Growth Biology Research Articles

A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. However, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. Here, we describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies for stacking genes and traits to address many impending environmental and agricultural challenges.

BIOLOGY AND INTRINSIC GROWTH RATE OF EARWIG (Euborellia annulata)

Earwig (Euborellia annulata) is a potential predator of corn borer (Ostrinia furnacalis), one of the most important pests of corn. To include the use of predator in integrated pest management (IPM) to control the pest, it is necessary to understand the basic information of the predator. This study aimed to know biology and intrinsic growth rate of the predator feed on an artificial media (dog food). Ten pairs of newly emerging adults of the predator were placed in a small plastic container containing a mixture of soil and sand (1:1 v/v) supplemented with an artificial food. The average temperature and relative humidity during the study were kept at 27.9-30.3oC and 76.7-92.3%, respectively. The biological aspects of the predator evaluated were number of eggs laid, hatched, and died, as well as its oviposition period and adult mortality. The intrinsic growth rate was studied from a group of 200 newly laid eggs and results were analyzed based on the method of Birch. The biological aspects study showed that number of eggs laid by a single female of E. annulata was 86-166, which were laid five times in a group of 9-45 eggs. The nymph consists of five instars. Length of nymphs varied ranging from 4 to 13 mm depends on their instar. The fifth instar nymph period was 4-6 days for female and 2-3 days for male. The period of first mating was shorter; the shortest was 2 minutes and the longest one was 70 minutes. Both male and female were able to do mating several times at an interval of several seconds or minutes. Pre-oviposition period was 6-13 days. The eggs were deposited five times, the first, second, third, fourth, and fifth oviposition period were 7-22 days, 7-21 days, 7-18 days, 11-18 days, and 11-21 days, respectively. The oviposition period was 32-59 days and postoviposition period was 21-51 days. Ratio between male and female was 1.4:1.0. The average natural mortality of E. annulata was 10.5% which means that 89.5% of deposited eggs hatched became nymphs. The study also revealed that the intrinsic growth rate (r) of the predator was 0.0772, net reproductive rate (R0) 80.16, limited growth rate (λ) 1.17, nymph stage period 39-46 days, and adult longevity of male and female were 57-75 and 61-89 days, respectively. The study implies that E. annulata is potential to be incorporated in IPM for controlling corn borer.

BIOLOGY AND INTRINSIC GROWTH RATE OF EARWIG (Euborellia annulata)

Earwig (Euborellia annulata) is a potential predator of corn borer (Ostrinia furnacalis), one of the most important pests of corn. To include the use of predator in integrated pest management (IPM) to control the pest, it is necessary to understand the basic information of the predator. This study aimed to know biology and intrinsic growth rate of the predator feed on an artificial media (dog food). Ten pairs of newly emerging adults of the predator were placed in a small plastic container containing a mixture of soil and sand (1:1 v/v) supplemented with an artificial food. The average temperature and relative humidity during the study were kept at 27.9-30.3oC and 76.7-92.3%, respectively. The biological aspects of the predator evaluated were number of eggs laid, hatched, and died, as well as its oviposition period and adult mortality. The intrinsic growth rate was studied from a group of 200 newly laid eggs and results were analyzed based on the method of Birch. The biological aspects study showed that number of eggs laid by a single female of E. annulata was 86-166, which were laid five times in a group of 9-45 eggs. The nymph consists of five instars. Length of nymphs varied ranging from 4 to 13 mm depends on their instar. The fifth instar nymph period was 4-6 days for female and 2-3 days for male. The period of first mating was shorter; the shortest was 2 minutes and the longest one was 70 minutes. Both male and female were able to do mating several times at an interval of several seconds or minutes. Pre-oviposition period was 6-13 days. The eggs were deposited five times, the first, second, third, fourth, and fifth oviposition period were 7-22 days, 7-21 days, 7-18 days, 11-18 days, and 11-21 days, respectively. The oviposition period was 32-59 days and postoviposition period was 21-51 days. Ratio between male and female was 1.4:1.0. The average natural mortality of E. annulata was 10.5% which means that 89.5% of deposited eggs hatched became nymphs. The study also revealed that the intrinsic growth rate (r) of the predator was 0.0772, net reproductive rate (R0) 80.16, limited growth rate (λ) 1.17, nymph stage period 39-46 days, and adult longevity of male and female were 57-75 and 61-89 days, respectively. The study implies that E. annulata is potential to be incorporated in IPM for controlling corn borer.

