bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage
Authors: Yang Zerui , Xie Chunzhu , Huang Yuying , An Wenli , Liu Shanshan , Huang Song , Zheng Xiasheng 
Published: July 2021

Background
The borneol chemotype of Cinnamomum camphora (BCC), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in BCC used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in BCC’s monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of BCC induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in BCC.

Results
Gas chromatography–mass spectrometry analysis detected 14 monoterpenes and seven sesquiterpenes. All but two monoterpenes underwent a significantly increased accumulation after the MD treatment. RNA sequencing data revealed that 10 TPS, 82 MYB, 70 AP2/ERF, 38 BHLH, 31 WRKY, and 29 bZIP unigenes responded to the MD treatment. A correlation analysis revealed that three monoterpene synthase genes (CcTPS1, CcTPS3, CcTPS4) highly correlated with multiple monoterpenes, namely D-borneol, camphor, and bornyl acetate, which could be responsible for monoterpenoid biosynthesis in BCC. Furthermore, five WRKY, 15 MYB, 10 ERF/AP2, five bZIP, and two BHLH genes had strong, positive correlations with CcTPS1 or CcTPS4, judging by their high coefficient values (R2 > 0.8). The bioinformatics results were verified by quantitative real-time PCR.

Conclusion
This study provides insight into the genes involved in the biosynthesis and regulation of monoterpene in BCC and thus provides a pool of candidate genes for future mechanistic analyses of how monoterpenes accumulate in BCC.
Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis
Authors: Zhang Han , Yue Pan , Tong Xinxin , Gao Tinghui , Peng Ting , Guo Jinlin 
Published: July 2021

Background
Ophiocordyceps sinensis is a species endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. Although O. sinensis has been cultivated since the past few years, whether cultivated O. sinensis can completely replace wild O. sinensis remains to be determined.

Methods
To explore the differences of O. sinensis grown in varied environments, we conducted morphological and transcriptomic comparisons between wild and cultivated samples who with the same genetic background.

Results
The results of morphological anatomy showed that there were significant differences between wild and cultivated O. sinensis, which were caused by different growth environments. Then, a total of 9,360 transcripts were identified using Illumina paired-end sequencing. Differential expression analysis revealed that 73.89% differentially expressed genes (DEGs) were upregulated in O. sinensis grown under natural conditions compared with that grown under artificial conditions. Functional enrichment analysis showed that some key DEGs related to fatty acid metabolism, including acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-ketoacyl-CoA thiolase, and acetyl-CoA acetyltransferase, were upregulated in wild O. sinensis. Furthermore, gas chromatography-mass spectrometry results confirmed that the fatty acid content of wild O. sinensis was significantly higher than that of cultivated O. sinensis and that unsaturated fatty acids accounted for a larger proportion.

Conclusion
These results provide a theoretical insight to the molecular regulation mechanism that causes differences between wild and cultivated O. sinensis and improving artificial breeding.
In silico-driven analysis of theGlossina morsitans morsitansantennae transcriptome in response to repellent or attractant compounds
Authors: Gakii Consolata , Bwana Billiah Kemunto , Mugambi Grace Gathoni , Mukoya Esther , Mireji Paul O. , Rimiru Richard 
Published: July 2021

BackgroundHigh-throughput sequencing generates large volumes of biological data that must be interpreted to make meaningful inference on the biological function. Problems arise due to the large number of characteristicsp(dimensions) that describe each record [n] in the database. Feature selection using a subset of variables extracted from the large datasets is one of the approaches towards solving this problem.MethodologyIn this study we analyzed the transcriptome ofGlossina morsitans morsitans(Tsetsefly) antennae after exposure to either a repellant (δ-nonalactone) or an attractant (ε-nonalactone). We identified 308 genes that were upregulated or downregulated due to exposure to a repellant (δ-nonalactone) or an attractant (ε-nonalactone) respectively. Weighted gene coexpression network analysis was used to cluster the genes into 12 modules and filter unconnected genes. Discretized and association rule mining was used to find association between genes thereby predicting the putative function of unannotated genes.Results and discussionAmong the significantly expressed chemosensory genes (FDR < 0.05) in response to Ɛ-nonalactone were gustatory receptors (GrIA and Gr28b), ionotrophic receptors (Ir41a and Ir75a), odorant binding proteins (Obp99b, Obp99d, Obp59a and Obp28a) and the odorant receptor (Or67d). Several non-chemosensory genes with no assigned function in the NCBI database were co-expressed with the chemosensory genes. Exposure to a repellent (δ-nonalactone) did not show any significant change between the treatment and control samples. We generated a coexpression network with 276 edges and 130 nodes. Genes CAH3, Ahcy, Ir64a, Or67c, Ir8a and Or67a had node degree values above 11 and therefore could be regarded as the top hub genes in the network. Association rule mining showed a relation between various genes based on their appearance in the same itemsets as consequent and antecedent.
Ayurvedic Management of Chronic Pancreatitis in Adolescent Girl: A Case Report
Authors: Sawarkar Gaurav , Sawarkar Punam 
Published: July 2021

