Atta mexicana waste dumps are hot spots of soil nutrients in an urban Neotropical cloud forest environment

相似文献   

Identification of survival-related alternative splicing signatures in acute myeloid leukemia

Aberrant RNA alternative splicing (AS) variants play critical roles in tumorigenesis and prognosis in human cancers. Here, we conducted a comprehensive profiling of aberrant AS events in acute myeloid leukemia (AML). RNA AS profile, including seven AS types, and the percent spliced in (PSI) value for each patient were generated by SpliceSeq using RNA-seq data from TCGA. Univariate followed by multivariate Cox regression analysis were used to identify survival-related AS events and develop the AS signatures. A nomogram was developed, and its predictive efficacy was assessed. About 27,892 AS events and 3,178 events were associated with overall survival (OS) after strict filtering. Parent genes of survival-associated AS events were mainly enriched in leukemia-associated processes including chromatin modification, autophagy, and T-cell receptor signaling pathway. The 10 AS signature based on seven types of AS events showed better efficacy in predicting OS of patients than those built on a single AS event type. The area under curve (AUC) value of the 10 AS signature for 3-year OS was 0.91. Gene set enrichment analysis (GSEA) confirmed that these survival-related AS events contribute to AML progression. Moreover, the nomogram showed good predictive performance for patient''s prognosis. Finally, the correlation network of AS variants with splicing factor genes found potential important regulatory genes in AML. The present study presented a systematic analysis of survival-related AS events and developed AS signatures for predicting the patient’s survival. Further studies are needed to validate the signatures in independent AML cohorts and might provide a promising perspective for developing therapeutic targets.     

Long‐term selection for litter size in swine results in shifts in allelic frequency in regions involved in reproductive processes

High‐density genotype data were analyzed in three lines of swine that express substantial variation in sow fertility to uncover regions of the genome potentially influenced during selection for litter size traits. The experimental lines examined include the Nebraska Index Line (NIL), which has been subjected to long‐term selection for litter size; a control line derived from the same population that founded NIL; and a commercial Duroc × Hampshire (D × H) population, in which no selection for litter size was practiced. Regions of the genome potentially affected by selection for litter size traits in NIL were determined by multiple lines of evidence, including altered allelic frequency compared to the other lines, loss of heterozygosity and relative extended haplotype homozygosity. Additionally, a genome‐wide association study for litter size traits was conducted in a population based on NIL and commercial maternal line genetics. Several genomic regions identified as putative signatures of selection overlapped with QTL for litter size traits. One of these regions, located on SSC2 (13–14 Mb), includes the candidate gene P2X3R, which plays a role in implantation and sustained release of hormones associated with reproductive processes. Sequencing identified synonymous SNPs in P2X3R that are fixed in NIL but polymorphic with nearly equal frequencies in the D × H line, indicating a potential role of P2X3R in sow fertility. These results suggest that data derived from these lines can help to uncover and understand a portion of the genetic variance associated with fertility traits in swine.     

Group chorusing as an intragroup signal in the greater ani,a communally breeding bird

Group living often requires maintaining dynamic and varied relationships with fellow group members, while simultaneously monitoring and interacting with external competitors. Group members in many social species vocalize together to produce duets or choruses—coordinated, often conspicuous vocal displays—that may play a role in these interactions. Compared with male–female duets, however, relatively little research exists on the function and adaptive significance of group choruses, which involve three or more individuals. Here we investigate chorusing behavior in the greater ani (Crotophaga major), a communally breeding cuckoo that nests in stable social groups of four to eight unrelated individuals. Groups may remain together for several years on the same nesting territory, and groups occasionally destroy each other's clutches in conflicts over high-quality territories. We asked whether the raucous, highly stereotyped choruses performed by ani groups are primarily used for intra- or intergroup communication, and whether they contain information about the identity of the social group and the number of birds vocalizing. Behavioral observations and acoustic recordings from three breeding seasons revealed that choruses typically occurred during social interactions within the group (78% of choruses) or in response to a predator or extra-group individual (17%) and only rarely in intergroup interactions (4%). Consistent with this finding, choruses did not reliably reflect the number of birds vocalizing, and we found only limited evidence for group-specific acoustic signatures (driven by a single group whose choruses were highly distinct). These results suggest that group choruses play an important role in intra-group signaling, potentially in contexts such as group formation, reinforcement of social bonds within the group, and/or collective decision-making, and they motivate new research questions about the role of collective signaling in social evolution.     

