bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility
Authors: Trentini Filippo , Manna Adriana , Balbo Nicoletta , Marziano Valentina , Guzzetta Giorgio , Merler Stefano , Ajelli Marco , Poletti Piero , Melegaro Alessia
Published: November 2021

Background

After a rapid upsurge of COVID-19 cases in Italy during the fall of 2020, the government introduced a three-tiered restriction system aimed at increasing physical distancing. The Ministry of Health, after periodic epidemiological risk assessments, assigned a tier to each of the 21 Italian regions and autonomous provinces (AP). It is still unclear to what extent these different measures altered mixing patterns and how quickly the population adapted their social interactions to continuous changes in restrictions.

Methods and findings

We conducted a survey between July 2020 and March 2021 to monitor changes in social contact patterns among individuals in the metropolitan city of Milan, Italy, which was hardly hit by the second wave of COVID-19 pandemic. The number of contacts during periods characterized by different levels of restrictions was analyzed through negative binomial regression models and age-specific contact matrices were estimated under the different tiers. Relying on the empirically estimated mixing patterns, we quantified relative changes in SARS-CoV-2 transmission potential associated with the different tiers.

As tighter restrictions were implemented during the fall of 2020, a progressive reduction in the mean number of contacts recorded by study participants was observed: from 16.4% under mild restrictions (yellow tier), to 45.6% under strong restrictions (red tier). Higher restrictions levels were also found to increase the relative contribution of contacts occurring within the household. The SARS-CoV-2 reproduction number was estimated to decrease by 18.7% (95%CI: 4.6-30.8), 33.4% (95%CI: 22.7-43.2), and 50.2% (95%CI: 40.9-57.7) under the yellow, orange, and red tiers, respectively.

Conclusions

Our results give an important quantification of the expected contribution of different restriction levels in shaping social contacts and decreasing the transmission potential of SARS-CoV-2. These estimates can find an operational use in anticipating the effect that the implementation of these tiered restriction can have on SARS-CoV-2 reproduction number under an evolving epidemiological situation.
Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 cell differentiation
Authors: Duddu Atchuta Srinivas , Majumdar Sauma Suvra , Sahoo Sarthak , Jhunjhunwala Siddharth , Jolly Mohit Kumar
Published: November 2021

Naïve helper (CD4+) T-cells can differentiate into distinct functional subsets including Th1, Th2, and Th17 phenotypes. Each of these phenotypes has a ‘master regulator’ – T-bet (Th1), GATA3 (Th2) and RORγT (Th17) – that inhibits the other two master regulators. Such mutual repression among them at a transcriptional level can enable multistability, giving rise to six experimentally observed phenotypes – Th1, Th2, Th17, hybrid Th/Th2, hybrid Th2/Th17 and hybrid Th1/Th17. However, the dynamics of switching among these phenotypes, particularly in the case of epigenetic influence, remains unclear. Here, through mathematical modeling, we investigated the coupled transcription-epigenetic dynamics in a three-node mutually repressing network to elucidate how epigenetic changes mediated by any ‘master regulator’ can influence the transition rates among different cellular phenotypes. We show that the degree of plasticity exhibited by one phenotype depends on relative strength and duration of mutual epigenetic repression mediated among the master regulators in a three-node network. Further, our model predictions can offer putative mechanisms underlying relatively higher plasticity of Th17 phenotype as observedin vitroandin vivo. Together, our modeling framework characterizes phenotypic plasticity and heterogeneity as an outcome of emergent dynamics of a three-node regulatory network, such as the one mediated by T-bet/GATA3/RORγT.
CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7
Authors: Tan Yong Zi , Abbas Yazan M. , Wu Jing Ze , Wu Di , Hesketh Geoffrey G. , Bueler Stephanie A. , Gingras Anne-Claude , Robinson Carol V. , Grinstein Sergio , Rubinstein John L.
Published: November 2021

V-ATPases are rotary proton pumps that serve as signaling hubs with numerous proposed binding partners in cells. We used cryoEM combined with exhaustive focused classification to detect endogenous proteins that associate with V-ATPase from porcine kidney. A super-stoichiometric copy of subunit C was found in ~3% of complexes, while an additional ~1.6% of complexes bound mEAK-7, a protein with proposed roles in dauer formation in nematodes and mTOR signaling in mammals. High-resolution cryoEM of porcine kidney V-ATPase with recombinant mEAK-7 shows that mEAK-7’s TLDc domain interacts with V-ATPase’s stator while its C-terminal α helix binds V-ATPase’s rotor. This crosslink would be expected to inhibit rotary catalysis. However, unlike inhibition of yeast V-ATPase by the TLDc protein Oxr1p, exogenous mEAK-7 does not inhibit V-ATPase and mEAK-7 overexpression in cells does not alter lysosomal or phagosomal pH. Instead, cryoEM suggests that interaction of mEAK-7 with V-ATPase is disrupted by ATP-induced rotation of the rotor. Comparison of Oxr1p and mEAK-7 binding explains this difference. Together, these results show that differences in V-ATPase binding by TLDc domain-containing proteins can lead to effects ranging from strong inhibition to formation of labile interactions that are sensitive to the enzyme’s activity.
Missing interactions: the current state of multispecies connectivity analysis
Authors: Wood Sylvia L.R. , Martins Kyle T. , Dumais-Lalonde Véronique , Tanguy Olivier , Maure Fanny , Denis Annick St. , Rayfield Bronwyn , Martin Amanda E. , Gonzalez Andrew
Published: November 2021

