False Exclusion: A Case to Embed Predator Performance in Classical Population Models

We argue that predator-prey dynamics, a cornerstone of ecology, can be driven by insufficiently explored aspects of predator performance that are inherently prey dependent: that is, these have been falsely excluded. Classical (Lotka-Volterra–based) models tend to consider only prey-dependent ingestion rate. We highlight three other prey-dependent responses and provide empirically derived functions to describe them. These functions introduce neglected nonlinearities and threshold behaviors into dynamic models, leading to unexpected outcomes: specifically, as prey abundance increases predators (1) become less efficient at using prey; (2) initially allocate resources toward survival and then allocate resources toward reproduction; and (3) are less likely to die. Based on experiments using model zooplankton, we explore the consequences of including these functions in the classical structure and show that they alter qualitative and quantitative dynamics of an empirically informed generic predator-prey model. Through bifurcation analysis, our revised structure predicts (1) predator extinctions, where the classical structure allows persistence; (2) predator survival, where the classical structure drives predators toward extinction; and (3) greater stability through smaller amplitude of cycles, relative to the classical structure. Then, by exploring parameter space, we show how these responses alter predictions of predator-prey stability and competition between predators. In light of our results, we suggest that classical assumptions about predator responses to prey abundance should be reevaluated

O-GlcNAcylation of core components of the translation initiation machinery regulates protein synthesis

Protein synthesis is essential for cell growth, proliferation, and survival. Protein synthesis is a tightly regulated process that involves multiple mechanisms. Deregulation of protein synthesis is considered as a key factor in the development and progression of a number of diseases, such as cancer. Here we show that the dynamic modification of proteins by O-linked β-N-acetyl-glucosamine (O-GlcNAcylation) regulates translation initiation by modifying core initiation factors eIF4A and eIF4G, respectively. Mechanistically, site-specific O-GlcNAcylation of eIF4A on Ser322/323 disrupts the formation of the translation initiation complex by perturbing its interaction with eIF4G. In addition, O-GlcNAcylation inhibits the duplex unwinding activity of eIF4A, leading to impaired protein synthesis, and decreased cell proliferation. In contrast, site-specific O-GlcNAcylation of eIF4G on Ser61 promotes its interaction with poly(A)-binding protein (PABP) and poly(A) mRNA. Depletion of eIF4G O-GlcNAcylation results in inhibition of protein synthesis, cell proliferation, and soft agar colony formation. The differential glycosylation of eIF4A and eIF4G appears to be regulated in the initiation complex to fine-tune protein synthesis. Our study thus expands the current understanding of protein synthesis, and adds another dimension of complexity to translational control of cellular proteins

Optoelectronic properties of atomically thin ReSSe with weak interlayer coupling

Rhenium dichalcogenides, such as ReS2 and ReSe2, have attracted a lot of interests due to the weak interlayered coupling in these materials. Studies of rhenium based dichalcogenide alloys will help us understand the differences between binary rhenium dichalcogenides. They will also extend the applications of two-dimensional (2D) materials through alloying. In this work, we studied the optoelectronic properties of ReSSe with a S and Se ratio of 1 : 1. The band gap of the ReSSe alloy is investigated by optical absorption spectra as well as theoretical calculations. The alloy shows weak interlayered coupling, as evidenced by the Raman spectrum. A field-effect transistor based on ReSSe shows typical n-type behavior with a mobility of about 3 cm2 V-1 s-1 and an on/off ratio of 105, together with the in-plane anisotropic conductivity. The device also shows good photoresponse properties, with a photoresponsivity of 8 A W-1. The results demonstrated here will provide new avenues for the study of 2D materials with weak interlayer interactions and in-plane anisotropy

An evidence-based framework for predicting the impact of differing autotroph-heterotroph thermal sensitivities on consumer-prey dynamics

Increased temperature accelerates vital rates, influencing microbial population and wider ecosystem dynamics, for example, the predicted increases in cyanobacterial blooms associated with global warming. However, heterotrophic and mixotrophic protists, which are dominant grazers of microalgae, may be more thermally sensitive than autotrophs, and thus prey could be suppressed as temperature rises. Theoretical and meta-analyses have begun to address this issue, but an appropriate framework linking experimental data with theory is lacking. Using ecophysiological data to develop a novel model structure, we provide the first validation of this thermal sensitivity hypothesis: increased temperature improves the consumer’s ability to control the autotrophic prey. Specifically, the model accounts for temperature effects on auto- and mixotrophs and ingestion, growth and mortality rates, using an ecologically and economically important system (cyanobacteria grazed by a mixotrophic flagellate). Once established, we show the model to be a good predictor of temperature impacts on consumer–prey dynamics by comparing simulations with microcosm observations. Then, through simulations, we indicate our conclusions remain valid, even with large changes in bottom-up factors (prey growth and carrying capacity). In conclusion, we show that rising temperature could, counterintuitively, reduce the propensity for microalgal blooms to occur and, critically, provide a novel model framework for needed, continued assessment

