| 51091. |
- Marquez Molins, Joan, et al.
(författare)
-
Hop stunt viroid infection induces heterochromatin reorganization
- 2024
-
Ingår i: New Phytologist. - 0028-646X .- 1469-8137. ; 243, s. 2351-2367
-
Tidskriftsartikel (refereegranskat)abstract
- Viroids are pathogenic noncoding RNAs that completely rely on their host molecularmachinery to accomplish their life cycle. Several interactions between viroids and their hostmolecular machinery have been identified, including interference with epigenetic mechanismssuch as DNA methylation. Despite this, whether viroids influence changes in other epigeneticmarks such as histone modifications remained unknown. Epigenetic regulation is particularlyimportant during pathogenesis processes because it might be a key regulator of the dynamismof the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultativeand constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatinimmunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 andH3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2,with a tendency to decrease the levels of repressive epigenetic marks through infection pro-gression. These epigenetic changes are connected to the transcriptional regulation of theirexpected targets, genes, and transposable elements. Indeed, several genes related to thedefense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, pro-viding further information about the complexity of the multiple layers of interactions betweenpathogens/viroids and hosts/plants.
|
|
| 51092. |
- Marquez Molins, Joan
(författare)
-
Uncovered diversity of infectious circular RNAs: A new paradigm for the minimal parasites?
- 2024
-
Ingår i: npj viruses. - 2948-1767. ; 2
-
Tidskriftsartikel (refereegranskat)abstract
- Infectious circular RNAs (circRNAs) have been considered as biological oddities only occurring in plants, with limited exceptions. However, a great diversity of viroid-like circRNAs has been recently uncovered by the high-throughput exploration of transcriptomic data of geographically and ecologically diverse niches. In my opinion, this suggests a change in basic assumptions regarding our knowledge about these minimal parasites. The potentially infectious circRNAs found are diverse in size, type of ribozymes, encoded proteins and potential host organisms. The distinction between viroids and RNA viruses has been blurred by the detection of circular mitoviruses and ambiviruses which encode for their own RNA-dependent RNA polymerase. Thus, their taxonomic classification might pose a challenge because of the apparent extensive horizontal transfer and recombination of sequences. Many aspects of the predicted circRNAs remain to be uncovered, such as their pathogenicity or host range, and experimental validations are essential. For example, viroid-like circRNAs similar in size to plant viroids have been found to replicate and cause symptoms in fungi, with an isolate being the smallest replicon characterized so far. Despite an ancestral prebiotic origin for viroid-like sequences has been proposed, their dependence of viral or cellular proteins seems, to my view, more compatible with a cellular escape and/or viral genome reduction. This wide variety of potentially infectious agents might pose a biohazard concern of which we were previously unaware, and thus it would be convenient that more efforts are assigned for their characterization.
|
|
| 51093. |
- Márquez-Zacarías, Pedro, et al.
(författare)
-
Why have aggregative multicellular organisms stayed simple?
- 2021
-
Ingår i: Current Genetics. - : Springer. - 0172-8083 .- 1432-0983. ; 67:6, s. 871-876
-
Forskningsöversikt (refereegranskat)abstract
- Multicellularity has evolved numerous times across the tree of life. One of the most fundamental distinctions among multicellular organisms is their developmental mode: whether they stay together during growth and develop clonally, or form a group through the aggregation of free-living cells. The five eukaryotic lineages to independently evolve complex multicellularity (animals, plants, red algae, brown algae, and fungi) all develop clonally. This fact has largely been explained through social evolutionary theory’s lens of cooperation and conflict, where cheating within non-clonal groups has the potential to undermine multicellular adaptation. Multicellular organisms that form groups via aggregation could mitigate the costs of cheating by evolving kin recognition systems that prevent the formation of chimeric groups. However, recent work suggests that selection for the ability to aggregate quickly may constrain the evolution of highly specific kin recognition, sowing the seeds for persistent evolutionary conflict. Importantly, other features of aggregative multicellular life cycles may independently act to constrain the evolution of complex multicellularity. All known aggregative multicellular organisms are facultatively multicellular (as opposed to obligately multicellular), allowing unicellular-level adaptation to environmental selection. Because they primarily exist in a unicellular state, it may be difficult for aggregative multicellular organisms to evolve multicellular traits that carry pleiotropic cell-level fitness costs. Thus, even in the absence of social conflict, aggregative multicellular organisms may have limited potential for the evolution of complex multicellularity.
|
|
| 51094. |
- Marquina, Daniel, et al.
