Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclic-di-GMP is required for corneal infection by Pseudomonas aeruginosa and modulates host immunity

Biofilms are extremely tolerant toward antimicrobial treatment and host immune clearance due to their distinct physiology and protection by extracellular polymeric substances. Bis-(3´-5´)-cyclic dimeric guanosine monophosphate (c-di-GMP) is an essential messenger that regulates biofilm formation by a wide range of bacteria. However, there is a lack of physiological characterization of biofilms in vivo as well as the roles of c-di-GMP signaling in mediating host-biofilm interactions. Here, we employed dual RNA-Seq to characterize the host and pathogen transcriptomes during Pseudomonas aeruginosa infection using a mouse keratitis model. In vivo P. aeruginosa biofilms maintained a distinct physiology compared with in vitro P. aeruginosa biofilms, with enhanced virulence and iron uptake capacity. C-di-GMP synthesis was enhanced in P. aeruginosa cells in vivo, potentially due to down-regulation of the expression of several phosphodiesterases (e.g., DipA, NbdA). Increased intracellular c-di-GMP levels were required for long-term ocular colonization of P. aeruginosa and impaired host innate immunity.
PEAPOD limits developmental plasticity in Arabidopsis

Higher plants utilise developmental plasticity to adapt to changes in the environment, especially to variations in light. Much of this change in growth and development involves the light-mediated regulation of multiple hormone pathways. However, despite considerable progress towards understanding the molecular processes controlling light signalling and hormone activity, regulatory mechanisms preventing exaggerated plant developmental responses are not well understood. Here I report that the PPD regulatory complex has a crucial role in limiting developmental plasticity in Arabidopsis. Reductions in PPD or KIX8/9 gene expression resulted in; tolerance to ABA inhibition of seed germination, hypocotyl elongation, increases in stomata on hypocotyls, cambial cell proliferation and seed weight, and delayed flowering. Transcript profiling and analyses of hormone responses and genetic interactions established PPD modulates developmental plasticity, mainly by a combination of transcriptional activation and repression of genes controlling CRY/PHY light signalling and ABA, auxin, brassinosteroid, cytokinin and gibberellin homeostasis.
Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single-nucleotide Polymorphism Markers

The level and extent of linkage disequilibrium (LD) and effective population size (Ne) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas, using 61 single-nucleotide polymorphisms. Significant differences were detected in the average r2 between the selected lines and wild population for both syntenic and nonsyntenic loci with LD beyond population-specific critical values (P<0.05). Moreover, the proportions of syntenic and nonsyntenic loci with the expected LD level in the wild population were lower than that in the selected lines. Taken together, the LD level of the selected lines was higher than that of the wild population. The extent of LD analysis showed that a short range of LD (0–0.23 cM) was detected in the four populations, and the decay distance was lower in the wild population than in the selected lines. Ne values ranged from 47.6 to 58.5 in the selected lines and ranged from 527.9 to 709.6 with infinite upper limits in the wild population. Further variance analysis of LD demonstrated that genetic drift and epistatic selection might account for the increased LD levels in selected lines. The LD information will be valuable for further association study and marker-assisted selection in oysters.
The role of WRKY transcription factors in plants

The WRKY proteins are one of the largest families of transcriptional regulators in plants. Their biosynthesis is induced during certain stages of plant development and upon pathogen infection. A single WRKY transcription factor may be involved in the regulation of several apparently disparate processes. Their hallmark is strong conservation of the DNA binding domain which contains an invariant WRKYGQK amino acid sequence and a zinc binding motif. However, the overall sequences of individual representatives are highly divergent. Little is known about the 3D-structure of the WRKY proteins. Up to date there have only been results of structural strudies of DNA binding domain available. In this review, the biological function as well the structural studies of the WRKY proteins have been recapitulated.
The Genetic History of Northern Europe

