Effects of integrated plant nutrition systems with fertilizer deep placement on rice yields and nitrogen use efficiency under different irrigation regimes.

Improved fertilizer management, with a combination of organic and inorganic inputs, has the potential to enhance rice yield while maintaining soil health. However, studies on the effects of broadcast prilled urea (PU) and urea deep placement (UDP) applied in combination with organic inputs (poultry litter [PL] and vermicompost [VC]), as integrated plant nutrition systems (IPNSs), on rice yields and nitrogen use efficiency (NUE) under alternate wetting and drying (AWD) irrigation are limited. We conducted field experiments during the dry and wet seasons of 2018, 2019, and 2020 to investigate the effects of fertilizer treatments, including control (no nitrogen), UDP, PU, and IPNSs (PU + VC, PU + PL, and UDP + PL) on rice yield and NUE under two irrigation regimes - AWD and continuous flooding (CF).

Genomic Complexity as a Biomarker to De-Escalate Adjuvant Imatinib Treatment in High-Risk Gastrointestinal Stromal Tumor.

Purpose: Adjuvant imatinib treatment is recommended for patients with localized gastrointestinal stromal tumor (GIST) at high risk of recurrence. Almost half of high-risk patients are cured by surgery alone, indicating a need for improved selection of patients for adjuvant therapy. The aim of this study was to investigate if genomic tumor complexity could be used as a prognostic biomarker.

Structural Organization of Human Full-Length PAR3 and the aPKC-PAR6 Complex.

The tripartite partition defect (PAR) polarity complex, which includes the proteins PAR3, atypical protein kinase C (aPKC), and PAR6, is a major regulator of cellular polarity. It is highly conserved and expressed in various tissues. Its largest component, PAR3, controls protein-protein interactions of the PAR complex with a variety of interaction partners, and PAR3 self-association is critical for the formation of filament-like structures.

Mitigating greenhouse gas emissions from irrigated rice cultivation through improved fertilizer and water management.

Greenhouse gas (GHG) emissions from agriculture sector play an important role for global warming and climate change. Thus, it is necessary to find out GHG emissions mitigation strategies from rice cultivation. The efficient management of nitrogen fertilizer using urea deep placement (UDP) and the use of the water-saving alternate wetting and drying (AWD) irrigation could mitigate greenhouse gas (GHG) emissions and reduce environmental pollution.

An assessment of irrigated rice cultivation with different crop establishment practices in Vietnam.

Overuse of seed and chemical inputs is a major constraint for sustainable rice production in Vietnam. In this study, two seasons of field trials were conducted to compare different crop establishment practices for rice production in the Mekong River Delta using environmental and economic sustainability performance indicators. The indicators including energy efficiency, agronomic use efficiency, net income, and greenhouse gas emissions (GHGEs) were quantified based on four treatments including manual broadcast-seeding, blower seeding, drum seeding, and mechanized transplanting.

Evolutionary patterns of chromosomal instability and mismatch repair deficiency in proximal and distal colorectal cancer.

Aim: Colorectal carcinomas (CRCs) progress through heterogeneous pathways. The aim of this study was to analyse whether or not the cytogenetic evolution of CRC is linked to tumour site, level of chromosomal imbalance and metastasis.

Method: A set of therapy-naïve pT3 CRCs comprising 26 proximal and 49 distal pT3 CRCs was studied by combining immunohistochemistry of mismatch repair (MMR) proteins, microsatellite analyses and molecular karyotyping as well as clinical parameters.

Expression of the Neural REST/NRSF-SIN3 Transcriptional Corepressor Complex as a Target for Small-Molecule Inhibitors.

The repressor element 1 (RE1) silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) modulates the expression of genes with RE1/neuron-restrictive silencing element (RE1/NRSE) sites by recruiting the switch independent 3 (SIN3) factor and the REST corepressor (COREST) to its N and C-terminal repressor domain, respectively. Both, SIN3 and COREST assemble into protein complexes that are composed of multiple subunits including a druggable histone deacetylase (HDAC) enzyme. The SIN3 core complex comprises the eponymous proteins SIN3A or SIN3B, the catalytically active proteins HDAC1 or HDAC2, the histone chaperone retinoblastoma-associated protein 46/retinoblastoma-binding protein 7 (RBAP46/RBBP7) or RBAP48/RBBP4, the SIN3-associated protein 30 (SAP30), and the suppressor of defective silencing 3 (SDS3).

