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Organic shiso grown in Italy is now available
is an important ingredient in the preparation of sushi and kombucha
especially popular for high-end preparations
L'Orto di Mimì grows both red and green shiso
so much so that it is possible to say that an Italian shiso has been born
hitherto closely linked to Japan on a par with wasabi
The company was set up by chef Antonio D'Angelo (photo above) and was recently awarded the European prize for the best certified organic "Japanese Farm"
The plant belongs to the Lamiaceae family and is an aromatic herb with jagged leaves and a distinctive scent
The scientific head of the project is Andrea Tessadrelli
who explains the details of this difficult and complex cultivation
was selected by us at L'Orto di Mimì after research that lasted over 4 years
and which included stimulation and foliar fertilisation with micro and macroelements to make the colour a very deep red that does not change depending on the temperature
It is therefore an improved variety also distinguished by the tenderness of the leaf blade."
Shiso production will continue in cold greenhouses until late November
"We have both dried leaves and pre-developed plants so leaves can be harvested autonomously
Each plant produces over a hundred leaves per cycle
and our market is expanding not only to Italy but abroad as well."
more tannic and pungent and ideal for fermenting
Cultivating shiso in the Po Valley immediately seemed like a difficult undertaking
but the stubbornness of D'Angelo and his collaborators prevailed: "It certainly wasn't easy
organic aromatic herb with the organoleptic characteristics required by the market."
For more information:L'Orto di MimìVia Macina, 25030Castel Mella (Brescia)[email protected]www.lortodimimi.com
Frontpage photo: © L'ORTO DI MIMI'
FreshPublishers © 2005-2025 FreshPlaza.com
The cultivation of wasabi (Eutrema japonicum)
a brassica native to Japan that is widely used in the kitchen
is proving successful in Italy for the first time
the grated rhizome is used to accompany raw fish
but the leaves are also fried in tempura and the stems are used for making the traditional kizami
which has always been closely linked to Japan
is now also taking place at the L'Orto di Mimì farm in the Brescia province
set up by chef Antonio D'Angelo and recently awarded as the best certified organic 'Japanese Farm' in Europe
Talking about this successful project is D'Angelo himself who
supported from a technical-scientific point of view by his collaborator Andrea Tessadrelli
wasabi is one of the most difficult crops in the world
Over 15 months pass between planting and the first harvest
which greatly increases the risks involved in production
the first harvest partially took place in 2022 with a taste identical to the Japanese original
yet initially with some differences in colour and epidermis due to the excessive heat."
Producing wasabi in Italy seemed an impossible task at first
but Tessadrelli took up D'Angelo's challenge
"We recreated an environment similar to the Japanese one from scratch
including constantly flowing water at a controlled temperature and trees to reduce solar radiation
creating wind currents with a thermal cooling function."
The added value of Orto di Mimì was to focus on know-how and scientific research right from the start
focusing on the plants that demonstrated the best characteristics from an agronomic and nutritional point of view
Tessadrelli adds that "from my first day in this company
I have always been convinced that you cannot replicate an exotic crop without investing in research and breeding
a variety that can adapt and thrive even at our latitudes
we have crossed and improved several varieties over the years
We have now reached the stage of worldwide registration of Fant1
a unique hybrid that is resistant up to 40° Celsius and boasts abundant
opaque foliage and a rhizome with a good specific weight
He concludes: "The company already has four years of intensive research and development behind it
with a lot of investments made to try and get the first results
but now we are proud to have our own variety to grow and propagate
with constant attention to varietal improvement
We are only at the beginning and we are very confident
knowing that we have reached a goal that was previously unimaginable."
