scholarly journals Phenotyping single-cell motility in microfluidic confinement

2021 ◽  
Author(s):  
Samuel A Bentley ◽  
Vasileios Anagnostidis ◽  
Hannah Laeverenz Schlogelhofer ◽  
Fabrice Gielen ◽  
Kirsty Y Wan
Keyword(s):  
Single Cell ◽  
Genetic Basis ◽  
Marine Alga ◽  
Reaction Network ◽  
Droplet Microfluidics ◽  
Model Species ◽  
Active Systems ◽  
Locomotor Behaviour ◽  
Cellular Excitability ◽  
First Time

At all scales, the movement patterns of organisms serve as dynamic read-outs of their behaviour and physiology. We devised a novel droplet microfluidics assay to encapsulate single algal microswimmers inside closed arenas, and comprehensively studied their roaming behaviour subject to a large number of environmental stimuli. We compared two model species, Chlamydomonas reinhardtii (freshwater alga, 2 cilia), and Pyramimonas octopus (marine alga, 8 cilia), and detailed their highly-stereotyped behaviours and the emergence of a trio of macroscopic swimming states (smooth-forward, quiescent, tumbling or excitable backward). Harnessing ultralong timeseries statistics, we reconstructed the species-dependent reaction network that underlies the choice of locomotor behaviour in these aneural organisms, and discovered the presence of macroscopic non-equilibrium probability fluxes in these active systems. We also revealed for the first time how microswimmer motility changes instantaneously when a chemical is added to their microhabitat, by inducing deterministic fusion between paired droplets - one containing a trapped cell, and the other, a pharmacological agent that perturbs cellular excitability. By coupling single-cell entrapment with unprecedented tracking resolution, speed and duration, our approach offers unique and potent opportunities for diagnostics, drug-screening, and for querying the genetic basis of micro-organismal behaviour.

NEW VARIETIES OF CURRANTS AND GOOSEBERRY BREEDING PLANTS

1970 ◽  
pp. 41-46
Author(s):  
O. D. Golyaeva ◽  
O. V. Kurashev ◽  
S. D. Knyazev ◽  
А. Yu. Bakhotskaya
Keyword(s):  
Powdery Mildew ◽  
Genetic Basis ◽  
Black Currant ◽  
Leaf Spots ◽  
Agricultural Sciences ◽  
Berry Crops ◽  
New Varieties ◽  
First Time ◽  
Red Currant

The main goal of the scientific institution was and remains to improve the assortment of fruit and berry crops for the development of domestic horticulture. Black currant breeding at VNIISPK was started by A.F Tamarova and continued by the doctor of agricultural Sciences T.P.Ogoltsova and doctor of agricultural Sciences S.D. Knyazev. A long-term breeding program has been developed. The main goals of the program are to create black currant cultivars with continuous resistance to diseases, first of all powdery mildew, as wells resistance to pests, i.e. bud mite. As a result of the long-term work, over 40 black currant cultivars have been developed, 14 of them are zoned. Red currant breeding was led by the candidate of agricultural Sciences L.V. Bayanova; since 2001 the work has been continued by the candidate of agricultural Sciences O.D. Golyaeva. ‘Heinemanns Rote Spӓtlese’, the descendant of R. multiflorum Kit., was involved in the red currant breeding for the first time in Russia. On its genetic basis, a series of late maturing cultivars with long and dense racemes was created. At the Institute, in total 21cultivars of red currants have been developed, 13 of them are zoned. At present, red currant cultivars make up 25.5% of the zoned assortment in Russia. The first research on gooseberries was stated by V.P. Semakin and A.F Tamarova; since 1992 the systematic gooseberry breeding has been carried out by the candidate of agricultural Sciences O.V. Kurashev. On the basis of Grossularia robusta, we have created gooseberry forms that are resistant to powdery mildew and leaf spots. These forms are highly productive, weakly thorned, having bush habit suitable for mechanized harvest. The result of breeding activities was the transfer of 6 gooseberry cultivars to State agricultural testing: ‘Solnechny Zaychik’, ‘Nekrasovsky’, ‘Yupiter’, ‘Zemlianichny’, ‘Moryachok’ and ‘Discovery’.

scholarly journals Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1212
Author(s):  
J. Spencer Johnston ◽  
Carl E. Hjelmen
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Basis ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Complete Genomic Sequence ◽  
Special Issue ◽  
Model Species ◽  
Road Map ◽  
Generation Sequencing ◽  
Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

scholarly journals Massively parallel, time-resolved single-cell RNA sequencing with scNT-Seq

2019 ◽  
Author(s):  
Qi Qiu ◽  
Peng Hu ◽  
Kiya W. Govek ◽  
Pablo G. Camara ◽  
Hao Wu
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Temporal Dynamics ◽  
Embryonic Stem ◽  
Droplet Microfluidics ◽  
Massively Parallel ◽  
Specific Gene ◽  
Time Resolved ◽  
Single Cell Rna Sequencing ◽  
Rna Biogenesis

