Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Fusarium solani f. sp. pisi (Fsp) Responsive Genes in Pisum sativum

Pisum sativum (pea) is rapidly emerging as an inexpensive and major contributor to the plant-derived protein market. Due to its nitrogen-fixation capability, short life cycle, and low water usage, pea is a useful cover-and-break crop that requires minimal external inputs. It is critical for sustainable agriculture and indispensable for future food security. Root rot in pea, caused by the fungal pathogen Fusarium solani f. sp. pisi (Fsp), can result in a 15-60% reduction in yield. It is urgent to understand the molecular basis of Fsp interaction in pea to develop root rot tolerant cultivars. A complementary genetics and gene expression approach was undertaken in this study to identify Fsp-responsive genes in four tolerant and four susceptible pea genotypes. Time course RNAseq was performed on both sets of genotypes after Fsp challenge. Analysis of the transcriptome data resulted in the identification of 42,905 differentially expressed contigs (DECs). Interestingly, the vast majority of DECs were overexpressed in the susceptible genotypes at all sampling time points, rather than in the tolerant genotypes. Gene expression and GO enrichment analyses revealed genes coding for receptor-mediated endocytosis, sugar transporters, salicylic acid synthesis and signaling, and cell death were overexpressed in the susceptible genotypes. In the tolerant genotypes, genes involved in exocytosis, and secretion by cell, the anthocyanin synthesis pathway, as well as the DRR230 gene, a pathogenesis-related (PR) gene, were overexpressed. The complementary genetic and RNAseq approach has yielded a set of potential genes that could be targeted for improved tolerance against root rot in P. sativum. Fsp challenge produced a futile transcriptomic response in the susceptible genotypes. This type of response is hypothesized to be related to the speed at which the pathogen infestation advances in the susceptible genotypes, and the preexisting level of disease-preparedness in the tolerant genotypes.
A molecular mechanism for LINC complex branching by structurally diverse SUN-KASH 6:6 assemblies

The LINC complex mechanically couples cytoskeletal and nuclear components across the nuclear envelope to fulfil a myriad of cellular functions, including nuclear shape and positioning, hearing and meiotic chromosome movements. The canonical model of the LINC complex is of individual linear nucleocytoskeletal linkages provided by 3:3 interactions between SUN and KASH proteins. Here, we provide crystallographic and biophysical evidence that SUN-KASH is a constitutive 6:6 complex in which two SUN trimers interact back-to-back. A common SUN-KASH topology is achieved through structurally diverse 6:6 interaction mechanisms by distinct KASH proteins, including zinc-coordination by Nesprin-4. The SUN-KASH 6:6 complex is incompatible with the current model of a linear LINC complex and instead suggests the formation of a branched LINC complex network. In this model, SUN-KASH 6:6 complexes act as nodes for force distribution and integration between adjacent SUN and KASH molecules, enabling the coordinated transduction of large forces across the nuclear envelope.
Working groups, gender and publication impact of Canada’s ecology and evolution faculty

A critical part of science is the extraction of general principles by synthesizing results from many different studies or disciplines. In the fields of ecology and evolution, a popular method to conduct synthesis science is in working groups – that is, research collaborations based around intensive week-long meetings. We present in this report an analysis of the impact of working group participation and gender on the publication impact of ecology and evolution faculty at Canadian universities who were research active over the last three decades (N=1408). Women are underrepresented in this research population relative to the general population, and even the Canadian faculty population. Participation in working groups not only benefits science, but also benefits the researchers involved by accelerating the temporal increase in their H-index. However, this benefit is particularly driven by senior male researchers. The effect is weaker for female researchers and even negative for researchers within 4 years of their PhD. However, gender does not affect current participation rates in working groups, nor reported indirect benefits – such as future collaborations, funding and data resources. The results of this study suggest that working groups can act as career catalysts for researchers, but that – as in many areas of science – there are challenging issues of equity that require action. Because the H-index is a cumulative measure, gender inequities from before the turn of the millenium may still be distorting the perceived publication impact of today’s research-active faculty.
Consumer Attitudes Toward Use of Probiotic Cultures

ABSTRACT: Some probiotic cultures appear to modulate the immune system, improve lactose intolerance, resolvesome bacterial and viral diarrheal diseases, reduce symptoms associated with inflammatory bowel disease, lowerblood cholesterol, and protect against some cancers. Focus groups were used to determine consumer familiaritywith probiotic bacteria and response to benefits, information source, potential health claims, and dietary sources.Some consumers were skeptical that probiotic cultures could be effective. Information is more credible if it isconsistent with existing beliefs and endorsed by recognized health experts. Consumers aware of “friendly bacteria”in yogurt were more likely to accept the potential benefits of probiotic cultures than consumers unaware of benefi-cial bacteria. Some consumers were so sensitive to the risks of pathogenic bacteria that the concept of beneficialbacteria was not credible.Keywords: probiotics, cultures, yogurt, consumer attitudes Introduction P ROBIOTIC CULTURES ARE LIVE MICROBIAL FOOD INGREDIENTS THAT
Psi promotes Drosophila wing growth through transcriptional repression of key developmental networks