Designing effective habitat and protected area networks, which sustain species-rich communities is a critical conservation challenge. Recent decades have witnessed the emergence of new computational methods for analyzing and prioritizing the connectivity needs of multiple species. We argue that the goal of multispecies connectivity prioritizations be the long-term persistence of a set of species in a landscape and suggest the index of metapopulation capacity as one metric by which to assess and compare the effectiveness of proposed network designs. Here we present a review of the literature based on 77 papers published between 2010 and 2020, in which we assess the current state and recent advances in multispecies connectivity analysis in terrestrial ecosystems. We summarize the four most employed analytical methods, compare their data requirements, and provide an overview of studies comparing results from multiple methods. We explicitly look at approaches for integrating multiple species considerations into reserve design and identify novel approaches being developed to overcome computational and theoretical challenges posed by multispecies connectivity analyses. We conclude that, while advances have been made over the past decade, the field remains nascent in its ability to integrate multiple species interactions into analytical approaches to connectivity. Furthermore, the field is hampered in its ability to provide robust connectivity assessments for lack of a clear definition and goal for multispecies connectivity, as well as a lack of common metrics for their comparison.
An ex vivo culture model of kidney podocyte injury reveals mechanosensitive, synaptopodin-templating, sarcomere-like structures
Authors: Jiang Shumeng , Alisafaei Farid , Yuan Hong , Peng Xiangjun , Huang Yin-Yuan , Miner Jeffrey H. , Genin Guy M. , Suleiman Hani Y.
Published: November 2021

Chronic kidney diseases are widespread and incurable. The biophysical mechanisms underlying them are unclear, in part because material systems for reconstituting the microenvironment of the relevant kidney cells are limited. A critical question is how kidney podocytes (glomerular epithelial cells) regenerate the foot processes of the filtration apparatus following injury. Recently identified sarcomere-like structures (SLSs) with periodically spaced myosin IIA (a contractile protein) and synaptopodin (an actin-associated protein) appear in injured podocytes in vivo. We hypothesized that SLSs template synaptopodin in the initial stages of recovery, and tested this hypothesis by developing an ex vivo culture system that models both kidney physiology and pathophysiology. SLSs were observed in vitro for the first time as podocytes migrated out of harvested kidney glomeruli onto micropatterns of physiologically relevant proteins. SLSs emerged over two days, and cells formed foot process-like extensions from these periodically spaced proteins. SLS distributions and morphology were sensitive to actomyosin inhibitors, substrate stiffness, and extracellular matrix proteins associated with pathology. These results indicate a role for mechanobiological factors in podocyte recovery from injury, and suggest SLSs as a target for therapeutic intervention.
Age-dependent increased sag amplitude in human pyramidal neurons dampens baseline cortical activity
Authors: Guet-McCreight Alexandre , Chameh Homeira Moradi , Mahallati Sara , Wishart Margaret , Tripathy Shreejoy J. , Valiante Taufik A. , Hay Etay
Published: November 2021

Aging involves various neurobiological changes, although their effect on brain function in humans remains poorly understood. The growing availability of human neuronal and circuit data provides opportunities for uncovering age-dependent changes of brain networks and for constraining models to predict consequences on brain activity. Here we found increased sag voltage amplitude in human middle temporal gyrus layer 5 pyramidal neurons from older subjects, and captured this effect in biophysical models of younger and older pyramidal neurons. We used these models to simulate detailed layer 5 microcircuits and found lower baseline firing in older pyramidal neuron microcircuits, with minimal effect on response. We then validated the predicted reduced baseline firing using extracellular multi-electrode recordings from human brain slices of different ages. Our results thus report changes in human pyramidal neuron input integration properties and provide fundamental insights on the neuronal mechanisms of altered cortical excitability and resting state activity in human aging.
Tubular obstruction induced polycystin upregulation is pro-fibrotic and induced a severe cystic phenotype in adult mice with autosomal dominant polycystic kidney disease: the coexistence of polycystin loss and gain function in ADPKD
Authors: Wu Ming , Wang Yanzhe , Jing Ying , Chen Dongping , Xing Yufeng , Bai Yanfang , Huang Di , Zhou Yijing , Hu Jinghua , Zhuang Shougang , Ye Chaoyang
Published: November 2021

Mutations inPKD1(encoding polycystin-1) orPKD2(encoding polycystin-2) gene cause autosomal dominant polycystic kidney disease (ADPKD), however high levels of polycystins are detected in renal tissues of ADPKD patients. Animal studies showed that loss and gain of function of polycystins are both pathogenic and can induce cystic phenotype in the kidney, which are associated with enhanced renal fibrosis. Recent studies showed that increased expression of polycystins contributes to organ fibrosis. However, the role of polycystins in renal tubulointerstitial fibrosis remains unclear. In this study, we demonstrated that polycystin-1 or polycystin-2 was highly expressed in the kidney of two different fibrotic mouse models and positively correlated with expression of collagen-I. Pharmaceutical inhibition of polycystin-2 with triptolide or genetic knockout of polycystin-2 reduced the expression of epithelial-mesenchymal transition (EMT) markers and deposition of extracellular matrix proteins in fibrotic kidneys. Similarly, conditional knockout ofPkd1gene also attenuated renal fibrosis in mouse models. Thus, we further hypothesized that inhibition of polycystins delays cyst growth by mitigating renal fibrosis. Here, we showed that polycystin-1 or polycystin-2 was up-regulated inPkd2orPkd1mice respectively and tightly correlated with the growth of renal cysts and fibrosis development. Genetic deletion of both polycystin-1 and polycystin-2 retarded cyst growth inPkd1orPkd2mice. Finally, we deleted pkd1 gene in a fibrosis triggered adult ADPKD mouse model at different time point before or after the fibrotic injury. We showed that early and long-term inactivation ofPkd1delayed fibrosis triggered renal cyst growth in adultPkd1mice as compared with mice with late and short-term inactivation ofPkd1gene. We conclude that tubular obstruction induced polycystin up-regulation is pro-fibrotic and accelerates cyst growth through enhancing renal interstitial fibrosis in ADPKD mice. Our study indicates that ADPKD is caused by both loss and gain function of polycystins. Reduction of the aberrant upregulation of polycystins in cystic kidneys is a therapeutic option for ADPKD patients.

