Miracle-dz/UniFAR-FTUs huggingface dataset:
HSP90 buffers newly induced mutations in massively mutated plant lines

Robustness to both genetic and environmental change is an emergent feature of living systems. Loss of phenotypic robustness can be associated with increased penetrance of genetic variation. In model organisms and in humans, the phenotypic consequences of standing genetic variation can be buffered by the molecular chaperone HSP90. However, it has been argued that HSP90 has the opposite effect on newly introduced genetic variation. To test the buffering effect of HSP90 on new mutations, we introduced vast numbers of mutations into wild-type and HSP90-reduced plants and assessed embryonic lethality and early seedling phenotypes for thousands of offspring. Although the levels of newly introduced mutations were similar in the two backgrounds, the HSP90-reduced plants showed a significantly greater frequency of embryonic lethality and severe phenotypic abnormalities, consistent with higher penetrance and expressivity of newly introduced genetic variation. We further demonstrate that some mutant phenotypes were heritable in an HSP90-dependent manner, and we map candidate HSP90-dependent polymorphisms. Moreover, both sequence and phenotypic analyses of wild-type and HSP90-reduced plants suggest that the HSP90-dependent phenotypes are largely due the newly introduced mutations rather than to an increased mutation rate in HSP90-reduced plants. Taken together, our results support a model in which HSP90 buffers newly introduced mutations, and the phenotypic consequences of such mutations outweigh those of mutations arising de novo in response to HSP90 perturbation.
Development of a Pseudomonas putida cell-free protein synthesis platform for rapid screening of gene regulatory elements

Abstract Cell-free protein synthesis (CFPS) systems enable the production of protein without the use of living, intact cells. An emerging area of interest is to use CFPS systems to characterize individual elements for genetic programs [e.g. promoters, ribosome binding sites (RBS)]. To enable this research area, robust CFPS systems must be developed from new chassis organisms. One such chassis is the Gram-negative Pseudomonas bacteria, which have been studied extensively for their diverse metabolism with promises in the field of bioremediation and biosynthesis. Here, we report the development and optimization of a high-yielding (198 ± 5.9 µg/ml) batch CFPS system from Pseudomonas putida ATCC 12633. Importantly, both circular and linear DNA templates can be applied directly to the CFPS reaction to program protein synthesis. Therefore, it is possible to prepare hundreds or even thousands of DNA templates without time-consuming cloning work. This opens the possibility to rapidly assess and validate genetic part performance in vitro before performing experiments in cells. To validate the P. putida CFPS system as a platform for prototyping genetic parts, we designed and constructed a library consisting of 15 different RBSs upstream of the reporter protein sfGFP, which covered an order of magnitude range in expression. Looking forward, our P. putida CFPS platform will not only expand the protein synthesis toolkit for synthetic biology but also serve as a platform in expediting the screening and prototyping of gene regulatory elements.
Increased Populations of Endangered Cranes After Amur River Flood

Abstract. Dam construction on the Zeya River, which is an important tributary of the Amur River in Far East Russia, has caused significant declines in water levels and frequency of floods in the adjacent floodplains since 1980. However, an extreme flood event occurred in 2013. Populations of six crane species were monitored before and after these drastic water level changes at Muraviovka Park in Far East Russia, an important breeding and stop-over site. Individuals were counted by territory mapping during the breeding season (2000–2015) and by roosting site counts during autumn migration (2006–2015). The objective of this study was to evaluate whether changes in water levels had a significant impact on local and migratory crane populations. We found a positive effect of flooding on numbers of breeding Red-crowned Cranes (Grus japonensis) and White-naped Cranes (Antigone vipio), as well as on numbers of roosting Hooded Cranes (Grus monacha) in autumn. Siberian Cranes (Leucogeranus leucogeranus) were only observed after the wetlands were flooded. The results of this study highlight the importance of elevated Amur River water levels for crane populations of global importance.
Evaluation of chitosan and alginate immobilized Methylobacterium oryzae CBMB20 on tomato plant growth

