SeedQuant: a deep learning-based tool for assessing stimulant and inhibitor activity on root parasitic seeds

Witchweeds (Striga spp.) and broomrapes (Orobanchaceae and Phelipanche spp.) are root parasitic plants that infest many crops in warm and temperate zones, causing enormous yield losses and endangering global food security. Seeds of these obligate parasites require rhizospheric, host-released stimulants to germinate, which opens up possibilities for controlling them by applying specific germination inhibitors or synthetic stimulants that induce lethal germination in the host’s absence. To determine their effect on germination, root exudates or synthetic stimulants/inhibitors are usually applied to parasitic seeds in in vitro bioassays, followed by assessment of germination ratios. Although these protocols are very sensitive, the germination recording process is laborious, representing a challenge for researchers and impeding high-throughput screens. Here, we developed an automatic seed census tool to count and discriminate germinated seeds (GS) from non-GS. We combined deep learning, a powerful data-driven framework that can accelerate the procedure and increase its accuracy, for object detection with computer vision latest development based on the Faster Region-based Convolutional Neural Network algorithm. Our method showed an accuracy of 94% in counting seeds of Striga hermonthica and reduced the required time from approximately 5 min to 5 s per image. Our proposed software, SeedQuant, will be of great help for seed germination bioassays and enable high-throughput screening for germination stimulants/inhibitors. SeedQuant is an open-source software that can be further trained to count different types of seeds for research purposes.     

Raman microspectroscopy reveals long‐term extracellular activity of chlamydiae

The phylum Chlamydiae consists exclusively of obligate intracellular bacteria. Some of them are formidable pathogens of humans, while others occur as symbionts of amoebae. These genetically intractable bacteria possess a developmental cycle consisting of replicative reticulate bodies and infectious elementary bodies, which are believed to be physiologically inactive. Confocal Raman microspectroscopy was applied to differentiate between reticulate bodies and elementary bodies of Protochlamydia amoebophila and to demonstrate in situ the labelling of this amoeba symbiont after addition of isotope‐labelled phenylalanine. Unexpectedly, uptake of this amino acid was also observed for both developmental stages for up to 3 weeks, if incubated extracellularly with labelled phenylalanine, and P. amoebophila remained infective during this period. Furthermore, P. amoebophila energizes its membrane and performs protein synthesis outside of its host. Importantly, amino acid uptake and protein synthesis after extended extracellular incubation could also be demonstrated for the human pathogen Chlamydia trachomatis, which synthesizes stress‐related proteins under these conditions as shown by 2‐D gel electrophoresis and MALDI‐TOF/TOF mass spectrometry. These findings change our perception of chlamydial biology and reveal that host‐free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms.     

Phylogenetic analysis of Aedes species distributed in Taif Province,Saudi Arabia,based on mitochondrial COX1 sequences

As Aedes mosquitoes are the predominant carriers of arboviruses responsible for global dengue fever and chikungunya outbreaks, understanding their genetic diversity and population structure can enhance dengue prevention and vector control efforts. Although sympatric cryptic species have been acknowledged in Aedes species subgroups in Southeast Asia, little information is available regarding the occurrence and dispersal of cryptic Aedes species in Saudi Arabia. In the present investigation, we intend to analyze genetic variations and perform a phylogenetic study of sympatric Aedes samples collected from various locations in Taif Province, Saudi Arabia. The locus of mitochondrial DNA cytochrome c oxidase subunit 1 (COX1, analyzed with DNA barcoding) was utilized to determine genetic variance and to build phylogenetic trees. For species identification, the COX1 sequences of Aedes samples from Taif Province were compared with those of Aedes samples from GenBank (National Center for Biotechnology Information, NCBI). To identify phylogenetic relationships and genetic variability, phylogenetic trees were created using Taif Province samples, GenBank A. albopictus samples, and GenBank A. aegypti samples. The phylogenetic analysis revealed that some Taif samples (A3, A7, F2, F4, F1, A4, A1, F9 and F6) were closer to A. aegypti and A. albopictus samples from Africa and East Asia, especially Kenya and Malaysia. Whereas other samples (F9, F6, A4, F1 and A1) were closer to the GenBank A. aegypti samples KP843383 (Thailand), HM399357(Australia), MK533632 (Kenya), KX420460 (Kenya), KU495081 (Australia) and MF179160 (China) than the remaining Taif samples. Overall, our findings demonstrate that examining the genetic diversity and phylogenetic linkages of Aedes samples can aid in understanding the evolution of Aedes cryptic species in the western regions of Saudi Arabia.     

Cardioprotective effect of des-Aspartate-angiotensin-I (DAA-I) on cytokine gene expression profile in ligation model of myocardial infarction

We investigate the influence of des-Aspartate-angiotensin-I (DAA-I) on the cytokine expression profile in a rodent model of myocardial infarction. Myocardial infarction model was created in female Wistar rats by coronary artery ligation. Animals were randomized to receive intravenously either a daily dose of 1.2 mug DAA-I/kg body weight (group 1; n = 60) or saline (group 2; n = 60) for 14 days after infarction. Heart function was assessed by echocardiography. Animals were euthanized at 1, 3, 7, 14 and 31 days. Morphometric analysis using tetrazolium chloride staining revealed that infarct size was reduced by 32.2% (p < 0.05) in group 1 after 14 days of DAA-I treatment. Left ventricular ejection fraction in group 1 improved significantly (73.4%) as compared to group 2 (47.7%; p < 0.001). Immunostaining for immune cells at the infarct site showed that CD8+ lymphocytes infiltration at the infarct site declined in group 1 (15 +/- 5 cells) as compared to group 2 (50 +/- 6 cells; p < 0.001). Infiltration of monocytes and macrophages remained high at day 14 in group 2 (126 +/- 40 cells) as compared to group 1 (49 +/- 11 cells; p = 0.006). Multiplex PCR was done for differential gene expression of various pro-inflammatory cytokines. IL-6, TNF-alpha, TGF-beta and GM-CSF expression were significantly down-regulated in the infarct, peri-infarct and contra-lateral zones of the left ventricle in group 1 as compared to group 2. IL-6, TGF-beta and GM-CSF expression started to decline from day 1 of DAA-I treatment while TNF-alpha expression only reduced after 7 days of DAA-I treatment. We conclude that DAA-I prevented infarct expansion through suppression of inflammatory cytokines and immune cell infiltration in the infarct region.     

