Erythrodermic mycosis fungoides: A case report.

BACKGROUND: Mycosis fungoides is the most common primary cutaneous T-cell lymphoma, whereas generalized erythroderma is rare. In this report, we describe a case of mycosis fungoides with generalized erythroderma using complete clinical data and [18F]fluoroDglucose positron emission tomography/computed tomography (18F-FDG PET/CT) images. CASE SUMMARY: Systemic skin redness with desquamation for three years confirmed mycosis fungoides within one month. The patient underwent left axillary lymphadenectomy biopsy; pathological biopsy suggested abnormal T-cell lesions consistent with mycosis fungoides involving lymph nodes. The patient received methotrexate, 5 mg twice weekly, as part of their chemotherapy regimen. Patients January half after discharge, no obvious cause of high fever, left axillary lymph nodes with red heat pain, and rupture entered our hospital for treatment. CONCLUSION: The 18F-FDG PET/CT is essential for early diagnosis and timely treatment.

Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach.

BACKGROUND: Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities. RESULTS: Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity. CONCLUSIONS: In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.

Identification of T-DNA structure and insertion site in transgenic crops using targeted capture sequencing.

The commercialization of GE crops requires a rigorous safety assessment, which includes a precise DNA level characterization of inserted T-DNA. In the past, several strategies have been developed for identifying T-DNA insertion sites including, Southern blot and different PCR-based methods. However, these methods are often challenging to scale up for screening of dozens of transgenic events and for crops with complex genomes, like potato. Here, we report using target capture sequencing (TCS) to characterize the T-DNA structure and insertion sites of 34 transgenic events in potato. This T-DNA is an 18 kb fragment between left and right borders and carries three resistance (R) genes (RB, Rpi-blb2 and Rpi-vnt1.1 genes) that result in complete resistance to late blight disease. Using TCS, we obtained a high sequence read coverage within the T-DNA and junction regions. We identified the T-DNA breakpoints on either ends for 85% of the transgenic events. About 74% of the transgenic events had their T-DNA with 3R gene sequences intact. The flanking sequences of the T-DNA were from the potato genome for half of the transgenic events, and about a third (11) of the transgenic events have a single T-DNA insertion mapped into the potato genome, of which five events do not interrupt an existing potato gene. The TCS results were confirmed using PCR and Sanger sequencing for 6 of the best transgenic events representing 20% of the transgenic events suitable for regulatory approval. These results demonstrate the wide applicability of TCS for the precise T-DNA insertion characterization in transgenic crops.

Assessment of fetal left atrial volume and function using a novel left atrial volume tracking method.

BACKGROUND: Several fetal cardiovascular structural defects may alter the hemodynamics of the cardiac chambers resulting in changes in chamber sizes. Quantitative measurements of the sizes of cardiac chambers can augment the diagnostic power of fetal echocardiography. AIMS: Using a new left atrial volume tracking (LAVT) method, time-left atrial volume curves (TLAVCs) can be automatically obtained. The goal of this study was to examine whether this method can be used to evaluate left atrial volume (LAV) and provide reference values for LAV and indices of left atrial function in normal human fetuses. METHODS: Two hundred and four normal human fetuses were enrolled. Using LAVT, the maximal left atrial volume (LAVmax) and minimal left atrial volume (LAVmin) were measured from TLAVCs. Left atrial ejection fraction (EF) was calculated. The maximal left atrial area (LAAmax) and minimal left atrial area (LAAmin) were measured using manual method tracing. RESULTS: Between 21 and 40 weeks, mean LAVmax increased from 0.27 ml to 4.15 ml, and mean LAVmin increased from 0.13 ml to 2.26 ml, respectively, while the EF remained stable at around 0.43. From 21 to 40 weeks, mean LAAmax increased from 0.61 cm2 to 2.64 cm2, and mean LAAmin increased from 0.34 cm2 to 1.53 cm2. CONCLUSIONS: This study establishes reference values for fetal LAV during the second half of gestation. The LAVT method appears to be feasible in estimating fetal LAV and shows potential for assessing left atrial function.

