phenotypic characterisation
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PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261677
Author(s):  
Dorota Litwinek ◽  
Jakub Boreczek ◽  
Halina Gambuś ◽  
Krzysztof Buksa ◽  
Wiktor Berski ◽  
...  

Starter cultures composed of lactic acid bacteria (LAB) were developed based on the genotypic and phenotypic characterisation of isolates belonging to dominant groups of bacteria in spontaneous rye wholemeal sourdoughs. Combinations of strains have been evaluated on an industrial scale in the sourdough fermentation process. Wholemeal rye bread was prepared using sourdoughs obtained with 3 new starter cultures, and compared to bread made using the commercial culture (LV2). All newly developed cultures used for the preparation of wholemeal rye bread allowed to obtain better quality products as compared to the LV2 based bread. The best results were obtained when the culture containing Lactiplantibacillus plantarum 2MI8 and exopolysaccharide (EPS)-producing Weissella confusa/cibaria 6PI3 strains was applied. The addition of yeast during sourdough breads production, especially the one prepared from mentioned above starter culture, significantly improved their organoleptic properties, their volume and crumb moisture was increased, and also the crumb acidity and hardness was reduced. Fermentation of rye wholemeal dough, especially without the yeast addition, resulted in a significant reduction in the content of higher inositol phosphates as compared to the applied flour, which is associated with improved bioavailability of minerals. The results of this study prove that the investigated new starter cultures can be successfully applied in wholemeal rye bread production.


Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 161
Author(s):  
Danuta Wójcik ◽  
Monika Marat ◽  
Agnieszka Marasek-Ciołakowska ◽  
Krzysztof Klamkowski ◽  
Zbigniew Buler ◽  
...  

Polyploidization is an important source of variability for plant breeding. Polyploids are often characterised by increased resistance to biotic and abiotic stresses. Since drought and pathogen attack are the main threats to apple cultivation, obtaining new sources of resistance is an important issue for apple breeding. The newly obtained autotetraploid clones of apple cv. ‘Redchief’ showed superior resistance to fire blight. The aim of the presented research was the in-depth phenotypic characterisation of ‘Redchief’ tetraploids and assessment of their response to drought at the physiological and genetic level. The growth of own-rooted five-year-old trees of ‘Redchief’ tetraploids was poor compared with diploids; all growth parameters—the number and length of current season shoots, the total length of current season shoots per tree and the cross-section area of the trunk—were reduced in tetraploid clones. Grafting on M9 rootstock improved the growth characteristics of ‘Redchief’ tetraploids. Compared with diploid plants, the leaves of tetraploids were thicker, with altered shape, higher chlorophyll content, and larger stomata, but the stomatal density decreased. The leaf anatomical structure of tetraploids was changed, the adaxial and abaxial epidermis and both types of mesophyll were significantly thicker than in diploids. Moreover, the pollen grains of tetraploids were larger, but their viability and germination were reduced. Under conditions of limited water supply, the reduction in growth parameters was smaller and the physiological parameters were higher in the ‘Redchief’ tetraploid clone 4x-25 than in diploid plants. The expression of APX gene was higher in tetraploids than in diploids 15 days after drought stress induction. The results suggest the enhanced drought tolerance of the studied ‘Redchief’ autotetraploid clone compared with its diploid counterpart.


Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6386
Author(s):  
Antonio J. Ruiz-Rodríguez ◽  
Maria P. Molina-Vallejo ◽  
Inés Aznar-Peralta ◽  
Cristina González Puga ◽  
Inés Cañas García ◽  
...  

The isolation of circulating tumour cells (CTCs) in colorectal cancer (CRC) mostly relies on the expression of epithelial markers such as EpCAM, and phenotypic characterisation is usually performed under fluorescence microscopy with only one or two additional markers. This limits the ability to detect different CTC subpopulations based on multiple markers. The aim of this work was to develop a novel protocol combining two platforms (IsoFluxTM and ImageStream®X) to improve CTC evaluation. Cancer cell lines and peripheral blood from healthy donors were used to evaluate the efficiency of each platform independently and in combination. Peripheral blood was extracted from 16 early CRC patients (before loco-regional surgery) to demonstrate the suitability of the protocol for CTC assessment. Additionally, peripheral blood was extracted from nine patients one month after surgery to validate the utility of our protocol for identifying CTC subpopulation changes over time. Results: Our protocol had a mean recovery efficiency of 69.5% and a limit of detection of at least four cells per millilitre. We developed an analysis method to reduce noise from magnetic beads used for CTC isolation. CTCs were isolated from CRC patients with a median of 37 CTCs (IQ 13.0–85.5) at baseline. CTCs from CRC patients were significantly (p < 0.0001) larger than cytokeratin (CK)-negative cells, and patients were stratified into two groups based on BRAFV600E and PD-L1 expression on CK-positive cells. The changes observed over time included not only the number of CTCs but also their distribution into four different subpopulations defined according to BRAFV600E and PD-L1 positivity. We developed a novel protocol for semi-automatic CTC isolation and phenotypic characterisation by combining two platforms. Assessment of CTCs from early CRC patients using our protocol allowed the identification of two clusters of patients with changing phenotypes over time.


