Ascertainment Bias and the Pattern of Nucleotide Diversity at the Human ALDH2 Locus in a Japanese Population

Many East Asian human populations harbor a high-frequency deficiency allele for the aldehyde dehydrogenase 2 (ALDH2) enzyme, a critical protein involved in the metabolism of ethanol. Here we use resequencing and long-range SNP haplotype data from a Japanese sample to test whether patterns of nucleotide diversity and linkage disequilibrium at this locus are compatible with a standard neutral model of evolution. Examination of the pattern of polymorphism at a locus such as this, where the frequency of a common allele is known a priori, introduces an ascertainment bias that must be corrected for in analyses of the frequency spectrum of polymorphisms. We apply a flexible and generally applicable simulation approach to correct for this bias in our ALDH2 data and, also, to explore the effect of bias on the commonly used summary statistics Tajima’s D, Fu and Li’s D, and Fay and Wu’s H. Our study finds no evidence that the pattern of genetic variation at ALDH2 differs from that expected under a standard neutral model. However, our general examination of ascertainment bias indicates that a priori knowledge of segregating alleles greatly affects the expected distributions of summary statistics. Under many parameter combinations we find that ascertainment bias introduces an elevated rate of false positives when summary statistics are used to test for deviations from a standard neutral model. However, we also show that over a wide range of conditions the power of all summary statistics can be greatly increased by incorporating prior knowledge of segregating alleles. [Reviewing Editor: Dr. Martin Kreitman]     

Altered cerebral glucose and acetate metabolism in succinic semialdehyde dehydrogenase-deficient mice: evidence for glial dysfunction and reduced glutamate/glutamine cycling

Succinic semialdehyde dehydrogenase (SSADH) catalyzes the NADP-dependent oxidation of succinic semialdehyde to succinate, the final step of the GABA shunt pathway. SSADH deficiency in humans is associated with excessive elevation of GABA and γ-hydroxybutyrate (GHB). Recent studies of SSADH-null mice show that elevated GABA and GHB are accompanied by reduced glutamine, a known precursor of the neurotransmitters glutamate and GABA. In this study, cerebral metabolism was investigated in urethane-anesthetized SSADH-null and wild-type 17-day-old mice by intraperitoneal infusion of [1,6-¹³C₂]glucose or [2-¹³C]acetate for different periods. Cortical extracts were prepared and measured using high-resolution ¹H-[¹³C] NMR spectroscopy. Compared with wild-type, levels of GABA, GHB, aspartate, and alanine were significantly higher in SSADH-null cortex, whereas glutamate, glutamine, and taurine were lower. ¹³C Labeling from [1,6-¹³C₂]glucose, which is metabolized in neurons and glia, was significantly lower (expressed as μmol of ¹³C incorporated per gram of brain tissue) for glutamate-(C4,C3), glutamine-C4, succinate-(C3/2), and aspartate-C3 in SSADH-null cortex, whereas Ala-C3 was higher and GABA-C2 unchanged. ¹³C Labeling from [2-¹³C]acetate, a glial substrate, was lower mainly in glutamine-C4 and glutamate-(C4,C3). GHB was labeled by both substrates in SSADH-null mice consistent with GABA as precursor. Our findings indicate that SSADH deficiency is associated with major alterations in glutamate and glutamine metabolism in glia and neurons with surprisingly lesser effects on GABA synthesis.     

Identification of two novel phytosiderophores secreted by perennial grasses

It has been suggested that some perennial grasses secrete phytosiderophores in response to iron (Fe) deficiency, but the compounds have not been identified. Here, we identified and characterized the phytosiderophores secreted by two perennial grasses, Lolium perenne cv. Tove and Poa pratensis cv. Baron. Root exudates were collected from the roots of Fe-deficient grasses and then purified with various chromatographies. The structure of the purified compounds was determined using both nuclear magnetic resonance and fast atom bombardment mass spectrometry. Both species secreted phytosiderophores in response to Fe deficiency, and the amount of phytosiderophores secreted increased with the development of Fe deficiency. The type of phytosiderophores secreted differed with plant species; L. perenne cv. Tove secreted 3-epihydroxy-2'-deoxymugineic acid (epiHDMA), 2'-deoxymugineic acid (DMA) and an unknown compound, whereas P. pratensis cv. Baron secreted DMA, avenic acid A (AVA) and an unknown compound. Purification and subsequent analysis with nuclear magnetic resonance and mass led to identification of the two novel phytosiderophores; 3-hydroxy-2'-deoxymugineic acid (HDMA) from L. perenne, and 2'-hydroxyavenic acid A (HAVA) from P. pratensis. Both novel phytosiderophores have similar chelating activity to known phytosiderophores.     