Nonflammable Localized High-Concentration Electrolytes with Long-Term Cycling Stability for High-Performance Li Metal Batteries.

High-concentration electrolytes (HCEs) can effectively enhance interface stability and cycle performance of Li metal batteries (LMBs). However, HCEs suffer from low ionic conductivity, high viscosity, high cost, and high density. Herein, fluorobenzene (FB) diluted localized high-concentration electrolytes (LHCEs) consisting of lithium bis(fluorosulfonyl)imide (LiFSI)/triethyl phosphate (TEP)/FB are developed. 2.3 M LHCE can reserve concentrated Li+-FSI--TEP solvation structures. Diluent FB possesses low density, low viscosity, low cost, low dielectric constant, low LUMO, and a good fluorine-donating property, which can significantly reduce viscosity, improve ionic conductivity, promote the formation of LiF-rich SEI, and enhance interaction of Li+-TEP and Li+-FSI- ion-pairs of the electrolytes. 2.3 M LHCE is a highly safe nonflammable electrolyte. 2.3 M LHCE can effectively inhibit dendrite growth on Li metal anode. 2.3 M LHCE endows LiFePO4 cells with good rate capability (discharge capacity of 112.7 mAh g-1 at 5 C rate) and excellent cycling performance (capacity retention of 95.4% after 1000 cycles). 2.3 M LHCE also shows good compatibility with LiNi0.8Co0.1Mn0.1O2 and exhibits outstanding cycle stability (capacity retention of 86.4% after 500 cycles). Therefore, 2.3 M LHCE is a promising electrolyte for practical applications in LMBs.

Using single cell type proteomics to identify Al-induced proteomes in outer layer cells and interior tissues in the apical meristem/cell division regions of tomato root-tips.

Aluminum (Al) toxicity primarily targets the root tips, inhibiting root growth and function and leading to crop yield losses on acidic soils. Previously we reported using laser capture microdissection (LCM) proteomics to identify Al-induced proteins in the outer layer cells in the transitional zone of tomato root-tips. This study aims to further characterize Al-induced proteomic dynamics from the outer to interior tissues, thus providing a panoramic view reflecting Al resistance in the root tip as a whole in tomatoes. Three types of cells were isolated via LCM from the basal 350-400 µm (below cell elongation regions) of root tips using tomato (Solanum lycopersicum) 'Micro-Tom' plants. Type I and Type II were from Al-treated plants. Type I included cells of the outer three layers, i.e., the epidermis and cortex initials and the quiescent center (QC) in root apical meristem (RAM), and Type II possessed the interior tissues of the same region. Type III contained cells from the non-Al-treated root tips collected in the same region as Type I. Two tandem mass tag (TMT) proteomics analyses with three biological replicates for each sample type were conducted. The TMTexp1 (comparing Type I and Type II) identified 6575 quantifiable proteins and 178 different abundance proteins (DAPs). The TMTexp2 (comparing Type I and Type III) identified 7197 quantifiable proteins and 162 DAPs. Among all quantified proteins (7685) from the two TMT experiments, 6088 (79%) proteins, including 313 DAPs (92% of the 340 total), were identified in all tissues. A model reflecting the tissue-specific Al-resistance mechanism was proposed, in which the level of the citrate transporter MATE protein, involved in Al exclusion, accumulated to the highest level in the outer-layer cells but decreased toward the interior of root-tips (which concurs with the tissue-specific importance in Al resistance). Proteins for biosynthesis of ethylene and jasmonic acid, proteolytic enzymes, stress-responsive proteins, and cell wall modeling were affected by Al treatment, some in a cell type-specific manner. The KEGG metabolite pathways enriched with these DAPs changed depending on the cell types. This study demonstrated the advantage of using the tissue/cell-specific analysis for identifying proteins and their dynamic changes directly associated with Al resistance in the root-tip region. The proteomics datasets have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (https://www.ebi.ac.uk/pride/) with the dataset identifier as PXD021994 under project title: Proteomics studies of outer and inner cellular layers of tomato root-tips for Al stress, Project DOI: 10.6019/ PXD021994; and PXD018234 under Project title: Al-induced root proteomics changes in stress-acclimated tomato plant, Project DOI: https://doi.org/10.6019/PXD018234. SIGNIFICANCE: This paper presents the method of using laser capture microdissection (LCM) to collect homogenous cell-type specific tissue samples from the outer layers and inner central regions of tomato root-tips. The tandem mass tag-proteomics analysis showed that the outer-layer cells expressed proteomes that were different from the inner tissues of Al-treated root-tips; proteins related to resistance/tolerance to Al toxicity were highly accumulated in the outer-layer cells. Furthermore, the Al-treated outer-layer cells expressed proteomes which were different from the non-Al treated counterpart cells. This study has provided the first dataset of proteins differentiating from the outer to inner layers of cells in Al-treated root-tips. It provided convincing experimental evidences demonstrating the single-cell type proteomics as a powerful analytical approach to identify Al tolerance mechanisms in plants. The analytical procedure of LCM-tandem mass tag-quantitative proteomics analysis has a broad application for proteomics analysis of spatially separated cells in complex tissues.

