Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation

Short tandem repeat (STR) typing continues to be the primary workhorse in forensic DNA profiling. Therefore, the present review discusses the prominent role of STR marker in criminal justice system. All over the world, deoxyribonucleic acid (DNA) profiling provides evidence that may be used to convict criminals, as an irrefutable proof of wrongful convictions, invaluable links to the actual perpetrators of crimes, and could also deter some offenders from committing more serious offences. Clearly, DNA profiling tools have also aided forensic scientists to re-evaluate old cases that were considered closed as a result of inadequate evidence. In carrying out this review, a comprehensive electronic literature search using PubMed, ScienceDirect, Google Scholar and Google Search were used, and all works meeting the subject matter were considered, including reviews, retrospective studies, observational studies and original articles. Case reports presented here, further demonstrates the crucial role of forensic DNA profiling in mitigating and providing compelling evidence for the resolution of crimes. For case report 1, there was a 100% match between the DNA recovered from the items found in the crime scene, and the suspect's DNA sample collected via buccal swab following 15 STR loci examination. Case report 2 further highlights the indispensable contribution of DNA database in solving crime. Therefore, it has become very necessary for developing countries like Nigeria to develop a national DNA database and make policies and legislatures that will further expand and enable the practice of forensic genetics, particularly DNA profiling.

Seasonality of temperate forest photosynthesis and daytime respiration

Terrestrial ecosystems currently offset one-quarter of anthropogenic carbon dioxide (CO2) emissions because of a slight imbalance between global terrestrial photosynthesis and respiration. Understanding what controls these two biological fluxes is therefore crucial to predicting climate change. Yet there is no way of directly measuring the photosynthesis or daytime respiration of a whole ecosystem of interacting organisms; instead, these fluxes are generally inferred from measurements of net ecosystem-atmosphere CO2 exchange (NEE), in a way that is based on assumed ecosystem-scale responses to the environment. The consequent view of temperate deciduous forests (an important CO2 sink) is that, first, ecosystem respiration is greater during the day than at night; and second, ecosystem photosynthetic light-use efficiency peaks after leaf expansion in spring and then declines, presumably because of leaf ageing or water stress. This view has underlain the development of terrestrial biosphere models used in climate prediction and of remote sensing indices of global biosphere productivity. Here, we use new isotopic instrumentation to determine ecosystem photosynthesis and daytime respiration in a temperate deciduous forest over a three-year period. We find that ecosystem respiration is lower during the day than at night-the first robust evidence of the inhibition of leaf respiration by light at the ecosystem scale. Because they do not capture this effect, standard approaches overestimate ecosystem photosynthesis and daytime respiration in the first half of the growing season at our site, and inaccurately portray ecosystem photosynthetic light-use efficiency. These findings revise our understanding of forest-atmosphere carbon exchange, and provide a basis for investigating how leaf-level physiological dynamics manifest at the canopy scale in other ecosystems.

Diel patterns of autotrophic and heterotrophic respiration among phenological stages

Improved understanding of the links between aboveground production and allocation of photosynthate to belowground processes and the temporal variation in those links is needed to interpret observations of belowground carbon cycling processes. Here, we show that combining a trenching manipulation with high-frequency soil respiration measurements in a temperate hardwood forest permitted identification of the temporally variable influence of roots on diel and seasonal patterns of soil respiration. The presence of roots in an untrenched plot caused larger daily amplitude and a 2-3 h delay in peak soil CO2 efflux relative to a root-free trenched plot. These effects cannot be explained by differences in soil temperature, and they were significant only when a canopy was present during the growing season. This experiment demonstrated that canopy processes affect soil CO2 efflux rates and patterns at hourly and seasonal time scales, and it provides evidence that root and microbial processes respond differently to environmental factors.

