Relative Amino Acid Composition Signatures of Organisms and Environments

Background

Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment.

Methodologies/Principal Findings

To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny.

Conclusions

Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.     

Differential Regulation of MAPK Phosphorylation in the Dorsal Hippocampus in Response to Prolonged Morphine Withdrawal-Induced Depressive-Like Symptoms in Mice

Depression is one of the most frequent neuropsychiatric comorbidities associated with opiate addiction. Mitogen activated protein kinase (MAPK) and MAPK phosphatase (MKP) are involved in drug addiction and depression. However, the potential role of MAPK and MKP in depression caused by morphine withdrawal remains unclear. We utilized a mouse model of repeated morphine administration to examine the molecular mechanisms that contribute to prolonged withdrawal induced depressive-like behaviors. Depressive-like behaviors were significant at 1 week after withdrawal and worsened over time. Phospho-ERK (extracellular signal-regulated protein kinase) was decreased and MKP-1 was elevated in the hippocampus, and JNK (c-Jun N-terminal protein kinase), p38 (p38 protein kinase) and MKP-3 were unaffected. A pharmacological blockade of MKP-1 by intra-hippocampal sanguinarine (SA) infusion prevented the development of depressive-like behaviors and resulted in relatively normal levels of MKP-1 and phospho-ERK after withdrawal. Our findings support the association between hippocampal MAPK phosphorylation and prolonged morphine withdrawal-induced depression, and emphasize the MKP-1 as an negative regulator of the ERK phosphorylation that contributes to depression.     

Insulin-Producing Cells Derived from Human Embryonic Stem Cells: Comparison of Definitive Endoderm- and Nestin-Positive Progenitor-Based Differentiation Strategies

Human embryonic stem cells (hESCs) are pluripotent and capable of undergoing multilineage differentiation into highly specialized cells including pancreatic islet cells. Thus, they represent a novel alternative source for targeted therapies and regenerative medicine for diabetes. Significant progress has been made in differentiating hESCs toward pancreatic lineages. One approach is based on the similarities of pancreatic β cell and neuroepithelial development. Nestin-positive cells are selected as pancreatic β cell precursors and further differentiated to secrete insulin. The other approach is based on our knowledge of developmental biology in which the differentiation protocol sequentially reproduces the individual steps that are known in normal β cell ontogenesis during fetal pancreatic development. In the present study, the hESC cell line PKU1.1 was induced to differentiate into insulin-producing cells (IPCs) using both protocols. The differentiation process was dynamically investigated and the similarities and differences between both strategies were explored. Our results show that IPCs can be successfully induced with both differentiation strategies. The resulting IPCs from both protocols shared many similar features with pancreatic islet cells, but not mature, functional β cells. However, these differently-derived IPC cell types displayed specific morphologies and different expression levels of pancreatic islet development-related markers. These data not only broaden our outlook on hESC differentiation into IPCs, but also extend the full potential of these processes for regenerative medicine in diabetes.     

Design and Optimization of Planting Process Parameters for 2ZYX-2 Type Green Onion Ditching and Transplanting Machine

Considering the current low level of mechanization for domestic green onion planting and the high labor intensity of artificial planting, a 2ZYX-2 green onion ditching and transplanting machine, which can complete ditching, ridging, transplanting, repression, soil covering and other operations, is designed in this study. The Central Composite test design method was carried out with the speed of the transplanting machine, the depth of the opener and the horizontal position of the opener as the experimental factors and with the qualification ratio of perpendicularity, the variation coefficient of the plant spacing and the qualification ratio of the planting depth as the test index. Through the analysis of the model interaction and response surface, the change laws that the influence the machine’s forward speed, the depth of the opener and the horizontal position of the opener were studied. The regression model was optimized by Design-Expert 8.0.6 software, and the accuracy of the predicted results was verified by experiments. The optimal working parameters showed that the forward speed of the machine was 0.06 m/s, the depth of the opener was 102 mm, and the horizontal position of the opener was 29 mm. Under conditions of optimal working parameters, the qualification rate of the verticality was 86.83%, the coefficient of variation for the plant spacing was 2.77, and the pass rate of planting depth was 88.26%. The research related to the thesis can provide a reference for the mechanized planting of green onion, which is of great significance to the cost-effectiveness of the green onion industry.     

