Growth Biology Research Articles

Functional genomics of human skeletal development and the patterning of height heritability.

Underlying variation in height are regulatory changes to chondrocytes, cartilage cells comprising long-bone growth plates. Currently, we lack knowledge on epigenetic regulation and gene expression of chondrocytes sampled across the human skeleton, and therefore we cannot understand basic regulatory mechanisms controlling height biology. We first rectify this issue by generating extensive epigenetic and transcriptomic maps from chondrocytes sampled from different growth plates across developing human skeletons, discovering novel regulatory networks shaping human bone/joint development. Next, using these maps in tandem with height genome-wide association study (GWAS) signals, we disentangle the regulatory impacts that skeletal element-specific versus global-acting variants have on skeletal growth, revealing the prime importance of regulatory pleiotropy in controlling height variation. Finally, as height is highly heritable, and thus often the test case for complex-trait genetics, we leverage these datasets within a testable omnigenic model framework to discover novel chondrocyte developmental modules and peripheral-acting factors shaping height biology and skeletal growth.

A user-friendly CRISPR/Cas9 system for mutagenesis of Neurosporacrassa

As a widely used eukaryotic model organism, Neurosporacrassa offers advantages in genetic studies due to its diverse biology and rapid growth. Traditional genetic manipulation methods, such as homologous recombination, require a considerable amount of time and effort. In this study, we present an easy-to-use CRIPSR/Cas9 system for N.crassa, in which the cas9 sequence is incorporated into the fungal genome and naked guide RNA is introduced via electroporation. Our approach eliminates the need for constructing multiple vectors, speeding up the mutagenesis process. Using cyclosporin-resistant-1 (csr-1) as a selectable marker gene, we achieved 100% editing efficiency under selection conditions. Furthermore, we successfully edited the non-selectable gene N-acylethanolamineamidohydrolase-2 (naa-2), demonstrating the versatility of the system. Combining gRNAs targeting csr-1 and naa-2 simultaneously increased the probability of finding mutants carrying the non-selectable mutation. The system is not only user-friendly but also effective, providing a rapid and efficient method for generating loss-of-function mutants in N.crassa compared to traditional methods.

A framework for the integration of development and evolution: The forgotten legacy of James Meadows Rendel

The historical challenges to bridge the gaps between developmental biology and population or statistical genetics under the explanatory dominance of the Modern Evolutionary Synthesis during the 20th century have been thoroughly documented. However, although several attempts to integrate these fields have been made, most have been deemed unsuccessful. As an example of those efforts, in this paper I discuss the work of James Meadows Rendel, a student of J. B. S. Haldane and disciple of Conrad Hal Waddington. I present his largely forgotten or unrecognized, but innovative, ideas about canalization and the role of development in phylogeny as a valuable piece to connect these fields that could still have important ramifications for today's evolutionary biology. In fact, it is expected that the legacy of J. M. Rendel will be rediscovered, and more importantly, incorporated and extended by future researchers, in light of the growth of evolutionary developmental biology in the last decades. What is more, this case offers a chance to critically revisit standard historiographies about the dichotomy between developmental and population genetics research frameworks in 20th century biology.

The allometric growth relationship between electricity consumption and economics in China.

Electric power is the basic industry of a modern country. The rapid development of the power industry has promoted economic development and social progress. With the establishment of the carbon neutrality target of carbon peak, China's power industry is also facing new situations and new challenges. This paper innovatively introduces the concept of allometric growth in biology, and uses the data of provincial electricity consumption and economic development from 1972 to 2017, to study the allometric growth relationship between electricity consumption and economics in China at multiple scales. Combined with the spatial autocorrelation analysis method, the temporal and spatial characteristics of allometric growth between electricity consumption and economic development were researched based on the analysis of spatial correlation of GDP electricity consumption intensity. The results show that: (1) The provincial GDP electricity consumption intensity shows an aggregate distribution, and the local aggregate pattern changed significantly from 1972 to 2017. (2) The High-High Cluster gradually disappeared, and the Low-Low Cluster moved southward, appearing in the middle and lower reaches of the Yangtze River. (3) The differential growth coefficient of electricity consumption and economic development increased initially and decreased from 1972 to 2017. (4) GDP would increase by 7.4%, 20.1%, and 15.6% in the simulation of electricity consumption, increasing 10% at the three stages of China's economic development. (5) The allometric growth coefficients of electricity consumption and economic development are very different in the three economic belts, eight economic zones, and provinces with different characteristics at the different stages of economic development. Formulating differentiated regulation policies for regional economic development and electricity consumption will be conducive to the coordinated development of electric power production and the national economy.