Research highlights

Polycystin1 and polycystin-2 are up-regulated in fibrotic kidneys

Inhibition or deletion of polycystins inhibits EMT and attenuates renal tubulointerstitial fibrosis

Upregulation of polycystin1 or polycystin-2 is positively correlated with fibrosis progression and renal cyst growth in ADPKD mice

Double knockout of Pkd1 and Pkd2 gene inhibits renal cyst growth in ADPKD mice

Long-term deletion of Pkd1 gene delayed fibrosis triggered renal cyst growth in ADPKD mice
The Biosynthetic Costs of Amino Acids at the Base of the Food Chain Determine Their Use in Higher-order Consumer Genomes
Authors: Ortega Javier Gómez , Tyagi Sonika , Mirth Christen K. , Piper Matthew D. W.
Published: November 2021

Dietary nutrient composition is essential for shaping important fitness traits and behaviours. Many organisms are protein limited and for Drosophila melanogaster, this limitation manifests at the level of the single most limiting essential Amino Acid (AA) in the diet. The identity of this AA and its effects on female fecundity is readily predictable by a procedure called exome matching in which the sum of AAs encoded by a consumer’s exome is used to predict the relative proportion of AAs required in its diet. However, the exome matching calculation does not weight AA contributions to the overall profile by protein size or expression. Here we update the exome matching calculation to include these weightings. Surprisingly, although nearly half of the transcriptome is differentially expressed when comparing male and female flies, we found that creating transcriptome-weighted exome matched diets for each sex did not enhance their fecundity over that supported by exome matching alone. These data indicate that while organisms may require different amounts of dietary protein across conditions, the relative proportion of the constituent AAs remains constant. Interestingly, we also found remarkable conservation of exome matched AA profiles across taxa and that the composition of these profiles could be explained by the metabolic costs of microbial AA synthesis. Thus, it appears that bioenergetic constraints amongst autotrophs shape the relative proportion of AAs that are available across trophic levels and that that this constrains biomass composition.
Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry
Authors: Hardigan Michael A. , Feldmann Mitchell J. , Pincot Dominique D.A. , Famula Randi A. , Vachev Michaela V. , Madera Mary A. , Zerbe Philipp , Mars Kristin , Peluso Paul , Rank David , Ou Shujun , Saski Christopher A. , Acharya Charlotte B. , Cole Glenn S. , Yocca Alan E. , Platts Adrian E. , Edger Patrick P. , Knapp Steven J.
Published: November 2021

The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its wild progenitors are outbred octoploids (2n = 8x = 56) in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the day-neutral octoploidF. × ananassahybrid ‘Royal Royce’ from the University of California. Our goal was to produce subgenome-and haplotype-resolved assemblies of all 56 chromosomes, accurately reconstructing the parental haploid chromosome complements. Previous work has demonstrated that partitioning sequences by parental phase supports direct assembly of haplotypes in heterozygous diploid species. We leveraged the accuracy of HiFi sequence data with pedigree-informed sequencing to partition long read sequences by phase, and reduce the downstream risk of subgenomic chimeras during assembly. We were able to utilize an octoploid strawberry recombination breakpoint map containing 3.6 M variants to identify and break chimeric junctions, and perform scaffolding of the phase-1 and phase-2 octoploid assemblies. The N50 contiguity of the phase-1 and phase-2 assemblies prior to scaffolding and gap-filling was 11 Mb. The final haploid assembly represented seven of 28 chromosomes in a single contiguous sequence, and averaged fewer than three gaps per pseudomolecule. Additionally, we re-annotated the octoploid genome to produce a customF. × ananassarepeat library and improved set of gene models based on IsoSeq transcript data and an expansive RNA-seq expression atlas. Here we present ‘FaRR1’, a gold-standard reference genome ofF. × ananassacultivar ‘Royal Royce’ to assist future genomic research and molecular breeding of allo-octoploid strawberry.
Controlled and Selective Photo-oxidation of Amyloid-β Fibrils by Oligomericp-Phenylene Ethynylenes
Authors: Fanni Adeline M. , Okoye Daniel , Monge Florencia A. , Hammond Julia , Maghsoodi Fahimeh , Martin Tye D. , Brinkley Gabriella , Phipps M. Lisa , Evans Deborah G. , Martinez Jennifer S. , Whitten David G. , Chi Eva Y.
Published: November 2021

