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2021 ◽  
Vol 112 ◽  
pp. 103483
Jing Liu ◽  
Fukang Yang ◽  
Shan Chong ◽  
Qingzhi Wen ◽  
Qianguo Lin

2021 ◽  
Vol 72 (3) ◽  
pp. 627-634
R. K. PAL ◽  
P. K. KINGRA ◽  
S. K. MISHRA ◽  

The DSSAT module for cotton crop has been evaluated as a tool to predict the crop growth and yield response to microclimatic modifications. In this context, multi-location field experiments were laid out at Bathinda and Faridkot, districts of Punjab during Kharif 2018 with Bt-cotton hybrid RCH 773 BGII and sown at three times, i.e., April 30, May 15 and May 30 with two row orientations (North-South : N-S and East-West : E-W) and three plant spacing’s (67.5 cm × 45.0 cm, 67.5 cm × 60.0 cm and 67.5 cm × 75.0 cm) in factorial split plot design and replicated by three times. The model output in terms of simulated phenology showed close proximity over observed value having R2 of 0.51 and 0.61 at Bathinda and 0.43 and 0.87 at Faridkot anthesis and maturity, respectively. Among study locations, observed and simulated LAI ranged from 2.7 to 3.7 and 1.8 to 3.0. Simulated seed cotton yield was found significantly higher with the crop sown on 30th April (3053 and 3274 kg ha-1) than 30th May sowing (2392 and 2511 kg ha-1) at Bathinda and Faridkot, respectively, which was in good agreement with observed yield having higher value of d-stat (0.84 for Bathinda and 0.89 for Faridkot) and R2 (0.75 for Bathinda and 0.83 for Faridkot). Moreover, higher seed cotton yield was simulated under East-West row direction along with wider plant spacing (67.5 × 75 cm) at both locations. Overall, CROPGRO-cotton model can be used as research tool for the prediction of cotton phenology and yield and to explore site-specific adoption strategies such as appropriate sowing time, row orientation and plant spacing to sustain cotton productivity under changing climatic conditions.

2021 ◽  
Vol 9 ◽  
Yu Chen ◽  
Dingpeng Zhang ◽  
Xiaohong Zhang ◽  
Zhen Wang ◽  
Chuan-Fa Liu ◽  

Asparaginyl endopeptidases (AEPs) or legumains are Asn/Asp (Asx)-specific proteases that break peptide bonds, but also function as peptide asparaginyl ligases (PALs) that make peptide bonds. This ligase activity can be used for site-specific protein modifications in biochemical and biotechnological applications. Although AEPs are common, PALs are rare. We previously proposed ligase activity determinants (LADs) of these enzymes that could determine whether they catalyze formation or breakage of peptide bonds. LADs are key residues forming the S2 and S1′ substrate-binding pockets flanking the S1 active site. Here, we build on the LAD hypothesis with the engineering of ligases from proteases by mutating the S2 and S1′ pockets of VcAEP, an AEP from Viola canadensis. Wild type VcAEP yields <5% cyclic product from a linear substrate at pH 6.5, whereas the single mutants VcAEP-V238A (Vc1a) and VcAEP-Y168A (Vc1b) targeting the S2 and S1′ substrate-binding pockets yielded 34 and 61% cyclic products, respectively. The double mutant VcAEP-V238A/Y168A (Vc1c) targeting both the S2 and S1′ substrate-binding pockets yielded >90% cyclic products. Vc1c had cyclization efficiency of 917,759 M−1s−1, which is one of the fastest rates for ligases yet reported. Vc1c is useful for protein engineering applications, including labeling of DARPins and cell surface MCF-7, as well as producing cyclic protein sfGFP. Together, our work validates the importance of LADs for AEP ligase activity and provides valuable tools for site-specific modification of proteins and biologics.