PpERF1b-like enhances lignin synthesis in pear (Pyrus pyrifolia) 'hard-end' fruit.

The hard-end is a disorder of pear fruit, however, the mechanisms underlying its development remain unknown. In this study, we found that the hard-end fruit contained a higher transcript abundance level of ethylene-response factor 1b-like (PpERF1b-like) and released more ethylene compared to normal pear. In the ethephon treated normal fruit, flesh tissues accumulated more lignin together with elevated expression of PpERF1b-like. Overexpressing PpERF1b-like transiently in fruit and stably in callus increased lignin accumulation and the expression of lignin biosynthesis genes; the opposite results were observed in fruit showing repressed expression of PpERF1b-like. These results confirmed the role of PpERF1b-like in promoting hard-end formation through promoting lignin synthesis. This study provided valuable information for further clarifying the regulation of hard-end formation in pear.

Non-sterile fermentation of food waste using thermophilic and alkaliphilic Bacillus licheniformis YNP5-TSU for 2,3-butanediol production.

Conversion of food waste into 2,3-butanediol (2,3-BDO) via microbial fermentation provides a promising way to reduce waste disposal to landfills and produce sustainable chemicals. However, sterilization of food waste, an energy- and capital-costly process, is generally required before fermentation to avoid any contamination, which reduces the energy net output and economic feasibility of food waste fermentation. In this study, we investigated the non-sterile fermentation of food waste to produce 2,3-BDO using a newly isolated thermophilic and alkaliphilic B. licheniformis YNP5-TSU. Three unitary food waste samples (i.e., pepper, pineapple, cabbage wastes) and one miscellaneous food waste mixture were respectively inoculated with B. licheniformis YNP5-TSU under non-sterile conditions. At 50 °C and an initial pH of 9.0, B. licheniformis YNP5-TSU was able to consume all sugars in food waste and produce 5.2, 5.9, 5.9 and 4.3 g/L of 2,3-BDO within 24 h from pepper, pineapple, cabbage and miscellaneous wastes, respectively, corresponding to a yield of 0.40, 0.38, 0.41 and 0.41 g 2,3-BDO/g sugar. These 2,3-BDO concentrations and yields from the non-sterile fermentations were comparable to those from the traditional sterile fermentations, which produced 4.0-6.8 g/L of 2,3-BDO with yields of 0.31-0.48 g 2,3-BDO/g sugar. Moreover, B. licheniformis was able to ferment various food wastes (pepper, pineapple and miscellaneous wastes) without any external nutrient addition and produce similar 2,3-BDO quantities. The non-sterile fermentation of food waste using novel thermophilic and alkaliphilic B. licheniformis YNP5-TSU provides a robust and energy-efficient approach to convert food waste to high-value chemicals.

Genotypic variation of flavonols and antioxidant capacity in broccoli.