(författare)
-
Evaluation of non-destructive extraction protocols for metabarcoding of insects
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Researchers in the field of insect diversity can greatly benefit from DNA metabarcoding due to its accuracy, low cost and short processing time compared to manual sorting and identification. But most existing metabarcoding protocols require homogenization of the sample, thus prohibiting any further work on the captured individuals. A mild digestion of the tissue by incubation of the specimens in a lysis buffer has been proposed as an alternative to sample homogenization. Several mild lysis protocols have been presented but they have not been properly evaluated against each other. Here, we analyze the effects of two different mild lysis buffers (one more aggressive than the other), two different incubation times, and two different DNA purification methods (a manual precipitation method and an automated robotic protocol) on metabarcoding performance. Performance was measured as the accuracy of retrieving the true composition of mock insect communities using two different mitochondrial markers (COI and 16S). We found that the variation in concentration and purity of the DNA extracts produced by the different lysis treatments and purification methods had little effect on the recovery of species. However, the two lysis treatments differed significantly in how well they allowed quantification of species abundances. Digestion in the gentler buffer and for a shorter time resulted in metabarcoding results that were more representative of the original sample, while a more aggressive buffer or a longer incubation reduced the values of alpha diversity and increased the differences between metabarcoding results and the true species- abundance distribution. In summary, our results show that the details of non-destructive DNA metabarcoding protocols can have a significant effect on performance. Specifically, our results suggest that a short and mild lysis treatment is the best choice for recovering the true composition of the processed sample. Short and mild lysis protocols not only improve accuracy, they also come with a lower cost and a faster processing time.
|
|
| 51095. |
- Marquina, Daniel, et al.
(författare)
-
The effect of ethanol concentration on the preservation of insects for biodiversity studies
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- 1. Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well. Highly concentrated ethanol (95-100 %), preferred as a DNA preservative for molecular biology, has generally been assumed to make specimens brittle and prone to breaking. However, systematic studies of the correlation between ethanol concentration and specimen preservation are lacking.2. Here, we tested how preservative ethanol concentration in combination with different sample handling regimes affect the integrity of seven insect species representing four orders, and differing substantially in the level of sclerotization. After the treatments, we counted the number of appendages (legs, wings, antennae or heads) that each specimen had lost.3. We found that high ethanol concentrations indeed induce brittleness in insects. However, the magnitude and nature of the effect varied strikingly among species. In general, ethanol concentrations at or above 90 % made the insects more brittle and resulted in more shriveling, but insects with more robust or sclerotized exoskeletons actually retained more of their appendages at high concentrations. Surprisingly, neither freezing the samples nor drying the insects after immersion in ethanol had a negative effect on the loss of appendages. However, the morphology of the insects was severely damaged if they were allowed to dry.4. While higher ethanol concentrations might positively affect long-term DNA preservation, there is a clear trade-off between collecting and preserving insects for morphological examination and genetic analysis, since the optimal ethanol concentration for the latter is detrimental for the former and vice versa. The trade-off needs to be considered in large insect biodiversity surveys and other projects aiming to combine molecular work with traditional morphology-based characterization of the samples.
|
|
| 51096. |
|
|
| 51097. |
- Marschinke, Franziska, et al.