Cold acclimation was partially impaired in boron deficient Norway spruce seedlings

Susceptibility of trees to freezing injury has been suggested to increase in boron (B) deficiency but there is no experimental evidence to support this proposition. In this study, Norway spruce (Picea abies L. Karst.) seedlings were cultivated for two growing seasons in deficient, intermediate and ‘optimal’ B levels. Cold hardening of the seedlings was measured after the second growing season. Freezing tolerance in tips of shoots, needles, stems and roots was determined by controlled freezing tests and electrolyte leakage method, and that of buds, in addition, by differential thermal analysis (DTA). Electrical impedance was used to monitor changes in the apoplastic space during cold acclimation. Root dry weight and shoot height growth were lower in B deficiency. Cold acclimation of buds and stems was reduced by B deficiency. When hardened seedlings were subjected to subzero temperatures for 3 weeks, extracellular electrical resistance of stems became the highest at the lowest B supply which was probably due to decreased desiccation tolerance. As a conclusion, susceptibility to freezing damage may be increased by B deficiency in Norway spruce trees.     

Nitrogen deficiency as well as phosphorus deficiency in sorghum promotes the production and exudation of 5-deoxystrigol,the host recognition signal for arbuscular mycorrhizal fungi and root parasites

Strigolactones released from plant roots induce hyphal branching of symbiotic arbuscular mycorrhizal (AM) fungi and germination of root parasitic weeds, Striga and Orobanche spp. We already demonstrated that, in red clover plants (Trifolium pratense L.), a host for both AM fungi and the root holoparasitic plant Orobanche minor Sm., reduced supply of phosphorus (P) but not of other elements examined (N, K, Ca, Mg) in the culture medium significantly promoted the secretion of a strigolactone, orobanchol, by the roots of this plant. Here we show that in the case of sorghum [Sorghum bicolor (L.) Moench], a host of both the root hemiparasitic plant Striga hermonthica and AM fungi, N deficiency as well as P deficiency markedly enhanced the secretion of a strigolactone, 5-deoxystrigol. The 5-deoxystrigol content in sorghum root tissues also increased under both N deficiency and P deficiency, comparable to the increase in the root exudates. These results suggest that strigolactones may be rapidly released after their production in the roots. Unlike the situation in the roots, neither N nor P deficiency affected the low content of 5-deoxystrigol in sorghum shoot tissues.     

A negative regulatory role for auxin in sulphate deficiency response in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Sulphate is a major macronutrient required for the synthesis of the sulphur (S)-containing amino acid cysteine and thus is critical for cellular metabolism, growth and development and response to various abiotic and biotic stresses. A recent genome-wide expression study suggested that several auxin-inducible genes were up-regulated by S deficiency in Arabidopsis. Here, we examined the relationship between auxin signaling and S deficiency. Investigation of DR5::GUS expression patterns indicates that auxin accumulation and/or response is suppressed by S deficiency. Consistently, S deficiency resulted in the suppression of lateral root development, but the axr1-3 mutant was insensitive to this response. Furthermore, the activation of the promoter for the putative thioglucosidase gene (At2g44460) by S deficiency was suppressed by auxin, cytokinin and abscisic acid (ABA). Interestingly, the activation of At2g44460 by S deficiency is regulated by the availability of carbon and nitrogen nutrients in a tissue-specific manner. These results demonstrate that auxin plays a negative role in signaling to S deficiency. Given that activation of the genes encoding the sulphate transporter SULTR1;2 and 5′-adenylylsulphate reductase APR2 are suppressed by cytokinin only, we hypothesize that while cytokinin may play an important role in general S deficiency response, auxin might be only involved in a subset of S deficiency responses such as the release of thiol groups from the S storage sources. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Reduction of Fe(II)EDTA-NO by a newly isolated <Emphasis Type="Italic">Pseudomonas</Emphasis> sp. strain DN-2 in NO<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript> scrubber solution

