Large Scale Screening of Rhizospheric Allelopathic Bacteria and Their Potential for the Biocontrol of Wheat-Associated Weeds

Conventional weed control practices have generated serious issues related to the environment and human health. Therefore, there is a demand for the development of alternative techniques for sustainable agriculture. The present study performed a large-scale screening of allelopathic bacteria from the rhizosphere of weeds and wheat to obtain biological weed control inoculants in the cultivation of wheat. Initially, around 400 strains of rhizobacteria were isolated from the rhizosphere of weeds as well as wheat that grows in areas of chronic weed invasions. A series of the screen was performed on these strains, including the release of phytotoxic metabolites, growth inhibition of sensitive Escherichia coli, growth inhibition of indicator plant of lettuce, agar bioassays on five weeds, and agar bioassay on wheat. Firstly, 22.6% (89 strains) of the total strains were cyanogenic, and among the cyanogenic strains, 21.3% (19 strains) were inhibitory to the growth of sensitive E. coli. Then, these 19 strains were tested using lettuce seedling bioassay to show that eight strains suppressed, nine strains promoted, and two strains remained ineffective on the growth. These 19 strains were further applied to weeds and wheat on agar bioassays. The results indicated that dry matter of broad-leaved dock, wild oat, little seed canary grass, and common lambs’ quarter were reduced by eight strains (23.1–68.1%), seven strains (38.5–80.2%), eight strains (16.5–69.4%), and three strains (27.5–50.0%), respectively. Five strains suppressed the growth of wheat, nine strains increased its dry matter (12.8–47.9%), and five remained ineffective. Altogether, the strains that selectively inhibit weeds, while retaining normal growth of wheat, can offer good opportunities for the development of biological weed control in the cultivation of wheat.

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Field Performance of Allelopathic Bacteria for Biological Weed Control in Wheat: Innovative, Sustainable and Eco-Friendly Approach for Enhanced Crop Production

Sustainability ◽

10.3390/su12218936 ◽

2020 ◽

Vol 12 (21) ◽

pp. 8936

Author(s):

Tasawar Abbas ◽

Zahir Ahmad Zahir ◽

Muhammad Naveed ◽

Mona S. Alwahibi ◽

Mohamed Soliman Elshikh ◽

...

Keyword(s):

Grain Yield ◽

Weed Control ◽

Field Trial ◽

Weed Suppression ◽

Control Technique ◽

Biological Weed Control ◽

Wild Oat ◽

Weed Invasion ◽

Canary Grass ◽

Pot Trial

Application of allelopathic bacteria (AB) for weed suppression may be helpful to solve various environmental challenges posed by conventional weed control techniques. In our earlier studies, around 400 strains of rhizobacteria of five weeds and wheat were isolated, screened for production of phytotoxic substances, and tested for phytotoxic activity on wild oat and little seed canary grass, and possible effects on wheat under laboratory conditions. We obtained 13 strains inhibitory to wild oat (Avena fatua L.) and 11 to little seed canary grass (Phalaris minor Retz.). Five of these (13 and 11) strains also suppressed wheat (Triticum aestivum L.) while others either stimulated or remained ineffective on wheat in separate bioassays. The success of any weed biocontrol technique, however, depends on its response under field conditions. Therefore, the present study was conducted to investigate biological weed control of the five most efficient strains of AB under natural conditions in pot and field trials. Wheat was artificially invaded with wild oat in the pot trial through seeding. Wheat of the field trial was artificially invaded with wild oat and little seed canary through seeding. The selected strains belonged to pseudomonads (Pseudomonas putida, P. fluorescence, P. aeruginosa, and P. alcaligenes) and their inocula were prepared using sterilized peat. The inoculated seeds of wild oat and wheat were sown together in a pot trial. The inoculated seeds of wild oat, little seed canary grass, and wheat were sown together in the field experiment. The field was selected based on chronic infestation of these weeds. However, weed invasion was ensured by adding seeds of weeds (inoculated with the respective strains of AB, according to treatment plan). A severe invasion of wild oat was observed in the pot trial, which reduced the grain yield of infested wheat up to 60.8%. The effectiveness of applied strains controlled 22.0–76.3% loss of grain yield of infested wheat. Weed invasion in the field trial reduced the grain yield of the crop up to 56.3% and effectiveness of the applied strains controlled 29.0–60.7% loss of grain yield of infested wheat. The study of other agronomic, physiological, and chemical parameters of the crop and weeds supported these findings. Harnessing the potential of these strains exhibited in our studies may be helpful to introduce an innovative, sustainable, and eco-friendly weed control technique for production of wheat.

