Critical stage and key natural mortality factors of Hypothenemus hampei in commercial coffee plantations

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Critical stage and key natural mortality factors of Hypothenemus hampei in commercial coffee plantations

Predators ants, parasitoids, entomopathogenic fungi, and malformations during the Hyphothenemus hampei life cycle caused 75.34% of the mortalities seen within their populations. Adult mortality is the principal factor that regulates the size of populations of this insect. Predatory ants were the key mortality factor for H. hampei.


Abstract

The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae), is one of the most important coffee pests, and is present in almost all countries producing this crop, causing annual losses of US$350 million. Natural factors regulate H. hampei populations in coffee crops. Ecological life table analysis is a robust tool that allows the estimation of the mortality caused by these factors. Therefore, the main objective of this study was to determine the critical stage and the key mortality factors affecting H. hampei in the field. Data for constructing life tables were collected over 2 years in six coffee plantations in the regions of Paula Cândido and Viçosa, Minas Gerais State, Brazil. The average mortality of H. hampei was 75.34% ± 5.85%. The mortality at each developmental stage was 24.32% ± 2.83% (eggs), 7.29% ± 1.01% (first instar), 11.58% ± 1.46% (second instar), 9.68% ± 1.10% (third instar), 7.45% ± 1.01% (pupa), and 15.02% ± 1.29% (adult; n = 124). The mortality factors observed and quantified in this study were parasitism by Prorops nasuta (Hymenoptera: Bethylidae), predation by ants (Crematogaster spp., Pheidole spp. and Solenopsis spp.), physiological disorders and fungal infection by Beauveria bassiana and Metarhizium anisopliae. The critical mortality stage of H. hampei was the adult stage. The key factors for mortality of H. hampei adults were predatory ants, followed by B. bassiana and malformations (these insects had deformities in the head, wings, legs, or abdomen). This information is essential to conserve the activities of natural enemies and, thus maintain H. hampei natural mortality factors in coffee plantations, reducing damage to the crops and the need for excessive insecticide interventions.

The structure of a Lactobacillus helveticus chlorogenic acid esterase and the dynamics of its insertion domain provide insights into substrate binding

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The structure of a Lactobacillus helveticus chlorogenic acid esterase and the dynamics of its insertion domain provide insights into substrate binding

Chlorogenic acid esterases are biotechnologically useful enzymes that hydrolyze unwanted chlorogenic acid in foods, thereby improving their sensory properties. This work determines how two residues on hairpin loops above the active site influence substrate binding and turnover in a bacterial chlorogenic acid esterase.


Chlorogenic acid esterases (ChlEs) are a useful class of enzymes that hydrolyze chlorogenic acid (CGA) into caffeic and quinic acids. ChlEs can break down CGA in foods to improve their sensory properties and release caffeic acid in the digestive system to improve the absorption of bioactive compounds. This work presents the structure, molecular dynamics, and biochemical characterization of a ChlE from Lactobacillus helveticus (Lh). Molecular dynamics simulations suggest that substrate access to the active site of LhChlE is modulated by two hairpin loops above the active site. Docking simulations and mutational analysis suggest that two residues within the loops, Gln145 and Lys164, are important for CGA binding. Lys164 provides a slight substrate preference for CGA, whereas Gln145 is required for efficient turnover. This work is the first to examine the dynamics of a bacterial ChlE and provides insights on substrate binding preference and turnover in this type of enzyme.

Source‐sink patterns on coffee trees related to annual climate variability: An approach through stable isotopes analysis

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Source-sink patterns on coffee trees related to annual climate variability: An approach through stable isotopes analysis

This study highlights the importance of using stable isotope analysis as a reference point for long-term coffee ecophysiological studies. We have provided evidence to support the hypothesis that variations in the δ13C and δ15N values for the dry matter of bulk material from leaves, heterotrophic organs, and the cellulose in the growth tree rings of coffee trees have temporal and spatial patterns that suggest the differential use of substrates and signals the influence of the climate on the growth and phenology of the trees.


Abstract

Stable isotopic determination constitutes a useful tool to identify the processes that control the dynamics of the carbon and nitrogen flow in plants, unravelling the mechanisms of their differential investment under different environments. This work aimed to evaluate the spatiotemporal variation of source-sink patterns of coffee trees under field conditions in response to climatic conditions through the assessment of stable isotopes. For this purpose, stems, leaves, and fruit samples from coffee trees were collected following a temporal pattern based on the region's climatic characteristics and the plant's phenology and a spatial pattern considering different parts of the canopy. The carbon and nitrogen percentage content, the C/N ratio, and the carbon and nitrogen isotopic compositions (δ13C and δ15N) were determined for all samples. The basal portion of the orthotropic branch was also considered for the isotopic analysis of the tree's growth rings. The results obtained were correlated with the climatic variables of the region through a Pearson correlation analysis (p < .05). Coffee plants showed traditional δ13C values of C3 plants. Temporal δ13C variation was associated with the different growth rates between phenological stages and the use of substrates produced at different times under different environmental conditions leading to differences in photosynthetic discrimination. Spatial δ13C variation was observed with heterotrophic tissues isotopically heavier than leaves, with a significant decrease trend in δ13C values from the top (upper third) to the bottom (lower third), associated with ecophysiological differences between the canopy, isotopic fractionation processes downstream of photosynthetic carbon discrimination, and the fixation of C from other pools. Temporal δ15N variation was associated with the precipitation rates in the region and the fertilization distribution across the tree, while the spatial variation was with the plant's nitrogen assimilation and translocation patterns. The tree growth rings isotopic analyses showed isotopic differences between growth rings of the same plant addressed by the climatic conditions, with precipitation being the primary climatic determinant influencing the fixation and discrimination against 13C. Our results highlight the importance of using stable isotope analysis as a reference point for coffee ecophysiological studies to characterize how the temporal and spatial patterns of δ13C and δ15N emerge and signal the influence of climate on the source-sink relationship of coffee trees under field conditions.