ABSTRACT Methylobacterium oryzae CBMB20, a promising plant growth promoting bacteria (PGPB) and a biocontrol agent, was immobilized in different formulations such as wet chitosan, dry chitosan, wet alginate and dry alginate and were tested for tomato plant growth promotion. Chitosan solution (1.5%) with pH 5.5–6.0 and 90 min contact time was found optimal for immobilization. The chitosan formulations showed better entrapment efficiency and good degradability resistance apart from slow release of cells under prolonged incubation. Survivability of bacteria (80%) was observed in wet chitosan formulation even after 90 days of storage at 4°C. The spermosphere survival of bacteria was high in both dry and wet chitosan formulations applied soils even after 21 days under greenhouse conditions. While the alginate formulation degraded fully, partial degradation of chitosan formulation was observed even after 30 days, indicating its ability to support the survival of M. oryzae CBMB20 in soil. Plants inoculated with wet chitosan formulation registered 1.3 fold increase in the shoot and root length and dry weight compared to other treatments. Hence, chitosan formulation supporting better plant growth compared to alginate will be a better carrier for taking bacteria to the plant rhizosphere and thereby promote plant growth.
Développements méthodologiques pour l'identification in silico des métalloprotéines dans les protéomes bactériens : le cas des protéines à centre Fer-Soufre

Jusqu’a 40% des proteines sont connues pour fixer des metaux, ces heteroatomes jouant un role capital dans la regulation, la catalyse ou le maintien de la structure de ces proteines. Ces metalloproteines sont ubiquitaires et d’une importance primordiale dans les trois domaines du vivant. Cependant, les methodes actuelles dediees a l’identification des membres de cette grande famille dans les proteomes bacteriens sont soit inadaptees pour des approches a grande echelle, soit presentent des performances relativement limitees en l’absence d’une structure tridimensionnelle resolue. Dans ce contexte, differents outils d’analyse de sequence ont ete testes, en recherchant des descripteurs de ces proteines (e.g. motifs, domaines conserves, empreintes phylogenetiques). Pour pallier le relatif manque de sensibilite de ceux-ci, de nouveaux descripteurs ont ete construits, dedies specifiquement a l’identification des proteines a centre fer-soufre : (i) des profils de co-conservation des ligands du metal et (ii) des profile-HMMs adaptes a la detection d’homologues distants. Les pouvoirs predictifs respectifs de ces categories de descripteurs ont ete evalues sur un jeu de proteines fer-soufre expertise, en les considerant soit separement soit en combinaison. L’ensemble de ces descripteurs a finalement ete integre dans un modele lineaire generalise en utilisant la technique d’elastic-net. Le modele predictif obtenu a ete evalue sur le proteome complet d’Escherichia coli, sur lequel il atteint une precision de 89% et une sensibilite de 83%. Enfin, il a ete applique a environ 300 proteomes pour explorer differentes relations biologiques comme l’abondance relative des proteines Fe-S et la tolerance a l’oxygene des organismes auxquelles elles appartiennent.
Development of a Plaque Reduction Assay as an Antiphage Activity Evaluation Method

DOI: 10.7508/rmm.2015. 03.005 Abstract Background: Antiviral screening of newly isolated or synthesized compounds is an important matter which requires a reliable antiviral test. In order to address this issue, development of a rapid antiphage test has been conducted. To achieve this goal, the antiphage activity of three antiviral drugs (Acyclovir, Lamivudine and Trifluridine) against phage CP51 which infects Bacillus cereus (ATCC 10876) was investigated. Materials and Methods: Phage lysate was prepared by inoculation of bacterial culture with few phage plaques. The number of phage has to be about one million units per milliliter. The antiviral drugs were dissolved in suitable solvents and different concentrations of each drug were prepared. Phage lysate (0.1ml) mixed with appropriate amount of each drug. After 30 minutes incubation at ambient temperature or without any incubation, 500 μl inoculum of 5 hours old liquid culture of B.cereus was added to the mixture. Then, melted top agar (1.4-1.9 ml) was subjoined at the end and the final admixture was immediately seeded on the solid PA agar. After 24 h, plaques were counted. Results: Out of three drugs, only trifluridine significantly decreased the plaque forming unit ratio (p<0.05) at higher concentration (133 μg/ml). The results of preincubation and non-incubation methods did not show any significant differences (p>0.05). Conclusion: This study supported the development of one rapid qualitative and quantitative antiphage assay.
Adapting sampling effort to assess the population establishment of Torymus sinensis, the biocontrol agent of the chestnut gallwasp

