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opencc-zeroJan 2022View details →

Data from: Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane

Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER (TFL)-like genes. As expected, these genes all show very high homology to their corresponding genes in Sorghum, and also to FT-like, MFT-like, and TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot. High expression levels of ScFT3 in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that ScFT3 is likely to play a role in floral induction in sugarcane; however, other sugarcane FT-like genes may also be involved in the flowering process.

Fig. 4. Callichimaeraperplexa n. gen. n in Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Fig. 4. Callichimaeraperplexa n. gen. n. sp., reconstruction. (A and B) Line drawing of dorsal (A) and ventral (B) views. Colorsdenoteconvergent traitswith other decapod groups: light gray, dorsal carapace, similar to some lobsters and †Palaeocorystidae (Brachyura: Raninoida); dark gray, large eyes, similar to †Ekalakia (Dromiacea: †Glaessneropsidae) and several homoloids; red, pediform mxp3 bearing acrista dentata, similarto lobsters, most anomurans, and early-branching brachyurans (Homolodromioidea, most Homoloidea); yellow, spanner-like P1, similar to Hippoidea (Anomura), Raninoidea (Brachyura), and †Retrorsichela; green, flattened paddle-like legs P2 and P3, similar to Matutidae (Brachyura: Eubrachyura); blue, reduced legs P4 and P5, as in hermit crabs (Anomura: Paguroidea), podotreme brachyurans (e.g., Homolodromioidea and Cyclodorippoidea) and early-branchingeubrachyurans (e.g., Dorippoidea); orange, sternites S5 and S6 similar to †Retrorsichela, and Heikeopsis (Eubrachyura: Dorippoidea); and purple, symmetrical pleon lacksarticulatedrings anduropods/uropodal plates, likemost brachyurans. (C and D) Digital reconstruction. (C) Dorsal view. (D) Ventralview. A, pleon; Cx, coxa;Is, ischium; Ma, manus. Scalebar,10 mm. See movies S1 and S2 anddata file S2 for three-dimensional (3D) viewableand printable models. Line drawings by J.L. and 3D reconstructions by A.D.

Fig. 3 in Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Fig. 3. Pleon and sexual dimorphism in Callichimaera perplexa n. gen. n. sp., lower Upper Cretaceous, Colombia. (A) Paratype IMG p881217, female, dorsal view showing thelegs 2 to 5 and thepleonites 1 to 4, two of them bearing anaxialtubercle. (B) Paratype IGMp881209b, female,showing the unfoldedpleon in lateralview and pleonites 2 to 5 andmultiple pairs of pleopods (white arrows). (C) Paratype MUN-STRI 27045-06, female, dorsalview, showing pleonites 1 to 6, theroundish telson, and the lack of uropods or uropodal plates. (D and E) Paratype IGM p881202, male. (D) Ventral view showing the chelipeds, pereopods, and pleon with sclerotized gonopods 1 and 2 [white box; see (E)]. (E) Close-upof sclerotized male gonopods 1 and 2 (white arrows), anarrow pleonite 6, anelongate telson,and the lackof uropods oruropodal plates. (F) Linedrawing of (E). (G) Paratype MUN-STRI 27045-09, a very small individual, possibly a megalopa or early postlarvalstage, preserving small and slender legs 2 and 3 compared to adult forms [see (I)]. (H) Paratype IGM p881220, juvenile, with legs 2 and 3, the pleon bearingan axial tubercle, and with a bifidrostrum anda pairof largecompoundeyesbearinghexagonalfacets (Fig.2G). (I) Paratype IGMp881206,adult female, ventralviewpreservingspanner-likechelipeds,longoar-likelegsor P2 and P3, reduced andslender legsor P4 and P5, and abroad pleon. G1 and G2, malegonopods 1 and 2; Pl1 to Pl6, pleonites 1 to 6; T, telson. All specimens were photographed dry; specimens in (A), (C), (D), and (G) to (I) were coated with ammonium chloride; specimens in (B) and (E) were uncoated. Photos by J.L.

