Ribonucleic acid (RNA) quantification is an essential technique in biology. There has been remarkable progress in RNA quantification techniques over the recent years; however, the specificity of these techniques to quantify a very small amount of RNA is doubtful because of factors which can inhibit precise quantification. To develop a technique that leads to the most sensitive RNA quantification, these problems must be overcome. In this article, we first review the factors that inhibit precise quantification of RNA: the quality of RNA, secondary structure of RNA, efficiency of the enzyme reaction, annealing conditions, limitations of the experimental protocol and equipment, and detection sensitivity of the equipment. Next, we discuss the possible methods which contribute to these factors: RNA quality control focused on target RNA degradation, isothermal amplification, techniques for avoiding amplification errors, RNase H-dependent PCR, targeting using a fluorescent-labeled probe, targeting using a padlock probe, bridged/locked nucleic acid (BNA/LNA) and peptide nucleic acid (PNA), and the clustered regularly interspaced short palindromic repeat (CRISPR) system. One of the goals for the development of an ultrasensitive RNA quantification technique is the absolute quantification of RNA. Here, we discuss the techniques used for this type of RNA quantification.

Citrus ‘Harumi’ is a mandarin-type cultivar and shows a wide range of fruit size, which affects fruit quality such as sugar and acid contents. In citrus, fruit size also affects the degree of physiological disorder which become a big problem during storage. Thus, making fruit with equal and appropriate size is very important. Fruit thinning is one of the most important techniques to adjust fruit size by controlling the fruit number. Basically, fruit thinning has been conducted using a criterion based on leaf and fruit ratio (L/F) or fruit number per canopy volume. In this review, several thinning criteria for ‘Harumi’ and other citrus varieties are compared, and the pros and cons are discussed. In some citrus varieties, storage is necessary to adjust shipping time. During the storage, some physiological disorders occurred in peel, flesh and whole fruit. The occurrence of physiological disorders was influenced by citrus variety, fruit size and environmental conditions during storage. In ‘Harumi’ which is classified to easy-peeling variety, small fruit showed serious weight loss and peel wrinkle, while rind puffing and dehydration of flesh were big problems in large fruit during storage. Polyethylene (PE) bag wrapping has been used to decrease the fruit weight loss and to prevent the occurrence of some physiological disorders in tight-skin citrus varieties. However, the influences of PE wrapping on easy-peeling citrus is unclear. In this study, the researches on storage conditions, feature, and cause of physiological disorders during storage are also reviewed, and the effects of PE wrapping are discussed to improve storage condition in ‘Harumi’.

The Fusarium fujikuroi species complex (FFSC) is a cosmopolitan fungal lineage with production of a broad spectrum of secondary metabolites including mycotoxins, pigments and plant hormones. The FFSC includes many important plant pathogens. Fusarium fujikuroi, a member of the FFSC, causes rice bakane disease and has been recognized as the exclusive gibberellin (GA) producer for a long time. However, other species such as Fusarium proliferatum, Fusarium sacchari and Fusarium konzum in the FFSC were also identified to produce GA in recent 20 years. GA biosynthesis is conferred by a gene cluster including 7 adjacent genes (GA gene cluster). Expression of the GA genes is activated under limited nitrogen conditions. GA low- or non-production in most FFSC species was revealed to attribute to a partial deletion of the GA gene cluster, malfunction or low expression of the GA genes although the cause has not been fully elucidated. It has been reported that transcriptional factors, signaling components, global regulators and histone modification are involved in regulation of the GA gene expression.

Fumonisin is a worldwide mycotoxin that has devastating implications for human and animal health and food security. The principal source of fumonisin contamination is the members of the Fusarium fujikuroi species complex (FFSC). A cluster (FUM gene cluster) of 16 co-expressed genes (FUM) responsible for fumonisin biosynthesis has been identified and characterized in Fusarium verticillioides. The FUM gene cluster has been detected from other members of the FFSC. In this review, the fumonisin production ability and the status of the FUM gene cluster in 3 clades (African, American, and Asian) of the FFSC have been presented. The comprehensive studies revealed that intraspecific variation is caused by several types of mutations in the FUM gene cluster. In addition, we summarized the regulatory genes involving fumonisin biosynthesis. A comparative study of fumonisin production ability and regulatory mechanism of fumonisin biosynthesis provides valuable insight for control of the mycotoxin contamination.