Mitigation of greenhouse gas emissions and reduced irrigation water use in rice production through water-saving irrigation scheduling, reduced tillage and fertiliser application strategies.

Rice production systems are the largest anthropogenic wetlands on earth and feed more than half of the world's population. However, they are also a major source of global anthropogenic greenhouse gas (GHG) emissions. Several agronomic strategies have been proposed to improve water-use efficiency and reduce GHG emissions.

E-cadherin to P-cadherin switching in lobular breast cancer with tubular elements.

Loss of E-cadherin expression due to mutation of the CDH1 gene is a characteristic feature of invasive lobular breast cancer (ILBC). Beta-catenin, which binds to the cytoplasmic domain of E-cadherin, is simultaneously downregulated, reflecting disassembly of adherens junctions (AJs) and loss of cell adhesion. E-cadherin to P-cadherin expression switching can rescue AJs and cell adhesion.

Effects of water management on greenhouse gas emissions from farmers' rice fields in Bangladesh.

Alternate wetting and drying (AWD) irrigation in lowland rice cultivation increases water use efficiency and could reduce greenhouse gas (GHG) emissions compared to the farmers' practice of continuous flooding (CF). However, there is a dearth of studies on the impacts of water management on methane (CH) and nitrous oxide (NO) emissions in Bangladesh. Multi-location field experiments were conducted during the dry seasons of 2018 and 2019 to determine the baseline emissions of CH and NO from rice fields and compare the emissions from AWD irrigation and CF.

An assessment of irrigated rice production energy efficiency and environmental footprint with in-field and off-field rice straw management practices.

The research provided scientific evidences for improved rice straw management. Rice cultivation with in-field burning of rice straw is the worst option with the lowest energy efficiency and highest air pollution emission. This article comprises a comparative assessment of energy efficiency and the environmental footprint of rice production using four different rice straw management scenarios, namely, straw retained, straw burned, partial straw removal, and complete straw removal.

The FlpTRAP system for purification of specific, endogenous chromatin regions.

The repressor element 1-silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) binds to repressor element 1/neuron-restrictive silencer element (RE1/NRSE) sites in the genome and recruits effector proteins to repress its target genes. Here, we developed the FlpTRAP system to isolate endogenously assembled DNA-protein complexes such as the REST/NRSF complex. In the FlpTRAP system, we take advantage of the step-arrest variant of the Flp recombinase, FlpH305L, which, in the presence of Flp recognition target (FRT) DNA, accumulates as FRT DNA-protein adduct.

Optimal thresholds of risk parameters for gastrointestinal stromal tumors.

Background: Gastrointestinal stromal tumors (GIST) are the most frequent mesenchymal neoplasms of the gastrointestinal tract with highly variable potential for relapse. Tumor size and mitotic index (MI) are major risk factors that predict the outcome of GIST patients. Recent risk stratification schemes include some or all of the empirical size thresholds of 2 cm, 5 cm, and 10 cm and MI thresholds of 5 per 50 high-power fields (hpf) and 10 per 50 hpf.

The ATPase BRG1/SMARCA4 is a protein interaction platform that recruits BAF subunits and the transcriptional repressor REST/NRSF in neural progenitor cells.

The BAF complex (SWI/SNF) is an ATP-dependent chromatin remodeler that adapts the structural organization of the chromatin. Despite a growing understanding of the composition of BAF in different cell types, the interaction network within the BAF complex is poorly understood. Here, we characterized an isoform of the BRG1/SMARCA4 ATPase expressed in human neural progenitor cells.

Modulating the Expression Strength of the Baculovirus/Insect Cell Expression System: A Toolbox Applied to the Human Tumor Suppressor SMARCB1/SNF5.

The human tumor suppressor SMARCB1/INI1/SNF5/BAF47 (SNF5) is a core subunit of the multi-subunit ATP-dependent chromatin remodeling complex SWI/SNF, also known as Brahma/Brahma-related gene 1 (BRM/BRG1)-associated factor (BAF). Experimental studies of SWI/SNF are currently considerably limited by the low cellular abundance of this complex; thus, recombinant protein production represents a key to obtain the SWI/SNF proteins for molecular and structural studies. While the expression of mammalian proteins in bacteria is often difficult, the baculovirus/insect cell expression system can overcome limitations of prokaryotic expression systems and facilitate the co-expression of multiple proteins.

Paddy soil drainage influences residue carbon contribution to methane emissions.