ABSTRACT Torymus sinensis Kamijo is to date the most effective controlling agent of the chestnut gallwasp Dryocosmus kuriphilus. The procedure to evaluate the parasitism rate of T. sinensis consists of dissecting D. kuriphilus galls collected in the field and checking them for its presence. Such a procedure is, however, time-consuming. Using a space-for-time substitution approach, by creating a temporal gradient within 15 sites and by means of bootstrap simulations, we analysed the effect of different sampling efforts on the precision of evaluating the success of T. sinensis release and the evolution of its parasitism rate towards biocontrol. Results show that after the first release, 200 galls are required to assess its presence with a 1% failure rate. Once T. sinensis is established, 100 galls are generally sufficient to estimate its parasitism rate by accepting a (median) percentage of error of 14% in the second year and 6% and 3% in the third and fourth year, respectively. Finally, we propose a series of design options to reduce the sampling effort according to the targeted accuracy level and as a function of the obtained parasitism rate.
First Record of Octopus insularis Leite and Haimovici, 2008 in the Octopus Fishery of a Marine Protected Area in the Gulf of Mexico

ABSTRACT The octopus fishery in Mexico is supported by two species, Octopus maya and an Octopus vulgaris-like species that teuthologists have named O. vulgaris type I. The main fishery species off the Yucatan Peninsula is O. maya, whereas the O. vulgaris-like species historically has supported the octopus fishery off the Mexican east coast. Management policies protect this species in the Veracruz Reef System (VRS) in the Gulf of Mexico, where artisanal fisherman catches it; however, specimens of O. vulgaris type I harvested in this reef system share haplotypes with Octopus insularis, and they cluster together in a strongly supported monophyletic clade. The species O. insularis does not belong to the O. vulgaris complex, as it was previously believed; it is related to the American octopuses, O. maya and Octopus mimus. The results indicate that O. insularis is distributed from the Gulf of Mexico to the coastal waters off southern Brazil and imply that the octopus fishery in the VRS is based on a misidentified species.
Human-mediated processes affecting distribution and genetic structure of Squalidus multimaculatus, a freshwater cyprinid with small spatial range

ABSTRACT Endemic species typically have a narrow niche breadth, and are likely more vulnerable to extinction than more widespread taxa. Squalidus multimaculatus is a small cyprinid endemic to the Korean Peninsula, and its reported geographical range was restricted to several small rivers located along the southeast coast. Several populations of S. multimaculatus have supposedly been subject to a variety of recent anthropogenic actions. Here, we analyzed the pattern of genetic diversity within and among populations of S. multimaculatus using nine microsatellite loci to quantify the relative contributions of human-mediated processes to the contemporary distribution and genetic structure. Overall, low levels of genetic diversity were exhibited in the populations of S. multimaculatus. Genetic differentiations among populations were not completely represented by their geographical proximity, likely resulting from the low intrapopulation genetic variability and anthropogenic transplants. The most conspicuous outcome of the anthropogenic activities was the introgression of alleles from a closely related species, S. gracilis majimae. Our study showed that anthropogenic transplanting, even with only a small number of individuals, can challenge our conservation goal to maintain the species integrity that has long been shaped in evolutionary processes.
Biomonitoring Study on Workers Occupationally Exposed to Automobile Fuels