PENGEMBANGAN PERANGKAT PEMBELAJARAN KOOPERATIF PADA BIOLOGI PERKEMBANGAN HEWAN

This research focused on developing cooperative learning materials for biology of animal growth. This research therefore aimed designing teaching instructional, testing validity and testing practicality of the implementation of the materials upon the topic of animal growth in biology. This research employed research and development design. The first phase dealt with reconstruction or designing learning materials and the instrument that were used in cooperative learning. Next, testing instrument validity was done by expert. In the last phase, limited try out was conducted to figure out the practicality. The findings showed that learning materials and the supporting instruments were valid. Such learning materials included syllabus, lesson plans, students’ lab sheets, concept map manual and students’ achievement evaluation sheet. Implementation practicality was assessed from the cooperative learning process and students’ responses. The findings showed that the learning process was suitable with prepared syllabus and lesson plans, and students’ responses toward learning process was in good category. Kata kunci : pembelajaran kooperatif, perangkat, instrumen, biologi perkembangan hewan

A Computational Approach of the French Flag Model to Connect Growth and Specification in Developmental Biology

The study of the mechanisms that link the global system behavior to the interaction of its parts is an important issue to the field of complex systems. This occurs in many natural systems in biology, ecology and physics. Nature-inspired computation tries to capture and exploit natural solutions in order to solve real problems in many different fields such as telecommunication networks, architecture and urban spaces design, sociology or economy planning. The main purpose of the present research is the creation of a computational path connecting a set of low-level interactions with high-level emerging behaviors. The low-level interactions are modeled by very simple neighbor binary rules. The upper level highlights a regular pattern formation. This framework has been applied to approach the pattern formation in the vertebrate limb development under the scope of the French Flag model. We have developed a four-level theoretical framework. The lowest level defines a set of neighbor binary rules. The second level comes from the iterative application of these rules on sequences of binary values. The resulting sequences are interpreted as arithmetic function values, in binary or decimal representation. The third level highlights a set of computational primitives that have the capability to build directly the function values. Any function can be carried out by means of a particular combination of these primitives, denoted seed behavior. In the fourth level, the emergent behavioral effect is highlighted as a scaling process of the seed behavior. Some functions that have been defined by the four-level framework have been successfully applied to model the French Flag model (progressive specification, intercalary specification and early specification) which is a well-known approach to the pattern formation in the vertebrate limb development. Our empirical research highlights it is possible to develop a computational model which connects very simple rules to complex behavioral patterns. The way consists of a hierarchical organization of computing embedded steps. Our model provides a numerical and geometrical counterpart to the French Flag model and therefore proves its capability to be a formal basis to the case of vertebrate limb development. These encouraging results suggest as a future work the improvement in this model. The composition of functions must be explored as well as new combinations of building primitives in order to identify more emergent effects. More, the relevance of quantitative emergent effects must be highlighted in future applications to natural cases. It is expected that the development of these operations will help addressing new issues such as truncation and graft in vertebrate limbs.

Topics in differential geometry associated with position vector fields on Euclidean submanifolds

The position vector field is the most elementary and natural geometric object on a Euclidean submanifold. The purpose of this article is to survey six research topics in differential geometry in which the position vector field plays very important roles. In this article we also explain the relationship between position vector fields and mechanics, dynamics, and D’Arcy Thompson’s law of natural growth in biology.

