Miracle-dz/UniFAR-FTUs huggingface dataset:
A prediction: granule cells can perform linearly non-separable computations

Multiple studies show how dendrites might extend some neurons’ computational capacity. Past works most often focus on pyramidal cells which have an extended dendritic tree where voltage can vary independently; pyramidal neurons’ dendrites emit local spikes turning dendritic branches into local non-linear subunits. However, these studies leave a large fraction of the nervous system unexplored. Here, we study a neuron with a modest dendritic and non-spiking dendrites. Granule cells’ dendrites do not spike and these cells’ membrane voltage remain constant over the neuron. This study uses a conjunction of Boolean algebra and biophysical modelling to predict that Granule cells can perform linearly non-separable computations. In a previous study, we found a linearly non-separable Boolean function possible to implement without dendritic spikes, we coined this computation the feature binding problem. In the present work, we use the intrinsic saturation of synaptic conductance to implement this computation in a biophysical model. An integrate and fire, cannot perform such type of computations. Confirming our prediction would change how we understand the nervous system.
Spectrogram cross-correlation can be used to measure the complexity of bird vocalizations

Birdsong is an important signal in mate attraction and territorial defense. Quantifying the complexity of these songs can shed light on individual fitness, sexual selection, and behavior. Several techniques have been used to quantify song complexity and be broadly categorized into diversity indices, measures of stationary probabilities, and measures of sequential variations. However, these methods are unable to account for important acoustic features like the frequency bandwidth and the variety in the shape of syllables which are an integral part of these vocal signals. This study proposes a new complexity measure that considers intra-song note variability and calculates a weighted index for birdsongs using spectral cross-correlation. We compared the previously described methods to understand the advantages and limitations based on the factors that would be affecting the complexity of songs. We developed a new method- Note Variability Index (NVI), which incorporates the spectral features of notes while quantifying complexity. This measure alleviates the need for manual annotations of notes that can be error-prone. We used Spectrogram Cross-Correlation (SPCC) to compare notes within a song and used the output values to quantify song complexity. To check for the efficacy of the new method, we generated synthetic songs to caricature extremes in song complexity and compared selected conventional complexity measures along with the NVI. We provide case-specific limitations of these methods. Additionally, to examine the efficacy of this new method in real-world scenarios, we used natural birdsongs from multiple species across the globe with varying song structures to compare conventional methods with NVI. To our knowledge, NVI is the only song complexity method that captures the variation of spectral features of notes in songs where the conventional methods fail to distinguish between similar song structures with different note types. As NVI does not need a manual classification of notes, it can be easily implemented for any type of birdsong with existing sound analysis softwares; it is very quick, avoids the possible biases in note classification, and can possibly be automated for large datasets in the future.
Transmission of ‘Candidatus Anaplasma camelii’ to laboratory animals by camel-specific keds, Hippobosca camelina

