Pterin-based pigmentation in animals

Pterins are one of the major sources of bright coloration in animals. They are produced endogenously, participate in vital physiological processes and serve a variety of signalling functions. Despite their ubiquity in nature, pterin-based pigmentation has received little attention when compared to other major pigment classes. Here, we summarize major aspects relating to pterin pigmentation in animals, from its long history of research to recent genomic studies on the molecular mechanisms underlying its evolution. We argue that pterins have intermediate characteristics (endogenously produced, typically bright) between two well-studied pigment types, melanins (endogenously produced, typically cryptic) and carotenoids (dietary uptake, typically bright), providing unique opportunities to address general questions about the biology of coloration, from the mechanisms that determine how different types of pigmentation evolve to discussions on honest signalling hypotheses. Crucial gaps persist in our knowledge on the molecular basis underlying the production and deposition of pterins. We thus highlight the need for functional studies on systems amenable for laboratory manipulation, but also on systems that exhibit natural variation in pterin pigmentation. The wealth of potential model species, coupled with recent technological and analytical advances, make this a promising time to advance research on pterin-based pigmentation in animals.

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Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

International Journal of Molecular Sciences ◽

10.3390/ijms21217934 ◽

2020 ◽

Vol 21 (21) ◽

pp. 7934

Author(s):

Thiago Mateus Rosa-Santos ◽

Renan Gonçalves da Silva ◽

Poornasree Kumar ◽

Pratibha Kottapalli ◽

Chiquito Crasto ◽

...

Keyword(s):

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Arable Land ◽

Aluminum Tolerance ◽

Aluminum Stress ◽

Physiological Processes ◽

Aluminum Ions ◽

Detoxification Mechanism ◽

Genomic Studies

Some metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al3+) can be very toxic, especially in acidic soils. Considerable parts of the world’s arable land are acidic in nature; mechanistically elucidating a plant’s response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar.

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Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

10.20944/preprints202010.0158.v1 ◽

2020 ◽

Author(s):

Thiago Mateus Rosa-Santos ◽

Renan Gonçalves da Silva ◽

Poornasree Kumar ◽

Pratibha Kottapalli ◽

Chiquito Crasto ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Aluminum Tolerance ◽

Differentially Expressed ◽

Rna Seq ◽

Aluminum Stress ◽

Physiological Processes ◽

Aluminum Ions ◽

Detoxification Mechanism ◽

Genomic Studies

Sugarcane is an important sugar-source crop. As any other plant, it can be exposed to several abiotic stress conditions. Though some metals contribute to critical physiological processes in plants, the presence of aluminum ions (Al3+) can be very toxic. In order to develop plants that flourish in acidic soils, it is critical to gain insights into the molecular mechanisms of sugarcane response to aluminum stress. To determine the genes involved in sugarcane response to aluminum stress we generated 372 million paired-end RNA sequencing reads, from roots of CTC-2 and RB855453 two contrasting cultivars. Data normalization resulted in 162,161 contigs and 97,335 trinity genes. After the read cutoff, the differentially expressed genes were 4,858 in CTC-2 and 1,307 in the RB855453, Treatment Vs Control, respectively. The differentially expressed genes were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and down regulated in RB855453 (sensitive cultivar). Here, we present the first root-transcriptome of sugarcane under aluminum stress. The results and conclusions of this study provide a valuable resource for future genetic and genomic studies in sugarcane. This transcriptome analysis points out that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with the lateral root formation and activation of redox enzymes. Following our results, we present here, a hypothetical model for the aluminum tolerance in CTC-2 cultivar.

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Extracellular domains play different roles in gap junction formation and docking compatibility

Biochemical Journal ◽

10.1042/bj20131162 ◽

2014 ◽

Vol 458 (1) ◽

pp. 1-10 ◽

Cited By ~ 34

Author(s):

Donglin Bai ◽

Ao Hong Wang

Keyword(s):

Gap Junction ◽

Molecular Mechanisms ◽

Bond Forming ◽

Functional Studies ◽

Extracellular Domains ◽

Physiological Processes ◽

Recent Developments ◽

Non Covalent Interactions ◽

Alignment Analysis ◽

Heterotypic Channels

GJ (gap junction) channels mediate direct intercellular communication and play an important role in many physiological processes. Six connexins oligomerize to form a hemichannel and two hemichannels dock together end-to-end to form a GJ channel. Connexin extracellular domains (E1 and E2) have been shown to be important for the docking, but the molecular mechanisms behind the docking and formation of GJ channels are not clear. Recent developments in atomic GJ structure and functional studies on a series of connexin mutants revealed that E1 and E2 are likely to play different roles in the docking. Non-covalent interactions at the docking interface, including hydrogen bonds, are predicted to form between interdocked extracellular domains. Protein sequence alignment analysis on the docking compatible/incompatible connexins indicate that the E1 domain is important for the formation of the GJ channel and the E2 domain is important in the docking compatibility in heterotypic channels. Interestingly, the hydrogen-bond forming or equivalent residues in both E1 and E2 domains are mutational hot spots for connexin-linked human diseases. Understanding the molecular mechanisms of GJ docking can assist us to develop novel strategies in rescuing the disease-linked connexin mutants.