Background- Chronic pancreatitis is the primary life-threatening nutritional & metabolic condition of gastrointestinal system that becomes a significant threat to the children's growth and induces educational loss due to recurrent hospitalization. Its mortality rate in childhood is up to 10 %. Malnutrition is one of the primary causes of pancreatitis in children. Modern science provides various types of medical and surgical therapies for Chronic pancreatitis, but it is realized that more research is needed for its management satisfactorily.
Aim - To study the efficacy of Ayurvedic management of chronic pancreatitis induced due to Malnutrition in an adolescent girl.
Material & Methods- It is a single case study of 12 years old teenage girl who was presented herself predominantly with pain in the epi-gastric region (recurrent attacks-especially after intake of the fatty or heavy meal), tenderness in the epi-gastric area, loss of appetite, fever on and off, general malaise, loss of weight, constipation (intermittent), anxious & uncomfortable mental irritation since one & half month. After taking conservative treatment from modern science for one & a half months, she did not get satisfactory relief & therefore; she was advised to under ERCP. However, the patient & her relative was not willing to undergo the same, that’s they approached Panchakarma OPD. After examination, she was advised for Shodhana(Panchtikta & Guduchyadi Niruha Vasti) & Shaman Chikitsa(Amruttotara Kashayam, Arogyavardhini Vati, Kumariasava; Dhanvantara Kashayam, Avipattikar Churna), Panchatikta Ghrita with Vasant Kusumakar Rasa- 10tab+Guduchi Satva- 20gm + Shatavari Churna- 15gm+ Ashwagandha Choorna-15 gm with honey.
Observation & Results- After 16 months of regular treatment, the patient has become entirely symptom-free & to date, there was no need for hospitalization. There was no educational loss due to ill-health.
Discussion:-Utilizing the basic concepts of Ayurveda(Nidanpanchaka), Jirna Jwarahara, Yakrutottejak, Pramehaghna, or pancreatic-protective, Mrudu Virechak, Bruhana (Shamana & Bruhana Snehapana), Rasayana Chikitsa was planned in this case which showed the promising result.
Conclusion- Ayurvedic management with Shodhana & Shamana Chikitsa based on the fundamentals of Ayurveda is effective in Chronic pancreatitis induced due to Malnutrition in children, which may become a ray of hope for pediatric patients.
Plant Secondary Metabolism
Authors: Sato Fumihiko 
Published: July 2021

Abstract

Plants synthesise an extraordinary array of natural products that usually do not play a role in their growth and development and thus are traditionally referred to as secondary metabolites. However, recent advances in plant sciences have revealed that these compounds not only function in response to environmental stimuli but also play more basic roles in plant growth. Secondary metabolites have several important roles in plants: they protect against herbivores and microbial infection and act as signals for symbiotic bacteria and mycorrhiza, attractants for pollinators and seed‐dispersing animals, allelopathic agents in natural habitats, physical and chemical barriers to abiotic stressors such as UV and evaporation and endogenous regulators of plant growth hormones. Many secondary metabolites are also useful for mankind as dyes, essential oils, flavouring agents, pesticides, pharmaceuticals, tanning agents and so on. Rapid advances in the metabolic engineering and synthetic biology of secondary metabolites have revealed novel physiological roles of these secondary metabolites in plants.

Key Concepts

Plants synthesise an extraordinary array of natural products, with large structural diversity and complexity: terpenoids, phenolics, alkaloids and so on.

Terpenoids and phenolics are ubiquitous in plant kingdom, whereas alkaloids are more specific to taxonomic groups or plant species.

Secondary metabolites are produced in environmental responses and development.

Secondary metabolites have multiple functions in defence and growth.

Secondary metabolites are mainly classified based on the biosynthetic pathways; for example terpenoids from isopentenyl pyrophosphate, phenolics (mainly phenylpropanoids) from shikimate and alkaloids from amino acids.

Advances in molecular biology and analytical chemistries including transcriptomics, metabolomics and functional genomics identified many missing biosynthetic enzymes in pathway.

