bluuebunny/crossref_metadata_2025 huggingface dataset:
Lesion Shedding Model: unraveling site-specific contributions to ctDNA
Authors: Rhrissorrakrai Kahn , Utro Filippo , Levovitz Chaya , Parida Laxmi
Published: January 2021

Sampling circulating tumor DNA (ctDNA) using liquid biopsies offers clinically important benefits for monitoring cancer progression. A single ctDNA sample represents a mixture of shed tumor DNA from all known and unknown lesions within a patient. Although shedding levels have been suggested to hold the key to identifying targetable lesions and uncovering treatment resistance mechanisms, the amount of DNA shed by any one specific lesion is still not well characterized. We designed the Lesion Shedding Model (LSM) to order lesions from the strongest to the poorest shedding for a given patient. By characterizing the lesion-specific ctDNA shedding levels, we can better understand the mechanisms of shedding and more accurately interpret ctDNA assays to improve their clinical impact. We verified the accuracy of the LSM under controlled conditions using a simulation approach as well as testing the model on three cancer patients. The LSM obtained an accurate partial order of the lesions according to their assigned shedding levels in simulations and its accuracy in identifying the top shedding lesion was not impacted by number of lesions. Applying LSM to three cancer patients, we found that indeed there were lesions that consistently shed more than others into the patients’ blood. In two of the patients, the top shedding lesion was one of the only clinically progressing lesions at the time of biopsy suggesting a connection between high ctDNA shedding and clinical progression. The LSM provides a much needed framework with which to understand ctDNA shedding and interpret ctDNA assays.

Availability

Binary is available athttps://github.com/ComputationalGenomics/LSM
Two softwood GUX clades are responsible for distinct glucuronic acid patterns on xylan
Authors: Lyczakowski Jan J , Yu Li , Terrett Oliver M , Fleischmann Christina , Temple Henry , Thorlby Glenn , Sorieul Mathias , Dupree Paul
Published: January 2021

Wood of coniferous (softwood) trees, is a globally significant carbon sink and an important source of biomass for industrial applications. Despite its importance, very little is known about the genetic basis of softwood biosynthesis. Glucomannan and xylan are the main hemicelluloses in softwood secondary cell walls. Xylan interacts with the cellulose fibrils in a two-fold screw configuration. Moreover, we have shown that xylan GUX (GlucUronic acid substitution of Xylan)-dependent branching with glucuronic acid is critical for biomass recalcitrance. Here, we investigated the decoration patterns of xylan by softwood GUX enzymes. Usingin vitroandin plantaassays we demonstrate that two distinct clades of conifer GUX enzymes are active glucuronyltransferases. Interestingly, these enzymes have different specific activities, with one adding evenly spaced GlcA branches and the other one being also capable of glucuronidating two consecutive xyloses. Since xylan patterning might modulate xylan-cellulose and xylan-lignin interactions, our result further the understanding of softwood biosynthesis and can contribute to strategies aimed at modifying softwood cell wall properties.
Fluoxetine acts concomitantly on dorsal and ventral hippocampus to Trk-dependently modulate the extinction of fear memory
Authors: Diniz Cassiano Ricardo Alves Faria , da Silva Leandro Antero , Domingos Luana Barreto , Sonego Andreza Buzolin , Moraes Leonardo Resstel Barbosa , Joca Sâmia
Published: January 2021

Background

Hippocampus can be divided along its longitudinal axis into dorsal and ventral parts. Both are usually committed to modulate different aspects of behavior and stress response. However, it is not clear whether the hippocampal subregions could differently modulate the effect of antidepressant drugs. Since fluoxetine (FLX) effect on extinction of aversive memory is well known to depend on hippocampal BDNF levels, we hypothesized that the hippocampal subregions might play different roles in fluoxetine efficacy in decreasing fear response.

Method

Wistar rats were fear-cued conditioned and treated chronically with fluoxetine to enhance their subsequent extinction memory. First, FLX effect on BDNF levels was assessed considering the dorsal (dHC) and ventral (vHC) hippocampus apart. Then, K252a (a functional Trk blocker) was infused either into the dHC or vHC to assay its interaction with FLX treatment over the fear response. Next, BDNF was directly infused into either the dHC or vHC to compare its behavioral effects with FLX. Finally, FLX effect on c-Fos expression was evaluated also considering the dHC and vHC apart, along with subareas of amygdala and medial prefrontal cortex.

Results

Chronic FLX treatment increased BDNF in the dHC, whereas BDNF was increased in the vHC after acute treatment only. K252a infused after the extinction protocol into either dHC or vHC was able to prevent FLX effect on fear response. BDNF directly infused into the dHC increased fear response, however its administration into the vHC induced an opposite effect. Besides, a negative correlation between the fear response and c-Fos expression was observed after chronic FLX treatment specifically in the dHC CA3/CA1 and vHC CA1/DG.

