bluuebunny/crossref_metadata_2025 huggingface dataset:
Ablation of palladin in adult heart causes dilated cardiomyopathy associated with intercalated disc abnormalities
Authors: Mastrototaro Giuseppina , Carullo Pierluigi , Zhang Jianlin , Scellini Beatrice , Piroddi Nicoletta , Nemska Simona , Filomena Maria Carmela , Serio Simone , Otey Carol A , Tesi Chiara , Emrich Fabian , Linke Wolfgang A. , Poggesi Corrado , Boncompagni Simona , Bang Marie-Louise
Published: May 2022

Palladin (PALLD) belongs to the PALLD/myopalladin (MYPN)/myotilin family of actin-associated immunoglobulin-containing proteins in the sarcomeric Z-line. PALLD is ubiquitously expressed in several isoforms and its longest 200 kDa isoform, predominantly expressed in striated muscle, shows high structural homology to MYPN. MYPN gene mutations are associated with human cardiomyopathies, whereas the role of PALLD in the heart has remained unknown, partly due to embryonic lethality of PALLD knockout mice. In a yeast two-hybrid screening, CARP/Ankrd1 and FHOD1 were identified as novel interaction partners of PALLD’s N-terminal region. To study the role of PALLD in the heart, we generated conditional (cPKO) and inducible (cPKOi) cardiomyocyte-specific PALLD knockout mice. While cPKO mice exhibited no pathological phenotype, ablation of PALLD in adult cPKOi mice caused progressive cardiac dilation and systolic dysfunction, associated with reduced cardiomyocyte contractility, intercalated disc abnormalities, and fibrosis, demonstrating that PALLD is essential for normal cardiac function. Double cPKO and MYPN knockout mice exhibited a similar phenotype as MKO mice, suggesting that MYPN does not compensate for the loss of PALLD in cPKO mice. Transcript levels of MYPN and the PALLD long isoform were significantly increased in myocardial tissue from human dilated cardiomyopathy patients, suggesting a role of PALLD in cardiac disease.
Extensive uORF translation from HIV-1 transcripts conditions DDX3 dependency for expression of main ORFs and elicits specific T cell immune responses in infected individuals
Authors: Labaronne Emmanuel , Décimo Didier , Bertrand Lisa , Guiguettaz Laura , Sohier Thibault J.M. , Cluet David , Vivet-Boubou Valérie , Dahoui Clara , François Pauline , Hatin Isabelle , Lambotte Olivier , Samri Assia , Autran Brigitte , Etienne Lucie , Goujon Caroline , Paillart Jean-Christophe , Namy Olivier , Ramirez Berta Cecilia , Ohlmann Théophile , Moris Arnaud , Ricci Emiliano P.
Published: May 2022

Human immunodeficiency virus type-1 (HIV-1) is a complex retrovirus which relies on alternative splicing, translational and post-translational mechanisms to produce more than 15 functional proteins from its single ∼10kb transcriptional unit. Here, we have applied ribosome profiling and nascent protein labeling at different time points during infection of CD4+ T lymphocytes to characterize the translational landscape of cellular and viral transcripts during the course of infection. Our results indicate a strong impact of viral infection on host cellular transcript levels but a modest impact on global translation rates. Analysis of ribosome profiling reads from viral transcripts reveals extensive and productive non-AUG translation of small peptides from multiple upstream open reading-frames (uORFs) located in the 5’ long terminal repeat. Remarkably, these uORFs derived peptides elicit specific T cell responses in HIV-infected individuals. uORFs are conserved among other retroviruses and, together with the TAR sequence, condition the dependency on DDX3 for efficient translation of the main viral open-reading frames.
CORK1, a LRR-Malectin Receptor Kinase for Cellooligomer Perception in Arabidopsis thaliana
Authors: Tseng Yu-Heng , Scholz Sandra S. , Fliegmann Judith , Krüger Thomas , Gandhi Akanksha , Kniemeyer Olaf , Brakhage Axel A. , Oelmüller Ralf
Published: May 2022

