Miracle-dz/UniFAR-FTUs huggingface dataset:
The Biocontrol Agent and Insect Pathogen Photorhabdus luminescens Interacts with Plant Roots

Insect-pathogenic Photorhabdus luminescens bacteria are widely used in biocontrol strategies against pests. Very little is known about the life of these bacteria in the rhizosphere. Here, we show that P. luminescens can specifically react to and interact with plant roots. Understanding the adaptation of P. luminescens in the rhizosphere is highly important for the biotechnological application of entomopathogenic bacteria and could improve future sustainable pest management in agriculture. ABSTRACT The number of sustainable agriculture techniques to improve pest management and environmental safety is rising, as biological control agents are used to enhance disease resistance and abiotic stress tolerance in crops. Here, we investigated the capacity of the Photorhabdus luminescens secondary variant to react to plant root exudates and their behavior toward microorganisms in the rhizosphere. P. luminescens is known to live in symbiosis with entomopathogenic nematodes (EPNs) and to be highly pathogenic toward insects. The P. luminescens-EPN relationship has been widely studied, and this combination has been used as a biological control agent; however, not much attention has been paid to the putative lifestyle of P. luminescens in the rhizosphere. We performed transcriptome analysis to show how P. luminescens responds to plant root exudates. The analysis highlighted genes involved in chitin degradation, biofilm regulation, formation of flagella, and type VI secretion system. Furthermore, we provide evidence that P. luminescens can inhibit growth of phytopathogenic fungi. Finally, we demonstrated a specific interaction of P. luminescens with plant roots. Understanding the role and the function of this bacterium in the rhizosphere might accelerate the progress in biocontrol manipulation and elucidate the peculiar mechanisms adopted by plant growth-promoting rhizobacteria in plant root interactions. IMPORTANCE Insect-pathogenic Photorhabdus luminescens bacteria are widely used in biocontrol strategies against pests. Very little is known about the life of these bacteria in the rhizosphere. Here, we show that P. luminescens can specifically react to and interact with plant roots. Understanding the adaptation of P. luminescens in the rhizosphere is highly important for the biotechnological application of entomopathogenic bacteria and could improve future sustainable pest management in agriculture.
From inhibitors to target site genes and beyond—herbicidal inhibitors as powerful tools for functional genomics

Abstract With rapid progress being made in deciphering plant genomic sequences, determining the function of these genes is one of the main challenges that plant molecular biologists face today. Herbicidal inhibitors have been very useful for understanding gene function in at least two examples, represented by herbicidal inhibitors of hydroxyphenylpyruvate dioxygenase (HPPD) and deoxyxylulosephosphate reductoisomerase (DXR). In the first, an albino mutant of Arabidopsis isolated during the study of carotenoid biosynthesis was found to have an intact carotenoid biosynthetic pathway. A number of “bleaching herbicides” in development at about the same time (e.g., sulcotrione) produced similar symptoms by strongly inhibiting HPPD, a key enzyme in plastoquinone biosynthesis. Examination of the Arabidopsis mutant revealed that the HPPD gene had been inactivated in the albino plants. Inhibition of the HPPD pathway also led to reduced levels of tocopherol (vitamin E), an end product of the pathway. Further studies and manipulation of the pathway produced plants with significantly higher levels of vitamin E. This result is a clear demonstration of how an herbicidal inhibitor was able to lead to the identification of a gene that was responsible for a particular phenotype. As a second example, identification of fosmidomycin as a specific inhibitor of DXR in the recently elucidated nonmevalonate pathway of isopentenyl pyrophosphate (IPP) biosynthesis was instrumental in furthering the understanding of an important route to synthesis of many important terpenoid products. Nomenclature: Fosmidomycin, 3-(N-formyl-N-hydroxyamino)propylphosphonic acid; sulcotrione; Arabidopsis mutant.
First report of Western Flower Thrips, Frankliniella occidentalis (Pergande) (Thripidae: Thysanoptera) from India- A Potential Havoc to Indian agriculture

Western Flower thrips (WFT), Frankliniella occidentalis (Pergande) is being reported for the first time from India based on specimens collected on tomato. It is the most economically important species in the insect Order Thysanoptera damaging wide variety of crops as a sucking pest and vector for plant viruses.
Rapid HIV Progression Is Associated with Extensive Ongoing Somatic Hypermutation