MORAL AND EDUCATIONAL PRINCIPLES IN THE WORKS OF IMAM KHOMEINI

The present article aims at studying the moral and educational principles and basics from Imam Khomeini’s viewpoint and seeks to answer to these questions: what is the position of the moral and educational principles in the works and ideas of Imam Khomeini? What is the position of moral and educational principles and methods in the works of Imam Khomeini? What are elements of anthropological education from Khomeini’s viewpoint? This research is of descriptive-analytical method. This article reviewing works and ideas of Imam Khomeini attempts to extract moral and educational principles from his perspective. The findings indicate that Imam Khomeini regards education as an important function in education system of Islamic society based on rules including principle of priority of self-correction over correcting others, principle of self-refinement priority over teaching, the principle of training continuity, the principle of repetition and indoctrination, the principle of directionality of training, and the principle of attractionism. Also, goals of education from Imam’s idea includes as following. Natural growth which is growth in physic and biology, intellectual growth which is fostering reasoning is spiritual growth and nurturing movements of heart and imagination, scientific and political development. Moreover, in order to achieve a full human education from Imam Khomeini’s viewpoint it should be based on methods as 1. Way of thinking 2. How to stimulate awareness and insight 3 Way of emotional motivation 4 Lessoning way 5 Reverence and encouragement 6 Repetition and indoctrination 7 How to use enemy 8 Calculation method 9 Advice and benevolence method 10 Pattern. Anthropological foundations of education in Imam Khomeini’s viewpoint are: discontinuous intrinsic relationship with God, truth- and justice-seeking, in search of perfection and love of completeness, desire to happiness and eternal prosperity, and a will to benevolence and freedom.

Effect of different diets on biology, reproductive variables and life and fertility tables of Harmonia axyridis (Pallas) (Coleoptera, Coccinellidae)

The biology, reproductive variables and population growth indicators of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) fed on three diets, namely Cinara atlantica (Wilson, 1919) (Hemiptera: Aphididae), Brevicoryne brassicae (Linnaeus, 1758) (Hemiptera: Aphididae), and frozen eggs of Anagasta kuehniella (Zeller, 1879) (Lepidoptera: Pyralidae), were evaluated. With all three diets, birth rate was higher than mortality, resulting in positive rm values and thus indicating population growth. Under the conditions used in the experiments, H. axyridis was able to survive, develop and reproduce normally. This demonstrates that are different kind of food that can be essential for supporting the reproduction of some species of Coccinellidae, but not with the same optimization of preferred prey.

A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis.

Reproduction in fishes and other vertebrates represents the timely coordination of many endocrine factors that culminate in the production of mature, viable gametes. In recent years there has been rapid growth in understanding fish reproductive biology, which has been motivated in part by recognition of the potential effects that climate change, habitat destruction and contaminant exposure can have on natural and cultured fish populations. New approaches to understanding the impacts of these stressors are being developed that require a systems biology approach with more biologically accurate and detailed mathematical models. We have developed a multi-scale mathematical model of the female rainbow trout hypothalamus-pituitary-ovary-liver axis to use as a tool to help understand the functioning of the system and for extrapolation of laboratory findings of stressor impacts on specific components of the axis. The model describes the essential endocrine components of the female rainbow trout reproductive axis. The model also describes the stage specific growth of maturing oocytes within the ovary and permits the presence of sub-populations of oocytes at different stages of development. Model formulation and parametrization was largely based on previously published in vivo and in vitro data in rainbow trout and new data on the synthesis of gonadotropins in the pituitary. Model predictions were validated against several previously published data sets for annual changes in gonadotropins and estradiol in rainbow trout. Estimates of select model parameters can be obtained from in vitro assays using either quantitative (direct estimation of rate constants) or qualitative (relative change from control values) approaches. This is an important aspect of mathematical models as in vitro, cell-based assays are expected to provide the bulk of experimental data for future risk assessments and will require quantitative physiological models to extrapolate across biological scales.