Conclusion

Both dHC and vHC are important for the Trk-dependent FLX effect on extinction memory, although a discrepancy on the fear response was observed with the direct infusion of BDNF into the dHC or vHC.
Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamineN-oxide
Authors: Hoyles Lesley , Pontifex Matthew G. , Rodriguez-Ramiro Ildefonso , Anis-Alavi M. Areeb , Jelane Khadija S. , Snelling Tom , Solito Egle , Fonseca Sonia , Carvalho Ana L. , Carding Simon R. , Müller Michael , Glen Robert C. , Vauzour David , McArthur Simon
Published: January 2021

Background

Communication between the gut microbiota and the brain is primarily mediatedviasoluble microbe-derived metabolites, but the details of this pathway remain poorly defined. Methylamines produced by microbial metabolism of dietary choline and L-carnitine have received attention due to their proposed association with vascular disease, but their effects upon the cerebrovascular circulation have hitherto not been studied.

Results

Here we use an integratedin vitro/in vivoapproach to show that physiologically relevant concentrations of the dietary methylamine trimethylamineN-oxide (TMAO) enhanced blood-brain barrier (BBB) integrity and protected it from inflammatory insult, acting through the tight junction regulator annexin A1. In contrast, the TMAO precursor trimethylamine (TMA) impaired BBB function and disrupted tight junction integrity. Moreover, we show that long-term exposure to TMAO protects murine cognitive function from inflammatory challenge, acting to limit astrocyte and microglial reactivity in a brain region-specific manner.

Conclusion

Our findings demonstrate the mechanisms through which microbiome-associated methylamines directly interact with the mammalian BBB, with consequences for cerebrovascular and cognitive function.
Female immunity protects from cutaneous squamous cell carcinoma
Authors: Budden Timothy , Gaudy-Marqueste Caroline , Craig Sarah , Hu Yuan , Earnshaw Charles , Gurung Shilpa , Ra Amelle , Akhras Victoria , Shenjere Patrick , Green Ruth , Jamieson Lynne , Lear John , Motta Luisa , Caulín Carlos , Oudit Deemesh , Furney Simon J , Virós Amaya
Published: January 2021

Purpose

Cancer susceptibility and mortality are higher in males, and the mutational and transcriptomic landscape of cancer differs by sex. The current assumption is that men are at higher risk of epithelial cancers as they expose more to carcinogens and accumulate more damage than women. We present data showing women are more protected from aggressive cutaneous squamous cell carcinoma (cSCC) due to strong immune activation.

Methods

We explored clinical and molecular sexual disparity in immunocompetent and immunosuppressed patients (N= 738, N=160) with carcinoma cSCC, in FVB/N mice exposed to equal doses of DMBA, and in human keratinocytes by whole exome sequencing, bulk and single cell RNA sequencing.

Results

We show cSCC is more aggressive in men, and immunocompetent women develop mild cSCC, later in life. To test if sex drives disparity, we exposed male and female mice to equal doses of carcinogen, and found males present more aggressive, metastatic cSCC than females. Critically, females activate cancer immune-related expression pathways and CD4 and CD8 T cell infiltration independently of mutations. In contrast, males increase the rate of mitoses and proliferation in response to carcinogen. Human female skin and keratinocytes also activate immune-cancer fighting pathways and immune cells at ultraviolet radiation-damaged sites. Critically, a compromised immune system leads to high-risk, aggressive cSCC specifically in women.

Conclusions

This work shows the immune response is sex biased in cSCC, and highlights female immunity offers greater protection than male immunity.
Impaired refinement of kinematic variability in Huntington disease mice on an automated home-cage forelimb motor task
Authors: Woodard Cameron L. , Sepers Marja D. , Raymond Lynn A.
Published: January 2021

The effective development of novel therapies in mouse models of neurological disorders relies on behavioural assessments that provide accurate read-outs of neuronal dysfunction and/or degeneration. We designed an automated behavioural testing system (‘PiPaw’) which integrates an operant lever-pulling task directly into the mouse home-cage. This task is accessible to group-housed mice 24-hours per day, enabling high-throughput longitudinal analysis of forelimb motor learning. Moreover, this design eliminates the need for exposure to novel environments and minimizes experimenter interaction, significantly reducing two of the largest stressors associated with animal behaviour. Mice improved their performance of this task over one week of testing by reducing inter-trial variability of reward-related kinematic parameters (pull amplitude or peak velocity). In addition, mice displayed short-term improvements in reward rate, and a concomitant decrease in movement variability, over the course of brief (<10 minutes) bouts of task engagement. We used this system to assess motor learning in mouse models of the inherited neurodegenerative disorder, Huntington disease (HD). Despite having no baseline differences in task performance, Q175-FDN HD mice were unable to modulate the variability of their movements in order to increase reward on either short or long timescales. Task training was associated with a decrease in the amplitude of spontaneous excitatory activity recorded from striatal medium spiny neurons in the hemisphere contralateral to the trained forelimb in wildtype mice; however, no such changes were observed in Q175-FDN mice. This behavioural screening platform should prove useful for preclinical drug trials towards improved treatments in HD and other neurological disorders.

