Evolution of a functionally diverse swarm via a novel decentralised quality-diversity algorithm

The inferior colliculus (IC) receives prominent projections from centralized neuromodulatory systems. These systems include extra-auditory clusters of cholinergic, dopaminergic, noradrenergic, and serotonergic neurons. Although these modulatory sites are not explicitly part of the auditory system, they receive projections from primary auditory regions and are responsive to acoustic stimuli. This bidirectional influence suggests the existence of auditory-modulatory feedback loops. A characteristic of neuromodulatory centers is that they integrate inputs from anatomically widespread and functionally diverse sets of brain regions. This connectivity gives neuromodulatory systems the potential to import information into the auditory system on situational variables that accompany acoustic stimuli, such as context, internal state, or experience. Once released, neuromodulators functionally reconfigure auditory circuitry through a variety of receptors expressed by auditory neurons. In addition to shaping ascending auditory information, neuromodulation within the IC influences behaviors that arise subcortically, such as prepulse inhibition of the startle response. Neuromodulatory systems therefore provide a route for integrative behavioral information to access auditory processing from its earliest levels.

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Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences

BMC Research Notes ◽

10.1186/s13104-021-05477-z ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Siddhartha Kundu

Keyword(s):

Amino Acid ◽

Water Molecule ◽

Active Site ◽

Ferrous Iron ◽

Web Server ◽

Protein Sequences ◽

Diverse Group ◽

And Function ◽

Functionally Diverse ◽

Haem Iron

Abstract Objective Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. Results This work reports the implementation of $$Fe\left(2\right)OG$$ F e 2 O G , a web server with dual functionality and an extension of previous work on i2OGdd enzymes $$\left(Fe\left(2\right)OG\equiv \{H2OGpred,DB2OG\}\right)$$ F e 2 O G ≡ { H 2 O G p r e d , D B 2 O G } . $$Fe\left(2\right)OG$$ F e 2 O G , in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. $$Fe\left(2\right)OG$$ F e 2 O G , utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. $$Fe\left(2\right)OG$$ F e 2 O G , also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. $$Fe(2)OG$$ F e ( 2 ) O G , is freely available (http://204.152.217.16/Fe2OG.html) and supersedes all previous versions, i.e., H2OGpred, DB2OG.

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Identification of the Genetic Basis of Response to de-Acclimation in Winter Barley

International Journal of Molecular Sciences ◽

10.3390/ijms22031057 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1057

Author(s):

Magdalena Wójcik-Jagła ◽

Agata Daszkowska-Golec ◽

Anna Fiust ◽

Przemysław Kopeć ◽

Marcin Rapacz

Keyword(s):

Enzyme Activity ◽

Stress Response ◽

Genetic Basis ◽

Differential Expression Analysis ◽

Winter Barley ◽

Developmental Changes ◽

Molecular Regulation ◽

Quantitative Real Time Pcr ◽

Breeding Lines ◽

Functionally Diverse

Mechanisms involved in the de-acclimation of herbaceous plants caused by warm periods during winter are poorly understood. This study identifies the genes associated with this mechanism in winter barley. Seedlings of eight accessions (four tolerant and four susceptible to de-acclimation cultivars and advanced breeding lines) were cold acclimated for three weeks and de-acclimated at 12 °C/5 °C (day/night) for one week. We performed differential expression analysis using RNA sequencing. In addition, reverse-transcription quantitative real-time PCR and enzyme activity analyses were used to investigate changes in the expression of selected genes. The number of transcripts with accumulation level changed in opposite directions during acclimation and de-acclimation was much lower than the number of transcripts with level changed exclusively during one of these processes. The de-acclimation-susceptible accessions showed changes in the expression of a higher number of functionally diverse genes during de-acclimation. Transcripts associated with stress response, especially oxidoreductases, were the most abundant in this group. The results provide novel evidence for the distinct molecular regulation of cold acclimation and de-acclimation. Upregulation of genes controlling developmental changes, typical for spring de-acclimation, was not observed during mid-winter de-acclimation. Mid-winter de-acclimation seems to be perceived as an opportunity to regenerate after stress. Unfortunately, it is competitive to remain in the cold-acclimated state. This study shows that the response to mid-winter de-acclimation is far more expansive in de-acclimation-susceptible cultivars, suggesting that a reduced response to the rising temperature is crucial for de-acclimation tolerance.

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Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1

Nature Communications ◽

10.1038/s41467-021-23876-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Bo Zhang ◽

Diyin Luo ◽

Yu Li ◽

Vanja Perčulija ◽

Jing Chen ◽

...