Key Points HIV RPs are an understudied patient population. Globally, IgG SHM is inversely correlated with disease progression. Longitudinal lineage tracking reveals ongoing SHM with disrupted selection in RPs. The Ab response to HIV is of great interest, particularly in the context of a protective vaccine and broadly neutralizing Abs, but research is typically geared toward elite controllers because of their ability to successfully control the virus. In this study, we studied the evolution of the Ab repertoire over the first year of HIV infection in people classified as rapid progressors (RP) compared with typical progressors. HIV RPs are an important yet understudied group of HIV patients classified by a rapid decline in CD4 counts and accelerated development of AIDS. We found that the global IgG somatic hypermutation load negatively correlated with disease progression, possibly because of exaggerated isotype switching of unmutated sequences in patients with low CD4 counts. We measured Ab sequence evolution over time using longitudinal samples taken during the early stages of infection and 1 year postinfection. Within clonal lineages spanning both timepoints, visit 2–derived sequences harbored considerably more mutations than their visit 1 relatives. Despite extensive ongoing somatic hypermutation, the initially strong signs of Ag selection pressure observed in visit 1–derived sequences decayed by visit 2. These data suggest that excessive immune activation in RPs leads to a hyperactive B cell response that fails to confer protection.
IN VITRO SCREENING OF SUGARCANE CULTIVAR Co 86032 FOR SALINITY TOLERANCE

Salt tolerant sugarcane mutants were isolated using in vitro UV mutagenesis-selection and regeneration under NaCl salt stress. Embryogenic callus cultures of popular sugarcane cultivar Co 86032 were established from young meristematic leaf whorls on MS basal medium supplemented with 4 mg l -1 containing 2% sucrose and 0.7% agar. When different concentrations of NaCl were used for assessing its lethal dosage for selection, calli failed to grow beyond 50mM NaCl concentration. Besides, callus culture exposed to UV radiation exhibited lower decline in survival and calli growth and differentiation up to 125mM NaCl (3.054 mg RGR) concentration was observed. From observations, three NaCl concentrations (75, 100, 125mM) were considered for studies on in vitro mutagenesisselection. The sugarcane calli exposed to 75mM NaCl accumulated higher proline (5.5265 µmol) than that in the control. Total soluble protein content also was higher at 125mM NaCl concentration (0.637 mg ml -1 of enzyme extract from stressed calli). The genetic variability among the selected variants was analyzed using Random Amplified Polymorphic DNA (RAPD) technique. RAPD analysis resolved 77 polymorphic bands with 63.11% total polymorphism. The primer RC15 produced four polymorphic bands of total 19 bands. The primer amplified the salt tolerant samples of 25mM to 150mM, but failed to amplify the sample of 175mM. The primer RC 16 amplified a 250bp band in all the salt tolerant samples but produced two unique bands at approximately 400 and 550 bp in 75mM and 125mM salt stressed lines. The primer OPS 09 produced eight amplicons at the highest salt concentration (175mM) probably indicating the amplification of lethal gene responsible for callus mortality. The results highlighted the need for proper assessment of induced variability by salinity stress to provide a better understanding of sugarcane cultivation under such stress conditions.
Sex-specific growth effects in protogynous hermaphrodites

We demonstrate sex-specific decoupling of otolith growth and somatic growth in two species of protogynous parrotfishes, Scarus frenatus and Chlorurus sordidus. Otoliths of both species increased in size consistently through life, even though somatic growth rate decreased with age (age effect). Furthermore, in S. frenatus, otoliths from terminal males were smaller than otoliths from females, despite males being larger than females of the same age. This demonstrates the presence of a sex-specific growth effect, where otoliths of fast-growing individuals (males) are smaller than otoliths of slow-growing individuals (females). The sex-specific growth effect for S. frenatus was most pronounced during the early life history, which suggests that only the fastest-growing females change sex to male. A sex-specific growth effect was also evident in C. sordidus, although it was not statistically significant because of greater variation in the otolith size of terminal males of this species. Our results demonstrate th.
Fine-Scale Habitat Selection by Female Forest-Dwelling Caribou in Managed Boreal Forest: Empirical Evidence of a Seasonal Shift between Foraging Opportunities and Antipredator Strategies