Recent ancient DNA studies have revealed that the genetic history of modern Europeans was shaped by a series of migration and admixture events between deeply diverged groups. While these events are well described in Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here we report genome-wide DNA data from 24 ancient North Europeans ranging from ∼7,500 to 200 calBCE spanning the transition from a hunter-gatherer to an agricultural lifestyle, as well as the adoption of bronze metallurgy. We show that Scandinavia was settled after the retreat of the glacial ice sheets from a southern and a northern route, and that the first Scandinavian Neolithic farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Western European Mesolithic hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers until around 2,900 calBCE when the arrival of steppe pastoralists introduced a major shift in economy and established wide-reaching networks of contact within the Corded Ware Complex.
Effects of Aerosols on Cloud Albedo: Evaluation of Twomey's Parameterization of Cloud Susceptibility Using Measurements of Ship Tracks.

Abstract Airborne measurements from the Meteorological Research Flight’s Hercules C-130 and the University of Washington’s Convair C-131A during the Monterey Area Ship Track field project are used to evaluate Twomey’s analytic expression for cloud susceptibility, which describes the sensitivity of cloud albedo to changes in droplet concentrations. This expression incorporates assumptions about cloud physics, such as the independence of the cloud liquid water content and the width of the droplet size distribution on droplet concentrations. Averaged over all 69 ship track penetrations, cloud liquid water content decreased slightly and the droplet size distributions broadened from the ambient values. For the 17 cases for which albedos were measured during overflights, Twomey’s parameterization represents the trend of albedo changes with droplet concentrations remarkably well, passing through the midpoints of the considerable spread in the data. The fortuitous agreement results from compensating changes in cl.
Sistemas de labranza y densidades de la batata: calidad del suelo y de las raíces tuberosas

The aim of this work was to determine the effect of tillage systems and seeding densities in sweet potato (Ipomoea batata (L) Lamb. ). The study was held on the Central University of Venezuela, in the year of 2014. The degrees of severity of soil degradation and its correspondence with the scales of preference based on unit weight and dimensions of the tuberous root were determined. An arrangement of slots was used, where the tillage systems (TS) were assigned to the parcels and the seeding densities (SD) were assigned to slots. The TS consisted on vertical farming with a chisel (LC), with disc plowing (LA), conventional with three passes of the disc harrow (LCo) and a minimum with a pass of disc harrow (LM). The Ds were of 0,25 cm (D1) and 0,15 cm (D2) in the line. The physical quality of the soil was superior in the LA treatments. In these, the combination with the longest planting distances (LA-D1) favored the highest postharvest quality. On the contrary, the chisel treatments promoted the least acceptances among consumers. The light to moderate severity of soil degradation did not explain the postharvest quality variation. It is inferred on the lower rate in water movement in LD, that promoted and excess in humidity and a lower quality in the tuberous root.
Gibbago trianthemae Simmons, a Biocontrol Agent of Horse Purslane Weed: Research and Prospect

Trianthema portulacastrum L. (commonly known as horse purslane) is a noxious weed of several economically important field crops in tropical regions of the world. An intensive work on the screening of the biocontrol agents was accomplished through in vitro epidemic study to control weed populations. The foliar disease symptoms on infected weed plants caused by fungal pathogens represented as round to irregular maroon spots with dark borders and the epidemic was identified as leaf spot disease. The pathogen allied with the infection of horse purslane was isolated from infectious propagules by inoculation of leaf bites on a nutrient medium, potato dextrose agar (PDA). The causal agent of leaf spot was confirmed as Gibbago trianthemae Simmons by Koch’s postulates. The mycoherbicide ability of G. trianthemae has been examined through visual (standard area diagram) and statistical methods (analysis of variance using the Microsoft Office Excel-Data Analysis Tool Pack 2007). The results revealed that the pathogen causes significantly (P < 0.05) severe infection on host weed and destructs the weed population by leaf spot diseases. The findings of the research suggested that the isolate G. trianthemae is highly virulent and host-specific, and recommended for further studies as a promising biocontrol agent against horse purslane weed.
Rôle de la protéine EB2 du virus d'Epstein-Barr dans le métabolisme des ARN messagers