Protecting tobacco plants from O3 injury by Bacillus velezensis with production of acetoin

Plant growth-promoting rhizobacteria (PGPRs) confer benefits to crops by producing volatile organic compounds (VOCs) to trigger induced systemic tolerance (IST). Here we show that Bacillus velezensis GJ11, a kind of PGPRs, produce VOCs such as 2,3-butanediol and acetoin to trigger IST and cause stomatal closure against O₃ injury in tobacco plants. Compared to 2,3-butanediol, acetoin was more effective on triggering IST against O₃ injury. The bdh-knockout strain GJ11Δbdh with a blocked metabolic pathway from acetoin to 2,3-butanediol produced more acetoin triggering stronger IST against O₃ injury than GJ11. Both acetoin and GJ11Δbdh effectively enhance the antioxidant enzymes activity (e.g. superoxide dismutase and catalases) that is favorable for scavenging the reactive oxygen species like H₂O₂ in leaves after exposure to O₃. Consequently, less H₂O₂ accumulation was observed, and reasonably less chlorophylls and proteins were damaged by H₂O₂ in the tobacco leaves treated with acetoin or GJ11Δbdh. The field experiment also showed that both acetoin and GJ11Δbdh could protect tobacco plants from O₃ injury after application by root-drench. This study provides new insights into the role of rhizobacterial B. velezensis and its volatile component of acetoin in triggering defense responses against stresses such as O₃ in plants.     

Exogenous Spermidine Promotes Somatic Embryogenesis of <i>Cunninghamia lanceolata</i> by Altering the Endogenous Phytohormone Content

In order to study how exogenous hormones in C. lanceolata (gymnosperm) regulate somatic embryogenesis, we measured the endogenous phytohormones of two genotypes with different somatic embryogenesis efficiency and found that an increase in endogenous concentrations of IAA and ABA may be correlated to more efficient somatic embryogenesis. By applying exogenous spermidine, we found that exogenous hormones may affect somatic embryogenesis efficiency through affecting the endogenous phytohormone content. Based on these results, further studies can be conducted whereby the concentration of exogenous hormones or the levels of endogenous phytohormones by molecular methods are regulated to promote somatic embryogenesis. Our research may benefit the long-term economic output of the forestry industry and lays the foundation to studying the molecular mechanism that controls somatic embryogenesis efficiency.     

Knockout of SlNPR1 enhances tomato plants resistance against Botrytis cinerea by modulating ROS homeostasis and JA/ET signaling pathways

Tomato is one of the most popular horticultural crops, and many commercial tomato cultivars are particularly susceptible to Botrytis cinerea. Non-expressor of pathogenesis-related gene 1 (NPR1) is a critical component of the plant defense mechanisms. However, our understanding of how SlNPR1 influences disease resistance in tomato is still limited. In this study, two independent slnpr1 mutants were used to study the role of SlNPR1 in tomato resistance against B. cinerea. Compared to (WT), slnpr1 leaves exhibited enhanced resistance against B. cinerea with smaller lesion sizes, higher activities of chitinase (CHI), β-1, 3-glucanases (GLU) and phenylalanine ammonia-lyase (PAL), and significantly increased expressions of pathogenesis-related genes (PRs). The increased activities of peroxidase (POD), ascorbate peroxidase (APX) and decreased catalase (CAT) activities collectively regulated reactive oxygen species (ROS) homeostasis in slnpr1 mutants. The integrity of the cell wall in slnpr1 mutants was maintained. Moreover, the enhanced resistance was further reflected by induction of defense genes involved in jasmonic acid (JA) and ethylene (ET) signaling pathways. Taken together, these findings revealed that knocking out SlNPR1 resulted in increased activities of defense enzymes, changes in ROS homeostasis and integrity of cell walls, and activation of JA and ET pathways, which confers resistance against B. cinerea in tomato plants.