The RRM-mediated RNA binding activity in T. brucei RAP1 is essential for VSG monoallelic expression.

Trypanosoma brucei is a protozoan parasite that causes human African trypanosomiasis. Its major surface antigen VSG is expressed from subtelomeric loci in a strictly monoallelic manner. We previously showed that the telomere protein TbRAP1 binds dsDNA through its 737RKRRR741 patch to silence VSGs globally. How TbRAP1 permits expression of the single active VSG is unknown. Through NMR structural analysis, we unexpectedly identify an RNA Recognition Motif (RRM) in TbRAP1, which is unprecedented for RAP1 homologs. Assisted by the 737RKRRR741 patch, TbRAP1 RRM recognizes consensus sequences of VSG 3'UTRs in vitro and binds the active VSG RNA in vivo. Mutating conserved RRM residues abolishes the RNA binding activity, significantly decreases the active VSG RNA level, and derepresses silent VSGs. The competition between TbRAP1's RNA and dsDNA binding activities suggests a VSG monoallelic expression mechanism in which the active VSG's abundant RNA antagonizes TbRAP1's silencing effect, thereby sustaining its full-level expression.We thank Dr. Donny Licatolasi, Dr. Anton Komar, Dr. Kurt Runge, and Catherine Z. Wang for their comments on the manuscript. This work is supported by an NIH R01 grant AI066095 (Li), an NIH S10 grant S10OD025252 (Li), Research Grants Council grants PolyU 151062/18M, 15103819, 15106421, R5050-18 and AoE/M-09/12 (Zhao), Shenzhen Basic Research Programs of China JCYJ20170818104619974 & JCYJ20210324133803009 (Zhao). Shenzhen Basic Research Program of China JCYJ20220818100215033 (Zhang). Research Grants Council grant C4041-18E (Wong, Zhang, Zhao). The publication cost is partly supported by GRHD at CSU and by PolyU.S

Eclipsing Binaries From the CSTAR Project at Dome A, Antarctica

The Chinese Small Telescope ARray (CSTAR) has observed an area around the Celestial South Pole at Dome A since 2008. About $20,000$ light curves in the i band were obtained lasting from March to July, 2008. The photometric precision achieves about 4 mmag at i = 7.5 and 20 mmag at i = 12 within a 30 s exposure time. These light curves are analyzed using Lomb--Scargle, Phase Dispersion Minimization, and Box Least Squares methods to search for periodic signals. False positives may appear as a variable signature caused by contaminating stars and the observation mode of CSTAR. Therefore the period and position of each variable candidate are checked to eliminate false positives. Eclipsing binaries are removed by visual inspection, frequency spectrum analysis and locally linear embedding technique. We identify 53 eclipsing binaries in the field of view of CSTAR, containing 24 detached binaries, 8 semi-detached binaries, 18 contact binaries, and 3 ellipsoidal variables. To derive the parameters of these binaries, we use the Eclipsing Binaries via Artificial Intelligence (EBAI) method. The primary and the secondary eclipse timing variations (ETVs) for semi-detached and contact systems are analyzed. Correlated primary and secondary ETVs confirmed by false alarm tests may indicate an unseen perturbing companion. Through ETV analysis, we identify two triple systems (CSTAR J084612.64-883342.9 and CSTAR J220502.55-895206.7). The orbital parameters of the third body in CSTAR J220502.55-895206.7 are derived using a simple dynamical model.Comment: 41 pages, 12 figures; published online in ApJ