Significance Statement

In order to develop effective therapies for neurological disorders such as Huntington disease (HD), it’s important to be able to accurately and reliably assess the behaviour of mouse models of these conditions. Moreover, these behavioural assessments should provide an accurate readout of underlying neuronal dysfunction and/or degeneration. In this paper, we employed an automated behavioural testing system to assess motor learning in mice within their home-cage. Using this system, we were able to study motor abnormalities in HD mice with an unprecedented level of detail, and identified a specific behavioural deficit associated with an underlying impairment in striatal neuronal plasticity. These results validate the usefulness of this system for assessing behaviour in mouse models of HD and other neurological disorders.
Glucose inhibits haemostasis and accelerates diet-induced hyperlipidaemia in zebrafish larvae
Authors: Morris Simone , Cholan Pradeep Manuneedhi , Britton Warwick J , Oehlers Stefan H
Published: January 2021

Hyperglycaemia damages the microvasculature in part through the reduced recruitment of immune cells and interference with platelet signalling, leading to poor wound healing and accelerated lipid deposition in mammals. We investigated the utility of zebrafish larvae to model the effect of glucose on neutrophil and macrophage recruitment to a tail wound, wound-induced haemostasis, and chicken egg yolk feed challenge-induced hyperlipidaemia by supplementing larvae with exogenous glucose by immersion or injection. Neither method of glucose supplementation affected the recruitment of neutrophils and macrophages following tail transection. Glucose injection reduced thrombocyte retention and fibrin plug formation while only thrombocyte retention was reduced by glucose immersion following tail transection. We observed accelerated lipid accumulation in glucose-injected larvae challenged with high fat chicken egg yolk feeding. Our study identifies conserved and divergent effects of high glucose on inflammation, haemostasis, and hyperlipidaemia in zebrafish larvae compared to mammals.
Validation of the Munich Actimetry Sleep Detection Algorithm for estimating sleep-wake patterns from activity recordings
Authors: Loock Ann-Sophie , Sullivan Ameena Khan , Reis Catia , Paiva Teresa , Ghotbi Neda , Pilz Luisa K. , Biller Anna M. , Molenda Carmen , Vuori-Brodowski Maria , Roenneberg Till , Winnebeck Eva C.
Published: January 2021

Periods of sleep and wakefulness can be estimated from wrist-locomotor activity recordings via algorithms that identify periods of relative activity and inactivity. Here, we evaluated the performance of our Munich Actimetry Sleep Detection Algorithm (MASDA). MASDA uses a moving 24-hour-threshold and correlation procedure estimating relatively consolidated periods of sleep and wake.

MASDA was validated against sleep logs and polysomnography. Sleep-log validation was performed on 2 field samples collected over 54 and 34 days (median) in 34 adolescents and 28 young adults. Polysomnographic validation was performed on a clinical sample of 23 individuals undergoing 1 night of polysomnography. Epoch-by-epoch analyses were conducted and comparisons of sleep measures via Bland-Altman plots and correlations.

Compared with sleep logs, MASDA classified sleep with a median sensitivity of 80% (IQR = 75-86%) and specificity of 91% (87-92%). Mean onset and offset times were highly correlated (r = 0.86-0.91). Compared with polysomnography, MASDA reached a median sensitivity of 92% (85-100%), but low specificity of 33% (10-98%), owing to the low frequency of wake episodes in the nighttime polysomnographic recordings. MASDA overestimated sleep onset (~21 min) and underestimated wake after sleep onset (~26 min), while not performing systematically different from polysomnography in other sleep parameters.

These results demonstrate the validity of MASDA to faithfully estimate sleep-wake patterns in field studies. With its good performance across day- and nighttime, it enables analyses of sleep-wake patterns in long recordings performed to assess circadian and sleep regularity and is therefore an excellent objective alternative to sleep logs in field settings.
Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematics and revealed by a three dimensional computational framework
Authors: Auddya Debabrata , Zhang Xiaoxuan , Gulati Rahul , Vasan Ritvik , Garikipati Krishna , Rangamani Padmini , Rudraraju Shiva
Published: January 2021

Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modeling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modeling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff-Love thin-shell kinematics, Helfrich-energy based mechanics, and state-of-the-art numerical techniques for modeling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modeling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a 3D space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modeling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a “phase diagram” for its symmetric and broken-symmetry states.
AP2 regulates Thickveins trafficking through Rab11 to attenuate NMJ growth signaling inDrosophila
Authors: Dwivedi Manish Kumar , Choudhury Saumitra Dey , Patnaik Abhinandan , Mishra Shirish , Padinjat Raghu , Kumar Vimlesh
Published: January 2021