La regulation post-transcriptionnelle de l’expression genique est basee sur un reseau complexe et dynamique d’interactions ARN-proteines. Un defi important est de comprendre les mecanismes par lesquels ces proteines de liaison a l’ARN (RBPs) influencent chaque etape du metabolisme des ARNm. Les travaux realises au cours de cette these ont permis de caracteriser de nouvelles fonctions de la RBP virale EB2 qui est indispensable a la production du virus d’Epstein-Barr (EBV). Des travaux anterieurs ont montre qu’EB2 favorise l’accumulation cytoplasmique de la majorite des ARNm viraux, dont la caracteristique est d’etre transcrit a partir de genes sans intron. Nous montrons que le role d’EB2 ne se limite pas a celui de facteur d’export des ARNm car cette RBP stabilise aussi ses ARNm cibles dans le noyau en les protegeant de la degradation par l’exosome. Nos resultats indiquent qu’en absence d’EB2 : (i) certains ARNm viraux sont instables car ils contiennent des sites cryptiques d’epissage ; (ii) le facteur d’epissage SRSF3 destabilise ces ARNm en interagissant a la fois avec l’exosome et le complexe NEXT, un des cofacteurs nucleaires de l’exosome. Par ailleurs, nous montrons egalement qu’EB2 est associee aux polysomes et stimule efficacement la traduction de ses ARNm cibles, en interagissant avec les facteurs d’initiation de la traduction eIF4G et PABP. Le developpement d’un nouveau systeme de traduction in vitro nous a permis de montrer que l’effet d’EB2 sur la traduction necessite le passage nucleaire de ses ARNm cibles. Ainsi, l’ensemble de nos travaux demontre le role cle d’une RBP virale dans le couplage entre les etapes nucleaires et cytoplasmiques de la biogenese des ARNm.
Performance of Asalio (Lepidium sativum L.) genotypes under semi-arid condition of middle Gujarat.

Asalio (Lepidium sativum L.), is a low water requiring medicinal herb: the roots, leaves and seeds are used for different medicinal preparations. A field experiment was conducted to assess the response of five important lines (No. 99, No. 31, No. 37, No. 16 and No. 53) and one cultivar (GA-1) of Asalio in terms of leaf photosynthetic characteristics, growth and grain yield. The results revealed that there was wide variability in different genotypes with regard to all these above parameters. A line, No. 16 exhibited maximum growth in terms of all these characters. Maximum seed yield of 18.1 q ha-1 was also obtained in No. 16 with a harvest index (HI) of 32.2 % and test weight (1000 seed weight) of 1.76 g, which was the maximum among all the genotypes. The significant variability among the genotypes with respect to all these above determinants indicates the utility of the line No. 16 under semi-arid condition.
Shrimp quality and safety management along the supply chain in Benin

Abstract This thesis focuses on quality and safety management of tropical shrimp (Penaeus spp.) using Benin (West Africa) as an example of a shrimp exporting country. The entire supply chain, from fishing areas (brackish waters) to shrimp processing plants, was investigated. The steps of the chain prior to shrimp processing at the freezer plants were critical for shrimp quality and safety because of prevailing temperature abuse and inappropriate hygienic conditions. Combining culture-dependent (plate counts) and culture independent (DGGE, clone libraries analysis) approaches, it was found that bacterial concentration in shrimps was higher than that of their surrounding water and sediment. Conversely, bacterial diversity was higher in water or sediment than in shrimps. At species level, distinct bacterial communities were associated with sediment, water or shrimp samples. Spoilage evaluation of shrimps showed that during storage at 0oC, Pseudomonas spp. were dominant, whereas at 7oC and 28oC, H2S-producing bacteria were the dominant group of microorganisms. An empirical model predicting shrimp shelf-life as a function of constant storage temperature was developed. Isolates producing strong off-odor were identified by 16S rRNA sequencing as mainly lactic acid bacteria (LAB) and Enterobacteriaceae at 28oC or 7oC and Pseudomonas spp. and LAB (Carnobacterium maltaromaticum) at 0oC. The fastest growing isolates namely, Pseudomonas psychrophila and C. maltaromaticum were selected for their spoilage activity and for modeling studies. P. psychrophila had a higher growth rate and a higher spoilage activity at 0 to 15oC, while at 28oC, C. maltaromaticum had a higher growth rate. Models predicting the growth of pseudomonads in shrimps as a function of temperature were constructed. These models were validated under dynamic storage temperatures simulating actual temperature fluctuation in the supply chain. Using different risk classification approaches, the main foodborne pathogen risks identified were Vibrio parahaemolyticus and Salmonella. The management of the risks posed by the main pathogens was addressed using different scenarios to meet the set food safety objectives. Based on quantitative and ecological studies, this thesis developed tools that can be used in decision-making regarding tropical shrimp quality and safety management.
δ56Fe in seabird guano reveals extensive recycling of iron in the Southern Ocean ecosystem