Flavonols are gaining increasing interests due to their diverse health benefits for humans. Broccoli is a main flavonol source in our diet, but the genetic variation of flavonols and their correlation with antioxidant capacity remain to be understood. Here, we examined variations of the two major flavonols kaempferol and quercetin in florets and leaves of 15 diverse broccoli accessions by ultra-performance liquid chromatography. Broccoli accumulated more kaempferol than quercetin in most of the accessions tested, with the ratios varying from 4.4 to 27.9 in leaves and 0.4 to 4.4 in florets. Total flavonoids showed 2.5-fold and 3.3-fold differences in leaves and florets of these accessions, respectively. Principle component analysis revealed that flavonols, along with the key biosynthetic pathway genes, correlated with antioxidant capacity related indicators. This study provides important information for broccoli flavonol genotypic variations and correlation with antioxidant capacity, and will facilitate the development of flavonol enriched cultivars in broccoli.

Proteome profile changes during poly-hydroxybutyrate intracellular mobilization in gram positive Bacillus cereus tsu1.

BACKGROUND: Bacillus cereus is a bacterial species which grows efficiently on a wide range of carbon sources and accumulates biopolymer poly-hydroxybutyrate (PHB) up to 80% cell dry weight. PHB is an aliphatic polymer produced and stored intracellularly as a reservoir of carbon and energy, its mobilization is a key biological process for sporulation in Bacillus spp. Previously, B. cereus tsu1 was isolated and cultured on rapeseed cake substrate (RCS), with maximum of PHB accumulation reached within 12 h, and depleted after 48 h. Fore-spore and spore structure were observed after 24 h culture. RESULTS: Quantitative proteomic analysis of B. cereus tsu1 identified 2952 quantifiable proteins, and 244 significantly changed proteins (SCPs) in the 24 h:12 h pair of samples, and 325 SCPs in the 48 h:12 h pair of samples. Based on gene ontology classification analysis, biological processes enriched only in the 24 h:12 h SCPs include purine nucleotide metabolism, protein folding, metal ion homeostasis, response to stress, carboxylic acid catabolism, and cellular amino acid catabolism. The 48 h:12 h SCPs were enriched into processes including carbohydrate metabolism, protein metabolism, oxidative phosphorylation, and formation of translation ternary structure. A key enzyme for PHB metabolism, poly(R)-hydroxyalkanoic acid synthase (PhaC, KGT44865) accumulated significantly higher in 12 h-culture. Sporulation related proteins SigF and SpoEII were significantly higher in 24 h-samples. Enzymes for nitrate respiration and fermentation accumulated to the highest abundance level in 48 h-culture. CONCLUSIONS: Changes in proteome of B. cereus tsu1 during PHB intracellular mobilization were characterized in this study. The key enzyme PhaC for PHB synthesis increased significantly after 12 h-culture which supports the highest PHB accumulation at this time point. The protein abundance level of SpoIIE and SigF also increased, correlating with sporulation in 24 h-culture. Enzymes for nitrate respiration and fermentation were significantly induced in 48 h-culture which indicates the depletion of oxygen at this stage and carbon flow towards fermentative growth. Results from this study provide insights into proteome profile changes during PHB accumulation and reuse, which can be applied to achieve a higher PHB yield and to improve bacterial growth performance and stress resistance.

Al-induced proteomics changes in tomato plants over-expressing a glyoxalase I gene.

