Correction: Neglecting the fallow season can significantly underestimate annual methane emissions in Mediterranean rice fields.

[This corrects the article DOI: 10.1371/journal.pone.0198081.].

Neglecting the fallow season can significantly underestimate annual methane emissions in Mediterranean rice fields.

Paddy rice fields are one of the most important sources of anthropogenic methane. Improving the accuracy in the CH4 budget is fundamental to identify strategies to mitigate climate change. Such improvement requires a mechanistic understanding of the complex interactions between environmental and agronomic factors determining CH4 emissions, and also the characterization of the annual temporal CH4 emissions pattern in the whole crop cycle. Hence, both the growing and fallow seasons must be included. However, most of the previous research has been based on single-factor analyses that are focused on the growing season. In order to fill this gap, a study was conducted in a Mediterranean rice agrosystem (Ebre Delta, Catalonia) following a farm-to-farm approach with the purpose of 1) evaluating the cumulative and temporal pattern of CH4 emission, and 2) conducting a multi-variate analyses to assess the associative pattern, relative contribution and temporal variation of the main explanatory variables concerning the observed CH4 emissions. Measurements of CH4 emissions and agronomic and environmental parameters in 15 commercial rice fields were monitored monthly, during a whole crop field cycle. The temporal pattern of CH4 emission followed a bi-modal distribution peaking in August and October. The cumulative annual CH4 emissions from rice fields amounted 314 kg CH4 kg ha-1, of which ca. 70% were emitted during the fallow season. The main controlling factors of the CH4 emission rate in the growing season were positive related to water level and plant cover, while soil redox was negatively related. The main controlling factors in the fallow season were water level (negatively related, conversely to the growing season), as well as straw incorporation and soil temperature (positively related). The results of this study highlight the importance of the often neglected fallow season in the accurate estimation of CH4 emissions and, thus, the necessity of measurement programs that cover the whole crop field cycle. This information is the first step for setting effective mitigation strategies based on straw and water management.

Electrophoretic characterization of the Mammalian nuclear matrix proteome, nuclear envelope, nucleoli and covalently bound ADP-ribose polymers: potential applications to cancer.

BACKGROUND/AIM: Nucleic acid metabolism is biochemically compartmentalized to the nucleus. Thus, it is necessary to define the proteome of the various macromolecular structures within this organelle. MATERIALS AND METHODS: We isolated the nuclear matrix (NM) fraction from rat liver by sequential centrifugation steps at 13,000 rpm, staggered between endogenous nuclease treatment for 2 h at 37°C, followed by high-salt (H.S.; 2.0 M NaCl) and non-ionic detergent extractions (0.1%- or 1.0% Triton X-100) to eliminate the bulk of chromosomal DNA/RNA, histone proteins and the nuclear envelope (NE). RESULTS: Integrity of the NM and NE structures was confirmed by electron microscopy. Next, we analyzed the NM proteome on a 20% polyacrylamide gel using the PhastSystem. We observed the absence of histone proteins and the characteristic presence of the lamins by Coomassie blue staining. By contrast, upon silver staining, following electrophoretic separation with a Tris-Borate-EDTA buffer, we observed the NM-associated nucleic RNA and protein-free ADP-ribose polymers. While polymers are found in much lower concentration than RNA in NM, they were purified by affinity chromatography on boronate resin prior to electrophoresis. We observed the electrophoretic resolution of free ADP-ribose chains (5-25 units) by silver staining. CONCLUSION: The significance of our observations to cancer studies and carcinogenesis is discussed.

Genetic composition of six miniSTR in a Brazilian Mulatto sample population.

The present study characterizes the genetic variability of Mulatto population based on the polymorphism of six miniSTR autosomal loci, known as Non Codis 01 and 02 (NC01 and NC02) and evaluate their applicability in forensic genetics. A sample of 102 unrelated Brazilian mulattoes were genotyped for miniSTR loci D1S1677, D2S441, D4S2364 (miniplex NC02) and 45 individuals for D10S1248, D14S1434, D22S1045 (miniplex NC01). No significant deviations from Hardy-Weinberg equilibrium expectations were detected. The combined power of discrimination (PD) and mean power of exclusion (PE) were 0.999996 and 0.98991, respectively. The results also support the effectiveness of the NC01and NC02 miniplexes for human identification.

Texas population substructure and its impact on estimating the rarity of Y STR haplotypes from DNA evidence*.