Photodynamic therapy (PDT) has been explored as a therapeutic strategy to clear toxic amyloid aggregates involved in neurodegenerative disorders such as Alzheimer’s disease. A major limitation of PDT is off-target oxidation, which can be lethal for the surrounding cells. We have shown that a novel class of oligo-p-phenylene ethynylene-based compounds (OPEs) exhibit selective binding and fluorescence turn-on in the presence of pre-fibrillar and fibrillar aggregates of disease-relevant proteins such as amyloid-β (Aβ) and α-synuclein. Concomitant with fluorescence turn-on, OPE also photosensitizes singlet oxygen under illumination through the generation of a triplet state, pointing to the potential application of OPEs as photosensitizers in PDT. Herein, we investigated the photosensitizing activity of an anionic OPE for the photo-oxidation of toxic Aβ aggregates and compared its efficacy to the well-known but non-selective photosensitizer methylene blue (MB). Our results show that while MB photo-oxidized both monomeric and fibrillar conformers of Aβ40, OPE oxidized only Aβ40 fibrils, targeting two histidine residues on the fibril surface and a methionine residue located in the fibril core. Oxidized fibrils were shorter and more dispersed, but retained the characteristic β-sheet rich fibrillar structure and the ability to seed further fibril growth. Importantly, the oxidized fibrils displayed low toxicity. We have thus discovered a class of novel theranostics for the simultaneous detection and oxidization of amyloid aggregates. Importantly, the selectivity of OPE’s photosensitizing activity overcomes the limitation of off-target oxidation of currently available photosensitizers, and represents a significant advancement of PDT as a viable strategy to treat neurodegenerative disorders.
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing
Authors: Marini Simone , Mora Rodrigo A. , Boucher Christina , Noyes Noelle , Prosperi Mattia
Published: November 2021

Antimicrobial resistance (AMR) is a growing threat to public health and farming at large. In clinical and veterinary practice, timely characterization of the antibiotic susceptibility profile of bacterial infections is a crucial step in optimizing treatment. High-throughput sequencing is a promising option for clinical point-of-care and ecological surveillance, opening the opportunity to develop genotyping-based AMR determination as a possibly faster alternative to phenotypic testing. In the present work, we compare the performance of state-of-the-art methods for detection of AMR using high-throughput sequencing data from clinical settings. We consider five computational approaches based on alignment (AMRPlusPlus), deep learning (DeepARG), k-mer genomic signatures (KARGA, ResFinder) or hidden Markov models (Meta-MARC). We use an extensive collection of 585 isolates with available AMR resistance profiles determined by phenotypic tests across nine antibiotic classes. We show how the prediction landscape of AMR classifiers is highly heterogeneous, with balanced accuracy varying from 0.40 to 0.92. Although some algorithms—ResFinder, KARGA, and AMRPlusPlus– exhibit overall better balanced accuracy than others, the high per-AMR-class variance and related findings suggest that: (1) all algorithms might be subject to sampling bias present both in data repositories used for training and experimental/clinical settings; and (2) a portion of clinical samples might contain uncharacterized AMR genes that the algorithms—mostly trained on known AMR genes—fail to generalize upon. These results lead us to formulate practical advice for software configuration and application, and give suggestions for future study designs to further develop AMR prediction tools from proof-of-concept to bedside.
Synergy of color and motion vision for detecting approaching objects inDrosophila
Authors: Longden Kit D. , Rogers Edward M. , Nern Aljoscha , Dionne Heather , Reiser Michael B.
Published: November 2021

Color and motion are used by many species to identify salient moving objects. They are processed largely independently, but color contributes to motion processing in humans, for example, enabling moving colored objects to be detected when their luminance matches the background. Here, we demonstrate an unexpected, additional contribution of color to motion vision inDrosophila. We show that behavioral ON-motion responses are more sensitive to UV than for OFF-motion, and we identify cellular pathways connecting UV-sensitive R7 photoreceptors to ON and OFF-motion-sensitive T4 and T5 cells, using neurogenetics and calcium imaging. Remarkably, the synergy of color and motion vision enhances the detection of approaching UV discs, but not green discs with the same chromatic contrast, and we show how this generalizes for visual systems with ON and OFF pathways. Our results provide a computational and circuit basis for how color enhances motion vision to favor the detection of saliently colored objects.
Chigno/CG11180 and SUMO are Chinmo-Interacting Proteins with a Role in Drosophila Testes Stem Cells
Authors: Rinehart Leanna , Stewart Wendy E. , Luffman Natalie , Wawersik Matthew , Kerscher Oliver
Published: November 2021