Delayed Solid Tumor Presentations in Adolescent and Young Adults Patients in the Bronx.

Adolescent and young adults (AYAs) require support from their parents and caregivers. While there are formal programs available for patients with complex medical problems, <20% of pediatric practices are performing transition readiness processes in patients aged 12-17 years to effective transition. Although cancer is the most common cause of disease-related death in AYAs in high-income countries, AYA oncology patients have not attained the same clinical improvements as pediatric patients, and their outcomes remain poorer. While there are published data on an expected degree of lag time for patients presenting with solid tumors, due to the underlying biology and slow growth of the cancer, we have recently witnessed extreme delays in the presentation to medical care. In this article, we share the cases of two young adults.

Synthesis of queuine by colonic gut microbiome via cross‐feeding

AbstractQueuine (Que) is an essential micronutrient, and its deficiency will lead to errors in tRNA modification and protein misfold, further to diseases. Meanwhile, the content of Que in food will be further reduced due to the modern planting pattern and processing. In this study, an idea, synthetic biology of gut microbiome, was introduced to meet people's demand for Que. Further, various food can be used as a media for promoting the growth of synthetic biology of flora and the concentrations of Que. Through this research, gut bacteria (Escherichia coli K12, Bacteroides fragilis ATCC25285, and Lactobacillus reuteri DSM20058) with abilities of Que independent synthesis in vitro were selected, and higher productivity of Que was fulfilled through the above three strains cocultivation via cross‐feeding. Moreover, the effect of Que on the structure of microbiome was also studied, in order to figure out the continuous synthesis of Que by this coculture system in colonic situation. Que could enhance bacterial α‐diversity, increase the abundance of Limosilactobacillus, Pediococcus, and Lactobacillus, while decrease the abundance of Eschi‐Shigella. Three bacteria combination intervention changed intestinal microbial composition, and distribution of enzymes transglycozyme, QueA, and QueG that involved in last three steps of Que synthesis in microorganisms was significantly changed. These results provide an experimental basis for colonic synthesis of Que via food intervention to solve the deficiency Que in human body. Here, we regard gut microbes as a fermentation system in human body, providing a constant supply of tiny but important substance that humans need.

The Saddleback Deformity in Teleost Fish: Identification of a Unique Global Hotspot in Eastern Australia

The saddleback deformity, an abnormality of the dorsal fin and profile, lacking one to all of the dorsal spines, accompanied by shape, number and position abnormalities of associated pterygiophores, has been reported in teleosts under culture conditions and in the wild in many locations throughout the world, including North and South America, Asia, Australia, Europe, India and the Middle East. A unique global hotspot for saddleback deformities in wild teleosts is the southeast Queensland Australia coastal region between 26° S and 28° S. At this location the incidence of saddleback has been relatively stable but very high at about 10% of individual teleosts taken in the associated fishery since 1997. Opinions on causation have focused on two possibilities, a developmental defect associated with water pollution or a physical injury. The range of skeletal deformities is vastly different in cultured teleosts compared with those occurring in the wild. There is now mounting evidence that physical injury is causing saddleback in teleosts in southeast Queensland Australia. Such injury could be caused by predatory behaviour of piscivorous fish or birds, parasites, or escapement or release from fishing nets and other fishing gear. Population mortality rates associated with saddleback in southeast Queensland are unknown, but expected to be high. The high level of occurrence of saddleback in teleosts in southeast Queensland Australia together with the good understanding of their fisheries biology (age and growth rates, reproductive biology, habitat dependence) and stock assessments of the associated fisheries provide excellent opportunities for further research which would add to the scientific understanding of the saddleback deformity in teleosts throughout the world. A recommendation from this review is that support should be sought by research providers (universities and Government research agencies) from routine annual funding offers from the Australian and Queensland Governments to achieve an increase in the scientific understanding of the saddleback deformity.

Accentuating the positive and eliminating the negative: Efficacy of TiO2 as digestibility index marker for poultry nutrition studies.