New Frontiers in Language Evolution and Development.

This article introduces the Special Issue and its focus on research in language evolution with emphasis on theory as well as computational and robotic modeling. A key theme is based on the growth of evolutionary developmental biology or evo-devo. The Special Issue consists of 13 articles organized in two sections: A) Theoretical foundations and B) Modeling and simulation studies. All the papers are interdisciplinary in nature, encompassing work in biological and linguistic foundations for the study of language evolution as well as a variety of computational and robotic modeling efforts shedding light on how language may be developed and may have evolved.

Molecular Dimensions of Gastric Cancer: Translational and Clinical Perspectives.

Gastric cancer is a global health burden and has the highest incidence in East Asia. This disease is complex in nature because it arises from multiple interactions of genetic, local environmental, and host factors, resulting in biological heterogeneity. This genetic intricacy converges on molecular characteristics reflecting the pathophysiology, tumor biology, and clinical outcome. Therefore, understanding the molecular characteristics at a genomic level is pivotal to improving the clinical care of patients with gastric cancer. A recent landmark study, The Cancer Genome Atlas (TCGA) project, showed the molecular landscape of gastric cancer through a comprehensive molecular evaluation of 295 primary gastric cancers. The proposed molecular classification divided gastric cancer into four subtypes: Epstein-Barr virus–positive, microsatellite unstable, genomic stable, and chromosomal instability. This information will be taken into account in future clinical trials and will be translated into clinical therapeutic decisions. To fully realize the clinical benefit, many challenges must be overcome. Rapid growth of high-throughput biology and functional validation of molecular targets will further deepen our knowledge of molecular dimensions of this cancer, allowing for personalized precision medicine.

Automation, consolidation, and integration in autoimmune diagnostics.

Over the past two decades, we have witnessed an extraordinary change in autoimmune diagnostics, characterized by the progressive evolution of analytical technologies, the availability of new tests, and the explosive growth of molecular biology and proteomics. Aside from these huge improvements, organizational changes have also occurred which brought about a more modern vision of the autoimmune laboratory. The introduction of automation (for harmonization of testing, reduction of human error, reduction of handling steps, increase of productivity, decrease of turnaround time, improvement of safety), consolidation (combining different analytical technologies or strategies on one instrument or on one group of connected instruments) and integration (linking analytical instruments or group of instruments with pre- and post-analytical devices) opened a new era in immunodiagnostics. In this article, we review the most important changes that have occurred in autoimmune diagnostics and present some models related to the introduction of automation in the autoimmunology laboratory, such as automated indirect immunofluorescence and changes in the two-step strategy for detection of autoantibodies; automated monoplex immunoassays and reduction of turnaround time; and automated multiplex immunoassays for autoantibody profiling.

Plenty of proteins

The growth of structural biology brings new challenges for the world's protein data archive.

Antimicrobial stewardship: the role of scientists?

We continue to be warned about the risk of antibiotic resistance. This campaign has targeted medicine and agriculture, asking these industries to pay attention to the risks of widespread resistance and to cut the use of antibiotics wherever possible. However, there has been little to no mention of the widespread use of antibiotics in the scientific research community. As scientists we use antibiotics and antibiotic resistance as fundamental tools for our research; almost all conventional plasmids use an antibiotic resistance gene as a selectable marker, offering us an easy method of screening. With molecular biology and genetics at the heart of many research disciplines, these tools are ubiquitous. Scientists have a responsibility to monitor and reduce our use of antibiotics. With the growth and fast advancement of synthetic biology, it is timely for us to consider other options and to teach the next generation of researchers by example how to truly value antibiotics by using them more responsibly.