Cell wall integrity (CWI) maintenance is central for plant cells. Mechanical or chemical distortions, pH changes, or breakdown products of cell wall polysaccharides activate plasma membrane-localized receptors and induce appropriate downstream responses. Microbial interactions alter or destroy the structure of the plant cell wall, connecting CWI maintenance to immune responses. Cellulose is the major polysaccharide in the primary and secondary cell wall. Its breakdown generates short-chain cellooligomers which induce Ca2+-dependent CWI responses. We have shown here that these responses require the malectin domain-containing CELLOOLIGOMER-RECEPTOR KINASE 1 (CORK1) in Arabidopsis. CORK1 is required for cellooligomer-induced cytoplasmic Ca2+ elevation, reactive oxygen species (ROS) production, mitogen associated protein kinase (MAPK) activation, cellulose synthase phosphorylation, and the regulation of CWI-related genes including those involved in biosynthesis of cell wall material, secondary metabolites and tryptophan. Phosphoproteome analyses identified early targets involved in signaling, cellulose synthesis, the endoplasmatic reticulum/Golgi secretory pathway, cell wall repair and immune responses. Two conserved phenylalanine residues in the malectin domain are crucial for CORK1 function. We propose that cellulose breakdown products bind to the malectin domain in CORK1, indicating its role as a novel receptor kinase for CWI maintenance.
In situ structure of a dimeric hibernating ribosome from a eukaryotic intracellular pathogen
Authors: McLaren Mathew , Gil-Diez Patricia , Isupov Michail N. , Conners Rebecca , Gambelli Lavinia , Gold Vicki , Walter Andreas , Connell Sean R. , Williams Bryony , Daum Bertram
Published: May 2022

Translational control is an essential process for the cell to adapt to varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be shut down almost entirely by inhibiting ribosomal function. Here we investigated eukaryotic hibernating ribosomes from the microsporidian parasite Spraguea lophii in situ by a combination of cryo-electron tomography (cryoET) and single particle cryoEM. We show that microsporidian spores contain ribosomes primed for host cell invasion and thus shed new light on the infection mechanism of this important pathogen. Prior to host infection, virtually all ribosomes are locked in the 100 S dimeric state, which appears to be formed by a unique dimerization mechanism that is distinct from its bacterial counterparts. Within the dimer, the hibernation factor MDF1 is bound within the E site, locking the L1 stalk in a closed conformation, and thus preventing the translation of mRNAs to polypeptides.
NSF/αSNAP2-mediated cis-SNARE complex disassembly precedes membrane fusion generating the cell plate during Arabidopsis cytokinesis
Authors: Park Misoon , Mayer Ulrike , Jürgens Gerd
Published: May 2022

Eukaryotic membrane fusion requires trans-SNARE complexes bridging the gap between adjacent membranes (Jahn and Scheller, 2006). Fusion between a transport vesicle and its target membrane transforms the trans-into a cis-SNARE complex. The latter interacts with the hexameric AAA+-ATPase NSF and its co-factor αSNAP, forming a 20S complex (Zhou et al., 2015; Zhao and Brunner, 2016). ATPase activity disassembles the SNARE complex into Qa-SNARE, which folds back onto itself, and its partners (Huang et al., 2019; Kim et al., 2021). Fusion of identical membranes has a different sequence of events (Baker and Hughson, 2016). The fusion partners each have cis-SNARE complexes to be broken up by NSF and αSNAP. The Qa-SNARE monomers are then stabilized by interaction with Sec1-type regulators (SM proteins) to form trans-SNARE complexes, as shown for the yeast vacuole (Baker et al., 2015). Membrane fusion in Arabidopsis cytokinesis is formally akin to vacuolar fusion (Müller and Jürgens, 2016). Membrane vesicles fuse with one another to form the partitioning membrane known as cell plate. Cis-SNARE complexes of cytokinesis-specific Qa-SNARE KNOLLE and its SNARE partners are assembled at the ER and delivered by traffic via Golgi/TGN to the cell division plane (Karnahl and Park et al., 2017). SM protein KEULE is required for the formation of trans-SNARE complexes between adjacent membrane vesicles (Park et al., 2012). Here, we identify the missing NSF-type AAA+-ATPase and its adaptor αSNAP2 required for disassembly of KNOLLE cis-SNARE complexes. In addition, we show that NSF is also required for other trafficking pathways and interacts with the respective Q-SNAREs. In conclusion, the SNARE complex disassembly machinery is conserved in plants and plays a unique essential role in cytokinesis.
The activation of mGluR4 rescues parallel fiber LTP, motor learning and social behavior in a mouse model of Fragile X Syndrome
Authors: Martín Ricardo , Suárez-Pinilla Alberto Samuel , García-Font Nuria , Laguna-Luque M. Luisa , López-Ramos Juan C. , Oset-Gasque María Jesús , Gruart Agnes , Delgado-García José M. , Torres Magdalena , Sánchez-Prieto José
Published: May 2022