Inert digestibility index markers such as titanium dioxide are universally accepted to provide simple measurement of digestive tract retention and relative digestibility in poultry feeding trials. Their use underpins industry practice: specifically dosing regimens for adjunct enzymes added to animal feed. Among these, phytases, enzymes that degrade dietary phytate, inositol hexakisphosphate, represent a billion-dollar sector in an industry that raises ca. 70 billion chickens/annum. Unbeknown to the feed enzyme sector, is the growth in cell biology of use of titanium dioxide for enrichment of inositol phosphates from extracts of cells and tissues. The adoption of titanium dioxide in cell biology arises from its affinity under acid conditions for phosphates, suggesting that in feeding trial contexts that target phytate degradation this marker may not be as inert as assumed. We show that feed grade titanium dioxide enriches a mixed population of higher and lower inositol phosphates from acid solutions. Additionally, we compared the extractable inositol phosphates in gizzard and ileal digesta of 21day old male Ross 308 broilers fed three phytase doses (0, 500 and 6000 FTU/kg feed) and one inositol dose (2g/kg feed). This experiment was performed with or without titanium dioxide added as a digestibility index marker at a level of 0.5%, with all diets fed for 21 days. Analysis yielded no significant difference in effect of phytase inclusion in the presence or absence of titanium dioxide. Thus, despite the utility of titanium dioxide for recovery of inositol phosphates from biological samples, it seems that its use as an inert marker in digestibility trials is justified-as its inclusion in mash diets does not interfere with the recovery of inositol phosphates from digesta samples.

Microbial Production of Mevalonate.

Mevalonate, an important intermediate product of the mevalonate pathway, has a broad spectrum of applications. With the rapid growth of metabolic engineering and synthetic biology, mevalonate biosynthesis by microorganisms is feasible and holds great promise in the future. In this review, we summarize the applications of mevalonate and its derivatives and describe the biosynthesis pathways of mevalonate. The current status of mevalonate biosynthesis is also detailed with an emphasis on metabolic engineering strategies to enhance mevalonate production in typical industrial organisms, including Escherichia coli, Saccharomyces cerevisiae, and Pseudomonas putida, suggesting new insights for the efficient production of biosynthesized mevalonate.

Population Growth Parameters of Helicoverpa armigera (Hübner) on Various Legume Seeds Reveal Potential Tolerance Traits

Helicoverpa armigera (Hübner) is a key polyphagous pest with global spread that causes economic damage to agricultural crops. It is commonly managed by synthetic insecticides, which can cause negative impacts on the environment and human health, as well as toxicity to natural enemies. Hence, investigations into alternative pest management approaches such as the use of resistant host plant cultivars against H. armigera is important. In this study, the effects of various legume seeds based on meridic diets were evaluated using biology and population growth parameters of H. armigera under laboratory conditions. The results indicated that the shortest developmental time and pupal incubation periods occurred on white kidney bean Dehghan, while the longest periods occurred on broad bean Mahta. The intrinsic rate of population increase (r) was highest when H. armigera was reared on white kidney bean Dehghan and cowpea Arabi, and the lowest when reared on broad bean Mahta and common bean Khomein. Furthermore, the highest net reproductive rate (R0) occurred on white kidney bean Dehghan and the lowest on common bean Khomein. Cluster analysis revealed that white kidney bean Dehghan and cowpea Arabi were the most susceptible hosts, while common bean Khomein, and broad beans Feyz and Mahta were the poorest and perhaps least susceptible hosts for population growth of H. armigera. Our results suggest that the selective use of certain bean cultivars as potential sources of antibiosis against this pest may be useful as part of an integrated management program.

Complementary Role of Fishers' Experiential Knowledge to Conventional Science in Terms of Species-Specific Biological Traits and Population Changes in Azorean Waters.