Psi, the sole FUSE Binding Protein (FUBP) family single stranded DNA/RNA binding protein in Drosophila, is essential for proper cell and tissue growth, however its mechanism of function remains unclear. Here we use Targeted DamID combined with RNA-sequencing to generate the first genome-wide binding and expression profiles for Psi. Surprisingly, we demonstrate Psi drives growth in the Drosophila wing through transcriptional repression of key developmental pathways (e.g. Wnt, Notch and TGFβ). Thus, Psi patterns tissue growth by directly repressing transcription of developmental growth suppressors. Analysis of direct Psi targets identified novel growth inhibitors, including Tolkin (Zinc metallopeptidase implicated in TGFβ signalling), Ephexin (Rho-GEF) and emp (CD36 scavenger receptor-related protein). Their depletion not only suppressed impaired growth associated with Psi knockdown, but alone was sufficient to drive wing overgrowth. Thus, Psi drives wing growth twofold, through direct activation of Myc and through transcriptional repression of growth inhibitors comprising core developmental pathways.
Combined knockout of Lrrk2 and Rab29 does not result in behavioral abnormalities in vivo

Coding mutations in the LRRK2 gene, encoding for a large protein kinase, have been shown to cause familial Parkinson’s disease (PD). The immediate biological consequence of LRRK2 mutations is to increase kinase activity, leading to the suggestion that inhibition of this enzyme might be useful therapeutically to slow disease progression. Genome-wide association studies have identified the chromosomal loci around LRRK2 and one of its proposed substrates, RAB29, as contributors towards the lifetime risk of sporadic PD. Considering the evidence for interactions between LRRK2 and RAB29 on the genetic and protein levels, here we generated a double knockout mouse model and determined whether there are any consequences on brain function with aging. From a battery of motor and non-motor behavioral tests, we noted only that 18-24 month Rab29-/- and double (Lrrk2-/-/Rab29-/-) knockout mice had diminished locomotor behavior in open field compared to wildtype mice. However, no genotype differences were seen in number of substantia nigra pars compacta (SNc) dopamine neurons or in tyrosine hydroxylase levels in the SNc and striatum, which might reflect a PD-like pathology. These results suggest that depletion of both Lrrk2 and Rab29 is tolerated, at least in mice, and support that this pathway might be able to be safely targeted for therapeutics in humans. Significance statement Genetic variation in LRRK2 that result in elevated kinase activity can cause Parkinson’s disease (PD), suggesting LRRK2 inhibition as a therapeutic strategy. RAB29, a substrate of LRRK2, has also been associated with increased PD risk. Evidence exists for an interactive relationship between LRRK2 and RAB29. Mouse models lacking either LRRK2 or RAB29 do not show brain pathologies. We hypothesized that the loss of both targets would result in additive effects across in vivo and post-mortem assessments in aging mice. We found that loss of both LRRK2 and RAB29 did not result in significant behavioral deficits or dopamine neuron loss. This evidence suggests that chronic inhibition of this pathway should be tolerated clinically.
Mu-Opioids Suppress GABAergic Synaptic Transmission onto Orbitofrontal Cortex Pyramidal Neurons with Subregional Selectivity