Agriculture plays an important role in Indonesia, but it is often neglected by various parties. As a result, farmers face many problems particularly when it comes to selling their products. The solution is to strengthen the agricultural institutions, especially the auction market. This institution has proven to provide many benefits for all parties. Farmers' products are sold in large quantities at high prices and strengthen the existence of farmer groups. Consumers also get high-quality products while the industry will get a continual supply of raw materials. For the economy, the auction market has been shown to improve agricultural trade efficiency and contribute to government revenue. However, the auction market's performance is still not optimal due to ack of rigorous rules, lack of quantity and quality human resources, lack of funds and infrastructure, competition with traders, and weak support from other parties. The auction market needs to make a good collaboration with suppliers, buyers, financial institutions, and the government.

Mounting evidence elucidates the impact of gut microbiota on the maintenance of host’s physical and psychological conditions. The gut microbiota can produce its effects through neural, endocrine, and immune pathways. Specific gut members, such as lactobacilli and bifidobacteria, have shown unique abilities to affect the host’s mental health, and hence, they are called psychobiotics. Several studies, on both rodents and humans, have confirmed the role of Bifidobacterium in the regulation of anxiety, mood, cognition, and pain. Here, we summarize the currently available evidence that suggests the roles of bifidobacteria in gut microbiota–brain communication and highlight the prospects of this research field. The action of Bifidobacterium has been found to be strain specific. We discuss here the currently reported mechanisms of action of different Bifidobacterium strains. However, more strategic investigations are needed to fully understand the detailed mechanisms of action of Bifidobacterium as psychobiotic bacteria.

Food insecurity throughout Sub-Saharan African countries is a common problem and needs a sustainable solution to improve crop yield production, rather than agricultural area expansion. Vegetables are important in sustaining the livelihood of many small-scale and subsistence farmers throughout Sub-Saharan African and contain vitamins, minerals, and essential amino acids, none has cholesterol and most are low in fat and calories. Vegetables also high in fiber, which helps keep the digestive system healthy. Vegetable production in Sub-Saharan Africa faces numerous agronomic constraints that will have to be overcome to feed the increasing population and to fight malnutrition. Major areas on the continent consequently experience nutrient limitation as a major yield gap component, especially in densely populated areas. Now a day one possible solution may come from insect farming, a growing industry with broad potential. Black soldier fly (Hermetia illucens L) feces (frass) may have great potential as a valuable organic bio-fertilizer by positively affecting soil fertility and ultimately vegetable yields. However, the understanding of this positive effect of frass is still limited in our community and very few researchers are trying to determine the effects of this bio-fertilizer on vegetable growth and soil fertility amendment and to explore the utilization of this waste product as a novel organic bio-fertilizer. As nitrogen and phosphorus uptake observed in plots treated with black soldier fly frass fertilizer compared to plots treated with the commercial organic and mineral fertilizers could be attributed to better supply and availability of nutrients from the newly introduced frass fertilize. Clearly black soldier fly frass fertilizer performed better than commercial and inorganic fertilizer. Therefore, further study and awareness creation should be conducted to promote the feasibility of black soldier fly frass bio-fertilizer application in vegetable production and its role in soil fertility amendment.

The use of synthetic chemicals has increased drastically due to industrialization and urbanization. However, the long-term and indiscriminate use of these chemicals has a negative impact on environment and human health; thus, public concerns about the hazardous effects of such synthetic chemicals are increasing day by day. To solve these problems, the exploitation of potential alternatives has become a major challenge, and the admiration of beneficial microbes is increasing due to their safe and environment-friendly nature. Microbes can mitigate the hazardous effects of synthetic chemicals by reducing their use and toxicity. Lysinibacillus species are gram-positive, spore-forming, motile bacteria. This genus was previously designated as Bacillus spp. under the family Bacillaceae of the phylum Firmicutes. For a long period of time, Lysinibacillus is well-known for its insecticidal activity against various insects, including mosquitoes, which are the vector of several human diseases. In addition, some Lysinibacillus species have a potential for heavy metal remediation. In recent years, Lysinibacillus spp. are attracting the researchers’ attention as plant growth-promoting and disease control agents, which would be used as alternatives to agrochemicals. This study gives an overview of the entomopathogenic, bioremediation, plant growth-promoting, and biological disease control abilities of the genus Lysinibacillus.