Combining scientific information with fishers' perceptions may be a robust approach for directing decision-makers working with marine ecosystems. This is particularly the case when baseline data on a vulnerable stock are poor, as the integration of fishers' experiential knowledge can help fill data gaps, as well as inform legitimate management actions, and empower fishing communities in resource management. This study aimed to analyze fishers' knowledge regarding the biology (reproduction, growth, and maximum size) and temporal changes in the abundance and size of six commercially important marine species (red porgy Pagrus pagrus, veined squid Loligo forbesii, blue jack mackerel Trachurus picturatus, blackspot seabream Pagellus bogaraveo, blackbelly rosefish Helicolenus dactylopterus, and European conger Conger conger) in the Azores small-scale communities. Additionally, a comparison between fishers' knowledge and available scientific information was performed to determine the former's value and its possible complementarity with the latter. A total of 105 fishers were surveyed in the nine islands of the archipelago. The results demonstrated a reasonable level of agreement between the information from fishers and scientific literature on the species-specific spawning seasons and growth rates. The median values of size at maturity and maximum length were not statistically different between data sources. Most participants indicated size and abundance trends that were consistent with the literature. This study highlights the usefulness of fishers' perceptions in improving knowledge about species characteristics and temporal changes in commercially exploited stocks, especially when scientific research is limited, but further research should be encouraged to improve the reliability and consistency of these results.

The methanogen core and pangenome: conservation and variability across biology's growth temperature extremes.

Temperature is a key variable in biological processes. However, a complete understanding of biological temperature adaptation is lacking, in part because of the unique constraints among different evolutionary lineages and physiological groups. Here we compared the genomes of cultivated psychrotolerant and thermotolerant methanogens, which are physiologically related and span growth temperatures from -2.5°C to 122°C. Despite being phylogenetically distributed amongst three phyla in the archaea, the genomic core of cultivated methanogens comprises about one-third of a given genome, while the genome fraction shared by any two organisms decreases with increasing phylogenetic distance between them. Increased methanogenic growth temperature is associated with reduced genome size, and thermotolerant organisms-which are distributed across the archaeal tree-have larger core genome fractions, suggesting that genome size is governed by temperature rather than phylogeny. Thermotolerant methanogens are enriched in metal and other transporters, and psychrotolerant methanogens are enriched in proteins related to structure and motility. Observed amino acid compositional differences between temperature groups include proteome charge, polarity and unfolding entropy. Our results suggest that in the methanogens, shared physiology maintains a large, conserved genomic core even across large phylogenetic distances and biology's temperature extremes.

Biology, predatory potential and growth parameters of the syrphid fly, Scaeva pyrastri (L.) (Diptera: Syrphidae) feeding on the cabbage aphid, Brevicoryne brassicae (L.)

BackgroundScaeva pyrastri (L.) (Diptera: Syrphidae) is a large-size Palaearctic region syrphid fly. The larval stage of S. pyrastri is aphidophagous in nature, while the adults are efficient pollinators of various crops. Therefore, this study was carried out to investigate the predation efficacy, biology and population growth parameters of S. pyrastri on the cabbage aphid, Brevicoryne brassicae (L.) (Hemiptera: Aphididae) as prey using age–stage-specific two-sex fertility table.ResultsThe results showed that the mean total larval development duration was 8.31 days and the pre-adult stage was 19.82 ± 0.25 days long. In the adult stage, the mean longevity of female (18.57 ± 0.37 days) was longer than that of the male (15.50 ± 0.17 days). The adult pre-ovipositional, ovipositional and post-ovipositional periods were 4.25 ± 0.25, 8.50 ± 0.46 and 3.25 ± 0.31 days, respectively, and the mean female’s fecundity was 37.75 ± 1.16 eggs per female. The two-sex fertility table indicated that the age-specific fecundity (mx) increased gradually peaking at the 27th day of pivotal age (2.71 eggs per day) and decreased thereafter. The life expectancy of female was observed on the 18th (20.25 days) and 19th day (16.44 days) in the female and male flies, respectively. The female attained the maximum reproductive value (vxj) on the 25th day, which was 26.05 eggs needed to produce one individual. The population growth parameters indicated that the population had a net reproduction rate of 15.10 ± 4.19 offspring per individual and a true generation time of 28.86 ± 0.28 days. The intrinsic rate of increase was greater than zero (0.093 ± 0.011) and the finite rate of increase (λ) was greater than one (1.098 ± 0.012), which indicated that B. brassicae was the suitable prey for S. pyrastri. The values related to the number of aphids consumed by the larvae were: a net predation rate (Co) of 377.06 ± 26.54 nymphs and finite predation rate (ω) of 19.58 ± 0.78.ConclusionsScaeva pyrastri had a considerable predatory potential and fitted well for the biological control of aphids, especially B. brassicae. However the field potential is still unknown; thus, this study will be helpful in determining the field efficacy of S. pyrastri against B. brassicae.