2021 ◽  
Vol 11 ◽  
Author(s):  
Drew Maclean ◽  
Maria Tsakok ◽  
Fergus Gleeson ◽  
David J. Breen ◽  
Robert Goldin ◽  
...  

Colorectal liver metastases (CRLM) have heterogenous histopathological and immunohistochemical phenotypes, which are associated with variable responses to treatment and outcomes. However, this information is usually only available after resection, and therefore of limited value in treatment planning. Improved techniques for in vivo disease assessment, which can characterise the variable tumour biology, would support further personalization of management strategies. Advanced imaging of CRLM including multiparametric MRI and functional imaging techniques have the potential to provide clinically-actionable phenotypic characterisation. This includes assessment of the tumour-liver interface, internal tumour components and treatment response. Advanced analysis techniques, including radiomics and machine learning now have a growing role in assessment of imaging, providing high-dimensional imaging feature extraction which can be linked to clinical relevant tumour phenotypes, such as a the Consensus Molecular Subtypes (CMS). In this review, we outline how imaging techniques could reproducibly characterize the histopathological features of CRLM, with several matched imaging and histology examples to illustrate these features, and discuss the oncological relevance of these features. Finally, we discuss the future challenges and opportunities of CRLM imaging, with a focus on the potential value of advanced analytics including radiomics and artificial intelligence, to help inform future research in this rapidly moving field.


BMJ Open ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. e048073
Author(s):  
Igor C Johansen ◽  
Priscila T Rodrigues ◽  
Juliana Tonini ◽  
Joseph Vinetz ◽  
Marcia C Castro ◽  
...  

PurposeThis population-based open cohort study aims to investigate biological and sociodemographic drivers of malaria transmission in the main urban hotspot of Amazonian Brazil.ParticipantsNearly 20% of the households in the northwestern town of Mâncio Lima were randomly selected and 2690 participants were enrolled since April 2018. Sociodemographic, housing quality, occupational, behavioural and morbidity information and travel histories were collected during consecutive study visits. Blood samples from participants>3 months old were used for malaria diagnosis and human genetic studies; samples from participants with laboratory-confirmed malaria have been cryopreserved for genetic and phenotypic characterisation of parasites. Serology was introduced in 2020 to measure the prevalence and longevity of SARS-CoV-2 IgG antibodies.Findings to dateMalaria prevalence rates were low (up to 1.0% for Plasmodium vivax and 0.6% for P. falciparum) during five consecutive cross-sectional surveys between April–May 2018 and October–November 2020; 63% of infections diagnosed by microscopy were asymptomatic. Malaria risk is heterogeneously distributed, with 20% study participants contributing 86% of the overall burden of P. vivax infection. Adult males are at greatest risk of infection and human mobility across the urban–rural interface may contribute to sustained malaria transmission. Local P. vivax parasites are genetically diverse and fragmented into discrete inbred lineages that remain stable across space and time.Future plansTwo follow-up visits, with similar study protocols, are planned in 2021. We aim to identify high-risk individuals that fuel onwards malaria transmission and represent a priority target for more intensive and effective control interventions.Trial registration numberNCT03689036.


Author(s):  
Micael Widerström ◽  
Marc Stegger ◽  
Anders Johansson ◽  
Bharat Kumar Gurram ◽  
Anders Rhod Larsen ◽  
...  

