repeat (STR) loci HUMVWA, HUMFES, HUMF13A01 and of the variable number of tandem repeat (VNTR) locus D1S80 were determined in a Filipino population from Metro Manila (103 individuals) by use of the polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis (PAGE). The exact test demonstrated that all four loci had no deviations from Hardy-Weinberg equilibrium (HWE) with the only reservation that the exact test p-value for F13A01 is weak. The discriminating power is 0.82 for D1S80, and the expected exclusion chance is 0.85 for F13A01, 0.83 for FES, and 0.93 for VWA. The observed heterozygosity rates are 0.63 for D1S80, 0.66 for F13A01, 0.67 for FES, and 0.80 for VWA. The exact test for independance between all loci gave a p-value of 0.0195. This is the first time that Filipino population data of DNA loci of forensic importance are reported.

In vitro response of embryos from different provenances of Pinus caribaea var. hondurensis Morelet

The tissue culture response of embryo explants of four fast- and slow-growing provenances of Pinus caribaea var. hondurensis was investigated. Treatments included adventitious bud induction and development with benzyladenine (BA) at different concentrations and exposure periods, root induction with naphthaleneacetic acid (NAA) and indolebutyric acid (IBA) and cullus production with combinations of NAA, 2, 4-dichlorophenoxyacetic acid (2, 4-d), BA and kinetin. Fast-growing provenances produced nodules earlier on the cotyledonary surface, developed shoots earlier from induced buds and produced more shoots per surviving embryo at lower BA concentrations tested compared with slow-growing provenances. On the other hand, calluses of the slow-growing provenance, La Mosquitia, grew faster on media supplemented with cytokinins and auxins compared with those grown on media supplemented with auxin only. This reaction was not observed with fast-growing provenances. It is suggested that cytokinins in fast-growing provenances promted organized development more efficiently than in slow-growing provenances.

Adsorption and uptake of nickel by Chlamydomonas acidophilus

The interest in the study of the interactions between microorganisms and heavy metal ion species is long standing. Many algae, bacteria and fungi are known to be capable of sequestering and accumulating metal species from dilute solutions and concentrating them on or within the structure of microorganisms [1–10]. The adsorption and property of microbes is brought about by the presence of different species of functional groups on the cell surface, such as amines, carboxyl, phosphate, imidazole, hydroxyl, and sulfhydryl [3, 4, 11]. This metal—microbial complexation can be an ion-exchange process, and may be chemical or electrostatic in nature [12]. Using microbes that accumulate and concentrate heavy metals to decontaminate waste-streams emanating from mining operations, refining, electroplating and metal finishing plants may be used to control pollution and retrieve toxic metals from the environment.