Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Projection From the Deep Cerebellar Nuclei to the Hippocampus via the Ventrolateral and Laterodorsal Thalamus in Mice

The cerebellar involvement in cognitive functions such as attention, language, working memory, emotion, goal-directed behavior and spatial navigation is constantly growing. However, an exact connectivity map between the hippocampus and cerebellum in mice is still unknown. Here, we conducted a tracing study to identify the sequence of transsynaptic, cerebellar-hippocampal connections in the mouse brain using combinations of Recombinant adeno-associated virus (rAAV) and pseudotyped deletion-mutant rabies (RABV) viruses. Stereotaxic injection of a primarily anterograde rAAV-WGA (wheat germ agglutinin)-Cre tracer virus in the deep cerebellar nuclei (DCN) of a Cre-dependent tdTomato reporter mouse resulted in strong tdTomato labeling in hippocampal CA1 neurons, retrosplenial cortex (RSC), rhinal cortex (RC) as well as thalamic and cerebellar areas. Whereas hippocampal injections with the retrograde tracer virus rAAV-TTC (tetanus toxin C fragment)-eGFP, displayed eGFP positive cells in the rhinal cortex and subiculum. To determine the sequence of mono-transsynaptic connections between the cerebellum and hippocampus, we used the retrograde tracer RABVΔG-eGFP(EnvA). The tracing revealed a direct connection from the dentate gyrus (DG) in the hippocampus to the RSC, RC and subiculum (S), which are monosynaptically connected to thalamic laterodorsal and ventrolateral areas. These thalamic nuclei are directly connected to cerebellar fastigial (FN), interposed (IntP) and lateral (Lat) nuclei, discovering a new projection route from the fastigial to the laterodorsal thalamic nucleus in the mouse brain. Collectively, our findings suggest a new cerebellar-hippocampal connection via the laterodorsal and ventrolateral thalamus to RSC, RC and S. These results strengthen the notion of the cerebellum’s involvement in cognitive functions such as spatial navigation via a polysynaptic circuitry.
The Determination of Population Development and Infestation Rate of Mediterranean Fruit Fly (Ceratitis capitata (Wied)) in Peach Orchards in Meram (Konya) Province

This study was carried out in 2017 and 2018 in Meram district (Konya) in order to determine the population development and infestation rate of the Mediterranean fruit fly (MFF) ( Ceratitis capitata (Wied)) (Dip.: Tephritidae) in the peach orchards. In the study, traps called Decis Trap were used to catch the adults of the MFF. As a result of the study, adult population development determined different in two years, two population peaks occurred in 2017 and four times in 2018. The pest may give two to four generation in Meram district according to climatic conditions and years. The first adults of the MFF appeared in 2017 in the third week of August and were active for four months, and appeared in 2018 in the third week of July and were determined to be active in the nature for about five months. In addition to the results of the study conducted in the years 2017-2018, the infestation rates were 5% and 2% in Ekmekkocu, 3% and 2% in Hasankoy, 96% and 96% in Hatip, 94% and 100% in Karahuyuk, 0% and 2% in Yenibahce location, respectively. Farmers are advised to use Decis Trap at the beginning of July and to carry out other maintenance work in orchards, especially the destruction of the fruit falling on the ground.
DECOMPOSIÇÃO DA PALHADA DE UROCHLOA RUZIZIENSIS EM DIFERENTES SISTEMAS DE SEMEADURA E CORREÇÃO DO SOLO

