Global Warming Potential Is Not an Ecosystem Property

Ecosystems - Greenhouse gas metrics and ecosystem greenhouse gas fluxes should not be confounded with each other, either conceptually or in the language that we use to describe them. The global...     

Pyrimidine Biosynthesis Is Not an Essential Function for Trypanosoma brucei Bloodstream Forms

Background

African trypanosomes are capable of both pyrimidine biosynthesis and salvage of preformed pyrimidines from the host, but it is unknown whether either process is essential to the parasite.

Methodology/Principal Findings

Pyrimidine requirements for growth were investigated using strictly pyrimidine-free media, with or without single added pyrimidine sources. Growth rates of wild-type bloodstream form Trypanosoma brucei brucei were unchanged in pyrimidine-free medium. The essentiality of the de novo pyrimidine biosynthesis pathway was studied by knocking out the PYR6-5 locus that produces a fusion product of orotate phosphoribosyltransferase (OPRT) and Orotidine Monophosphate Decarboxylase (OMPDCase). The pyrimidine auxotroph was dependent on a suitable extracellular pyrimidine source. Pyrimidine starvation was rapidly lethal and non-reversible, causing incomplete DNA content in new cells. The phenotype could be rescued by addition of uracil; supplementation with uridine, 2′deoxyuridine, and cytidine allowed a diminished growth rate and density. PYR6-5⁻/⁻ trypanosomes were more sensitive to pyrimidine antimetabolites and displayed increased uracil transport rates and uridine phosphorylase activity. Pyrimidine auxotrophs were able to infect mice although the infection developed much more slowly than infection with the parental, prototrophic trypanosome line.

Conclusions/Significance

Pyrimidine salvage was not an essential function for bloodstream T. b. brucei. However, trypanosomes lacking de novo pyrimidine biosynthesis are completely dependent on an extracellular pyrimidine source, strongly preferring uracil, and display reduced infectivity. As T. brucei are able to salvage sufficient pyrimidines from the host environment, the pyrimidine biosynthesis pathway is not a viable drug target, although any interruption of pyrimidine supply was lethal.     

Conservation Research Is Not Happening Where It Is Most Needed

Target 19, set by the Convention on Biological Diversity, seeks to improve the knowledge, science base, and technologies relating to biodiversity. We will fail to achieve this target unless prolific biases in the field of conservation science are addressed. We reveal that comparatively less research is undertaken in the world’s most biodiverse countries, the science conducted in these countries is often not led by researchers based in-country, and these scientists are also underrepresented in important international fora. Mitigating these biases requires wide-ranging solutions: reforming open access publishing policies, enhancing science communication strategies, changing author attribution practices, improving representation in international processes, and strengthening infrastructure and human capacity for research in countries where it is most needed.In the environmental sciences, the scientific process generates evidence for policies and practices. Published evidence indicates that the quality standards associated with peer review have been met. Publishing also provides others with access to the evidence being shared, and increasingly, to the data and methodological processes underlying it. There are, however, strong biases in the peer-reviewed literature.Biodiversity and the threats to its persistence are not uniformly distributed across the globe and therefore some areas demand comparatively greater scientific attention. If research is biased away from the most biodiverse areas, then this will accentuate the impacts of the global biodiversity crisis and reduce our capacity to protect and manage the natural ecosystems that underpin human well-being. Target 19 of the Convention on Biodiversity (CBD) states that “By 2020, knowledge, the science base, and technologies relating to biodiversity, its values, functioning, status and trends, and the consequences of its loss, are improved, widely shared and transferred, and applied” [1]. Biases in conservation science will prevent us from achieving this target.We conducted the first comprehensive analysis of publishing trends of the conservation science literature. We identified all publications from 2014 on the topic of “conservation” in the research areas of environmental sciences, ecology, biodiversity conservation, plant sciences, zoology, and geography. We searched both the Thomson Reuters Zoological Records and Web of Science Core Collection databases, which returned 10,036 scientific publications (from 1,061 journals), after the duplicate, unrelated, and incomplete records were removed. For a subset of these publications (n = 7,593, or 81%), we manually identified at least one topic country, and we determined the relative conservation importance of these countries for mammal conservation [2] as well as a broader definition of conservation importance that considers richness of vascular plants, endemic species, and functional species [3].The countries for which knowledge is sparse coincide with where research is most urgently needed. The top five countries, ranked according to relative importance for mammal conservation (i.e, Indonesia, Madagascar, Peru, Mexico, and Australia), were represented in 11.9% of the publications (Fig 1). If we consider the broader definition of conservation importance that reflects the richness of vascular plants, endemic species, and functional species, then the top five countries (i.e., Ecuador, Costa Rica, Panama, the Dominican Republic, and Papua New Guinea) are the focus of only 1.6% of publications (4,5], will continue to be populated with biased data.Open in a separate windowFig 1Global distribution of publications on biodiversity conservation (S1 Data).

Table 1

Publishing trends and representation in the International Union for Conservation of Nature (IUCN) Specialist Groups or the Intergovernmental Panel on Biodiversity and Ecosystem Services (IPBES) for (A) the countries ranked highest in terms of importance for mammal conservation [2], (B) the countries ranked highest in terms of biodiversity [3], and (C) the United States and United Kingdom, for the purposes of comparison (S1 Data).