Abstract: Forest harvesting is a major cause of habitat alteration negatively affecting forest-dwelling caribou (Rangifer tarandus caribou) in the boreal forest. In order to identify female caribou habitat requirements, we conducted a fine-scale habitat selection analysis in a managed forest of eastern Canada. Five land-cover types used by 8 female caribou during 2 periods (winter and snow-free) were considered to characterize structural attributes, ground cover, and lichen abundance at 320 GPS locations and at 200 random points within home ranges. Because caribou rely on a limited food supply in winter, we predicted that they would select sites of higher biomass of terrestrial and/or arboreal lichens. Since female caribou (especially those with calves) are more vulnerable to predation during the snow-free period, we predicted that they would select sites where predation would be reduced by a denser hiding cover (i.e., high basal area, shrub height, and/or lateral cover) or by a lower forage availability for alternative prey (i.e., low shrub density). Within each land-cover type, comparisons between used and random sites were conducted using an exploratory PCA analysis followed by conditional logistic regressions. Our results demonstrated that, in winter, female caribou selected sites with higher terrestrial lichen biomass or ericaceous shrub cover in old spruce stands and old cutovers. During the snow-free period, female caribou did not select sites of denser hiding cover. However, well-regenerated shrub layer was avoided during both periods, suggesting that caribou avoided sites containing abundant forage attractive to moose and, consequently, wolf. At a fine scale, forest management should focus on protecting sites or stands with a high biomass of terrestrial lichens. Silvicultural practices that prevent cutovers from regenerating into areas with abundant moose forage should also be favoured. Nomenclature: Marie-Victorin, 1995; Farrar, 1996; Brodo et al., 2001, Feldhamer et al., 2003.
The development of integrated crop management in agricultural crops: comparisons with conventional methods.

The development of chemical pesticides enabled farmers to abandon more traditional control strategies, but an over-reliance on the use of chemicals led to problems of resistance and environmental damage. A more advanced system, integrated crop management, has been developed which involves the use of both chemical and cultural methods; a number of trials carried out in the UK and Europe have shown that this approach is both economically viable and environmental beneficial compared with the conventional alternative.
Shedding light on human cerebral lipofuscin: An explorative study on identification and quantification

Increased oxidative stress has been associated with several neurodegenerative diseases such as Alzheimer's disease, but also with neurological diseases sharing pathophysiological pathways like epilepsy. Lipofuscin is a nondegradable end‐product of oxidative stress; its cerebral presence reflects the cumulative amount of oxidative stress the brain has endured. In this study, we have observed prominent autofluorescent particles in the pial arterial wall and in neocortical parenchyma of young, drug‐resistant epilepsy patients (18–28 years old) who underwent resective brain surgery (n = 6), as well as in older control patients (n = 3). With fluorescence spectroscopic imaging, brightfield microscopy, histochemistry and fluorescence lifetime imaging, these autofluorescent particles were identified as the age pigment lipofuscin. An evaluation of these lipofuscin particles using Imaris© software allowed robust quantification, while the 3D properties allowed visualization of the complex configuration. We elaborate on the usefulness of lipofuscin as a marker of cumulative oxidative stress in the brain. Furthermore, we speculate on the observed differences in particle size and density that we found between young patients and older controls, which could imply a role for lipofuscin in the pathophysiology of epilepsy and possibly other neurological diseases.
Biological activities of extracts from Andaman Sea sponges, Thailand

