Antiferromagnetically ordered topological semimetals in Hubbard model with spin-orbit coupling.

We examine the possible existence of Dirac semimetal with magnetic order in a two-dimensional system with a nonsymmorphic symmetry by using the Hartree-Fock mean-field theory within the Hubbard model. We locate the region in the second-neighbor spin-orbit coupling vs Hubbard interaction phase diagram, where such a state is stabilized. The edge states for the ribbons along two orthogonal directions concerning the orientation of in-plane magnetic moments are obtained. Finally, the effect of the in-plane magnetic field, which results in the stabilization of the Weyl semimetallic (WSM) state, and the nature of the edge states corresponding to the WSM state for ribbon geometries are also explored.

Automated Platform for the Plasmid Construction Process.

There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J5 DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.

Management of a Large Dentigerous Cyst with Enucleation and Packing Open with BIPP in 9-year-old Child: A Case Report.

Dentigerous cyst is also known as follicular cyst. It is an odontogenic cyst of developmental origin. The dentigerous cyst involves impacted, embedded or submerged tooth by expansion of its follicle. The normal follicular space is mostly 3-4 mm but with dentigerous cyst it can be 5 mm or more. These are second most commonly occurring odontogenic cysts and literature shows occurrence of 24% among true cysts of jaw. It is most commonly associated with mandibular 3rd molar followed by maxillary canine and third molar. Radiographically occurring as unilocular radiolucency around an impacted tooth. In our case the cyst was a large dentigerous cyst occurring in 9-year-old child having mixed dentition. Complete enucleation of the cystic lesion and packing open with bismuth iodoform paraffin paste (BIPP) was done. BIPP dressing was changed at regular intervels and more than 60% of bone formation was complete in around 5 months which was evident on the radiograph. Conclusion: Methods employed for elimination include enucleation, decompression marsupialization but the treatment modality also depends upon age, existing dentition, location and size of the lesion. How to cite this article: Gaur G, Agarwal P, Goyal G, et al. Management of a Large Dentigerous Cyst with Enucleation and Packing Open with BIPP in 9-year-old Child: A Case Report. Int J Clin Pediatr Dent 2023;16(3):515-517.

Semimetallic spin-density wave state in iron pnictides.

We examine the existence of semimetallic spin-density wave (SDW) states in iron pnictides. In the experimentally observed metallic SDW state, the symmetry-protected Dirac cones are located away from the Fermi surface giving rise to tiny pockets and there are also additional Fermi pockets such as one around Γ. We find that the location of a pair of Dirac points with respect to the Fermi surface exhibits significant sensitivity to the orbital splitting between thedxzanddyzorbitals. Besides, in the presence of orbital splitting, the Fermi pockets not associated with the Dirac cones, can be suppressed so that a semimetallic SDW state can be realized. We explain these findings in terms of difference in the slopes and orbital contents of the bands which form the Dirac cone, and obtain the necessary conditions dependent on these two and other parameters for the coexisting Dirac semimetallic and SDW states. Additionally, the topologically protected edge states are studied in the ribbon geometry when the same are oriented either alongxoryaxes.

Novel variant CPLANE 1: c.5051C>A (p.Ser1684Ter) in an Indian neonate with Joubert syndrome.

Joubert syndrome (JS) is a rare ciliopathy that presents with the triad of hypotonia, developmental delay and molar tooth sign (MTS) in brain MRI. Next-generation sequencing has identified about 35 genes which are known to cause JS of which CPLANE 1 mutation is found in 8%-10% of cases. We report a case of JS in an Indian neonate who presented with hypotonia, dysmorphic facies, polydactyly, syndactyly and occipital encephalocele. MRI of the brain revealed MTS, and compound heterozygous mutations in CPLANE 1 gene were detected by clinical exome sequencing, one of them a novel variant CPLANE 1: c.5051C>A (p.Ser1684Ter) in exon 26, which was inherited from the parents.

Colorimetric Assaying of Exosomal Metabolic Biomarkers.

Exosomes released into the extracellular matrix have been reported to contain metabolic biomarkers of various diseases. These intraluminal vesicles are typically found in blood, urine, saliva, breast milk, cerebrospinal fluid, semen, amniotic fluid, and ascites. Analysis of exosomal content with specific profiles of DNA, microRNA, proteins, and lipids can mirror their cellular origin and physiological state. Therefore, exosomal cargos may reflect the physiological processes at cellular level and can potentially be used as biomarkers. Herein, we report an optical detection method for assaying exosomal biomarkers that supersedes the state-of-the-art time consuming and laborious assays such as ELISA and NTA. The proposed assay monitors the changes in optical properties of poly(3-(4-methyl-3'-thienyloxy) propyltriethylammonium bromide) upon interacting with aptamers/peptide nucleic acids in the presence or absence of target biomarkers. As a proof of concept, this study demonstrates facile assaying of microRNA, DNA, and advanced glycation end products in exosomes isolated from human plasma with detection levels of ~1.2, 0.04, and 0.35 fM/exosome, respectively. Thus, the obtained results illustrate that the proposed methodology is applicable for rapid and facile detection of generic exosomal biomarkers for facilitating diseases diagnosis.