Fragile X patients and mice lacking the Fragile X Mental Retardation Protein (FMRP) suffer from multiple behavioral alterations, including deficits in motor learning. We found that enhanced synaptic vesicle (SV) docking in cerebellar parallel fiber to Purkinje cell Fmr1KO synapses was associated with enhanced asynchronous release, which not only occludes further potentiation, but it also compromises presynaptic parallel fiber long-term potentiation (PF-LTP). A reduction in extracellular Ca2+ restored the readily releasable pool (RRP) size, rescuing β adrenergic receptor-mediated potentiation and parallel fiber LTP. Interestingly, VU 0155041, a selective positive allosteric modulator of mGluR4, also restored both the RRP size and parallel fiber LTP. Moreover, when injected into Fmr1KO mice, VU 0155041 improved motor learning in skilled reaching, classical eyeblink conditioning and vestibuloocular reflex (VOR) tests, as well as improving the social behavior of these mice. Thus, pharmacological activation of mGluRs may offer therapeutic relief for motor learning and social deficits in Fragile X Syndrome.
The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases
Authors: Chen Zhongbo , Reynolds Regina H. , Pardiñas Antonio F. , Gagliano Taliun Sarah A. , van Rheenen Wouter , Lin Kuang , Shatunov Aleksey , Gustavsson Emil K. , Fogh Isabella , Jones Ashley R. , Robberecht Wim , Corcia Philippe , Chiò Adriano , Shaw Pamela J. , Morrison Karen E. , Veldink Jan H. , van den Berg Leonard H. , Shaw Christopher E. , Powell John F. , Silani Vincenzo , Hardy John A. , Houlden Henry , Owen Michael J. , Turner Martin R. , Ryten Mina , Al-Chalabi Ammar
Published: May 2022

Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions.

We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimer’s disease, amyotrophic lateral sclerosis and Parkinson’s disease.

We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimer’s disease, amyotrophic lateral sclerosis and Parkinson’s disease,, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk.

These findings provide insight into the origins of neurodegenerative disorders within the evolution ofHomo sapiensand addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.
Transcription factor binding sites are frequently under accelerated evolution in primates
Authors: Zhang Xinru , Huang Yi-Fei
Published: May 2022

Recent comparative genomic studies have identified many human accelerated elements (HARs) with elevated substitution rates in the human lineage. However, it remains unknown to what extent transcription factor binding sites (TFBSs) are under accelerated evolution in humans and other primates. Here, we introduce two pooling-based phylogenetic methods with dramatically enhanced sensitivity to examine accelerated evolution in TFBSs. Using these new methods, we show that more than 6,000 TFBSs annotated in the human genome have experienced accelerated evolution in Hominini, apes, and Old World monkeys. Although these TFBSs individually show relatively weak signals of accelerated evolution, they collectively are more abundant than HARs. Also, we show that accelerated evolution in Pol III binding sites may be driven by lineage-specific positive selection, whereas accelerated evolution in other TFBSs might be driven by nonadaptive evolutionary forces. Finally, the accelerated TFBSs are enriched around neurodevelopmental and pluripotency genes, suggesting that accelerated evolution in TFBSs may drive the divergence of neurodevelopmental processes between primates.
The Features Underlying the Memorability of Objects
Authors: Kramer Max A. , Hebart Martin N. , Baker Chris I. , Bainbridge Wilma A.
Published: May 2022

What makes certain images more memorable than others? While much of memory research has focused on participant effects, recent studies employing a stimulus-centric perspective have sparked debate on the determinants of memory, including the roles of semantic and visual features and whether the most prototypical or atypical items are best remembered. Prior studies have typically relied on constrained stimulus sets, limiting a generalized view of the features underlying what we remember. Here, we collected 1+ million memory ratings for a naturalistic dataset of 26,107 object images designed to comprehensively sample concrete objects. We establish a model of object features that is predictive of image memorability and examined whether memorability could be accounted for by the typicality of the objects. We find that semantic features exert a stronger influence than perceptual features on what we remember and that the relationship between memorability and typicality is more complex than a simple positive or negative association alone.

