Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis B virus and human immunodeficiency virus co-infection: impact on transmission and

There is overwhelming evidence of a strong association between human immunodeficiency virus (HIV) and hepatitis B virus (HBV) infections in areas of low endemicity for both viruses, due to shared risk factors. There is also much evidence that HIV modifies the natural history of HBV infection in these areas: co-infected individuals are more likely to be HBV chronic carriers, with higher levels of HBV infectivity, than HIV-negative individuals. Also, immunosuppression brought about by HIV infection reduces persistence of anti-HBs in previously immune and vaccinated individuals, and can cause HBV reactivation or reinfection in those previously exposed to HBV. Furthermore, HIV infection increases the risk of death from liver disease in HBV co-infected individuals, and this risk increases when these patients are treated with highly active anti-retroviral therapy. However, extensive research has found no convincing evidence that HBV impacts on the transmission and natural history of HIV infection. However, the growing body of literature from sub-Saharan Africa (where both HIV and HBV are endemic, and where the majority of the population have been exposed to HBV long before the time of reaching sexual maturity and being exposed to HIV) stands in sharp contrast with the above findings. In this region, it is clear that the prevalence of HBV in HIV-positive individuals is seldom significantly increased, especially in healthy individuals; and when it is significantly increased, it is not increased to the same extent as in HBV-naive populations. Also, it is expected that these increases will be caused mainly by reactivation or re-infection.
Natural tags reveal populations of Conservation Dependent school shark use different pupping areas

Knowledge of reproductive movements and sources of recruitment in highly mobile species is important to understand population-level resilience and to manage recovery in populations depleted by human interference. Management of the school shark Galeorhinus galeus (Linnaeus, 1758), a Conservation Dependent species in Australia subject to a national recovery strategy after stock collapse from overfishing, has long assumed obligate female migration to pupping areas in the southeast of their range. We used post-natal elemental signatures of individuals from 3 cohorts born in 1996 to 1998 as a proxy to test whether females use common pupping areas. Environmental or biological factors that differ among pupping areas can give rise to unique trace element signatures in shark vertebrae that act as natural tags and can be used to assess relative contributions from recruitment sources to adult populations. We compared post-natal signatures from sharks caught in 2 regions, South Australia in the northwest of the species’ range and Bass Strait in the southeast, using laser ablation inductively coupled mass spectrometry. Signatures were similar between regions for 1 cohort, suggesting high use of shared or similar pupping areas, but differed for the 2 remaining cohorts. Region of capture could also be accurately predicted (>75%) based on post-natal signatures, refuting the long-held view that all females use common pupping areas. We conclude that female movements and reproductive strategies are likely more plastic than previously assumed, highlighting the need to clarify them and their potential effects on resilience and conservation.
Nitrogen deposition influences the response of Potentilla tanacetifolia to phosphorus addition

Phosphorus is an essential macronutrient for all livingplants and plant production. Simultaneously, atmospheric nitrogendeposition also affects plant productivity at a global scale. However,few studies have investigated how plants respond to P addition whilesimultaneously considering N deposition. We investigated plant biomass,nutrient status and stoichiometric ratios on Potentilla tanacetifoliain response to P fertilization under contrasting N addition ratesin a typical meadow steppe in Inner Mongolia, China. Abovegroundbiomass of P. tanacetifolia increased under increasing levels of P fertilizationunder conditions of N addition. However, there was no significantchange in biomass when only phosphorus was added. Plantleaf and stem P concentrations increased linearly with P additionwhen there was no N addition. Our results suggest that increasedplant P nutrition under P addition will not turn into plant growthenhancement unless N demands are also satisfied. Nitrogen additionsignificantly increased leaf N concentrations, and leaf and seed N:Pratios, when there was no P fertilization. Nevertheless, the effects ofN addition were weakened, and eventually disappeared when P fertilizationrates increased. This indicates that N-induced alterationsof the plant nutrition status and stoichiometric ratios were P availability-dependent. Overall, our results suggest that multiple-nutrientconstraints and their interactions must be considered when assessingplant nutrient and growth responses to nutrient enrichment.
The protective roles of NLRs during infection and tumor progression