Planetary transit candidates in the CSTAR field: analysis of the 2008 data

The Chinese Small Telescope ARray (CSTAR) is a group of four identical, fully automated, static 14.5 cm telescopes. CSTAR is located at Dome A, Antarctica and covers 20 deg2 of sky around the South Celestial Pole. The installation is designed to provide high-cadence photometry for the purpose of monitoring the quality of the astronomical observing conditions at Dome A and detecting transiting exoplanets. CSTAR has been operational since 2008, and has taken a rich and high-precision photometric data set of 10,690 stars. In the first observing season, we obtained 291,911 qualified science frames with 20 s integrations in the i band. Photometric precision reaches 4 mmag at 20 s cadence at i = 7.5 and is 20 mmag at i = 12. Using robust detection methods, 10 promising exoplanet candidates were found. Four of these were found to be giants using spectroscopic follow-up. All of these transit candidates are presented here along with the discussion of their detailed properties as well as the follow-up observations

Physiological and Transcriptional Responses of Industrial Rapeseed (Brassica napus) Seedlings to Drought and Salinity Stress

Abiotic stress greatly inhibits crop growth and reduces yields. However, little is known about the transcriptomic changes that occur in the industrial oilseed crop, rapeseed (Brassica napus), in response to abiotic stress. In this study, we examined the physiological and transcriptional responses of rapeseed to drought (simulated by treatment with 15% (w/v) polyethylene glycol (PEG) 6000) and salinity (150 mM NaCl) stress. Proline contents in young seedlings greatly increased under both conditions after 3 h of treatment, whereas the levels of antioxidant enzymes remained unchanged. We assembled transcripts from the leaves and roots of rapeseed and performed BLASTN searches against the rapeseed genome database for the first time. Gene ontology analysis indicated that DEGs involved in catalytic activity, metabolic process, and response to stimulus were highly enriched. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that differentially expressed genes (DEGs) from the categories metabolic pathways and biosynthesis of secondary metabolites were highly enriched. We determined that myeloblastosis (MYB), NAM/ATAF1-2/CUC2 (NAC), and APETALA2/ethylene-responsive element binding proteins (AP2-EREBP) transcription factors function as major switches that control downstream gene expression and that proline plays a role under short-term abiotic stress treatment due to increased expression of synthesis and decreased expression of degradation. Furthermore, many common genes function in the response to both types of stress in this rapeseed

Versatile Site-Selective Protein Reaction Guided by WW Domain–Peptide Motif Interaction

A short, flexible, and unstructured peptide tag that has versatile and facile use in protein labeling applications is highly desirable. Here, we report an 11-residue peptide tag with an internal cysteine (a W-tag, derived from a Comm PY peptide motif that is known to bind with Nedd4 WW3* domain) that can be installed at different regions of the target protein without compromising its covalent reactivity with the reactive label (a 35-residue synthetic Nedd4 WW3* domain derivative). This versatility is explained by the unique structural features of the reaction. NMR analysis reveals that both the W-tag peptide and reactive Nedd4 WW3* protein are unstructured before they encounter each other. The binding interaction of the two induces noticeable structural changes and promotes global folding. Consequently, the reactive cysteine residue at W-tag and the electrophilic chloroacetyl group at Nedd4 WW3* domain are positioned to be in close proximity, inducing an intermolecular covalent cross-linking. The covalent linkage in turn stabilizes the folding of the protein complex. This unique multistep mechanism renders this labeling reaction amenable to different sites of the proteins of interest: installation of the tag at N- and C-termini, in the flexible linker region, in the loop region, and the extracellular terminus of target proteins exhibited comparable reactivity. This work therefore represents the first proximity-induced cysteine reaction based on the unique binding features of WW domains that demonstrates unprecedented versatility

Asperuloside Prevents Peri-Implantitis via Suppression of NF-κB and ERK1/2 on Rats

