Local adaptive evolution of two distinct clades of Beijing and T families of Mycobacterium tuberculosis in Chongqing: a Bayesian population structure and phylogenetic study.

BACKGROUND: Beijing sub-pedigree 2 (BSP2) and T sub-lineage 6 (TSL6) are two clades belonging to Beijing and T family of Mycobacterium tuberculosis (MTB), respectively, defined by Bayesian population structure analysis based on 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR). Globally, over 99% of BSP2 and 89% of TSL6 isolates were distributed in Chongqing, suggesting their possible local adaptive evolution. The objective of this paper is to explore whether BSP2 and TSL6 originated by their local adaptive evolution from the specific isolates of Beijing and T families in Chongqing. METHODS: The genotyping data of 16 090 MTB isolates were collected from laboratory collection, published literatures and SITVIT database before subjected to Bayesian population structure analysis based on 24-loci MIRU-VNTR. Spacer Oligonucleotide Forest (Spoligoforest) and 24-loci MIRU-VNTR-based minimum spanning tree (MST) were used to explore their phylogenetic pathways, with Bayesian demographic analysis for exploring the recent demographic change of TSL6. RESULTS: Phylogenetic analysis suggested that BSP2 and TSL6 in Chongqing may evolve from BSP4 and TSL5, respectively, which were locally predominant in Tibet and Jiangsu, respectively. Spoligoforest showed that Beijing and T families were genetically distant, while the convergence of the MIRU-VNTR pattern of BSP2 and TSL6 was revealed by WebLogo. The demographic analysis concluded that the recent demographic change of TSL6 might take 111.25 years. CONCLUSIONS: BSP2 and TSL6 clades might originate from BSP4 and TSL5, respectively, by their local adaptive evolution in Chongqing. Our study suggests MIRU-VNTR be combined with other robust markers for a more comprehensive genotyping approach, especially for families of clades with the same MIRU-VNTR pattern.

An Eco- and User-Friendly Herbicide.

The increasing use of pesticides in agriculture and gardening has caused severe deterioration to both the ecosystem and the health of users (human beings), so there is an urgent need for eco- and user-friendly pesticides. Among a variety of herbicides, paraquat (PQ), frequently used as an effective herbicidal agent worldwide, is well-known for its serious toxicity that has killed, and harmed, thousands of people and countless wildlife such as fish. Herein, we present a facile supramolecular formulation of PQ@cucurbit[7]uril (PQ@CB[7]), prepared by simply mixing PQ with equivalent (molar) CB[7] in water. With addition of CB[7], PQ's cellular uptake was dramatically inhibited. The reactive oxygen species (ROS) generation and the associated apoptosis otherwise induced by PQ in cellular models were both reduced, resulting in increased cellular viability. In a wildtype zebrafish model that is a typical fragile wildlife species in the ecosystem, the supramolecular formulation exhibited significantly reduced hepatotoxicity and increased survival rate, in comparison with those of the fish exposed to free PQ. In a mouse model that is clinically relevant to human being, the administration of PQ@CB[7] significantly alleviated major organ injuries and unusual hematological parameters that were otherwise induced by free PQ, resulting in a significantly increased survival rate. Meanwhile, this formulation maintained effective herbicidal activity that was equivalent to that of free PQ. Taken together, this facile supramolecular PQ formulation is providing not only an extremely rare example of an eco- and user-friendly herbicide that has been desired for decades but also a practical solution for green agriculture.

Skeletal muscle proteome analysis provides insights on high altitude adaptation of yaks.

The differences in proteome profile of longissimus thoracis (LT) muscles of yak (Bos grunniens) and cattle (Bos taurus) were investigated employing isobaric tag for relative and absolute quantification (iTRAQ) approach to identify differentially expressed proteins and to understand the cellular level adaptations of yaks to high altitudes. Fifty-two proteins were differentially expressed in the two species, among which 20 were up-regulated and 32 were down-regulated in yaks. Gene ontology (GO) annotation revealed that most of the differentially expressed proteins were involved in the molecular function of protein binding, catalytic activity, and structural activity. Protein-protein interaction analysis recognized 24 proteins (involved in structural integrity, calcium ion regulation, and energy metabolism), as key nodes in biological interaction networks. These findings indicated that mammals living at high altitudes could possibly generate energy by pronounced protein catabolism and glycolysis compared with those living in the plains. The key differentially expressed proteins included calsequestrin 1, prostaglandin reductase 1 and ATP synthase subunit O, which were possibly associated with the cellular and biochemical adaptation of yaks to high altitude. These key proteins may be exploited as candidate proteins for mammalian adaptation to high altitudes.

Brassinosteroid Signaling in Plant⁻Microbe Interactions.

As sessile organisms, plants are frequently exposed to different stress conditions caused by either biotic or abiotic factors. Understanding the mechanisms that underlie plant interaction with the biotic and abiotic environments is fundamental to both plant biotechnology and sustainable agriculture. Brassinosteroids (BRs) are a group of plant-specific steroidal compounds essential for normal growth and development. Recent research evidence indicates that BRs are also actively involved in plant⁻environment interactions and play important roles in shaping plant fitness and the growth⁻defense trade-offs. In this minireview, we focus our attention on recent advances in the understanding of BR functions in modulating plant interactions with different pathogenic microbes, with particular focus on how BR signaling primes the plant innate immunity pathways and achieves a trade-off between growth and immunity.