The Utilization of Polymerase Chain Reaction, DNA Barcoding and Bioinformatics in Identifying Plant Species

Bioinformatics and DNA barcoding is a process used to identify plants, animals, and fungi. DNA barcoding in plants utilizes a key variable region in the genome, the RuBisCo large subunit (RbcL) on Chloroplast DNA. Once the DNA is extracted, Polymerase Chain Reaction (PCR) amplifies that region and that sample is sent off for sequencing. Bioinformatics and DNA barcoding helps taxonomists determine the sequence of the RbcL gene as well as obtain a unique barcode that can be used to identify plants. Several plant species from our local campus were sequenced and identified using the previously described methods

Design and evaluation of synthetic RNA-based incoherent feed-forward loop circuits

RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization

Modelling upper respiratory viral load dynamics of SARS-CoV-2.

Relationships between viral load, severity of illness, and transmissibility of virus are fundamental to understanding pathogenesis and devising better therapeutic and prevention strategies for COVID-19. Here we present within-host modelling of viral load dynamics observed in the upper respiratory tract (URT), drawing upon 2172 serial measurements from 605 subjects, collected from 17 different studies. We developed a mechanistic model to describe viral load dynamics and host response and contrast this with simpler mixed-effects regression analysis of peak viral load and its subsequent decline. We observed wide variation in URT viral load between individuals, over 5 orders of magnitude, at any given point in time since symptom onset. This variation was not explained by age, sex, or severity of illness, and these variables were not associated with the modelled early or late phases of immune-mediated control of viral load. We explored the application of the mechanistic model to identify measured immune responses associated with the control of the viral load. Neutralising antibodies correlated strongly with modelled immune-mediated control of viral load amongst subjects who produced neutralising antibodies. Our models can be used to identify host and viral factors which control URT viral load dynamics, informing future treatment and transmission blocking interventions

Discordant and heterogeneous clinically relevant genomic alterations in circulating tumor cells vs plasma DNA from men with metastatic castration resistant prostate cancer

Circulating tumor cell (CTC) and cellâ free (cf) DNAâ based genomic alterations are increasingly being used for clinical decisionâ making in oncology. However, the concordance and discordance between paired CTC and cfDNA genomic profiles remain largely unknown. We performed comparative genomic hybridization (CGH) on CTCs and cfDNA, and lowâ pass whole genome sequencing (lpWGS) on cfDNA to characterize genomic alterations (CNA) and tumor content in two independent prospective studies of 93 men with mCRPC treated with enzalutamide/abiraterone, or radiumâ 223. Comprehensive analysis of 69 patient CTCs and 72 cfDNA samples from 93 men with mCRPC, including 64 paired samples, identified common concordant gains in FOXA1, AR, and MYC, and losses in BRCA1, PTEN, and RB1 between CTCs and cfDNA. Concordant PTEN loss and discordant BRCA2 gain were associated with significantly worse outcomes in Epic ARâ V7 negative men with mCRPC treated with abiraterone/enzalutamide. We identified and externally validated CTCâ specific genomic alternations that were discordant in paired cfDNA, even in samples with high tumor content. These CTC/cfDNAâ discordant regions included key genomic regulators of lineage plasticity, osteomimicry, and cellular differentiation, including MYCN gain in CTCs (31%) that was rarely detected in cfDNA. CTC MYCN gain was associated with poor clinical outcomes in ARâ V7 negative men and small cell transformation. In conclusion, we demonstrated concordance of multiple genomic alterations across CTC and cfDNA platforms; however, some genomic alterations displayed substantial discordance between CTC DNA and cfDNA despite the use of identical copy number analysis methods, suggesting tumor heterogeneity and divergent evolution associated with poor clinical outcomes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153751/1/gcc22824.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153751/2/gcc22824_am.pd