ABSTRACT Petrol products remain unavoidable environmental pollutants as well as serious health hazards. Hence, the present study was undertaken amongst 70 petrol pump attendants and 70 Control subjects to evaluate the effects of exposure. The Exposed Group was further divided into two groups (Addiction and Non-addiction). Urinary phenol measurement, haematological analysis and Reactive Oxygen Species (ROS) parameters such as Super oxide dismutase (SOD), Catalase (CAT), Glutathione (GSH) and Glutathione peroxidise (G-Px) were performed in serum. The haematological parameters were found to be within normal range. Urinary phenol levels and the ROS parameters were significantly increased in Exposed Group. Further, the ROS levels were significantly increased in Addicted group as compared to the Non-addicted group. The results showed a positive correlation between exposure and its effects on enzyme activity. Long term occupational exposure to automobile fuel may be linked to oxidative stress which can further alleviate due to confounding factors.
Dealing with food shortage: larval dispersal behaviour and survival on non‐prey food of the hoverfly Episyrphus balteatus

1. Predatory larvae often have to face food shortages during their development, and thus the ability to disperse and find new feeding sites is crucial for survival. However, the dispersal capacity of predatory larvae, the host finding cues employed, and their use of alternative food sources are largely unknown. These aspects of the foraging behaviour of the aphidophagous hoverfly (Episyrphus balteatus De Geer) larvae were investigated in the present study.
Spatio-temporal regulation of Dachsous proteins during Drosophila development

Transcriptional regulation is one of the main mechanisms involved in tissue morphogenesis to give rise to functional organs with characteristic shapes. The Drosophila dachsous (ds) gene plays a key role in tissue development and tumorigenesis by controlling planar cell polarity (PCP), tissue growth, patterning and mitochondrial activity, among other processes. Disturbance of ds expression during Drosophila development results in alterations of the function and morphology of a wide range of embryonic and larval tissues. Similarly, in humans, mutations in the DCHS1 gene cause severe congenital malformations due to a global impairment affecting the normal formation of many tissues and organs. However, the transcriptional mechanism governing the expression of ds gene remains poorly understood. Here, we perform transcriptional analysis of ds expression and identify novel embryonic Ds proteins not expressed in larvae. The comparative analysis of Ds proteins and the exon expression pattern in/of two regulatory alleles such as dsD36 and ds38K further suggests the existence of specific transcriptional ds variants at different stages. Furthermore, a search for regulatory elements that control the spatial and temporal pattern of ds revealed the presence of cis-regulatory elements located in the intronic regions, which regulate the expression of these Ds proteins. Finally, using the Drosophila wing as model to perform a functional analysis, we show that wing growth and PCP are differentially regulated by Ds proteins expressed in different regions of wing disc. The present findings reveal that the complex regulation of the ds gene ensures the expression of specific Ds protein isoforms at different developmental stages in order to activate the cell-specific molecular programs required for tissue morphogenesis.
A possible IDO1- TSP1 role in breast cancer dormancy

Disseminated breast cancer cells have been found in the perivascular niche of lung, brain and bone marrow. Research has suggested that thrombospondin 1 (TSP1), an antiangiogenic protein secreted by endothelial cells, is involved in cancer dormancy. My research aims to clarify the role of TSP1 in cancer dormancy. On the other hand, breast tumours overexpress indoleamine 2,3-dioxygenase (IDO1) which degrades intracellular tryptophan, a key amino acid of TSP1. I aim to investigate whether cancer cells induce endothelial IDO1 expression and therefore limit TSP1 synthesis. I hypothesize that the decrease of TSP1 might enable cancer cell proliferation and angiogenesis. To evaluate whether endothelial cells can induce cancer dormancy, MDA-MB-231 cells were cultured on the top of an endothelial monolayer or treated with endothelial conditioned medium. Ki67, p21 and cell cycle analysis showed that endothelial cells induce cell cycle arrest in MDA-MB-231 cells but not senescence. ki67 was also decreased when MDA-MB-231 cells were cultured with TSP1. MDA-MB-231 revealed to be more resistant to docetaxel, a breast cancer drug, when pre-cultured with TSP1. Conditioned medium experiments showed that MDA-MB-231 cells are capable of inducing endothelial IDO1 expression and it also increased tryptophan degradation, which was prevented by siRNA IDO1 knockdown. Interestingly, endothelial TSP1 secretion was revealed to be decreased under low tryptophan concentration. Immunohistochemistry of breast cancer tissue showed that there was a negative correlation between vascular IDO1 and stromal TSP1. IFNγ, a potent inducer of IDO1, showed to be able to induce endothelial IDO1 and a decrease in endothelial TSP1. Taken together, the data presented here suggests that endothelial cells induce breast cancer dormancy and drug resistance via TSP1. My research also suggests that an IFNγ/IDO1 pathway might decrease TSP1 synthesis leading to cancer cell proliferation and angiogenesis.
Structural Characterisation of Human Kinases using a Library-Based Construct Screening Approach