A novel statistical method for rare-variant association studies in general pedigrees

In this paper, the authors discuss a novel statistical method for rare-variant association studies in general pedigrees for quantitative traits. This method uses a retrospective view that treats the traits as fixed and the genotypes as random, which accounts for complex and undefined ascertainment of families

OsMADS1 represses microRNA172 in elongation of palea/lemma development in Rice

Specification of floral organ identity is critical for the establishment of floral morphology and inflorescence architecture. Although multiple genes are involved in the regulation of floral organogenesis, our understanding of the underlying regulating network is still fragmentary. MADs-box genes are principle members in the ABC model that characterized floral organs. OsMADS1 specifies the determinacy of spikelet meristem and lemma/palea identity in rice. However, the pathway through which OsMADS1 regulates floral organs remains elusive; here, we identified the miR172 family as possible regulators downstream of OsMADS1. Genetic study revealed that overexpression of each miR172 gene resulted in elongated lemma/palea and indeterminacy of the floret, which resemble the phenotype of osmads1 mutant. On the contrary, overexpression of each target APETALA2 (AP2) genes resulted in shortened palea/lemma. Expression level and specificity of miR172 was greatly influenced by OsMADS1, as revealed by Northern blot analysis and In situ hybridization. Genetically, AP2-3 and AP2-2 over expression complemented the elongation and inconsistent development of the lemma/palea in OsMADS1RNAi transgenic plants. Our results suggested that in rice, OsMADS1 and miR172s/AP2s formed a regulatory network involved in floral organ development, particularly the elongation of the lemma and the palea

Comparative Transcriptome Analysis Reveals Gene Expression Differences in Eggplant (<i>Solanum melongena</i> L.) Fruits with Different Brightness

Fruit brightness is an important quality trait that affects the market value of eggplant. However, few studies have been conducted on eggplant brightness. In this study, we aimed to identify genes related to this trait in three varieties of eggplant with different fruit brightness between 14 and 22 days after pollination. Using RNA-Seq Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, we found that wax- and cutin-related pathways and differentially expressed genes displayed significant differences among different development stages and varieties. Scanning electron microscopy revealed that the wax layer was thinner in ‘30-1’ and ‘QPCQ’ than in ‘22-1’. Gas chromatography-mass spectrometry analysis revealed that wax content was significantly lower in ‘30-1’ than in ‘22-1’, which indicated that wax may be an important factor determining fruit brightness. We further identified and analyzed the KCS gene family, which encodes the rate-limiting enzyme of FA elongation in wax synthesis. The results provide an insight into the molecular mechanisms of fruit brightness in eggplants and further eggplant breeding programs

Chalcone synthase (CHS) family members analysis from eggplant (Solanum melongena L.) in the flavonoid biosynthetic pathway and expression patterns in response to heat stress.

Enzymes of the chalcone synthase (CHS) family participate in the synthesis of multiple secondary metabolites in plants, fungi and bacteria. CHS showed a significant correlation with the accumulation patterns of anthocyanin. The peel color, which is primarily determined by the content of anthocyanin, is an economically important trait for eggplants that is affected by heat stress. A total of 7 CHS (SmCHS1-7) putative genes were identified in a genome-wide analysis of eggplants (S. melongena L.). The SmCHS genes were distributed on 7 scaffolds and were classified into 3 clusters. Phylogenetic relationship analysis showed that 73 CHS genes from 7 Solanaceae species were classified into 10 groups. SmCHS5, SmCHS6 and SmCHS7 were continuously down-regulated under 38°C and 45°C treatment, while SmCHS4 was up-regulated under 38°C but showed little change at 45°C in peel. Expression profiles of key anthocyanin biosynthesis gene families showed that the PAL, 4CL and AN11 genes were primarily expressed in all five tissues. The CHI, F3H, F3'5'H, DFR, 3GT and bHLH1 genes were expressed in flower and peel. Under heat stress, the expression level of 52 key genes were reduced. In contrast, the expression patterns of eight key genes similar to SmCHS4 were up-regulated at a treatment of 38°C for 3 hour. Comparative analysis of putative CHS protein evolutionary relationships, cis-regulatory elements, and regulatory networks indicated that SmCHS gene family has a conserved gene structure and functional diversification. SmCHS showed two or more expression patterns, these results of this study may facilitate further research to understand the regulatory mechanism governing peel color in eggplants