Compromised endocytosis in neurons leads to synapse overgrowth and altered organization of synaptic proteins. However, the molecular players and the signaling pathways which regulate the process remains poorly understood. Here we show that σ2-adaptin, one of the subunits of the AP2-complex, genetically interacts with BMP type I receptor, Thickveins (Tkv), and Daughter against decapentaplegic (Dad), two of the components of BMP signaling. We found that mutations in σ2-adaptin lead to an accumulation of Tkv receptors at the NMJ and results in a significant reduction in Tkv-positive early endosomes in the presynaptic terminals. Interestingly, the level of small GTPase Rab11 was significantly reduced in the σ2-adaptin mutant synapses. Consistent with the role of σ2-adaptin and Rab11 in the regulation of the same signaling pathway, a mutation in Rab11 or overexpression of a GDP-locked form of Rab11 (Rab11S25N) phenocopies the morphological and signaling defects of the σ2-adaptin mutants. Finally, we demonstrate thatσ2-adaptinmutants show an accumulation of large vesicles and massive membranous structures, akin to endosomes at the synapse. Thus, we propose a model in which AP2 regulates Tkv internalization and recycling through a process that requires Rab11 activity to control the synaptic growth.
A comparative baseline of coral disease across the central Red Sea
Authors: Aeby Greta Smith , Shore Amanda , Jensen Thor , Ziegler Maren , Work Thierry , Voolstra Christian R.
Published: January 2021

The Red Sea is a unique environment for corals with a strong environmental gradient characterized by temperature extremes and high salinities, but minimal terrestrial runoff or riverine input and their associated pollution. Disease surveys were conducted along 22 reefs in the central Red Sea along the Saudi Arabian coast in October 2015, which coincided with a bleaching event. Our objectives were to 1) document types, prevalence, and distribution of coral diseases in a region with minimal terrestrial input, 2) compare regional differences in diseases and bleaching along a latitudinal gradient of environmental conditions, and 3) use histopathology to characterize disease lesions at the cellular level. Coral reefs of the central Red Sea had a widespread but a surprisingly low prevalence of disease (<0.5%), based on the examination of >75,750 colonies. Twenty diseases were recorded affecting 16 coral taxa and included black band disease, white syndromes, endolithic hypermycosis, skeletal eroding band, growth anomalies and focal bleached patches. The three most common diseases wereAcroporawhite syndrome (59.1% of the survey sites),Poritesgrowth anomalies (40.9%), andPoriteswhite syndrome (31.8%). Over half of the coral genera within transects had lesions and corals from the generaAcropora, MilleporaandLobophylliawere the most commonly affected. Cell-associated microbial aggregates were found in four coral genera resembling patterns found in the Indo-Pacific. Differences in disease prevalence, coral cover, amount of heat stress as measured by degree heating weeks (DHW) and extent of bleaching was evident among sites. Disease prevalence was not explained by coral cover or DHW, and a negative relationship between coral bleaching and disease prevalence was found. The northern-most sites off the coast of Yanbu had the highest average DHW values but absence of bleaching and the highest average disease prevalence was recorded. Our study provides a foundation and baseline data for coral disease prevalence in the Red Sea, which is projected to increase as a consequence of increased frequency and severity of ocean warming.
Collective Regulation of Metabolism, Development and Longevity Through a
Socially Exchanged Fluid
Authors: Hakala SM , Meurville M-P , Stumpe M , LeBoeuf AC
Published: January 2021

Socially exchanged fluids, like seminal fluid and milk, allow individuals to
molecularly influence conspecifics. Many social insects have a social
circulatory system, where food and endogenously produced molecules are
transferred mouth-to-mouth (stomodeal trophallaxis), connecting all the
individuals in the society. To understand how these endogenous molecules relate
to colony life, we used quantitative proteomics to investigate the trophallactic
fluid within colonies of the carpenter ant Camponotus
floridanus. We show that different stages of the colony life
cycle circulate different types of proteins: young colonies prioritize direct
carbohydrate processing; mature colonies prioritize accumulation and
transmission of stored resources. Further, colonies circulate proteins
implicated in oxidative stress, ageing, and social insect caste determination,
potentially acting as superorganismal hormones. Brood-caring individuals that
are also closer to the queen in the social network (nurses) showed higher
abundance of oxidative stress-related proteins. Thus, trophallaxis behavior
provides a mechanism for distributed metabolism in social insect
societies.
Reaching to inhibit a prepotent response: a wearable 3-axis accelerometer kinematic analysis
Authors: Angeli Alessia , Valori Irene , Farroni Teresa , Marfia Gustavo
Published: January 2021

