Miracle-dz/UniFAR-FTUs huggingface dataset:
ArdC protein overpasses the recipient hsdRMS restriction system broadening conjugation host range

Plasmids, when transferred by conjugation, must overpass restriction-modification systems of the recipient cell. We demonstrate that protein ArdC, encoded by broad host range plasmid R388, was required for conjugation from Escherichia coli to Pseudomonas putida, but not from E. coli to E. coli. Surprisingly, expression of ardC was required in the recipient cells, but not in the donor cells. Besides, ardC was not required for conjugation if the hsdRMS system was deleted in P. putida recipient cells. Thus, ArdC has antirestriction activity against HsdRMS system, and consequently broadens R388 plasmid host range. The crystal structure of ArdC was solved both in the absence and in the presence of Mn2+. ArdC is composed of a non-specific ssDNA binding N-terminal domain and a C-terminal metalloprotease domain, although the metalloprotease activity is not needed for antirestriction function. We also observed by RNA-seq that ArdC-dependent conjugation triggers an SOS response in the P. putida recipient cells. Our findings give new insights, and open new questions, into the antirestriction strategies developed by plasmids to counteract bacterial restriction strategies.
Bioflocculation technique for microalgal harvesting and wastewater nutrient recovery

Fungal assist microalgal cultivation is getting substantial considerations due to the highly efficiency of bioflocculation process without requirements of added chemicals and little bit energy input. So, Fungi pelletization-assisted microalgal cultivation were applied for improving algal harvesting process and nutrient recovery as step wise for wastewater treatment. Two strains of microalgae (Nannochloropsis salina and Chlorella salina) and three species of fungi (Penicillium chrysogenum, Aspergillus niger and Aspergillus fumigatus) were used to evaluate the effect of fungi–algae pelletization process on wastewater recovery. After 48 hour of cultivation, the highest flocculation efficiency (98.9%) was recorded by A. fumigatus assist C. salina, while the lowest percentage (85.9%) recorded by A. niger assist N. Salina. The highest nutrient removal percentage was for nitrite by A. niger assist C. salina /tap water (98.4%) followed by phosphate A. fumigates assist N. salina/sea and tap water (90.9%), then ammonia by A. fumigates assist N. salina /seawater (89.5%). This study concluded that the bioflocculation technique is a highly promising compared to traditional algal harvesting techniques and other biological wastewater treatment methods.
Morphological and molecular identification of two Florida populations of foliar nematodes (Aphelenchoides spp.) isolated from strawberry with notes on their phytoparasitic status

vi RESUMO . viii GENERAL INTRODUCTION . 1 LITERATURE CITED . 3 Morphological and Molecular Identification of Two Florida Populations of Foliar Nematodes (Aphelenchoides spp.) Isolated from Strawberry with notes on their Phytoparasitic Status. 5 Abstract . 5 Introduction . 6 Materials and Methods . 8 Results . 13 Discussion . 19 Acknowledgements . 22 Tables legends . 24 Figure legends . 44 Literature cited . 55
Inclusion of mesquite pod meal (Prosopis juliflora) in diets for nile tilapia (Oreochromis niloticus) juveniles

Alternative feeds are used to include or replace conventional ingredients in fish diets to generate regional socioeconomic sustainability and maintain the growth performance of fish. The objective of this study was to evaluate the effect of mesquite pod meal (MPM) in extruded diets for Nile tilapia juveniles fed graded levels of inclusion (26, 32, 38, 44, and 50%). Growth performance variables of plasma metabolites, enzymatic activities and haematological parameters were evaluated. Fish were fed at 6% of biomass for 45 days. Four-hundred Nile tilapias juveniles (11.5 ± 0.18 g) were distributed into twenty-500L aquaria in recirculation system. Significant differences of treatments on performance parameters, feed conversion ratio and survival were observed. Among the metabolic parameters, glycemia was altered (P 0.05) by the inclusion of MPM. Hematological variables did not change (P>0.05). It was concluded that MPM can be included up to 38.67% in diets for Nile tilapia juveniles without impairing performance, metabolism, enzymatic activities and health.
ALMOPOL: A Cross-pollination and Nut Set Simulation Model for Almond

ALMOPOL is an interactive computer-based model that simulates the interactions of weather, bloom phenology, blossom quality, and honey bee foraging behavior that culminate in almond [Prunus dulcis (Mill) D. A. Webb] nut set. ALMOPOL enables users to enter orchard conditions, colonies per hectare, and foragers per colony. Information concerning honey bee foraging behaviors and blossom quality (i.e., a blossom's probability of setting a nut if cross-pollinated) can also be entered interactively into the program. Hence, nut set estimates are specific for a given set of weather, orchard, bee behavior, and blossom quality conditions. A description of the logic and data used in ALMOPOL's construction is included.
Distribution of mercury‐cycling genes in the Arctic and equatorial Pacific Oceans and their relationship to mercury speciation