Francisella tularensis is a small Gram-negative cocco-bacilli and the causative agent of the disease tularemia. During infection escape of F. tularensis into the cytosol from the phagosome leads to activation of the AIM2 inflammasome in macrophages. Upon activation of the AIM2 inflammasome caspase-1 is autocatalytically cleaved into its active form, which subsequently cleaves IL-1β and IL-18 into their mature forms that are secreted. Both IL-1β and IL-18 have an important role in the innate immune response to F. tularensis. We have identified 5-formyltetrahydrofolate cycloligase (FTL_0724) as a novel virulence factor for F. tularenesis live vaccine strain (LVS). Infection of macrophages with an F. tularenesis FTL_0724 mutant lead to increased AIM2 inflammasome-dependent IL-1β and IL-18 secretion and pyroptosis. Mice infected with F. tularenesis FTL_0724 mutant strain exhibited decreased mortality compared to mice challenged with wild type LVS. In contrast, macrophages challenged with a F. tularenesis LVS rluD pseudouridine synthase (FTL_0699) mutant exhibited a marked decrease in IL-1β and IL-18 secretion compared to macrophages infected with wild type LVS. In concert, mice challenged with F. tularenesis FTL_0699 exhibited increased mortality. Together these data demonstrate two novel F. tularenesis LVS genes that are capable of modulating inflammasome activation and pathogen virulence.
Benthic foraminiferal patchiness – revisited

Abstract. Many benthic organisms show aggregated distribution patterns due to the spatial heterogeneity of niches or food availability. In particular, high-abundance patches of benthic foraminifera have been reported that extend from centimetres to metres in diameter in salt marshes or shallow waters. The dimensions of spatial variations of shelf or deep-sea foraminiferal abundances have not yet been identified. Therefore, we studied the distribution of Globobulimina turgida dwelling in the 0–3 cm surface sediment at 118 m water depth in the Alsbäck Deep, Gullmar Fjord, Sweden. Standing stock data from 58 randomly replicated samples depicted a log-normal distribution of G. turgida with weak evidence for an aggregated distribution on a decimetre scale. A model simulation with different patch sizes, outlines, and impedances yielded no significant correlation with the observed variability of G. turgida standing stocks. Instead, a perfect match with a random log-normal distribution of population densities was obtained. The data–model comparison revealed that foraminiferal populations in the Gullmar Fjord were not moulded by any underlying spatial structure beyond 10 cm diameter. Log-normal population densities also characterise data from contiguous, gridded, or random sample replicates reported in the literature. Here, a centimetre-scale heterogeneity was found and interpreted to be a result of asexual reproduction events and restricted mobility of juveniles. Standing stocks of G. turgida from the Alsbäck Deep temporal data series from 1994 to 2021 showed two distinct cohorts of samples of either high or low densities. These cohorts are considered to represent two distinct ecological settings: hypoxic and well-ventilated conditions in the Gullmar Fjord. Environmental forcing is therefore considered to impact the population structure of benthic foraminifera rather than their reproduction dynamics.
Activity patterns of breeding Hen Harriers Circus cyaneus assessed using nest cameras

ABSTRACT Nest camera footage from 13 Hen Harrier Circus cyaneus nests was analysed to document patterns of adult attendance, incubation, brooding and prey delivery rates. Nest attendance was high throughout the incubation stage and began to decrease when chicks were five days old. Chick provisioning increased gradually after hatching and peaked when the chicks were five days old. Daily activity rates were highest during the middle of the day, from 08:00 to 19:00 hours.
Recombination between co-infecting herpesviruses occurs where replication compartments coalesce

