Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

1. Introduction and Overview. 2. Detecting Influential Observations and Outliers. 3. Detecting and Assessing Collinearity. 4. Applications and Remedies. 5. Research Issues and Directions for Extensions. Bibliography. Author Index. Subject Index.

Regression Diagnostics: Identifying Influential Data and Sources of Collinearity

Positive ions that are available in soils absorb on grain surfaces. The total sum of cations that can be absorbed bij a soil/sediment at a certain PH is defined by the cation-exchange capacity (CEC, in meq g-1: mol equivalents per gram). The uptake of cations is an important parameter in agriculture and the larger the CEC, the more cations can be absorbed to the soil. The CEC depends highly on the pH of soil and sediments, where the CEC decreases with decreasing PH (increasing acidity). The exchange of ions on sediments occurs commonly fast on geological time scales, but the kinetics of adsorption in natural environments is still poorly understood. The strength of the bonding between the cations and the sediments varies from weak Van der Waals bondings (physical adsorption) to strong chemical bonds. The CEC is widely used for agricultural assessment because it is a measure of general soil fertility as well as an indicator of structural stability because CED is capabel of enhancing development of shrinkage cracks. The list below shows the CEC for different types of minerals. The data indicate that the CEC can vary over 2 orders of magnitude for various types of , minerals and can vary one order of magnitude within one soil type. Cation exchange capacity for different types of sediment (Eisma, 1992; Locher and de Bakker, 1990):

Cation exchange capacity.

Differentiation and secondary metabolism are correlated processes in fungi that respond to light. In
Aspergillus nidulans
, light inhibits sexual reproduction as well as secondary metabolism. We identified
the heterotrimeric
velvet
complex VelB/VeA/LaeA connecting light-responding developmental
regulation and control of secondary metabolism. VeA, which is primarily expressed in the dark,
physically interacts with VelB, which is expressed during sexual development. VeA bridges VelB to the
nuclear master regulator of secondary metabolism, LaeA. Deletion of either
velB
or
veA
results in
defects in both sexual fruiting-body formation and the production of secondary metabolites.

VelB/VeA/LaeA Complex CoordinatesLight Signal with Fungal Developmentand Secondary Metabolism

Legumes and many nonleguminous plants enter symbiotic interactions with microbes, and it is poorly understood how host plants respond to promote beneficial, symbiotic microbial interactions while suppressing those that are deleterious or pathogenic. Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide (nt) "phased" intervals, a pattern formed by DICER-LIKE 4 (DCL4) processing. A search for phased siRNAs (phasiRNAs) found at least 114 Medicago loci, the majority of which were defense-related NB-LRR-encoding genes. We identified three highly abundant 22-nt microRNA (miRNA) families that target conserved domains in these NB-LRRs and trigger the production of trans-acting siRNAs. High levels of small RNAs were matched to >60% of all ∼540 encoded Medicago NB-LRRs; in the potato, a model for mycorrhizal interactions, phasiRNAs were also produced from NB-LRRs. DCL2 and SGS3 transcripts were also cleaved by these 22-nt miRNAs, generating phasiRNAs, suggesting synchronization between silencing and pathogen defense pathways. In addition, a new example of apparent "two-hit" phasiRNA processing was identified. Our data reveal complex tasiRNA-based regulation of NB-LRRs that potentially evolved to facilitate symbiotic interactions and demonstrate miRNAs as master regulators of a large gene family via the targeting of highly conserved, protein-coding motifs, a new paradigm for miRNA function.

microRNAs as Master Regulators of the Plant NB-LRR Defense Gene Family via the Production of Phased, Trans-acting siRNAs