Humans are exposed to potentially harmful amounts of the neurotoxin monomethylmercury (MMHg) through consumption of marine fish and mammals. However, the pathways of MMHg production and bioaccumulation in the ocean remain elusive. In anaerobic environments, inorganic mercury (Hg) can be methylated to MMHg through an enzymatic pathway involving the hgcAB gene cluster. Recently, hgcA‐like genes have been discovered in oxygenated marine water, suggesting the hgcAB methylation pathway, or a close analog, may also be relevant in the ocean. Using polymerase chain reaction amplification and shotgun metagenomics, we searched for but did not find the hgcAB gene cluster in Arctic Ocean seawater. However, we detected Hg‐cycling genes from the mer operon (including organomercury lyase, merB), and hgcA‐like paralogs (i.e., cdhD) in Arctic Ocean metagenomes. Our analysis of Hg biogeochemistry and marine microbial genomics suggests that various microorganisms and metabolisms, and not just the hgcAB pathway, are important for Hg methylation in the ocean.
The diagnostic chronic lymphocytic leukaemia genome by nanopore sequencing

Chronic lymphocytic leukaemia (CLL) is characterised by considerable clinical and biological heterogeneity, with specific recurrent genomic alterations, including TP53 mutations, deletions of chromosome 17p, and IgHV mutational status, impacting on response to chemo-immunotherapy and targeted agents. Consequently, diagnostic screening for these predictive biomarkers is recommended in both national and international clinical guidelines. Current conventional methods, including fluorescent in-situ hybridisation and Sanger sequencing, exhibit shortcomings in terms of cost, speed and sensitivity, and even second-generation sequencing methods encounter technical limitations imposed by short-read lengths and bio-informatics analysis. The MinION platform from Oxford Nanopore Technologies generates exceptionally long (1-100kbp) read lengths in a short period of time and at low cost, making it a good candidate for diagnostic testing. In this paper, we present a nanopore-based CLL-specific screening assay, to simultaneously screen for both TP53 mutations and del17p13.1, as well as determining the IgHV mutation status for a single patient in one sequencing run. We sequenced 11 CLL patients and were able to generate a full diagnostic dataset for all. We identified somatic SNVs and indels in the coding region of TP53, and demonstrate that, following error correction of the data, we could accurately define the somatically hypermutated IgHV region in all patients. We also demonstrated the ability of the MinION platform to detect large-scale genomic deletions through low-coverage whole-genome sequencing. We conclude that nanopore sequencing has the potential to provide accurate, low-cost and rapid diagnostic information, which could be applied to other cancer types.
Deciphering the rules underlying xenogeneic silencing and counter-silencing of Lsr2-like proteins

Lsr2-like nucleoid-associated proteins play an important role as xenogeneic silencers (XS) of horizontally acquired genomic regions in actinobacteria. In this study, we systematically analyzed the in vivo constraints underlying silencing and counter-silencing of the Lsr2-like protein CgpS in Corynebacterium glutamicum. Genome-wide analysis revealed binding of CgpS to regions featuring a distinct drop in GC-profile close to the transcription start site (TSS), but also identified an overrepresented motif with multiple A/T steps at the nucleation site of the nucleoprotein complex. Binding of specific transcription factors (TFs) may oppose XS activity leading to counter-silencing. Following a synthetic counter-silencing approach, target gene activation was realized by inserting operator sites of an effector-responsive TF within various CgpS target promoters resulting in an increased promoter activity upon TF binding. Analysis of reporter constructs revealed maximal counter-silencing when the TF operator site was inserted at the position of maximal CgpS coverage. This principle was implemented in a synthetic toggle switch, which features a robust and reversible response to effector availability highlighting the potential for biotechnological applications. Altogether, our results provide comprehensive insights into how Lsr2 silencing and counter-silencing shapes evolutionary network expansion in this medically- and biotechnologically-relevant bacterial phylum. IMPORTANCE In actinobacteria, Lsr2-like nucleoid-associated proteins function as xenogeneic silencers (XS) of horizontally acquired genomic regions, including viral elements, virulence gene clusters in Mycobacterium tuberculosis, and genes involved in cryptic specialized metabolism in Streptomyces species. Consequently, a detailed mechanistic understanding of Lsr2 binding in vivo is relevant as a potential drug target and for the identification novel bioactive compounds. Here, we followed an in vivo approach to investigate the rules underlying xenogeneic silencing and counter-silencing of the Lsr2-like XS CgpS from Corynebacterium glutamicum. Our results demonstrated that CgpS distinguishes between self and foreign by recognizing a distinct drop in GC-profile in combination with a short, sequence specific motif at the nucleation site. Following a synthetic counter-silencer approach, we studied the potential and constraints of transcription factors to counteract CgpS silencing thereby facilitating the integration of new genetic traits into host regulatory networks.
Multi-modal communication: Song sparrows increase signal redundancy in noise

Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has been on communication in a single modality. Consequently, how multimodal communication is affected by anthropogenic noise is relatively poorly understood. Here we ask whether song sparrows (Melospiza melodia) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (1) that song sparrows will shift signaling effort to the visual modality (the multi-modal shift hypothesis), and (2) that they will increase redundancy of their multi-modal signaling (the back-up hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signaling effort to visual modality (i.e., wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase redundancy of their multi-modal signals, which may aid in robustness of the communication system.
Predictive masking is associated with a system-wide reconfiguration of neural populations in the human visual cortex

The human visual system masks the perceptual consequences of retinal or cortical lesion-induced scotomas by predicting what is missing from nearby regions of the visual field. To reveal the neural mechanisms underlying this remarkable capacity, known as predictive masking, we used fMRI and neural modeling to track changes in cortical population receptive fields (pRFs) and connectivity in response to the introduction of an artificial scotoma (AS). Consistent with predictive masking, we found that extrastriate areas increased their sampling of the V1 region outside the AS projection zone. Moreover, throughout the visual field and hierarchy, pRFs shifted their preferred position towards the AS border. A gain field model, centered at this border, accounted for these shifts, especially for extrastriate areas. This suggests that a system-wide reconfiguration of neural populations in response to a change in visual input is guided by extrastriate signals and underlies the predictive masking of scotomas.
Interrelationships among attitudes toward and practice of nutrition and health of prepaid health plan members

approved: _ . -. Elizabeth ^Fbhnson, Ph.D. Interrelationships among attitudes toward and practice of nutrition and health were determined from results of 335 responses to a survey mailed to members of a prepaid health plan in Portland, Oregon, in the Spring of 1981. The scales used to test attitudes included Subjective Index of General Well-Being, Health Locus of Control and the attitude "nutrition is important". Nutrition practices were determined from a one-day food record analyzed using Pennington's index nutrients. Health practices, including smoking, alcohol consumption, physical activity, hours of sleep, body weight in relation to standards and meal frequency, were analyzed to form a health practice score. Demographic characteristics of the population, including sex, age, marital status, employment status, education and income, were determined and correlated with all attitudes and practices. Interrelationships were tested using Pearson r and Chi-square correlations and multiple regression analysis. The population studied was characterized as married, employed, well educated and middle income. They felt well and in control of their health. Approximately 52 percent practiced several desirable health practices, about 90 percent had a positive attitude toward nutrition and only 22 percent scored above at least 66 percent of Dietary Nutrient Score considered adequate for adults while 33 percent had diets which did not meet 50 percent of this score. This study using members of a prepaid health plan supports the existing literature. Nutrition attitude, "nutrition is important," is correlated to nutrient intake. Health attitudes, general well-being and health locus of control, were correlated to health practices. In this study correlations among general well-being, health locus of control, nutrition attitude, health practices and nutrition practices were noted, however the correlations were not large enough to be predictive. Further study is recommended to define and develop these relationships. Interrelationships Among Attitudes Toward and Practice of Nutrition and Health of Prepaid Health Plan Members by Jan Morgan Daoust A THESIS submitted to Oregon State University in partial fulfillment of the requirements for the degree of Master of Science Completed April 30, 198 2 Commencement June, 1982
Cis-Regulatory Accessibility Directs Muller Glial Development and Regenerative Capacity

Diseases and damage to the retina lead to losses in retinal neurons and eventual visual impairment. Although the mammalian retina has no inherent regenerative capabilities, fish have robust regeneration from Müller glia (MG). Recently, we have shown that driving expression of Ascl1 in adult mouse MG stimulates neurogenesis similar to fish regeneration. The regeneration observed in the mouse is limited in the variety of neurons that can be derived from MG; Ascl1-expressing MG primarily generate bipolar cells. To better understand the limits of MG-based regeneration in mouse retinas, we used ATAC- and RNA-seq to compare newborn progenitors with MG. Our analysis demonstrated striking similarities between MG and progenitors, with losses in regulatory motifs for neurogenesis genes. Young MG were found to have intermediate expression profiles and accessible DNA, which is mirrored in the ability of Ascl1 to direct bipolar neurogenesis in young MG. When comparing what makes bipolar and photoreceptor cells distinct from glial cells, we find that bipolar-specific accessible regions are more frequently linked to bHLH motifs and Ascl1 binding, indicating that Ascl1 preferentially binds to bipolar regions. Overall, our analysis indicates a loss of neurogenic gene expression and motif accessibility during glial maturation that may prevent efficient reprogramming.
Heterospecific song quality as social information for settlement decisions: an experimental approach in a wild bird