Maintenance of sexual identity on the cellular level ensures the proper function of sexually dimorphic genes expressed in the brain and gonads. Disruption of genes that regulate sex maintenance alters the cellular structure of these tissues and leads to infertility and diseases, such as diabetes, obesity, and gonadal cancers. Sex maintenance in the testis of Drosophila melanogaster depends on the previously identified gene chinmo (Chronologically inappropriate morphogenesis). Chinmo’s effect on testis differentiation has been investigated in detail, but there is still much to be elucidated about its structure, function, and interactions with other proteins. Using a two-hybrid screen, we find that Chinmo interacts with itself, the small ubiquitin-like modifier SUMO, the novel protein CG11180, and four other proteins (CG4318, Ova (Ovaries absent), Taf3 (TBP-associated factor 3), and CG18269). Since both Chinmo and CG11180 contain sumoylation sites and SUMO-interacting motifs (SIMs), we analyzed their interaction in more detail. Using site-directed mutagenesis of a unique SIM in CG11180, we demonstrate that Chinmo’s interaction with CG11180 is SUMOdependent. Furthermore, to assess the functional relevance of both SUMO and CG11180, we performed RNAi-mediated knockdown of both proteins in somatic cells of the Drosophila testis. Using this approach, we find that CG11180 and SUMO are required in somatic cells of adult testes, and that reduction of either protein causes formation of germ cell tumors. Overall, our work indicates that SUMO functionally links Chinmo and CG11180 in somatic cells of the adult Drosophila testis. Consistent with the CG11180 knockdown phenotype in male testes, and to underscore its connection to Chinmo, we propose the name Childless Gambino (Chigno) for CG11180.
Sulcal depth in prefrontal cortex: A novel predictor of working memory performance
Authors: Yao Jewelia K. , Voorhies Willa I. , Miller Jacob A. , Bunge Silvia A. , Weiner Kevin S.
Published: November 2021

The neuroanatomical changes that underpin cognitive development is of major interest in neuroscience. Of the many aspects of neuroanatomy to consider, tertiary sulci are particularly appealing as they emerge last in gestation, show a protracted development after birth, and are either human- or hominoid-specific. Thus, they are ideal targets for exploring morphological-cognitive relationships with cognitive skills, such as verbal working memory (WM), that also show protracted development. Yet, the relationship between sulcal morphology and verbal WM is unknown, either in development or more generally. To fill this gap, we adopted a data-driven approach with cross-validation to examine the relationship between sulcal depth in lateral prefrontal cortex (LPFC) and verbal WM in 60 participants ages 6-18. These analyses identified nine left, but not right, LPFC sulci (of which six were tertiary) whose depth predicted verbal WM performance. Most of these sulci are located within and around contours of functionally defined parcellations of LPFC proposed previously. This sulcal depth model out-performed models with age or cortical thickness. Taken together, these findings contribute to building empirical support for a classic theory that tertiary sulci serve as landmarks in association cortices that contribute to aspects of human behavior that show a protracted development.
MTG16 (CBFA2T3) regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors
Authors: Brown Rachel E. , Jacobse Justin , Anant Shruti A. , Blunt Koral M. , Chen Bob , Vega Paige N. , Jones Chase T. , Pilat Jennifer M. , Revetta Frank , Gorby Aidan H. , Stengel Kristy R. , Choksi Yash A. , Palin Kimmo , Piazuelo M. Blanca , Washington M. Kay , Lau Ken S. , Goettel Jeremy A. , Hiebert Scott W. , Short Sarah P. , Williams Christopher S.
Published: November 2021

Aberrant epithelial differentiation and regeneration contribute to colon pathologies including inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). MTG16 (CBFA2T3) is a transcriptional corepressor expressed in the colonic epithelium. MTG16 deficiency in mice exacerbates colitis and increases tumor burden in CAC, though the underlying mechanisms remain unclear. Here, we identified MTG16 as a central mediator of epithelial differentiation, promoting goblet and restraining enteroendocrine cell development in homeostasis and enabling regeneration following dextran sulfate sodium (DSS)-induced colitis. Transcriptomic analyses implicated increased E box-binding transcription factor (E protein) activity in MTG16-deficient colon crypts. Using a novel mouse model with a point mutation that disrupts MTG16:E protein complex formation (Mtg16P209T), we established that MTG16 exerts control over colonic epithelial differentiation and regeneration by repressing E protein-mediated transcription. Mimicking murine colitis,MTG16expression was increased in biopsies from patients with active IBD compared to unaffected controls. Finally, uncoupling MTG16:E protein interactions only partially phenocopied the enhanced tumorigenicity ofMtg16-/-colon in the azoxymethane(AOM)/DSS-induced model of CAC, indicating that MTG16 protects from tumorigenesis through additional mechanisms. Collectively, our results demonstrate that MTG16, via its repression of E protein targets, is a key regulator of cell fate decisions during colon homeostasis, colitis, and cancer.

Graphical Abstract
Identification of key interactions of benzimidazole resistance-associated amino acid mutations inAscarisβ-tubulins by molecular docking simulations
Authors: Jones Ben P. , van Vliet Arnoud H.M. , LaCourse E. James , Betson Martha
Published: November 2021

Ascarisspecies are soil-transmitted helminths that infect humans and livestock mainly in low and middle-income countries. Benzimidazole (BZ) class drugs have predominated for many years in the treatment ofAscarisinfections, but persistent use of BZs has already led to widespread resistance in other nematodes, and treatment failure is emerging forAscaris. Benzimidazoles act by binding to β-tubulin proteins and destabilising microtubules. Three mutations in the β-tubulin protein family are associated with BZ resistance. Seven shared β-tubulin isotypes were identified inAscaris lumbricoidesandA. suumgenomes. Benzimidazoles were predicted to bind to all β-tubulin isotypes usingin silicodocking, demonstrating that the selectivity of BZs to interact with one or two β-tubulin isotypes is likely the result of isotype expression levels affecting the frequency of interaction.Ascarisβ-tubulin isotype A clusters with helminth β-tubulins previously shown to interact with BZ. Molecular dynamics simulations using β-tubulin isotype A highlighted the key role of amino acid E198 in BZ-β-tubulin interactions. Simulations indicated that mutations at amino acids E198A and F200Y alter binding of BZ, whereas there was no obvious effect of the F167Y mutation. In conclusion, the key interactions vital for BZ binding with β-tubulins have been identified and show how mutations can lead to resistance in nematodes.
Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct and long-read sequencing
Authors: Tavakoli Sepideh , Nabizadehmashhadtoroghi Mohammad , Makhamreh Amr , Gamper Howard , McCormick Caroline A. , Rezapour Neda K. , Hou Ya-Ming , Wanunu Meni , Rouhanifard Sara H.
Published: November 2021

