Browse Articles

A basic framework to explain splice-site choice in eukaryotes

Abstract Changes in splicing can mediate phenotypic variation, ranging from flowering time differences in plants to genetic diseases in humans. Splicing changes occur due to differences in splice-site strength, often influenced by genetic variation and the environment. How genetic variation influences splice-site strength remains poorly understood, largely because splice-site usage across transcriptomes has not been empirically quantified. Here, we quantify the use of individual splice-sites in Arabidopsis, Drosophila and humans and treat these measurements as molecular phenotypes to map variation in splice-site usage through GWAS. We carry out more than 130,000 GWAS with splice-site usage phenotypes, cataloguing genetic variation associated with changes in the usage of individual splice-sites across transcriptomes. We find that most of the common, genetically controlled variation in splicing is cis and there are no major trans hotspots in the three species analyzed. We group splice-sites based on GT[N]4 or [N]4AG sequence, quantify their average use, develop a ranking and show that these hexamer rankings provide a simple and comparable feature across species to explain most of the splice-site choice. Transcriptome analyses in several species suggest that hexamer rankings offer a rule that helps explain splice-site choices, forming a basis for a shared splicing logic in eukaryotes.

Association between physical activity and academic achievement in adolescents mediated by self-concept and physical and mental health

Interrogating ABCC1 and CASP1 as key players in epigallocatechin gallate’s action against radiotherapy-resistant nasopharyngeal carcinoma

Sustainable electromagnetic interference shielding materials from cellulose-grafted n-type polymers

Comparative techno functional, physio chemical and pasting properties of pigmented (Kavuni) rice land races of India

The axial tip clearance leakage analysis of the squealer blade tip for the liquid-ring pump

Age-related constraints on the spatial geometry of the brain

Abstract Age-related structural brain changes may be better captured by assessing complex spatial geometric differences rather than isolated changes to individual regions. We applied an analytic method to quantify age-related changes to the spatial anatomy of the brain by measuring expansion and compression of global brain shape and the distance between cross-hemisphere homologous regions. To test how global brain shape and regional distances are affected by aging, we analyzed 2603 structural MRIs (range: 30−97 years). Increasing age was associated with global expansion across inferior-anterior gradients, global compression across superior-posterior gradients, and regional expansion between frontotemporal homologues. Specific patterns of global and regional expansion and compression were further associated with clinical impairment and distinctly related to deficits in various cognitive domains. These findings suggest that changes to the complex spatial anatomy and geometry of the aging brain may be associated with reduced efficiency and cognitive dysfunction in older adults.

The effect of urban agglomeration land use zoning on sustainable development goals

An experimental approach varying piston geometry for optimization of diesel engine performance and emissions using prioritized clustering approach

RNA polymerase II is a polar roadblock to a progressing DNA fork

Abstract Transcription–replication conflicts threaten genome stability. Although head-on conflicts are more detrimental and prone to R-loop formation than co-directional conflicts, the cause of this RNA polymerase roadblock polarity remains unclear, and proposed structures of these R-loops are speculative. Here, we examine the Pol II roadblock to a DNA fork advanced by mechanical unzipping to mimic replisome progression. We found that a head-on Pol II with a minimal transcript resists disruption more strongly, revealing inherent polarity. Moreover, an elongating Pol II with a long RNA transcript becomes an even more potent roadblock, mediated by RNA–DNA hybrid formation. Surprisingly, when a Pol II collides with the DNA fork head-on and becomes backtracked, a hybrid can form in front of Pol II, creating a topological lock that traps Pol II at the fork. Our findings capture the basal properties of Pol II interactions with a DNA fork, revealing significant implications for transcription–replication conflicts.

Effects of biochar from populus alba × populus berolinensis and pinus sylvestris var. mongolica application on soil physicochemical properties

Study on the grouting repair performance of shield tunnel segments based on high-fluidity slurry

Effect of the gut microbiota-derived tryptophan metabolite indole-3-acetic acid in pneumonia

Investigating the effects of miR-526b and miR-655 on doxorubicin sensitivity in breast cancer

ITGB6 promotes tumor recurrence and metastasis by mediating the resistance of daughter cells of PGCCs to anoikis

Long-term homeostasis in microbial consortia via auxotrophic cross-feeding

IL6/STAT3 induced GRWD1 mediates aerobic glycolysis via P53/GLUT1 signal axis in colon carcinoma

Enhanced IoT threat detection using Graph-Regularized neural networks optimized by Sea-Lion algorithm

Disentangling dispersion from mean reveals true heterogeneity-diversity relationships

Abstract Understanding the effect of heterogeneity is fundamental to numerous fields. In community ecology, classical theory postulates that habitat heterogeneity determines niche dimensionality and drives biodiversity. However, disparate heterogeneity-diversity relationships have been empirically observed, generating increasingly complex theoretical developments. Here we show that spurious heterogeneity-diversity relationships and subsequent theories arise as artifacts of heterogeneity measures that are mean-biased for bounded continuous variables. To solve this, we derive an alternative mean-independent measure of heterogeneity for beta and gamma distributed variables that disentangles statistical dispersion from mean. Using the mean-independent measure of heterogeneity, true monotonic positive heterogeneity-diversity relationships, consistent with classical theory, are revealed in data previously presented as evidence for both hump-shaped heterogeneity-diversity relationships and theories of an area-heterogeneity trade-off for biodiversity. This work sheds light on the source of conflicting results that have hindered understanding of heterogeneity relationships in broader ecology and numerous other fields. The mean-independent measure of heterogeneity is provided as a solution, essential for understanding true mean-independent heterogeneity relationships in wider research.

Investigation on the wind erosion resistance of aeolian sand solidified by enzyme mineralization combined with fiber reinforcement

Abstract Sandstorms can lead to atmospheric pollution, soil degradation and health damage, which the origin of frequent outbreaks is that traditional methods cannot effectively solve the solidified of aeolian sand. Enzyme induced calcium carbonate precipitation (EICP) combined with basalt fiber reinforcement (BFR) or wool fiber reinforcement (WFR) method can significantly improved the strength and reduced the brittle fracture of sand. Based on the wind tunnel model test, this paper analyzed the effect of wind velocity (v), erosion angle (α), and erosion cycles (N) on the erosion resistance of aeolian sand solidified by EICP with BFR or WFR. According to analyzed the anti-erosion mechanism of aeolian sand, the erosion modulus model was established considered the effects of wind velocity and erosion angle. The results showed that compared with loose aeolian sand, EICP-solidified sand formed a hard layer on the surface, and the mass loss rate (η) increased with increasing of wind velocity, erosion angle and erosion cycles. Under the strongest erosion condition, the η of loose sand, EICP, EICP-BFR and EICP-WFR solidified aeolian sand reached 88.79%, 63.55%, 55.57% and 52.40%, respectively. As the number of erosion cycles increases, the η of EICP-solidified aeolian sand rises from 1.46 to 7.59%, that of EICP-BFR-solidified sand from 0.82 to 6.41%, and that of EICP-WFR-solidified sand from 0.71 to 6.26%. The addition of fiber can effectively promoted the cementation of CaCO3 crystal, improved the surface strength and wind erosion resistance, and reduced the quality loss of aeolian sand. The experimental results agreed well with the model prediction results, which validated the reliability of erosion modulus model. The research results can provide a guideline for aeolian sand solidified in desert area.