Peri-implantitis is characterized by inflammatory cell infiltration and hyperactivation of the osteoclasts surrounding dental implants which can result in bone resorption and ultimately implant failure. Therefore, coordinating the activity of inflammatory response and bone-resorbing osteoclasts is crucial for the prevention of peri-implantitis. Asperuloside (ASP), an iridoid glycoside, has significant anti-inflammatory activities, suggesting the great potential in attenuating peri-implantitis bone resorption. A ligature-induced peri-implantitis model in the maxilla of rats was established, and the effects of ASP on preventing peri-implantitis were evaluated after four weeks of ligation using micro-CT and histological staining. RT-PCR, western blotting, tartrate-resistant acid phosphatase (TRAP), and immunofluorescent staining were conducted on osteoclasts to confirm the mechanisms of ASP on osteoclastogenesis. The results show that ASP could lead to attenuation of alveolar bone resorption in peri-implantitis by inhibiting osteoclast formation and decreasing pro-inflammatory cytokine levels in vivo. Furthermore, ASP could inhibit osteoclastogenesis by downregulating expression levels of transcription factors nuclear factor of activated T-cell (NFATc1) via restraining the activations of nuclear factor kappa beta (NF-κB) and the phosphorylation of extracellular signal-related kinase 1/2 (ERK1/2). In conclusion, ASP could significantly attenuate bone resorption in peri-implantitis via inhibition of osteoclastogenesis by suppressing NF-κB and ERK1/2 signaling pathways activations

An unbiased method of measuring the ratio of two data sets

International audienceIn certain cases of astronomical data analysis, the meaningful physical quantity to extract is the ratio $R$ between two data sets. Examples include the lensing ratio, the interloper rate in spectroscopic redshift samples, the decay rate of gravitational potential and $E_G$ to test gravity. However, simply taking the ratio of the two data sets is biased, since it renders (even statistical) errors in the denominator into systematic errors in $R$. Furthermore, it is not optimal in minimizing statistical errors of $R$. Based on the Bayesian analysis and the usual assumption of Gaussian error in the data, we derive an analytical expression of the posterior PDF $P(R)$. This result enables fast and unbiased $R$ measurement, with minimal statistical errors. Furthermore, it relies on no underlying model other than the proportionality relation between the two data sets. Even more generally, it applies to the cases where the proportionality relation holds for the underlying physics/statistics instead of the two data sets directly. It also applies to the case of multiple ratios ($R\rightarrow {\bf R}=(R_1,R_2,\cdots)$). We take the lensing ratio as an example to demonstrate our method. We take lenses as DESI imaging survey galaxies, and sources as DECaLS cosmic shear and \emph{Planck} CMB lensing. We restrict the analysis to the ratio between CMB lensing and cosmic shear. The resulting $P(R$), for multiple lens-shear pairs, are all nearly Gaussian. The S/N of measured $R$ ranges from $5.3$ to $8.4$. We perform several tests to verify the robustness of the above result

An unbiased method of measuring the ratio of two data sets

In certain cases of astronomical data analysis, the meaningful physical quantity to extract is the ratio $R$ between two data sets. Examples include the lensing ratio, the interloper rate in spectroscopic redshift samples, the decay rate of gravitational potential and $E_G$ to test gravity. However, simply taking the ratio of the two data sets is biased, since it renders (even statistical) errors in the denominator into systematic errors in $R$. Furthermore, it is not optimal in minimizing statistical errors of $R$. Based on the Bayesian analysis and the usual assumption of Gaussian error in the data, we derive an analytical expression of the posterior PDF $P(R)$. This result enables fast and unbiased $R$ measurement, with minimal statistical errors. Furthermore, it relies on no underlying model other than the proportionality relation between the two data sets. Even more generally, it applies to the cases where the proportionality relation holds for the underlying physics/statistics instead of the two data sets directly. It also applies to the case of multiple ratios ($R\rightarrow {\bf R}=(R_1,R_2,\cdots)$). We take the lensing ratio as an example to demonstrate our method. We take lenses as DESI imaging survey galaxies, and sources as DECaLS cosmic shear and \emph{Planck} CMB lensing. We restrict the analysis to the ratio between CMB lensing and cosmic shear. The resulting $P(R$), for multiple lens-shear pairs, are all nearly Gaussian. The S/N of measured $R$ ranges from $5.3$ to $8.4$. We perform several tests to verify the robustness of the above result