Assigning functionality to cysteines by base editing of cancer dependency genes

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Nature Chemical Biology, Published online: 02 October 2023; doi:10.1038/s41589-023-01428-w

Determining which covalent binding events impact protein function is challenging. Now, a strategy has been reported that integrates base editing and chemical proteomics to infer the functionality of ligandable cysteines in cancer dependency proteins by quantifying the impact of their missense mutation on cancer cell proliferation.

Manipulating table beet growth using exogeneous gibberellic acid 3 in New York, USA

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Manipulating table beet growth using exogeneous gibberellic acid 3 in New York, USA

Table beets are grown in New York, USA for processing into cans and jars (left) for which their suitability is dictated by quality and root shoulder diameter.


Abstract

Table beet (Beta vulgaris ssp. vulgaris) root suitability for processing into cans and jars is dictated by quality and shoulder diameter (crown width). For shoulder diameter, roots are sorted into six classes and those in the small (19.1–44.5 mm) and small/medium (44.6–40.8 mm) classes are considered suitable. Smaller (≤19 mm) roots are usually lost in harvesting while larger (≥40.9 mm) roots are typically discarded. Exogenous (foliar-applied) gibberellic acid 3 (GA3) may alter source-sink carbohydrate partitioning with potential advantages for processing table beet producers. Small plot replicated trials were conducted in each of 3 years (2020, 2021 and 2022) to evaluate the effect and optimal timing of exogenous GA3 on table beet yield components in New York, USA. GA3 was applied as ProGibb at 30 ppm in all trials and as ProGibb at 30 ppm and FalGro 2X LV at 67 ppm (label rates) in 2022. GA3 as ProGibb resulted in significant increases in foliar health attributes (leaf blade length and width, petiole diameter, normalized difference vegetative index and dry weight of foliage). GA3 as ProGibb significantly reduced average root shoulder diameter and affected the percentage of roots in various size categories. The percentage of tiny roots (<19 mm) was significantly decreased while the percentage of small roots was increased. The percentage of small/medium roots were unaffected. In 2022, the percentage of small roots was significantly increased compared to nontreated plots but was not significantly different between GA3 as either ProGibb or FalGro applied at 42 or 62 Days after Planting (DAP). Exogenous GA3 had no consistent, significant effect on the severity of the foliar disease, Cercospora leaf spot. The significant increase in foliar health attributes from GA3 is beneficial for harvest that relies upon top pulling machinery. Increases in the percentage of small roots and reductions in tiny roots can reduce wasted crop input investments. The optimal number of GA3 applications was seasonally dependent, ranging from a single application at 40 or 62 DAP in 2 years, to two applications in 2021. GA3 applications late (>80 DAP) in the cropping season had no significant effect on foliar health attributes or root yield components. The implications of these results on the New York table beet processing industry are discussed.

Deroceras laeve as a potential agricultural pest in Darjeeling Himalayas, India: Palatability and preference of economically important plants

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Deroceras laeve as a potential agricultural pest in Darjeeling Himalayas, India: Palatability and preference of economically important plants

The plant food preference and palatability of the slug Deroceras laeve, reported from Darjeeling Himalayas, India, was assessed. The pumpkin leaf was consumed maximally by D. laeve while mint leaf was least consumed, though the fecundity was higher in lettuce and cabbage diet. Apart from being positively linked with body mass, the consumption rate of D. laeve was considerably higher than the controphic slug, Meghimatium bilineatum.