Abstract Prosthetic joint infection (PJI) is a feared and challenging to diagnose complication after arthroplasty, with Staphylococcus epidermidis as the major pathogen. One important criteria to define PJI is the detection of phenotypically indistinguishable microorganisms with identical antibiotic susceptibility pattern in at least two different samples. However, owing to phenotypical variation within genetic clones and clonal variation within a phenotype, the criteria may be ambiguous. We investigated the extent of diversity among coagulase-negative staphylococci (CoNS) in PJI and characterised S. epidermidis isolates from PJI samples, specifically multiple S. epidermidis isolates identified in individual PJI patients. We performed a retrospective cohort study on 62 consecutive patients with PJI caused by CoNS from two hospitals in Northern Sweden. In 16/62 (26%) PJIs, multiple S. epidermidis isolates were available for whole-genome analyses. Hospital-adapted multidrug-resistant genetic clones of S. epidermidis were identified in samples from 40/62 (65%) of the patients using a combination of pulsed-field gel electrophoresis and multilocus sequence typing. Whole-genome sequencing showed the presence of multiple sequence types (STs) in 7/16 (44%) PJIs where multiple S. epidermidis isolates were available. Within-patient phenotypical variation in the antibiotic susceptibility and/or whole-genome antibiotic resistance gene content was frequent (11/16, 69%) among isolates with the same ST. The results highlight the ambiguity of S. epidermidis phenotypic characterisation as a diagnostic method in PJI and call for larger systematic studies for determining the frequency of CoNS diversity in PJIs, the implications of such diversity for microbiological diagnostics, and the therapeutic outcomes in patients.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jodie A. Watkins ◽  
James J. P. Alix ◽  
Pamela J. Shaw ◽  
Richard J. Mead

AbstractThe majority of preclinical studies in ALS have relied on transgenic models with overexpression of mutant human superoxide dismutase 1 (SOD1), widely regarded to have failed in terms of translation of therapeutic effects. However, there are still no widely accepted models of other genetic subtypes of ALS. The majority of patients show ubiquitinated cytoplasmic inclusions of TAR DNA binding protein of 43 kilodaltons (TDP-43) in spinal motor neurons at the end stage of disease and a small proportion have mutations in TARDBP, the gene encoding TDP-43. TDP-43 transgenic mouse models have been produced, but have not been widely adopted. Here, we characterised one of these models available from the Jackson Laboratory in detail. Compared to TDP-43WT mice, TDP-43Q331K mice had 43% less hindlimb muscle mass at 6 months and a 73% reduction in hindlimb compound muscle action potential at 8 months of age. Rotarod and gait analysis indicated motor system decline with elevated weight gain. At the molecular level, the lack of TDP-43 cellular pathology was confirmed with a surprising increase in nuclear TDP-43 in motor neurons. Power analysis indicated group sizes of 12–14 mice are needed to detect 10–20% changes in measured parameters with a power of 80%, providing valid readouts for preclinical testing. Overall, this model may represent a useful component of multi-model pre-clinical therapeutic studies for ALS.


2021 ◽  
pp. 1-8
Author(s):  
Junwei Zhong ◽  
Bing You ◽  
Ke Xu ◽  
Xiaohui Zhang ◽  
Yue Xie ◽  
...  

2021 ◽  
pp. 1098612X2110321
Author(s):  
Matthew Green ◽  
Laurent Garosi ◽  
Claire Bessant ◽  
Mark Lowrie

Objectives The aim of this study was to identify the phenotypic features of a paroxysmal dyskinesia observed in Sphynx cats. Methods The owners of affected Sphynx cats were invited to provide video footage of abnormal episodes for review. Those that demonstrated episodes consistent with paroxysmal dyskinesia were then invited to complete an online questionnaire designed to allow further characterisation. Results Ten Sphynx cats were included in the study. All affected cats were <4 years of age at the onset of the episodes (range 0.5–4.0). The episodes had a duration of <5 mins in 9/10 cats (range 0.5–10), while episode frequency was variable between and within individual cats. The episodes were characterised by impaired ambulation due to muscle hypertonicity, most commonly affecting the hips and pelvic limbs (9/10) and shoulders and thoracic limbs (8/10). The head and neck (6/10), tail (5/10), and back and abdomen (3/10) were also involved in some cats. Sudden movement, excitement and stress were identified as possible triggers for the episodes in three cats. Therapeutic intervention was not attempted in 7/10 cases, although two cats were reported to become free of the episodes while receiving acetazolamide. The two cats that were followed beyond 2 years from onset entered spontaneous remission. None of the owners believed that the abnormal episodes had affected the quality of life of their cat. Conclusions and relevance The phenotype of paroxysmal dyskinesia in Sphynx cats presented in this study appears to share similarities with paroxysmal kinesigenic dyskinesia described in human classification systems. Some cats appear to achieve episode freedom spontaneously. Subsequent research should focus on evaluating response to treatment and determining an underlying genetic cause.


Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 680
Author(s):  
Thuy T. P. Mai ◽  
Craig M. Hardner ◽  
Mobashwer M. Alam ◽  
Robert J. Henry ◽  
Bruce L. Topp

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.


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