Cell Cycle Arrest Protein CDKN2C Is Not an HBV Host Factor

In summary, we demonstrated here that elevated CDKN2C expression was positively correlated with the proliferation state of the parenchymal liver cells, suggesting that CDKN2C expression in necro-inflammatory liver tissues, even though markedly upregulated, was not enough to facilitate the expression of the HBV host factor genes since it failed to repress cell cycle progression. Likewise, no correlation between CDKN2C expression and HBV replication in HBV-infected patients owing to the absence of CDKN2C expression in hepatocytes dominated in quiescent status and animal experiments also confirmed that CDKN2C cannot promote HBV replication in vivo. In conclusion, it is neither CDKN2C nor other single cell cycle specific gene itself, but instead the cell cycle arrest induced by them promotes HBV replication in patients with HBV infection. Hence, it is improper to term these genes as HBV host factors.     

The Barley Magnesium Chelatase 150-kD Subunit Is Not an Abscisic Acid Receptor

Magnesium chelatase is the first unique enzyme of the chlorophyll biosynthetic pathway. It is composed of three gene products of which the largest is 150 kD. This protein was recently identified as an abscisic acid receptor in Arabidopsis (Arabidopsis thaliana). We have evaluated whether the barley (Hordeum vulgare) magnesium chelatase large subunit, XanF, could be a receptor for the phytohormone. The study involved analysis of recombinant magnesium chelatase protein as well as several induced chlorophyll-deficient magnesium chelatase mutants with defects identified at the gene and protein levels. Abscisic acid had no effect on magnesium chelatase activity and binding to the barley 150-kD protein could not be shown. Magnesium chelatase mutants showed a wild-type response in respect to postgermination growth and stomatal aperture. Our results question the function of the large magnesium chelatase subunit as an abscisic acid receptor.     

Stepwise Folding of an Autotransporter Passenger Domain Is Not Essential for Its Secretion

Autotransporters are a superfamily of virulence proteins produced by Gram-negative bacteria. They consist of an N-terminal β-helical domain (“passenger domain”) that is secreted into the extracellular space and a C-terminal β-barrel domain (“β-domain”) that anchors the protein to the outer membrane. Because the periplasm lacks ATP, vectorial folding of the passenger domain in a C-to-N-terminal direction has been proposed to drive the secretion reaction. Consistent with this hypothesis, mutations that disrupt the folding of the C terminus of the passenger domain of the Escherichia coli O157:H7 autotransporter EspP have been shown to cause strong secretion defects. Here, we show that point mutations introduced at specific locations near the middle or N terminus of the EspP β-helix that perturb folding also impair secretion, but to a lesser degree. Surprisingly, we found that even multiple mutations that potentially abolish the stability of several consecutive rungs of the β-helix only moderately reduce secretion efficiency. Although these results provide evidence that the free energy derived from passenger domain folding contributes to secretion efficiency, they also suggest that a significant fraction of the energy required for secretion is derived from another source.     

FNDC5/Irisin Is Not Only a Myokine but Also an Adipokine

Exercise provides clear beneficial effects for the prevention of numerous diseases. However, many of the molecular events responsible for the curative and protective role of exercise remain elusive. The recent discovery of FNDC5/irisin protein that is liberated by muscle tissue in response to exercise might be an important finding with regard to this unsolved mechanism. The most striking aspect of this myokine is its alleged capacity to drive brown-fat development of white fat and thermogenesis. However, the nature and secretion form of this new protein is controversial. The present study reveals that rat skeletal muscle secretes a 25 kDa form of FNDC5, while the 12 kDa/irisin theoretical peptide was not detected. More importantly, this study is the first to reveal that white adipose tissue (WAT) also secretes FNDC5; hence, it may also behave as an adipokine. Our data using rat adipose tissue explants secretomes proves that visceral adipose tissue (VAT), and especially subcutaneous adipose tissue (SAT), express and secrete FNDC5. We also show that short-term periods of endurance exercise training induced FNDC5 secretion by SAT and VAT. Moreover, we observed that WAT significantly reduced FNDC5 secretion in fasting animals. Interestingly, WAT of obese animals over-secreted this hormone, which might suggest a type of resistance. Because 72% of circulating FNDC5/irisin was previously attributed to muscle secretion, our findings suggest a muscle-adipose tissue crosstalk through a regulatory feedback mechanism.     

When an ATPase Is Not an ATPase: at Low Temperatures the C-Terminal Domain of the ABC Transporter CvaB Is a GTPase

The ATP-binding cassette (ABC) transporters belong to a large superfamily of proteins which share a common function and a common nucleotide-binding domain. The CvaB protein from Escherichia coli is a member of the bacterial ABC exporter subfamily and is essential for the export of the peptide antibiotic colicin V. Here we report that, surprisingly, the CvaB carboxyl-terminal nucleotide-binding domain (BCTD) can be preferentially cross-linked to GTP but not to ATP at low temperatures. The cross-linking is Mg²⁺ and Mn²⁺ dependent. However, BCTD possesses similar GTPase and ATPase activities at 37°C, with the same kinetic parameters and with similar responses to inhibitors. Moreover, a point mutation (D654H) in CvaB that completely abolishes colicin V secretion severely impairs both GTPase and ATPase activities in the corresponding BCTD, indicating that the two activities are from the same enzyme. Interestingly, hydrolysis activity of ATP is much more cold sensitive than that of GTP: BCTD possesses mainly GTP hydrolysis activity at 10°C, consistent with the cross-linking results. These findings suggest a novel mechanism for an ABC protein-mediated transport with specificity for GTP hydrolysis.