Significant alterations of the novel 15 gene signature identified from macrophage-tumor interactions in breast cancer

Background

Tumor microenvironment is composed of a largely altered extracellular matrix with different cell types. The complex interplay between macrophages and tumor cells through several soluble factors and signaling is an important factor in breast cancer progression.

Development and validation of a novel epigenetic signature for predicting prognosis in colon cancer

Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse-free survival of colon cancer patients. Public microarray datasets were acquired from the Gene Expression Omnibus databases: GSE39582, GSE17538, GSE33113, and GSE37892 set. Patients from GSE39582 set were randomized 1:1 into training and internal validation series. Patients were divided into high-risk and low-risk groups in training series based on a set of 11 epigenetic factors (p < .001). The good reproducibility for the prognostic value of the epigenetic signature was confirmed in the internal validation series (p < .001), external validation series (a combination of GSE17538 set, GSE33113 set, and GSE37892 set; p = .018), and entire series (p < .001). Furthermore, a nomogram, which integrated the epigenetic signature, pathological stage, and postoperative chemotherapy, was developed based on the GSE39582 set. The time-dependent receiver operating characteristic curve at 1 year demonstrated that the comprehensive signature presented superior prognostic value than the pathological stage. In conclusion, an epigenetic signature, which could be utilized to divide colon cancer patients into two groups with significantly different risk of relapse, was established. This biomarker would aid in identifying patients who require an intensive follow-up and aggressive therapeutic intervention.     

Tamoxifen therapy benefit predictive signature combining with prognostic signature in surgical-only ER-positive breast cancer

Tamoxifen treatment is important assistant for estrogen-receptor-positive breast cancer (BRCA) after resection. This study aimed to identify signatures for predicting the prognosis of patients with BRCA after tamoxifen treatment. Data of gene-specific DNA methylation (DM), as well as the corresponding clinical data for the patients with BRCA, were obtained from The Cancer Genome Atlas and followed by systematic bioinformatics analyses. After mapping these DM CPG sites onto genes, we finally obtained 352 relapse-free survival (RFS) associated DM genes, with which 61,776 gene pairs were combined, including 1,614 gene pairs related to RFS. An 11 gene-pair signature was identified to cluster the 189 patients with BRCA into the surgical low-risk group (136 patients) and high-risk group (53 patients). Then, we further identified a tamoxifen-predictive signature that could classify surgical high-risk patients with significant differences on RFS. Combining surgical-only prognostic signature and tamoxifen-predictive signature, patients were clustered into surgical-only low-risk group, tamoxifen nonbenefit group, and tamoxifen benefit group. In conclusion, we identified that the gene pair PDHA2–APRT could serve as a potential prognostic biomarker for patients with BRCA after tamoxifen treatment.     

澳大利亚Floreana岛达尔文小树雀喙型与其鸣唱的不相关性

鸟类鸣唱的功能通常是吸引配偶,对于建立繁殖隔离也是非常重要的。现有的研究认为鸟类鸣唱表演可能受到鸟类喙型变化的影响。达尔文鸣雀是一类用来验证喙型和鸣唱表演关系的模型物种,前人的研究认为较低的元音演奏与更大的喙相关。本文用在Floreana岛屿生活的达尔文小树雀(Camarhynchus parvulus)来验证喙型和元音演奏的关系。结果显示,喙型大小与元音演奏之间无相关性。这个发现与过去对小树雀中的研究结果相似,但却与达尔文鸣雀中更大体型的鸟类研究结果相反。讨论了研究结果在物种的生态分化和生态变异之间的前后关系。