Affimer sandwich probes for stable and robust lateral flow assaying.

Lateral flow assays (LFAs) widely deployed for on-site diagnosis have predominantly utilized antibodies as recognition molecules. Antibodies with limited thermal stability deteriorate the performance of the LFA over time. Herein, we demonstrate a stable and robust LFA by utilizing thermally stable peptide-based 12-14 kDa affimers as recognition molecules, in lieu of conventional protein-based antibodies to analyze complex samples with a significantly improved shelf life at room temperature. The model system studied here is that of interleukin-8 (IL8) biomarker for validating the efficacy of the proposed approach, using a pair of affimer probes that demonstrates dual functionality of capturing and reporting. Affimers immobilized on the test zone of LFA serve as capture probes for IL8-affimer-MB complexes. Whereas affimers conjugated with the MBs that enable extraction of IL8 from the sample matrix serve as reporters for visual detection. The MB complexes captured at the test zone resulted in brownish test bands that enable concentration-dependent detection of IL8. The assay yielded sensitive visual detection of IL8 at ng/mL levels (~ 0.1 ng/mL and 1 ng/mL in buffer and human plasma, respectively), within 20 min, using sample volumes of ~ 100 µL. Importantly, the stability of affimer-incorporated LFA improved significantly in contrast to antibody-incorporated LFA over time, even when stored at 4 °C. Therefore, the proposed affimer-based LFA in conjunction with MBs offer stable and reliable detection of biomarkers at clinically relevant concentration ranges in complicated matrices, even without requiring cold storage, hence, offering a promising avenue for on-site diagnosis in resource-limited settings.

Repurposing a microfluidic formulation device for automated DNA construction.

Microfluidic applications have expanded greatly over the past decade. For the most part, however, each microfluidics platform is developed with a specific task in mind, rather than as a general-purpose device with a wide-range of functionality. Here, we show how a microfluidic system, originally developed to investigate protein phase behavior, can be modified and repurposed for another application, namely DNA construction. We added new programable controllers to direct the flow of reagents across the chip. We designed the assembly of a combinatorial Golden Gate DNA library using TeselaGen DESIGN software and used the repurposed microfluidics platform to assemble the designed library from off-chip prepared DNA assembly pieces. Further experiments verified the sequences and function of the on-chip assembled DNA constructs.

Stoichiometric Tuning of PNA Probes to Au0.8Ag0.2 Alloy Nanoparticles for Visual Detection of Nucleic Acids in Plasma.

Standard detection methods for nucleic acids, an important class of diagnostic biomarkers, are often laborious and cumbersome. In need for development of facile methodologies, localized surface plasmon resonance (LSPR) assays have been widely explored for both spectroscopic and visual detection of nucleic acids. Our sensing approach is based on monitoring changes in the LSPR band due to interaction between peptide nucleic acid (PNA) and plasmonic nanoparticles (NPs) in the presence/absence of target nucleic acid. We have investigated the importance of tuning the stoichiometry of PNA to NPs to enable "naked-eye" detection of nucleic acids at clinically relevant concentration ranges. Assaying in plasma is achieved by incorporation of silver in gold NPs (AuNPs) via an alloying process. The synthesized gold/silver alloy NPs reduce nonspecific adsorption of proteinaceous interferents in plasma. Furthermore, the gold/silver alloy NPs absorb in the most sensitive cyan to green transition zone (∼500 nm) yielding highly competitive visual limits of detection (LODs). The visual LOD (calculated objectively using the ΔE algorithm) for a model microRNA (mir21) using a productive combination of stoichiometric tuning of the PNA to NP ratio and compositional tuning of the NPs in buffer and plasma extract equals 200 pM (∼250 times lower than existing reports) and 3 nM, respectively. We envision that the proposed LSPR assay based on Au0.8Ag0.2NPs offers an avenue for rapid and sensitive on-site detection of nucleic acids in complex matrixes in combination with efficient target extraction kits.

Adenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel Isopentanol.