For more information L'Orto di MimìVia Macina, 25030Castel Mella (Brescia)[email protected]www.lortodimimi.com
Metrics details
Skeletal muscle satellite cells are quiescent adult resident stem cells that activate
proliferate and differentiate to generate myofibres following injury
They harbour a robust proliferation potential and self-renewing capacity enabling lifelong muscle regeneration
Although several classes of microRNAs were shown to regulate adult myogenesis
systematic examination of stage-specific microRNAs during lineage progression from the quiescent state is lacking
Here we provide a genome-wide assessment of the expression of small RNAs during the quiescence/activation transition and differentiation by RNA-sequencing
We show that the majority of small RNAs present in quiescent
activated and differentiated muscle cells belong to the microRNA class
by comparing expression in distinct cell states
we report a massive and dynamic regulation of microRNAs
highlighting their pivotal role in regulation of quiescence
We also identify a number of microRNAs with reliable and specific expression in quiescence including several maternally-expressed miRNAs generated at the imprinted Dlk1-Dio3 locus
the majority of class-switching miRNAs are associated with the quiescence/activation transition suggesting a poised program that is actively repressed
These data constitute a key resource for functional analyses of miRNAs in skeletal myogenesis
in the regulation of stem cell self-renewal and tissue homeostasis
a subset of proliferating satellite cells self-renew in their niche by reversibly exiting the cell cycle
skeletal myogenesis is a tractable model to study the regulation of quiescence
As previous quantitative and differential data obtained using RT-qPCR or miRNA-microarrays were limited to the quantification of known molecules
we performed an unbiased analysis of small-RNA profiles from stem to differentiated cells in adult myogenesis
Our data provide a key resource for functional studies of the involvement of small-RNAs - including miRNAs
and more broadly in the regulation of stem cell self-renewal and tissue homeostasis
Unbiased identification of stage specific small RNAs during lineage progression from muscle stem cells
(A) Quiescent satellite cells were isolated after digestion of resting limb muscles and diaphragm from adult Tg:Pax7-nGFP mice by FACS using GFP fluorescence
An aliquot was cultured in vitro for 60 h or 7 days
and the remainder was lysed directly for RNA extraction
After size selecting 15–35 nucleotides small RNAs on a polyacrylamide gel
sequencing libraries were prepared and analysed
(B) Schematic representation of lineage progression in adult skeletal muscle
activated and differentiated samples are represented
Immuno-fluorescence images confirmed the cellular identity of the 3 populations (i) quiescent satellite cells: Pax7(+)
Myod(−); Activated satellite cells/myoblasts: Pax7(+)
MyoD(+); Differentiated muscle cells: Pax7(−) Myog(+)
Note the presence of rare self-renewing “reserve cells” expressing Pax7 in the differentiated sample
(C) Sequenced small RNA corresponded overwhelmingly to miRNAs in all 3 samples
and showed low contamination by degraded tRNA
Despite the inclusion of the 25–32 nt size range in the analysis
whereas reads mapping to intronic regions were identified in particular in the quiescent samples (>5% reads)
(D) 412 and 231 miRNAs were detected in at least one sample type more than 10 or 100 times
(E) Frequency histogram displaying the miRNAs distribution according to their expression levels in all 3 samples highlight their large dynamic range in expression
Other classes of small RNAs and in particular piRNAs were not detected in our samples
We subsequently focused on the expression profiles of miRNAs
This observation underscored the importance of robust normalization of the datasets to avoid skewing of the expression profiles as a result of the high expression of a limited number of miRNAs
Identification of differentially expressed miRNAs during myogenic lineage progression
(A) Scatter plot of miRNA expression level in Quiescent vs
Results are presented as the median of log transformed normalized counts for each miRNA
249 showed a modulation that reached statistical significance in the 3 pairwise comparisons (corrected p-value ≤ 0.001)
Statistically significant up- or down-regulated miRNAs were coloured in yellow and blue
(D) Heatmap presenting 4 classes of differentially expressed miRNAs identified by K-means clustering
MicroRNAs are involved in the regulation of all processes – quiescence
activation and self-renewal and differentiation
and a large number of miRNAs with expression specific of one particular state were identified
whereas low expression is blue as in previous panels
We then grouped the differentially expressed miRNAs according to their expression profiles using K-means clustering which reveals 4 classes (Fig. 2D and Supplementary Table S2)
