Inbreeding in Chinese fir: Insights into the adaptive growth traits of selfed progeny from mRNA, miRNA, and copy number variation.

PREMISE: The impact of inbreeding on biological processes is well documented in individuals with severe inbreeding depression. However, the biological processes influencing the adaptive growth of normal selfed individuals are unknown. Here, we aimed to investigate how inbreeding affects gene expression for adaptive growth of normal selfed seedlings from a self-fertilizing parent in Chinese fir (Cunninghamia lanceolata). METHODS: Using RNA-seq data from above- and underground tissues of abnormal and normal selfed seedlings, we analyzed GO biological processes network. We also sequenced small RNAs in the aboveground tissues and measured the copy number variations (CNV) of the hub genes. RESULTS: Phenotypic fitness analysis revealed that the normal seedlings were better adapted than their abnormal counterparts. Upregulated differentially expressed genes (DEGs) were associated with development processes, and downregulated DEGs were mainly enriched in fundamental metabolism and stress response. Results of mRNA-miRNA parallel sequencing revealed that upregulated target genes were predominantly associated with development, highlighting their crucial role in phosphorylation in signal transduction networks. We also discovered a moderate correlation (0.1328 < R2 < 0.6257) between CNV and gene expression levels for three hub genes (TMKL1, GT2, and RHY1A). CONCLUSIONS: We uncovered the key biological processes underpinning the growth of normal selfed seedlings and established the relationship between CNV and the expression levels of hub genes in selfed seedlings. Understanding the candidate genes involved in the growth of selfed seedlings will help us comprehend the genetic mechanisms behind inbreeding depression in the evolutionary biology of plants.

Evaluation and prediction of individual growth trajectories.

BACKGROUND: Conventional growth charts offer limited guidance to track individual growth. AIM: To explore new approaches to improve the evaluation and prediction of individual growth trajectories. SUBJECTS AND METHODS: We generalise the conditional SDS gain to multiple historical measurements, using the Cole correlation model to find correlations at exact ages, the sweep operator to find regression weights and a specified longitudinal reference. We explain the various steps of the methodology and validate and demonstrate the method using empirical data from the SMOCC study with 1985 children measured during ten visits at ages 0-2 years. RESULTS: The method performs according to statistical theory. We apply the method to estimate the referral rates for a given screening policy. We visualise the child's trajectory as an adaptive growth chart featuring two new graphical elements: amplitude (for evaluation) and flag (for prediction). The relevant calculations take about 1 millisecond per child. CONCLUSION: Longitudinal references capture the dynamic nature of child growth. The adaptive growth chart for individual monitoring works with exact ages, corrects for regression to the mean, has a known distribution at any pair of ages and is fast. We recommend the method for evaluating and predicting individual child growth.

Tissue Adaptation to Environmental Cues by Symmetric and Asymmetric Division Modes of Intestinal Stem Cells.

Tissues must adapt to the different external stimuli so that organisms can survive in their environments. The intestine is a vital organ involved in food processing and absorption, as well as in innate immune response. Its adaptation to environmental cues such as diet and biotic/abiotic stress involves regulation of the proliferative rate and a switch of division mode (asymmetric versus symmetric) of intestinal stem cells (ISC). In this review, we outline the current comprehension of the physiological and molecular mechanisms implicated in stem cell division modes in the adult Drosophila midgut. We present the signaling pathways and polarity cues that control the mitotic spindle orientation, which is the terminal determinant ensuring execution of the division mode. We review these events during gut homeostasis, as well as during its response to nutrient availability, bacterial infection, chemical damage, and aging. JNK signaling acts as a central player, being involved in each of these conditions as a direct regulator of spindle orientation. The studies of the mechanisms regulating ISC divisions allow a better understanding of how adult stem cells integrate different signals to control tissue plasticity, and of how various diseases, notably cancers, arise from their alterations.

FCS-like zinc finger 6 and 10 repress SnRK1 signalling in Arabidopsis.

SNF1-related protein kinase 1 (SnRK1) is a central regulator of plant growth during energy starvation. The FCS-like zinc finger (FLZ) proteins have recently been identified as adaptor proteins which facilitate the interaction of SnRK1 with other proteins. In this study, we found that two starvation-induced FLZ genes, FLZ6 and FLZ10, work as repressors of SnRK1 signalling. The reduced expression of these genes resulted in an increase in the level of SnRK1α1, which is the major catalytic subunit of SnRK1. This lead to a concomitant increase in phosphorylated protein and SnRK1 activity in the flz6 and flz10 mutants. FLZ6 and FLZ10 specifically interact with SnRK1α subunits in the cytoplasmic foci, which co-localized with the endoplasmic reticulum. In physiological assays, similar to the SnRK1α1 overexpression line, flz mutants showed compromised growth. Further, growth promotion in response to favourable growth conditions was found to be attenuated in the mutants. The enhanced SnRK1 activity in the mutants resulted in a reduction in the level of phosphorylated RIBOSOMAL S6 KINASE and the expression of E2Fa and its targets, indicating that TARGET OF RAPAMYCIN-dependent promotion of protein synthesis and cell cycle progression is impaired. Taken together, this study uncovers a plant-specific modulation of SnRK1 signalling.