Reproductive ecology of buzz-pollinated <i>Ouratea spectabilis</i> trees (Ochnaceae) in Brazilian Cerrados

Abstract. Ouratea spectabilis is a ubiquitous tree species in the Brazilian savannas, or Cerrados, where it plays an important ecological role. We studied its anthesis phenology, pollination biology, pollen viability, and pollen tube growth, and executed a set of intra- and interspecific experimental crosses to determine its mechanisms of incompatibility and reproductive ecology. The species presents a specialized buzz pollination syndrome and is served by a small array of specialized pollinator species. It is a mostly self-incompatible species, and although self-pollination is possible, it strongly reduces fertility, with reproductive outputs for hand self-pollination similar to those of interspecific crosses with the co-generic species O. hexasperma. Incompatibility with another commonly co-occurring co-generic species, O. floribunda, was complete, with a null fruit set, as occurred for the autonomous apomixis tests. Our pollen tube growth observations indicate that incompatibility occurs at the style, and is thus pre-zygotic. All three Ouratea species presented very high pollen viability. Manual pollen supplementation did not increase seed sets. Nevertheless, even after excess manual pollen supplementation, seed-to-ovule ratios were only 30%. Such limits are common in stressful environments, and fruit production for most Cerrado species is reported to be regularly under those levels. The apparent ubiquity of this fertility limit among Cerrado species poses interesting ecological questions, such as the role of environmental stress on reproduction and the potential overproduction of ovules as an evolutionary strategy to deal with seed predation – questions which deserve further research in the future.

Computational pharmacokinetics and in vitro-in vivo correlation of anti-diabetic synergistic phyto-composite blend.

Despite tremendous strides in modern medicine stringent control over insulin resistance or restoration of normoglycemia has not yet been achieved. With the growth of molecular biology, omics technologies, docking studies, and in silico pharmacology, modulators of enzymes and receptors affecting the molecular pathogenesis of the disease are being considered as the latest targets for anti-diabetic therapy. Therapeutic molecular targets are now being developed basing on the up or down regulation of different signaling pathways affecting the disease. Phytosynergistic anti-diabetic therapy is in vogue both with classical and non-classical medicinal systems. However its chemo-profiling, structural and pharmacokinetic validation awaits providing recognition to such formulations for international acceptance. Translational health research with its focus on benchside product development and its sequential transition to patient bedside puts the pharma RDs to a challenge to develop bio-waiver protocols. Pharmacokinetic simulation models and establishment of in vitro-in vivo correlation can help to replace in vivo bioavailability studies and provide means of quality control for scale up and post approval modification. This review attempts to bring different shades highlighting phyto-synergy, molecular targeting of antidiabetic agents via different signaling pathways and bio-waiver studies under a single umbrella.

Magnetic nanotechnology to study and promote axon growth

After injury of the central and peripheral nervous systems, functional recovery is impaired by axon regeneration failure. Various approaches for promoting axon growth have been attempted but their low efficacy has prevented them from being clinically applicable. It is possible that in spite of all the research that has been performed regarding axon growth, we are still missing key aspects of axon growth biology that are essential in order to design effective treatments for axon regeneration. Most of what we know about how an axon grows has been discovered by using tools that delete, add, block, or activate macromolecules in the whole cell and by looking at its corresponding effect on axon growth. Less is known about the spatiotemporal actions of macromolecules and organelles at the growth cone and its relation with axon growth. Macromolecules and organelles are heterogeneously distributed in the cell and their resulting function depends heavily on when and where they exert their actions. We need tools that allow us to manipulate these macromolecules and organelles in a temporal window during which axon growth events are taking place. The development of such tools will provide enhanced knowledge of how an axon grows and lead to design more effective therapies to promote axon growth.