The present work explores the distinctive contribution of motor planning and control to human reaching movements. In particular, the movements were triggered by the selection of a prepotent response (Dominant) or, instead, by the inhibition of the prepotent response, that required the selection of an alternative one (Non-dominant). To this aim, we adapted aGo/No-Gotask to investigate both the dominant and non-dominant movements of a cohort of 19 adults, utilizing kinematic measures to discriminate between the planning and control components of the two actions. To sample such measures, a low-cost, easy to use, 3-axis wrist worn accelerometer was put to good use to obtain raw acceleration data and to compute and break down its velocity components. The values obtained with such task indicate that with the inhibition of a prepotent response, the selection and execution of the alternative one yields both a longer reaction time and movement duration. Moreover, the peak velocity occurred later in time with respect to the dominant response, revealing that participants tended to indulge more in motor planning rather than in adjusting their movement along the way. Finally, comparing such results to the findings obtained by other means in literature, we discuss the feasibility of an accelerometer-based analysis to disentangle distinctive cognitive mechanisms of human movements.
Fish primary embryonic stem cells self-assemble into retinal tissue mirroringin vivoearly eye development
Authors: Zilova Lucie , Weinhardt Venera , Tavhelidse Tinatini , Thumberger Thomas , Wittbrodt Joachim
Published: January 2021

Organoids derived from pluripotent stem cells promise the solution to current challenges in basic and biomedical research. Further progress and widespread applications are however limited by long developmental time, variable success, and lack of direct comparison to anin vivoreference. To overcome those limitations, we derived organoids from rapidly developing teleosts. We demonstrate how primary embryonic stem cells from zebrafish and medaka efficiently self-organize into anterior neural structures, particularly retina. Within four days, blastula-stage cell aggregates reproducibly execute key steps of eye development: retinal specification, morphogenesis and differentiation. The number of aggregated cells as well as genetic factors crucially impacted upon the concomitant morphological changes that were intriguingly reflecting thein vivosituation. High reproducibility and rapid development of fish-derived organoids in combination with advanced genome editing techniques immediately allow addressing aspects of development and disease, and systematically probing the impact of the physical environment on morphogenesis and differentiation.
Th17 immunity in the colon is controlled by two novel subsets of colon-specific mononuclear phagocytes
Authors: Huang Hsin-I , Jewell Mark L. , Youssef Nourhan , Huang Min-Nung , Hauser Elizabeth R. , Fee Brian E. , Rudemiller Nathan P. , Privratsky Jamie R. , Zhang Junyi J. , Reyes Estefany , Wang Donghai , Taylor Gregory A. , Gunn Michael D. , Ko Dennis C. , Cook Donald N. , Chandramohan Vidyalakshmi , Crowley Steven D. , Hammer Gianna Elena
Published: January 2021

Intestinal immunity is coordinated by specialized mononuclear phagocyte populations, constituted by a diversity of cell subsets. Although the cell subsets constituting the mononuclear phagocyte network are thought to be similar in both small and large intestine, these organs have distinct anatomy, microbial composition, and immunological demands. Whether these distinctions demand organ-specific mononuclear phagocyte populations with dedicated organ-specific roles in immunity are unknown. Here we implement a new strategy to subset murine intestinal mononuclear phagocytes and identify two novel subsets which are colon-specific: a macrophage subset and a Th17-inducing dendritic cell (DC) subset. Colon-specific DCs and macrophages co-expressed CD24 and CD14, and surprisingly, both were dependent on the transcription factor IRF4. Novel IRF4-dependent CD14+CD24+macrophages were markedly distinct from conventional macrophages and failed to express classical markers including CX3CR1, CD64 and CD88, and surprisingly expressed little IL-10, which was otherwise robustly expressed by all other intestinal macrophages. We further found that colon-specific CD14+CD24+mononuclear phagocytes were essential for Th17 immunity in the colon, and provide definitive evidence that colon and small intestine have distinct antigen presenting cell requirements for Th17 immunity. Our findings reveal unappreciated organ-specific diversity of intestine-resident mononuclear phagocytes and organ-specific requirements for Th17 immunity.
BnaA03.WRKY28, interacting with BnaA09.VQ12, acts as a brake factor of activated BnWRKY33-mediated resistance outburst againstSclerotinia sclerotioruminBrassica napus
Authors: Zhang Ka , Liu Fei , Wang Zhixin , Zhuo Chenjian , Hu Kaining , Li Xiaoxia , Wen Jing , Yi Bin , Shen Jinxiong , Ma Chaozhi , Fu Tingdong , Tu Jinxing
Published: January 2021

Sclerotinia sclerotiorumcauses substantial damage to the growth ofBrassica napus(rapeseed) and makes a significant loss of crop yield. The plant innate immune system may be the primary solution to defense againstS. sclerotiorumfor rapeseed. Here, we identify that BnWRKY33, a transcription factor in the innate immune pathway, can be rapidly phosphorylated and activated by the MAPK cascade after rapeseed is infected withS. sclerotiorum. In the MAPK cascade, activated BnaA03.MKK4 phosphorylates and activates BnaA06.MPK3 and BnaC03.MPK3. The activated BnMPK3 acts on the substrate BnWRKY33 to enhance its transcriptional activity and trigger a transcriptional burst ofBnWRKY33, which helps plants effectively resist the pathogenic fungi by enhancing the expression of phytoalexin synthesis-related genes. With constant infection,BnaA03.WRKY28andBnaA09.VQ12are induced, and BnaA03.WRKY28 physically interacts with BnaA09.VQ12 to form a protein complex. BnaA03.WRKY28 preferentially binds to the promoter ofBnWRKY33with the help of BnaA09.VQ12. Compared with activated BnWRKY33, BnaA03.WRKY28 has a lower transcriptional activity on downstreamBnWRKY33, which leads to weaker resistance againstS. sclerotiorumfor rapeseed in the later stage of infection. Furthermore, the inducedBnaA03.WRKY28may promote axillary bud activity and axillary meristem initiation by regulating the expression of branching-related genes (such asBnBRC1), thus promoting the formation of branches in the leaf axils.