Accumulating genome sequencing data revealed that molecular evolution of secondary metabolism is based on the gene duplication and neofunctionalisation.

Many secondary metabolites are used for mankind as dyes, essential oils, flavouring agents, pesticides, pharmaceuticals, tanning agents and so on.

Metabolic engineering characterises the functions of pathway and also improves the production of secondary metabolites.

Reconstruction of biosynthetic pathways enables the production of plant‐derived secondary metabolites in heterologous hosts, such as
Escherichia coli
and yeast.
Tepidimonas
Authors: Albuquerque Luciana , Egas Conceição 
Published: July 2021

Abstract

Te.pi.di.mo'nas. L. masc. adj.
tepidus
warm; Gr. fem. n.
monas
unit, monad; N.L. fem. n.
Tepidimonas
warm monad.

Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / Tepidimonas

The genus
Tepidimonas
comprises eight species with validly published names,
Tepidimonas alkaliphilus, T. aquatica
,
T. charontis
,
T. fonticaldi
,
T. ignava
,
T. sediminis
,
T. taiwanensis,
and
T. thermarum
. These organisms form short rod‐shaped cells with motility. Cells stain Gram‐negative, and endospores are not observed. Colonies are nonpigmented. The species of the genus
Tepidimonas
are moderately thermophilic and strictly aerobic. Possess cytochrome
c
oxidase and are catalase‐positive. The organisms are chemoorganotrophic and mixotrophic. Growth factors are necessary for growth in minimal defined medium for some species. Organic acids and amino acids are used as carbon and energy sources; carbohydrates are used only by one species. Thiosulfate is oxidized to sulfate. The major respiratory quinone of these species is ubiquinone 8 (U‐8). The major polar lipids are phosphatidylethanolamine (PE) and phosphatidylglycerol (PG); diphosphatidylglycerol (DPG), one unidentified aminolipid, and additional unidentified phospholipids are also present. Fatty acids are primarily straight‐chain saturated and monounsaturated. Isolated from hydrothermal areas and from a domestic hot water tank.

DNA G + C content (mol%)
: 67.9–71.6 (HPLC).

DNA G + C content (%)
: 66.6–71.8 (genome).

Type species
:
Tepidimonas ignava
Moreira et al. 2000
VP
.
Fervidobacterium Emendation
Authors: L'Haridon Stéphane , Farrell Anne , Zhaxybayeva Olga , Nesbø Camilla L. 
Published: July 2021

Abstract

Fer.vi.do.bac.te'ri.um. L. masc. adj.
fervidus
hot: Gr. neut. n.
bakterion
a small rod: N.L. neut. n.
Fervidobacterium
a rod that grow at higher temperatures.

Thermotogota / Thermotogae / Thermotogales / Fervidobacteriaceae / Fervidobacterium emendation

The genus
Fervidobacterium
is currently composed of seven described species (
Fervidobacterium changbaicum
,
Fervidobacterium gondwanense
,
Fervidobacterium islandicum
,
Fervidobacterium nodosum
,
Fervidobacterium pennivorans
,
Fervidobacterium riparium
, and
Fervidobacterium thailandense
). They are members of the phylum
Thermotogota
, class
Thermotogae
, order
Thermotogales
, and family
Fervidobacteriaceae
. Similar to other
Thermotogota
,
Fervidobacterium
spp. are obligately
anaerobic heterotrophs
. They are
thermophilic
or
hyperthermophilic
, with optimum growth temperature of 60–80°C and optimal pH of 6.5–7.8. However, unlike other described
Thermotogota
,
Fervidobacterium
spp.
grow only at low salinity
(0–0.5% NaCl).
Sulfur is reduced to H

2

S
and stimulates growth, while molecular hydrogen inhibits growth. The cells are Gram‐negative rods and occur individually, in pairs, in filaments, in chains of up to 17 cells in one chain, or as spherical rotund bodies where 10 or more cells share an outer membrane. The majority of the individual cells produce terminal protuberances on one end of the cell (spheroids). Cells size about 0.4–0.6 × 1–40 μm. The cells are sensitive to inhibitors of cell‐wall, protein, and nucleic acid biosynthesis. Known habitats are terrestrial geothermal systems. The genus has also been detected in several types of anthropogenic environments: oil sands, tailing ponds, effluent of pulp and paper industry, and thermophilic microbial fuel cells. Several isolates have important uses in biotechnology; for instance, keratinophilic isolates are known to degrade feathers.

DNA G + C content (mol%)
: 35–45.8.