Anaplasmosis, caused by infection with bacteria of the genus Anaplasma is an important veterinary and zoonotic disease. The characterization of transmission has concentrated on ticks and little is known about non-tick vectors of livestock anaplasmosis. This study investigated the presence of Anaplasma spp. in camels in northern Kenya and whether the hematophagous camel ked, Hippobosca camelina, acts as a vector. Camels (n = 976) and > 10,000 keds were sampled over a three-year study period and the presence of Anaplasma species was determined by PCR-based assays targeting the Anaplasmataceae 16S rRNA gene. Camels were infected by ‘Candidatus Anaplasma camelii’ occurring from 63 - 78% during the dry (September 2017), wet (June-July 2018), and late wet seasons (July-August 2019). 10 - 29% of camel keds harbored ‘Ca. Anaplasma camelii’ acquired from infected camels during blood feeding. We determined whether Anaplasma positive camel keds could transmit ‘Ca. Anaplasma camelii’ to small laboratory animals via blood-feeding. We show competence in pathogen transmission and subsequent infection in mice and rabbits by both direct detection in blood smears and subsequent molecular identification by PCR. Transmission of ‘Ca. Anaplasma camelii’ to mice (8 - 47%) and rabbits (25%) occurred readily after ked bites. Hence, we demonstrate, for the first time, the potential of H. camelina as a vector of anaplasmosis. This key finding provides the basis for establishing ked control programmes for improvement of livestock and human health. Author summary Hematophagous flies such as Tabanids and Stomoxys, among other biting flies, are mechanical transmitters of various pathogens such as African trypanosomes and Anaplasma species. However, little is known about the role of common camel-specific biting keds (also known as camel flies or louse flies, genus Hippobosca) in pathogen transmission. Keds inflict painful bites to access host blood, and in the process may transmit bacterial hemopathogens frequently detected in both camels and their keds. We confirmed by experimental blood-feeding, gene amplification, and amplicon sequencing that camel keds can transmit “Candidatus Anaplasma camelii” from naturally-infected camels to healthy mice and rabbits. The high prevalence of camel anaplasmosis throughout the year in northern Kenya could be explained by the infestation camel-specific H. camelina, whose capacity as efficient fliers, unlike ticks, promotes disease transmission and maintenance within and among camel herds. Although this study focused on the transmission of Anaplasma sp. by camel keds, it is possible that other hemopathogens could also be transmitted by these flies through a similar mechanism. Notably, in the absence of their preferred hosts, keds occasionally bite humans and other vertebrates they come across in order to acquire bloodmeals, and in the process could transmit zoonotic pathogens.
THEM6-mediated lipid remodelling sustains stress resistance in cancer

Despite the clinical benefit of androgen-deprivation therapy (ADT), the majority of patients with advanced prostate cancer (PCa) ultimately develop lethal castration-resistant prostate cancer (CRPC). In this study, we identified thioesterase superfamily member 6 (THEM6) as a marker of ADT resistance in PCa. In patients, THEM6 expression correlates with progressive disease and is associated with poor survival. THEM6 deletion reduces in vivo tumour growth and restores castration sensitivity in orthograft models of CRPC. Mechanistically, THEM6 is located at the endoplasmic reticulum (ER) membrane and controls lipid homeostasis by regulating intracellular levels of ether lipids. Consequently, THEM6 loss in CRPC cells significantly alters ER function, reducing de novo sterol biosynthesis and preventing lipid-mediated induction of ATF4. Finally, we show that THEM6 is required for the establishment of the MYC-induced stress response. Thus, similar to PCa, THEM6 loss significantly impairs tumorigenesis in the MYC-dependent subtype of triple negative breast cancer. Altogether, our results highlight THEM6 as a novel component of the treatment-induced stress response and a promising target for the treatment of CRPC and MYC-driven cancer.
Genome sequencing and functional genes comparison between Sphingopyxis USTB-05 and Sphingomonas morindae NBD5