Three sampled populations of unrelated males--African American, Caucasian, and Hispanic, all from Texas-were typed for 16 Y short tandem repeat (STR) markers using the AmpFlSTR Yfiler kit. These samples also were typed previously for the 13 core CODIS autosomal STR loci. Most of the 16 marker haplotypes (2478 out of 2551 distinct haplotypes) were observed only once in the data sets. Haplotype diversities were 99.88%, 99.89%, and 99.87% for the African American, Caucasian, and Hispanic sample populations, respectively. F(ST) values were very small when a haplotype comprised 10-16 markers. This suggests that inclusion of substructure correction is not required. However, haplotypes consisting of fewer loci may require the inclusion of F(ST) corrections. The testing of independence of autosomal and Y STRs supports the proposition that the frequencies of autosomal and Y STR profiles can be combined using the product rule.

Mutation rates at Y chromosome short tandem repeats in Texas populations.

Father-son pairs from three populations (African American, Caucasian, and Hispanic) of Texas were typed for the 17 Y STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR YfilerTM kit. With 49,578 allele transfers, 102 mutations were detected. One three-step and four two-step mutations were found, and all others (95.1%) were one-step mutations. The number of gains (48) and losses (54) of repeats were nearly similar. The average mutation rate in the total population is 2.1 x 10(-3) per locus (95% CI (1.7-2.5)x10(-3)). African Americans showed a higher mutation rate (3.0 x 10(-3); 95% CI (2.4-4.0)x10(-3)) than the Caucasians (1.7 x 10(-3); 95% CI (1.1-2.5)x10(-3)) and Hispanics (1.5 x 10(-3); 95% CI (1.0-2.2)x10(-3)), but grouped by repeat-lengths, such differences were not significant. Mutation is correlated with relative length of alleles, i.e., longer alleles are more likely to mutate compared with the shorter ones at the same locus. Mutation rates are also correlated with the absolute number of repeats, namely, alleles with higher number of repeats are more likely to mutate than the shorter ones (p-value=0.030). Finally, occurrences of none, one, and two mutations over the father-son transmission of alleles were consistent with the assumption of independence of mutation rates across loci.

Null allele sequence structure at the DYS448 locus and implications for profile interpretation.

Null alleles can occur with any PCR-based STR typing system. They generally are due to deletions within the target region or primer binding sites or by primer binding site mutations that destabilize hybridization of at least one of the primers flanking the target region. Although not common, null types were detected at the DYS448 locus in seven out of 1,005 unrelated males in the Hispanic population. Of these DYS448 null types, four individuals displayed an apparent duplication at the DYS437 locus. The additional allele observed at the DYS437 locus is in actuality a smaller-sized DYS448 amplicon, which is the result of a deletion of the invariant N42 base pair domain and downstream repeats within the DYS448 locus. Thus, some DYS448 null types are not truly null. A true DYS448 null allele carried numerous primer binding site variants and a large deletion including the N42 base pair domain and surrounding or downstream repeat regions. The presence of null alleles is not a real concern for interpretation of Y STR loci evidence; current methods for interpreting Y STR profiles easily accommodate such phenomena.

Validation of male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex.

Y chromosome-specific short tandem repeat (Y-STR) analysis has become another widely accepted tool for human identification. The PowerPlex Y System is a fluorescent multiplex that includes the 12 loci: DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. This panel of markers incorporates the 9-locus European minimal haplotype (EMH) loci recommended by the International Y-STR User Group and the 11-locus set recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Described here are inter-laboratory results from 17 developmental validation studies of the PowerPlex Y System and include the following results: (a) samples distributed between laboratories and commercial standards produced expected and reproducible haplotypes; (b) use of common amplification and detection instruments were successfully demonstrated; (c) full profiles were obtained with standard 30 and 32 cycle amplification protocols and cycle number (24-28 cycles) could be modified to match different substrates (such as direct amplification of FTA paper); (d) complete profiles were observed with reaction volumes from 6.25 to 50 microL; (e) minimal impact was observed with variation of enzyme concentration; (f) full haplotypes were observed with 0.5-2x primer concentrations; however, relative yield between loci varied with concentration; (g) reduction of magnesium to 1mM (1.5 mM standard) resulted in minimal amplification, while only partial loss of yield was observed with 1.25 mM magnesium; (h) decreasing the annealing temperature by 2-4 degrees C did not generate artifacts or locus dropout and most laboratories observed full amplification with the annealing temperature increased by 2 degrees C and significant locus dropout with a 4 degrees C increase in annealing temperature; (i) amplification of individual loci with primers used in the multiplex produced the same alleles as observed with the multiplex amplification; (j) all laboratories observed full amplification with >or = 125 pg of male template with partial and/or complete profiles observed using 30-62.5 pg of DNA; (k) analysis of < or = 500 ng of female DNA did not yield amplification products; (l) the minor male component of a male/female mixture was observed with < or =1200-fold excess female DNA with the majority of alleles still observed with 10,000-fold excess female; (m) male/male mixtures produced full profiles from the minor contributor with 10-20-fold excess of the major contributor; (n) average stutter for each locus; (o) precision of sizing were determined; (p) human-specificity studies displayed amplification products only with some primate samples; and (q) reanalysis of 102 non-probative casework samples from 65 cases produced results consistent with original findings and in some instances additional identification of a minor male contributor to a male/female mixture was obtained. In general, the PowerPlex Y System was shown to have the sensitivity, specificity and reliability required for forensic DNA analysis.

Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America.

A total of 2443 male individuals, previously typed for the 13 CODIS STR loci, distributed across the five North American population groups African American, Asian, Caucasian, Hispanic, and Native American were typed for the Y-STR loci DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 using the PowerPlex Y System. All population samples were highly polymorphic for the 12 Y-STR loci with the marker DYS385a/b being the most polymorphic across all sample populations. The Native American population groups demonstrated the lowest genetic diversity, most notably at the DYS393 and DYS437 loci. Almost all of the 12-locus haplotypes observed in the sample populations were represented only once in the database. Haplotype diversities were greater than 99.6% for the African Americans, Caucasians, Hispanics, and Asians. The Native Americans had the lowest haplotype diversities (Apaches, 97.0%; Navajo, 98.1%). Population substructure effects were greater for Y-haplotypes, compared with that for the autosomal loci. For the apportionment of variance for the 12 Y-STRs, the within sample population variation was the largest component (>98% for each major population group and approximately 97% in Native Americans), and the variance component contributed by the major population groups was less than the individual component, but much greater than among sample populations within a major group (11.79% versus 1.02% for African Americans/Caucasians/Hispanics and 15.35% versus 1.25% for all five major populations). When each major population is analyzed individually, the R(ST) values were low but showed significant among group heterogeneity. In 692 confirmed father-son pairs, 14 mutation events were observed with the average rate of 1.57x10(-3)/locus/generation (a 95% confidence bound of 0.83x10(-3) to 2.69x10(-3)). Since the Y-STR loci reside on the non-recombining region of the Y chromosome, the counting method is one approach suggested for conveying an estimate of the rarity of the Y-haplotype. Because the Y-STR loci are not all in disequilibrium to the same extent, the counting method is a very conservative approach. The data also support that autosomal STR frequencies can be multiplied by the upper bound frequency estimate of a Y-haplotype in the individual population group or those pooled into major population groups (i.e., Caucasian, African American, Hispanic, and Asian). These analyses support use of the haplotype population data for estimating Y-STR profile frequencies for populations residing in North America.

Leaf morphology, photochemistry and water status changes in resprouting Quercus ilex during drought.

Functional and morphological (structural) characteristics of Quercus ilex L. leaves under drought stress were studied in the forest and in a nursery. We compared undisturbed individuals (controls) with resprouts emerging after clear-cut or excision. When soil water availability was high, gas-exchange was similar in resprouts and controls, despite higher midday leaf water potential, midday leaf hydration and relative water content (RWC). In moderate drought, stomatal closure was found to limit photosynthesis in controls, and in severe drought non-stomatal limitations of photosynthesis were also greater than in resprouts. Leaf structure and chemical composition changed under drought stress. Leaves tended to be smaller in controls with increasing drought, and resprouts had larger leaves and lower leaf mass area (LMA). The relationship between nitrogen (N) content and LMA implied lower N investment in photosynthetic components in controls, which could be responsible for their increased non-stomatal limitation of photosynthesis. Changes were more apparent in leaf density (D) and thickness (T), components of LMA. Decreases in D were related to reductions in cell wall components: hemicellulose, cellulose and lignin. In resprouts, reduced D and leaf T accounted for the higher mesophyll conductance (gmes) to CO2 measured.

Validation of a male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex.