Metabolism, which is a flow of metabolites, is orchestrated by gene expression, and it is in turn regulated by metabolites. Some of the metabolites are known to act as signaling molecules that regulate metabolism and also developmental processes in plants. Here we summarize findings about metabolites-directed gene regulation, focusing on primary metabolites including sugars and organic acids. Abundant soluble sugars such as sucrose and glucose are known to induce genes involved in starch storage, synthesis and degradation. These sugars also activate anthocyanin biosynthesis and suppress photosynthetic genes, both of which promote photoprotection responses. Several kinases, like hexokinase, sucrose non-fermenting1-related kinase 1 and target of rapamycin kinase have been identified, which are the major regulators of transcriptional regulation by these sugars. Although less studied than sugars, metabolites constituting the TCA cycle are good candidates of signaling molecules, because they are located in the primary metabolism adjacent to the respiratory electron transport system and thus are reflected by both primary metabolism and redox status of the electron transport system. Some organic acids as citrate, malate and 2-oxoglutarate have also been known to be implicated in the regulation of gene expression. Deficiency or over accumulation of some primary metabolites not only modulate gene expression of the local metabolic enzymes to supplement distorted metabolism but produce signals to balance between bigger metabolic blocks like carbon and nitrogen metabolisms. Status of primary metabolites can also produce signals of overall energy levels of plants. Relationship of sugar signaling to reactive oxygen species signaling is also suggested.

The subject of livelihood dynamics in montane mainland Southeast Asia has been widely discussed by many researchers. Globalization that takes place through changes in the political system has most impacts on the diversity of livelihoods of rural communities. However, there are few studies of diversity in the field, and most focus on sectoral shifts and financial activities. We conducted an overview of the historical dynamics of rural livelihoods and its diversification, and used various indices to measure diversification. To reveal the complex diversity of rural livelihoods it is necessary to understand the general situation and patterns of livelihood diversification. This article highlights the diverse livelihood dynamics from two viewpoints of livelihood diversification; distress and progressive diversification, and case studies that can support these dynamics to illustrate the process of livelihood diversification and discuss the direction of the pattern of diversification to provide information for future research. This study suggested intensified focus on livelihood diversification to promote sustainable development in this region.

As the demand for local products increases, there has been a call to promote sago starch (Metroxylon sagu Rottb.) at the regional level in Indonesia. In this study, we examine the current status of the sago supply chain and its role in promoting rural development. Our study reveals the weak bargaining position sago farmers have due to inefficiencies in the sago supply chain and lack of market information. Furthermore, we also point out the direction in which future actions should be taken as guidelines in order to achieve a high level of efficiency along the sago supply chain. In particular, we highlight farm production management, logistical systems, agronomy, and knowledge and information as key dimensions of sago supply chain in the context of rural development.

Environmental pollution is one of the most critical issues concerning the quality of the environment and threatens the human safety due to bioaccumulation. The extensive application of pesticides causes great public concern about the negative impacts on the environment and human health. Herbicides have been used for weed management and to prevent the yield loss of agricultural products. In recent years, the environment’s quality is extensively considered due to the enormous pesticide application in agroecosystems. There are some different pathways for the degradation of herbicides in the environment, including biodegradation, chemical degradation, photodegradation, uptake by target or non-target plants, adsorption to soil particles and leaching. Assessing the environmental risks of herbicides before mass production, commercialization, and distribution is very important. The presence of herbicide residues in the environment has become a fundamental problem in many countries. Bioassay and analytical methods could identify, detect, and quantify herbicide residues in the environment. In this review paper, the fate, detection methods, and effect of herbicides on non-target plants have been discussed.

