Biotechnology has almost unlimited potential to change our lives in very exciting ways. Many of the chemical reactions that produce these products can be fully optimized by performing them at ...extremes of temperature, pressure, salinity, and pH for efficient and cost-effective outcomes. Fortunately, there are many organisms (extremophiles) that thrive in extreme environments found in nature and offer an excellent source of replacement enzymes in lieu of mesophilic ones currently used in these processes. In this review, I discuss the current uses and some potential new applications of extremophiles and their products, including enzymes, in biotechnology.
Despite the typical human notion that the Earth is a habitable planet, over three quarters of our planet is uninhabitable by us without assistance. The organisms that live and thrive in these ..."inhospitable" environments are known by the name extremophiles and are found in all Domains of Life. Despite our general lack of knowledge about them, they have already assisted humans in many ways and still have much more to give. In this review, I describe how they have adapted to live/thrive/survive in their niches, helped scientists unlock major scientific discoveries, advance the field of biotechnology, and inform us about the boundaries of Life and where we might find it in the Universe.
This work examined in detail the a priori prediction of the axial dispersion coefficient from available correlations versus obtaining both it and mass transfer information from experimental ...breakthrough data and the consequences that may arise when doing so based on using a 1-D axially dispersed plug flow model and its associated Danckwerts outlet boundary condition. These consequences mainly included determining the potential for erroneous extraction of the axial dispersion coefficient and/or the LDF mass transfer coefficient from experimental data, especially when nonplug flow conditions prevailed in the bed. Two adsorbent/adsorbate cases were considered, i.e., CO2 and H2O vapor in zeolite 5A, because they both experimentally exhibited significant nonplug flow behavior, and the H2O-zeolite 5A system exhibited unusual concentration front sharpening that destroyed the expected constant pattern behavior (CPB) when modeled with the 1-D axially dispersed plug flow model. Overall, this work showed that it was possible to extract accurate mass transfer and dispersion information from experimental breakthrough curves using a 1-D axial dispersed plug flow model when they were measured both inside and outside the bed. To ensure the extracted information was accurate, the inside the bed breakthrough curves and their derivatives from the model were plotted to confirm whether or not the adsorbate/adsorbent system was exhibiting CPB or any concentration front sharpening near the bed exit. Even when concentration front sharpening was occurring with the H2O-zeolite 5A system, it was still possible to use the experimental inside and outside the bed breakthrough curves to extract fundamental mass transfer and dispersion information from the 1-D axial dispersed plug flow model based on the systematic methodology developed in this work.
Dracunculus medinensis (Guinea worm) is a parasitic nematode that can cause the debilitating disease dracunculiasis (Guinea worm disease) in humans. The global Guinea Worm Eradication Program has led ...intervention and eradication efforts since the 1980s, and Guinea worm infections in people have decreased >99.99%. With the final goal of eradication drawing nearer, reports of animal infections from some remaining endemic countries pose unique challenges. Currently, confirmation of suspected Guinea worm infection relies on conventional molecular techniques such as polymerase chain reaction (PCR), which is not specific to Guinea worm and, therefore, requires sequencing of the PCR products to confirm the identity of suspect samples, a process that often takes a few weeks. To decrease the time required for species confirmation, we developed a quantitative PCR assay targeting the mitochondrial cytochrome b (cytb) gene of Guinea worm. Our assay has a limit of detection of 10 copies per reaction. The mean analytical parameters (± SE) were as follows: efficiency = 93.4 ± 7.7%, y-intercept = 40.93 ± 1.11, slope = -3.4896 ± 0.12, and the R.sup.2 = 0.999 ± 0.004. The assay did not amplify other nematodes found in Guinea worm-endemic regions and demonstrated 100% diagnostic sensitivity and specificity. Implementation of this quantitative PCR assay for Guinea worm identification could eliminate the need for DNA sequencing to confirm species. Thus, this approach can be implemented to provide more rapid confirmation of Guinea worm infections, leading to faster execution of Guinea worm interventions while increasing our understanding of infection patterns.
Dynamic instability, polarity, and spatiotemporal organization are hallmarks of the microtubule cytoskeleton that allow formation of complex structures such as the eukaryotic spindle. No similar ...structure has been identified in prokaryotes. The bacteriophage-encoded tubulin PhuZ is required to position DNA at mid-cell, without which infectivity is compromised. Here, we show that PhuZ filaments, like microtubules, stochastically switch from growing in a distinctly polar manner to catastrophic depolymerization (dynamic instability) both in vitro and in vivo. One end of each PhuZ filament is stably anchored near the cell pole to form a spindle-like array that orients the growing ends toward the phage nucleoid so as to position it near mid-cell. Our results demonstrate how a bacteriophage can harness the properties of a tubulin-like cytoskeleton for efficient propagation. This represents the first identification of a prokaryotic tubulin with the dynamic instability of microtubules and the ability to form a simplified bipolar spindle.
Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural ...diversity is poorly understood. Here, we determine a 7.1 Å cryo-electron microscopy reconstruction of the bacteriophage-encoded PhuZ filament and provide molecular-level insight into its cooperative assembly mechanism. The PhuZ family of tubulins is required to actively center the phage within infected host cells, facilitating efficient phage replication. Our reconstruction and derived model reveal the first example of a three-stranded tubulin filament. We show that the elongated C-terminal tail simultaneously stabilizes both longitudinal and lateral interactions, which in turn define filament architecture. Identified interaction surfaces are conserved within the PhuZ family, and their mutagenesis compromises polymerization in vitro and in vivo. Combining kinetic modeling of PhuZ filament assembly and structural data, we suggest a common filament structure and assembly mechanism for the PhuZ family of tubulins.
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•The phage tubulin homolog PhuZ forms a three-stranded filament•The extended PhuZ C terminus defines both longitudinal and lateral contacts•The PhuZ family of tubulins has a common filament structure and assembly mechanism
The bacteriophage-encoded PhuZ family of tubulins is required to actively center the phage within infected host cells, facilitating phage replication. Zehr et al. describe a 7.1 Å cryo-EM reconstruction of the PhuZ filament and reveal an unexpected three-stranded tubulin filament.
Archaea are prokaryotic organisms with simplified versions of eukaryotic transcription systems. Genes coding for the general transcription factors TBP and TFB are present in multiple copies in ...several Archaea, including Halobacterium sp. NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters.
We attempted to knock out all six TBP and seven TFB genes in Halobacterium sp. NRC-1 using the ura3-based gene deletion system. Knockouts were obtained for six out of thirteen genes, tbpCDF and tfbACG, indicating that they are not essential for cell viability under standard conditions. Screening of a population of 1,000 candidate mutants showed that genes which did not yield mutants contained less that 0.1% knockouts, strongly suggesting that they are essential. The transcriptomes of two mutants, Delta tbpD and DeltatfbA, were compared to the parental strain and showed coordinate down regulation of many genes. Over 500 out of 2,677 total genes were regulated in the Delta tbpD and DeltatfbA mutants with 363 regulated in both, indicating that over 10% of genes in both strains require the action of both TbpD and TfbA for normal transcription. Culturing studies on the Delta tbpD and DeltatfbA mutant strains showed them to grow more slowly than the wild-type at an elevated temperature, 49 degrees C, and they showed reduced viability at 56 degrees C, suggesting TbpD and TfbA are involved in the heat shock response. Alignment of TBP and TFB protein sequences suggested the expansion of the TBP gene family, especially in Halobacterium sp. NRC-1, and TFB gene family in representatives of five different genera of haloarchaea in which genome sequences are available.
Six of thirteen TBP and TFB genes of Halobacterium sp. NRC-1 are non-essential under standard growth conditions. TbpD and TfbA coordinate the expression of over 10% of the genes in the NRC-1 genome. The Delta tbpD and DeltatfbA mutant strains are temperature sensitive, possibly as a result of down regulation of heat shock genes. Sequence alignments suggest the existence of several families of TBP and TFB transcription factors in Halobacterium which may function in transcription of different classes of genes.
Precious metals supported on ferrimagnetic particles have a diverse range of uses in catalysis. However, fabrication using synthetic methods results in potentially high environmental and economic ...costs. Here we show a novel biotechnological route for the synthesis of a heterogeneous catalyst consisting of reactive palladium nanoparticles arrayed on a nanoscale biomagnetite support. The magnetic support was synthesized at ambient temperature by the Fe(III)-reducing bacterium, Geobacter sulfurreducens, and facilitated ease of recovery of the catalyst with superior performance due to reduced agglomeration (versus conventional colloidal Pd nanoparticles). Surface arrays of palladium nanoparticles were deposited on the nanomagnetite using a simple one-step method without the need to modify the biomineral surface, most likely due to an organic coating priming the surface for Pd adsorption, which was produced by the bacterial culture during the formation of the nanoparticles. A combination of EXAFS and XPS showed the Pd nanoparticles on the magnetite to be predominantly metallic in nature. The Pd0−biomagnetite was tested for catalytic activity in the Heck reaction coupling iodobenzene to ethyl acrylate or styrene. Rates of reaction were equal to or superior to those obtained with an equimolar amount of a commercial colloidal palladium catalyst, and near complete conversion to ethyl cinnamate or stilbene was achieved within 90 and 180 min, respectively.