Sphingomonadaceae has a large number of strains that can biodegrade hepatotoxins or environmental pollutants. The latest research reported that certain strains can also produce lutein. Based on the third-generation sequencing technology, we analyzed the whole genome sequence and compared related functional genes of two strains of Sphingomonadaceae isolated from different habitats. The genome of Sphingopyxis USTB-05 was 4,679,489 bp and contained 4312 protein coding genes. The 4,239,716 bp nuclear genome of Sphingomonas morindae NBD5, harboring 3882 protein coding genes, has two sets of chromosomes. Both strains had lutein synthesis metabolism pathway sharing identical synthetic genes of crtB, crtE, crtI, crtQ, crtL, crtR, atoB, dxs, dxr, ispD, ispE, ispDF, gcpE, ispG, ispH, ispA, ispB and ispU. Sphingopyxis USTB-05 had hepatotoxins microcystins and nodularin metabolic pathways related to 16 genes (ald, ansA, gdhA, crnA, phy, ocd, hypdh, spuC, nspC, speE, murI, murD, murC, hmgL, bioA and glsA), while these genes were not found in Sphingomonas morindae NBD5. The unique protein sequences of strain NBD5 and strain USTB-05 were 155 and 199, respectively. The analysis of whole genome of the two Sphingomonadaceae strains provides insights into prokaryote evolution, the new pathway for lutein production and the new genes for environmental pollutant biodegradation. IMPORTANCE Understanding the functional genes related to the special functions of strains is essential for humans to utilize microbial resources. The ability of Sphingopyxis USTB-05 to degrade hepatotoxins microcystins and nodularin has been studied in depth, however the complete metabolic process still needs further elucidation. Sphingomonas morindae NBD5 can produce lutein, and it is necessary to determine whether there is a new pathway of lutein. In this study, the whole genome sequencing of Sphingopyxis USTB-05 and Sphingomonas morindae NBD5 were performed for the first time. Lutein synthesis metabolic pathways and synthetic genes were discovered in Sphingomonadaceae. We predicted the existence of new lutein synthesis pathways and revealed most of the genes of the new synthesis pathways. A comparative analysis of the functional genes of the two strains revealed that Sphingopyxis USTB-05 contains a large number of functional genes related to the biodegradation of hepatotoxins or hexachlorocyclohexane. Among them, the functional genes related to the biodegradation and metabolism of hexachlorocyclohexane had not been previously reported. These findings lay the foundation for the biosynthesis of lutein using Sphingomonas morindae NBD5 or Sphingopyxis USTB-05 and the application of Sphingopyxis USTB-05 for the biodegradation of hepatotoxins microcystins and nodularin or environmental pollutants.
PCRedux: A Data Mining and Machine Learning Toolkit for qPCR Experiments

Motivation Quantitative Real-time PCR (qPCR) is a widely used -omics method for the precise quantification of nucleic acids, in which the result is associated with the presence/absence or quantity of a specific nucleic acid sequence. As the amount of qPCR data increases worldwide, the manual assessment of results becomes challenging and difficult to reproduce. To overcome this, some automatable characteristics of amplification curves have been described in the literature, often with an appropriate “rule of thumb”. Results We developed PCRedux to analyze and calculate 90 numerical qPCR amplification curve descriptors (‘‘features”) from large datasets of qPCR amplification curves that are aimed for interpretable machine learning and development of decision support systems. In a case study of a diverse dataset with 3181 positive, negative and ambiguous amplification curves, as assessed by three human raters, we demonstrate a sensitivity >99 % and specificity >97 % in detecting positive and negative amplification. PCRedux is unique as it goes beyond traditional qPCR analysis to capture curvature properties that improve the characterization and classification of amplification curves. The calculation of the features is reproducible and objective, since R is used as a controllable working environment. PCRedux is not a black box, but open source software following on the principle of mathematically interpretable features. These can be combined with user-defined labels for automatic multi-category classification and regression in machine learning. Availability https://cran.r-project.org/package=PCRedux. Web server: http://shtest.evrogen. net/PCRedux-app/. Documentation: https://PCRuniversum.github. io/PCRedux/.
Hypsugo stubbei sp. nov., a novel cryptic bat species of the genus Hypsugo (Vespertilionidae, Chiroptera, Mammalia) from Mongolia. Results of the Mongolian-German Biological Expeditions Since 1962, No. 347.