The orbitofrontal cortex (OFC) plays a critical role in evaluating outcomes in a changing environment. Administering opioids to the OFC can alter the hedonic reaction to food rewards and increase their consumption in a subregion-specific manner. However, it is unknown how mu-opioid signaling influences synaptic transmission in the OFC. Thus, we investigated the cellular actions of mu-opioids within distinct subregions of the OFC. Using in vitro patch-clamp electrophysiology in brain slices containing the OFC, we found that the mu-opioid agonist DAMGO produced a concentration-dependent inhibition of GABAergic synaptic transmission onto medial OFC (mOFC), but not lateral OFC (lOFC) neurons. This effect was mediated by presynaptic mu-opioid receptor activation of local parvalbumin (PV+)-expressing interneurons. The DAMGO-induced suppression of inhibition was long lasting and not reversed on washout of DAMGO or by application of the mu-opioid receptor antagonist CTAP, suggesting an inhibitory long-term depression (LTD) induced by an exogenous mu-opioid. We show that LTD at inhibitory synapses is dependent on downstream cAMP/protein kinase A (PKA) signaling, which differs between the mOFC and lOFC. Finally, we demonstrate that endogenous opioid release triggered via moderate physiological stimulation can induce LTD. Together, these results suggest that presynaptic mu-opioid stimulation of local PV+ interneurons induces a long-lasting suppression of GABAergic synaptic transmission, which depends on subregional differences in mu-opioid receptor coupling to the downstream cAMP/PKA intracellular cascade. These findings provide mechanistic insight into the opposing functional effects produced by mu-opioids within the OFC. SIGNIFICANCE STATEMENT Considering that both the orbitofrontal cortex (OFC) and the opioid system regulate reward, motivation, and food intake, understanding the role of opioid signaling within the OFC is fundamental for a mechanistic understanding of the sequelae for several psychiatric disorders. This study makes several novel observations. First, mu-opioids induce a long-lasting suppression of inhibitory synaptic transmission onto OFC pyramidal neurons in a regionally selective manner. Second, mu-opioids recruit parvalbumin inputs to suppress inhibitory synaptic transmission in the mOFC. Third, the regional selectivity of mu-opioid action of endogenous opioids is due to the efficacy of mu-opioid receptor coupling to the downstream cAMP/PKA intracellular cascades. These experiments are the first to reveal a cellular mechanism of opioid action within the OFC.
THE MAMMALIAN CELL-VIRUS RELATIONSHIP

All primary cell cultures tested from numerous human and rhesus monkey tissues were susceptible to Coxsackie A9 virus infection and were found to contain a specific A9 virus receptor. Ability of these cells to adsorb actively virus correlated with the presence of this receptor. Attachment of A9 virus to cell receptor was specifically enhanced by calcium and magnesium ions. Human cells established in continuous culture from pretested susceptible cultures were found to have lost A9 virus susceptibility and A9 receptors but not receptors for adsorption of type 1 poliovirus or B1, B3, B5 Coxsackie viruses. These cultures were able also to produce infectious A9 virus after exposure to viral RNA. Coxsackie A9 virus as well as type 1 poliovirus, inactivated following reaction with debris prepared from susceptible cells, could be recovered fully in infectious form by treatment of the inactive systems at low pH. Recovery of infectious A9 virus was also possible with a chelating compound. Coxsackie A9 virus could also be dissociated by means of low pH after adsorption onto susceptible cells for 2 minutes at 1°C. , but not after 1 hour incubation at 37°C. , indicating that viral host cell activity may be required in order for irreversible enterovirus attachment to take place.
BLM-dependent Break-Induced Replication handles DSBs in transcribed chromatin upon impaired RNA:DNA hybrids dissolution

Transcriptionally active loci are particularly prone to breakage and mounting evidence suggest that DNA Double-Strand Breaks arising in genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loops accumulation and dissolution. Here, we uncovered a critical function of the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in a R-loop dissolution-deficient background BLM switches from promoting Homologous Recombination to promoting Break-Induced Replication (BIR), which strongly impairs cell viability. Altogether our work unveils a role for BLM in BIR at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at these transcription-associated DSBs.
Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, Chromosome Conformation Capture (Hi-C), and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species.
Characterization of Antibiotic Resistant Salmonella spp Isolated from Chicken Eggs of Dhaka City

In present study, the occurrence of Salmonella in local chicken eggs and their pattern of antibiotic resistance were determined. 100 egg samples collected from different locations of Dhaka city were analysed and Salmonella spp were found in 8% of the samples. Among all presumptive Salmonella isolates, 8 isolates were confirmed as Salmonella enterica subsp . salamae (4%), Salmonella enterica subsp . indica (1%), Salmonella Paratyphi-A (1%), Salmonella bongori (1%) and Salmonella Choleraesuis (1%) on the basis of serotyping and biochemical analysis. These isolates were subjected to susceptibility test against 10 antibiotic disks. All the isolates were found chloramphenicol sensitive. The highest percentage of resistance (87.5%) was found to amoxicillin and ampicillin. Resistance against erythromycin, cephalexin, doxycycline hydrochloride, ceftazidime, doxycycline and nalidixic acid was also found significant ranging from 25% to 62.5%. Salmonella isolated from egg shell surface were found more antibiotic resistant than that of egg yolk and white. The present study suggests that poultry eggs are potential reservoir of antibiotic resistant Salmonellae. Keywords : Egg; Salmonella; Characterization; Antibiotic resistance. © 2011 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. doi:10.3329/jsr.v3i1. 6109 J. Sci. Res. 3 (1), 191-196 (2011)
Do Common Whitethroats (Sylvia communis) discriminate against alien eggs