Recombination between co-infecting herpesvirus DNA genomes is an important process affecting viral population diversity and evolution. Each herpes simplex virus type 1 (HSV-1) replication compartment (RC) derives from a single incoming genome and maintains a specific territory within the nucleus. This raises intriguing questions about where and when co-infecting viral genomes interact. To study the spatiotemporal requirements for inter-genomic recombination, we developed an assay with dual-color fluorescence in situ hybridization enabling detection of homologous recombination (HR) between different co-infecting HSV-1 pairs. Our results revealed that when viral RCs enlarge towards each other, there is detectable overlap of genomes from each virus. Infection with paired viruses that allow visualization of HR correlates with increased overlap of RCs. Taken together, these findings suggest that HR events take place during replication of HSV-1 DNA and are mainly confined to the periphery of RCs when they coalesce. Importance Homologous recombination is considered a major driving force of evolution since it generates and spreads genetic diversity. In the case of HSV-1, a ubiquitous human pathogen that causes significant morbidity and mortality, evidence of homologous recombination can be found frequently, both in vitro and in clinical isolates. Here we designed an experimental system to detect where and when recombination takes place between viral genomes during infection. We found that recombination events occur after viral DNA replication during the late stages of infection, and is prevalent at the interface of expanding viral replication compartments. Overall, our results provide spatial and temporal information regarding the process of HSV-1 replication and recombination, and these observations have implications for understanding the recombination restrictions of other DNA viruses and cellular DNA.
GENETIC POTENTIAL OF CHICKPEA GERMPLASM AGAINST Fusarium WILT (Fusarium oxysporum. f.sp. ciceris)

Sixty four advance lines of chickpea were evaluated against Fusarium wilt by sowing them in sick plot in research area of Plant Pathology Research Institute Faisalabad following augmented design to find out the resistance source. Three susceptible varieties CM-44, CM 72 and CM 2006 were used as check. Out of these 64 advance lines,7 lines TGxKo1, TGx1110, TGx1219, TG1307, TGx1232, TGx1218 and TGx1113 were found highly resistant ranging 0-10% plant mortality, 11 advance lines were resistant showing 11-20% plants mortality and 10 moderately resistant ranging 21-30% plant mortality. Remaining advance lines showed in susceptible and highly susceptible range showing 31-50% and more than 50% plant mortality, respectively. Highly resistant and resistant genotypes may be exploited for the development of resistant cultivars against wilt.
In Vitro Shoot Multiplication of Flacourtia jangomas (Lour.) Raeusch

Shoot bud multiplication was obtained in Flacourtia jangomas , a dioecious woody plant of medicinal as well as pomocultural value, by using nodal segment and shoot apex explants. The basal medium was MS medium supplemented with 3.0% sucrose and 0.8% agar. The optimum PGRs for establishment of culture were 1.0mg/l Kinetin and 0.1mg/l NAA. Maximum shoot buds were noted when transferred in MS medium with 5.0mg/l BAP and 0.1mg/l NAA for shoot multiplication. The cycle was repeated twice and 78-81 shoot buds was obtained per explants. Rooting was noted after 60 days in half strength MS with 3.0mg/l NAA. It was also obtained within 15 days by transferring shoot lets after a week from higher conc. (3.0mg/l) to a lower conc. (1.0mg/l) of NAA. After transferring to pots, about 40% of them survived.
Variation in Volume Production Through Clonal Deployment: Results From a Simulation Model to Minimize Risk for Both a Currently Known and Unknown Future Pest

Abstract A simulation model was developed to examine optimum patterns of deploying selected clones in the hypothetical situations of both a currently known pest and an unknown future pest. We modelled the interactions between Sitka spruce (Picea sitchensis (Bong.) Carr. ), an economically important forest tree in British Columbia and the northwestern U.S., and the spruce terminal weevil (Pissodes strobi (Peck)), a major pest in western spruces. The model is combined with the Province of British Columbia’s Tree and Stand Simulator (TASS) model to drive individual tree growth and stand establishment and development. Two clonal-sampling strategies are examined: a randomly drawn set of genotypes or clones, to depict the potential consequences of a new (e.g., exotic) or a previously unimportant natural pest attacking a ‘random’ set of genotypes, and a ‘fixed’ set of clones, emulating a ‘commercial’ or known set of clones for growth and resistance mechanisms. Simulations use a range of numbers of genotypes or clones (2, 6, 18 and 30), and three deployment patterns (a random mixture of ramets, single- clone blocks, and a mosaic of smaller clonal blocks), in one and five hectare (Ha) stands. Total merchantable timber volume on a per Ha basis at harvest age 80 is used to compare the various combinations and schemes. With both random and fixed chosen sets of clones, the random planting pattern (i.e., random mixture of ramets from the clonal set) produced the most volume. Eighteen randomly chosen clones generally produced more volume, than 2, 6 and 30 clones, but differences among 6, 18 and 30 clones were small in most cases, irrespective of planting pattern. For fixed clones, the use of more resistant clones with higher growth potential produced more volume; however, pure clonal blocks of the best clone were not better than a mixture of that clone and an inferior one. Reducing the effects of insect activity and attack on trees, by lowering the average annual temperature in the model, or turning off all insect ‘activity’, increased merchantable volume but did not change the optimum number of clones (~18) or deployment pattern (random mixture). Forestry agencies can weigh these findings against economic advantages of block plantings of similar genotypes, in the choice of an appropriate number of clones and a deployment strategy.
Molecular Mechanisms Regulating Mammalian Forebrain Development