Glyoxalase I (Gly I) is the first enzyme in the glutathionine-dependent glyoxalase pathway for detoxification of methylglyoxal (MG) under stress conditions. Transgenic tomato 'Money Maker' plants overexpressing tomato SlGlyI gene (tomato unigene accession SGN-U582631/Solyc09g082120.3.1) were generated and homozygous lines were obtained after four generations of self-pollination. In this study, SlGlyI-overepxressing line (GlyI), wild type (WT, negative control) and plants transformed with empty vector (ECtr, positive control), were subjected to Al-treatment by growing in Magnavaca's nutrient solution (pH 4.5) supplemented with 20 µM Al3+ ion activity. After 30 days of treatments, the fresh and dry weight of shoots and roots of plants from Al-treated conditions decreased significantly compared to the non-treated conditions for all the three lines. When compared across the three lines, root fresh and dry weight of GlyI was significant higher than WT and ECtr, whereas there was no difference in shoot tissues. The basal 5 mm root-tips of GlyI plants expressed a significantly higher level of glyoxalase activity under both non-Al-treated and Al-treated conditions compared to the two control lines. Under Al-treated condition, there was a significant increase in MG content in ECtr and WT lines, but not in GlyI line. Quantitative proteomics analysis using tandem mass tags mass spectrometry identified 4080 quantifiable proteins and 201 Al-induced differentially expressed proteins (DEPs) in root-tip tissues from GlyI, and 4273 proteins and 230 DEPs from ECtr. The Al-down-regulated DEPs were classified into molecular pathways of gene transcription, RNA splicing and protein biosynthesis in both GlyI and ECtr lines. The Al-induced DEPs in GlyI associated with tolerance to Al3+ and MG toxicity are involved in callose degradation, cell wall components (xylan acetylation and pectin degradation), oxidative stress (antioxidants) and turnover of Al-damaged epidermal cells, repair of damaged DNA, epigenetics, gene transcription, and protein translation. A protein-protein association network was constructed to aid the selection of proteins in the same pathway but differentially regulated in GlyI or ECtr lines. Proteomics data are available via ProteomeXchange with identifiers PXD009456 under project title '25Dec2017_Suping_XSexp2_ITAG3.2' for SlGlyI-overexpressing tomato plants and PXD009848 under project title '25Dec2017_Suping_XSexp3_ITAG3.2' for positive control ECtr line transformed with empty vector.

Comparative Proteomics of Root Apex and Root Elongation Zones Provides Insights into Molecular Mechanisms for Drought Stress and Recovery Adjustment in Switchgrass.

Switchgrass plants were grown in a Sandwich tube system to induce gradual drought stress by withholding watering. After 29 days, the leaf photosynthetic rate decreased significantly, compared to the control plants which were watered regularly. The drought-treated plants recovered to the same leaf water content after three days of re-watering. The root tip (1cm basal fragment, designated as RT1 hereafter) and the elongation/maturation zone (the next upper 1 cm tissue, designated as RT2 hereafter) tissues were collected at the 29th day of drought stress treatment, (named SDT for severe drought treated), after one (D1W) and three days (D3W) of re-watering. The tandem mass tags mass spectrometry-based quantitative proteomics analysis was performed to identify the proteomes, and drought-induced differentially accumulated proteins (DAPs). From RT1 tissues, 6156, 7687, and 7699 proteins were quantified, and 296, 535, and 384 DAPs were identified in the SDT, D1W, and D3W samples, respectively. From RT2 tissues, 7382, 7255, and 6883 proteins were quantified, and 393, 587, and 321 proteins DAPs were identified in the SDT, D1W, and D3W samples. Between RT1 and RT2 tissues, very few DAPs overlapped at SDT, but the number of such proteins increased during the recovery phase. A large number of hydrophilic proteins and stress-responsive proteins were induced during SDT and remained at a higher level during the recovery stages. A large number of DAPs in RT1 tissues maintained the same expression pattern throughout drought treatment and the recovery phases. The DAPs in RT1 tissues were classified in cell proliferation, mitotic cell division, and chromatin modification, and those in RT2 were placed in cell wall remodeling and cell expansion processes. This study provided information pertaining to root zone-specific proteome changes during drought and recover phases, which will allow us to select proteins (genes) as better defined targets for developing drought tolerant plants. The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD017441.

The Al-induced proteomes of epidermal and outer cortical cells in root apex of cherry tomato 'LA 2710'.

