Electrophoretic behavior of the H+-ATPase proteolipid from bovine heart mitochondria

The proteolipid subunit of H⁺-ATPase was labeled by [¹⁴C]N,N-dicyclohexylcarbodiimide in bovine heart mitochondria. The radioactive labeling was followed using various systems of sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). When using discontinuous SDS-PAGE (Laemmli, U.K., 1970,Nature (London)227, 680–685) a monomeric (Mr 7600±1500) and a dimeric form (Mr 17,800±1200) of the proteolipid were detected, while only the monomeric form was found on urea (8 M) containing gels (SDS-PAGE according to Laemmli; or Swank, R. T., and Munkers, K. D., 1971,Anal. Biochem. 39, 462–477). When using SDS-PAGE with Na-P_i buffer (Weber, K., and Osborn, M., 1969,J. Biol. Chem. 244, 4406–4442), only a dimeric form of the proteolipid (Mr 15,000±1000) was detected. Experimental data indicate that the different patterns of proteolipid separation are related to the presence of the two distinct proteolipid conformations in the SDS solution.     

Effects of fertigation scheme on N uptake and N use efficiency in cotton

While fertigation can increase fertilizer use efficiency, there is an uncertainly as to whether the fertilizer should be introduced at the beginning of the irrigation or at the end, or introduced during irrigation. Our objective was to determine the effect of different fertigation schemes on nitrogen (N) uptake and N use efficiency (NUE) in cotton plants. A pot experiment was conducted under greenhouse conditions in year 2004 and 2005. According to the application timing of nitrogen (N) fertilizer solution and water (W) involved in an irrigation cycle, four nitrogen fertigation schemes [nitrogen applied at the beginning of the irrigation cycle (N–W), nitrogen applied at the end of the irrigation cycle (W–N), nitrogen applied in the middle of the irrigation cycle (W–N–W) and nitrogen applied throughout the irrigation cycle (N&W)] were employed in a completely randomized design with four replications. Cotton was grown in plastic containers with a volume of 84 l, which were filled with a clay loam soil and fertilized with 6.4 g of N per pot as unlabeled and ¹⁵N-labeled urea for 2004 and 2005, respectively. Plant total dry matter (DM) and N content in N–W was significantly higher than in N&W in both seasons, but these were not consistent for W–N and W–N–W treatments. In year 2005, a significantly higher nitrogen derived from fertilizer (NDFF) for the whole plant was found in W–N and N–W than that in W–N–W and N&W. Fertigation scheme had a consistent effect on total NUE: N–W had the highest NUE for the whole plant, but this was not significantly different from W–N. Treatments W–N and W–N–W had similar total NUE, and N&W had the lowest total NUE. After harvesting, the total residual fertilizer N in the soil was highest in W–N, lowest in N–W, but this was not significantly different from N&W and W–N–W treatments. Total residual NO₃–N in the soil in N&W and W–N treatments was 20.7 and 21.2% higher than that in N–W, respectively. The total ¹⁵N recovery was not statistically significant between the four fertigation schemes. In this study, the fertigation scheme N–W (nitrogen applied at the beginning of an irrigation cycle) increased DM accumulation, N uptake and NUE of cotton. This study indicates that Nitrogen application at the beginning of an irrigation cycle has an advantage on N uptake and NUE of cotton. Therefore, NUE could be enhanced by optimizing fertilization schemes with drip irrigation.     

Genomic data reject the hypothesis of a prosimian primate clade

The phylogenetic position of tarsiers within the primates has been a controversial subject for over a century. Despite numerous morphological and molecular studies, there has been weak support for grouping tarsiers with either strepsirrhine primates in a prosimian clade or with anthropoids in a haplorrhine clade. Here, we take advantage of the recently released whole genome assembly of the Philippine tarsier, Tarsius syrichta, in order to infer the phylogenetic relationship of Tarsius within the order Primates. We also present estimates of divergence times within the primates. Using a 1.26 million base pair multiple sequence alignment derived from 1078 orthologous genes, we provide overwhelming statistical support for the presence of a haplorrhine clade. We also present divergence date estimates using local relaxed molecular clock methods. The estimated time of the most recent common ancestor of extant Primates ranged from 64.9 Ma to 72.6 Ma, and haplorrhines were estimated to have a most recent common ancestor between 58.9 Ma and 68.6 Ma. Examination of rates of nucleotide substitution in the three major extant primate clades show that anthropoids have a slower substitution rate than either strepsirrhines or tarsiers. Our results provide the framework on which primate morphological, reproductive, and genomic features can be reconstructed in the broader context of mammalian phylogeny.     