Type species
:
Fervidobacterium nodosum
Patel et al. 1985, VL19.
Hyphobacterium
Authors: Sun Cong 
Published: July 2021

Abstract

Hy.pho.bac.te'ri.um. Gr. fem. n.
hyphê
a web, thread; L. neut. n.
bacterium
a small rod; N.L. neut. n.
Hyphobacterium
a thread‐producing rod.

Proteobacteria / Alphaproteobacteria / Caulobacterales / Hyphomonadaceae / Hyphobacterium

The genus
Hyphobacterium
accommodates mesophilic, neutrophilic, and chemoorganotrophic bacteria. Cells of the genus
Hyphobacterium
are Gram‐stain‐negative, aerobic, non‐spore‐forming, and oval‐to‐rod‐shaped, multiply by binary fission and show two lifetypes, one with a prostheca for attachment to other objects and the other with a polar flagellum for motility. Growth occurs in a wide range of NaCl concentrations (1–6%) and temperatures (10–45°C). No growth is observed without NaCl. Catalase‐ and oxidase‐positive.
Hyphobacterium
members can utilize substrates including monosaccharides, oligosaccharides, and organic acids. Cells contain both glycolipids and phospholipids, indicating that the habitat or the phosphorus accumulation mechanism of
Hyphobacterium
strains may differ from its closely related members. The main glycolipids are monoglycosyl diglyceride (MGDG), glucuronopyranosyl diglyceride (GUDG), and sulfoquinovosyl diacylglycerol (SQDG), and the main phospholipids are phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and phosphatidylinositol (PI). The major isoprenoid quinone is ubiquinone‐10 (Q‐10). The most abundant fatty acid is C
18:1
ω7
c
with or without iso‐C
17:1
ω9
c
. The known habitat is seawater.

DNA G + C content (mol%)
: 59.8 (HPLC); 60.9 (genome sequence).

Type species
:
Hyphobacterium vulgare
Sun et al. 2017
VP
.
Salinivirga
Authors: Fardeau Marie‐Laure , Spring Stefan 
Published: July 2021

Abstract

Sa.li.ni.vir'ga. L. neut. n.
salinum
salt‐cellar; L. fem. n. virga rod; N.L. fem. n.
Salinivirga
a saline rod.

Bacteroidetes / Bacteroidia / Marinilabiliales / Salinivirgaceae / Salinivirga

The genus
Salinivirga
comprises one species with validly published name,
Salinivirga cyanobacteriivorans,
which was isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein‐rich extracts of
Arthrospira
(formerly
Spirulina platensis
) as substrate. The species of the genus is Gram‐negative‐staining, anaerobic, mesophilic, and moderately halophilic, with a strictly fermentative metabolism. Cells are straight to slightly curved slender, not motile rods, which occur singly or in pairs. No flagella or spores are formed. The major cellular fatty acids are iso‐C
15:0
and iso‐C
17:0
3OH. The polar lipid composition is complex, comprising phosphatidylethanolamine and several distinct unidentified polar lipids, including aminolipids and glycolipids. The main respiratory lipoquinone is menaquinone 7 (MK7). Tests for oxidase and catalase are negative. Nutrient requirements are complex (trypticase peptone, tryptone, and yeast extract). The only available genome sequence of this genus belongs to the nomenclatural type
Salinivirga cyanobacteriivorans
L21‐Spi‐D4
T
. It has a size of 4.81 Mb and contains 3,884 protein‐coding genes and 59 RNA genes. Phylogenetic analyses based on almost complete 16S RNA gene sequences placed the genus within the family
Salinivirgaceae
.

DNA G + C content (mol%)
: 39.0 (sequence analysis).

Type species
:
Salinivirga cyanobacteriivorans
Ben Hania et al. 2017, VL176.
Candidatus
Nanohalobium
Authors: Messina Enzo , La Cono Violetta , Rohde Manfred , Sorokin Dmitry Y. , Oren Aharon , Yakimov Michail M. 
Published: July 2021

Abstract

Na.no.ha.lo'bi.um. Gr. masc. n.
nanos
a dwarf; Gr. masc. n.
hals
,
halos
salt; Gr. masc. n.
bios
life; N.L. neut. n.
Nanohalobium
small organism living in salt.

