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Fulltext Whole-Genome Sequencing Reveals a New Genospecies of Methylobacterium sp. GXS13, Isolated from Vitis vinifera L. Xylem Sap

Lai WX, Gan HM, Hudson AO, Savka MA

Genome Announc, 2016;4(1).
PMID: 26847900 DOI: 10.1128/genomeA.01695-15

The whole-genome sequence of a new genospecies of Methylobacterium sp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server.

Matched MeSH terms: Xylem
Exploration of cassava plant xylem for water treatment: preparation, characterization and filtration capability

Hashim A, Hashim NA, Mohd Junaidi MU, Kamarudin D, Hussain MA

Water Sci Technol, 2022 Sep;86(5):1055-1065.
PMID: 36358045 DOI: 10.2166/wst.2022.253

Flood is among the natural disasters that commonly happened in Malaysia every year. During the flood, victims faced clean water shortages and deterioration of the environment resulting in long waiting times for aid to access. Hence, affordable and efficient filters are needed to supply clean water in the affected areas. Application of xylem tissue inside plant stem has the potential as a filter for water filtration. This research focuses on xylem tissue in Malaysian tropical plants from cassava stem. Cassava stems were prepared in a small-scale set-up as the xylem was used as a filter. Effects of cross-sectional area and hydrostatic pressure were analyzed and the results showed a directly proportional relationship with permeate flow rate. Upon filtration with red dye solution, total dye removal was achieved using a xylem with a minimal length of 3 cm and onwards. While for bacteria removal, E. coli bacteria have been removed when tested with a bacteria count plate. Thus, this study demonstrated the potential of the xylem tissue of the cassava plant as affordable and available natural raw materials to be used as water filters during an emergency.

Matched MeSH terms: Xylem
Fulltext Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - potential regulatory sequences in monolignol biosynthetic pathway

Ong SS, Wickneswari R

BMC Genomics, 2011 Nov 30;12 Suppl 3(Suppl 3):S13.
PMID: 22369296 DOI: 10.1186/1471-2164-12-S3-S13

BACKGROUND: Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15-35% of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem.
RESULTS: In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41%) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21%). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing. Differential expression of the small RNAs between secondary xylem tissues with contrasting lignin content suggests that a cascade of miRNAs play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species.
CONCLUSIONS: Our study critically demonstrated the roles of small RNAs during secondary wall formation. Comparison of the expression pattern of small RNAs between secondary xylem tissues with contrasting lignin content strongly indicated that small RNAs play a key regulatory role during lignin biosynthesis. Our analyses suggest an evolutionary mechanism for miRNA targets on the basis of the length of their 5' and 3' UTRs and their cellular roles. The results obtained can be used to better understand the roles of small RNAs during lignin biosynthesis and for the development of gene constructs for silencing of specific genes involved in monolignol biosynthesis with minimal effect on plant fitness and viability. For the first time, small RNAs were proven to play an important regulatory role during lignin biosynthesis in A. mangium.

Matched MeSH terms: Xylem/genetics; Xylem/metabolism
Growth and anatomical responses in xanthostemon chrysanthus as influenced by paclobutrazol and potassium nitrate

Nazarudin MA, Tsan F, Adzmi Y, Normaniza O

Sains Malaysiana, 2015;44:483-489.

A study was conducted to determine the effects of a plant growth regulator (paclobutrazol, PBZ) and commercial
fertilizer (Krista-K Plus) as a source of potassium nitrate (KNO3
) on the growth of Xanthostemon chrysantus. It was
also attempted to investigate the anatomical changes in the leaf and stem after the treatment. Nine treatments, i.e.
control (no PBZ and Krista-K Plus application), 0 PBZ gL-1 + 100 g Krista-K Plus, 0 PBZ gL-1 + 200 g Krista-K Plus,
0.125 PBZ gL-1 + 0 g Krista-K Plus, 0.125 PBZ gL-1 + 100 g Krista-K Plus, 0.125 PBZ gL-1 + 200 g Krista-K Plus, 0.25
PBZ gL-1 + 0 g Krista-K Plus, 0.25 PBZ gL-1 + 100 g Krista-K Plus and 0.25 PBZ gL-1 + 200 g Krista-K Plus, were
tested. PBZ was soil drenched at the commencement of the study while Krista-K Plus was applied at three-month
intervals. Plant growth performances such as tree height, diameter at breast height, canopy diameter and leaf area
were recorded monthly throughout the study period. Stem and leaf samples were collected before the application
of treatments and after six months of treatments for anatomical observation by using electron microscope. Plant
height, diameter at breast height, crown diameter and leaf area were significantly reduced with the application of
PBZ. Palisade parenchyma thickness was increased by 33.83% with 0.25 PBZ gL-1 + 200 g Krista-K Plus, while only
2.44% increment recorded in the control tree. Xylem thickness in the stem was reduced by 21.81% after treated with
the highest dosage of PBZ, while the control tree only had 1.78% increment. Spongy parenchyma thickness in the leaf
was unaffected. However, palisade parenchyma was found the thickest after combined treatment with 0.25 PBZ gL-1
+ 200 g Krista-K Plus. Micrograph images of the cross-section of leaf lamina and stem showed that the cells were
tightly arranged in response to the application of PBZ.