A change from phalanx to guerrilla growth form is an effective strategy to acclimate to sedimentation in a wetland sedge species Carex brevicuspis (Cyperaceae)

The rhizomatous sedge Carex brevicuspis can produce clumping ramets from shortened rhizomes (phalanx) and spreading ramets from elongated rhizomes (guerrilla) to form a combined clonal growth form. In this paper, changes in clonal growth and biomass allocation pattern of C. brevicuspis in response to sedimentation were studied. Four sedimentation depths (0, 3, 6, and 9 cm) were applied to 48 ramets in a randomized block design. Plants were harvested after 20 weeks. With increasing sedimentation depth, the proportion of spreading ramets to total ramets increased from 19.6% in 0 cm to 92.9% in 9 cm sedimentation treatments, whereas that of clumping ramets decreased from 80.4% to 7.1%, indicating a change of clonal growth form from phalanx to guerrilla as a response to sedimentation. With increasing sedimentation depth, biomass allocation to shoots and roots did not change, but rhizome mass ratio increased from 2.7% in 0 cm to 7.2% in 9 cm sedimentation treatments, suggesting that production of long rhizomes changes biomass allocation pattern. The results show that plasticity of clonal growth forms, by which more spreading ramets are produced, is an effective strategy to avoid sedimentation stress under our experimental conditions.     

Effect of NBD chloride (4-chloro-7-nitrobenzo-2-oxa-1,3-diazole) on the pyridine nucleotide transhydrogenase of Escherichia coli.

Pyridine nucleotide transhydrogenases of bacterial cytosolic membranes and mitochondrial inner membranes are proton pumps in which hydride transfer between NADP(+) and NAD(+) is coupled to proton translocation across cytosolic or mitochondrial membranes. The pyridine nucleotide transhydrogenase of Escherichia coli is composed of two subunits (alpha and beta). Three domains are recognized. The extrinsic cytosolic domain 1 of the amino-terminal region of the alpha subunit bears the NAD(H)-binding site. The NADP(H)-binding site is present in domain 3, the extrinsic cytosolic carboxyl-terminal region of the beta subunit. Domain 2 is composed of the membrane-intrinsic carboxyl-terminal region of the alpha subunit and the membrane-intrinsic amino-terminal region of the beta subunit. Treatment of the transhydrogenase of E. coli with 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD chloride) inhibited enzyme activity. Analysis of inhibition revealed that several sites on the enzyme were involved. NBD chloride modified two (betaCys-147 and betaCys-260) of the seven cysteine residues present in the transhydrogenase. Modification of betaCys-260 in domain 2 resulted in inhibition of enzyme activity. Modification of residues other than cysteine residues also resulted in inhibition of transhydrogenation as shown by use of a cysteine-free mutant enzyme. The beta subunit was modified by NBD chloride to a greater extent than the alpha subunit. Reaction of domain 2 and domain 3 was prevented by NADPH. Modification of domain 3 is probably not associated with inhibition of enzyme activity. Modification of domain 2 of the beta subunit resulted in a decreased binding affinity for NADPH at its binding site in domain 3. The product resulting from the reaction of NBD chloride with NADPH was a very effective inhibitor of transhydrogenation. In experiments with NBD chloride in the presence of NADPH it is likely that all of the sites of reaction described above will contribute to the inhibition observed. The NBD-NADPH adduct will likely be more useful than NBD chloride in investigations of the pyridine nucleotide transhydrogenase.     