Na região Centro-Oeste, a Urochloa ruziziensis tem sido utilizada como cobertura do solo, devido à facilidade de dessecação. Assim, objetivou-se, com o presente estudo, avaliar a taxa de decomposição da Urochloa ruziziensis em sistemas de semeadura direta e convencional, submetidos a diferentes doses de calcário e de gesso agrícola, em um Latossolo Vermelho distroférrico, no Cerrado. O delineamento experimental foi o de blocos ao acaso, em esquema de parcelas subdivididas, quatro repetições. Nas parcelas, foram avaliados os sistemas de semeadura direta (SSD) e convencional (SSC) e, nas subparcelas, as doses de calcário e de gesso. Foram coletadas sacolas contendo os resíduos vegetais depositados no solo (25, 50, 100 e 150 dias após semeadura da soja). Foi usado o modelo matemático exponencial negativo para descrever a decomposição dos resíduos e a liberação de Ca, Mg, K e P, sendo calculados a constante de decomposição (k) e o tempo de meia-vida (T1/2). Em 86 dias a massa seca contida nas sacolas de decomposição foi reduzida à metade, em ambos os sistemas de plantio empregado, sendo eles sistema de semeadura convencional (SSC) e sistema de semeadura direta (SSD). No SSC verificaram-se maiores taxas de decomposição. No SSD foram determinados os menores teores de K nas sacolas de decomposição. Nos sistemas em que houve aplicação de calcário e de gesso, as constantes de decomposição foram maiores para os elementos Ca e Mg.
Instant Ocean Versus Natural Seawater: Impacts on Aspects of Reproduction and Development in Three Marine Invertebrates

Marine invertebrate larvae have often been reared in artificial rather than natural seawater, either for convenience or to avoid potentially confounding effects of unknown contaminants. This study sought to determine the impact of artificial seawater on various aspects of development for three marine invertebrate species. We examined the impact of Instant Ocean on growth, survival, and fecundity of the deposit-feeding polychaete Capitella teleta at 2 salinities: 24 and 34 ppt; the impact on survival, growth rate, and time to metamorphic competence for the slipper limpet Crepidula fornicata; and the impact on larval growth for the sea star Asterias forbesi. Juveniles of C. teleta survived better in natural seawater than in Instant Ocean at both salinities but at the higher salinity grew more quickly in Instant Ocean; fecundity was not significantly affected by the type of seawater used at either salinity. Using Instant Ocean in place of natural seawater had no pronounced impact on the survival of C. fornicata larvae or on how long it took them to become competent to metamorphose; however, larvae grew somewhat more quickly in Instant Ocean than in natural seawater for the first 4 days of development, but by day 7 they were about 4.5% larger if they had been reared in seawater. The type of seawater used affected the growth of A. forbesi larvae, with larvae growing significantly more slowly in Instant Ocean than in natural seawater, no matter how growth was measured. In conclusion, our results suggest that although Instant Ocean may be a reasonable substitute for natural seawater for work with some species, using it may affect experimental outcomes in some aspects of work with other species.
Time-Dependent Changes in Morphostructural Properties and Relative Abundances of Contributors in Pleurotus ostreatus/Pseudomonas alcaliphila Mixed Biofilms

Pleurotus ostreatus dual biofilms with bacteria are known to be involved in rock phosphate solubilization, endophytic colonization, and even in nitrogen fixation. Despite these relevant implications, no information is currently available on the architecture of P. ostreatus-based dual biofilms. In addition to this, there is a limited amount of information regarding the estimation of the temporal changes in the relative abundances of the partners in such binary systems. To address these issues, a dual biofilm model system with this fungus was prepared by using Pseudomonas alcaliphila 34 as the bacterial partner due to its very fast biofilm-forming ability. The application of the bacterial inoculum to already settled fungal biofilm on a polystyrene surface coated with hydroxyapatite was the most efficient approach to the production of the mixed system the ultrastructure of which was investigated by a multi-microscopy approach. Transmission electron microscopy analysis showed that the adhesion of bacterial cells onto the mycelial cell wall appeared to be mediated by the presence of an abundant layer of extracellular matrix (ECM). Scanning electron microscopy analysis showed that ECM filaments of bacterial origin formed initially a reticular structure that assumed a tabular semblance after 72 h, thus overshadowing the underlying mycelial network. Across the thickness of the mixed biofilms, the presence of an extensive network of channels with large aggregates of viable bacteria located on the edges of their lumina was found by confocal laser scanning microscopy; on the outermost biofilm layer, a significant fraction of dead bacterial cells was evident. Albeit with tangible differences, similar results regarding the estimation of the temporal shifts in the relative abundances of the two partners were obtained by two independent methods, the former relying on qPCR targeting of 16S and 18S rRNA genes and the latter on ester-linked fatty acid methyl esters analysis.
Haematology of Jaffarabadi buffaloes on an established farm: Effect of various physiological parameters