Sesbania species grow mainly in tropical and subtropical regions of the world as multipurpose legume crops. These are very important part of sustainable agriculture and also for diverse industrial or other uses. But their production has compromised due to lack of interest among farmers and presence of constraints, rendering it appropriate to use as a food crop. Improvement has lagged in Sesbania species because of the unavailability of the gene pool, along with self-incompatibility in closely related species. Lacunae in improvement of its species could overcome with the help of biotechnological tools that could transfer genes in distantly related species, too. Mostly, an efficient and reproducible regeneration system is a prerequisite for efficient transgenic plant production. However, progress has made towards invitro regeneration in various Sesbania species such as S. bispinosa, S. grandiflora, S. sesban using hypocotyl explants and using cotyledonary node explants in S. drumondii and S.rostrata. Considerable success has also been obtained in plant regeneration via somatic embryos in S. sesban and via protoplasts in S. bispinosa. But, till date only in S. drumondii one report on generation of transgenic plants is available, where T0 plants have been obtained using cotyledonary node explants. In this regard, the current paper highlights the in vitro regeneration and genetic transformation protocols developed so far in Sesbania species along with future directives towards improvement of this important genus.

Indonesia experiences various disasters that affect human life in the economic and social aspects. Those disasters also affect the agriculture sector, and farmers have to face destroyed land and crop loss. The lives of farmers become more vulnerable. This paper presents the various disasters in Indonesia that affect agriculture, how the farmers’ lives get affected, and how the farmers cope with the impacts of the disasters with various mitigation strategies. Management of disaster risk reduction is being conducted by farmers with their local wisdom such as using predicting climate change with pranata mangsa in Java, and applying pikukuh for earthquake resistant house construction in Badduy Tribe. It is supported by the relevant stakeholders that, time by time, gets more support with advanced sciences. Farmers do have their own ways to cope with disasters, but other parties’ involvement is needed to make disaster risk reduction management more effective such as through education or direct and indirect aids. Farmers cannot work along for the disaster mitigation, therefore good inter stakeholder coordination is needed.

Bakanae disease, caused by Fusarium fujikuroi, is a serious problem in rice production. This disease is widespread across the world and leads to substantial yield losses. F. fujikuroi is known to produce various secondary metabolites, including the plant hormone gibberellin, which induces typical bakanae symptoms. In this article, authors overviewed the methods for controlling bakanae disease, including the use of host resistance, chemical compounds, biocontrol agents, natural products, and physical methods. Although various strategies have been applied to control bakanae disease, the disease is not yet completely prevented. Authors discuss the advantages and disadvantages of these various methods. In addition, the mode of action of major fungicides and the resistance mechanisms to these fungicides were outlined. These information contribute to the development of more effective methods for controlling bakanae disease.

In West Africa (WA), there are high rates of poverty, population growth rate and food insecurity, and most agricultural productions are conducted at mostly an un-mechanized level, with almost a complete reliance on rain-fed conditions. This review provides an overview of climate change across WA and its impacts on key horticultural crop groups (vegetables, plantations, fruits, roots and tubers). The review also identifies areas within WA where these crops may be more or less vulnerable to changing climatic conditions. Empirical studies using climate change models were synthesized and analyzed for reliable future climate projection effects on the production of region horticultural crops. The two climatic variables likely to have the greatest effects on the horticultural crops in the region are temperature and precipitation, with the latter considered to be of superior influence. As climate change continues to intensify with time, so does its impact on rain-fed horticulture. The study showed that the Sahel areas of the region would be the most affected and that horticulture production in that part would be significantly impacted. The study found that the impact of climate change on the WA region is not uniform across the different ecosystems. Therefore, its effects on horticultural crops will also differ across the region: in some areas, the crop yields would increase, while in others it might decrease depending on the type of plant and the ecology being considered. This creates an urgent need to understand and synthesize the responses of horticultural crops to climate change and identify adaptation options. Adaptation actions and strategies are all discussed, education, the introduction of new cultivars, the development of effective cropping systems, the transference of skills from other regions, and the expansion of farmer-government-NGO collaborations.

The water-soluble dietary fiber, pectin, is a polysaccharide present in the cell wall of terrestrial plants. It is a polymer of d-galacturonic acid polymerized by alpha-1,4 linkages and has side chains composed of 13 different sugars. Due to its complex chemical structure, pectin has a number of physical characteristics, including gelling properties and viscosity, and has physiological functions in vivo. The degree of esterification of the pectin main chain affects gelling. In addition, the side chain structure has been shown to affect antitumor activity and regulation of intestinal immunity, which are well-known physiological functions of pectin, and the rhamnogalacturonan-I region is particularly important. This review discusses the correlations between the molecular structure of pectin and its functions. Not only that, we will discuss the mechanisms and physiological significance of small intestinal villus morphological changes, which is still a mysterious function of pectin.