TEASER

Semantic versus perceptual features more heavily influence what we remember, and memorability cannot be reduced to typicality.
HIV-1 Rev-RRE Functional Activity in Primary Isolates is Highly Dependent on Minimal Context-Dependent Changes in Rev
Authors: Dzhivhuho Godfrey , Holsey Jordan , Honeycutt Ethan , O’Farrell Heather , Rekosh David , Hammarskjold Marie-Louise , Jackson Patrick E. H.
Published: May 2022

During HIV infection, intron-containing viral mRNAs have to be exported efficiently from the host cell nucleus to the cytoplasm in order to complete the replication cycle. To overcome cellular restrictions to export incompletely spliced transcripts, HIV encodes a protein, Rev, that is constitutively expressed from a completely spliced transcript. Rev is then imported into the nucleus where it binds to an RNA structure on intron-containing viral mRNAs called the Rev Response Element (RRE). Bound Rev multimerizes and recruits cellular factors that permit the nuclear export of the resulting ribonucleoprotein complex. Primary HIV isolates display substantial variation in the functional activity of the Rev-RRE axis, which may permit viral adaptation to differing immune environments. We describe two subtype G primary isolates with disparate Rev activity. Rev activity was correlated within vitrofitness of replication-competent viral constructs. Amino acid differences within the oligomerziation domain, but not within the arginine-rich motif or nuclear export signal, determined the different levels of Rev activity. Two specific amino acid substitutions were demonstrated to be able to alter the low-activity Rev to a high-activity phenotype. However, introducing the original amino acids from the the low activity Rev into high activity Rev in this position did not result in significant alterations in activity, highlighting the importance of the broader sequence context for functional activity. These results demonstrate that studies of Rev and RRE activity variation, which may have broader implications for HIV transmission and pathogenesis, should include sequences from primary isolates, as findings using only laboratory-adapted strains cannot be generalized.
Actin cytoskeleton signaling via MRTF/SRF entrains circadian clock
Authors: Xiong Xuekai , Li Weini , Nam Jin , Qu Meng , Kay Steve A. , Ma Ke
Published: May 2022

The circadian clock is entrained to daily environmental cues. Integrin-linked intracellular signaling via actin cytoskeleton dynamics transduces extracellular matrix interactions to Myocardin-related Transcription Factor (MRTF)/Serum Response Factor (SRF)-mediated transcription. Actin cytoskeleton organization in liver displays diurnal oscillations and SRF-MRTF activity exert transcriptional control to entrain clock. By interrogating disparate upstream events involved in actin cytoskeleton-MRTF-A/SRF signaling cascade, here we show that this signaling cascade transduce cellular niche cues to modulate circadian clock function. Pharmacological inhibitions of MRTF-A/SRF, by disrupting actin polymerization or blocking ROCK kinase, induced period lengthening with augmented clock amplitude, and genetic loss-of-functions of Srf or Mrtf-a mimic that of actin-depolymerizing agents. In contrast, actin-polymerization induced by Jasplakinolide shortened period with attenuated amplitude. In addition, interfering with cell-matrix interaction through blockade of integrin, inhibition of focal adhesion kinase or attenuating matrix rigidity led to reduced period length while enhancing amplitude. Mechanistically, we identify that core clock repressors, Per2, Nr1d1, and Nfil3, are direct transcriptional targets of MRTF-A/SRF in mediating actin dynamic-induced clock response. Collectively, our findings defined an integrin-actin cytoskeleton-MRTF/SRF pathway in linking clock entrainment with extracellular microenvironment that may facilitate cellular adaptation to its physical niche.