Availability of iron limits productivity in the Southern Ocean where vast regions of high‐nitrogen low‐chlorophyll conditions are punctuated by hotspots of production surrounding the subAntarctic islands. Here, we compare patterns in accumulation of iron, as indicated by [Fe] and Fe : C (from Wing et al. ), with proxies for uptake of iron within food webs, as indicated by Fe : Al and δ56Fe within the subAntarctic Auckland Island ecosystem. We compare these proxies for dynamics of iron within egested material collected from six seabird species, representing three distinct foraging guilds. Fractions of biogenic iron, estimated from Fe : Al, were lowest in the coastal foraging guild (0.83 ± 0.01), and higher in the oceanic and predator guilds (0.94 ± 0.01 and 0.95 ± 0.01), consistent with high rates of biological recycling. The isotopic ratio of iron 56Fe/54Fe, reported as δ56Fe, is depleted in the heavy isotope 56Fe by recycling in the microbial loop, and is likely further depleted in 56Fe when taken up by animals within the food web. δ56Fe was most negative for the oceanic foraging group indicating intensive recycling (−1.16 ± 0.16‰), most positive in the coastal group where direct lithogenic sources of iron are more available (−0.14 ± 0.15‰), and intermediate in the predatory group, representing a mixture and possible fractionation within food webs (−0.37 ± 0.14‰). These data reveal strong contrasts in bioaccumulation and recycling of iron between coastal and oceanic food webs, and important interactions between marine food web structure and biogeochemical processes supporting productivity in the Southern Ocean.
Resolving sky island speciation in populations of East African Adolfus alleni (Sauria, Lacertidae)

The genus Adolfus Sternfeld, 1912 currently contains three species from Equatorial Africa. Two of these occur in widespread, lowto mid-elevation habitats, but Adolfus alleni is only known from four montane peaks (Aberdares, Mt. Kenya, Cherangani Hills, Mt. Elgon) in Kenya and Uganda. An integrative approach using 58 morphological characters and genetic analyses of mitochondrial (16S and cyt b) and nuclear (c-mos and RAG1) DNA sequence data revealed differences between these populations, and indicated that A. alleni is a complex of at least two cryptic species. Herein, we describe the populations from the Aberdares and Mount Elgon as a new species, and restrict A. alleni to Mount Kenya. This action underscores the importance of conservation strategies to protect these montane peaks, which may harbour additional, unique evolutionary lineages.
Evaluation of Experimental Hybrids in Early Growth Stages for Cold Tolerance in Maize

To evaluate fifteen experimental hybrids at early seedling stages in winter season of northern India, a study was conducted during Rabi seasons of 2013-14 and 2014-15 with three checks. The experiment was laid out in Randomized Block Design with two replications and observations were recorded fortnightly from third week of December to last week of February. Cold stress significantly reduced the survival rate, seedling height, leaf appearance rate and leaf area in genotypes. Experimental hybrids, 12007x EL-KRNL-7, 12007 x A-89 and 131026 x131023 out-performed the superior check under cold conditions. Cold tolerant hybrids for early growth stages identified may be recommended for northern India in winter season after undergoing multi location yield trials. Further these hybrids can be utilized in breeding programmes.
GLYCOGEN SYNTHASE KINASE-3 BETA PROTEIN INHIBITION BY SELECTED PHYTOCOMPOUNDS IN SILICO