‘Switch to love, switch to kill—dose and light co-regulate iron single-atom nanozyme to modulate cell fate

Remote control of cells and the regulation of cell events at the molecular level are of great interest to the biomedical field. In addition to mechanical forces and genes, chemical compounds and light play pivotal roles in regulating cell fate, which have boosted the fast growth of biology. Herein, we synthesized light-regulated, atomically dispersed Fe-N4 immobilized on a carbon substrate nanozyme (Fe-N/C single atom catalysts), whose peroxidase- and catalase-like properties can be enhanced by 120% and 135%, respectively, under 808-nm laser irradiation through the photothermal effect of Fe-N/C. Interestingly, a switch to love/switch to kill interaction between Fe-N/C dose and near-infrared (NIR) light co-regulating the Fe-N/C nanozyme to modulate cell fate was discovered. Based on this, we found that under NIR light irradiation, when the dose of Fe-N/C is low, it can scavenge more reactive oxygen species (ROS) and achieve cell protection; when the dose of Fe-N/C is too high, it tended to lead to cell apoptosis. This work not only provides an effective strategy for the regulation of nanozyme activity but also realizes the dual-functional application of nanozyme materials for the treatment of some specific diseases.

Competition between cell types under cell cycle regulation with apoptosis

Competition between different cell types plays a crucial role in bacterial ecology, developmental biology, and tumor growth. We study how cells compete in 2D by using both a mean field theory and particle-based simulations. We employ a mechanical model that incorporates a stylized form of cell cycle regulation to control cell division events. This is extended to treat multiple cell types with different rates of programed cell death (apoptosis) and characteristic cell-cycle control pressures. Analytic predictions for the invasion speed and the coexistence line are in agreement with simulations. Synchronization in the cell division/apoptosis events can emerge, leading to oscillations in pressure and cell-cycle activity. We also study the invasion or elimination of small (pre)cancerous colonies. We show how a Laplace pressure at the colony interface, here controlled by differential cell adhesion, shifts the coexistence line; there are cell types that can invade when starting from a large colony but will be eliminated if the colony is small.

Hands-on training in structural biology, a tool for sustainable development in Africa series 4.

ABSTRACTStructural biology is an essential tool for understanding the molecular basis of diseases, which can guide the rational design of new drugs, vaccines, and the optimisation of existing medicines. However, most African countries do not conduct structural biology research due to limited resources, lack of trained persons, and an exodus of skilled scientists. The most urgent requirement is to build on the emerging centres in Africa – some well-established, others growing. This can be achieved through workshops that improve networking, grow skills, and develop mechanisms for access to light source beamlines for defining X-ray structures across the continent. These would encourage the growth of structural biology, which is central to understanding biological functions and developing new antimicrobials and other drugs. In this light, a hands-on training workshop in structural biology series 4 was organised by BioStruct-Africa and the Malaria Research and Training Center (MRTC) in Bamako, Mali, to help bridge this gap. The workshop was hosted by MRTC from the 25th to 28th of April 2022. Through a series of lectures and practicals, the workshop enlightened the participants on how structural biology can be utilised to find solutions to the prevalent diseases in Africa. The short training gave them an overview of target selection, protein production and purification, structural determination techniques, and analysis in combination with high-throughput, structure-guided, fragment-based drug design.

Machine Learning for Endometrial Cancer Prediction and Prognostication.

Endometrial cancer (EC) is a prevalent uterine cancer that remains a major contributor to cancer-associated morbidity and mortality. EC diagnosed at advanced stages shows a poor therapeutic response. The clinically utilized EC diagnostic approaches are costly, time-consuming, and are not readily available to all patients. The rapid growth in computational biology has enticed substantial research attention from both data scientists and oncologists, leading to the development of rapid and cost-effective computer-aided cancer surveillance systems. Machine learning (ML), a subcategory of artificial intelligence, provides opportunities for drug discovery, early cancer diagnosis, effective treatment, and choice of treatment modalities. The application of ML approaches in EC diagnosis, therapies, and prognosis may be particularly relevant. Considering the significance of customized treatment and the growing trend of using ML approaches in cancer prediction and monitoring, a critical survey of ML utility in EC may provide impetus research in EC and assist oncologists, molecular biologists, biomedical engineers, and bioinformaticians to further collaborative research in EC. In this review, an overview of EC along with risk factors and diagnostic methods is discussed, followed by a comprehensive analysis of the potential ML modalities for prevention, screening, detection, and prognosis of EC patients.