2021 ◽  
Vol 12 (1) ◽  
Jinfeng Liu ◽  
Jinrong Yang ◽  
Xiao Cheng Zeng ◽  
Sotiris S. Xantheas ◽  
Kiyoshi Yagi ◽  

AbstractThe spectroscopic features of protonated water species in dilute acid solutions have been long sought after for understanding the microscopic behavior of the proton in water with gas-phase water clusters H+(H2O)n extensively studied as bottom-up model systems. We present a new protocol for the calculation of the infrared (IR) spectra of complex systems, which combines the fragment-based Coupled Cluster method and anharmonic vibrational quasi-degenerate perturbation theory, and demonstrate its accuracy towards the complete and accurate assignment of the IR spectrum of the H+(H2O)21 cluster. The site-specific IR spectral signatures reveal two distinct structures for the internal and surface four-coordinated water molecules, which are ice-like and liquid-like, respectively. The effect of inter-molecular interaction between water molecules is addressed, and the vibrational resonance is found between the O-H stretching fundamental and the bending overtone of the nearest neighboring water molecule. The revelation of the spectral signature of the excess proton offers deeper insight into the nature of charge accommodation in the extended hydrogen-bonding network underpinning this aqueous cluster.

2021 ◽  
Suxia Yang ◽  
Bin Yuan ◽  
Yuwen Peng ◽  
Shan Huang ◽  
Wei Chen ◽  

Abstract. Ambient nitrate has been of increasing concern in PM2.5, while there are still large uncertainties in quantifying the formation of nitrate aerosol. The formation pathways of nitrate aerosol at an urban site and a suburban site in the Pearl River Delta (PRD) are investigated using an observation-constrained box model. Throughout the campaigns, aerosol pollution episodes were constantly accompanied with the increase of nitrate concentrations and fractions at both urban and suburban sites. The simulations demonstrate that chemical reactions in the daytime and at night both contributed significantly to formation of nitrate in the boundary layer at the two sites. However, nighttime reactions predominately occurred aloft in the residual layer at the urban site and downward transport from the residual layer in the morning are important source (53 %) for surface nitrate at the urban site, whereas similar amounts of nitrate were produced in the nocturnal boundary layer and residual layer at the suburban site, which results in little downward transport of nitrate from the residual layer to the ground at the suburban site. We show that nitrate formation was in the volatile organic compounds (VOCs)-limited regime at the urban site, and in the transition regime at the suburban site, identical to the response of ozone at both sites. The reduction of VOCs emissions can be an efficient approach to mitigate nitrate in both urban and suburban areas through influencing hydroxyl radical (OH) and N2O5 production, which will also be beneficial for the synergistic control of regional ozone pollution. The results highlight that the relative importance of nitrate formation pathways can be site-specific, and the quantitative understanding of various pathways of nitrate formation will provide insights for developing nitrate mitigation strategies.

2021 ◽  
Vol 9 ◽  
Marco Roversi ◽  
Gianluca Mirra ◽  
Antonio Musolino ◽  
Domenico Barbuti ◽  
Laura Lancella ◽  

Objectives: The aim of this study is to provide new data on pediatrics spondylodiscitis for an optimal clinical management of this site-specific osteomyelitis.Methods: We reported 48 cases of pediatric spondylodiscitis and made three comparisons between: (1) tubercular and non-tubercular cases; (2) patients aged more or less than 5 years; (3) children with spondylodiscitis and 62 controls with non-vertebral osteomyelitis.Results: A higher rate of sequelae was reported in patients with tubercular spondylodiscitis, but no significant differences were noted at the cut-off of 5 years of age. Compared to non-vertebral osteomyelitis, pediatric spondylodiscitis affects younger children of both genders, usually presenting with afebrile back pain, and requiring longer time to admission, hospitalization, and antibiotic therapy.Conclusion: Pediatric spondylodiscitis is an insidious disease with a non-specific presentation in childhood and peculiarities of its own. However, when clinical remission is obtained by an early start of broad-spectrum antibiotics, prolonging the therapy does not improve, nor worsens, the outcome. Surgical management is mandatory in case of vertebral instability and neurological signs but can be avoided when the infection is promptly treated with antibiotic therapy.