Abstract

The invasion of the terrestrial ecosystem by gastropods has immense negative impacts on ecosystem functions, health, and agricultural plants. The non-native slug, Deroceras laeve (O. F. Müller, 1774), a recognised agricultural pest in native and invaded regions, was recently reported from the Darjeeling Himalayas, India. We assessed the plant palatability and preference of D. laeve using selected plants being farmed in Darjeeling Himalayas (basil, cabbage, coriander, lettuce, mint, pumpkin leaf, and spinach) by laboratory-based choice and non-choice experiments. Moreover, we evaluated the correlation between different chemical features of the plants with the consumption rate of D. laeve and observed the fecundity of D. laeve reared on different plant diets. The highest consumption rate of D. laeve was observed for pumpkin (12.99 ± 1.33 mg dry mass) and the lowest for mint (1.63 ± 0.13 mg dry mass), with a significant positive correlation between consumption rate and D. laeve body mass (for lettuce: R = .47, p = .0009 and other plant species: R = .52, p = .00004) was observed through the non-choice experiment. Moreover, the consumption rate of the non-native slug, D. laeve, was considerably higher than a controphic slug, Meghimatium bilineatum. In the choice experiment, D. laeve preferred lettuce, followed by pumpkin, cabbage, and coriander, even in the presence of detritus and significantly avoided spinach, mint, and basil. The consumption rate of D. laeve had a significant negative correlation with calcium (R = −.49, p = .003) and potassium (R = −.37, p = .03), and a positive correlation was observed for magnesium (R = .37, p = .03). However, no correlation was observed for zinc, silica, total carbohydrate, protein, and phenol content of the leaves. The highest fecundity of D. laeve was observed in the lettuce and cabbage diet, while no eggs were laid on the mint diet. Hence, the consumption of different leaves, irrespective of physical and chemical features (hairiness, amount of silicon, protein, carbohydrate, and phenol), suitable life history traits, and suitable habitats, may facilitate D. laeve as a potential agricultural pest in the Darjeeling Himalayas, India.

A historical perspective of macroautophagy regulation by biochemical and biomechanical stimuli

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A historical perspective of macroautophagy regulation by biochemical and biomechanical stimuli

Autophagy is stimulated by starvation (amino acids and/or glucose deprivation) and growth factor limitation. In addition, mechanical forces are also positive regulators of autophagy. Growth factors and mechanical forces trigger signaling from the cell surface including from the primary cilium (PC) whereas nutrients directly act intracellularly. Many of the stimuli that control autophagy converge on the kinases mTOR and AMPK.


Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates and organelles. The formation of the autophagosome, a double membrane-bound structure that sequesters cargoes before their delivery to the lysosome, is regulated by several stimuli in multicellular organisms. Pioneering studies in rat liver showed the importance of amino acids, insulin and glucagon in controlling macroautophagy. Thereafter, many studies have deciphered the signaling pathways downstream of these biochemical stimuli to control autophagosome formation. Two signaling hubs have emerged: the kinase mTOR, in a complex at the surface of lysosomes which is sensitive to nutrients and hormones; and AMPK, which is sensitive to the cellular energetic status. Besides nutritional, hormonal and energetic fluctuations, many organs have to respond to mechanical forces (compression, stretching and shear stress). Recent studies have shown the importance of mechanotransduction in controlling macroautophagy. This regulation engages cell surface sensors, such as the primary cilium, in order to translate mechanical stimuli into biological responses.

The magnified view: from ancient trinkets to single nuclear pore complexes

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The magnified view: from ancient trinkets to single nuclear pore complexes

A journey from the polished quartz lenses in the eyes of an ancient Egyptian statue of a seated scribe, through the development of microscopes and towards modern electron microscopy. Recent advances in field emission scanning electron microscopy have made it possible to expose nuclei from human cells and to focus on individual nuclear pore complexes, comparing their architectural features.


A journey from the earliest known use of lenses and magnifying glasses in ancient times, through the development of microscopes and towards modern electron microscopy techniques. The evolving technology and improved microscopes enabled the discovery of intracellular organelles, the nucleus and nuclear pore complexes (NPCs). Current advances have led to composite three-dimensional models showing NPC structure in unprecedented detail but relying on the averaging of many images. A complementary approach is field emission scanning electron microscopy providing topographic surface images that are easily and intuitively interpreted by our brain. Recent advances in this technique have made it possible to expose nuclei from human cells and to focus on individual NPCs and their architectural features.

Structural dynamics at the active site of the cancer‐associated flavoenzyme NQO1 probed by chemical modification with PMSF

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Structural dynamics at the active site of the cancer-associated flavoenzyme NQO1 probed by chemical modification with PMSF

Human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoenzyme associated with a variety of human diseases, possesses high plasticity in the catalytic site. We report the crystal structure of NQO1 with phenylmethylsulfonyl fluoride (PMSF) covalently bound to the Tyr128 residue. We show that, unexpectedly, the catalytic activity of the enzyme was not abolished, indicating that the PMSF molecule does not limit the dynamics of this residue.


A large conformational heterogeneity of human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoprotein associated with various human diseases, has been observed to occur in the catalytic site of the enzyme. Here, we report the X-ray structure of NQO1 with phenylmethylsulfonyl fluoride (PMSF) at 1.6 Å resolution. Activity assays confirmed that, despite being covalently bound to the Tyr128 residue at the catalytic site, PMSF did not abolish NQO1 activity. This may indicate that the PMSF molecule does not reduce the high flexibility of Tyr128, thus allowing NADH and DCPIP substrates to bind to the enzyme. Our results show that targeting Tyr128, a key residue in NQO1 function, with small covalently bound molecules could possibly not be a good drug discovery strategy to inhibit this enzyme.