Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes

Kang, Zhen; Zhang, Junli; Jin, Peng; Yang, Shuli

doi:10.1080/21655979.2015.1011029

Cited by 20 publications

(7 citation statements)

References 40 publications

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“…This is consistent with their sense organs being poorly compatible with terrestrial locomotion (small eyes, small semicircular canals; [ 20 ]). Both sedimentological and isotopic evidence suggests that remingtonocetids lived in coastal marine environments [ 6 , 10 , 21 ]. The specimens of Remingtonocetus domandaensis Gingerich et al, [ 22 ] that we analyze here came from the early middle Eocene (middle Lutetian) of Pakistan.…”

Section: Introductionmentioning

confidence: 99%

Transition of Eocene Whales from Land to Sea: Evidence from Bone Microstructure

et al. 2015

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Cetacea are secondarily aquatic amniotes that underwent their land-to-sea transition during the Eocene. Primitive forms, called archaeocetes, include five families with distinct degrees of adaptation to an aquatic life, swimming mode and abilities that remain difficult to estimate. The lifestyle of early cetaceans is investigated by analysis of microanatomical features in postcranial elements of archaeocetes. We document the internal structure of long bones, ribs and vertebrae in fifteen specimens belonging to the three more derived archaeocete families — Remingtonocetidae, Protocetidae, and Basilosauridae — using microtomography and virtual thin-sectioning. This enables us to discuss the osseous specializations observed in these taxa and to comment on their possible swimming behavior. All these taxa display bone mass increase (BMI) in their ribs, which lack an open medullary cavity, and in their femora, whereas their vertebrae are essentially spongious. Humeri and femora show opposite trends in microanatomical specialization in the progressive independence of cetaceans from a terrestrial environment. Humeri change from very compact to spongious, which is in accordance with the progressive loss of propulsive role for the forelimbs, which were used instead for steering and stabilizing. Conversely, hind-limbs in basilosaurids became strongly reduced with no involvement in locomotion but display strong osteosclerosis in the femora. Our study confirms that Remingtonocetidae and Protocetidae were almost exclusively aquatic in locomotion for the taxa sampled, which probably were shallow water suspended swimmers. Basilosaurids display osseous specializations similar to those of modern cetaceans and are considered more active open-sea swimmers. This study highlights the strong need for homologous sections in comparative microanatomical studies, and the importance of combining information from several bones of the same taxon for improved functional interpretation.

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Section: Introductionmentioning

confidence: 99%

Transition of Eocene Whales from Land to Sea: Evidence from Bone Microstructure

et al. 2015

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“…Some strains were relevance to serious illness such as ribo-type 176, 244, 27, 17, 78 by encoding or destroying genes for different enzymes [ 14 ]. While as the separation of more detailed strains with the technology advances, it seems to be more diversification than previously record [ 34 , 35 ]. But no reports related to serious diseases found till now.…”

Section: Resultsmentioning

confidence: 99%

Complete genome sequence of the Clostridium difficile LCL126

et al. 2021

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Clostridium difficile (C. difficile) is a kind of obligate anaerobic gram-positive Bacillus related with intestinal diseases and antibiotic treatment. In present study, the C. difficile genome was studied employing met genomic technology. Genome sequencing identified C. difficile LCL126 has total size of 4,301,949 bp with a 27.97% of GC content. Specifically, 4119 predicted coding genes, 188 repeat sequences, 13 prophages and 8 gene islands were detected. Additionally, gene function analysis aspect of the function annotation, effector, and virulence were concluded that total of 3367 cluster of orthologous groups of proteins genes and classified into 24 categories, while the most outstanding class was metabolic process (1533) and catalytic activity (1498). The carbohydrate-active enzymes have been detected 127 genes, pathogenicity analysis revealed that 133 reduced and 22 increased virulence (hypervirulence) genes, while 54 unaffected and 10 loss of pathogenicity genes were found. Furthermore, perform the visualization and methylation expression were revealed that the dominant types comprised m4C, m5C, and m6C with the number of 6989, 36,666, and 3534, respectively. Overall, whole genome sequence information of C. difficile LCL126 was obtained and functional prediction was revealed its possible toxicological potential genes existence.

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“…With modular design and minute-scale temporal resolution, FLARE offers an important system in neuroscience to measure responses to inputs as varied as calcium channels and engineered ligand-receptor pairs, finding numerous approaches that extend even beyond Ca 2+ to result in transcription factor release [195]. These advances can be accelerated with implementation of synthetic biology strategies for directed evolution of proteins (see review by Kang et al [196]), which must involve detailed biochemical and biophysical characterization complemented by computational strategies to reduce the costs of empirical optimization [197].…”

Section: Calcium-dependent Transcription Factorsmentioning

confidence: 99%

Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology

Saha

2021

Biomolecules

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Since the 1970s, the emergence and expansion of novel methods for calcium ion (Ca2+) detection have found diverse applications in vitro and in vivo across a series of model animal systems. Matched with advances in fluorescence imaging techniques, the improvements in the functional range and stability of various calcium indicators have significantly enhanced more accurate study of intracellular Ca2+ dynamics and its effects on cell signaling, growth, differentiation, and regulation. Nonetheless, the current limitations broadly presented by organic calcium dyes, genetically encoded calcium indicators, and calcium-responsive nanoparticles suggest a potential path toward more rapid optimization by taking advantage of a synthetic biology approach. This engineering-oriented discipline applies principles of modularity and standardization to redesign and interrogate endogenous biological systems. This review will elucidate how novel synthetic biology technologies constructed for eukaryotic systems can offer a promising toolkit for interfacing with calcium signaling and overcoming barriers in order to accelerate the process of Ca2+ detection optimization.

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Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes

Abstract: (2015) Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes, Bioengineered, 6:3,[136][137][138][139][140]

Cited by 20 publications

References 40 publications

Transition of Eocene Whales from Land to Sea: Evidence from Bone Microstructure

Transition of Eocene Whales from Land to Sea: Evidence from Bone Microstructure

Complete genome sequence of the Clostridium difficile LCL126

Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology

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