The occurrence of two members of the genus Hypsugo, namely H. alaschanicus and H. savii caucasicus, have been reported for Mongolia in the literature. Due to various taxonomic reassignments within and between genera, the number of records for the genus Hypsugo in Mongolia is quite scarce and sometimes not resolved at species or subspecies level. Despite recognition of the two above-mentioned species, recent reports based on genetic analyses describe only new and further records of H. alaschanicus. Thus, it exists a large uncertainty regarding the occurrence and distribution of H. savii caucasicus in Mongolia. Here, our efforts in gaining a deeper understanding towards the occurrence and distribution of Hypsugo species in Mongolia are described. A combination of genetic and morphological analyses of collected material from Hypsugo specimens revealed the existence of a genetically largely distant Hypsugo clade. Therefore, a new and cryptic Hypsugo species is proposed which is named after Prof. Dr. Michael Stubbe for his continuous, long-standing and significant contributions into the biological exploration of Mongolia. Hypsugo stubbei sp. nov. differs by at least 8.4 % and 9 % to the closest Western Palearctic distributed H. cf. darwinii and H. savii as well as at least 11.3 % to the Easter Palearctic (including Mongolia) distributed H. alaschanicus based on the first 798 nucleotides of the gene encoding the mitochondrial ND1 (subunit one of NADH dehydrogenase). Neither a close proximity species based on the gene encoding the mitochondrial COI (cytochrome oxidase subunit one) could be found in publicly accessible nucleotide databases. While the cryptic H. stubbei sp. nov. reveals no obvious cranial and morphological differences, few external characteristics are dissimilar to both H. alaschanicus and H. savii (caucasicus). Currently, Hypsugo stubbei sp. nov. was found at four different locations in Mongolia. Among the 11 specimens captured, six facilitated a genetic assignment. Based on the current scarce data records, the species seems to occur mainly in the far west of Mongolia inhabiting semi-deserts and steppes up to high mountain areas. An overlapping distribution with H. alaschanicus cannot be excluded based on the limited data currently available.
Quantitative prey species detection in predator guts across multiple trophic levels by DNA shotgun sequencing

Metabarcoding has revolutionized the study of ecological communities, but PCR bias hampers quantitative analyses, as required in studies of trophic interactions. Direct DNA shotgun sequencing can avoid the amplification step when unassembled reads are mapped to a reference database, enabling identification and quantification of prey items. Two feeding bioassays tested the precision and accuracy of quantitative assessments with the coccinellids Harmonia axyridis and Hippodamia convergens, the chrysopid Chrysoperla externa, and the aphid Myzus persicae. Guts were dissected and the total DNA extracted was directly sent to sequence by Illumina HiSeq2500 (insert 350 bp, PE 250). Predator gut content reads were blasted against an arthropod mitochondrial DNA reference database for taxonomic assignment and the matches curated for false positive prey identification using a series of bioinformatics pipelines, mostly in R. Taxonomic assignment through KrakenUnique, which is based on the counts of unique k-mers, was compared. In a Prey Quantity bioassay, the number of prey reads was correlated to the amount of prey consumed and the elapsed time since consumption. In a Direct and Indirect Predation bioassay, prey was detectable in the predator 6 h after feeding (direct predation) and the prey’s prior prey was detectable 3 h after feeding (indirect predation). Detection of indirect predation was related to the species-specific decay rates of the two predators, but not to the order of predation. We demonstrate that degraded prey DNA was quantifiable across trophic levels with high accuracy (98.4% positive predictive value) and taxonomic resolution.
Regulation of neurogenesis and gliogenesis by the matricellular protein CCN2 in the mouse retina

Cellular communication network (CCN) 2 is an extracellular matrix protein with cell type- and context-dependent functions. Using a combination of mouse genetics and omic approaches, we show that CCN2 is expressed in early embryonic retinal progenitor cells (RPCs) and becomes restricted to fully differentiated Müller glial cells (MGCs) thereafter. Germline deletion of CCN2 in mice decreases BrdU labeling, reduces RPC pool, and impairs the competency of remaining RPCs to generate early and late born retinal cell types. Retinal hypocellularity and microphthalmia ensue. The transcriptomic changes associated with CCN2 inactivation include reduced marker and transcriptional regulator genes of retinal ganglion cells, photoreceptors and MGCs. Yap (Yes-associated protein), a singular node for transcriptional regulation of growth and differentiation genes, is also a target of CCN2 signals. In an organotypic model of ex vivo cultured embryonic retinas, CCN2 and YAP immunoreactivity signals overlap. Lentivirus-mediated YAP expression in CCN2-deficient retinal explants increases the number of differentiating Sox9-positive MGCs. Taken together, our data indicate that CCN2 controls the proliferative and differentiation potentials of RPCs ultimately endowing, a subpopulation thereof, with Müller glial cell fate. Summary statement A CCN2-YAP regulatory axis controls retinal progenitor cell growth and lineage commitment to neuronal and glial cell fates.
Genetic diversity in facultatively sexual populations and its implications for the origins of self-incompatibility in algae and fungi