The status of chocolate as functional food is still questionable for some other people as chocolate can also give some adverse effect due to its high fat and sugar content. To overcome this issue, some attempts have made by food scientist to produce chocolate with high potential health benefits and minimum adverse effects such as by fat reduction, sugar replacement and probiotic supplementation. Some of sugar replacer are providentially identified as prebiotic substances. This review, therefore, deeply discuss the potential use of probiotics and sugar replacer in chocolate. The health benefit as well as the effect on the consumer acceptance are also covered as chocolate reformulation may result in the alteration on the chocolate characteristic. Moreover, the regulation in chocolate manufacturing and functional food from different regulatory boards are covered in this review as the guidelines to answer challenges and opportunities in developing functional chocolate. This review also clearly shows a possible direction of designing probiotic chocolate in the future that has not been fully explored until to date.

Water is an essential input for agricultural development and irrigated agriculture. However, groundwater reliance is rising due to lack of canal water and is often inferior quality, costly, scarce, and ultimately expensive for smallholders. Moreover, as hunger rises daily due to population growth, additional irrigation water systems are needed to extend the cropping patterns. Therefore, wastewater (WW) use in agriculture has been increased on a growing scale over the last decades due to its fertilizing capacity and decrease in canal water and freshwater availability. It enhances soil productivity by contributing organic matter contents and preserves water and nutrients for plants. Various traditional treatments such as primary, secondary, and tertiary treatments are being used, but more working is required due to health and environmental issues. Therefore, the end product of tertiary treatments could be mixed with different water sources (for dilution), phytoremediator plants in channels and use of microbes that eat waste food could be adopted because the maximum crop yield is primarily determined by water quality, as well as climatic conditions, water management practices, chemical and physical soil properties. Besides, we can minimize the all-potential risks associated with agricultural activities and production via strengthened strategies, systemic dialogues, and financial frameworks. The present review discusses WW irrigation are that it provides a safer water source to the farmers and has the beneficial elements of providing essential plant nutrients after treatment and environmental sustainability.

This paper talks about the constraints of ginger farming and its future perspective in Fiji. Ginger is recognized as a significant product in Fiji due to the potential the crop has for food, income benefit, and providing work to the farmers. However, the industry is facing many drawbacks. The main ginger farming constraints in Fiji viz. access to quality planting material, access to water, loss of expertise, soil-borne pathogens like Pythium soft rot and nematodes infestation, pest infestation whereby the presence of scale insect intercepts with the requiring quarantine interventions, unsatisfactory result of pre-planting hot water dip treatment, land and differentiation in rural Fiji (Land tenure) and exporting fresh ginger to high market prices explains how the local ginger produced are not attaining high niche markets.

Waste disposal is a serious global environmental threat resulting in heavy metal pollution. Contaminated soil with heavy metals has become a concern for agricultural scientists because of the progress made in agricultural product safety. Heavy metals are metalloids with biological toxicity. The most common are arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), lead (Pb), and zinc (Zn). These metals exist throughout the terrestrial environment and produced from anthropogenic and natural activities. Recently, the landfills have been reported as persecutor to soil contamination, but still, there is no promising way proposed for the waste disposal management in some developing countries. This is the biggest threat to the soil, crops, and the communities living around the dumpsites. Soil polluted with heavy metals result in human health risks, groundwater pollution, plant phytotoxicity and decline in crop and soil production. Absorption of heavy metals through plant roots is the major pathway in which heavy metals penetrate the food chain and their successive crowding along the food chain is a critical threat to animal and human health. The previous findings reported that soil, vegetables, and other food crops around dumpsites are contaminated with heavy metals. The soil contaminated with heavy metals is a leading cause of vegetables and other crops contamination, which is a cause of adverse health outcomes in developing countries’ cities. Therefore, there is an urgent need for continuous monitoring of heavy metals in different open dumpsites. The necessary measures to reduce the high concentration of heavy metals in the soil and crops should be put in place. This paper aimed to review the harmful impacts of heavy metal contamination to the soil and crops grown in the vicinity of dumpsites, but also several techniques treating heavy metals pollution in the soil were discussed in this review.