Melatonin is a multifunctional signaling molecule, ubiquitously distributed in different parts of plants and responsible for stimulating several physiological responses to adverse environmental conditions. In the current review, we showed that the biosynthesis of melatonin occurred in plants by themselves, and accumulation of melatonin fluctuated sharply by modulating its biosynthesis and metabolic pathways under stress conditions. Melatonin, with its precursors and derivatives, acted as a powerful growth regulator, bio-stimulator, and antioxidant, which delayed leaf senescence, lessened photosynthesis inhibition, and improved redox homeostasis and the antioxidant system through a direct scavenging of reactive oxygen species (ROS) and reactive nitrogen species (RNS) under abiotic and biotic stress conditions. In addition, exogenous melatonin boosted the growth, photosynthetic, and antioxidant activities in plants, confirming their tolerances against drought, unfavorable temperatures, salinity, heavy metals, acid rain, and pathogens. However, future research, together with recent advancements, would support emerging new approaches to adopt strategies in overcoming the effect of hazardous environments on crops and may have potential implications in expanding crop cultivation against harsh conditions. Thus, farming communities and consumers will benefit from elucidating food safety concerns.

https://www.mdpi.com/1422-0067/20/5/1040/pdf

Melatonin Mediates Enhancement of Stress Tolerance in Plants

Carbon Catabolite Repression (CCR) has fascinated scientists and researchers around the globe for the past few decades. This important mechanism allows preferential utilization of an energy-efficient and readily available carbon source over relatively less easily accessible carbon sources. This mechanism helps microorganisms to obtain maximum amount of glucose in order to keep pace with their metabolism. Microorganisms assimilate glucose and highly favorable sugars before switching to less-favored sources of carbon such as organic acids and alcohols. In CCR of filamentous fungi, CreA acts as a transcription factor, which is regulated to some extent by ubiquitination. CreD-HulA ubiquitination ligase complex helps in CreA ubiquitination, while CreB-CreC deubiquitination (DUB) complex removes ubiquitin from CreA, which causes its activation. CCR of fungi also involves some very crucial elements such as Hexokinases, cAMP, Protein Kinase (PKA), Ras proteins, G protein-coupled receptor (GPCR), Adenylate cyclase, RcoA and SnfA. Thorough study of molecular mechanism of CCR is important for understanding growth, conidiation, virulence and survival of filamentous fungi. This review is a comprehensive revision of the regulation of CCR in filamentous fungi as well as an updated summary of key regulators, regulation of different CCR-dependent mechanisms and its impact on various physical characteristics of filamentous fungi.

https://www.mdpi.com/1422-0067/19/1/48/pdf

Carbon Catabolite Repression in Filamentous Fungi

Plant defense against fungal pathogens by antagonistic fungi with Trichoderma in focus.

The diamondback moth (DBM), Plutella xylostella (Lepidoptera: Plutellidae) is a very destructive crucifer-specialized pest that has resulted in significant crop losses worldwide. DBM is well attracted to glucosinolates (which act as fingerprints and essential for herbivores in host plant recognition) containing crucifers such as wintercress, Barbarea vulgaris (Brassicaceae) despite poor larval survival on it due to high-to-low concentration of saponins and generally to other plants in the genus Barbarea. B. vulgaris build up resistance against DBM and other herbivorous insects using glucosinulates which are used in plant defense. Aside glucosinolates, Barbarea genus also contains triterpenoid saponins, which are toxic to insects and act as feeding deterrents for plant specialist herbivores (such as DBM). Previous studies have found interesting relationship between the host plant and secondary metabolite contents, which indicate that attraction or resistance to specialist herbivore DBM, is due to higher concentrations of glucosinolates and saponins in younger leaves in contrast to the older leaves of Barbarea genus. As a response to this phenomenon, herbivores as DBM has developed a strategy of defense against these plant biochemicals. Because there is a lack of full knowledge in understanding bioactive molecules (such as saponins) role in plant defense against plant herbivores. Thus, in this review, we discuss the role of secondary plant metabolites in plant defense mechanisms against the specialist herbivores. In the future, trials by plant breeders could aim at transferring these bioactive molecules against herbivore to cash crops.

https://www.mdpi.com/1420-3049/24/11/2067/pdf

Role of Saponins in Plant Defense Against Specialist Herbivores

Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.

https://www.mdpi.com/1422-0067/19/2/515/pdf

Waqar Islam

Papers

Melatonin Mediates Enhancement of Stress Tolerance in Plants

Carbon Catabolite Repression in Filamentous Fungi

Plant defense against fungal pathogens by antagonistic fungi with Trichoderma in focus.

Role of Saponins in Plant Defense Against Specialist Herbivores

Plant Responses to Pathogen Attack: Small RNAs in Focus