One-sentence summary

Under constant infection bySclerotinia sclerotiorum, BnaA03.WRKY28 interacts with BnaA09.VQ12 and takes precedence over phosphorylated BnWRKY33 to bind to theBnWRKY33promoter, thereby weakening resistance but promoting branching.
Does insect herbivory suppress ecosystem productivity? Evidence from a temperate woodland
Authors: Visakorpi Kristiina , Gripenberg Sofia , Malhi Yadvinder , Riutta Terhi
Published: January 2021

Our current understanding of the relationship between insect herbivory and ecosystem productivity is limited. Previous studies have typically quantified only leaf area loss, or have been conducted during outbreak years. These set-ups often ignore the physiological changes taking place in the remaining plant tissue after insect attack, or may not represent typical, non-outbreak herbivore densities. Here, we estimate the amount of carbon lost to insect herbivory in a temperate deciduous woodland both through leaf area loss and, notably, through changes in leaf gas exchange in non-consumed leaves under non-outbreak densities of insects. We calculate how net primary productivity changes with decreasing and increasing levels of herbivory, and estimate what proportion of the carbon involved in the leaf area loss is transferred further in the food web. We estimate that the net primary productivity of an oak stand under ambient levels of herbivory is 54 - 69% lower than that of a completely intact stand. The effect of herbivory quantified only as leaf area loss (0.1 Mg C ha−1yr−1) is considerably smaller than when the effects of herbivory on leaf physiology are included (8.5 Mg C ha−1yr−1). We propose that the effect of herbivory on primary productivity is non-linear and mainly determined by changes in leaf gas exchange. We call for replicated studies in other systems to validate the relationship between insect herbivory and ecosystem productivity described here.
Exploring the prognostic value of SCARF1 in non-small cell lung cancers
Authors: Patten Daniel A. , Shetty Shishir
Published: January 2021

Scavenger receptor class F member 1 (SCARF1) has previously been shown to be highly expressed within the human liver, hold prognostic value in hepatocellular carcinoma and mediate the specific recruitment of leukocytes to liver sinusoidal endothelial cells; however, to date, the liver remains the only major organ in which SCARF1 has been explored in any detail. Here, we utilised publically-available RNA-sequencing data from The Cancer Genome Atlas (TGCA) to identify the lungs as a site of significantSCARF1expression and attribute the majority of its expression to endothelial cell populations. Next, we show thatSCARF1expression is significantly reduced in two histologically distinct types of non-small cell lung carcinoma cancers (NSCLCs), lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), compared to non-tumoural tissues. Interestingly, loss ofSCARF1expression was associated with aggressive tumour biology in LUAD tissues, but not in LUSC. Furthermore, increasedSCARF1expression was highly prognostic of better overall survival in LUAD tumour tissues, but this was again in contrast to LUSC tumours, in whichSCARF1held no prognostic value. Finally, we showed thatSCARF1is widely expressed in tumour endothelial cells of non-small cell lung cancers and that its total expression in LUAD tumour tissues correlated with immune score and CD4+T cell infiltration. This study represents the first detailed exploration ofSCARF1expression in normal and diseased human lung tissues and further highlights the prognostic value and therapeutic potential of SCARF1 in immunologically active cancers.
ssDNA recombineering boostsin vivoevolution of nanobodies displayed on bacterial surfaces
Authors: Al-ramahi Yamal , Nyerges Akos , Margolles Yago , Cerdán Lidia , Ferenc Gyorgyi , Pál Csaba , Fernández Luis Ángel , de Lorenzo Víctor
Published: January 2021

In vivoevolution of antibodies facilitates emergence of novel target specificities from pre-existing clones. In this work we show how mutagenic ssDNA recombineering of camel-derived nanobodies encoded in a bacterial genome enables clonal hyper-diversification and the rise of new properties. As a proof-of-principle we used a nanobody recognizing the antigen TirM from enterohaemorrhagicE. coli(EHEC) and evolved it towards the otherwise not recognized TirM antigen from enteropathogenicE. coli(EPEC). To this end,E. colicells displaying on their surface this nanobody fused to the intimin outer membrane anchor domain were subjected to multiple rounds of mutagenic ssDNA recombineering targeted to the CDR1, CDR2 and CDR3 regions of its genomically encoded VHHsequence. Binders to the new antigen (EPEC TirM) were then selected upon immunomagnetic capture of bacteria bearing the corresponding nanobody variants. As a result, several modified nanobodies were identified which maintained recognition of EHEC TirM but acquired the ability to bind the new antigen with high affinity (Kd ~20 nM). The results highlight the power of combining evolutionary properties of bacteriain vivowith oligonucleotide synthesisin vitrofor the sake of focusing diversification to specific segments of a gene (or protein thereof) of interest. Our experimental workflow empowers the evolution of nanobodies displayed on the surface of bacterial cells for a large number of potential applications in medical and industrial biotechnology.
Pervasive false brain connectivity from electrophysiological signals
Authors: Pascual-Marqui Roberto D. , Achermann Peter , Faber Pascal , Kinoshita Toshihiko , Kochi Kieko , Nishida Keiichiro , Yoshimura Masafumi
Published: January 2021