Soil respiration at mean annual temperature predicts annual total across vegetation types and biomes

Soil respiration (SR) constitutes the largest flux of CO(2) from terrestrial ecosystems to the atmosphere. However, there still exist considerable uncertainties as to its actual magnitude, as well as its spatial and interannual variability. Based on a reanalysis and synthesis of 80 site-years for 57 forests, plantations, savannas, shrublands and grasslands from boreal to tropical climates we present evidence that total annual SR is closely related to SR at mean annual soil temperature (SR(MAT)), irrespective of the type of ecosystem and biome. This is theoretically expected for non water-limited ecosystems within most of the globally occurring range of annual temperature variability and sensitivity (Q(10)). We further show that for seasonally dry sites where annual precipitation (P) is lower than potential evapotranspiration (PET), annual SR can be predicted from wet season SR(MAT) corrected for a factor related to P/PET. Our finding indicates that it can be sufficient to measure SR(MAT) for obtaining a well constrained estimate of its annual total. This should substantially increase our capacity for assessing the spatial distribution of soil CO(2) emissions across ecosystems, landscapes and regions, and thereby contribute to improving the spatial resolution of a major component of the global carbon cycle.

Environmental Parameters Regulating Gaseous Nitrogen Losses from Two Forested Ecosystems via Nitrification and Denitrification

Gaseous N losses from disturbed and reference forested watersheds at the Coweeta Hydrologic Laboratory in western North Carolina were studied by in situ N(2)O diffusion measurements and laboratory incubations throughout a 10-month period. Soil temperature, percent base saturation, and water-filled pore space accounted for 43% of the variation in in situ N(2)O diffusion measurements. Laboratory incubations distinguished the gaseous N products of nitrification and denitrification. Nitrifying activity, ambient NO(3), and nitrification N(2)O were positively correlated with percent base saturation. However, differences between watersheds in soil N substrate caused by presence of leguminous black locust in the disturbed watershed were confounded with differences in soil acidity. Denitrification was most strongly affected by soil moisture, which in turn was determined by precipitation events and slope position. Gaseous N losses from well-drained midslope and toeslope landscape positions appeared to be minor relative to other N transformations. Favorable conditions for denitrification occurred at a poorly drained site near the stream of the disturbed watershed. Laboratory incubations revealed high rates of NO(3) reduction in these soils. We speculate that the riparian zone is a major site of depletion of NO(3) from the soil solution via denitrification.

A genetic linkage map for Arctic char (Salvelinus alpinus): evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents

We constructed a genetic linkage map for Arctic char (Salvelinus alpinus) using two backcrosses between genetically divergent strains. Forty-six linkage groups (expected = 39-41) and 19 homeologous affinities (expected = 25) were identified using 184 microsatellites, 129 amplified fragment length polymorphisms (AFLPs), 13 type I gene markers, and one phenotypic marker, SEX. Twenty-six markers remain unlinked. Female map distance (9.92 Morgans) was substantially higher than male map distance (3.90 Morgans) based on the most complete parental information (i.e., the F1 hybrids). Female recombination rates were often significantly higher than those of males across all pairwise comparisons within homologous chromosomal segments (average female to male ratios within families was 1.69:1). The female hybrid parent had significantly higher recombination rates than the pure strain female parent. Segregation distortion was detected in four linkage groups (4, 8, 13, 20) for both families. In family 3, only the largest fish were sampled for genotyping, suggesting that segregation distortion may represent regions possessing influences on growth. In family 2, almost all cases showing segregation distortion involved markers in the female hybrid parent.

Emissions of nitrous oxide and nitric oxide from soils of native and exotic ecosystems of the Amazon and Cerrado regions of Brazil

This paper reviews reports of nitrous oxide (N2O) and nitric oxide (NO) emissions from soils of the Amazon and Cerrado regions of Brazil. N2O is a stable greenhouse gas in the troposphere and participates in ozone-destroying reactions in the stratosphere, whereas NO participates in tropospheric photochemical reactions that produce ozone. Tropical forests and savannas are important sources of atmospheric N2O and NO, but rapid land use change could be affecting these soil emissions of N oxide gases. The five published estimates for annual emissions of N2O from soils of mature Amazonian forests are remarkably consistent, ranging from 1.4 to 2.4 kg N ha(-1) year(-1), with a mean of 2.0 kg N ha(-1) year(-1). Estimates of annual emissions of NO from Amazonian forests are also remarkably similar, ranging from 1.4 to 1.7 kg N ha(-1) year(-1), with a mean of 1.5 kg N ha(-1) year(-1). Although a doubling or tripling of N2O has been observed in some young (< or = 2 years) cattle pastures relative to mature forests, most Amazonian pastures have lower emissions than the forests that they replace, indicating that forest-to-pasture conversion has, on balance, probably reduced regional emissions slightly (<10%). Secondary forests also have lower soil emissions than mature forests. The same patterns apply for NO emissions in Amazonia. At the only site in Cerrado where vegetation measurements have been made N2O emissions were below detection limits and NO emissions were modest (approximately 0.4 kg N ha(-1) year(-1)). Emissions of NO doubled after fire and increased by a factor of ten after wetting dry soil, but these pulses lasted only a few hours to days. As in Amazonian pastures, NO emissions appear to decline with pasture age. Detectable emissions of N2O have been measured in soybean and corn fields in the Cerrado region, but they are modest relative to fluxes measured in more humid tropical agricultural regions. No measurements of NO from agricultural soils in the Cerrado region have been made, but we speculate that they could be more important than N2O emissions in this relatively dry climate. While a consistent pattern is emerging from these studies in the Amazon region, far too few data exist for the Cerrado region to assess the impact of land use changes on N oxide emissions.