This paper reports a laser capture microdissection-tandem mass tag-quantitative proteomics analysis of Al-sensitive cells in root tips. Cherry tomato (Solanum lycopersicum var. cerasiforme 'LA2710') seedlings were treated under 15 µM Al3+ activity for 13 d. Root-tip longitudinal fresh frozen tissue sections of 10 µm thickness were prepared. The Al-sensitive root zone and cells were determined using histochemical analysis of root-tips and micro-sections. A procedure for collecting the Al-sensitive cells using laser capture microdissection-protein extraction-tandem mass tag-proteomics analysis was developed. Proteomics analysis of 18 µg protein/sample with three biological replicates per treatment condition identified 3879 quantifiable proteins each associated with two or more unique peptides. Quantified proteins constituted a broad range of Kyoto Encyclopedia of Genes and Genomes pathways when searched in the annotated tomato genome. Differentially expressed proteins between the Al-treated and non-Al treated control conditions were identified, including 128 Al-up-regulated and 32 Al-down-regulated proteins. Analysis of functional pathways and protein-protein interaction networks showed that the Al-down-regulated proteins are involved in transcription and translation, and the Al-up-regulated proteins are associated with antioxidant and detoxification and protein quality control processes. The proteomics data are available via ProteomeXchange with identifier PXD010459 under project title 'LCM-quantitative proteomics analysis of Al-sensitive tomato root cells'. SIGNIFICANCE: This paper presents an efficient laser capture microdissection-tandem mass tag-quantitative proteomics analysis platform for the analysis of Al sensitive root cells. The analytical procedure has a broad application for proteomics analysis of spatially separated cells from complex tissues. This study has provided a comprehensive proteomics dataset expressed in the epidermal and outer-cortical cells at root-tip transition zone of Al-treated tomato seedlings. The proteomes from the Al-sensitive root cells are valuable resources for understanding and improving Al tolerance in plants.

PpNAC187 Enhances Lignin Synthesis in 'Whangkeumbae' Pear (Pyrus pyrifolia) 'Hard-End' Fruit.

A disorder in pears that is known as 'hard-end' fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of 'Whangkeumbae' pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of 'Whangkeumbae' fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR and PpCOMT transcripts was observed, which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in the control plants that were transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.

Overexpression of Pear (Pyrus pyrifolia) CAD2 in Tomato Affects Lignin Content.

PpCAD2 was originally isolated from the 'Wangkumbae' pear (Pyrus pyrifolia Nakai), and it encodes for cinnamyl alcohol dehydrogenase (CAD), which is a key enzyme in the lignin biosynthesis pathway. In order to verify the function of PpCAD2, transgenic tomato (Solanum lycopersicum) 'Micro-Tom' plants were generated using over-expression constructs via the agrobacterium-mediated transformation method. The results showed that the PpCAD2 over-expression transgenic tomato plant had a strong growth vigor. Furthermore, these PpCAD2 over-expression transgenic tomato plants contained a higher lignin content and CAD enzymatic activity in the stem, leaf and fruit pericarp tissues, and formed a greater number of vessel elements in the stem and leaf vein, compared to wild type tomato plants. This study clearly indicated that overexpressing PpCAD2 increased the lignin deposition of transgenic tomato plants, and thus validated the function of PpCAD2 in lignin biosynthesis.

Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives.

Microbes are ubiquitously distributed in nature and are a critical part of the holobiont fitness. They are perceived as the most potential biochemical reservoir of inordinately diverse and multi-functional enzymes. The robust nature of the microbial enzymes with thermostability, pH stability and multi-functionality make them potential candidates for the efficient biotechnological processes under diverse physio-chemical conditions. The need for sustainable solutions to various environmental challenges has further surged the demand for industrial enzymes. Fueled by the recent advent of recombinant DNA technology, genetic engineering, and high-throughput sequencing and omics techniques, numerous microbial enzymes have been developed and further exploited for various industrial and therapeutic applications. Most of the hydrolytic enzymes (protease being the dominant hydrolytic enzyme) have broad range of industrial uses such as food and feed processing, polymer synthesis, production of pharmaceuticals, manufactures of detergents, paper and textiles, and bio-fuel refinery. In this review article, after a short overview of microbial enzymes, an approach has been made to highlight and discuss their potential relevance in biotechnological applications and industrial bio-processes, significant biochemical characteristics of the microbial enzymes, and various tools that are revitalizing the novel enzymes discovery.