ABSTRACTSingle-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal dynamics of RNA biogenesis and decay. Here we present single-cell new transcript tagging sequencing (scNT-Seq), a method for massively parallel analysis of newly-transcribed and pre-existing RNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking metabolically labeled newly-transcribed RNAs with T-to-C substitutions. By simultaneously measuring new and old transcriptomes, scNT-Seq reveals neuronal subtype-specific gene regulatory networks and time-resolved RNA trajectories in response to brief (minutes) versus sustained (hours) neuronal activation. Integrating scNT-Seq with genetic perturbation reveals that DNA methylcytosine dioxygenases may inhibit stepwise transition from pluripotent embryonic stem cell state to intermediate and totipotent two-cell-embryo-like (2C-like) states by promoting global RNA biogenesis. Furthermore, pulse-chase scNT-Seq enables transcriptome-wide measurements of RNA stability in rare 2C-like cells. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms.

scholarly journals CHEMICAL CONSTITUENTS AND BIOACTIVITY OF Codium amplivesiculatum SETCHELL N. L.GARDNER (CHLOROPHYTA; BRYOPSIDALES)

2013 ◽  
Vol 28 (2) ◽  
pp. 1
Author(s):  
A. Marín -Álvarez ◽  
J. I. Murrillo -Álvarez ◽  
M. Muñoz -Ochoa ◽  
G. M. Molina -Salinas
Keyword(s):  
Staphylococcus Aureus ◽  
Silica Gel ◽  
Vibrio Parahaemolyticus ◽  
Marine Alga ◽  
Chemical Constituents ◽  
Ethanol Extract ◽  
Solvent Mixtures ◽  
Bioactive Substances ◽  
First Time ◽  
Tuberculosis Activity

In search of bioactive substances from Mexican marine organisms, crude ethanol-extract from the marine alga Codium amplivesiculatum was fractionated in chromatographic columns of silica gel at 60 Å (230-400 mesh) using solvent mixtures of increasing polarity. All the fractions were submitted to antibacterial assays. The major metabolite from an anti-tuberculosis fraction (MIC = 100 μg mL–1) was purified and identified as 1-octodecanol (1). The anti-tuberculosis activity was attributed to 1 with bases in previous reports. In addition, clerosterol (2) was obtained by crystallization from an active fraction against Staphylococcus aureus and Vibrio parahaemolyticus (MIC = 125 and 250 μg mL–1, respectively). Both structures were established by interpretation and comparison of infrared and 1H NMR spectroscopic data. In contrast with other studies, 2 showed a non-significant cytotoxicity against the cell line PC-3 (% GI = 21.05 ± 0.3 at 50 μg mL–1). To our knowledge, these metabolites are reported for the first time from C. amplivesiculatum, and this is one of very rare reports of saturated long-chain alcohols isolated from chlorophytes. Constituyentes químicos y bioactividad de Codium amplivesiculatum Con el propósito de descubrir sustancias bioactivas a partir de organismos marinos encontrados en México, se fraccionó el extracto crudo etanólico de Codium amplivesiculatum en columnas cromatográficas de sílica gel 60 Å (230-400 de malla) utilizando mezclas de solventes de polaridad creciente. Todas las fracciones se sometieron a ensayos antibacterianos. El principal metabolito de la fracción activa antituberculosis (MIC = 100 μg mL-1), fue purificado e identificado como 1-octodecanol (1). La actividad antituberculosis, basada en reportes previos, se atribuyó al compuesto 1. Además, se obtuvo clerosterol (2) por cristalización de una fracción activa frente a Staphylococcus aureus y Vibrio parahaemolyticus (MIC = 125 y 250 μg mL-1, respectivamente). Las dos estructuras fueron inferidas mediante interpretación y comparación de datos obtenidos por espectroscopía de IR-ATR y 1H RMN. En contraste con otros estudios, el compuesto 2 mostró una citotoxicidad no significativa contra la línea celular PC-3 (% IC = 21.05 ± 0.3 a 50 μg mL–1). Hasta donde sabemos, estos metabolitos se reportan por primera vez en C. amplivesiculatum y 1-octadecanol es un reporte muy raro de alcohol de cadena larga aislado de clorofitas.

Inertial-ordering-assisted droplet microfluidics for high-throughput single-cell RNA-sequencing

Lab on a Chip ◽  
2018 ◽  
Vol 18 (5) ◽  
pp. 775-784 ◽  
Author(s):  
Hui-Sung Moon ◽  
Kwanghwi Je ◽  
Jae-Woong Min ◽  
Donghyun Park ◽  
Kyung-Yeon Han ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput ◽  
Droplet Microfluidics ◽  
Single Cell Rna Sequencing ◽  
Spiral Microchannel

We developed a modified high-throughput droplet barcoding technique for single-cell Drop-Seq via introduction of hydrodynamic ordering in a spiral microchannel.

scholarly journals Unexpected Geographic Variability of the Free Running Period in the Linden Bug Pyrrhocoris apterus