Toward automated nucleic acid enzyme selection

Methods for automation of nucleic acid selections are being developed. The selection of aptamers has been successfully automated using a Biomek 2000 workstation. Several binding species with nanomolar affinities were isolated from diverse populations. Automation of a deoxyribozyme ligase selection is in progress. The process requires eleven times more robotic manipulations than an aptamer selection. The random sequence pool contained a 5' iodine residue and the ligation substrate contained a 3' phosphorothioate. Initially, a manual deoxyribozyme ligase selection was performed. Thirteen rounds of selection yielded ligators with a 400-fold increase in activity over the initial pool. Several difficulties were encountered during the automation of DNA catalyst selection, including effectively washing bead-bound DNA, pipetting 50% glycerol solutions, purifying single strand DNA, and monitoring the progress of the selection as it is performed. Nonetheless, automated selection experiments for deoxyribozyme ligases were carried out starting from either a naive pool or round eight of the manually selected pool. In both instances, the first round of selection revealed an increase in ligase activity. However, this activity was lost in subsequent rounds. A possible cause could be mispriming during the unmonitored PCR reactions. Potential solutions include pool redesign, fewer PCR cycles, and integration of a fluorescence microtiter plate reader to allow robotic 'observation' of the selections as they progress.

Glycobiology of Plasmodium falciparum

The human malaria parasite, Plasmodium falciparum, has as its only glycoconjugate GPI anchors. These structures, present in essentially all parasite surface proteins, are associated with disease pathology. In contrast, the parasite depends for essential recognition events on saccharides associated with host cell glycoproteins and proteoglycans.

Control of cation concentrations in stream waters by surface soil processes in an Amazonian watershed

The chemical composition of ground waters and stream waters is thought to be determined primarily by weathering of parent rock. In relatively young soils such as those occurring in most temperate ecosystems, dissolution of primary minerals by carbonic acid is the predominant weathering pathway that liberates Ca2+, Mg2+ and K+ and generates alkalinity in the hydrosphere. But control of water chemistry in old and highly weathered soils that have lost reservoirs of primary minerals (a common feature of many tropical soils) is less well understood. Here we present soil and water chemistry data from a 10,000-hectare watershed on highly weathered soil in the Brazilian Amazon. Streamwater cation concentrations and alkalinity are positively correlated to each other and to streamwater discharge, suggesting that cations and bicarbonate are mainly flushed from surface soil layers by rainfall rather than being the products of deep soil weathering carried by groundwater flow. These patterns contrast with the seasonal patterns widely recognized in temperate ecosystems with less strongly weathered soils. In this particular watershed, partial forest clearing and burning 30 years previously enriched the soils in cations and so may have increased the observed wet season leaching of cations. Nevertheless, annual inputs and outputs of cations from the watershed are low and nearly balanced, and thus soil cations from forest burning will remain available for forest regrowth over the next few decades. Our observations suggest that increased root and microbial respiration during the wet season generates CO2 that drives cation-bicarbonate leaching, resulting in a biologically mediated process of surface soil exchange controlling the streamwater inputs of cations and alkalinity from these highly weathered soils.