Rice LTG1 is involved in adaptive growth and fitness under low ambient temperature.

Low temperature (LT) is one of the most prevalent factors limiting the productivity and geographical distribution of rice (Oryza sativa L.). Although significant progress has been made in elucidating the effect of LT on seed germination and reproductive development in rice, the genetic component affecting vegetative growth under LT remains poorly understood. Here, we report that rice cultivars harboring the dominant LTG1 (Low Temperature Growth 1) allele are more tolerant to LT (15-25°C, a temperature range prevalent in high-altitude, temperate zones and high-latitude areas), than those with the ltg1 allele. Using a map-based cloning strategy, we show that LTG1 encodes a casein kinase I. A functional nucleotide polymorphism was identified in the coding region of LTG1, causing a single amino acid substitution (I357K) that is associated with the growth rate, heading date and yield of rice plants grown at LT. We present evidence that LTG1 affects rice growth at LT via an auxin-dependent process(es). Furthermore, phylogenetic analysis of this locus suggests that the ltg1 haplotype arose before the domestication of rice in tropical climates. Together, our data demonstrate that LTG1 plays an important role in the adaptive growth and fitness of rice cultivars under conditions of low ambient temperature.

Protandry, sexual size dimorphism, and adaptive growth.

Adaptive growth refers to the strategic adjustment of growth rate by individuals to maximize some component of fitness. The concept of adaptive growth proliferated in the 1990s, in part due to an influential theoretical paper by Peter Abrams and colleagues. In their 1996 paper, Abrams et al. explored the effects of time stress on optimal growth rate, development time, and adult size in seasonal organisms. In this review, I explore how the concept of adaptive growth informs our understanding of protandry (the earlier arrival of males to sites of reproduction than females) and sexual size dimorphism in seasonal organisms. I conclude that growth rate variation is an important mechanism that helps to conserve optimal levels of protandry and sexual size dimorphism in changing environments.

Developmental Aspects of Cardiac Adaptation to Increased Workload.

The heart is capable of extensive adaptive growth in response to the demands of the body. When the heart is confronted with an increased workload over a prolonged period, it tends to cope with the situation by increasing its muscle mass. The adaptive growth response of the cardiac muscle changes significantly during phylogenetic and ontogenetic development. Cold-blooded animals maintain the ability for cardiomyocyte proliferation even in adults. On the other hand, the extent of proliferation during ontogenetic development in warm-blooded species shows significant temporal limitations: whereas fetal and neonatal cardiac myocytes express proliferative potential (hyperplasia), after birth proliferation declines and the heart grows almost exclusively by hypertrophy. It is, therefore, understandable that the regulation of the cardiac growth response to the increased workload also differs significantly during development. The pressure overload (aortic constriction) induced in animals before the switch from hyperplastic to hypertrophic growth leads to a specific type of left ventricular hypertrophy which, in contrast with the same stimulus applied in adulthood, is characterized by hyperplasia of cardiomyocytes, capillary angiogenesis and biogenesis of collagenous structures, proportional to the growth of myocytes. These studies suggest that timing may be of crucial importance in neonatal cardiac interventions in humans: early definitive repairs of selected congenital heart disease may be more beneficial for the long-term results of surgical treatment.

Nutrient-driven dedifferentiation of enteroendocrine cells promotes adaptive intestinal growth in Drosophila.

Post-developmental organ resizing improves organismal fitness under constantly changing nutrient environments. Although stem cell abundance is a fundamental determinant of adaptive resizing, our understanding of its underlying mechanisms remains primarily limited to the regulation of stem cell division. Here, we demonstrate that nutrient fluctuation induces dedifferentiation in the Drosophila adult midgut to drive adaptive intestinal growth. From lineage tracing and single-cell RNA sequencing, we identify a subpopulation of enteroendocrine (EE) cells that convert into functional intestinal stem cells (ISCs) in response to dietary glucose and amino acids by activating the JAK-STAT pathway. Genetic ablation of EE-derived ISCs severely impairs ISC expansion and midgut growth despite the retention of resident ISCs, and in silico modeling further indicates that EE dedifferentiation enables an efficient increase in the midgut cell number while maintaining epithelial cell composition. Our findings identify a physiologically induced dedifferentiation that ensures ISC expansion during adaptive organ growth in concert with nutrient conditions.

Adaptive Response and Transcriptomic Analysis of Flax (Linum usitatissimum L.) Seedlings to Salt Stress.

