Correction: Double triage to identify poorly annotated genes in maize: The missing link in community curation.

[This corrects the article DOI: 10.1371/journal.pone.

Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.

Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.

Estimated GFR in autosomal dominant polycystic kidney disease: errors of an unpredictable method.

Background: Autosomal dominant polycystic kidney disease (ADPKD) causes about 10% of cases of end stage renal disease. Disease progression rate is heterogeneous. Tolvaptan is presently the only specific therapeutic option to slow kidney function decline in adults at risk of rapidly progressing ADPKD with chronic kidney disease (CKD) stages 1-4.

Varicocoele embolization with sclerosing agents leads to lower radiation exposure and procedural costs than coils: Data from a real-life before and after study.

Objectives: To investigate clinical outcomes, radiation exposure and procedural costs associated with percutaneous varicocoele embolization using coils and sclerosing agents (SAs) in a cohort of young-adult men.

Materials And Methods: Data from consecutive men treated with percutaneous varicocoele embolization using coils and SA between 2017 and 2021 were analyzed. The allocation was based on a change of policy occurred in June 2020 with the substitution of coils with SA (before and after study).

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud.

MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues from four maize strains (B73, NC350, W22, TIL11) by RNA-Seq, Chip-Seq, RAMPAGE, and small RNA sequencing. To facilitate reproducible science and provide both human and machine access to the MaizeCODE data, we enhanced SciApps, a cloud-based portal, for analysis and distribution of both raw data and analysis results.

Double triage to identify poorly annotated genes in maize: The missing link in community curation.

The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer.

In Situ Localization of Small RNAs in Plants.

Small RNAs have vital roles in numerous aspects of plant biology. Deciphering their precise contributions requires knowledge of a small RNA's spatiotemporal pattern of accumulation. The in situ hybridization protocol described here takes advantage of locked nucleic acid (LNA) oligonucleotide probes to visualize small RNA expression at the cellular level with high sensitivity and specificity.

Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals.

Mobile small RNAs serve as local positional signals in development and coordinate stress responses across the plant. Despite its central importance, an understanding of how the cell-to-cell movement of small RNAs is governed is lacking. Here, we show that miRNA mobility is precisely regulated through a gating mechanism polarised at defined cell-cell interfaces.

Peripheral blood CD34+ percentage at hematological recovery after chemotherapy is a good early predictor of harvest: a single-center experience.

Several algorithms for early prediction of poor-mobilizing patients after chemotherapy and granulocyte colony-stimulating factor administration have been proposed. They generally define peripheral blood cut-off levels of CD34+ cells at a fixed day after starting chemotherapy, mostly with cyclophosphamide. To define an algorithm for early addition of plerixafor regardless of the chemotherapy regimen used, we retrospectively analyzed 280 chemomobilization attempts in 236 patients treated at our institution between 2002 and 2012.

The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2.

Polycomb-repressive complexes (PRCs) ensure the correct spatiotemporal expression of numerous key developmental regulators. Despite their pivotal role, how PRCs are recruited to specific targets remains largely unsolved, particularly in plants. Here we show that the Arabidopsis ASYMMETRIC LEAVES complex physically interacts with PRC2 and recruits this complex to the homeobox genes BREVIPEDICELLUS and KNAT2 to stably silence these stem cell regulators in differentiating leaves.

In situ hybridization for the precise localization of transcripts in plants.

With the advances in genomics research of the past decade, plant biology has seen numerous studies presenting large-scale quantitative analyses of gene expression. Microarray and next generation sequencing approaches are being used to investigate developmental, physiological and stress response processes, dissect epigenetic and small RNA pathways, and build large gene regulatory networks(1-3). While these techniques facilitate the simultaneous analysis of large gene sets, they typically provide a very limited spatiotemporal resolution of gene expression changes.

Melon Resistance to Cucurbit yellow stunting disorder virus Is Characterized by Reduced Virus Accumulation.

ABSTRACT The pattern of accumulation of Cucurbit yellow stunting disorder virus (CYSDV; genus Crinivirus, family Closteroviridae) RNA has been analyzed in several cucurbit accessions. In susceptible accessions of melon (Cucumis melo), cucumber (Cucumis sativus), marrow (Cucurbita maxima), and squash (Cucurbita pepo), CYSDV RNA accumulation peaked during the first to second week postinoculation in the first to third leaf above the inoculated one; younger leaves showed very low or undetectable levels of CYSDV. Three melon accessions previously shown to remain asymptomatic after CYSDV inoculation under natural conditions were also assayed for their susceptibility to CYSDV.

Effect of microbial transglutaminase on the protein fractions of rice, pea and their blends.

Background: Transglutaminase (TG) is a transferase that has been used for crosslinking proteins. In general, those interactions are promoted within proteins of the same nature, and very few studies have been conducted for creating new bonds between proteins from different sources catalysed by TG. The effect of TG on the protein fractions of rice flour, pea protein isolate and their blends was studied by using different electrophoretic analyses (simple sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and multistaking SDS-PAGE under reducing and non-reducing conditions).

EcoTILLING for the identification of allelic variants of melon eIF4E, a factor that controls virus susceptibility.

Background: Translation initiation factors of the 4E and 4G protein families mediate resistance to several RNA plant viruses in the natural diversity of crops. Particularly, a single point mutation in melon eukaryotic translation initiation factor 4E (eIF4E) controls resistance to Melon necrotic spot virus (MNSV) in melon. Identification of allelic variants within natural populations by EcoTILLING has become a rapid genotype discovery method.