The evolutionary mechanism that drove the establishment of self-incompatibility in early sexual eukaryotes is still a debated topic. While a number of competing hypotheses have been proposed, many have not received detailed theoretical attention. In particular, the hypothesis that self-incompatibility increases the benefits of genetic recombination in sexual haploids has been comparatively understudied. In this paper we address this topic by mathematically deriving how the probability of mating with a genetically distinct individual changes as a function of the presence or absence of self-incompatible mating type classes. We find that although populations with mating types successfully engage in sexual reproduction less frequently than their self-compatible competitors, they can nevertheless engage in useful sex with genetically distinct partners more frequently. This conclusion holds when the number of sexual reproductive events per generation is low (i.e. in small populations with low rates of facultative sexual reproduction). Finally we demonstrate the potential for frequency-dependent selection in competitive dynamics between self-compatible and self-incompatible types. These analytic results provide a baseline for studying the sex advantage enhancer model for the evolutionary origin of mating types within each specific hypothesis for the evolution of recombination. PACS 87.23. -n Ecology and evolution, 87.23. Kg Dynamics of evolution, 02.50. Ey Stochastic processes 2000 MSC 37N25: Dynamical systems in biology, 60J70: Applications of diffusion theory (population genetics, absorption problems, etc.)
Synapse development is regulated by microglial THIK-1 K+ channels

Significance Microglia are the brain’s resident immune cells, surveying the brain with motile processes, which can remove pathogens but also prune unnecessary junctions between the neurons (synapses). A potassium channel, THIK-1, in the microglial membrane allows efflux of potassium from these cells and thereby regulates their membrane voltage as well as their process motility and release of inflammatory mediators. Here, using THIK-1–blocking drugs and THIK-1–deficient mice, we demonstrate that THIK-1 controls removal of synaptic material by microglia, which reduces the number of functional synapses in the developing brain. Microglia are the resident immune cells of the central nervous system. They constantly survey the brain parenchyma for redundant synapses, debris, or dying cells, which they remove through phagocytosis. Microglial ramification, motility, and cytokine release are regulated by tonically active THIK-1 K+ channels on the microglial plasma membrane. Here, we examined whether these channels also play a role in phagocytosis. Using pharmacological blockers and THIK-1 knockout (KO) mice, we found that a lack of THIK-1 activity approximately halved both microglial phagocytosis and marker levels for the lysosomes that degrade phagocytically removed material. These changes may reflect a decrease of intracellular [Ca2+]i activity, which was observed when THIK-1 activity was reduced, since buffering [Ca2+]i reduced phagocytosis. Less phagocytosis is expected to result in impaired pruning of synapses. In the hippocampus, mice lacking THIK-1 expression had an increased number of anatomically and electrophysiologically defined glutamatergic synapses during development. This resulted from an increased number of presynaptic terminals, caused by impaired removal by THIK-1 KO microglia. The dependence of synapse number on THIK-1 K+ channels, which control microglial surveillance and phagocytic ability, implies that changes in the THIK-1 expression level in disease states may contribute to altering neural circuit function.
Organ-specific microbiota enhances the terrestrial lifestyle of a brachyuran

14 The transition to terrestrial environments has occurred repeatedly and at different geological 15 times in arthropods, but almost no information is available about the role of symbiotic 16 microbiota in such process. Here we investigated the associated microbiota of a terrestrial 17 brachyuran crab, Chiromantes haematocheir, using a targeted metagenomic approach. 18 Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs 19 and environmental matrices to profile microbial communities. We found stable and organ20 specific communities of microorganisms associated to the gut and the gills of the crabs, the 21 former involved in the digestion of vascular plant tissues. These communities were mainly 22 composed by prokaryotic organisms and significantly differed from the fungi-dominated ones 23 present in the environment. Our results suggest that the establishment of a specific, stable 24 microbiota may be crucial to drive evolutionary transitions, as colonization of terrestrial 25