Climate change necessitates the development of CO2 neutral or negative routes to chemicals currently produced from fossil carbon. In this paper we demonstrate a pathway from the renewable resource glucose to next generation biofuel isopentanol by pairing the isovaleryl-CoA biosynthesis pathway from Myxococcus xanthus and a butyryl-CoA reductase from Clostridium acetobutylicum. The best plasmid and Escherichia coli strain combination makes 80.50 ± 8.08 (SD) mg/L of isopentanol after 36 h under microaerobic conditions with an oleyl alcohol overlay. In addition, the system also shows a strong preference for isopentanol production over prenol in microaerobic conditions. Finally, the pathway requires zero adenosine triphosphate and can be paired theoretically with nonoxidative glycolysis, the combination being redox balanced from glucose thus avoiding unnecessary carbon loss as CO2. These pathway properties make the isovaleryl-CoA pathway an attractive isopentanol production route for further optimization.

Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning.

The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, we report on implementation of two DBTL cycles to optimize 1-dodecanol production from glucose using 60 engineered Escherichia coli MG1655 strains. The first DBTL cycle employed a simple strategy to learn efficiently from a relatively small number of strains (36), wherein only the choice of ribosome-binding sites and an acyl-ACP/acyl-CoA reductase were modulated in a single pathway operon including genes encoding a thioesterase (UcFatB1), an acyl-ACP/acyl-CoA reductase (Maqu_2507, Maqu_2220, or Acr1), and an acyl-CoA synthetase (FadD). Measured variables included concentrations of dodecanol and all proteins in the engineered pathway. We used the data produced in the first DBTL cycle to train several machine-learning algorithms and to suggest protein profiles for the second DBTL cycle that would increase production. These strategies resulted in a 21% increase in dodecanol titer in Cycle 2 (up to 0.83 g/L, which is more than 6-fold greater than previously reported batch values for minimal medium). Beyond specific lessons learned about optimizing dodecanol titer in E. coli, this study had findings of broader relevance across synthetic biology applications, such as the importance of sequencing checks on plasmids in production strains as well as in cloning strains, and the critical need for more accurate protein expression predictive tools.

Parallel Integration and Chromosomal Expansion of Metabolic Pathways.

Robust fermentation of biomass-derived sugars into bioproducts demands the reliable microbial expression of metabolic pathways. Plasmid-based expression systems may suffer from instability and result in highly variable titers, rates, and yields. An established mitigation approach, chemical induced chromosomal expansion (CIChE), expands a singly integrated pathway to plasmid-like copy numbers while maintaining stability in the absence of antibiotic selection pressure. Here, we report parallel integration and chromosomal expansion (PIACE), extensions to CIChE that enable independent expansions of pathway components across multiple loci, use suicide vectors to achieve high-efficiency site-specific integration of sequence-validated multigene components, and introduce a heat-curable plasmid to obviate recA deletion post pathway expansion. We applied PIACE to stabilize an isopentenol pathway across three loci in E. coli DH1 and then generate libraries of pathway component copy number variants to screen for improved titers. Polynomial regressor statistical modeling of the production screening data suggests that increasing copy numbers of all isopentenol pathway components would further improve titers.

Sentinel Surveillance for Congenital Rubella Syndrome - India, 2016-2017.

Rubella infection during pregnancy can result in miscarriage, fetal death, stillbirth, or a constellation of congenital malformations known as congenital rubella syndrome (CRS). The 11 countries in the World Health Organization (WHO) South-East Asia Region are committed to the elimination of measles and control of rubella and CRS by 2020. Until 2016, when the Government of India's Ministry of Health and Family Welfare and the Indian Council of Medical Research initiated surveillance for CRS in five sentinel sites, India did not conduct systematic surveillance for CRS. During the first 8 months of surveillance, 207 patients with suspected CRS were identified. Based on clinical details and serologic investigations, 72 (34.8%) cases were classified as laboratory-confirmed CRS, four (1.9%) as congenital rubella infection, 11 (5.3%) as clinically compatible cases, and 120 (58.0%) were excluded as noncases. The experience gained during the first phase of surveillance will be useful in expanding the surveillance network, and data from the surveillance network will be used to help monitor progress toward control of rubella and CRS in India.

Nanoplasmonic Sensing from the Human Vision Perspective.

Localized surface plasmon resonance (LSPR) constitutes a versatile technique for biodetection, exploiting the sensitivity of plasmonic nanostructures to small changes in refractive index. The optical shift in the LSPR band caused by molecular interactions in the vicinity of the nanostructures are typically <5 nm and can readily be detected by a spectrophotometer. Widespread use of LSPR-based sensors require cost-effective devices and would benefit from sensing schemes that enables use of very simple spectrophotometers or even naked-eye detection. This paper describes a new strategy facilitating visualization of minute optical responses in nanoplasmonic bioassays by taking into account the physiology of human color vision. We demonstrate, using a set of nine different plasmonic nanoparticles, that the cyan to green transition zone at ∼500 nm is optimal for naked-eye detection of color changes. In this wavelength range, it is possible to detect a color change corresponding to a wavelength shift of ∼2-3 nm induced by refractive index changes in the medium or by molecular binding to the surface of the nanoparticles. This strategy also can be utilized to improve the performance of aggregation-based nanoplasmonic colorimetric assays, which enables semiquantitative naked-eye detection of matrix metalloproteinase 7 (MMP7) activity at concentrations that are at least 5 times lower than previously reported assays using spherical gold nanoparticles. We foresee significant potential of this strategy in medical diagnostic and environmental monitoring, especially in situations where basic laboratory infrastructure is sparse or even nonexistent. Finally, we demonstrate that the developed concept can be used in combination with cell phone technology and red-green-blue (RGB) analysis for sensitive and quantitative detection of MMP7.

Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme.

Prodiginines, which are tripyrrole alkaloids displaying a wide array of bioactivities, occur as linear and cyclic congeners. Identification of an unclustered biosynthetic gene led to the discovery of the enzyme responsible for catalyzing the regiospecific C-H activation and cyclization of prodigiosin to cycloprodigiosin in Pseudoalteromonas rubra. This enzyme is related to alkylglycerol monooxygenase and unrelated to RedG, the Rieske oxygenase that produces cyclized prodiginines in Streptomyces, implying convergent evolution.

A Versatile Microfluidic Device for Automating Synthetic Biology.

New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.

PR-PR: cross-platform laboratory automation system.

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.

Simultaneous cell growth and ethanol production from cellulose by an engineered yeast consortium displaying a functional mini-cellulosome.

BACKGROUND: The recalcitrant nature of cellulosic materials and the high cost of enzymes required for efficient hydrolysis are the major impeding steps to their practical usage for ethanol production. Ideally, a recombinant microorganism, possessing the capability to utilize cellulose for simultaneous growth and ethanol production, is of great interest. We have reported recently the use of a yeast consortium for the functional presentation of a mini-cellulosome structure onto the yeast surface by exploiting the specific interaction of different cohesin-dockerin pairs. In this study, we engineered a yeast consortium capable of displaying a functional mini-cellulosome for the simultaneous growth and ethanol production on phosphoric acid swollen cellulose (PASC). RESULTS: A yeast consortium composed of four different populations was engineered to display a functional mini-cellulosome containing an endoglucanase, an exoglucanase and a ß-glucosidase. The resulting consortium was demonstrated to utilize PASC for growth and ethanol production. The final ethanol production of 1.25 g/L corresponded to 87% of the theoretical value and was 3-fold higher than a similar yeast consortium secreting only the three cellulases. Quantitative PCR was used to enumerate the dynamics of each individual yeast population for the two consortia. Results indicated that the slight difference in cell growth cannot explain the 3-fold increase in PASC hydrolysis and ethanol production. Instead, the substantial increase in ethanol production is consistent with the reported synergistic effect on cellulose hydrolysis using the displayed mini-cellulosome. CONCLUSIONS: This report represents a significant step towards the goal of cellulosic ethanol production. This engineered yeast consortium displaying a functional mini-cellulosome demonstrated not only the ability to grow on the released sugars from PASC but also a 3-fold higher ethanol production than a similar yeast consortium secreting only the three cellulases. The use of more complex cellulosomal structures may further improve the overall efficiency for ethanol production.

Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production.

In this paper, we report the surface assembly of a functional minicellulosome by using a synthetic yeast consortium. The basic design of the consortium consisted of four different engineered yeast strains capable of either displaying a trifunctional scaffoldin, Scaf-ctf (SC), carrying three divergent cohesin domains from Clostridium thermocellum (t), Clostridium cellulolyticum (c), and Ruminococcus flavefaciens (f), or secreting one of the three corresponding dockerin-tagged cellulases (endoglucanase [AT], exoglucanase [EC/CB], or ß-glucosidase [BF]). The secreted cellulases were docked onto the displayed Scaf-ctf in a highly organized manner based on the specific interaction of the three cohesin-dockerin pairs employed, resulting in the assembly of a functional minicellulosome on the yeast surface. By exploiting the modular nature of each population to provide a unique building block for the minicellulosome structure, the overall cellulosome assembly, cellulose hydrolysis, and ethanol production were easily fine-tuned by adjusting the ratio of different populations in the consortium. The optimized consortium consisted of a SC:AT:CB:BF ratio of 7:2:4:2 and produced almost twice the level of ethanol (1.87 g/liter) as a consortium with an equal ratio of the different populations. The final ethanol yield of 0.475 g of ethanol/g of cellulose consumed also corresponded to 93% of the theoretical value. This result confirms the use of a synthetic biology approach for the synergistic saccharification and fermentation of cellulose to ethanol by using a yeast consortium displaying a functional minicellulosome.