Fig. 6 in Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Fig. 6. Convergent decarcinized body forms in various families of false and true crabs and convergent appendages in swimming and/or fossorial arthropods. (A to I) Decarcinized crabs. (A to D) Anomura. (A to C) Molecrabs,Hippoidea: (A) Hippidae, Hippamarmorata, Taiwan.(B) Blepharipodidae: Blepharipodaoccidentalis. (C) Albuneidae: Albunea occulta, Taiwan. (D) Porcelain crabs, Galatheoidea: Porcellanidae: Euceramus panatelus, Panama. (E to I) Brachyura. (E and F) Frog crabs, Raninoidea: Raninidae: (E) Raninoides benedicti, Panamá. (F) Symethis sp. Panamá. (G and H) Masked burrowing crabs, Eubrachyura: Corystoidea: Corystidae: (G) Corystes cassivelaunus, Belgium. (H) Jonas distinctus, Taiwan. (I) Chimera crab, †Callichimaeroidea: Callichimaeridae: Callichimaeraperplexa n. gen. n. sp., Cenomanian-Turonian (95 to 90 Ma ago) of Colombia. (J to Q) Otheraquatic arthropods with modified appendages for swimming and/or digging. (J) Sea scorpions, Chelicerata: †Eurypterida: Eurypterusremipes, YPM 211521, upper Silurian, New York. (K to M) Insecta. (K) Coleoptera: Dytiscidae: Cybisterfimbriolatus, YPMENT.959234; (L) Hemiptera: Corixidae: Hesperocorixa kennicottii, YPM ENT.452851; (M) Hemiptera: Notonectidae: Notonectaundulate, last instarnymph, Alberta, Canada. (N) Isopoda: Munnopsidae: Munnopsis longiremis, USNM 113282, Baja California, Mexico. (O to Q) Brachyura. (O) Orithyioidea: Orithyiidae: Orithyia sinica, USNM 134243, China. (P) Calappoidea: Matutidae: Matutavictor. (Q) Portunoidea:Portunidae:Arenaeus cribrarius. Photosby T. Y. Chan (A, C, and H), C. Boyko (B), A. Anker (D, E, and N), J.L. (F and O), H. Hillewaert (G), J. Utrup (J), E. Lazo-Wasem (K and L), J. Acorn (M), and O. Radosta (P and Q).

Fig. 2 in Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Fig. 2. Dorsal, frontal, and ocular features in Callichimaera perplexa n. gen. n. sp., from the mid-Cretaceous of Colombia. (A and B) Paratype MUN-STRI 27044-02, showing three specimensin dorsal view (left), ventral view (right), and anisolated dorsal carapace (bottom center). (A) Color image. (B) Inverted color image highlighting details of thecarapace outlines, clawsand legs, andlarge eyes. (C) Paratype IMGp881203, dorsalview, showingdetails of thecarapace groovesandridgesandthelackof true orbits. (D) Paratype IMGp881218, dorsal view, showing details of dorsal carapace, claws, andlarge oar-like legs 2 and 3. (E and F) Paratype IGM p881209a.(E) Scanning electron microscope (SEM) image showing details of large compound eye, optical lobe, rostrum (R), and two pairs of short antennae between the eyes. (F) SEM showing aclose-upof theoptical lobe. (G) Paratype IGMp881220,SEM oflargeeyepreservingmostlyhexagonalfacetsinhexagonalarrangement (left box), althoughtheproximal cornea bears squarishfacets inorthogonal packing (right box). (H to J) Paratype IGMp881208, ventral view,(H) showing thelargeeyes and bifidrostrum,(I) SEMof ventral right eye, and (J) SEMof ventralleft eye.An1, antenna 1 orantennula; An2,antenna 2; Bcg, branchio-cardiac groove; Cg, cervical groove; E, compound eye; Lr,longitudinal ridge; Ol, opticallobe; Pfr, postfrontal longitudinal ridge; Pgr,protogastric longitudinal ridge.All specimenswere photographed dry; specimensin (C) and (D) were coated with ammonium chloride; specimens in (A), (B), and (E) to (J) were uncoated. Photos by J.L.