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Large carabids enhance weed seed removal in organic fields and in large-scale, but not small-scale agriculture

Landscape Ecology ◽

10.1007/s10980-020-01157-8 ◽

2020 ◽

Author(s):

Christina Fischer ◽

Friederike Riesch ◽

Teja Tscharntke ◽

Péter Batáry

Keyword(s):

Body Size ◽

Weed Control ◽

Large Scale ◽

Landscape Scale ◽

Agricultural Landscapes ◽

Biological Weed Control ◽

Seed Removal ◽

Weed Seed ◽

Activity Density ◽

Wheat Seeds

Abstract Context Biological weed control by seed predators is an ecosystem service reducing weed population densities in agricultural landscapes. Drivers of seed predation are manifold and may change with spatial scales considered. Objectives We aimed at identifying the functional identity of seed predators, food web interactions and feeding links between weed and wheat seeds, considering the causal relationships between local and landscape-scale patterns. Methods We investigated direct and indirect effects of local management intensity in winter wheat fields (organic vs. conventional farming), local crop characteristics (wheat density and height), edge effects, landscape composition (measured as land-use diversity) and configuration (edge length) on carabid beetles of different body size (large vs. small carabids), and removal of weed and wheat seeds. Results We showed the importance of indirect local- and landscape-scale effects for weed seed removal via the activity density, but not assemblage composition, of large, but not small carabids, which was driven by few ubiquitous species. The activity density of large carabids increased with decreasing wheat density and increasing wheat height, which was highest in organic fields and in landscapes with low compositional and configurational heterogeneity. Further, the availability of nutrient-rich wheat seeds enhanced weed seed removal rates. Conclusions We found highest weed seed removal via large carabids in organic fields in large-scale agricultural landscapes. Predator body size and species identity as well as the availability of additional food items need to be taken into account for better predicting the biological weed control potential and reducing the use of plant protection products.

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Immunogold labeling of CMP-KDO synthetase produced by recombinant E. Coli cells

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100128900 ◽

1987 ◽

Vol 45 ◽

pp. 924-925

Author(s):

F. A. Durum ◽

R. G. Goldman ◽

T. J. Bolling ◽

M. F. Miller

Keyword(s):

Inclusion Bodies ◽

Large Scale ◽

Recombinant Dna ◽

Test System ◽

Cell Protein ◽

Gram Negative Bacteria ◽

Cytoplasmic Inclusions ◽

Isolation And Purification ◽

E Coli ◽

Low Concentrations

CMP-KDO synthetase (CKS) is an enzyme which plays a key role in the synthesis of LPS, an outer membrane component unique to gram negative bacteria. CKS activates KDO to CMP-KDO for incorporation into LPS. The enzyme is normally present in low concentrations (0.02% of total cell protein) which makes it difficult to perform large scale isolation and purification. Recently, the gene for CKS from E. coli was cloned and various recombinant DNA constructs overproducing CKS several thousandfold (unpublished data) were derived. Interestingly, no cytoplasmic inclusions of overproduced CKS were observed by EM (Fig. 1) which is in contrast to other reports of large proteinaceous inclusion bodies in various overproducing recombinant strains. The present immunocytochemical study was undertaken to localize CKS in these cells.Immune labeling conditions were first optimized using a previously described cell-free test system. Briefly, this involves soaking small blocks of polymerized bovine serum albumin in purified CKS antigen and subjecting them to various fixation, embedding and immunochemical conditions.