The first consisted of 59 miRNAs whose expression was found to be associated specifically with quiescence
The second and third clusters comprised miRNAs either expressed during activation
or conversely silenced in this cell state; they represented 70 and 64 miRNAs
the last cluster was composed of miRNAs showing an increase in expression during commitment and differentiation
the most important transition was between quiescence and activation
where more than half of the differentially expressed miRNAs identified were specific to these states
This finding highlights the concerted role that miRNAs play during the regulation in this transition
Validation of miRNA regulation on in vivo activated satellite cells Histogram presenting parallel expression measured by small-RNAseq following in vitro culture compared to in vivo activated satellite cells and isolated single muscle fibres
(A–F) The trend in expression was confirmed for 6 out 6 tested miRNAs
and only miR-26a did not show the same amplitude of deregulation on in vivo activated samples
(G–J) identical results were obtained for activation specific miRNAs
thus validating the miRNA-sequencing data using an in vitro activation paradigm
Normalization based on cell number allowed to confirm the higher expression level of many miRNAs during quiescence
given the per-cell normalization we used in our RT-qPCR assay
our analysis leads us to propose that tens of miRNAs have higher levels of expression in quiescent vs
these findings suggest that the miRNAs over-expressed during quiescence are potent regulators that exert their effect in satellite cells
we also identified functions related to skeletal muscle tissue development (p-value < 5.9E-9)
regulation of ubiquitin-protein transferase activity (p-value < 6.6E-4) and somatic stem cell division (p-value < 1.1E-4)
Functional analysis of miRNA from the Dlk1-Dio3 locus expressed in quiescent satellite cells
(A) Schematic representation of the maternally expressed miR-127/miR-136 and miR-379/miR-410 gene cluster in the imprinted Dlk1-Dio3 locus located on mouse chromosome 12
Dlk1 and Dio3 are expressed from paternally inherited chromosome
(B) Heatmap representing the expression level of miRNAs from the Dlk1-Dio3 locus during lineage progression from quiescent to activated and differentiated satellite cells
The two miRNAs studied in more detail are highlighted with orange arrows
(C) Expression of coding and non-coding genes from the Dlk1-Dio3 locus in control and mutant mice
(D) Counting of satellite cell numbers on EDL muscle fibres from mutant and WT mice; n = 6–7 mice/genotype; ≥15 fibres/mice
The bar in the violin plot represents the median
(E) H&E staining of TA muscle sections from WT and miR-379/410 mutants 6 and 9 weeks after Notexin injury of muscle
(F) Anti-Myog staining (top) and EdU reaction (bottom) in satellite cells isolated from Dll1-Dio3 Control (WT) and mutant (KO) mice at 72 h and 24 h
Quantification of Myog+ and EdU+ cells at each time point revealed no difference between WT and KO satellite cells
anti-Myog stainings (top) and EdU reaction (bottom) in satellite cells isolated from Tg:Pax7-nGFP mice 72 h after Mimic-127
Mimic-379 or Scramble control transfection
Myogenin-positive and EdU positive cells at 72 h following Mimic-127
Expression levels of the corresponding genes in the dataset of Garcia-Prat et al
ITGB6 and CD44) are among candidates that could mediate the effect of miR-127 and miR-379
We observed an overall downregulation in quiescence of the several thousand mRNAs putatively targeted by quiescence miRNAs
These observations point to a collective control by miRNAs on the expression of specific mRNAs during these cell transitions
The number of miRNAs expressed in quiescence
and thus the number of potential targets identified complicated the global analysis of their function
using a restricted list of potential targets generated by combining 3 prediction tools
we found Gene Ontologies associated with regulation of muscle development
Having identified the overexpression of tens of miRNAs from two clusters located in the Dlk1-Dio3 locus in quiescent satellite cells
we investigated the impact of the deletion of the miR-379/410 cluster in vivo
Our observation that this resulted in no overt regeneration phenotype or modulation of cell fates of isolated satellite cells leads us to speculate that other miRNAs have overlapping functions with this cluster
functional analysis by sustained expression of two miRNAs from the miR-127 and miR-379 loci resulted in a robust phenotype corresponding to an increase in Pax7 expression and reduced commitment towards differentiation
thereby indicating that these miRNAs promote the stem cell state
These findings suggest that these miRNAs play key roles in regulating satellite cell quiescence in adult resting muscles