We developed and applied a semi-quantitative method for high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of coverage and specific k-mer sequences are critical parameters for accurate basecalling. By adjusting these parameters for high-confidence U-to-C basecalling errors, we identified many known sites of pseudouridylation and uncovered new uridine-modified sites, many of which fall in k-mers that are known targets of pseudouridine synthases. Identified sites were validated using 1,000-mer synthetic RNA controls bearing a single pseudouridine in the center position which demonstrate systematical under-calling using our approach. We identify mRNAs with up to 7 unique modification sites. Our pipeline allows direct detection of low-, medium-, and high-occupancy pseudouridine modifications on native RNA molecules from nanopore sequencing data as well as multiple modifications on the same strand.
Kin17 drives dissociation of Mira from the centrosome in neuroblasts by regulating splicing of Flfl
Authors: Connell Marisa , Xie Yonggong , Chen Rui , Zhu Sijun
Published: November 2021

During asymmetric division of Drosophila neuroblasts, the fate determinant Prospero and its adaptor Miranda are segregated to the basal cortex through aPKC phosphorylation of Miranda and displacement from the apical cortex. Here we identify Kin17 as a novel regulator of Miranda localization during asymmetric cell division and loss of Kin17 or Protein Phosphatase 4 leads to aberrant localization of Miranda to the centrosome and cytoplasm and Prospero to the centrosome and nucleus. We report that dephosphorylation of Mira by Protein Phosphatase 4 at Serine-96 at the centrosome is required for the proper basal localization of Mira after being phosphorylated at the apical cortex. We further demonstrate that Kin17 regulates Miranda localization by promoting splicing of the transcript of a PP4 component Falafel. Taken together, our work reveals a novel mechanism that ensures proper basal localization of Miranda by preventing its aberrant localization to the centrosome during the asymmetric division.

Connell et al. show that proper segregation of cell fate determinant Miranda requires PP4-mediated dissociation of Miranda from the centrosome/spindle in Drosophila neuroblasts, a critical step that has been overlooked previously. Further, they identify a novel regulator of Miranda localization, Kin17, which promotes splicing of the transcript of the PP4 component Falafel.
Prediction of Kv11.1 potassium channel PAS-domain variants trafficking via machine learning
Authors: Immadisetty Kalyan , Fang Xuan , Hartle Cassandra M. , McCoy Thomas P. ,   Regeneron Genetics Center, Mirshahi Tooraj , Delisle Brian P. , Kekenes-Huskey Peter M.
Published: November 2021

1

Congenital long QT syndrome (LQTS) is characterized by a prolonged QT-interval on an electrocardiogram (ECG). An abnormal prolongation in the QT-interval increases the risk for fatal arrhythmias despite otherwise normal metrics of cardiac function. Genetic variants in several different cardiac ion channel genes, includingKCNH2, are known to cause LQTS. The population frequency of rare non-synonymous (missense) variants in LQTS-linked genes far outpaces the true incidence of the disease. Therefore, only a small percentage of missense variants identified in LQTS-linked genes are expected to associate with LQTS. Because of a lack of clear association between variants identified in LQTS-linked alleles and diseases, most variants are classified as variants of uncertain physiological significance (VUS). Here, we evaluated whether structure-based molecular dynamics (MD) simulations and machine learning (ML) can improve the identification of missense variants in LQTS-linked genes that associate with LQTS. To do this, we focused on investigatingKCNH2missense variants in the Kv11.1 channel protein shown to have wild type (WT) like or loss-of-function (LOF) phenotypesin vitro. We focused onKCNH2missense variants that disrupt normal Kv11.1 channel protein trafficking, as it is the most common LOF phenotype for LQTS-associated variants. Specifically, we used these computational techniques to correlate structural and dynamic changes in the Kv11.1 channel protein PAS domain (PASD) with Kv11.1 channel protein trafficking phenotypes. These simulations unveiled several molecular features, including the numbers of hydrating waters and H-Bonds, as well as FoldX scores, that are predictive of trafficking. We then used statistical and ML (Decision tree (DT), Random forest (RF), and Support vector machine (SVM)) techniques to classify variants using these simulation-derived features. Together with bioinformatics data, such as sequence conservation and folding energies, we were able to predict with reasonable accuracy (≈75%) whichKCNH2variants do not traffic normally. We conclude, structure-based simulations ofKCNH2variants localized to the Kv11.1 channel PASD led to a significant improvement (≈10%) in classification accuracy and this approach should therefore be considered to complement the classification of VUS in the Kv11.1 channel PASD.
SYMBIOSIS: Synthetic Manipulable Biobricks via Orthogonal Serine Integrase Systems
Authors: Ba Fang , Liu Yushi , Liu Wan-Qiu , Tian Xintong , Li Jian
Published: November 2021