Assessing local habitat quality via social cues provided by con- or heterospecific individuals sharing the same needs is a widespread strategy of social information use for breeding habitat selection. However, gathering information about putative competitors may involve agonistic costs. The use of social cues reflecting local habitat quality acquired from a distance, such as acoustic cues, could therefore be favoured. Bird songs are conspicuous signals commonly assumed to reliably reflect producer quality, and thereby local site quality. Birds of different species have been shown to be attracted to breeding sites by heterospecific songs, but whether they can use fine heterospecific song features as information on producer (and by extension habitat) quality remains unknown. We used a playback experiment in a wild population of collared flycatchers (Ficedula albicollis), a species known to eavesdrop on dominant great tits’ (Parus major) presence and performance, to test whether flycatchers preferred to settle near broadcasts of a high quality great tit song (i.e. song with large repertoire size, long strophes, high song rate), a low quality great tit song or a chaffinch song (control). Among old females, aggressive ones preferred to settle near broadcasts of high quality tit song and avoided broadcasts of low quality tit song, while less aggressive females preferred to settle near broadcasts of low quality tit song. Male personality or age did not influence settlement decisions. Our results show that collared flycatcher females use great tit song quality features as information for settlement decisions, though differently depending on their own competitive ability and/or previous experience with great tit songs. Our study therefore further illustrates the complex condition-dependent use of heterospecific social information for breeding habitat selection.
Motion Displaces Population Receptive Fields in the Direction Opposite to Motion

Motion signals can bias the perceived position of visual stimuli. While the apparent position of a stimulus is biased in the direction of motion, electro-physiological studies have shown that the receptive field (RF) of neurons is shifted in the direction opposite to motion, at least in cats and macaque monkeys. In humans, it remains unclear how motion signals affect population RF (pRF) estimates. We addressed this question using psychophysical measurements and functional magnetic resonance imaging (fMRI) at 7 Tesla. We systematically varied two factors: the motion direction of the carrier pattern (inward, outward and flicker motion) and the contrast of the mapping stimulus (low and high stimulus contrast). We observed that while physical positions were identical across all conditions, presence of low-contrast motion, but not high-contrast motion, shifted perceived stimulus position in the direction of motion. Correspondingly, we found that pRF estimates in early visual cortex were shifted against the direction of motion for low-contrast stimuli but not for high stimulus contrast. We offer an explanation in form of a model for why apertures are perceptually shifted in the direction of motion even though pRFs shift in the opposite direction.
The Seasonal Distribution of Wild Camels (Camelus ferus) in Relation to Changes of the Environmental Conditions in Mongolia

The wild camel (Camelus ferus) is a critically endangered large ungulate, surviving in just three distinct populations located in the Taklamakan Desert, China; deserts near Lop Nuur, China; and in China and Mongolia within and adjacent to Mongolia’s Great Gobi Strictly Protected Area (GGSPA). The population surviving in Mongolia remains poorly researched, but as few as 500 individuals may survive, although its distribution has remained relatively constant over the past 30 - 50 years. This study aimed at identifying potentially important environmental factors that influence the distribution of wild camels in Mongolia and predicting seasonal movement. We predicted distribution by season using presence only data and selected environmental predictors, including land surface temperature, normalized difference vegetation indices (NDVI), water sources, vegetation and soil. Model predictions revealed that land surface temperature in summer correlated significantly with wild camel distribution, with camels occurring in cooler areas. Abundance of biomass did not significantly correlate with camel distribution. Camels occurred in areas with intermediate levels of NDVI in most seasons, implying that they may base foraging decisions on forage quantity, not quality. Positive correlations of camel distribution with higher NDVI in summer (P = 0.03) suggests that they may prefer herbaceous species that appear after rainfall. Models indicate distance to water sources may be critical for camel distribution in all seasons. Camel occurrence correlated with areas containing shallow mountain soils in summer. Camels displayed no significant habitat correlations in other seasons, yet ranges differed among all seasons. Camels used a common region in spring, summer and autumn that we believe represents the core of the species’ annual range. Wild camel distribution during winter varied significantly from other seasons. Our modelling led to a predicted distribution range that was consistent with ranges described by previous research, indicating consistency between survey data and satellite tracking data.