Keyword(s):

Genome Editing ◽

Dna Cleavage ◽

Binary Complex ◽

Loop Formation ◽

Dna Duplex ◽

Target Dna ◽

Before And After ◽

Dna Strand ◽

Type V ◽

Functionally Diverse

AbstractCas12i is a newly identified member of the functionally diverse type V CRISPR-Cas effectors. Although Cas12i has the potential to serve as genome-editing tool, its structural and functional characteristics need to be investigated in more detail before effective application. Here we report the crystal structures of the Cas12i1 R-loop complexes before and after target DNA cleavage to elucidate the mechanisms underlying target DNA duplex unwinding, R-loop formation and cis cleavage. The structure of the R-loop complex after target DNA cleavage also provides information regarding trans cleavage. Besides, we report a crystal structure of the Cas12i1 binary complex interacting with a pseudo target oligonucleotide, which mimics target interrogation. Upon target DNA duplex binding, the Cas12i1 PAM-interacting cleft undergoes a remarkable open-to-closed adjustment. Notably, a zipper motif in the Helical-I domain facilitates unzipping of the target DNA duplex. Formation of the 19-bp crRNA-target DNA strand heteroduplex in the R-loop complexes triggers a conformational rearrangement and unleashes the DNase activity. This study provides valuable insights for developing Cas12i1 into a reliable genome-editing tool.

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Folding Control in the Path of Type 5 Secretion

Toxins ◽

10.3390/toxins13050341 ◽

2021 ◽

Vol 13 (5) ◽

pp. 341

Author(s):

Nathalie Dautin

Keyword(s):

Protein Folding ◽

Virulence Factors ◽

Secretion System ◽

Gram Negative Bacteria ◽

Secretion Systems ◽

Gram Negative ◽

Final Destination ◽

Cell Compartments ◽

Recent Addition ◽

Functionally Diverse

The type 5 secretion system (T5SS) is one of the more widespread secretion systems in Gram-negative bacteria. Proteins secreted by the T5SS are functionally diverse (toxins, adhesins, enzymes) and include numerous virulence factors. Mechanistically, the T5SS has long been considered the simplest of secretion systems, due to the paucity of proteins required for its functioning. Still, despite more than two decades of study, the exact process by which T5SS substrates attain their final destination and correct conformation is not totally deciphered. Moreover, the recent addition of new sub-families to the T5SS raises additional questions about this secretion mechanism. Central to the understanding of type 5 secretion is the question of protein folding, which needs to be carefully controlled in each of the bacterial cell compartments these proteins cross. Here, the biogenesis of proteins secreted by the Type 5 secretion system is discussed, with a focus on the various factors preventing or promoting protein folding during biogenesis.

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Role of Pirin, an Oxidative Stress Sensor Protein, in Epithelial Carcinogenesis

Biology ◽

10.3390/biology10020116 ◽

2021 ◽

Vol 10 (2) ◽

pp. 116

Author(s):

Francisco Perez-Dominguez ◽

Diego Carrillo-Beltrán ◽

Rancés Blanco ◽

Juan P. Muñoz ◽

Grettell León-Cruz ◽

...

Keyword(s):

Oxidative Stress ◽

Cancer Development ◽

Biological Factors ◽

Epithelial Cancers ◽

Physical Chemical ◽

Sensor Protein ◽

Cupin Superfamily ◽

Functionally Diverse ◽

Light Chain Enhancer

Pirin is an oxidative stress (OS) sensor belonging to the functionally diverse cupin superfamily of proteins. Pirin is a suggested quercetinase and transcriptional activator of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway. Its biological role in cancer development remains a novel area of study. This review presents accumulating evidence on the contribution of Pirin in epithelial cancers, involved signaling pathways, and as a suggested therapeutic target. Finally, we propose a model in which Pirin is upregulated by physical, chemical or biological factors involved in OS and cancer development.

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Neuroprotection resulting from insufficiency of RANBP2 is associated with the modulation of protein and lipid homeostasis of functionally diverse but linked pathways in response to oxidative stress

Disease Models & Mechanisms ◽

10.1242/dmm.004648 ◽

2010 ◽

Vol 3 (9-10) ◽

pp. 595-604 ◽

Cited By ~ 15

Author(s):

K.-i. Cho ◽

H. Yi ◽

N. Tserentsoodol ◽

K. Searle ◽

P. A. Ferreira

Keyword(s):

Oxidative Stress ◽

Lipid Homeostasis ◽

Functionally Diverse

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Nematode Hsp90: highly conserved but functionally diverse

Parasitology ◽

10.1017/s0031182014000304 ◽

2014 ◽

Vol 141 (9) ◽

pp. 1203-1215 ◽

Cited By ~ 4

Author(s):

VICTORIA GILLAN ◽

EILEEN DEVANEY

Keyword(s):

Life Cycle ◽

Heat Shock Protein 90 ◽

Ecological Niches ◽

Actual Number ◽

Host Organism ◽

Free Living ◽

Parasitic Species ◽

Free Living Nematode ◽

Functionally Diverse

SUMMARYNematodes are amongst the most successful and abundant organisms on the planet with approximately 30 000 species described, although the actual number of species is estimated to be one million or more. Despite sharing a relatively simple and invariant body plan, there is considerable diversity within the phylum. Nematodes have evolved to colonize most ecological niches, and can be free-living or can parasitize plants or animals to the detriment of the host organism. In this review we consider the role of heat shock protein 90 (Hsp90) in the nematode life cycle. We describe studies on Hsp90 in the free-living nematode Caenorhabditis elegans and comparative work on the parasitic species Brugia pahangi, and consider whether a dependence upon Hsp90 can be exploited for the control of parasitic species.

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