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Training Aides to Screen Children for Speech and Language Problems

Language Speech and Hearing Services in Schools ◽

10.1044/0161-1461.0704.236 ◽

1976 ◽

Vol 7 (4) ◽

pp. 236-241 ◽

Cited By ~ 5

Author(s):

Marisue Pickering ◽

William R. Dopheide

Keyword(s):

Rural Areas ◽

Large Scale ◽

School Personnel ◽

School Age Children ◽

Speech And Language ◽

Elementary School Age ◽

Evaluation Procedures ◽

Language Problems ◽

Competency Based ◽

Large Scale Screening

This report deals with an effort to begin the process of effectively identifying children in rural areas with speech and language problems using existing school personnel. A two-day competency-based workshop for the purpose of training aides to conduct a large-scale screening of speech and language problems in elementary-school-age children is described. Training strategies, implementation, and evaluation procedures are discussed.

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Identification of N-Substituted Triazolo-azetidines as Novel Antibacterials using pDualrep2 HTS Platform

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207322666190412165316 ◽

2019 ◽

Vol 22 (5) ◽

pp. 346-354

Author(s):

Yan A. Ivanenkov ◽

Renat S. Yamidanov ◽

Ilya A. Osterman ◽

Petr V. Sergiev ◽

Vladimir A. Aladinskiy ◽

...

Keyword(s):

Antibacterial Activity ◽

Large Scale ◽

Underlying Mechanism ◽

Luciferase Assay ◽

Reporter System ◽

E Coli ◽

Starting Point ◽

High Concentrations ◽

Mic Value

Aim and Objective: Antibiotic resistance is a serious constraint to the development of new effective antibacterials. Therefore, the discovery of the new antibacterials remains one of the main challenges in modern medicinal chemistry. This study was undertaken to identify novel molecules with antibacterial activity. Materials and Methods: Using our unique double-reporter system, in-house large-scale HTS campaign was conducted for the identification of antibacterial potency of small-molecule compounds. The construction allows us to visually assess the underlying mechanism of action. After the initial HTS and rescreen procedure, luciferase assay, C14-test, determination of MIC value and PrestoBlue test were carried out. Results: HTS rounds and rescreen campaign have revealed the antibacterial activity of a series of Nsubstituted triazolo-azetidines and their isosteric derivatives that has not been reported previously. Primary hit-molecule demonstrated a MIC value of 12.5 µg/mL against E. coli Δ tolC with signs of translation blockage and no SOS-response. Translation inhibition (26%, luciferase assay) was achieved at high concentrations up to 160 µg/mL, while no activity was found using C14-test. The compound did not demonstrate cytotoxicity in the PrestoBlue assay against a panel of eukaryotic cells. Within a series of direct structural analogues bearing the same or bioisosteric scaffold, compound 2 was found to have an improved antibacterial potency (MIC=6.25 µg/mL) close to Erythromycin (MIC=2.5-5 µg/mL) against the same strain. In contrast to the parent hit, this compound was more active and selective, and provided a robust IP position. Conclusion: N-substituted triazolo-azetidine scaffold may be used as a versatile starting point for the development of novel active and selective antibacterial compounds.

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Recent Progress in Machine Learning-based Prediction of Peptide Activity for Drug Discovery

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666190122151634 ◽

2019 ◽

Vol 19 (1) ◽

pp. 4-16 ◽

Cited By ~ 6

Author(s):

Qihui Wu ◽

Hanzhong Ke ◽

Dongli Li ◽

Qi Wang ◽

Jiansong Fang ◽

...

Keyword(s):

Machine Learning ◽

Drug Discovery ◽

Large Scale ◽

Recent Progress ◽

High Specificity ◽

Learning Approaches ◽

Anticancer Peptides ◽

The Past ◽

Traditional Approaches ◽

Large Scale Screening

Over the past decades, peptide as a therapeutic candidate has received increasing attention in drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory peptides (AIPs). It is considered that the peptides can regulate various complex diseases which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide- based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the peptide activity. In this review, we document the recent progress in machine learning-based prediction of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.