2021 ◽  
Vol 12 ◽  
Yong Zhang ◽  
Shanshan Zheng ◽  
Wanjun Zhao ◽  
Yonghong Mao ◽  
Wei Cao ◽  

Deciphering the glycosylation of the viral envelope (Env) glycoprotein is critical for evaluating viral escape from the host’s immune response and developing vaccines and antiviral drugs. However, it is still challenging to precisely decode the site-specific glycosylation characteristics of the highly glycosylated Env proteins, although glycoproteomics have made significant advances in mass spectrometry techniques and data analysis tools. Here, we present a hybrid dissociation technique, EThcD-sceHCD, by combining electron transfer/higher-energy collisional dissociation (EThcD) and stepped collision energy/higher-energy collisional dissociation (sceHCD) into a sequential glycoproteomic workflow. Following this scheme, we characterized site-specific N/O-glycosylation of the human immunodeficiency virus type 1 (HIV-1) Env protein gp120. The EThcD-sceHCD method increased the number of identified glycopeptides when compared with EThcD, while producing more comprehensive fragment ions than sceHCD for site-specific glycosylation analysis, especially for accurate O-glycosite assignment. Finally, eighteen N-glycosites and five O-glycosites with attached glycans were assigned unambiguously from heavily glycosylated gp120. These results indicate that our workflow can achieve improved performance for analysis of the N/O-glycosylation of a highly glycosylated protein containing numerous potential glycosites in one process. Knowledge of the glycosylation landscape of the Env glycoprotein will be useful for understanding of HIV-1 infection and development of vaccines and drugs.

PLoS Genetics ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. e1009863
Michaela A. Gold ◽  
Jenna M. Whalen ◽  
Karine Freon ◽  
Zixin Hong ◽  
Ismail Iraqui ◽  

Disease-associated trinucleotide repeats form secondary DNA structures that interfere with replication and repair. Replication has been implicated as a mechanism that can cause repeat expansions and contractions. However, because structure-forming repeats are also replication barriers, it has been unclear whether the instability occurs due to slippage during normal replication progression through the repeat, slippage or misalignment at a replication stall caused by the repeat, or during subsequent replication of the repeat by a restarted fork that has altered properties. In this study, we have specifically addressed the fidelity of a restarted fork as it replicates through a CAG/CTG repeat tract and its effect on repeat instability. To do this, we used a well-characterized site-specific replication fork barrier (RFB) system in fission yeast that creates an inducible and highly efficient stall that is known to restart by recombination-dependent replication (RDR), in combination with long CAG repeat tracts inserted at various distances and orientations with respect to the RFB. We find that replication by the restarted fork exhibits low fidelity through repeat sequences placed 2–7 kb from the RFB, exhibiting elevated levels of Rad52- and Rad8ScRad5/HsHLTF-dependent instability. CAG expansions and contractions are not elevated to the same degree when the tract is just in front or behind the barrier, suggesting that the long-traveling Polδ-Polδ restarted fork, rather than fork reversal or initial D-loop synthesis through the repeat during stalling and restart, is the greatest source of repeat instability. The switch in replication direction that occurs due to replication from a converging fork while the stalled fork is held at the barrier is also a significant contributor to the repeat instability profile. Our results shed light on a long-standing question of how fork stalling and RDR contribute to expansions and contractions of structure-forming trinucleotide repeats, and reveal that tolerance to replication stress by fork restart comes at the cost of increased instability of repetitive sequences.

2021 ◽  
Vol 352 ◽  
pp. 54-60
Praveen Kulkarni ◽  
Nicole Bens ◽  
Dhruv K. Karia ◽  
Craig F. Ferris

2021 ◽  
Maryam Abdulali Abdulla ◽  
Azenith Castillo

Total Petroleum Hydrocarbons (TPHs) and Polycyclic Aromatic Hydrocarbons (PAHs) are priority pollutants, which are known to be associated with petroleum products. They are released into the marine environment via accidental spillage, exploration and transportation. The present study aims to investigate the type, origin and weathering of petroleum in the coastal marine sediment of the western coastline of Qatar. Sixty-six surface sediment samples were collected along the western coastal area. The concentrations of organic hydrocarbons (TPHs and PAHs) were determined using GC-FID and GC-MS, respectively. Sediment characteristics including pH, temperature, TOC and particle size were also measured. The results indicated low concentrations of TPH (<0.001-0.246 µg/g dry weight sediment) and PAHs (<0.001-0.044 µg/g dry weight sediment). The concentrations for both organic pollutants were lower compared to the previous studies done within Qatar and in the Arabian Gulf and also indicated below the available permissible limit set by the Ministry of Municipality and Environment of Qatar and other Sediment Quality Guidelines (SQGs) used worldwide (NOAA). Pollution concentration profile is site specific where concentrations are high within the proximity of the source and derived from both direct inputs of petrogenic and pyrogenic contribution.

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