Serine integrases are emerging as one of the most powerful biological tools for synthetic biology. They have been widely used across genome engineering and genetic circuit design. However, developing serine integrase-based tools for directly/precisely manipulating synthetic biobricks is still missing. Here, we report SYMBIOSIS, a versatile method that can robustly manipulate DNA parts in vivo and in vitro. First, we proposed a “Keys match Locks” model to demonstrate that three orthogonal serine integrases are able to irreversibly and stably switch on seven synthetic biobricks with high accuracy in vivo. Then, we demonstrated that purified integrases can facilitate the assembly of “Donor” and “Acceptor” plasmids in vitro to construct composite plasmids. Finally, we used SYMBIOSIS to assemble different chromoprotein genes and create novel colored Escherichia coli. We anticipate that our SYMBIOSIS strategy will accelerate synthetic biobricks manipulation, genetic circuit design, and multiple plasmids assembly for synthetic biology with broad potential applications.
Amelioration of DSS-induced Acute Colitis in Mice by Recombinant Monomeric Human Interleukin-22
Authors: Kim Suhyun , Hong Eun-Hye , Lee Cheol-Ki , Ryu Yiseul , Jeong Hyunjin , Heo Seungnyeong , Lee Joong-jae , Ko Hyun-Jeong
Published: November 2021

Interleukin-22 (IL-22), a pleiotropic cytokine, is known to have a profound effect on the regeneration of damaged intestinal barriers. The tissue-protective properties of IL-22 are expected to be potentially exploited in the attenuation and treatment of colitis. However, because of the disease-promoting role of IL-22 in chronic inflammation, a comprehensive evaluation is required to translate IL-22 into the clinical domain. Here, we present the effective production of soluble human IL-22 in bacteria to prove whether recombinant IL-22 has the ability to ameliorate colitis and inflammation. IL-22 was expressed in the form of a biologically active monomer and a non-functional dimer. Monomeric IL-22 (mIL-22) was highly purified through a series of three separate chromatographic methods and an enzymatic reaction. We reveal that the resulting mIL-22 is correctly folded and is able to phosphorylate signal transducer and activator of transcription 3 in HT-29 cells. Subsequently, we demonstrate that mIL-22 enables the attenuation of dextran sodium sulfate-induced acute colitis in mice, as well as the suppression of pro-inflammatory cytokine production. Collectively, our results suggest that the recombinant mIL-22 is suitable to study the biological roles of endogenous IL-22 in immune responses and can be developed as a biological agent associated with inflammatory disorders.
Disease-linked mutations trigger exposure of a protein quality control degron in the DHFR protein
Authors: Kampmeyer Caroline , Larsen-Ledet Sven , Wagnkilde Morten Rose , Michelsen Mathias , Iversen Henriette K. M. , Nielsen Sofie V. , Lindemose Søren , Caregnato Alberto , Ravid Tommer , Stein Amelie , Teilum Kaare , Lindorff-Larsen Kresten , Hartmann-Petersen Rasmus
Published: November 2021

Degrons are short stretches of amino acids or structural motifs that are embedded in proteins. They mediate recognition by E3 ubiquitin-protein ligases and thus confer protein degradation via the ubiquitin-proteasome system. Well-described degrons include the N-degrons, destruction boxes, and the PIP degrons, which mediate the controlled degradation of various proteins including signaling components and cell cycle regulators. In comparison, the so-called protein quality control (PQC) degrons that mediate the degradation of structurally destabilized or misfolded proteins are not well described. Here, we show that disease-linked DHFR missense variants are structurally destabilized and chaperone-dependent proteasome targets. We systematically mapped regions within DHFR to assess those that act as cytosolic PQC degrons in yeast cells. Two regions, DHFR-Deg13-36 (here Deg1) and DHFR-Deg61-84 (here Deg2), act as degrons and conferred degradation to unrelated fusion partners. The proteasomal turnover of Deg2 was dependent on the molecular chaperone Hsp70. Structural analyses by NMR and hydrogen/deuterium exchange revealed that Deg2 is buried in wild-type DHFR, but becomes transiently exposed in the disease-linked missense variants.
Regulation of invasion-associated actin dynamics by the Chlamydia trachomatis effectors TarP and TmeA
Authors: Romero Matthew D. , Carabeo Rey A.
Published: November 2021

The obligate intracellular pathogen Chlamydia trachomatis manipulates the host actin cytoskeleton to assemble actin-rich structures that drive pathogen entry. The recent discovery of TmeA, which like TarP is an invasion-associated type III effector implicated in actin remodeling, raised questions regarding the nature of their functional interaction. Quantitative live-cell imaging of actin remodeling at invasion sites revealed differences in recruitment and turnover kinetics associated with TarP and TmeA pathways, with the former accounting for most of the robust actin dynamics at invasion sites. TarP-mediated recruitment of the actin nucleators formin and the Arp2/3 complex were crucial for rapid actin kinetics, generating a collaborative positive feedback loop that enhanced their respective actin-nucleating activities within invasion sites. In contrast, Fmn1 is neither recruited to invasion sites nor collaborates with Arp2/3 within the context of TmeA-associated actin recruitment. While the TarP-Fmn1-Arp2/3 signaling axis is responsible for the majority of actin dynamics, its inhibition had similar effects as deletion of TmeA on invasion efficiency, consistent with the proposed model that TarP and TmeA acting on different stages of the same invasion pathway.