Study was conducted on male and female Jaffarabadi buffaloes from one week of age to 36 months of age and at various lactating and non-lactating stages. The haematological parameters were determined using Auto Hemato Analyser and the data generated was analysed to note the differences between age, sex, lactating stages and non-lactating stages. Age had a significant (P<0.05) effect on TEC levels in both the sexes of Jaffarabadi buffaloes. Significant (P<0.05) difference was noted in the TEC during lactation, whereas non-significant effect was observed between non-lactating animals in Jaffarabadi species. The TEC in males were found to be lower than in females. Age exerted significant (P<0.05) effect on Hb. and PCV levels in Jaffarabadi males but had no significant influence in Jaffarabadi females. Non-significant differences were noted in Hb. and PCV levels at different lactating and non-lactating stages in Jaffarabadi buffaloes. Significant (P<0.05) effect of age was seen in Jaffarabadi males and Jaffarabadi females for MCV, MCH and in Jaffarabadi females for MCHC values. Non-significant difference existed between lactating stages for all three indices in Jaffarabadi buffaloes. Age exerted a significant (P<0.05) effect on TLC values in both the sexes of Jaffarabadi species. Non-significant difference was noted during lactation stages and between non-lactating stages in Jaffarabadi buffaloes.
Phosphorus fertilizer placement and rate affect soybean root growth and nutrient uptake in soil with high fertility

O manejo do fertilizante fósforo (P) pode alterar o crescimento da raiz e da parte aérea da soja, promovendo desequilíbrios morfológicos na planta. Com o objetivo de avaliar os ajustes morfológicos da soja (Glycine max (L.)) em diferentes colocações e taxas de adubação fosfatada em solo P, foi realizado um estudo em casa de vegetação com dois objetivos principais: 1) avaliar o efeito da adubação fosfatada sobre a raiz e acúmulo de biomassa na parte aérea e as alterações associadas no comprimento das raízes; e, 2) estimar o efeito das alterações do crescimento radicular na absorção de macro e micronutrientes na planta. Os tratamentos com fertilizantes foram: (1) transmissão P na superfície do solo (BR), (2) P5x5 cm (B) aplicada na faixa (B) e (3) banda profunda P a 20 cm de profundidade (DB); usando duas taxas: (1) 60 e (2) 120 kg P2O5 ha-1 em solo com alta fertilidade. Imagens de minirhizotron e medidas de SPAD foram realizadas uma vez por semana até o florescimento. O peso seco da raiz e da parte aérea, bem como a absorção total de macro e micronutrientes foram avaliados no mesmo estágio. O aumento dos níveis de P no solo promovidos pela adubação mostra um efeito negativo no peso seco da raiz na taxa de 60 kg P2O5 ha-1 e muito pouco estímulo à alocação de biomassa nas raízes quando a taxa de P foi aumentada para 120 kg P2O5 ha -1 em tratamentos B e DB. O tratamento de controlo (sem fertilizante) mostrou um comprimento de raiz 108% maior do que o tratamento com B-60. Essas alterações também alteraram a absorção de macro e micronutrientes e afetaram o teor de clorofila nas plantas de soja. O aumento dos níveis de P no solo promovidos pela adubação mostra um efeito negativo no peso seco da raiz na taxa de 60 kg P2O5 ha-1 e muito pouco estímulo à alocação de biomassa nas raízes quando a taxa de P foi aumentada para 120 kg P2O5 ha -1 em tratamentos B e DB. O tratamento de controlo (sem fertilizante) mostrou um comprimento de raiz 108% maior do que o tratamento com B-60. Essas alterações também alteraram a absorção de macro e micronutrientes e afetaram o teor de clorofila nas plantas de soja. O aumento dos níveis de P no solo promovidos pela adubação mostra um efeito negativo no peso seco da raiz na taxa de 60 kg P2O5 ha-1 e muito pouco estímulo à alocação de biomassa nas raízes quando a taxa de P foi aumentada para 120 kg P2O5 ha -1 em tratamentos B e DB. O tratamento de controlo (sem fertilizante) mostrou um comprimento de raiz 108% maior do que o tratamento com B-60. Essas alterações também alteraram a absorção de macro e micronutrientes e afetaram o teor de clorofila nas plantas de soja.
Bioecology and Efficacy of Aenasius bambawalei in Population Management of Invasive Mealybug, Phenacoccus solenopsis on Cotton Crop in Pakistan