Developmental stage-specific biosynthesis of glycosylphosphatidylinositol anchors in intraerythrocytic Plasmodium falciparum and its inhibition in a novel manner by mannosamine

Glycosylphosphatidylinositols (GPIs) are the major glycoconjugates in intraerythrocytic stage Plasmodium falciparum. Several functional proteins including merozoite surface protein 1 are anchored to the cell surface by GPI modification, and GPIs are vital to the parasite. Here, we studied the developmental stage-specific biosynthesis of GPIs by intraerythrocytic P. falciparum. The parasite synthesizes GPIs exclusively during the maturation of early trophozoites to late trophozoites but not during the development of rings to early trophozoites or late trophozoites to schizonts and merozoites. Mannosamine, an inhibitor of GPI biosynthesis, inhibits the growth of the parasite specifically at the trophozoite stage, preventing further development to schizonts and causing death. Mannosamine has no effect on the development of either rings to early trophozoites or late trophozoites to schizonts and merozoites. The analysis of GPIs and proteins synthesized by the parasite in the presence of mannosamine demonstrates that the effect is because of the inhibition of GPI biosynthesis. The data also show that mannosamine inhibits GPI biosynthesis by interfering with the addition of mannose to an inositol-acylated GlcN-phosphatidylinositol (PI) intermediate, which is distinctively different from the pattern seen in other organisms. In other systems, mannosamine inhibits GPI biosynthesis by interfering with either the transfer of a mannose residue to the Manalpha1-6Manalpha1-4GlcN-PI intermediate or the formation of ManN-Man-GlcN-PI, an aberrant GPI intermediate, which cannot be a substrate for further addition of mannose. Thus, the parasite GPI biosynthetic pathway could be a specific target for antimalarial drug development.

Glycosylation and proteolytic processing of 70 kDa C-terminal recombinant polypeptides of Plasmodium falciparum merozoite surface protein 1 expressed in mammalian cells

The cDNAs that encode the 70 kDa C-terminal portion of Plasmodium falciparum merozoite surface protein 1 (MSP-1), with or without an N-terminal signal peptide sequence and C-terminal glycosylphosphatidylinositol (GPI) signal sequence of MSP-1, were expressed in mammalian cell lines via recombinant vaccinia virus. The polypeptides were studied with respect to the nature of glycosylation, localization, and proteolytic processing. The polypeptides derived from the cDNAs that contained the N-terminal signal peptide were modified with N -linked high mannose type structures and low levels of O -linked oligosaccharides, whereas the polypeptides from the cDNAs that lacked the signal peptide were not glycosylated. The GPI anchor moiety is either absent or present at a very low level in the polypeptide expressed from the cDNA that contained both the signal peptide and GPI signal sequences. Together, these data establish that whereas the signal peptide of MSP-1 is functional, the GPI anchor signal is either nonfunctional or poorly functional in mammalian cells. The polypeptides expressed from the cDNAs that contained the signal peptide were proteolytically cleaved at their C-termini, whereas the polypeptides expressed from the cDNAs that lacked the signal peptide were uncleaved. While the polypeptide expressed from the cDNA containing both the signal peptide and GPI anchor signal was truncated by approximately 14 kDa at the C-terminus, the polypeptide derived from the cDNA with only the signal peptide was processed to remove approximately 6 kDa, also from the C-terminus. Furthermore, the polypeptides derived from cDNAs that lacked the signal peptide were exclusively localized intra-cellularly, the polypeptides from cDNAs that contained the signal peptide were predominantly intracellular, with low levels on the cell surface; none of the polypeptides was secreted into the culture medium to a detectable level. These results suggest that N -glycosylation alone is not sufficient for the efficient extracellular transport of the recombinant MSP-1 polypeptides through the secretory pathway in mammalian cells.

MUC1 upregulation by ethanol

MUC1 is a glycoprotein and its expression is altered in breast cancer. Mucin protects epithelia from the external hostile environment. The expression of mucin changes when epithelia come in contact with toxic agents such as ethanol. Previously, we characterized the expression and regulation of tracheo-bronchial mucin (TBM) gene. In the present study, we studied the effect of ethanol on the gene encoding mammary gland mucin MUC1 and observed that ethanol regulates MUC1 expression at the transcription level. Ethanol enhanced the expression of MUC1 mRNA in a dose- and time-dependent manner in MCF-7 cells. At 100 mM concentration (a concentration reported to be present in alcoholics), ethanol induced a three to five-fold increase in mucin transcription as determined by nuclear run on analysis. This concentration of ethanol does not affect the half-life of MUC1 mRNA.