Towards Phytopathogen Diagnostics? Coconut Bud Rot Pathogen Phytophthora palmivora Mycelial Proteome Analysis Informs Genome Annotation.

Planetary agriculture stands to benefit immensely from phytopathogen diagnostics, which would enable early detection of pathogens with harmful effects on crops. For example, Phytophthora palmivora is one of the most destructive phytopathogens affecting many economically important tropical crops such as coconut. P. palmivora causes diseases in over 200 host plants, and notably, the bud rot disease in coconut and oil palm, which is often lethal because it is usually detected at advanced stages of infection. Limited availability of large-scale omics datasets for P. palmivora is an important barrier for progress toward phytopathogen diagnostics. We report here the mycelial proteome of P. palmivora using high-resolution mass spectrometry analysis. We identified 8073 proteins in the mycelium. Gene Ontology-based functional classification of detected proteins revealed 4884, 4981, and 3044 proteins, respectively, with roles in biological processes, molecular functions, and cellular components. Proteins such as P-loop, NTPase, and WD40 domains with key roles in signal transduction pathways were identified. KEGG pathway analysis annotated 2467 proteins to various signaling pathways, such as phosphatidylinositol, Ca2+, and mitogen-activated protein kinase, and autophagy and cell cycle. These molecular substrates might possess vital roles in filamentous growth, sporangia formation, degradation of damaged cellular content, and recycling of nutrients in P. palmivora. This large-scale proteomics data and analyses pave the way for new insights on biology, genome annotation, and vegetative growth of the important plant pathogen P. palmivora. They also can help accelerate research on future phytopathogen diagnostics and preventive interventions.

Cloning data with unchanged estimates of estimable non-linear functions of parameters

Non-linear regression models occur in the fields of biology, banking, economics, and sociology, population and biological growth. The absolute growth, growth of humans, and most importantly, an economic variable is appropriately described by non-linear regression models. In this article, we present cloned datasets for bivariate and multivariate non-linear regression models with the same non-linear regression fit. The application of such cloned datasets is used for the confidentiality of sensitive data for publication purposes. In this article, we present cloned data sets which will yield the same fitted non-linear regression models.

Dietary Effects on Biological Parameters and Gut Microbiota of Harmonia axyridis.

The multicolored Asian lady beetle (Harmonia axyridis, H. axyridis, Coleoptera, and Coccinellidae) is an effective biocontrol agent against agricultural pests. Previous studies have suggested that amount, type, and the quality of food can directly affect the biological aspects of H. axyridis. In this study, we investigated the influence of the food sources (Acyrthosiphon pisum Harris, Diaphorina citri Kuwayama, and artificial diets) on the gut microbiota diversity and the biology, reproductive variables, and population growth indicators of H. axyridis. Three kinds of diets were considered in this study: (1) HY: the adult of A. pisum Harris (HY group); (2) HM: the adult of D. citri Kuwayama (HM group); (3) HR: artificial diets prepared by blending a portion of fresh homogenized pork liver (15 g), honey (3 g), distilled water (35 ml) (HR group). We found that gut microbiota composition and diversity and the biological parameters differed when H. axyridis was fed with different diets. The abundance of Enterobacteriaceae was the highest in the HM group, followed by HY group, and was the lowest in the HR group. The abundance of Staphylococcaceae was highest in the HR group. Among the gut fungi, Davidiellaceae and Wallemiaceae were the highest and lowest in the HY group; Incertae_sedis were the major gut fungi in the HR group. Meanwhile, the changes of biological parameters may be correlated with the changes of Streptococcaceae abundance, Micrococcaceae abundance, Staphylococcaceae abundance, and Enterobacteriaceae abundance in responds to diet changes. To sum up, these data suggest that different diets can influence the changes in adult H. axyridis gut microbiota, consequently affecting the biological parameters.