Biology and parasitization efficiency of Aenasius bambawalei Hayat (Hymenoptera: Encyrtidae) on mealybug, Phenacoccus solenopsis Tinsley were studied under laboratory condition. The rate of development of parasitoid varied on different life stages of mealybug. Total development time from oviposition to adult emergence was shortest on second instar followed by third instar and adult. Sex ratio of parasitoid also varied greatly on different life-stages. Keywords: Cotton, Phenacoccus solenopsis, Aenasius bambawalei DOI : 10.7176/JNSR/9-10-04 Publication date :May 31 st 2019
Using deep whole genome sequence, transcriptome and epigenome data to characterize the mutational burden of induced pluripotent stem cells

1. Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA. 2. Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA. 3. Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA. 4. Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA. 5. Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, CA.
Spatial community structure of groundfish is conserved across the Gulf of Alaska

The mechanisms structuring patterns of diversity and community composition can be difficult to identify in large, open ecological systems. However, it is important to understand what drives these patterns at larger scales, especially in the face of climate change and other pertur bations. The Gulf of Alaska (GOA) is an ideal study system because it has complex topography, climate-driven variability, and an on-going groundfish community survey. We used groundfish community data to examine the ecological theory underlying spatial diversity and community composition across 10 study areas in the GOA. We created geostatistically modeled groundfish abundance and biomass from the Alaska Fisheries Science Center trawl survey data (1984 to 2015) to address inherent errors in trawl observations. We found that species richness and alpha, beta, and functional diversity varied little both within and between study areas. However, turnover in community composition was significant along a longitudinal gradient, with differences driven by lower-abundance species. Fishing pressure had non-linear effects only on species richness and local diversity, while productivity was linearly related to beta diversity. We conclude that spatial patterns of diversity were not driven by disturbance, but were largely driven by environmental heterogeneity, because of the longitudinal turnover in community composition and high beta diversity (and thus low saturation). In addition, the invariant functional diversity but varying community composition together indicate functional redundancy in this ecosystem. Finally, the spatially invariant alpha and functional diversity show that the underlying community structure of the GOA groundfish community was conserved across this large marine ecosystem.
Population structure and genetic characterization of two native Danish sheep breeds

ABSTRACT Genetic diversity in livestock animals has become recognized as important genetic resource for future sustainable livestock production. Especially native breeds, adapted to their local environment, are of considerable interest. Here, we report a genome-wide characterization of two native Danish sheep breeds, the Danish Landrace sheep and the Danish White-Headed Marsh sheep. We investigated the genetic diversity both at national and European breed level using a European-derived reference panel. The native Danish breeds are genetically distinct from other Nordic breeds. Their closest relatives are Border Leicester, Galway, and Texel. Apart from gene flow between native Danish breeds, Texel admixture was most dominant. For Danish Landrace sheep, a population split into two genetically distinct sub-populations was detected. Compared to other livestock species, genomic inbreeding was moderate. However, among European-derived sheep the native Danish breeds were among the 10 most inbred investigated, illustrating the need for sustainable management strategies to preserve genetic diversity.
The ecology of parasite transmission during fauna translocations: Observations from the woylie (Bettongia penicillata)