Positive feedbacks in the fire dynamic of closed canopy tropical forests

The incidence and importance of fire in the Amazon have increased substantially during the past decade, but the effects of this disturbance force are still poorly understood. The forest fire dynamics in two regions of the eastern Amazon were studied. Accidental fires have affected nearly 50 percent of the remaining forests and have caused more deforestation than has intentional clearing in recent years. Forest fires create positive feedbacks in future fire susceptibility, fuel loading, and fire intensity. Unless current land use and fire use practices are changed, fire has the potential to transform large areas of tropical forest into scrub or savanna.

Cloning and characterization of the merozoite surface antigen 1 gene of Plasmodium berghei

Merozoite surface antigen 1 (MSA1) is a promising candidate for vaccine development against malaria parasites. Here, we report the complete nucleotide sequence of the gene encoding the precursor to this major surface antigen of Plasmodium berghei strain ANKA using cDNA library screening and polymerase chain reaction techniques. A single open reading frame of 5,376 basepairs encoding a protein with a calculated molecular mass of 197 kD was defined. The protein contains a putative signal peptide of 19 amino acids, a membrane anchor sequence of 18 residues, and shows two epidermal growth factor-like domains rich in Cys residues at the C-terminus. There are four repeat sequences of oligopeptides in the molecule: tetrapeptide (Ser-Thr-Thr-Thr), tripeptide (Pro-Thr-Pro and Pro-Ala-Ala), and dipeptide (Ser-Gly). Furthermore, three nine-residue stretches of a motif (Ala-Ser-Asn-Pro-Gly-Ala-Ser-Ala-Ser) are located near each other. All of these repeat sequences are unexceptionally located in the variable regions when compared with other MSA1 molecules. The molecule displays 79% overall identity to the analogous antigen of P. yoelii yoelii strain YM, 70% to that of P. chabaudi chabaudi strain AS, and 38% to that of P. falciparum strain Wellcome.

Protein glycosylation in the malaria parasite

The nature and extent of glycosylation in Plasmodium falciparum has long been controversial. It has been widely believed that O-glycosylation is the major carbohydrate modification in the intraerythrocytic stage of P. falciparum and that the parasite has no N-glycosylation capacity. Contrary to this, recent studies have demonstrated that P. falciparum has a low N-glycosylation capability, and O-glycosylation is either absent or present at an extremely low level, whereas glycosylphosphatidylinositol (GPI) anchor modification is common and is the major carbohydrate modification in parasite proteins. The GPI anchor moieties are essential for parasite survival. The parasite GPI anchors can activate signaling pathways in host cells, and thereby induce the expression of inflammatory cytokines, adhesion molecules and induced nitric oxide synthase (iNOS). This might cause erythrocyte sequestration, hypoglycemia, triglyceride lipogenesis and immune dysregulation. Thus, the parasite GPI anchor structure and biosynthetic pathways are attractive targets for antimalarial and/or antiparasite drug development, as discussed here by Channe Gowda and Eugene Davidson.

CFTR antisense phosphorothioate oligodeoxynucleotides (S-ODns) induce tracheo-bronchial mucin (TBM) mRNA expression in human airway mucosa

Mucus hypersecretion is a critical component of cystic fibrosis (CF) pathogenesis. The effects of dysfunction of the cystic fibrosis transmembrane regulator (CFTR) on mucin expression were examined using the tracheo-bronchial mucin (TBM) gene as an indicator. TBM mRNA expression was assessed in a human bronchial epithelial cell line (HBE1) and human nasal mucosal explants in vitro. Antisense phosphorothioate oligodeoxynucleotides (S-ODN) to TBM suppressed baseline expression of TBM mRNA in both systems, but had no effect on glyceraldehyde phosphate dehydrogenase mRNA (GAPDH) expression. Sense and missense (multiple scrambled control oligonucleotides) S-ODNs had no effect. 8Br-cAMP and PGE1 significantly elevated TBM mRNA expression. These increases were also specifically inhibited by the antisense S-ODNs. In order to induce a CF-like state, S-ODN to CFTR were added to explants. Antisense CFTR S-ODNs were anticipated to reduce the expression of cellular CFTR protein, and the level of CFTR function. Antisense, but not sense or missense, CFTR S-ODN significantly increased TBM mRNA expression. These data suggest that mucin hypersecretion in CF may be a direct consequence of CFTR dysfunction; the specific mechanism through which this effect is mediated is not known.