Association of Proteomics Changes with Al-Sensitive Root Zones in Switchgrass.

In this paper, we report on aluminum (Al)-induced root proteomic changes in switchgrass. After growth in a hydroponic culture system supplemented with 400 µM of Al, plants began to show signs of physiological stress such as a reduction in photosynthetic rate. At this time, the basal 2-cm long root tips were harvested and divided into two segments, each of 1-cm in length, for protein extraction. Al-induced changes in proteomes were identified using tandem mass tags mass spectrometry (TMT-MS)-based quantitative proteomics analysis. A total of 216 proteins (approximately 3.6% of total proteins) showed significant differences between non-Al treated control and treated groups with significant fold change (twice the standard deviation; FDR adjusted p-value < 0.05). The apical root tip tissues expressed more dramatic proteome changes (164 significantly changed proteins; 3.9% of total proteins quantified) compared to the elongation/maturation zones (52 significantly changed proteins, 1.1% of total proteins quantified). Significantly changed proteins from the apical 1-cm root apex tissues were clustered into 25 biological pathways; proteins involved in the cell cycle (rotamase FKBP 1 isoforms, and CDC48 protein) were all at a reduced abundance level compared to the non-treated control group. In the root elongation/maturation zone tissues, the identified proteins were placed into 18 pathways, among which proteins involved in secondary metabolism (lignin biosynthesis) were identified. Several STRING protein interaction networks were developed for these Al-induced significantly changed proteins. This study has identified a large number of Al-responsive proteins, including transcription factors, which will be used for exploring new Al tolerance genes and mechanisms. Data are available via ProteomeXchange with identifiers PXD008882 and PXD009125.

Effects of precipitation changes on switchgrass photosynthesis, growth, and biomass: A mesocosm experiment.

Climate changes, including chronic changes in precipitation amounts, will influence plant physiology and growth. However, such precipitation effects on switchgrass, a major bioenergy crop, have not been well investigated. We conducted a two-year precipitation simulation experiment using large pots (95 L) in an environmentally controlled greenhouse in Nashville, TN. Five precipitation treatments (ambient precipitation, and -50%, -33%, +33%, and +50% of ambient) were applied in a randomized complete block design with lowland "Alamo" switchgrass plants one year after they were established from tillers. The growing season progression of leaf physiology, tiller number, height, and aboveground biomass were determined each growing season. Precipitation treatments significantly affected leaf physiology, growth, and aboveground biomass. The photosynthetic rates in the wet (+50% and +33%) treatments were significantly enhanced by 15.9% and 8.1%, respectively, than the ambient treatment. Both leaf biomass and plant height were largely increased, resulting in dramatically increases in aboveground biomass by 56.5% and 49.6% in the +50% and +33% treatments, respectively. Compared to the ambient treatment, the drought (-33% and -50%) treatments did not influence leaf physiology, but the -50% treatment significantly reduced leaf biomass by 37.8%, plant height by 16.3%, and aboveground biomass by 38.9%. This study demonstrated that while switchgrass in general is a drought tolerant grass, severe drought significantly reduces Alamo's growth and biomass, and that high precipitation stimulates its photosynthesis and growth.

Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park.

Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel cellulolytic thermophiles. We report here the draft genome sequence of one of these isolates, Bacillus altitudinis YNP4-TSU.

Draft Genome Sequences of Three Cellulolytic Bacillus licheniformis Strains Isolated from Imperial Geyser, Amphitheater Springs, and Whiterock Springs inside Yellowstone National Park.

Novel cellulolytic microorganisms are becoming more important for rapidly growing biofuel industries. This paper reports the draft genome sequences of Bacillus licheniformis strains YNP2-TSU, YNP3-TSU, and YNP5-TSU. These cellulolytic isolates were collected from several hydrothermal features inside Yellowstone National Park.