Fig. 1 in Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Fig. 1. Ventraland appendicularfeatures in Callichimaera perplexa n. gen. n. sp., fromthemid-Cretaceous of Colombia. (A to C) Holotype IGM p881215.(A) Ventral view. (B) Close-up of sternal plates, sutures, and linea media (lm); the white arrow shows a spine in the third leg coxae. (C) Close-up of sternal crown, mandibles, and maxillipeds 2 and 3, thelatterbearingarowof spinesorcristadentata (cd) intheischium. (D and E) Paratype IGMp881196. (D) Ventralview. (E) Close-upof sternumand sutures. (F) Paratype IGM p881185, showingdetails of thespanner-like claw. (G to I) Paratype IGM p881214. (G) Close-up of the large oar-like legs 2 and 3. (H) Ventralview showing the sternites, claws, legs, and pleon. (I) Close-up of the reduced and slender legs 4 and 5. Ba, basis; Ca, carpus; Da, dactylus; Pr, propodus; Ma, mandibula; Me, merus; Mxp2 and Mxp3, second and third maxillipeds, respectively; P1, claw or cheliped; P2 to P5, pereopods or legs 2 to 5; Po, pollex or fixed finger tip; Pl, pleon or "abdomen"; S1 to S7, sternites 1 to 7; 4/5–6/7, sternal sutures. All specimens were photographed dry; specimens in (A), (D), (E), (G), and (H) were coated with ammonium chloride; specimensin (B), (C), (F), and (I) were uncoated. Photos by J.L.

Fig. 5 in Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Fig. 5. Phylogenetic relationships among the main families, superfamilies, and sections of "true" crabs or Brachyura. Tree topology after figs. S5 and S6. Each color and letter (encircled) represents one of the nine major brachyuran evolutionary branches. Dromiacea (red) (A) and Homoloida (purple) (B) are first known from the Jurassic, while †Callichimaeroida section nov. (dark blue) (C), †Torynommoida (light blue) (D), †Etyoida (dark green) (E), Raninoida (light green) (F), †Dakoticancroida (yellow) (G), Cyclodorippoida (orange) (H), and Eubrachyura or "higher" brachyurans (brown) (I) are all first known from the Cretaceous.Thick solid lines represent the ages of the first and last occurrences of each family within the main lineages. Dotted lines and daggers indicate extinct taxa; solid lines indicate living taxa. Black triangles indicate that in Anomura,decarcinization has occurred twice (anomuran clades not illustrated).White triangles indicate the three Brachyura lineages where decarcinization has occurred. Figure by J.L.

opencc-zeroJan 2022View details →

Post-association barrier to host switching maintained despite strong selection in a novel mutualism

Following a host shift, repeated co-passaging of a mutualistic pair is expected to increase fitness over time in one or both species. Without adaptation, a novel association may be evolutionarily short-lived as it is likely to be outcompeted by native pairings. Here we test whether experimental evolution can rescue a low-fitness novel pairing between two sympatric species of Steinernema nematodes and their symbiotic Xenorhabdus bacteria. Despite low mean fitness in the novel association, considerable variation in nematode reproduction was observed across replicate populations. We selected the most productive infections, co-passaging this novel mutualism nine times to determine whether selection could improve fitness of either or both partners. We found that neither partner showed increased fitness over time. Our results suggest that the variation in association success was not heritable and that mutational input was insufficient to allow evolution to facilitate this host shift. Thus, post-association costs of host switching may represent a formidable barrier to novel partnerships among sympatric mutualists.

opencc-by-4.0Nov 2021View details →

Comparative proteomic and metabolomic analyses of plasma reveal the novel biomarker panels for thyroid dysfunction