The halophilic archaea (haloarchaea) live in saline environments, which are found across the globe. In addition to salinity, these niches can be quite dynamic and experience extreme conditions such ...as low oxygen content, radiation (gamma and UV), pH and temperature. However, of all the naturally occurring stresses faced by the haloarchaea, only one, pH, has not been previously investigated in regard to the changes induced in the transcriptome. Therefore, we endeavored to determine the responses in three haloarchaea:
Halorubrum lacusprofundi (Hla),
Haloferax volcanii (Hvo), and
Halobacterium sp. NRC-1 (NRC-1) to growth under acidic and alkaline pH. Our observations showed that the transcriptomes of Hvo and NRC-1 regulated stress, motility, and ABC transporters in a similar manner, which is in line with previous reports from other prokaryotes when grown in an acidic environment. However, the pattern for Hla was more species specific. For alkaline stress, all three haloarchaea responded in a manner similar to well-studied archaea and bacteria showing the haloarchaeal response was general to prokaryotes. Additionally, we performed an analysis on the changes in the transcriptomes of the three haloarchaea when shifting from one pH extreme to the other. The results showed that the transcriptomes of all three haloarchaea respond more similarly when moving from alkaline to acidic conditions compared to a shift in the opposite direction. Interestingly, our studies also showed that individual genes of multiple paralogous gene families (
tbp,
tfb,
orc/
cdc6, etc.) found in the haloarchaea were regulated under specific stresses thereby providing evidence that they modulate the response to various environmental stresses. The studies described here are the first to catalog the changes in the haloarchaeal transcriptomes under growth in extreme pH and help us understand how life is able to thrive under all conditions present on Earth and, if present, on extraterrestrial bodies as well.
Spaceflight-associated neuro-ocular syndrome (SANS) occurs in 40% to 60% of National Aeronautics and Space Administration (NASA) International Space Station (ISS) astronauts who present postflight ...with ophthalmological findings and elevated intracranial pressure. The etiology of SANS is unknown; it is hypothesized that venous outflow congestion from the head and neck occurs because of microgravity, which is supported by the finding of internal jugular vein stagnant flow and thrombosis in some astronauts, but the impact on intracranial dural venous sinus structures remains unknown.
To clarify the potential risk of retrograde extension of clot intracranially among astronauts with internal jugular venous thrombosis by evaluating intracranial venous structures following spaceflight and to assess for any association between intracranial venous congestion and SANS.
This retrospective cohort study of all NASA astronauts who had undergone magnetic resonance (MR) venography at the time of the study included quantitative and qualitative assessments of the intracranial venous system on preflight and postflight MR venograms. Data were collected a mean (SD) of 525.8 (187.5) days before spaceflight and 2.0 (1.5) days after return to Earth. A semiautomated segmentation of the venogram images was used, which was then compared with a neuroradiologist's assessment.
A mean (SD) 184.3 (66.0) days of ISS spaceflight missions.
Dural venous sinus volumes before and after spaceflight.
A total of 12 astronauts (2 16.67% women; 10 83.33% men), with a mean (SD) age of 47.8 (5.8) years, were included. Overall, 4 astronauts (33.33%) met the diagnostic criteria for SANS. No dural venous sinus thrombosis was detected for any astronaut. Astronauts with SANS had significantly greater median (range) preflight to postflight increases in volume vs astronauts without SANS for all 3 venous sinus structures: superior sagittal sinus (13.40% 8.70% to 17.47% vs -2.66% -15.84% to 5.31%,; P = .004), right transverse/sigmoid sinus (17.15% 7.63% to 30.08% vs 0.77% -14.98% to 15.12%; P = .02), and left transverse/sigmoid sinus (9.40% 5.20% to 15.50% vs -1.40% -14.20% to 12.50%; P = .03). There was a positive correlation between the neuroradiologist's evaluation and the semiautomated method for the superior sagittal sinus (rpb = 0.64; P = .02) and the right transverse/sigmoid sinus (rpb = 0.58; P = .050).
These findings, in conjunction with the growing body of evidence of abnormal blood flow dynamics during spaceflight, suggest an association between intracranial venous congestion and SANS. Thus, there is an implication that individuals with increased venous sinus compliance may be at increased risk of developing SANS. These findings should be confirmed in a larger astronaut population and may contribute to understanding disorders of intracranial venous outflow on Earth.
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