Thirty six organic extracts were prepared from eighteen marine sponges collected from the Andaman Sea, Thailand. The extracts were examined for anti-malaria, anti-Microbacterium tuberculosis, anti-herpes simplex virus, antimicrobial, anti-acetylcholinesterase enzyme and cytotoxic activities. Four extracts showed anti-M. tuberculosis, one anti-malarial, twenty four antimicrobial and one extract exhibited cytotoxic activity. However, anti-acetylcholinesterase enzyme and anti-herpes simplex virus type 1 (HSV-1) activities were not recorded. Dichloromethane extracts prepared from Axinyssa sp. , Halichondria sp. and Chondrosia reticulata exhibited potential anti-M. tuberculosis at MIC 50, 100 and 200 mg/mL, respectively. The Hexane part of Phakellia ventilabrum extract showed anti-malarial activity (MIC= 2.8 mg/mL) while the dichloromethane extract showed anti-M. tuberculosis and cytotoxic activity with MIC 200 and IC50 7.1 mg/mL, respectively. Antimicrobial activity was found in both the hexane and dichloromethane parts of extracts.
First record of the common house gecko Hemidactylus frenatus Schlegel, 1836 and distribution extension of Phyllodactylus reissii Peters, 1862 in the Galápagos

Among introduced species in the Galapagos are three species of geckos – Gonatodes caudiscutatus , Lepidodactylus lugubris , Phyllodactylus reissii – occurring on the islands of Isabela, San Cristobal, and Santa Cruz. Here we report the first record of a fourth invasive species of gecko from Isabela, as well as the first record of P. reissii from the same island.
Radar detection of fluctuating targets in compound-Gaussian clutter

The paper deals with the detection of fluctuating targets in the presence of compound-Gaussian clutter. We show that the optimum receiver, according to the Neyman-Pearson criterion, is canonical in that its structure is independent of the clutter amplitude probability density function. Moreover it is interpretable as a conventional square law receiver with an adaptive threshold. The performance analysis shows that the proposed detector largely outperforms the conventional receiver. Unfortunately the Neyman-Pearson receiver is hardly implementable since it requires the knowledge of the target strength. Nevertheless it not only provides guidance for the design of suboptimal realizable detectors, but also its performance is an upper bound for those achievable by any other detector.
TRAF3 Acts as a Checkpoint of B Cell Receptor Signaling to Control Antibody Class Switch Recombination and Anergy

Key Points We identify checkpoints restricting the BCR-induced class switch recombination. TRAF3 maintains B cell homeostasis by fine-tuning the BCR signaling strength. The BCR recognizes foreign Ags to initiate humoral immunity that needs isotype-switched Abs generated via class switch recombination (CSR); however, stimulating the BCR in the absence of costimulation (e.g., CD40) does not induce CSR; thus, it remains elusive whether and how the BCR induces CSR mechanistically. Autoreactive B cells can maintain anergy via unresponsiveness of their BCRs to self-antigens. However, it remains unknown what molecule(s) restrict BCR signaling strength for licensing BCR-induced CSR and whether deficiency of such molecule(s) disrupts autoreactive B cell anergy and causes B cell–mediated diseases by modulating BCR signaling. In this study, we employ mouse models to show that the BCR’s capacity to induce CSR is restrained by B cell–intrinsic checkpoints TRAF3 and TRAF2, whose deletion in B cells enables the BCR to induce CSR in the absence of costimulation. TRAF3 deficiency permits BCR-induced CSR by elevating BCR-proximal signaling intensity. Furthermore, NF-κB2 is required for BCR-induced CSR in TRAF3-deficient B cells but not for CD40-induced or LPS-induced CSR, suggesting that TRAF3 restricts NF-κB2 activation to specifically limit the BCR’s ability to induce CSR. TRAF3 deficiency also disrupts autoreactive B cell anergy by elevating calcium influx in response to BCR stimulation, leading to lymphoid organ disorders and autoimmune manifestations. We showed that TRAF3 deficiency-associated autoimmune phenotypes can be rectified by limiting BCR repertoires or attenuating BCR signaling strength. Thus, our studies highlight the importance of TRAF3-mediated restraint on BCR signaling strength for controlling CSR, B cell homeostasis, and B cell–mediated disorders.
The correlation between ultrasonographic features, bFGF, and the local invasiveness of thyroid papillary carcinoma