Summary Statement

Kinetic analysis of actin recruitment during C. trachomatis invasion reveals TarP as the major contributor relative to TmeA, via its ability to facilitate collaboration between actin nucleators Formin 1 and Arp2/3.
The Conformational Plasticity of the Selectivity Filter Methionines Controls the In-Cell Cu(I) Uptake through the CTR1 transporter
Authors: Janoš Pavel , Aupič Jana , Ruthstein Sharon , Magistrato Alessandra
Published: November 2021

Copper is a trace element vital to many cellular functions. Yet its abnormal levels are toxic to cells, provoking a variety of severe diseases. The high affinity Copper Transporter 1 (CTR1), being the main in-cell copper (Cu(I)) entry route, tightly regulates its cellular uptake via a still elusive mechanism. Here, all-atoms simulations unlock the molecular terms of Cu(I) transport in eukaryotes disclosing that the two Methionine triads, forming the selectivity filter, play an unprecedented dual role both enabling selective Cu(I) transport and regulating its uptake-rate thanks to an intimate coupling between the conformational plasticity of their bulky side chains and the number of bound Cu(I) ions. Namely, the Met residues act as a gate reducing the Cu(I) import-rate when two ions simultaneously bind to CTR1. This may represent an elegant autoregulatory mechanism through which CTR1 protects the cells from excessively high, and hence toxic, in-cell Cu(I) levels. Overall, these outcomes resolve fundamental questions in CTR1 biology and open new windows of opportunity to tackle diseases associated with an imbalanced copper uptake.

Abstract Figure
Genome sequencing identifies three molecular diagnoses including a mosaic variant in the COL2A1 gene in an individual with Pol III–related leukodystrophy and Feingold syndrome
Authors: Muirhead Kayla J. , Clause Amanda R. , Schlachetzki Zinayida , Dubbs Holly , Perry Denise L. , Hagelstrom R. Tanner , Taft Ryan J. , Vanderver Adeline
Published: November 2021

Undiagnosed genetic disease imposes a significant burden on families and health-care resources, especially in cases with a complex phenotype. Here we present a child with suspected leukodystrophy in the context of additional features, including hearing loss, clinodactyly, rotated thumbs, tapered fingers, and simplified palmar crease. Trio genome sequencing (GS) identified three molecular diagnoses in this individual: compound heterozygous missense variants associated with polymerase III (Pol III)–related leukodystrophy, a 4-Mb de novo copy-number loss including the MYCN gene associated with Feingold syndrome, and a mosaic single-nucleotide variant associated with COL2A1-related disorders. These variants fully account for the individual's features, but also illustrate the potential for superimposed and unclear contributions of multiple diagnoses to an individual's overall presentation. This report demonstrates the advantage of GS in detection of multiple variant types, including low-level mosaic variants, and emphasizes the need for comprehensive genetic analysis and detailed clinical phenotyping to provide individuals and their families with the maximum benefit for clinical care and genetic counseling.
On the importance of accounting for alternative foraging tactics when assessing cognitive performance in wild animals
Authors: Vernouillet Alizée
Published: November 2021

Research Highlight: Reichert, S., Morand‐Ferron, J., Kulahci, I. G., Firth, J. A., Davidson, G. L., Crofts, S. J., & Quinn, J. L. (2021) Cognition and covariance in the producer–scrounger game. Journal of Animal Ecology, https://doi.org/10.1111/1365‐2656.13551. When foraging in groups, individuals can either acquire their own resources, as producers, or profit from the work of other individuals, as scroungers. Individuals vary in how much they rely on one foraging tactic over the other. Yet, each of these foraging tactics presents unique cognitive challenges. Using a field experiment with a mixed‐species flock of birds, Reichert et al. (2021) investigated how production learning (i.e. successfully feeding from their assigned rewarded feeder) and scrounging propensity (i.e. collecting food from a non‐assigned feeders by following another individual) are related at an individual level, as well as the repeatability of both production learning and scrounging propensity. The authors show that overall, (a) individuals learned to scrounge, (b) individuals who rely more on scrounging took longer to learn their assigned feeder and (c) variation in each cognitive trait was mostly explained by individual behavioural flexibility rather than by consistent differences between individuals. Since learning was negatively correlated with the use of an alternative foraging tactic (i.e. scrounging), results of this study also suggest that individual choice of foraging tactics should be considered when evaluating cognitive abilities in wild animals.
The impact of blowflies on pig cadaver decomposition on Yeongdo Island, Busan, South Korea
Authors: Park Sang‐Hyun , Baek Seung‐Ho , Moon Tae‐Young
Published: November 2021

The decomposition process is an important factor in forensics, and flies play a crucial role in the decomposition of animals and humans. However, there remains limited information on the effect of flies that attend death scenes. This study assesses the effect of the presence or absence of blowflies on the rate and process of cadaver decomposition in the spring, summer, and autumn from 2016 to 2020 on Yeongdo Island, Busan, South Korea. Nine blowfly species belonging to four genera in two subfamilies were sampled. The blowflies that approached the cadavers differed between seasons, but Chrysomya pinguis (Walker) was the dominant species regardless of the season. Blowfly presence on cadavers significantly affected the duration of the decomposition stage and the pattern of weight loss in nearly all scenarios. With the presence of blowflies, the decomposition rate was four times faster in spring, three times faster in summer, and nine times faster in autumn. These results show that the presence or absence of blowflies is an essential factor in the decomposition process of cadavers. Therefore, it should be taken into account when estimating postmortem intervals in medicolegal forensic entomology.