1.

Signals of brain electric neuronal activity, either invasively measured or non-invasively estimated, are commonly used for connectivity inference. One popular methodology assumes that the neural dynamics follow a multivariate autoregression, where the autoregressive coefficients represent the couplings among regions. If observation noise is present and ignored, as is common in practice, the estimated couplings are biased, affecting all forms of Granger-causality inference, both in time and in frequency domains. Significant nonsense coupling, i.e., nonsense connectivity, can appear when in reality there is none, since there is always observation noise in two possible forms: measurement noise, and activity from other brain regions due to volume conduction and low spatial resolution. This problem is critical, and is currently not being addressed, calling into question the validity of many Granger-causality reports in the literature. An estimation method that accounts for noise is based on an overdetermined system of high-order multivariate Yule-Walker equations, which give reduced variance estimators for the coupling coefficients of the unobserved signals. Simulation-based comparisons to other published methods are presented, demonstrating its adequate performance. In addition, simulation results are presented for a zero connectivity case with noisy observations, where the new method correctly reports no connectivity while classical analyses (as found in most software packages) report nonsense connectivity. For the sake of reproducible research, the supplementary material includes, in human readable format, all the time series data used here.
Macaque V1 responses to 2nd-order contrast-modulated stimuli and the possible subcortical and cortical contributions
Authors: Ju Nian-Sheng , Guan Shu-Chen , Tang Shi-Ming , Yu Cong
Published: January 2021

V1 neurons as linear filters supposedly only respond to 1st-order luminance-modulated (LM) stimuli, but not 2nd-order contrast-modulated (CM) ones. To solve this difficulty, filter-rectify-filter models are proposed, in which first-stage filters respond to CM stimulus elements, and the nonlinear-rectified outputs are summed by a second-stage filter for CM stimulus representation. Correspondingly, neurophysiological evidence shows V1/A17 neurons less responsive to CM stimuli than V2/A18 neurons. Here we used two-photon calcium imaging to demonstrate substantial V1 responses to CM gratings with unimodally distributed LM/CM preferences. Moreover, LM responses are suppressed by LM and CM adaptations regardless of orientation, but CM responses are more suppressed by same-orientation LM and CM adaptations than by orthogonal ones. While LM adaptation results agree with the Hubel-Wiesel view of LGN contributions to V1 orientation responses, CM adaptation results, which include both orientation-unspecific and specific components, may suggest similar subcortical contributions plus additional refinement by recurrent intracortical interactions.
Angular and Linear Speed Cells in the Parahippocampal Circuits
Authors: Spalla Davide , Treves Alessandro , Boccara Charlotte N.
Published: January 2021

An essential role of the hippocampal region is to integrate information to compute and update representations. How this transpires is highly debated. Many theories hinge on the integration of self-motion signals and the existence of continuous attractor networks (CAN). CAN models hypothesise that neurons coding for navigational correlates – such as position and direction – receive inputs from cells conjunctively coding for position, direction and self-motion. As yet, such conjunctive coding had not been found in the hippocampal region. Here, we report neurons coding for angular and linear velocity, distributed across the medial entorhinal cortex, the presubiculum and the parasubiculum. These self-motion neurons often conjunctively encoded position and/or direction, yet lacked a structured organisation, calling for the revision of current CAN models. These results offer insights as to how linear/angular speed – derivative in time of position/direction – may allow the updating of spatial representations, possibly uncovering a generalised algorithm to update any representation.
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT
Authors: Sarmashghi Shahab , Balaban Metin , Rachtman Eleonora , Touri Behrouz , Mirarab Siavash , Bafna Vineet
Published: January 2021