In a coevolutionary arms race between a brood parasite and its host, both species are expected to evolve adaptations and counteradaptations, such as egg mimicry and egg discrimination. The Common Whitethroat (Sylvia communis) is a regular Common Cuckoo (Cuculus canorus) host in some parts of its breeding range. We studied egg discrimination in the Whitethroat in the south-eastern part of the Czech Republic in an area where the Whitethroat is parasitised only occasionally. To investigate responses to parasitic eggs, in 34 nests either a non-mimetic or a mimetic (conspecific) egg was added. All 21 non-mimetic eggs were ejected. Of the 13 mimetic eggs, 7 were ejected and 6 eggs were accepted. No significant differences were found in intraclutch variation in egg appearance between acceptors and rejecters. Ejected mimetic eggs, however, showed greater contrast with host eggs than did the mimetic eggs that were accepted. Our experiments show that Whitethroats are persistent rejecters of alien eggs at the study site. This fact is discussed in the light of the host selection and host-parasite coevolution hypotheses.
Reactivation of latent infections with migration shapes population-level disease dynamics

Annual migration is common across animal taxa and can dramatically shape the spatial and temporal patterns of infectious disease. Although migration can decrease infection prevalence in some contexts, these energetically costly long-distance movements can also have immunosuppressive effects that may interact with transmission processes in complex ways. Here we develop a mechanistic model for the reactivation of latent infections driven by physiological changes or energetic costs associated with migration (i.e., “migratory relapse”) and its effects on disease dynamics. We determine conditions under which migratory relapse can amplify or reduce infection prevalence across pathogen and host traits (e.g., infectious periods, virulence, overwinter survival, timing of relapse) and transmission phenologies. We show that relapse at either the start or end of migration can dramatically increase prevalence across the annual cycle and may be crucial for maintaining pathogens with low transmissibility and short infectious periods in migratory populations. Conversely, relapse at the start of migration can reduce the prevalence of highly virulent pathogens by amplifying culling of infected hosts during costly migration, especially for highly transmissible pathogens and those transmitted during migration or the breeding season. Our study provides a mechanistic foundation for understanding the spatiotemporal patterns of relapsing infections in migratory hosts, with implications for zoonotic surveillance and understanding how infection patterns will respond to shifts in migratory propensity associated with environmental change. Further, our work suggests incorporating within-host processes into population-level models of pathogen transmission may be crucial for reconciling the range of migration–infection relationships observed across migratory species.
A normative account of confirmation bias during reinforcement learning

Reinforcement learning involves updating estimates of the value of states and actions on the basis of experience. Previous work has shown that in humans, reinforcement learning exhibits a confirmatory bias: when updating the value of a chosen option, estimates are revised more radically following positive than negative reward prediction errors, but the converse is observed when updating the unchosen option value estimate. Here, we simulate performance on a multi-arm bandit task to examine the consequences of a confirmatory bias for reward harvesting. We report a paradoxical finding: that confirmatory biases allow the agent to maximise reward relative to an unbiased updating rule. This principle holds over a wide range of experimental settings and is most influential when decisions are corrupted by noise. We show that this occurs because on average, confirmatory biases lead to overestimating the value of more valuable bandits, and underestimating the value of less valuable bandits, rendering decisions overall more robust in the face of noise. Our results show how apparently suboptimal learning policies can in fact be reward-maximising if decisions are made with finite computational precision.
Revision of the Australian species of Pleistodontes (Hymenoptera: Agaonidae) fig-pollinating wasps and their host-plant associations

The Australian species of Pleistodontes, fig-pollinating wasps, are revised. In Australia, 14 species of Ficus belonging to the Urostigma sect. Malvanthera are known. From these Ficus, 17 species of Pleistodontes are recorded, of which seven are described as new. All type material has been examined and four new specific synonymies are proposed. One species, P. regalis Grandi, is resurrected from synonymy, while another, P. nitens (Girault) is redescribed. A key to females of Australian Pleistodontes is provided. All species are defined by means of full morphological descriptions, diagnosis, SEM photographs and drawings. Lectotypes are designated for nine species. The known distribution of each species is also given. Host plant (Ficus) associations are re-assessed in the light of this work and the recent revision of Australian Ficus sect. Malvanthera. In most cases there is a one-to-one relationship between Ficus and Pleistodontes species; however, three notable exceptions are discussed. Finally, our morphological study suggests strongly that the genus Pleistodontes includes some species that pollinate fig flowers actively and others that effect only passive pollination. © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society, 2002, 136, 637−683.