2016 ◽  
Vol 31 (6) ◽  
pp. 568-576 ◽  
Author(s):  
Lenka Pivarciova ◽  
Hanka Vaneckova ◽  
Jan Provaznik ◽  
Bulah Chia-hsiang Wu ◽  
Martin Pivarci ◽  
...  
Keyword(s):  
Technological Progress ◽  
Genetic Basis ◽  
Model Organisms ◽  
Geographic Variability ◽  
Model Species ◽  
Pyrrhocoris Apterus ◽  
Free Running ◽  
Field Lines ◽  
Free Running Period ◽  
Remarkable Progress

Circadian clocks keep organisms in synchrony with external day-night cycles. The free running period (FRP) of the clock, however, is usually only close to—not exactly—24 h. Here, we explored the geographical variation in the FRP of the linden bug, Pyrrhocoris apterus, in 59 field-lines originating from a wide variety of localities representing geographically different environments. We have identified a remarkable range in the FRPs between field-lines, with the fastest clock at ~21 h and the slowest close to 28 h, a range comparable to the collections of clock mutants in model organisms. Similarly, field-lines differed in the percentage of rhythmic individuals, with a minimum of 13.8% and a maximum of 86.8%. Although the FRP correlates with the latitude and perhaps with the altitude of the locality, the actual function of this FRP diversity is currently unclear. With the recent technological progress of massive parallel sequencing and genome editing, we can expect remarkable progress in elucidating the genetic basis of similar geographic variants in P. apterus or in similar emerging model species of chronobiology.

scholarly journals Single-Cell Genomic Sequencing of Three Peritrichs (Protista, Ciliophora) Reveals Less Biased Stop Codon Usage and More Prevalent Programmed Ribosomal Frameshifting Than in Other Ciliates

2020 ◽  
Vol 7 ◽  
Author(s):  
Xiao Chen ◽  
Chundi Wang ◽  
Bo Pan ◽  
Borong Lu ◽  
Chao Li ◽  
...  
Keyword(s):  
Codon Usage ◽  
Single Cell ◽  
Stop Codon ◽  
Genomic Data ◽  
Evolutionary Strategy ◽  
Genomic Sequencing ◽  
Ribosomal Frameshifting ◽  
Genomic Features ◽  
First Time ◽  
Stop Codon Reassignment

Peritrichs are one of the largest groups of ciliates with over 1,000 species described so far. However, their genomic features are largely unknown. By single-cell genomic sequencing, we acquired the genomic data of three sessilid peritrichs (Cothurnia ceramicola, Vaginicola sp., and Zoothamnium sp. 2). Using genomic data from another 53 ciliates including 14 peritrichs, we reconstructed their evolutionary relationships and confirmed genome skimming as an efficient approach for expanding sampling. In addition, we profiled the stop codon usage and programmed ribosomal frameshifting (PRF) events in peritrichs for the first time. Our analysis reveals no evidence of stop codon reassignment for peritrichs, but they have prevalent +1 or -1 PRF events. These genomic features are distinguishable from other ciliates, and our observations suggest a unique evolutionary strategy for peritrichs.

scholarly journals Ultraviolet patterns of flowers revealed in polymer replica – caused by surface architecture

2019 ◽  
Vol 10 ◽  
pp. 459-466 ◽  
Author(s):  
Anna J Schulte ◽  
Matthias Mail ◽  
Lisa A Hahn ◽  
Wilhelm Barthlott
Keyword(s):  
Surface Structure ◽  
Uv Light ◽  
Model Species ◽  
Visual Signaling ◽  
Starting Point ◽  
Structure Lead ◽  
Replication Technique ◽  
First Time ◽  
Uv Reflection

Angiosperms and their pollinators are adapted in a close co-evolution. For both the plants and pollinators, the functioning of the visual signaling system is highly relevant for survival. As the frequency range of visual perception in many insects extends into the ultraviolet (UV) region, UV-patterns of plants play an important role in the flower–pollinator interaction. It is well known that many flowers contain UV-absorbing pigments in their petal cells, which are localized in vacuoles. However, the contribution of the petal surface microarchitecture to UV-reflection remains uncertain. The correlation between the surface structure and its reflective properties is also relevant for biomimetic applications, for example, in the field of photovoltaics. Based on previous work, we selected three model species with distinct UV-patterns to explore the possible contribution of the surface architecture to the UV-signaling. Using a replication technique, we transferred the petal surface structure onto a transparent polymer. Upon illumination with UV-light, we observed structural-based patterns in the replicas that were surprisingly comparable to those of the original petals. For the first time, this experiment has shown that the parameters of the surface structure lead to an enhancement in the amount of absorbed UV-radiation. Spectrophotometric measurements revealed up to 50% less reflection in the UV-absorbing regions than in the UV-reflecting areas. A comparative characterization of the micromorphology of the UV-reflecting and UV-absorbing areas showed that, in principle, a hierarchical surface structure results in more absorption. Therefore, the results of our experiments demonstrate the structural-based amplification of UV-reflection and provide a starting point for the design of bioinspired antireflective and respectively strongly absorbing surfaces.

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