Soil salinity constrains agricultural development in arid regions. Flax is an economically important crop in many countries, and screening or breeding salinity-resistant flax cultivars is necessary. Based on the previous screening of flaxseed cultivars C71 (salt-sensitive) and C116 (salt-tolerant) as test materials, flax seedlings stressed with different concentrations of NaCl (0, 100, 150, 200, and 250 mmol/L) for 21 days were used to investigate the effects of salt stress on the growth characteristics, osmotic regulators, and antioxidant capacity of these flax seedlings and to reveal the adaptive responses of flax seedlings to salt stress. The results showed that plant height and root length of flax were inhibited, with C116 showing lower growth than C71. The concentrations of osmotic adjustment substances such as soluble sugars, soluble proteins, and proline were higher in the resistant material, C116, than in the sensitive material, C71, under different concentrations of salt stress. Consistently, C116 showed a better rapid scavenging ability for reactive oxygen species (ROS) and maintained higher activities of antioxidant enzymes to balance salt injury stress by inhibiting growth under salt stress. A transcriptome analysis of flax revealed that genes related to defense and senescence were significantly upregulated, and genes related to the growth and development processes were significantly downregulated under salt stress. Our results indicated that one of the important adaptations to tolerance to high salt stress is complex physiological remediation by rapidly promoting transcriptional regulation in flax.

Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth.

Plant root architecture flexibly adapts to changing nitrate (NO3-) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3--mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3- in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3- availability. Under low-NO3- availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.

Feet first: Adaptive growth in magellanic penguin chicks.

Growing animals should allocate their limited resources in ways that maximize survival. Seabird chicks must balance the growth of features and fat reserves needed to survive on land with those needed to successfully fledge and survive at sea. We used a large, 34-year dataset to examine energy allocation in Magellanic penguin chicks. Based on the temporal trends in the selective pressures that chicks faced, we developed predictions relating to the timing of skeletal feature growth (Prediction 1), variation in skeletal feature size and shape (Prediction 2), and responses to periods of high energetic constraint (Prediction 3). We tested our predictions using descriptive statistics, generalized additive models, and principal component analysis. Nearly all of our predictions were supported. Chicks grew their feet first, then their flippers. They continued to grow their bill after fledging (Prediction 1). Variance in feature size increased in young chicks but declined before fledging; this variance was largely driven by overall size rather than by shape (Prediction 2). Chicks that died grew slower and varied more in feature size than those that fledged (Prediction 2). Skeletal features grew rapidly prior to thermoregulation and feet and flippers were 90% grown prior to juvenile feather growth; both thermoregulation and feather growth are energetically expensive (Prediction 3). To avoid starvation, chicks prioritized storing mass during the first 10 days after hatching; then, the body condition of chicks began to decline (Prediction 3). In contrast to our prediction of mass prioritization in young chicks, chicks that were relatively light for their age had high skeletal size to mass ratios. Chicks did not show evidence of reaching physiological growth limits (Prediction 3). By examining energy allocation patterns at fine temporal scales and in the context of detailed natural history data, we provide insight into the trade-offs faced by growing animals.

Opposing Post-transcriptional Control of InR by FMRP and LIN-28 Adjusts Stem Cell-Based Tissue Growth.

Although the intrinsic mechanisms that control whether stem cells divide symmetrically or asymmetrically underlie tissue growth and homeostasis, they remain poorly defined. We report that the RNA-binding protein fragile X mental retardation protein (FMRP) limits the symmetric division, and resulting expansion, of the stem cell population during adaptive intestinal growth in Drosophila. The elevated insulin sensitivity that FMRP-deficient progenitor cells display contributes to their accelerated expansion, which is suppressed by the depletion of insulin-signaling components. This FMRP activity is mediated solely via a second conserved RNA-binding protein, LIN-28, known to boost insulin signaling in stem cells. Via LIN-28, FMRP controls progenitor cell behavior by post-transcriptionally repressing the level of insulin receptor (InR). This study identifies the stem cell-based mechanism by which FMRP controls tissue adaptation, and it raises the possibility that defective adaptive growth underlies the accelerated growth, gastrointestinal, and other symptoms that affect fragile X syndrome patients.

The evolutionary traverse: a causal analysis.

This paper explores the process of adaptation to new methods in a simple model where the growth rate of labour supply is exogenously given and constant. It shows that competition for a primary input in short supply changes the mechanism of adaptation and its consequences: If surplus labour exists, differential capacity accumulation effectuates adaptation and leads to a logistic replacement pattern; but if labour is in short supply, 'growth predation' undermines the former mechanism and leads to an exponential replacement pattern. The consequences of the quantitative adjustment mechanisms for aggregate growth are discussed by means of a 'causal analysis', which focuses on the properties of the traverse between two full-employment steady states. The analysis reveals that different types of new methods lead to different adaptation paths and results. Overall, adaptation entails unsteady growth and it is not always the case that the diffusion of a new method boosts aggregate growth.