Water drainage is an important mitigation option for reducing CH (methane) emissions from residue-amended paddy soils. Several studies have indicated a long-term reduction in CH emissions, even after re-flooding, suggesting that the mechanism goes beyond creating temporary oxidized conditions in the soil. In this pot trial, the effects of different drainage patterns on straw-derived CH and CO (carbon dioxide) emissions were compared to identify the balance between straw-carbon CH and CO emissions influenced by soil aeration over different periods, including effects of drainage on emissions during re-flooding.

Folding and assembly defects of pyruvate dehydrogenase deficiency-related variants in the E1α subunit of the pyruvate dehydrogenase complex.

The pyruvate dehydrogenase complex (PDC) bridges glycolysis and the citric acid cycle. In human, PDC deficiency leads to severe neurodevelopmental delay and progressive neurodegeneration. The majority of cases are caused by variants in the gene encoding the PDC subunit E1α.

Increasing sensitivity of methane emission measurements in rice through deployment of 'closed chambers' at nighttime.

This study comprises field experiments on methane emissions from rice fields conducted with an Eddy-Covariance (EC) system as well as test runs for a modified closed chamber approach based on measurements at nighttime. The EC data set covers 4 cropping seasons with highly resolved emission rates (raw data in 10 Hz frequency have been aggregated to 30-min records). The diel patterns were very pronounced in the two dry seasons with peak emissions at early afternoon and low emissions at nighttime.

Vectors for Expression of Signal Peptide-Dependent Proteins in Baculovirus/Insect Cell Systems and Their Application to Expression and Purification of the High-Affinity Immunoglobulin Gamma Fc Receptor I in Complex with Its Gamma Chain.

Integral membrane proteins play a central role in various cellular functions and are important therapeutic targets. However, technical challenges in the overexpression and purification of membrane proteins often represent a limiting factor for biochemical and structural studies. Here, we constructed a set of vectors, derivatives of MultiBac vectors that can be used to express proteins with a cleavable N-terminal signal peptide in insect cells.

The effective mitigation of greenhouse gas emissions from rice paddies without compromising yield by early-season drainage.

Global rice production systems face two opposing challenges: the need to increase production to accommodate the world's growing population while simultaneously reducing greenhouse gas (GHG) emissions. Adaptations to drainage regimes are one of the most promising options for methane mitigation in rice production. Whereas several studies have focused on mid-season drainage (MD) to mitigate GHG emissions, early-season drainage (ED) varying in timing and duration has not been extensively studied.

Hemoglobin polymerization via disulfide bond formation in the hypoxia-tolerant turtle Trachemys scripta: implications for antioxidant defense and O transport.

The ability of many reptilian hemoglobins (Hbs) to form high-molecular weight polymers, albeit known for decades, has not been investigated in detail. Given that turtle Hbs often contain a high number of cysteine (Cys), potentially contributing to the red blood cell defense against reactive oxygen species, we have examined whether polymerization of Hb could occur via intermolecular disulfide bonds in red blood cells of freshwater turtle Trachemys scripta, a species that is highly tolerant of hypoxia and oxidative stress. We find that one of the two Hb isoforms of the hemolysate HbA is prone to polymerization in vitro into linear flexible chains of different size that are visible by electron microscopy but not the HbD isoform.

Subclonal analysis in a lobular breast cancer with classical and solid growth pattern mimicking a solid-papillary carcinoma.

Recently, a new variant of invasive lobular breast cancer (ILBC) with solid-papillary-like growth pattern has been described. We present a case of ILBC with solid-papillary-like growth pattern in the main tumour mass and classical invasive lobular growth pattern in adjacent satellite foci. The two tumour components were subjected to comprehensive molecular analyses.

Expression of Flp Protein in a Baculovirus/Insect Cell System for Biotechnological Applications.

The Saccharomyces cerevisiae Flp protein is a site-specific recombinase that recognizes and binds to the Flp recognition target (FRT) site, a specific sequence comprised of at least two inverted repeats separated by a spacer. Binding of four monomers of Flp is required to mediate recombination between two FRT sites. Because of its site-specific cleavage characteristics, Flp has been established as a genome engineering tool.

Synergistic anti-cancer effects of epigenetic drugs on medulloblastoma cells.

Purpose: Medulloblastomas are aggressive brain malignancies. While considerable progress has been made in the treatment of medulloblastoma patients with respect to overall survival, these patients are still at risk of developing neurologic and cognitive deficits as a result of anti-cancer therapies. It is hypothesized that targeted molecular therapies represent a better treatment option for medulloblastoma patients.