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Large-scale High-throughput Screening Revealed 5'-(carbonylamino)-2,3'- bithiophene-4'-carboxylate as Novel Template for Antibacterial Agents

Current Drug Discovery Technologies ◽

10.2174/1570163816666190603095521 ◽

2020 ◽

Vol 17 (5) ◽

pp. 716-724

Author(s):

Yan A. Ivanenkov ◽

Renat S. Yamidanov ◽

Ilya A. Osterman ◽

Petr V. Sergiev ◽

Vladimir A. Aladinskiy ◽

...

Keyword(s):

Antibacterial Activity ◽

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Antibacterial Agents ◽

Sos Response ◽

Luciferase Assay ◽

Translational Machinery ◽

E Coli ◽

New Class

Background: The key issue in the development of novel antimicrobials is a rapid expansion of new bacterial strains resistant to current antibiotics. Indeed, World Health Organization has reported that bacteria commonly causing infections in hospitals and in the community, e.g. E. Coli, K. pneumoniae and S. aureus, have high resistance vs the last generations of cephalosporins, carbapenems and fluoroquinolones. During the past decades, only few successful efforts to develop and launch new antibacterial medications have been performed. This study aims to identify new class of antibacterial agents using novel high-throughput screening technique. Methods: We have designed library containing 125K compounds not similar in structure (Tanimoto coeff.< 0.7) to that published previously as antibiotics. The HTS platform based on double reporter system pDualrep2 was used to distinguish between molecules able to block translational machinery or induce SOS-response in a model E. coli system. MICs for most active chemicals in LB and M9 medium were determined using broth microdilution assay. Results: In an attempt to discover novel classes of antibacterials, we performed HTS of a large-scale small molecule library using our unique screening platform. This approach permitted us to quickly and robustly evaluate a lot of compounds as well as to determine the mechanism of action in the case of compounds being either translational machinery inhibitors or DNA-damaging agents/replication blockers. HTS has resulted in several new structural classes of molecules exhibiting an attractive antibacterial activity. Herein, we report as promising antibacterials. Two most active compounds from this series showed MIC value of 1.2 (5) and 1.8 μg/mL (6) and good selectivity index. Compound 6 caused RFP induction and low SOS response. In vitro luciferase assay has revealed that it is able to slightly inhibit protein biosynthesis. Compound 5 was tested on several archival strains and exhibited slight activity against gram-negative bacteria and outstanding activity against S. aureus. The key structural requirements for antibacterial potency were also explored. We found, that the unsubstituted carboxylic group is crucial for antibacterial activity as well as the presence of bulky hydrophobic substituents at phenyl fragment. Conclusion: The obtained results provide a solid background for further characterization of the 5'- (carbonylamino)-2,3'-bithiophene-4'-carboxylate derivatives discussed herein as new class of antibacterials and their optimization campaign.

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Analytical Validation and Clinical Application of Rapid Serological Tests for SARS-CoV-2 Suitable for Large-Scale Screening

Diagnostics ◽

10.3390/diagnostics11050869 ◽

2021 ◽

Vol 11 (5) ◽

pp. 869

Author(s):

Amedeo De Nicolò ◽

Valeria Avataneo ◽

Jessica Cusato ◽

Alice Palermiti ◽

Jacopo Mula ◽

...

Keyword(s):