Abstract: Objectives: Thyroid dysfunction such as hypothyroidism (THO) and hyperthyroidism (THE) are the disease caused by pathological processes in the thyroid. The current diagnosis of thyroid dysfunction is variable because of ages and genders. The aim of this study was to explore the novel candidate biomarker panels for hypothyroidism and hyperthyroidism screening with mass spectrometry and bioinformatics. Methods: Plasma samples were collected from 15 THE patients, 9 THO patients, and 15 healthy controls. DIA-based proteomic and untargeted metabolomic analyses were performed to identify the novel biomarker panels for THO and THE. Finally, three candidate biomarkers were verified by ELISA in 34 samples. Results: A total of 2738 proteins and 6103 metabolites were identified, and 173 proteins and 2487 metabolites were found to be differentially expressed among THE, THO and control groups. The results of the ensemble feature selection, K-means clustering and the least absolute shrinkage and selection operator (LASSO) regression model showed that four proteins (C4A, C3/C5 convertase, APOL1, and ITIH4) and four metabolites (L-arginine, L-proline, cortisol, and cortisone) identified by plasma proteomics and metabolomics could help distinguish THO and THE patients from healthy controls. Conclusions: This study identified and verified two pairs of biomarker panels that can distinguish the THE and THO patients regardless of ages and genders. Consequently, our findings represent a comprehensive analyses of thyroid dysfunction plasma, which is significant for the clinical diagnosis.

opencc-by-4.0Feb 2022View details →

Novel Pixelwise Co-Registered Hematoxylin-Eosin and Multiphoton Microscopy Image Dataset for Human Colon Lesion Diagnosis

General Description: The dataset consists of a set of 50 samples of lesions obtained by colonoscopies and colectomies carried out between the years 2012 and 2017 at at Digestive Service at OSI Bilbao Basurto. These are 24 malignant neoplasms (adenocarcinoma), 19 preneoplastic lesions (adenoma) and 2 hyperplasia and 5 healthy tissues, obtained from 24 men and 19 women. The samples were diagnosed by the Pathological Anatomy Department at OSI Bilbao Basurto and the FFPE (Formalin-Fixed Paraffin-Embedded) blocks were stored in the Basque Biobank. All the samples were processed after signing Informed Consent and following standard operation procedures. The samples were scanned using a multiphoton microscope (Lens, Florence, Italy) both for multi-photon fluorescence (MPM) and second harmonic generation (SHG) and later stained with H&E (Hematoxylin & Eosin). The different image modalities were reconstructed and corregistered by performing non-rigid deformation (Tecnalia, Bilbao, Spain) allowing pixel correspondence among the different modalities. Pathologists from Basurto Hospital manually labeled the regions where the lession is present. Scale of current dataset is 0.5um/px. Technical Details: On the data_info.csv information for each sample is included: - SAMPLE_ID: Includes the tag "PICCOLO_XX_YY", where XX stands for the patient ID number and YY to the lesion suffix ID. - LESION_ID: The lesion is classified as healthy, hyperplasia, benign neoplasia, and malign neoplasia. - HISTOLOGICAL ANALYSIS: It includes informative test about the lesion. - GRADE: In the case for malign neoplasia universal grading system grade is included.

opencc-by-4.0Dec 2021View details →

Dataset from paper "Dynamic Concentration Factor: A Novel Parameter For The Rigorous Evaluation Of Solar Compound Parabolic Collectors"

<ul> <li>Dynamic Concentration Factor as a function of the beam angle (α) for CPC with different acceptance angles (θ), reflectivity (r) of the collector surface ranging from 0.0 to 1.0, and optical density ranging from 0.0 to 10.0</li> <li>Diffuse Dynamic Concentration factor for CPC with different acceptance angles (θ), reflectivity (r) of the collector surface ranging from 0.0 to 1.0, and optical density ranging from 0.0 to 10.0</li> <li>Experimental validation of the Dynamic Concentration Factor using actinometry results</li> <li>Independence test of Dynamic Concentration results of the number of rays cast in the software tool.</li> <li>Full-precision data of the Dynamic Concentration Factor as a function of the beam angle (α) for CPC with different acceptance angles (θ), reflectivity (r) of the collector surface ranging from 0.0 to 1.0, and optical density ranging from 0.0 to 10.0</li> </ul>

opencc-zeroMar 2022View details →

Data for Rapid phenotypic differentiation and local adaptation in Japanese knotweed s.l. (Reynoutria japonica and R. × bohemica, Polygonaceae) invading novel habitats