Biological reduction of nitric oxide (NO) chelated by ferrous ethylenediaminetetraacetate (Fe(II)EDTA) to N₂ is one of the core processes in a chemical absorption–biological reduction integrated technique for nitrogen oxide (NO _x ) removal from flue gases. A new isolate, identified as Pseudomonas sp. DN-2 by 16S rRNA sequence analysis, was able to reduce Fe(II)EDTA-NO. The specific reduction capacity as measured by NO was up to 4.17 mmol g DCW⁻¹ h⁻¹. Strain DN-2 can simultaneously use glucose and Fe(II)EDTA as electron donors for Fe(II)EDTA-NO reduction. Fe(III)EDTA, the oxidation of Fe(II)EDTA by oxygen, can also serve as electron acceptor by strain DN-2. The interdependency between various chemical species, e.g., Fe(II)EDTA-NO, Fe(II)EDTA, or Fe (III)EDTA, was investigated. Though each complex, e.g., Fe(II)EDTA-NO or Fe(III)EDTA, can be reduced by its own dedicated bacterial strain, strain DN-2 capable of reducing Fe(III)EDTA can enhance the regeneration of Fe(II)EDTA, hence can enlarge NO elimination capacity. Additionally, the inhibition of Fe(II)EDTA-NO on the Fe(III)EDTA reduction has been explored previously. Strain DN-2 is probably one of the major contributors for the continual removal of NO _x due to the high Fe(II)EDTA-NO reduction rate and the ability of Fe(III)EDTA reduction.     

Expression and secretion of a single-chain sweet protein monellin in <Emphasis Type="Italic">Bacillus subtilis</Emphasis> by <Emphasis Type="Italic">sacB</Emphasis> promoter and signal peptide

The sweet protein monellin gene was expressed in Bacillus subtilis under the control of the Bacillus subtilis sacB promoter and signal peptide sequence. A 294-bp DNA fragment, coding for sweet protein monellin, was ligated into the Escherichia coli/B. subtilis shuttle vector pHPC, producing pHPMS, which was subsequently transformed into B. subtilis QB1098, DB104, and DB403. The peptide efficiently directed the secretion of monellin from the recombinant B. subtilis cells. A maximum yield of monellin of 0.29 g protein l⁻¹ was obtained from the supernatant of B. subtilis DB403 harboring pHPMS. SDS-PAGE confirmed the purity of the recombinant product.     

Adaptation of photosynthesis under iron deficiency in maize

This paper explores the effects of high light stress on Fe-deficient plants. Maize (Zea mays) plants were grown under conditions of Fe deficiency and complete nutrition. Attached, intact leaves of Fe-deficient and control plants were used for gas exchange experiments under suboptimal, optimal and photoinhibitory illumination. Isolated chloroplasts were used to study photosynthetic electron transport system, compromised by the induction of Fe deficiency. The reaction centers of PS II (measured as reduction of Q, the primary electron acceptor of P 680) and PS I (measured as oxidation of P 700) were estimated from the amplitude of light induced absorbance change at 320 and 700 nm, respectively. Plants were subjected to photoinhibitory treatment for different time periods and isolated chloroplasts from these plants were used for electron transport studies. Carbon dioxide fixation in control as well as in Fe-deficient plants decreased in response to high light intensities. Total chlorophyll, P 700 and Q content in Fe-deficient chloroplasts decreased, while Chl a/b ratio and Q/P 700 ratio increased. However, electron transport through PS II suffered more after photoinhibitory treatment as compared to electron transport through PS I or whole chain. Electron transfer through PS I+PS II, excluding the water oxidation complex showed a decrease in Fe-deficient plants. However, electron transport through this part of the chain did not suffer much as a result of photoinhibition, suggesting a defect in the oxidising side of PS II.