While the extrinsic factors regulating neurogenesis in the developing forebrain have been widely studied, the mechanisms downstream of the various signaling pathways are relatively ill-defined. In particular, we focused on proteins that have been implicated in cognitive dysfunction. Here, we ask what role two cell intrinsic factors play in the development of two different neurogenic compartments in the forebrain. In the first part of the thesis, the transcription factor FoxP2, which is mutated in individuals who have specific language deficits, was identified to regulate neurogenesis in the developing cortex, in part by regulating the transition from the radial precursors to the transit amplifying intermediate progenitors. Moreover, we found that ectopic expression of the human homologue of the protein promotes neurogenesis in the murine cortex, thereby acting as a gain-of-function isoform. In the second part of the thesis, the histone acetyltransferase CREB-binding protein (CBP) was identified as regulating the generation of neurons from medial ganglionic eminence precursors, similar to its role in the developing cortex. But CBP also plays a more substantial role in the expression of late interneuron markers, suggesting that it is continuously required for the various stages of neurogenesis at least in the ventral neurogenic niche. Finally, similar to cortical precursors, the function of CBP in the ventral forebrain precursors is also dependent on histone acetylation. Together, these studies shed light on some of the key intrinsic players that regulate the differentiation of neural precursors in the embryonic murine forebrain, and they also suggest potential mechanisms for the pathogenesis of various cognitive dysfunctions.
The invasive kelp Undaria pinnatifida hosts an epifaunal assemblage similar to native seaweeds with comparable morphologies

Invasive seaweeds have the potential to disrupt ecosystem functioning if they are unsuitable hosts for the small mobile invertebrates (epifauna) that are an important trophic link between benthic primary producers and higher trophic levels. The Asian kelp Undaria pinnatifida has successfully invaded many coastal regions worldwide. We compared the epifaunal assemblage on U. pinnatifida with epifauna of 7 co-occurring, canopy-forming native brown seaweed species in southern New Zealand to help understand the effect of the invasive species on shallow subtidal ecosystems. The density, diversity and composition of epifauna across the 8 seaweeds were much more strongly related to host morphology than to the geographic origin of the host. U. pinnatifida and several native seaweeds with similarly simple morphologies supported relatively depauperate epifaunal assemblages dominated by copepods. More structurally complex native seaweeds supported more abundant and diverse epifaunal assemblages containing lower proportions of copepods and higher proportions of amphipods and other epifaunal groups. Our results indicate that abundances of epifauna at the ecosystem level will be reduced if U. pinnatifida displaces more structurally complex native seaweed species that host more diverse and dense epifaunal assemblages. The findings suggest that morphological complexity may be key to predicting the impacts of invasive seaweeds on epifaunal assemblages, and potentially on food webs, in other geographic regions.
Integrated Weed Management Strategies in Cover Crop—based, Organic Rotational No-Till Corn and Soybean in the Mid-Atlantic Region

