A naturally occurring promoter polymorphism of the Arabidopsis FUM2 gene causes expression variation,and is associated with metabolic and growth traits

Fumarate and malate are known intermediates of the TCA cycle, a mitochondrial metabolic pathway generating NADH for respiration. Arabidopsis thaliana and other Brassicaceae contain an additional cytosolic fumarase (FUM2) that functions in carbon assimilation and nitrogen use. Here, we report the identification of a hitherto unknown FUM2 promoter insertion/deletion (InDel) polymorphism found between the Col‐0 and C24 accessions, which also divides a large number of Arabidopsis accessions carrying either the Col‐0 or the C24 allele. The polymorphism consists of two stretches of 2.1 and 3.8 kb, which are both absent from the promotor region of Col‐0 FUM2. By analysing mutants as well as mapping and natural populations with contrasting FUM2 alleles, the promotor insertion was linked to reduced FUM2 mRNA expression, reduced fumarase activity and reduced fumarate/malate ratio in leaves. In a large population of 174 natural accessions, the polymorphism was also found to be associated with the fumarate/malate ratio, malate and fumarate levels, and with dry weight at 15 days after sowing (DAS). The association with biomass production was confirmed in an even larger (251) accession population for dry weight at 22 DAS. The dominant Col‐0 allele that results in increased fumarate/malate ratios and enhanced biomass production is predominantly found in central/eastern European accessions, whereas the C24 type allele is prevalent on the Iberian Peninsula, west of the Rhine and in the British Isles. Our findings support the role of FUM2 in diurnal carbon storage, and point to a growth advantage of accessions carrying the FUM2 Col‐0 allele.     

Studies on a Vibrio vulnificus Functional Ortholog of Escherichia coli RNase E Imply a Conserved Function of RNase E-like Enzymes in Bacteria

RNase E (Rne) plays a key role in the processing and degradation of RNA in Escherichia coli. In the genome of Vibrio vulnificus, one open reading frame potentially encodes a protein homologous to E. coli RNase E, designated RNase EV, which N-terminal (1-500 amino acids) has 86.4% amino acid identity to the N-terminal catalytic part of RNase E (N-Rne). Here, we report that both the full-length and the N-terminal part of RNase EV (N-RneV) functionally complement E. coli RNase E and their expression consequently supports normal growth of RNase E-depleted E. coli cells. E. coli cells expressing N-RneV showed copy numbers of ColE1-type plasmid similar to that of E. coli cells expressing N-Rne, indicating in vivo ribonucleolytic activity of N-RneV on RNA I, an antisense regulator of ColE1-type plasmid replication. In vitro cleavage assays further showed that N-RneV has cleavage activity and specificity of RNase E on RNase E-targeted sequence of RNA I (BR13). Our findings suggest that RNase E-like proteins have conserved enzymatic properties that determine substrate specificity across species.     

Horizontal Transfer of phnAc Dioxygenase Genes within One of Two Phenotypically and Genotypically Distinctive Naphthalene-Degrading Guilds from Adjacent Soil Environments

Several distinct naphthalene dioxygenases have been characterized to date, which provides the opportunity to investigate the ecological significance, relative distribution, and transmission modes of the different analogs. In this study, we showed that a group of naphthalene-degrading isolates from a polycyclic aromatic hydrocarbon (PAH)-contaminated hillside soil were phenotypically and genotypically distinct from naphthalene-degrading organisms isolated from adjacent, more highly contaminated seep sediments. Mineralization of ¹⁴C-labeled naphthalene by soil slurries suggested that the in situ seep community was more acclimated to PAHs than was the in situ hillside community. phnAc-like genes were present in diverse naphthalene-degrading isolates cultured from the hillside soil, while nahAc-like genes were found only among isolates cultured from the seep sediments. The presence of a highly conserved nahAc allele among gram-negative isolates from the coal tar-contaminated seep area provided evidence for in situ horizontal gene transfer and was reported previously (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330-2337, 1997). Natural horizontal transfer of the phnAc sequence was also suggested by a comparison of the phnAc and 16S ribosomal DNA sequences of the hillside isolates. Analysis of metabolites produced by cell suspensions and patterns of amplicons produced by PCR analysis suggested both genetic and metabolic diversity among the naphthalene-degrading isolates of the contaminated hillside. These results provide new insights into the distribution, diversity, and transfer of phnAc alleles and increase our understanding of the acclimation of microbial communities to pollutants.     

Estimation of forest carbon budget from land cover change in South and North Korea between 1981 and 2010

This paper quantified carbon budget in the past 30 years (1981–2010) and identified the impact of land cover change on carbon dynamics using vegetation integrated simulator for trace gases (VISIT) model. North Korea was converted from carbon sink to source with 10.72 ± 5.18 Tg C yr^?1 of net ecosystem production (NEP) in the 1980s, 3.00 ± 7.96 Tg C yr^?1 in the 1990s, and ?0.46 ± 5.13 Tg C yr^?1 in the 2000s. NEP in South Korea was 10.55 ± 1.09 Tg C yr^?1 in the 1980s, 10.47 ± 7.28 Tg C yr^?1 in the 1990s, and 6.32 ± 5.02 Tg C yr^?1 in the 2000s, showing a gradual decline. In North Korea, NEP was decreased by 0.52 Tg yr^?1 in the 1990s due to reduction of forest, and increased by 0.36 Tg yr^?1 in the 2000s due to expansion of cropland. In South Korea, it was decreased by 0.24 Tg yr^?1 in the 1990s as urban and built-up area expanded, and increased by 0.04 Tg yr^?1 in the 2000s with the expansion of forest. These results suggest the importance of forest and land cover management against deforestation for ensuring national carbon balance.     

Factors that Predict Negative Results of QuantiFERON-TB Gold In-Tube Test in Patients with Culture-Confirmed Tuberculosis: A Multicenter Retrospective Cohort Study

Background

Interferon-γ release assays such as the QuantiFERON-TB Gold In-Tube Test (QFT-GIT) are designed to detect Mycobacterium tuberculosis infections, whether latent or manifesting as disease. However, a substantial number of persons with culture-confirmed tuberculosis (TB) have negative QFT-GITs. Information on host factors contributing to false-negative and indeterminate results are limited.

Methods

A multicenter retrospective cohort study was performed with 1,264 culture-confirmed TB patients older than 18 years who were subjected to the QFT-GIT at one of the six hospitals between May 2007 and February 2014. Patients with human immunodeficiency virus infection were excluded. Clinical and laboratory data were collected in South Korea.

Results

Of all patients, 87.6% (1,107/1,264) were diagnosed with pulmonary TB and 12.4% (157/1,264) with extrapulmonary TB. The rate of negative results was 14.4% (182/1,264). The following factors were highly correlated with false-negative results in the QFT-GIT: advanced age (age ≥ 65 years, odds ratio [OR] 1.57, 95% confidence interval [CI] 1.03–2.39), bilateral disease as determined by chest radiography (OR 1.75, 95% CI 1.13–2.72), malignancy (OR 2.42, 95% CI 1.30–4.49), and lymphocytopenia (total lymphocyte count < 1.0 × 10⁹/L, OR 1.86, 95% CI 1.21–2.87).

Conclusions

Consequently, QFT-GIT results need to be interpreted with caution in patients with these host risk factors such as the elderly, bilateral disease on chest radiography, or malignancy, or lymphocytopenia.