Abstract The present study aimed to investigate the correlation between ultrasonographic features, basic fibroblast growth factor (bFGF), and the local invasiveness of papillary thyroid carcinoma (PTC). A total of 350 samples of thyroid nodules were collected. Routine ultrasonography was performed before the operation and routine pathological diagnosis and bFGF detection were performed after the operation. ’ These 350 samples of thyroid nodules included 90 samples of nodular goiter, 36 samples of focal thyroiditis, and 224 samples of PTC. A total of 326 thyroid nodules were examined for bFGF. The results revealed that the difference in the expression of bFGF between the benign and malignant groups was statistically significant (P < .05) and the difference in the positive expression of bFGF between the invasive and non-invasive PTC groups was statistically significant (P < .05). Whether the shape of PTC is regular or not and whether there is micro-calcification in PTC and other ultrasonographic features, the size and location of the lesions and the age of the patient help make a preliminary prediction of local invasiveness before the operation. Postoperative detection of bFGF is helpful for further risk assessments of PTC.
NF-κB Modulates TNF-α Production by Alveolar Macrophages in Asymptomatic HIV-Seropositive Individuals1

Local TNF-α production in different organs may affect HIV replication and pathogenesis. Alveolar macrophages (AMs) obtained by bronchoalveolar lavage from asymptomatic HIV-seropositive and HIV-seronegative individuals did not spontaneously release TNF-α, but LPS stimulation of these cells significantly increased TNF-α production. We tested whether NF-κB affects TNF-α production by AMs using N-tosyl-l-phenylalanine chloromethylketone (TPCK) or N-benzoyl-l-tyrosine ethyl ester (BTEE), which inhibit the degradation of IκB, or tricyclodecan-9-yl-xanthogenate-potassium (D609), which inhibits phospholipase C. Alveolar macrophages were exposed to LPS alone and with the chemical protease inhibitors TPCK, BTEE, and D609. NF-κB DNA binding induced by LPS treatment of AMs was inhibited by TPCK, BTEE, and D609. These agents also inhibited TNF-α mRNA and TNF-α protein production. After 24 h, the levels of TNF-α mRNA reached equilibrium, as assessed by RT-PCR. The levels of NF-κB mRNA remained constant under all conditions. The levels of IκB-α mRNA were similar after 30, 60, and 180 min, but the IκB-β mRNA concentration was initially low and increased over time under all conditions. IκB-α and IκB-β protein production was not affected by the chemical protease inhibitors. Our data show that TNF-α production by LPS-stimulated AMs from asymptomatic HIV-seropositive and -seronegative individuals is regulated via the phospholipase C pathway and by NF-κB DNA binding activity without obvious changes in IκB-α or IκB-β protein concentrations.
Effect of cold stress on cell membrane stability, chlorophyll a and b contain and proline accumulation in wheat (Triticum aiestivum L.) variety

The aim of this research was to determine the effect of cold stress on chlorophyll content, proline accumulation and the cell membrane stability of 15 bread wheat (Triticum aestivum L.) at two stage of growth (2 leaf stage and 4 leaf stage). Experiment was carried out in complete block design with tree replications at year 2009 in west Azerbaijan Agriculture science and research center laboratory. 15 cultivar (five genotypes with types winters names Sayson, Martin, Gaskoghen, C-82-12, C-81-14, 5 genotype with type intermediate including Alvand, Mahdavi, Zarrin, Marvdasht, Toos and five genotypes with type spring names Shiraz, Pishtaz, M-79-7, M-81-13 and Kavir) were sown in lab condition . According to the results, cold stress had a significant effect on chlorophyll a and b, total chlorophyll, prolin content and cell membrane stability. At the other hand variety and growing stage have significant effect on treats (P>0.01). The result showed that the M-81-13 with 53.05 mΩ EC has the highest cell membrane stability and the lowest EC was obtaining from gaskoghen with 18.987 mΩ. Also M-79-7 with 2.315 mg chlorophyll a per 1 g leaf fresh weight has highest chlorophyll content. It was determining the ratio of maximal chlorophyll content after cold stress is reliable and a method to determine the frost hardness of wheat variety. The proline content of the leaf however increased in both growth stages in all variety of wheat. Gaskoghen with 0.340 (μg/0.5 g dwt) in 2 leaf growing stage had the highest rate of proline amino acid and Marvdasht variety from inter mediate type in 4 leaf growing stage with 0.003 (μg/0.5 g dwt) had the lowest rate of proline. Key words: Wheat variety, chlorophyll content and proline.