C-2018: Human umbilical vein endothelial cell (HUVEC) response to interrupted cooling in the presence and absence of dimethyl sulfoxide

HUVECs were first successfully cultured in vitro in 1973, initiating the growth of modern vascular biology. Study into HUVEC cryopreservation has made it readily available for purchase, however the cryobiological response of HUVECs has not been fully investigated. Viability by membrane integrity of HUVECs as received from the supplier was 50 ± 2%, indicating that cryopreservation of HUVECs can be improved. Membrane hydraulic conductivity is an osmotic property which is necessary to simulate cryobiological response. HUVEC membrane hydraulic conductivity was measured and found to be 0.147 μm 3 /μm 2 /min/atm at 20 °C, less than fibroblasts and TF-1 cells, therefore being the slowest osmotically-responding cells studied using interrupted cooling. HUVECs were subjected to interrupted slow cooling without hold time (graded freezing) and rapid cooling interrupted with a hold time (two-step freezing) in the presence or absence of 10% Me 2 SO. Preliminary results show that HUVECs have higher viabilities from graded freezing than from two-step freezing, similar to previously studied fibroblasts but different from TF-1 cells. Optimal cooling procedures cannot solely be explained by hydraulic conductivity. Graded freezing at 1 °C/min in the presence of 10% Me 2 SO resulted in the best viability, with almost no damage from direct thaw after cooling to between −5 °C and −40 °C and a maximum of 66% HUVEC membrane integrity after cooling to −35 °C, plunging into liquid nitrogen and then thawing (plunge-thaw). Two-step freezing in the presence of 10% Me 2 SO resulted in almost no damage from direct thaw from as low as −15 °C. Lower experimental hold temperatures resulted in damage after direct thaw and the highest membrane integrity after plunge-thaw was 42% for a hold temperature of −25 °C. Interrupted cooling in the absence of Me 2 SO resulted in no HUVEC membrane integrity after plunge-thaw. The understanding gained from this investigation may lead to improved cryopreservation of HUVECs. Funding: CIHR.

Plasmodium falciparum transfected with ultra bright NanoLuc luciferase offers high sensitivity detection for the screening of growth and cellular trafficking inhibitors.

Drug discovery is a key part of malaria control and eradication strategies, and could benefit from sensitive and affordable assays to quantify parasite growth and to help identify the targets of potential anti-malarial compounds. Bioluminescence, achieved through expression of exogenous luciferases, is a powerful tool that has been applied in studies of several aspects of parasite biology and high throughput growth assays. We have expressed the new reporter NanoLuc (Nluc) luciferase in Plasmodium falciparum and showed it is at least 100 times brighter than the commonly used firefly luciferase. Nluc brightness was explored as a means to achieve a growth assay with higher sensitivity and lower cost. In addition we attempted to develop other screening assays that may help interrogate libraries of inhibitory compounds for their mechanism of action. To this end parasites were engineered to express Nluc in the cytoplasm, the parasitophorous vacuole that surrounds the intraerythrocytic parasite or exported to the red blood cell cytosol. As proof-of-concept, these parasites were used to develop functional screening assays for quantifying the effects of Brefeldin A, an inhibitor of protein secretion, and Furosemide, an inhibitor of new permeation pathways used by parasites to acquire plasma nutrients.

Using chemical genomics to study cell wall formation and cell growth in Arabidopsis thaliana and Penium margaritaceum.

The cell wall is directly involved in cell growth, and its ability to loosen and rearrange allows for cell expansion through the existing turgor pressure. Thus, information on cell wall deposition and rearrangement can provide insights into the overall plant growth. This chapter describes two methods that can be used to evaluate cell expansion (1) in the model plant Arabidopsis thaliana and (2) the model alga Penium margaritaceum. These methods are further used to screen for small molecules that induce cell growth phenotypic changes affecting cell wall. Identification of such small molecules is beneficial due to their posttranslational mechanism of action that can be controlled in a temporal and spatial manner. Chemical genomics has the ability to overcome issues of genetic redundancy and lethality, which can hinder traditional genetic methods. The identification of small molecules in these screens will provide useful information on plant cell wall biology and overall plant growth.