The cost of sequencing the genome is dropping at a much faster rate compared to assembling and finishing the genome. The use of lightly sampled genomes (genome-skims) could be transformative for genomic ecology, and results usingk-mers have shown the advantage of this approach in identification and phylogenetic placement of eukaryotic species. Here, we revisit the basic question of estimating genomic parameters such as genome length, coverage, and repeat structure, focusing specifically on estimating thek-mer repeat spectrum. We show using a mix of theoretical and empirical analysis that there are fundamental limitations to estimating thek-mer spectra due to ill-conditioned systems, and that has implications for other genomic parameters. We get around this problem using a novel constrained optimization approach (Spline Linear Programming), where the constraints are learned empirically. On reads simulated at 1X coverage from 66 genomes, our method, REPeat SPECTra Estimation (RESPECT), had<1.5% error in length estimation compared to 34% error previously achieved. In shotgun sequenced read samples with contaminants, RESPECT length estimates had median error 4%, in contrast to other methods that had median error 80%. Together, the results suggest that low-pass genomic sequencing can yield reliable estimates of the length and repeat content of the genome. The RESPECT software will be publicly available athttps://github.com/shahab-sarmashghi/RESPECT.git
SUFI:An automated approach to spectral unmixing of fluorescent multiplex images captured in mouse and postmortem human brain tissues
Authors: Sadashivaiah Vijay , Tippani Madhavi , Page Stephanie C. , Kwon Sang Ho. , Bach Svitlana V. , Bharadwaj Rahul A. , Hyde Thomas M. , Kleinman Joel E. , Jaffe Andrew E. , Maynard Kristen R.
Published: January 2021

Multispectral fluorescence imaging coupled with linear unmixing is a form of image data collection and analysis that uses multiple fluorescent dyes - each measuring a specific biological signal - that are simultaneously measured and subsequently “unmixed” to provide a read-out for each individual signal. This strategy allows for measuring multiple signals in a single data capture session - for example, multiple proteins or RNAs in tissue slices or cultured cells, but can often result in mixed signals and bleed-through problems across dyes. Existing spectral unmixing algorithms are not optimized for challenging biological specimens such as postmortem human brain tissue, and often require manual intervention to extract spectral signatures. We therefore developed an intuitive, automated, and flexible package calledSUFI: spectral unmixing of fluorescent images (https://github.com/LieberInstitute/SUFI). This package unmixes multispectral fluorescence images by automating the extraction of spectral signatures using Vertex Component Analysis, and then performs one of three unmixing algorithms derived from remote sensing. We demonstrate these remote sensing algorithms’ performance on four unique biological datasets and compare the results to unmixing results obtained using ZEN Black software (Zeiss). We lastly integrate our unmixing pipeline into the computational tooldotdotdotthat is used to quantify individual RNA transcripts at single cell resolution in intact tissues and perform differential expression analysis of smFISH data, and thereby provide a one-stop solution for multispectral fluorescence image analysis and quantification. In summary, we provide a robust, automated pipeline to assist biologists with improved spectral unmixing of multispectral fluorescence images.
Coronavirus-associated molecular mimicry through homology to a SARS-CoV-2 peptide could be leading to susceptibility in patients with HLA-A*02:01 and HLA-A*24:02 serotypes
Authors: Adiguzel Yekbun
Published: January 2021

This study aims to predict autoimmunity-related pathological mechanisms that possess risk for individuals with specific human leukocyte antigen (HLA) serotypes and shared by certain coronaviruses including SARS-CoV-2, based on homology to a SARS-CoV-2 peptide. With the given aim, 1-) coronavirus-associated sequences, which are homologous to the 15mer SARS-CoV-2 peptide CFLGYFCTCYFGLFC, are obtained. 2-) Human peptides that have at least 7 residue matches with those coronavirus sequences, and the SARS-CoV-2 15mer, are found. 3-) Epitope pairs, which are sourced by those aligned coronavirus and human sequences are identified. 4-) Epitope pairs that are predicted to bind strongly not only to the same HLA allele with each other but also to the same HLA allele as those of the respective alignment of the SARS-CoV-2 peptide are selected. Following are the identified proteins or peptides (with HLA-A*02:01 or HLA-A*24:02 epitopes), as described in 1-to-4: Immunoglobulin heavy chain junction regions, CRB1 isoform I precursor, slit homolog 2 protein, hCG1995581, hCG2028737, phospholipid phosphatase-related protein type 2. Among those, CRB1 isoform I precursor sequence with the predicted HLA-A*24:02 epitope aligns with the highest number of different sequences. Results imply autoimmunity risk in COVID-19 patients with HLA-A*02:01 and HLA-A*24:02 serotypes, through molecular mimicry, as a shared pathogenicity risk that can be prevalent upon getting infected with certain coronaviruses. These can pave way to improved risk groups’ assessment and autoimmunity treatment options, for COVID-19 and its associated diseases. Also, the approach in this study can be used to predict prospective pathologies of the transmissible variants in susceptible humans.
Human brain organoid networks
Authors: Sharf Tal , van der Molen Tjitse , Glasauer Stella M.K. , Guzman Elmer , Buccino Alessio P. , Luna Gabriel , Cheng Zhouwei , Audouard Morgane , Ranasinghe Kamalini G. , Kudo Kiwamu , Nagarajan Srikantan S. , Tovar Kenneth R. , Petzold Linda R. , Hierlemann Andreas , Hansma Paul K. , Kosik Kenneth S.
Published: January 2021

Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.