Hypoxia Adaptations in the Grey Wolf (Canis lupus chanco) from Qinghai-Tibet Plateau

The Tibetan grey wolf (Canis lupus chanco) occupies habitats on the Qinghai-Tibet Plateau, a high altitude (>3000 m) environment where low oxygen tension exerts unique selection pressure on individuals to adapt to hypoxic conditions. To identify genes involved in hypoxia adaptation, we generated complete genome sequences of nine Chinese wolves from high and low altitude populations at an average coverage of 25× coverage. We found that, beginning about 55,000 years ago, the highland Tibetan grey wolf suffered a more substantial population decline than lowland wolves. Positively selected hypoxia-related genes in highland wolves are enriched in the HIF signaling pathway (P = 1.57E-6), ATP binding (P = 5.62E-5), and response to an oxygen-containing compound (P≤5.30E-4). Of these positively selected hypoxia-related genes, three genes (EPAS1, ANGPT1, and RYR2) had at least one specific fixed non-synonymous SNP in highland wolves based on the nine genome data. Our re-sequencing studies on a large panel of individuals showed a frequency difference greater than 58% between highland and lowland wolves for these specific fixed non-synonymous SNPs and a high degree of LD surrounding the three genes, which imply strong selection. Past studies have shown that EPAS1 and ANGPT1 are important in the response to hypoxic stress, and RYR2 is involved in heart function. These three genes also exhibited significant signals of natural selection in high altitude human populations, which suggest similar evolutionary constraints on natural selection in wolves and humans of the Qinghai-Tibet Plateau.     

Relative Affinity of Calcium Pump Isoforms for Phospholamban Quantified by Fluorescence Resonance Energy Transfer

To investigate the regulation of SERCA1a [sarco(endo)plasmic reticulum calcium ATPase] and SERCA2a calcium pump isoforms by phospholamban (PLB), we quantified PLB-SERCA interactions by fluorescence resonance energy transfer (FRET) in live cells. For both SERCA1a and SERCA2a, FRET to PLB increased with increasing protein expression level to a maximum value corresponding to a probe separation distance of 64 Å. The data indicate that the respective regulatory complexes assume the same overall quaternary conformation. However, FRET measurements also revealed that PLB has a 50% higher apparent affinity for SERCA1a relative to SERCA2a. The results suggest that despite the structural similarities of the respective regulatory complexes, there is preferential binding of PLB to SERCA1a over SERCA2a. This apparent selectivity may have implications for biochemical studies in which SERCA1a is used as a substitute for SERCA2a. It may also be an important strategic consideration for therapeutic overexpression of SERCA isoforms in cardiac muscle.     

Metagenomic insights into the alteration of soil N-cycling-related microbiome and functions under long-term conversion of cropland to Miscanthus

Miscanthus spp. show excellent application prospects due to its bioenergy potential and multiple ecological services. Annual N export with biomass harvest from Miscanthus, even without fertilizer supplement, do not reduce soil N levels. The question arises regarding how Miscanthus can maintain stable soil N levels. Metagenomic strategies were used to reveal soil N-cycling-related microbiome and their functional contributions to processes of soil N-cycling based on the comparison among the bare land, cropland, 10-year Miscanthus × giganteus, and 15-year Miscanthus sacchariflorus fields. The results showed that, after long-term cropland-to-Miscanthus conversion (LCMC), 16 of 21 bacterial phyla and all the archaeal phyla exhibited significant changes. Soil microbial denitrification and nitrification functions were significantly weakened, and N fixation (NF) was significantly enhanced. The biosynthesis of amino acids, especially alanine, aspartate, and glutamate metabolism, in soil N-cycling-related microbiome was dramatically promoted. The genus Anaeromyxobacter contributed largely to the NF process after LCMC. Variations in the soil available potassium, available N, organic C, and total N contents drove a functional shift of soil microbiome from cropland to Miscanthus pattern. We conclude that Miscanthus can recruit Anaeromyxobacter communities to enhance NF benefiting its biomass sustainability and soil N balance.