Fauna translocations play a pivotal role in the management of threatened wildlife, though we are limited by our understanding of how the host-parasite community changes during translocation and in response to antiparasitic drug treatment. This project aimed to quantify changes in parasite community structure and host health in woylies following translocation, and in response to ivermectin treatment. This is the first study to evaluate changes to the broader parasite community in translocated and resident animals following translocation. During two fauna translocations to three different locations within south-western Australia, woylies were sampled for blood-borne, ecto- and gastrointestinal parasites, and morphometrics were measured. Prior to translocation, half of the translocated woylies were treated with ivermectin. Post-translocation monitoring was undertaken for up to 12 months following translocation. Destination site and time since translocation had the strongest effect on parasite dynamics and host health following translocation. Significant changes to the parasite community occurred within the first few months after translocation, and the parasite communities of translocated and resident woylies generally converged to become more similar over time, with failure of some parasite taxa to persist and new host-parasite associations emerging. Trypanosoma spp. richness and the prevalence of haemoparasite coinfection increased after translocation. Ivermectin treatment did not significantly reduce the prevalence/abundance of target parasites, or improve body condition in treated hosts. In translocated woylies, the presence of coccidia during the first three months following translocation, and increasing Strongyloides-like egg counts were associated with lower body condition. Results from this study highlight the importance of long-term parasite monitoring to better understand the biological implications (for individuals, populations and ecosystems) of wildlife translocations on host-parasite ecology. Insights gained from this study are broadly applicable to the management of threatened fauna and their parasite taxa, and enhance our fundamental understanding of the potential ecosystem impacts of wildlife translocations.
EGG PRODUCTION PERFORMANCE OF IMPROVED PHILIPPINE MALLARD DUCKS (Anas platyrhynchos) FED DIETS SUPPLEMENTED WITH FRESH TRICHANTHERA (Trichanthera gigantea) LEAVES

The nutritional values and feeding trial of fresh Trichanthera (Trichanthera gigantea) leaves for Improved Philippine Mallard Duck (IPMD) layers were examined. Proximate, calcium, phosphorus and energy contents of Trichanthera were analyzed. Its effects on egg production, fertility and hatchability were analyzed when used as part of a ration of IPMD on early lay performance. For the feeding trial, a total of 108 IPMD were randomly assigned in three treatments following Completely Randomized Design (CRD); each treatment had three replication with 12 ducks (2 drakes and 10 ducks) per replicate. The treatments were: without Trichanthera, with 50 g Trichanthera/duck/day and with 100 g Trichanthera/duck/day. When expressed on dry matter (DM) basis, Trichanthera contained 93.30% DM, 19.59% crude protein, 11.89% crude fiber, 2.33% crude fat, 20.15% ash, 4.47% calcium, 0.25% phosphorus and 2,310 kcal ME/kg. The combined intake of feed and Trichanthera was higher (P 0.05) by Trichanthera feeding. Egg quality, egg classification, fertility and hatchability of eggs, and quality of hatchling were not affected by Trichanthera. Numerically, higher IOFC (Php 47.43/duck) was attained from IPMD fed 100 g of Trichanthera/duck/day.
Progress in genetics of breeding for maize transformation ability

Maize (Zea mays) is the most widely grown crop grown and produced crop in the world. It is a foundational model for genomics and genetics. To meet the need of a growing population and climate change the current and future crop improvement efforts will comprise of the utilization of biotechnology-based approaches. This includes the functional analysis and discovery of agriculturally important genes for crop research and product development. Today, most crop genetic engineering systems use the transformation process. But there are limitations to the transformation process. The labor of creating transgenic events is the largest cost associated with the transformation production system. The culture process is the most time-consuming and has the highest labor cost of the system. Then once the trait is verified to be present the trait must be backcrossed into an elite line with better agronomic traits and good yield. The backcrossing process is time consuming and requires a large amount of greenhouse space. The major limitation of plant transformation is genotype dependency. To get more widely adoption of biotechnology and the transformation process for breeding it needs to become less expensive and time-consuming to produce transgenic lines. This can be achieved through discovery of the genetics behind callus formation and regeneration, so any elite line can be made transformable. The discovery of morphological genes like Bbm and Wus2 have made it possible to develop a genotype-independent transformation system in maize and other monocots.