PEARLS: Low Stellar Density Galaxies in the El Gordo Cluster Observed with JWST

A full understanding of how unusually large "Ultra Diffuse Galaxies" (UDGs) fit into our conventional understanding of dwarf galaxies remains elusive, despite the large number of objects identified locally. A natural extension of UDG research is the study of similar galaxies at higher redshift to establish how their properties may evolve over time. However, this has been a challenging task given how severely systematic effects and cosmological surface brightness dimming inhibit our ability to study low-surface brightness galaxies at high-$z$. Here, we present an identification of low stellar surface density galaxies (LDGs), likely the progenitors of local UDGs, at moderate redshift with deep near-IR observations of the El Gordo cluster at $z = 0.87$ with JWST. By stacking 8 NIRCAM filters, we are able to achieve an apparent surface brightness sensitivity of $24.59$ mag arcsec$^{-2}$, faint enough to be complete to the bright end of the LDG population. Our analysis identifies significant differences between this population and local UDGs, such as their color and size distributions, which suggest that UDG progenitors are bluer and more extended at high-$z$ than at $z = 0$. This suggests that multiple mechanisms are responsible for UDG formation and that prolonged transformation of cluster dwarfs is not a primary UDG formation mechanism at high-$z$. Furthermore, we find a slight overabundance of LDGs in El Gordo, and, in contrast to findings in local clusters, our analysis does not show a deficit of LDGs in the center of El Gordo, implying that tidal destruction of LDGs is significant between $z = 0.87$ and $z = 0$.Comment: Resubmitted to ApJ after minor revision

Are JWST/NIRCam color gradients in the lensed z=2.3 dusty star-forming galaxy El Anzuelo due to central dust attenuation or inside-out galaxy growth?

Gradients in the mass-to-light ratio of distant galaxies impede our ability to characterize their size and compactness. The long-wavelength filters of $JWST$'s NIRCam offer a significant step forward. For galaxies at Cosmic Noon ($z\sim2$), this regime corresponds to the rest-frame near-infrared, which is less biased towards young stars and captures emission from the bulk of a galaxy's stellar population. We present an initial analysis of an extraordinary lensed dusty star-forming galaxy (DSFG) at $z=2.3$ behind the $El~Gordo$ cluster ($z=0.87$), named $El~Anzuelo$ ("The Fishhook") after its partial Einstein-ring morphology. The FUV-NIR SED suggests an intrinsic star formation rate of $81^{+7}_{-2}~M_\odot~{\rm yr}^{-1}$ and dust attenuation $A_V\approx 1.6$, in line with other DSFGs on the star-forming main sequence. We develop a parametric lens model to reconstruct the source-plane structure of dust imaged by the Atacama Large Millimeter/submillimeter Array, far-UV to optical light from $Hubble$, and near-IR imaging with 8 filters of $JWST$/NIRCam, as part of the Prime Extragalactic Areas for Reionization and Lensing Science (PEARLS) program. The source-plane half-light radius is remarkably consistent from $\sim 1-4.5~\mu$m, despite a clear color gradient where the inferred galaxy center is redder than the outskirts. We interpret this to be the result of both a radially-decreasing gradient in attenuation and substantial spatial offsets between UV- and IR-emitting components. A spatial decomposition of the SED reveals modestly suppressed star formation in the inner kiloparsec, which suggests that we are witnessing the early stages of inside-out quenching.Comment: 29 pages, 11 figures, 5 tables. Accepted for publication in Ap

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

The JWST Discovery of the Triply-imaged Type Ia "Supernova H0pe" and Observations of the Galaxy Cluster PLCK G165.7+67.0

A Type Ia supernova (SN) at $z=1.78$ was discovered in James Webb Space Telescope Near Infrared Camera imaging of the galaxy cluster PLCK G165.7+67.0 (G165; $z = 0.35$). The SN is situated 1.5-2kpc from its host galaxy Arc 2 and appears in three different locations as a result of gravitational lensing by G165. These data can yield a value for Hubble's constant using time delays from this multiply-imaged SN Ia that we call "SN H0pe." Over the entire field we identified 21 image multiplicities, confirmed five of them using Near-Infrared Spectrograph (NIRspec), and constructed a new lens model that gives a total mass within 600kpc of ($2.6 \pm 0.3) \times 10^{14}$ M$_{\odot}$. The photometry uncovered a galaxy overdensity at Arc 2's redshift. NIRSpec confirmed six member galaxies, four of which surround Arc 2 with relative velocity $\lesssim$900 km s$^{-1}$ and projected physical extent $\lesssim$33 kpc. Arc 2 dominates the stellar mass ($(5.0 \pm 0.1) \times 10^{11}$ M$_{\odot}$), which is a factor of ten higher than other members of this compact galaxy group. These other group members have specific star formation rates (sSFR) of 2-260Gyr$^{-1}$ derived from the H$\alpha$-line flux corrected for stellar absorption, dust extinction, and slit losses. Another group centered on the dusty star forming galaxy Arc 1 is at $z=2.24$. The total SFR for the Arc 1 group ($gtrsim$ M$_{\odot}$ yr$^{-1}$) translates to a supernova rate of $\sim$1 SNe yr$^{-1}$, suggesting that regular monitoring of this cluster may yield additional SNe.Comment: 27 pages, submitted to Ap