Structural characterization of proteins is often hindered by insufficient amounts of soluble protein. A common approach is to isolate its separate domains, classically done by time-consuming iterations of design, generation and testing of constructs. An alternative approach is to generate a random library of all possible constructs by enzymatic DNA truncation and test them in one experiment for expression and solubility. In this work, the novel, directed evolution-type method Expression of Soluble Proteins by Random Incremental Truncations (ESPRIT) was used to explore the definition of protein domains. The biological focus was a set of multidomain protein kinases that has previously resisted soluble over-expression and structural characterisation. First, improvements in the method were developed to improve the quality and efficiency of the truncation libraries leading to better coverage of the diversity. Then, its application on a more characterised protein, DAPK1, demonstrated precise domain definition. Small variations of the constructs resulted in significantly different thermal stability and crystal packing, thus providing a means to resolve structures with alternative conformations. The method was also used for the identification of soluble variants of the complex between DAPK1 and its partner calmodulin where the minimal interaction region was shorter than previously reported. The application of the method to a series of difficult-to-express protein kinases resulted in rapid identification of incompatibility with E. coli over-expression for some of the targets. While attempts to rescue the low solubility the IKKb kinase catalytic domain were unsuccessful, additional screens on this protein identified soluble and regulatory domains that showed some functionality in vivo. Finally, it was demonstrated that constructs of the PI3Kb p110b catalytic domain with residual solubility in E. coli, identified from screening, could be expressed in insect cells at higher yields in soluble form.
Preparing for the worst: Evidence that older adults proactively downregulate negative affect

Age-related differences in processing emotional stimuli are well established. However, previous studies have only assessed the impact of age on emotional processing and encoding in response to, not in anticipation of, emotional stimuli. In the current study, we investigated age-related differences in the impact of emotional anticipation on affective responses and episodic memory for emotional images. Young and older were scanned while encoding negative and neutral images preceded by cues that were either valid or invalid predictors of image valence. Participants were asked to rate the emotional intensity of the images and to complete an episodic recognition task immediately after scanning. Using multivariate behavioral partial least squares (PLS) analysis, we found that young and older adults recruit the same set of brain regions to differentially support emotional processing during the anticipation of emotional images. Specifically, anticipatory recruitment of the amygdala, ventromedial PFC, and hippocampus in older adults predicts reduced memory for negative than neutral images for older adults and the opposite for young adults. Seed PLS analyses further show inverse coupling between the amygdala and ventromedial PFC activation following negative cues, consistent with the top-down spontaneous suppression of negative affect. To the best of our knowledge, this is the first study to provide evidence that the “positivity effect” seen in older adults’ memory performance is related to the spontaneous suppression of negative affect in anticipation of, not just in response to, negative stimuli.
A new species of Molineus (Nematoda: Molineidae) parasite of Procyon lotor (Mammalia: Carnivora) in Mexico with a taxonomic key for the species of the genus

Molineus lotoris n. sp. , parasite of the intestine of the raccoon Procyon lotor collected in Mexico is described and illustrated. The new species can be differentiated from the 27 species included in Molineus by a combination of traits: presence of a prominent and globular cephalic vesicle; spicules with 2 terminal processes, measuring 0.099–0.115 in length and by the number of synlophe ridges at mid-body level of males (17). In addition, a taxonomic key for the species included in Molineus is presented. Finally, some other nematode species collected in raccoons from several localities of Mexico are recorded, including two species not reported for this host in this country: Cameronecator urichi and Aonchotheca ( Aonchotheca ) putorii .