Addition of the MSA1 signal and anchor sequences to the malaria merozoite surface antigen 1 C-terminal region enhances immunogenicity when expressed by recombinant vaccinia virus

Genes encoding four different C-terminal fragments of a Plasmodium falciparum merozoite surface antigen were generated: MSA1C-(Si,A), containing signal and anchor regions of MSA1; MSA1C-(Si,nA), containing the signal but not the anchor; MSA1C-(nSi,A), containing the anchor but not the signal, and MSA1C-(nSi,nA) containing neither the signal nor the anchor region. Each gene was inserted into the thymidine kinase region of vaccinia virus, under the control of a synthetic strong early/ late promoter. When the plasmodial genes were expressed in cells infected by the recombinant vaccinia virus, the two proteins containing the signal region were transported to the surface of infected cells. Infection of mice and rabbits with the latter recombinant viruses stimulated C-terminal-specific antibody levels that were 10-80-fold higher than those induced by the two recombinant viruses without the signal region. The combination of the signal and anchor regions with the C-terminal MSA1 protein also generated the most effective neutralization in a P. falciparum invasion assay.

Saccharide anions as inhibitors of the malaria parasite

The asexual erythrocytic stage of Plasmodium falciparum was grown in culture in the presence or absence of glycoconjugate polyanions of varying structure, size and substitutions. Heparin, dextran sulfate, fucoidan and pentosan polysulfate had antimalarial IC50 values between one and 11 microg ml(-1). Constituent heparin disaccharides were ineffective against the malaria parasite and desulfation from either the O- or N-substitution sites of heparin or reduction of the uronic acid carboxyl group neutralized the antimalarial response to varying degrees. Immobilization of heparin onto agarose beads still permitted antimalarial activity suggesting that parasite uptake of the glycoconjugate is not required for inhibition. Accordingly, it is concluded that invasion of free parasites into the erythrocytes was inhibited rather than parasite maturation within the red cell. Merozoite surface antigen-1 was apparently prevented from binding to human erythrocytes in the presence of highly sulfated polyanions and, in a dose-dependent fashion, heparin.

RNA-RNA interaction and gene splicing

The precise excision of intervening sequences during RNA splicing is an interesting example of the high degree of specificity involved in biosynthesis processes. Self-splicing RNA precursors achieve this specificity primarily through intramolecular interactions whereas all other types of RNA splicing requires interaction between cellular factors and specific recognition signals in the RNA precursor. About twelve years ago, the in vitro splicing system was developed and a general scheme of the pre-mRNA was proposed (Hernandez and Keller, 1983; Krainer et al., 1984; Lin et al., 1985; Padgett et al., 1984; Ruskin et al., 1984). A fundamental question in the splicing field is how the 5' and 3' splice sites are recognized and paired during the splicing reaction. Recent work in the splicing field has established that a network of RNA interactions may form the structural foundation of the spliceosomes. Possible solutions to many unsolved puzzles are getting attention. RNA-RNA interactions now appear to underlie many aspects of substrate recognition, reaction partner juxtaposition and catalysis. In this article we have presented the latest mechanisms involved in the pre-mRNA splicing and their implication in applied research including cancer.

Transcriptional regulation of tracheo-bronchial mucin (TBM) gene by ethanol

The epithelia of the respiratory tract are protected by a mucin glycoprotein. The expression of mucin changes when epithelia come in contact with toxic agents such as ethanol. Previously, we have identified and characterized the expression of a tracheo-bronchial mucin (TBM) gene. In the present study, we observed that ethanol regulates TBM expression at the transcription level. Ethanol enhanced the expression of TBM mRNA in a dose- and time-dependent manner in HBE1 cells. At 100 mM concentration (a concentration reported to be present in alcoholics), ethanol induced an eight-fold increase in TBM transcription as determined by reporter gene expression analysis.