Y chromosome-specific short tandem repeat (Y-STR) analysis has become another widely accepted tool for human identification. The PowerPlex Y System is a fluorescent multiplex that includes the 12 loci: DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. This panel of markers incorporates the 9-locus European minimal haplotype (EMH) loci recommended by the International Y-STR User Group and the 11-locus set recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Described here are inter-laboratory results from 17 developmental validation studies of the PowerPlex Y System and include the following results: (a) samples distributed between laboratories and commercial standards produced expected and reproducible haplotypes; (b) use of common amplification and detection instruments were successfully demonstrated; (c) full profiles were obtained with standard 30 and 32 cycle amplification protocols and cycle number (24-28 cycles) could be modified to match different substrates (such as direct amplification of FTA paper); (d) complete profiles were observed with reaction volumes from 6.25 to 50 microL; (e) minimal impact was observed with variation of enzyme concentration; (f) full haplotypes were observed with 0.5-2x primer concentrations; however, relative yield between loci varied with concentration; (g) reduction of magnesium to 1mM (1.5 mM standard) resulted in minimal amplification, while only partial loss of yield was observed with 1.25 mM magnesium; (h) decreasing the annealing temperature by 2-4 degrees C did not generate artifacts or locus dropout and most laboratories observed full amplification with the annealing temperature increased by 2 degrees C and significant locus dropout with a 4 degrees C increase in annealing temperature; (i) amplification of individual loci with primers used in the multiplex produced the same alleles as observed with the multiplex amplification; (j) all laboratories observed full amplification with >or = 125 pg of male template with partial and/or complete profiles observed using 30-62.5 pg of DNA; (k) analysis of < or = 500 ng of female DNA did not yield amplification products; (l) the minor male component of a male/female mixture was observed with < or =1200-fold excess female DNA with the majority of alleles still observed with 10,000-fold excess female; (m) male/male mixtures produced full profiles from the minor contributor with 10-20-fold excess of the major contributor; (n) average stutter for each locus; (o) precision of sizing were determined; (p) human-specificity studies displayed amplification products only with some primate samples; and (q) reanalysis of 102 non-probative casework samples from 65 cases produced results consistent with original findings and in some instances additional identification of a minor male contributor to a male/female mixture was obtained. In general, the PowerPlex Y System was shown to have the sensitivity, specificity and reliability required for forensic DNA analysis.

Stomatal limitation to CO2 assimilation and down-regulation of photosynthesis in Quercus ilex resprouts in response to slowly imposed drought.

Holm oak (Quercus ilex L.) is native to hot, dry Mediterranean forests where limited water availability often reduces photosynthesis in many species, and forest fires are frequent. Holm oaks resprout after a disturbance, with improved photosynthetic activity and water relations compared with unburned plants. To better understand the role of water availability in this improvement, watering was withheld from container-grown plants, either intact (controls) or resprouts after excision of the shoot, to gradually obtain a wide range of soil water availabilities. At high water availability, gas exchange rates did not differ between controls and resprouts. At moderate soil dryness, net photosynthesis of control plants decreased as a result of increased stomatal limitation, whereas gas exchange rates of resprouts, which had higher midday and predawn leaf water potentials, were unchanged. Under severe drought, resprouts showed a less marked decline in gas exchange than controls and maintained photosystem II integrity, as indicated by chlorophyll fluorescence measurements. Photosynthesis was down-regulated in both plant types in response to reduced CO2 availability caused by high stomatal limitation. Lower non-stomatal limitations in resprouts than in control plants, as evidenced by higher carboxylation velocity and the capacity for ribulose-1,5-bisphosphate regeneration, conferred greater drought resistance under external constraints similar to summer conditions at midday.

Tumour necrosis factor-alpha uncouples respiration in isolated rat mitochondria.

Recent studies have demonstrated the existence of an intracellular (associated with mitochondria) tumour necrosis factor-alpha (TNF) binding protein. In an attempt to elucidate if this receptor could be involved in TNF action, we have incubated liver isolated mitochondria in the presence of recombinant murine TNF. The results show that the addition of TNF at concentrations as low as 10(-6) U/microl resulted in a clear uncoupling respiration of liver isolated mitochondria, therefore suggesting that TNF can indeed exert intracellular effects, which are possibly linked with its cytotoxic mechanism.

Variations in Quercus ilex chloroplast pigment content during summer stress: involvement in photoprotection according to principal component analysis.

We examined chloroplast pigment variation in holm oak (Quercus ilex L.) leaves for two periods under two climatic conditions, at midday during summer. We compared variation between control (unburned) plants and plants burned the preceding summer, since post-fire resprouts show higher photosynthetic rates and lower thermal energy dissipation. Principal component (PC) analysis was performed on nine pigment-content variables for the two periods separately. Two PC factors (PC1 and PC2) explained 83 and 84% of the variance of the data for each period. In both periods, PC1 was marked by positive loading of pigments associated with light absorption or structural function namely neoxanthin, lutein, ß-carotene, chlorophyll a, and chlorophyll b. These pigments were only affected by leaf age. In contrast, PC2 was marked by high loadings of xanthophyll-cycle pigments (associated with photoprotection), and lutein-5,6-epoxide. Leaf content of these pigments was affected by climatic conditions. In the situations considered in PC analysis (leaf types, periods), the lutein-5,6-epoxide content presented a variation pattern similar to that of violaxanthin, and was significantly correlated with thermal dissipation of excess energy (represented by non-photochemical quenching or NPQ). These results suggest a relationship of lutein and lutein-5,6-epoxide with photoprotection.