(författare)
-
The absence of CD47 promotes nerve fiber growth from cultured ventral mesencephalic dopamine neurons
- 2012
-
Ingår i: PLOS ONE. - : Public library of science. - 1932-6203. ; 7:9, s. e45218-
-
Tidskriftsartikel (refereegranskat)abstract
- In ventral mesencephalic organotypic tissue cultures, two timely separated sequences of nerve fiber growth have been observed. The first appearing nerve fiber pattern is a long-distance outgrowth that occurs before astrocytes start to proliferate and migrate to form an astrocytic monolayer that finally surrounds the tissue slice. These long-distance growing nerve fibers are retracted as the astrocytes migrate, and are followed by a secondary outgrowth. The secondary outgrowth is persistent in time but reaches short distances, comparable with outgrowth seen from a dopaminergic graft implanted to the brain. The present study was focused on the interaction between the astrocytes and the long-distance growing non-glial associated nerve fibers. Cross talk between astroglia and neurite formation might occur through the integrin-associated protein CD47. CD47 serves as a ligand for signal regulatory protein (SIRP) alpha and as a receptor for the extracellular matrix protein thrombospondin-1 (TSP-1). Embryonic day 14 ventral mesencephalic tissue from CD47(+/+) and CD47(-/-) mice was used to investigate astrocytic migration and the tyrosine hydroxylase (TH) -positive outgrowth that occurred remote from the astrocytes. TH-immunohistochemistry demonstrated that the non-glial-associated nerve fiber outgrowth in CD47(-/-) cultures reached significantly longer distances and higher density compared to nerve fibers formed in CD47(+/+) cultures at 14 days in vitro. These nerve fibers often had a dotted appearance in CD47(+/+) cultures. No difference in the astrocytic migration was observed. Further investigations revealed that the presence of CD47 in control culture did neither hamper non-glial-associated growth through SIRP alpha nor through TSP-1 since similar outgrowth was found in SIRP alpha mutant cultures and in CD47(+/+) cultures treated with blocking antibodies against the TSP-1, respectively, as in the control cultures. In conclusion, long-distance growing nerve fiber formation is promoted by the absence of CD47, even though the presence of astrocytes is not inhibited.
|
|
| 51098. |
- Marshall, Andrew G., et al.
(författare)
-
Spinal signalling of C-fiber mediated pleasant touch in humans
- 2019
-
Ingår i: eLIFE. - : ELIFE SCIENCES PUBLICATIONS LTD. - 2050-084X. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- C-tactile afferents form a distinct channel that encodes pleasant tactile stimulation. Prevailing views indicate they project, as with other unmyelinated afferents, in lamina I-spinothalamic pathways. However, we found that spinothalamic ablation in humans, whilst profoundly impairing pain, temperature and itch, had no effect on pleasant touch perception. Only discriminative touch deficits were seen. These findings preclude privileged C-tactile-lamina I-spinothalamic projections and imply integrated hedonic and discriminative spinal processing from the body.
|
|
| 51099. |
- Marshall, Charla, et al.
(författare)
-
Mitochondrial DNA haplogrouping to assist with the identification of unknown service members from the World War II Battle of Tarawa
- 2020
-
Ingår i: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 47
-
Tidskriftsartikel (refereegranskat)abstract
- The World War II Battle of Tarawa, 1943, was a devastating conflict that resulted in losses of more than 1100 American and 4690 Japanese troops. The United States government aims to identify and repatriate the remains of all missing American service members through the Defense Prisoner of War/Missing in Action (POW/MIA) Accounting Agency (DPAA) and its partners such as the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL). Remains associated with the Battle of Tarawa have been recovered from field excavations conducted by History Flight, a DPAA strategic partner, as well as from the National Memorial Cemetery of the Pacific (NMCP) in Hawaii where unknowns have been disinterred for identification. DNA testing at the AFMES-AFDIL has produced mitochondrial DNA (mtDNA) sequences from 1027 case samples to date. Haplogroup assignments indicate that more than one third (36.2 %) of field-collected samples are likely of Asian maternal ancestry. Therefore the field collections from the Tarawa battlefield comprise the remains of American service members but also those of foreign nationals from Asia. The mtDNA of the NMCP unknowns is similar in ancestry proportion to the family reference sample distribution. The DPAA uses the ancestry information gleaned from mtDNA sequence data in conjunction with anthropological evidence to make foreign national determinations. In this way, mtDNA haplogrouping is used to sort the commingled and fragmentary remains recovered from Tarawa between Americans and foreign nationals, which are then repatriated to their country of origin.
|
|
| 51100. |
- Marshall, Charla, et al.
(författare)
-
Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting
- 2020
-
Ingår i: Genes. - : MDPI. - 2073-4425. ; 11:10
-
Tidskriftsartikel (refereegranskat)abstract
- Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.
|
|