PREMISE: Many plant invaders like the Japanese knotweeds are thought to colonize new habitats with low genetic diversity. Such species provide an opportunity to study rapid adaptation to complex environmental conditions. METHODS: Using replicate reciprocal transplants of clones across three habitats, we described patterns of phenotypic response and assessed degree of local adaptation. KEY RESULTS: We found plants from beach habitats had decreased height, number of leaves, leaf area, and biomass allocation to roots and shoots compared to plants from marsh and roadside habitats when grown in their home habitat. In the marsh habitat, marsh plants were generally larger than beach plants, but not different from roadside plants. There were no differences among plants from different habitats grown in the roadside habitat. Despite this evidence of differentiation in beach and marsh habitats, we found mixed evidence for local adaptation. In their "home site" plants from the marsh habitat had greater biomass than plants from the beaches but not compared to plants from roadsides. Biomass comparisons in other habitats were either maladaptive or not significant. However, plants from the roadside had greater survival in their "home site" compared to foreign plants. There were no differences in survival in the other habitats. CONCLUSIONS: We found phenotypic differentiation associated with habitats despite the low reported genetic diversity for these populations. Our results partially support the hypothesis of local adaptation in marsh and roadside habitats. Identifying whether these patterns of differentiation result from genetic or heritable non-genetic mechanisms will require further work.

Raw Data for the article: Potential Anti-Metastatic Role of the Novel miR-CT3 in Tumor Angiogenesis and Osteosarcoma Invasion

Osteosarcoma (OS) is the most common primary bone tumor mainly occurring in young adults and derived from primitive bone-forming mesenchyme. OS develops in an intricate tumor microenvironment (TME) where cellular function regulated by microRNAs (miRNAs) may affect communication between OS cells and the surrounding TME. Therefore, miRNAs are considered potential therapeutic targets in cancer and one of the goals of research is to accurately define a specific signature of a miRNAs, which could reflect the phenotype of a particular tumor, such as OS. Through NGS approach, we previously found a specific molecular profile of miRNAs in OS and discovered 8 novel miRNAs. Among these, we deepen our knowledge on the fifth candidate renamed now miR-CT3. MiR-CT3 expression was low in OS cells when compared with human primary osteoblasts and healthy bone. Through TargetScan, VEGF-A was predicted as a potential biological target of miR-CT3 and luciferase assay confirmed it. We showed that enforced expression of miR-CT3 in two OS cell lines, SAOS-2 and MG-63, reduced expression of VEGF-A mRNA and protein, inhibiting tumor angiogenesis. Enforced expression of miR-CT3 also reduced OS cell migration and invasion as confirmed by soft agar colony formation assay. Interestingly, we found that miR-CT3 behaves inducing the activation of p38 MAP kinase pathway and modulating the epithelial-mesenchymal transition (EMT) proteins, in particular reducing Vimentin expression. Overall, our study highlights the novel role of miR-CT3 in regulating tumor angiogenesis and progression in OS cells, linking also to the modulation of EMT proteins.

opencc-by-4.0Jun 2022View details →

Dataset (II) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist

MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files) dataset I: systems SRL+Co, C-100 and BAY-1797 dataset I: each file contains all branched replicas and the main replica. dataset1:  C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b). dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches. dataset I: system SRL+Co ;each file contains one main replica dataset I: system BAY-1797; each file contains one main replica dataset II:system SRL ; each file contains one main replica.

opencc-by-4.0Jun 2022View details →

Dataset (I) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist

Supplementary Table S5 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S5. Repository data showing genes identified by MapMan in Giza 178 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose.  E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S4 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S4. Repository data showing genes identified by MapMan in Giza 177 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose. E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S2 - Article:Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S2. Repository data for the global analysis produced for cv Giza 177.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 177 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 177 up regulated genes.    D, GOEA results for Giza 177 down regulated genes.

Supplementary Table S3 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S3. Repository data for the global analysis produced for cv Giza 178.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 178 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 178 up regulated genes.    D, GOEA results for Giza 178 down regulated genes.