but instead increased self-renewal and decreased differentiation of satellite cells
The absence of a regeneration phenotype in the miR-379/410 mutant mice could be explained by compensations by other miRNAs expressed in quiescence targeting common targets
or other compensatory mechanisms during development following the germline deletion
The implication of a re-expression of the paternal allele of the miRNA-cluster is however unlikely
a maternally expressed ncRNAs that overlaps with the miR-379/411 cluster
was detected in satellite cells in mutant mice
the size of the locus to be deleted precludes the use of a cell type specific inducible Cre-recombinase under the control of Pax7 to study the role of these miRNAs in more detail
Future work will be required in gain or loss of function experiments to uncover the molecular function of additional differentially expressed miRNAs
and to identify their relevant targets in the context of induction and maintenance of quiescence
beyond the pivotal role of miR-489 and miR-195/497 already noted in Pax7-positive cells
identifying the signalling pathways upstream of these miRNAs will shed light on this tightly regulated biological process
our findings that a relatively significant variety of miRNAs are dedicated to negotiate the quiescence to activation states of muscle stem cells suggests that quiescence is actively repressed by this class of regulators
These results can impact on our views of genetic and epigenetic regulation of quiescence and how this critical cell state is regulated in homeostasis and trauma
All experiments with animals were performed under conditions established by the European Community and approved by the Ethics Committee at Institut Pasteur
EDL muscles were dissected and incubated in 0.1% w/v collagenase (Sigma
C0130)/DMEM for 1 h in a 37 °C shaking water bath
individual myofibres were either processed for RNA extraction to validate the RNA sequencing in differentiation conditions
or directly fixed in 4% paraformaldehyde (PFA
Freshly isolated satellite cells were seeded at 3,000 cells/cm2 in growth medium containing 1:1 DMEM:MCDB (Gibco and Sigma-Aldrich
respectively) supplemented with 20% serum FBS (Gibco) and 1% Ultroser G (Pall) on Matrigel coated flasks (BD Biosciences) and cultured in an incubator under physiological oxygen pressure (37 °C
cells were pulsed with the thymidine analogue 5-ethynyl-2′-deoxyuridine (EdU
2 h prior to fixation (ThermoFisher Click-iT Plus EdU kit
and cells were cultured for a total of 7 days to reach early differentiation
Freshly isolated satellite cells from Tg:Pax7-nGFP were transfected in suspension immediately after FACS with miRIDIAN microRNA hsa-miR-126-3p mimic (UCGUACCGUGAGUAAUAAUGCG
C310397) and Scramble Control#1 (UCACAACCUCCUAGAAAGAGUAGA; Dharmacon
CN-001000) at 200 nM final concentration using Lipofectamine 2000 (ThermoFisher) in Opti-MEM (Gibco)
3 volumes of fresh growth medium were added and cells were cultured for the indicated time
Cells and myofibers were fixed in 4% PFA for 5 min
permeabilised 5 min in 0.5% Triton-X100 (Sigma-Aldrich) and blocked in 10% normal goat-serum (Gibco) for 30 min at RT
Cells and fibres were then incubated with primary antibodies (Chick GFP
Samples were washed with 1X PBS three times and incubated with Alexa-conjugated secondary antibodies (Life Technologies
EdU staining was chemically revealed using the Click-iT Plus kit according to manufacturer’s recommendations (Life Technologies
Images were acquired using an upright fluorescent microscope (Zeiss)
Isolated TA muscles were fixed in PFA 2%/0.2% Triton/PBS 1X for 2 h at 4 °C
washed in PBS 1X overnight at 4 °C and incubated in 20% sucrose/PBS 1X for an additional 12 h
TA muscles were embedded in OCT and frozen in liquid nitrogen prior to cryosectioning (10 µm) and stained with Hematoxylin/Eosin
Images were acquired with Zeiss Axioscan microscope
quiescent cells were directly sorted into Trizol-LS reagent (Invitrogen)
and in-vitro cultured cells (activated at 60 hours and differentiated at 7 days) collected in Qiazol reagent (QIagen)
Total RNA was subsequently purified using the miRNeasy Mini Kit following the manufacturer's instructions (Qiagen)
Ten micrograms of total RNA obtained from several animals for the quiescent samples
were used for each biological replicate prepared for deep sequencing (i.e
2 replicates for the quiescent and differentiated samples
and 3 replicates for the in vitro activated sample)
For RT-qPCR validations all samples were extracted using the same methods (Trizol LS after FACS for quiescent and in-vivo activated satellite cells; Qiazol for isolated single fibres)
were isolated from quiescent and 48 h in vitro activated satellite cells using Direct-zol RNA Microprep (Zymo Research) according to manufacturer’s recommendations
Total RNA and small RNA ratio were quantified using the Agilent 2100 Bioanalyzer PicoChip and SmallChip and analyzed with 2100 Expert software