Nanohaloarchaeota / “Incertae sedis” / “Incertae sedis” / “Incertae sedis” / Candidatus Nanohalobium

The genus
Candidatus
Nanohalobium was established based on a genome sequence found after the enrichment, cultivation, and characterization of a binary association with its chitinolytic host, obtained from a crystallizer pond brine collected in the marine solar saltern Saline della Laguna of Trapani, Italy.
Ca
. Nanohalobium is phylogenetically affiliated with members of the
Ca
. Nanohaloarchaeota (
Candidatus
Haloredivivus,
Candidatus
Nanosalina, and
Candidatus
Nanosalinicola) of the archaeal DPANN superphylum. Cultivation experiments and analysis of the 0.97 Mb genome of
Ca
. Nanohalobium constans LC1Nh revealed that the organism has an organoheterotrophic, sugar‐fermenting lifestyle, lacking key anabolic machinery and any respiratory complexes. Additionally, the cultivation experiments revealed a remarkable mutualism of a nanohaloarchaeon–haloarchaeon association, namely the nanohaloarchaeon's ability to hydrolyze glycogen and starch to glucose, enabling the growth of
Halomicrobium
sp. LC1Hm in the absence of chitin. The low‐median isoelectric point for the predicted proteins suggests a “salt‐in” strategy used by the nanohaloarchaeon for osmotic balance. 16S rRNA gene sequences affiliated with
Ca
. Nanohalobium were recovered from other saltern ponds and hypersaline lakes worldwide.

DNA G + C content (mol%)
: 43.2 (genome).

Type species
:

Candidatus
Nanohalobium constans

, La Cono et al. 2020.
Novel 2D MBenes—Synthesis, Structure, and Biotechnological Potential
Authors: Jakubczak Michał , Szuplewska Aleksandra , Rozmysłowska‐Wojciechowska Anita , Rosenkranz Andreas , Jastrzębska Agnieszka Maria 
Published: July 2021

Abstract2D transition metal borides (MBenes) have emerged as promising post‐MXene materials with potential application in various biotechnological fields. Although they possess prospective bioactive properties due to boron in their structure, the experience gained from MXenes shows that an in‐depth understanding of their biological recognition and response as well as the exploration of their biological applications are highly challenging. This makes the identification of the most promising 2D MBenes for future biological research and final industrial applications rather complicated. Herein, MBenes are differentiated from MXenes and further untangled for their bioactivity‐generating features. It is expected that MBenes’ positive or negative biological impact on living organisms and different types of cells connect with their morphological, structural and physicochemical features in the context of relevant environments. Necessary toxicological data are also highlighted, which are key aspects to enable MBenes’ safe application in biotechnology and nanomedicine. Furthermore, a perspective for the rational development and design of novel biotechnological solutions based on MBenes is provided, which will meet the legal safety requirements for nanomaterials. In this regard, this work is an unprecedented contribution toward strategies for regulatory development for MBene/MXene‐type nanomaterials. It provides an inspiration for future biotechnological and nanotoxicological approaches using MBenes.
Integrin‐Targeted, Short Interfering RNA Nanocomplexes for Neuroblastoma Tumor‐Specific Delivery Achieve MYCN Silencing with Improved Survival
Authors: Tagalakis Aristides D. , Jayarajan Vignesh , Maeshima Ruhina , Ho Kin H. , Syed Farhatullah , Wu Lin‐Ping , Aldossary Ahmad M. , Munye Mustafa M. , Mistry Talisa , Ogunbiyi Olumide Kayode , Sala Arturo , Standing Joseph F. , Moghimi Seyed M. , Stoker Andrew W. , Hart Stephen L. 
Published: July 2021

AbstractThe authors aim to develop siRNA therapeutics for cancer that can be administered systemically to target tumors and retard their growth. The efficacy of systemic delivery of siRNA to tumors with nanoparticles based on lipids or polymers is often compromised by their rapid clearance from the circulation by the liver. Here, multifunctional cationic and anionic siRNA nanoparticle formulations are described, termed receptor‐targeted nanocomplexes (RTNs), that comprise peptides for siRNA packaging into nanoparticles and receptor‐mediated cell uptake, together with lipids that confer nanoparticles with stealth properties to enhance stability in the circulation, and fusogenic properties to enhance endosomal release within the cell. Intravenous administration of RTNs in mice leads to predominant accumulation in xenograft tumors, with very little detected in the liver, lung, or spleen. Although non‐targeted RTNs also enter the tumor, cell uptake appears to be RGD peptide‐dependent indicating integrin‐mediated uptake. RTNs with siRNA against MYCN (a member of the Myc family of transcription factors) in mice with MYCN‐amplified neuroblastoma tumors show significant retardation of xenograft tumor growth and enhanced survival. This study shows that RTN formulations can achieve specific tumor‐targeting, with minimal clearance by the liver and so enable delivery of tumor‐targeted siRNA therapeutics.