Early Diagnosis ◽

Real Time Pcr ◽

Large Scale ◽

High Sensitivity ◽

Analytical Validation ◽

Pcr Assay ◽

Serological Tests ◽

Flow Test ◽

Lateral Flow Test ◽

Large Scale Screening

Recently, large-scale screening for COVID-19 has presented a major challenge, limiting timely countermeasures. Therefore, the application of suitable rapid serological tests could provide useful information, however, little evidence regarding their robustness is currently available. In this work, we evaluated and compared the analytical performance of a rapid lateral-flow test (LFA) and a fast semiquantitative fluorescent immunoassay (FIA) for anti-nucleocapsid (anti-NC) antibodies, with the reverse transcriptase real-time PCR assay as the reference. In 222 patients, LFA showed poor sensitivity (55.9%) within two weeks from PCR, while later testing was more reliable (sensitivity of 85.7% and specificity of 93.1%). Moreover, in a subset of 100 patients, FIA showed high sensitivity (89.1%) and specificity (94.1%) after two weeks from PCR. The coupled application for the screening of 183 patients showed satisfactory concordance (K = 0.858). In conclusion, rapid serological tests were largely not useful for early diagnosis, but they showed good performance in later stages of infection. These could be useful for back-tracing and/or to identify potentially immune subjects.

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BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space

International Journal of Molecular Sciences ◽

10.3390/ijms22157773 ◽

2021 ◽

Vol 22 (15) ◽

pp. 7773

Author(s):

Neann Mathai ◽

Conrad Stork ◽

Johannes Kirchmair

Keyword(s):

Large Scale ◽

Computational Approach ◽

Large Sets ◽

Compound Libraries ◽

Wide Range ◽

Protein Space ◽

High Chance ◽

Large Scale Screening ◽

Early Drug ◽

Selection Of

Experimental screening of large sets of compounds against macromolecular targets is a key strategy to identify novel bioactivities. However, large-scale screening requires substantial experimental resources and is time-consuming and challenging. Therefore, small to medium-sized compound libraries with a high chance of producing genuine hits on an arbitrary protein of interest would be of great value to fields related to early drug discovery, in particular biochemical and cell research. Here, we present a computational approach that incorporates drug-likeness, predicted bioactivities, biological space coverage, and target novelty, to generate optimized compound libraries with maximized chances of producing genuine hits for a wide range of proteins. The computational approach evaluates drug-likeness with a set of established rules, predicts bioactivities with a validated, similarity-based approach, and optimizes the composition of small sets of compounds towards maximum target coverage and novelty. We found that, in comparison to the random selection of compounds for a library, our approach generates substantially improved compound sets. Quantified as the “fitness” of compound libraries, the calculated improvements ranged from +60% (for a library of 15,000 compounds) to +184% (for a library of 1000 compounds). The best of the optimized compound libraries prepared in this work are available for download as a dataset bundle (“BonMOLière”).

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Large-scale screening of natural genetic resource in the hydrocarbon-producing microalga Botrycoccus braunii identified novel fast-growing strains

Scientific Reports ◽

10.1038/s41598-021-86760-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Koji Kawamura ◽

Suzune Nishikawa ◽

Kotaro Hirano ◽

Ardianor Ardianor ◽

Rudy Agung Nugroho ◽

...

Keyword(s):

Large Scale ◽

Biomass Productivity ◽

Botryococcus Braunii ◽

Algal Biofuel ◽

Fast Growing ◽

Wild Strains ◽

Glass Tubes ◽

The Tropics ◽

Large Scale Screening ◽

Hydrocarbon Productivity

AbstractAlgal biofuel research aims to make a renewable, carbon–neutral biofuel by using oil-producing microalgae. The freshwater microalga Botryococcus braunii has received much attention due to its ability to accumulate large amounts of petroleum-like hydrocarbons but suffers from slow growth. We performed a large-scale screening of fast-growing strains with 180 strains isolated from 22 ponds located in a wide geographic range from the tropics to cool-temperate. A fast-growing strain, Showa, which recorded the highest productivities of algal hydrocarbons to date, was used as a benchmark. The initial screening was performed by monitoring optical densities in glass tubes and identified 9 wild strains with faster or equivalent growth rates to Showa. The biomass-based assessments showed that biomass and hydrocarbon productivities of these strains were 12–37% and 11–88% higher than that of Showa, respectively. One strain, OIT-678 established a new record of the fastest growth rate in the race B strains with a doubling time of 1.2 days. The OIT-678 had 36% higher biomass productivity, 34% higher hydrocarbon productivity, and 20% higher biomass density than Showa at the same cultivation conditions, suggesting the potential of the new strain to break the record for the highest productivities of hydrocarbons.

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