10 µg of total RNA (in 10 µl) were mixed with 10 µl of 2X TBE-Urea Sample Buffer (Invitrogen) and loaded in a well of a 15% polyacrylamide TBE-urea gel (Biorad)
the gel was soaked in a SYBR gold (Invitrogen) solution
and imaged on a Dark Reader transilluminator
The 18–35 nucleotide region was cut using a scalpel for each sample
and the RNA eluted in 300 µl of 0.3 M NaCl solution under rotation for 4 hours at room temperature
The eluate was transferred together with gel debris onto a Spin X cellulose acetate filter (VWR) and centrifuged for 2 minutes at 12,000 xg
Small RNAs were finally precipitated by addition of 1 μl of glycogen (Invitrogen) and 750 μl of room temperature 100% ethanol followed by an incubation at −80 °C for 30 min
and centrifugation for 25 min at 14,000 rpm and + 4 °C
The pellet was washed with 750 µl 75% Ethanol
dried and resuspended in 5 µl ultrapure water with 0.5 µl of RNAseOUT (Invitrogen)
Small RNAs purified on gel were mixed to 1 µl of 10 µM pre-adenylated 3′ Illumina linker V1.5 (5′-rAppATCTCGTATGCCGTCTTCTGCTTG/3ddC/-3′)
and further mixed with 1 µl of 10x T4 RNA-Ligase Truncated Reaction buffer
0.5 µl RNaseOut and 1.5 µl of T4 RNA Ligase 2 truncated (New England Biolabs)
0.5 µl of 5′-RNA adapter (5′-r(GUU CAG AGU UCU ACA GUC CGA CGA UC)-3′)
1 µl of 10 mM ATP and 1 µl T4 RNA ligase (Ambion) were added
and ligation was performed at 20 °C for 6 h
Adaptor ligated RNA in a volume of 4 µl were then mixed with 1 µl of 20 μM Solexa RT primer (5′-CAA GCA GAA GAC GGC ATA CGA-3′) and denatured at 70 °C and cooled on ice
Reverse transcription was then performed after addition of 2 µl 5x first strand buffer (Invitrogen)
0.5 µl_ RNase OUT and 1 µl SuperScript III Reverse Transcriptase (Invitrogen) at 50 °C for 1 h
The obtained cDNA was PCR-amplified by addition of 27 µl Ultra-pure water
1 µl of 25 µM Forward Primer (5′-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3′)
1 µl of 25 µM reverse Primer (5′-CAA GCA GAA GAC GGC ATA CGA-3′)
and 0.5 µl Phusion DNA Polymerase (Finnzymes) using 12 cycles 98 °C 10 sec/60 °C 30 sec/72 °C 15 sec
The library was finally purified on a 5% TBE PAGE gel
by cutting the region corresponding to the 92–106 bp (the ligated linkers corresponding to a 73 bp band visible on the gel)
The gel was crushed by centrifugation and eluted in 1X Elution buffer (Illumina) by rotation for 2 h at RT
The eluate was cleared using a Spin-X column and precipitated after addition of 1 µl of glycogen
10 µl of 3 M NaOAc and 325 µl of −20 °C 100% ethanol
followed by centrifugation for 20 min at 14,000 rpm
the sample was diluted to 10 nM and submitted to sequencing on a Solexa GA-IIX at the core sequencing facility
K-means clustering of differentially expressed miRNAs was performed using Cluster 3.0 (available at bonsai.hgc.jp/~mdehoon/software/cluster/software.htm) using normalized read count as input. After a step of median centering of expression level for each miRNA, clustering was perform using centered Pearson correlation with 1,000 iterations. The corresponding heatmap was generated using JavaTreeView (http://jtreeview.sourceforge.net)
Comparisons of expression level between the groups of transcripts in the different satellite cell states (i.e
quiescent or activated in vivo 3 days post injury) were performed using a Mann-Whitney test
The small RNA-seq data generated and analysed during the current study have been deposited in the ArrayExpress database at EMBL-EBI under accession number E-MTAB-5955 [https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5955]
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We acknowledge the Flow Cytometry Platform of the Technology Core-Center for Translational Science (CRT) and the Transcriptome and EpiGenome Platform of the Center for Innovation & Technological Research at Institut Pasteur for support in conducting this study
Centre National pour la Recherche Scientifique and the Agence Nationale de la Recherche (Laboratoire d’Excellence Revive
the European Research Council (Advanced Research Grant 332893) and the French Muscular Dystrophy Association (AFM-Téléthon)
was funded by the Fondation pour la Recherche Médicale (FRM)
We thank the ABC Facility of ANEXPLO Toulouse for mouse husbandry
Present address: Département de Cancérologie de l’Enfant et de l’Adolescent & UMR8203 “Vectorologie et Thérapeutiques Anticancéreuses”
Department of Developmental & Stem Cell Biology
Barbara Gayraud-Morel & Shahragim Tajbakhsh
Laboratoire de Biologie Moléculaire Eucaryote
The authors declare no competing interests
Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations
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DOI: https://doi.org/10.1038/s41598-018-21991-w
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Journal of Muscle Research and Cell Motility (2024)
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