Matched MeSH terms: Xylem
Fulltext Creating vessel elements in vitro: Towards a comprehensive understanding of the molecular basis of xylem vessel element differentiation

Tan TT, Demura T, Ohtani M

Plant Biotechnol (Tokyo), 2019;36(1):1-6.
PMID: 31275042 DOI: 10.5511/plantbiotechnology.18.1119b

Xylem is an essential conductive tissue in vascular plants, and secondary cell wall polymers found in xylem vessel elements, such as cellulose, hemicellulose, and lignin, are promising sustainable bioresources. Thus, understanding the molecular mechanisms underlying xylem vessel element differentiation is an important step towards increasing woody biomass and crop yields. Establishing in vitro induction systems, in which vessel element differentiation is induced by phytohormonal stimuli or by overexpression of specific transcription factors, has been vital to this research. In this review, we present an overview of these in vitro induction systems, and describe two recently developed in vitro induction systems, VISUAL (Vascular cell Induction culture System Using Arabidopsis Leaves) and the KDB system. Furthermore, we discuss the potentials and limitations of each of these new in vitro induction systems for advancing our understanding of the molecular mechanisms driving xylem vessel element differentiation.

Matched MeSH terms: Xylem
Removal of insecticide carbofuran from aqueous solutions by banana stalks activated carbon

Salman JM, Hameed BH

J Hazard Mater, 2010 Apr 15;176(1-3):814-9.
PMID: 20031311 DOI: 10.1016/j.jhazmat.2009.11.107

In this work, activated carbon was prepared from banana stalks (BSAC) waste to remove the insecticide carbofuran from aqueous solutions. The effects of contact time, initial carbofuran concentration, solution pH and temperature (30, 40 and 50 degrees C) were investigated. Adsorption isotherm, kinetics and thermodynamics of carbofuran on BSAC were studied. Equilibrium data were fitted to the Langmuir, Freundlich and Temkin isotherm models and the data best represented by the Langmuir isotherm. Thermodynamic parameters such as standard enthalpy (DeltaH(o)), standard entropy (DeltaS(o)) and standard free energy (DeltaG(o)) were evaluated. Regeneration efficiency of spent BSAC was studied using ethanol as a solvent. The efficiency was found to be in the range of 96.97-97.35%. The results indicated that the BSAC has good regeneration and reusability characteristics and can be used as alternative to present commercial activated carbon.

Matched MeSH terms: Xylem/chemistry
Decolorization of Acid Red 1 by Fenton-like process using rice husk ash-based catalyst

Daud NK, Hameed BH

J Hazard Mater, 2010 Apr 15;176(1-3):938-44.
PMID: 20042285 DOI: 10.1016/j.jhazmat.2009.11.130

The decolorization of Acid Red 1 (AR1) in aqueous solution was investigated by Fenton-like process. The effect of different reaction parameters such as different iron ions loading on rice husk ash (RHA), dosage of catalyst, initial pH, the initial hydrogen peroxide concentration ([H(2)O(2)](o)), the initial concentration of AR1 ([AR1](o)) and the reaction temperature on the decolorization of AR1 was studied. The optimal reacting conditions were found to be 0.070 wt.% of iron (III) oxide loading on RHA, dosage of catalyst=5.0 g L(-1), initial pH=2.0, [H(2)O(2)](o)=8 mM, [AR1](o)=50 mg L(-1) at temperature 30 degrees C. Under optimal condition, 96% decolorization efficiency of AR1 was achieved within 120 min of reaction.

Matched MeSH terms: Xylem/chemistry*
Fulltext Genome sequence of Methylobacterium sp. strain GXF4, a xylem-associated bacterium isolated from Vitis vinifera L. grapevine

Gan HM, Chew TH, Hudson AO, Savka MA

J Bacteriol, 2012 Sep;194(18):5157-8.
PMID: 22933776 DOI: 10.1128/JB.01201-12

Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium.

Matched MeSH terms: Xylem/microbiology
Fulltext Identification and analysis of expressed sequence tags present in xylem tissues of kelampayan (Neolamarckia cadamba (Roxb.) Bosser)

Ho WS, Pang SL, Abdullah J

Physiol Mol Biol Plants, 2014 Jul;20(3):393-7.
PMID: 25049467 DOI: 10.1007/s12298-014-0230-x

The large-scale genomic resource for kelampayan was generated from a developing xylem cDNA library. A total of 6,622 high quality expressed sequence tags (ESTs) were generated through high-throughput 5' EST sequencing of cDNA clones. The ESTs were analyzed and assembled to generate 4,728 xylogenesis unigenes distributed in 2,100 contigs and 2,628 singletons. About 59.3 % of the ESTs were assigned with putative identifications whereas 40.7 % of the sequences showed no significant similarity to any sequences in GenBank. Interestingly, most genes involved in lignin biosynthesis and several other cell wall biosynthesis genes were identified in the kelampayan EST database. The identified genes in this study will be candidates for functional genomics and association genetic studies in kelampayan aiming at the production of high value forests.

Matched MeSH terms: Xylem
Fulltext Mercury concentration data from Matang Mangrove Forest Reserve, Malaysia

Wolswijk G, Satyanarayana B, Le QD, Siau YF, Ali ANB, Saliu IS, et al.

Data Brief, 2020 Apr;29:105134.
PMID: 32016142 DOI: 10.1016/j.dib.2020.105134

This paper presents the results of mercury analysis on 786 abiotic (surface sediments) and biotic (plant and animal tissues) samples collected from 10 sites at Matang Mangrove Forest Reserve in Peninsular Malaysia. Sediment samples were collected at the surface level from both river bank and forest understory. Whereas plant tissues obtained from Rhizophora apiculata Blume and Rhizophora mucronata L. consisted of leaves (in four stages namely young, mature, senescent and decomposing), bark and roots (divided into xylem, cortex and epidermis), the animal samples were represented by muscle tissue of the gastropod Cassidula aurisfelis Bruguière and the cockle Tegillarca granosa L. The mercury concentration measurements were obtained through a cold vapor atomic absorption spectrometer. The core data have been analysed and interpreted in the paper "Distribution of mercury in sediments, plant and animal tissues in Matang Mangrove Forest Reserve, Malaysia" [1].

Matched MeSH terms: Xylem