Cover crop—based, organic rotational no-till (CCORNT) corn and soybean systems have been developed in the mid-Atlantic region to build soil health, increase management flexibility, and reduce labor. In this system, a roller-crimped cover crop mulch provides within-season weed suppression in no-till corn and soybean. A cropping system experiment was conducted in Pennsylvania, Maryland, and Delaware to test the cumulative effects of a multitactic weed management approach in a 3-yr hairy vetch/triticale—corn—cereal rye—soybean—winter wheat CCORNT rotation. Treatments included delayed planting dates (early, intermediate, late) and supplemental weed control using high-residue (HR) cultivation in no-till corn and soybean phases. In the no-till corn phase, HR cultivation decreased weed biomass relative to the uncultivated control by 58%, 23%, and 62% in Delaware, Maryland, and Pennsylvania, respectively. In the no-till soybean phase, HR cultivation decreased weed biomass relative to the uncultivated treatment planted in narrow rows (19 to 38 cm) by 20%, 41%, and 78% in Delaware, Maryland, and Pennsylvania, respectively. Common ragweed was more dominant in soybean (39% of total biomass) compared with corn (10% of total biomass), whereas giant foxtail and smooth pigweed were more dominant in corn, comprising 46% and 22% of total biomass, respectively. Common ragweed became less abundant as corn and soybean planting dates were delayed, whereas giant foxtail and smooth pigweed increased as a percentage of total biomass as planting dates were delayed. At the Pennsylvania location, inconsistent termination of cover crops with the roller-crimper resulted in volunteer cover crops in other phases of the rotation. Our results indicate that HR cultivation is necessary to achieve adequate weed control in CCORNT systems. Integration of winter grain or perennial forages into CCORNT systems will also be an important management tactic for truncating weed seedbank population increases. Nomenclature: Common ragweed, Ambrosia artemisiifolia L. ; giant foxtail, Setaria faberi Herrm. ; smooth pigweed, Amaranthus hybridus L. ; cereal rye, Secale cereale L. ; hairy vetch, Vicia villosa Roth; triticale, × Triticosecale Wittm. ex A. Camus [Secale × Triticum]; corn, Zea mays L. ; soybean, Glycine max (L.) Merr. ; winter wheat, Triticum aestivum L.
Positioning behavior according to individual color variation improves camouflage in novel habitats

Understanding how organisms interact with their environment is a key issue, especially in the current context of global change. We find that ground-perching grasshoppers colonizing urban pavements modify their camouflage and escape strategies depending on how well their body coloration resembles the pavement. A virtual predation experiment confirms that this adaptive behavioral flexibility allows individuals to reduce predation in their new environment.
High-throughput Analysis of Alternative Splicing Regulatory Networks that Control Cell Fate

Advances in high-throughput profiling technologies have revolutionized our view of transcriptome complexity and regulation. Alternative splicing (AS) is increasingly recognized as a widespread mechanism for gene regulation and is responsible for greatly expanding transcriptome and proteome diversity in metazoans. It is often controlled in a precise spatiotemporal manner by an intricate RNA-protein network. Given the extensive roles of AS in development and disease, understanding the molecular mechanisms underlying AS regulation is of critical importance. The main focus of my thesis is to develop and apply high-throughput strategies to systematically discover AS networks that control cell fate, as well as the factors and mechanisms that regulate these AS networks. By combining high-throughput RNA sequencing and splicing code analyses, I describe the identification of the muscleblind-like RNA binding proteins, MBNL1 and MBNL2, as conserved negative regulators of a large program of alternative exons that are differentially spliced between embryonic stem cells (ESCs)/induced pluripotent stem cells (iPSCs) and diverse non-ESCs/tissues. My results from this study provided the first evidence that AS regulatory networks play a central role in the core circuitry required for ESC pluripotency and iPSC reprogramming. Next, I present the development of a new multiplexed functional genomics screen whereby thousands of gene perturbations can be iii simultaneously assayed for effects on dozens of endogenous AS and gene expression events of interest. Using this system, I revealed a large network of novel positive and negative factors from multiple gene layers that regulate distinct subsets of AS events linked to ESC pluripotency, neural differentiation, and transitions in reprogramming. In summary, these studies have significantly broadened our knowledge of the global regulatory networks that determine cell fate decisions, and provided powerful tools for large-scale investigation of the regulation of AS and other RNA metabolic pathways in diverse cell types.