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An update on the diversity, ecology and biogeography of the Saccharomyces genus

FEMS Yeast Research ◽

10.1093/femsyr/foaa013 ◽

2020 ◽

Vol 20 (3) ◽

Cited By ~ 5

Author(s):

Haya Alsammar ◽

Daniela Delneri

Keyword(s):

Molecular Mechanisms ◽

Current Knowledge ◽

Phenotypic Diversity ◽

Evolutionary Process ◽

Cellular Biology ◽

Natural Environments ◽

Wild Strains ◽

Genomic Studies ◽

History Of ◽

Species Hybrids

ABSTRACT Saccharomyces cerevisiae is the most extensively studied yeast and, over the last century, provided insights on the physiology, genetics, cellular biology and molecular mechanisms of eukaryotes. More recently, the increase in the discovery of wild strains, species and hybrids of the genus Saccharomyces has shifted the attention towards studies on genome evolution, ecology and biogeography, with the yeast becoming a model system for population genomic studies. The genus currently comprises eight species, some of clear industrial importance, while others are confined to natural environments, such as wild forests devoid from human domestication activities. To date, numerous studies showed that some Saccharomyces species form genetically diverged populations that are structured by geography, ecology or domestication activity and that the yeast species can also hybridize readily both in natural and domesticated environments. Much emphasis is now placed on the evolutionary process that drives phenotypic diversity between species, hybrids and populations to allow adaptation to different niches. Here, we provide an update of the biodiversity, ecology and population structure of the Saccharomyces species, and recapitulate the current knowledge on the natural history of Saccharomyces genus.

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Curiosity: A behavioral biology perspective

10.31234/osf.io/rqa5b ◽

2021 ◽

Author(s):

Coltan Scrivner

Keyword(s):

Empirical Work ◽

Psychological Research ◽

Behavioral Biology ◽

History Of Research ◽

Different Types ◽

History Of ◽

Evolutionary Aspects ◽

Rich History ◽

Evolutionary Perspectives

Since Berlyne’s groundbreaking work in the 1960’s, curiosity has been a popular topic for psychological research. Despite a rich history of research, scientists have not been able to agree upon a single definition or taxonomy of curiosity. These diverging perspectives have led to a breadth of research that has yet to be integrated under one framework. Moreover, most research on curiosity has focused on neural mechanisms and ontogenetic characteristics, while the evolutionary aspects of curiosity have received little attention. I propose that research on curiosity can benefit from an evolutionary perspective, and more broadly from a biological perspective on information-gathering behavior. In this chapter, I synthesize the literature on curiosity from the perspective of behavioral biology – i.e., Tinbergen’s four questions. The behavioral biology framework provides a powerful lens through which questions about behavior can be asked and iterative empirical work and theoretical construction can take place. In particular, I argue that evolutionary perspectives on curiosity can help identify the “joints” of nature at which curiosity may be carved. By identifying the function of different types of

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Deubiquitinases: Modulators of Different Types of Regulated Cell Death

International Journal of Molecular Sciences ◽

10.3390/ijms22094352 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4352

Author(s):

Choong-Sil Lee ◽

Seungyeon Kim ◽

Gyuho Hwang ◽

Jaewhan Song

Keyword(s):

Cell Death ◽

Cell Fate ◽

Translational Regulation ◽

Molecular Mechanisms ◽

Regulatory Mechanisms ◽

Therapeutic Targeting ◽

Multiple Modalities ◽

Physiological Processes ◽

Regulated Cell Death ◽

Different Types

The mechanisms and physiological implications of regulated cell death (RCD) have been extensively studied. Among the regulatory mechanisms of RCD, ubiquitination and deubiquitination enable post-translational regulation of signaling by modulating substrate degradation and signal transduction. Deubiquitinases (DUBs) are involved in diverse molecular pathways of RCD. Some DUBs modulate multiple modalities of RCD by regulating various substrates and are powerful regulators of cell fate. However, the therapeutic targeting of DUB is limited, as the physiological consequences of modulating DUBs cannot be predicted. In this review, the mechanisms of DUBs that regulate multiple types of RCD are summarized. This comprehensive summary aims to improve our understanding of the complex DUB/RCD regulatory axis comprising various molecular mechanisms for diverse physiological processes. Additionally, this review will enable the understanding of the advantages of therapeutic targeting of DUBs and developing strategies to overcome the side effects associated with the therapeutic applications of DUB modulators.

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SOME MOLECULAR ASPECTS OF PLANT PEROXIDASE BIOSYNTHETIC STUDIES

10.31234/osf.io/8r3sy ◽

2020 ◽

Author(s):

Lungwani Muungo

Keyword(s):

Early History ◽

Reaction Products ◽

Animal Kingdom ◽

History Of Research ◽

Hydrogen Donors ◽

Different Types ◽

History Of ◽

Molecular Aspects ◽

First Time ◽

Biosynthetic Studies

The early history of research on peroxidase is most capably reviewed bySaunders et al (67). The first color reaction of biological material withguaiacum as substrate was noted in 1809, but the term peroxidase was usedfor the first time nearly a century later for an enzyme isolated from horseradish.In fact, peroxidase is widely distributed in the plant kingdom and also occurs in the animal kingdom. Many of the spectral aspects of this hemoproteinand its reaction products have been described in the above-mentioned textand elsewhere (e.g. 23). Different types of peroxidases were recognized, andan ever-increasing number of functions were ascribed to them, particularly inplant physiology (31). Therefore, while the basic chemical reactions ofperoxidase (E. C . 1.1 1.1. 7) are well established, namely that of the peroxidaticcycle involving H202 and a large array of hydrogen donors (23), the questionsof how its many isozymes function (31) and how its action in differentiation iscontrolled (68) remain largely unanswered. I do not review all publications onthese topics here. A comprehensive tabulation has appeared recently (31).Instead, I offer a critical review of certain aspects of peroxidase in terms ofstructure and biosynthesis.

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