Free fatty acids normalize a rosiglitazone-induced visfatin release

The detrimental effect of elevated free fatty acids (FFAs) on insulin sensitivity can be improved by thiazolidinediones (TZDs) in patients with type 2 diabetes mellitus. It is unknown whether this salutary action of TZD is associated with altered release of the insulin-mimetic adipocytokine visfatin. In this study, we investigated whether visfatin concentrations are altered by FFA and TZD treatment. In a randomized, double-blind, placebo-controlled, parallel-group study 16 healthy volunteers received an infusion of triglycerides/heparin to increase plasma FFA after 3 wk of treatment with rosiglitazone (8 mg/day, n = 8) or placebo (n = 8), and circulating plasma visfatin was measured. As a corollary, human adipocytes were incubated with synthetic fatty acids and rosiglitazone to assess visfatin release in vitro. The results were that rosiglitazone treatment increased systemic plasma visfatin concentrations from 0.6 +/- 0.1 to 1.7 +/- 0.2 ng/ml (P < 0.01). Lipid infusion caused a marked elevation of plasma FFA but had no effect on circulating visfatin in controls. In contrast, elevated visfatin concentrations in subjects receiving rosiglitazone were normalized by lipid infusion. In isolated adipocytes, visfatin was released into supernatant medium by acute addition and long-term treatment of rosiglitazone. This secretion was blocked by synthetic fatty acids and by inhibition of phosphatidylinositol 3-kinase or Akt. In conclusion, release of the insulin-mimetic visfatin may represent a major mechanism of metabolic TZD action. The presence of FFA antagonizes this action, which may have implications for visfatin bioactivity.     

Efficient transformation of thermotolerant methanol & strains of methylophilus spp. via electroporation

Plasmid transformation of three thermotolerant strains of methylotrophic bacterium Methylophilus spp. was investigated using three different methods. The plasmids could be transformed by electroporation and were stabily maintained in these methylotrophic bacteria. The calcium chloride (competent cell) method was successful only in the case of one of the three strains studied. Protoplast transformation of methylotrophic bacteria was not successful. The antibiotic resistance markers conferred resistance on the transformants, whereas the wild-type bacteria were sensitive to the antibiotics.     

A method for the approximation of the relative humidity in the upper human airways

In order to determine the growth of inhaled aerosol particles in the human respiratory tract the relative humidity in a lung model has been calculated using a numerical method. The computations take into account different types of airflows, enhanced transport mechanisms and an optimized wall temperature profile in the upper airways. These parameters are varied to fit experimental temperature data. Under certain conditions the corresponding relative humidity shows a maximum near the first bifurcation, which exceeds the final humidity in the alveoli. This high humidity forces dry NaC1 particles with diameters less than 0.5 μm to grow to their maximum size in the first bronchi. Thereafter the droplets loose water and reach their final size in the terminal bronchioles.     

Abbau und Umsetzung von lignifiziertem Pflanzenmaterial durch mikroskopische Bodenpilze

Zusammenfassung Es wird über eine Methode berichtet, an extrem dünnen Holzfolien die Abbauleistungen von Bodenpilzen zu messen.Aus einer Gesamtzahl von 280 geprüften Pilzarten wurden bei 27 mikroskopischen Pilzen mit hoher Aktivität Gewichtsabnahme und Reißfestigkeit von Ahornholz bestimmt.An Weizenstroh wurde mit einer Auswahl leistungsfähiger Pilze die Verminderung des Lignin- und Cellulosegehalts untersucht.Nach 120 Bebrütungstagen lag die Abnahme für Lignin zwischen 31 und 52%, für Cellulose zwischen 33 und 66%.Von den untersuchten Pilzen zeichneten sich Mammaria echinobotryoides, Hormiactis candida und Chaetomium piluliferum durch eine besonders starke Phenolproduktion aus.Die für alle geprüften Pilze mehr oder weniger typische Phenolproduktion stand in enger Beziehung zur Bildung von Huminstoffen, die bei der Rotte des Strohes auftraten.

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Decomposition and transformation of lignified plant material by microscopic soil fungi

Summary The use of ultra-thin foils prepared from maple wood for measuring the wood-destroying capacity of soil fungi is described.Data are given on the reduction of dry-weight and tensile strength by the action of 27 highly active species from a total number of 280 microfungi.The decrease in lignin and cellulose content of wheat straw was studied with a selected number of fungi.The percentage reduction after an incubation period of 120 days was found to be between 31 and 52% for lignin, 33 and 66% for cellulose content respectively.A remarkable production of phenols was found in liquid cultures of Mammaria echinobotryoides, Hormiactis candida and Chaetomium piluliferum.The phenol production was more or less typical for all the examined fungi. There was a close relationship between the phenol metabolism and dark humic acid-like substances occurring during the decomposition of straw.