Objectives: Bioactive phytocompounds are a rich source of chemopreventive substance. In the present investigation, docking study was performed for the selected bioactive phytocompounds such as oleanolic acid, ecdysterone, betaine, stigmasterol acetate, and cinnamic acid to evaluate their affinity to glycogen synthase kinase-3 beta (GSK-3β) protein, a wound-healing biomarker. 2-chloro-5-[4-(3-chloro-phenyl)-2, 5-dioxo-2,5-dihydro-1h- pyrrol-3-ylamino]-benzoic acid was used as an inhibitor for GSK-3β with minimum binding energy (−31.5 kcal/mol). Methods: Molecular docking study was conducted using AutoDock 4.2 version and the visualization result using Discover Studio 4.5. R esults: The docking analysis ranked the selected phytocompounds that have high theoretical scores to bind to the proteins. The binding mode of the phytocompounds that bound to all the target proteins with high affinity was studied. The simulation demonstrated that the protein-ligand complex stabilized by multiple hydrogen bonds (H-bonds) was preferentially formed at the catalytic site. The results highlighted in this study reveals that among the selected lead phytocompounds that docked into the active site of GSK-3β, ecdysterone showed acceptable 6 H-bond interactions with residues LYS85, TYR134, ARG141, GLN185, ASP200, PRO136 when compared to the reference compound with 5 H-bond interactions. C onclusion: Thus, based on the docking score ecdysterone could be considered as a novel compounds that can be used for experimental studies for the inhibition of GSK-3β kinase. These results can be helpful for further design of novel GSK-3β inhibitors. Ke ywords: Phytocompounds, Molecular docking, Simulation, Receptor, Ligand, Inhibition.
Surveillance and insecticide susceptibility status of Culicine mosquitoes in selected communities utilizing long-lasting insecticidal nets in Kwara state, Nigeria

Vector control programs in Nigeria are mostly targeted towards reducing the burden of malaria with less emphasis placed on other debilitating vector borne diseases such as dengue, yellow fever and filariasis. This study assessed the indoor resting densities and insecticide susceptibility status of Culex and Aedes mosquitoes in selected communities utilizing long-lasting insecticidal nets (LLIN) in Kwara State, Nigeria. Pyrethrum spray collections of indoor resting Aedes and Culex mosquitoes were conducted in three communities while adults of both mosquito species reared from larval collections were exposed to pyrethroid, organochlorine, and carbamate insecticides following WHO procedure. Results showed that the higher indoor resting densities of Culex quinquefasciatus (2.5 – 3.4) collected were not significantly (p>0.05) different from the Aedes aegypti (0.3 – 1.3) in all the communities. Carbamate resistance (≤ 81 % post exposure mortalities) was observed in both Culex (Ilota and Amoyo) and Aedes populations (Gaa-Bolorunduro). Aedes in Gaa-Bolorunduro and Ilota were fully susceptible (100 % mortality) to permethrin and DDT while the Culex population showed differential susceptibility (64 – 100%) to pyrethroid and organochlorine insecticides tested. These findings show focal insecticide resistance requiring specific intervention in each community based on the evidence provided by this study. Pyrethroid resistance status of the Culex quinquefasciatus in these areas may result in access of the vectors to net occupants leading to lower LLIN utilization rates among users. Environmental management strategy in addition to the use of effective insecticide will be most probable for management of vector borne diseases in these localities.
A Unique Ribosome Signature Reveals Bacterial Translation Initiation Sites

While methods for annotation of genes are increasingly reliable the exact identification of the translation initiation site remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. Using these unique signatures we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic samples, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and elongations of annotated coding sequences. These re-annotations are supported by the presence of Shine-Dalgarno sequences, structural and sequence based features and N-terminal peptides. Finally, our model identifies 61 novel genes previously undiscovered in the genome.