Paper 1: The JWST PEARLS View of the El Gordo Galaxy Cluster and of the Structure It Magnifies

The massive galaxy cluster El Gordo (z=0.87) imprints multitudes of gravitationally lensed arcs onto James Webb Space Telescope (JWST) Near-Infrared Camera (NIRCam) images. Eight bands of NIRCam imaging were obtained in the ``Prime Extragalactic Areas for Reionization and Lensing Science'' (``PEARLS'') program. PSF-matched photometry across Hubble Space Telescope (HST) and NIRCam filters supplies new photometric redshifts. A new light-traces-mass lens model based on 56 image multiplicities identifies the two mass peaks and yields a mass estimate within 500 kpc of ~(7.0 +/- 0.30) x 10^14 Msun. A search for substructure in the 140 cluster members with spectroscopic redshifts confirms the two main mass components. The southeastern mass peak that contains the BCG is more tightly bound than the northwestern one. The virial mass within 1.7 Mpc is (5.1 +/- 0.60) x 10^14 Msun, lower than the lensing mass. A significant transverse velocity component could mean the virial mass is underestimated. We contribute one new member to the previously known z=4.32 galaxy group. Intrinsic (delensed) positions of the five secure group members span a physical extent of ~60 kpc. Thirteen additional candidates selected by spectroscopic/photometric constraints are small and faint with a mean intrinsic luminosity ~2.2 mag fainter than L*. NIRCam imaging admits a fairly wide range of brightnesses and morphologies for the group members, suggesting a more diverse galaxy population in this galaxy overdensity.Comment: 24 pages, accepted by Ap

Tissue based biomarkers in non-clear cell RCC: Correlative analysis from the ASPEN clinical trial

Biomarkers are needed in patients with non-clear cell renal cell carcinomas (NC-RCC), particularly papillary renal cell carcinoma, in order to inform on initial treatment selection and identify potentially novel targets for therapy. We enrolled 108 patients in ASPEN, an international randomized open-label phase 2 trial of patients with metastatic papillary, chromophobe, or unclassified NC-RCC treated with the mTOR inhibitor everolimus (n=57) or the vascular endothelial growth factor (VEGF) receptor inhibitor sunitinib (n=51), stratified by MSKCC risk and histology. The primary endpoint was overall survival (OS) and secondary efficacy endpoints for this exploratory biomarker analysis were radiographic progression-free survival (rPFS) defined by intentionto- treat using the RECIST 1.1 criteria and radiographic response rates. Tissue biomarkers (n=78) of mTOR pathway activation (phospho-S6 and -Akt, c-kit) and VEGF pathway activation (HIF-1, c-MET) were prospectively explored in tumor tissue by immunohistochemistry prior to treatment and associated with clinical outcomes. We found that S6 activation was more common in poor-risk NC-RCC tumors and S6/Akt activation was associated with worse PFS and OS outcomes with both everolimus and sunitinib, while c-kit was commonly expressed in chromophobe tumors and associated with improved outcomes with both agents. C-MET was commonly expressed in papillary tumors and was associated with lower rates of radiographic response but did not predict PFS for either agent. In multivariable analysis, both pAkt and c-kit were statistically significant prognostic biomarkers of OS. No predictive biomarkers of treatment response were identified for clinical outcomes. Most biomarker subgroups had improved outcomes with sunitinib as compared to everolimus