Summary statement

Our study revealed the role of actin cytoskeleton-MRTF/SRF signaling in entraining circadian clock to its extracellular physical niche environment.
Characterization of the DNA binding domain of StbA, a key protein of a new type of DNA segregation system
Authors: Quèbre Valentin , del Campo Irene , Cuevas Ana , Siguier Patricia , Rech Jérôme , Le Phan Thai Nguyen , Ton-Hoang Bao , Cornet François , Bouet Jean-Yves , Moncalian Gabriel , de la Cruz Fernando , Guynet Catherine
Published: May 2022

Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 Å resolution. It folds into an HTH DNA-binding motif, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries the specific stbS DNA binding activity. A truncated version of StbA, deleted of its C-terminal domain, displays only partial activities in vivo, indicating that the non-conserved C-terminal domain is required for efficient segregation and subcellular plasmid positioning. The structure of StbA DNA-binding domain also provides some insight into how StbA monomers cooperate to repress transcription by binding to the stbDR and to form the segregation complex with stbS.
Decreased in vitro dihydroartemisinin sensitivity in malaria parasites infecting sickle cell disease patients
Authors: Gnondjui Albert A. , Toure Offianan A. , Ako Beranger A. , Koui Tossea S. , Assohoun Stanislas E. , Gbessi Eric A. , N’guessan Landry T. , Tuo Karim , Beourou Sylvain , Assi Serge-Brice , Yapo Francis A. , Sanogo Ibrahima , Jambou Ronan
Published: May 2022

Background

Partial ACTs treatment failure in Plasmodium falciparum malaria has been previously reported in sickle cell patients. The main purpose of this study was to investigate the in vitro susceptibility of clinical isolates to DHA to find out hypothesis backing up the reason of this poor therapeutic response.

Results

A total of 134 clinical isolates from patients attending health centers in Abidjan with uncomplicated Plasmodium falciparum malaria were selected. Hemoglobin HbAS, HbSS, HbAC, HbSC and HbAA were identified. Parasitemia and hemoglobin level at inclusion were lower in sickle cell patients with major forms than in patients with normal phenotype. A significant number of parasites with survival rates ranging from 14.68 to 33.75% were observed in clinical isolates from the SS phenotype. At inclusion, these resistant clinical isolates showed lower parasite densities, and patients had lower red blood cell count and hematocrit levels compared to those with susceptible clinical isolates. A low rate of parasitic growth has more often occurred with AS sickle cell phenotype. However, the decrease in in vitro sensitivity to DHA was not associated with Kelch 13-Propeller gene polymorphism.

Conclusion

This study highlights an in vitro decreased sensitivity to DHA, for clinical isolates collected from sickle cell SS patients living in Abidjan (Côte d’Ivoire), which is not related to the Pfkelch13 gene mutations. These clinical isolates may represent a health threat for sickle cell disease patients especially during crisis. Moreover, these results could suggest additional mechanisms of artemisinin resistance that need to be explored.
Effects of calcium-regulated autophagy on Candidatus Liberibacter solanacearum in carrot psyllid midguts
Authors: Sarkar Poulami , Jassar Ola , Ghanim Murad
Published: May 2022

Candidatus Liberibacter solanacearum (CLso) transmitted by the carrot psyllid, Bactericera trigonica causes carrot yellows in Israel, and has recently gained much importance due to the excessive economical loss. Understanding the interactions between CLso and the psyllid at the cellular level is fundamental for the disease management. Here, we demonstrate the role of calcium ATPase, cytosolic calcium and most importantly Beclin1 in regulating autophagy and its association with Liberibacter. Presence of CLso generates reactive oxygen species and induces the expression of the detoxification enzymes in the psyllid midguts. CLso also induces the expression of both sarco/endoplasmic reticulum Ca2+ pump (SERCA) and 1,4,5-trisphosphate receptors (ITPR) in the midguts, followed by high levels of calcium in the cytosol. Silencing these proteins individually disrupted the calcium levels in the cytosol leading to direct effects on autophagy and thus on Liberibacter. On the other hand, inhibiting Beclin1-phosphorylation through different calcium induced kinases altered the expression of autophagy and CLso abundance. This study establishes a direct correlation between cytosolic calcium levels, autophagy and CLso in the carrot psyllid midgut.
A guide for membrane potential measurements in Gram-negative bacteria using voltage-sensitive dyes
Authors: Buttress Jessica A. , Halte Manuel , te Winkel J. Derk , Erhardt Marc , Popp Philipp F. , Strahl Henrik
Published: May 2022

Transmembrane potential is one of the main bioenergetic parameters of bacterial cells, and is directly involved in energising key cellular processes such as transport, ATP synthesis, and motility. The most common approach to measure membrane potential levels is through use of voltage-sensitive fluorescent dyes. Such dyes either accumulate or are excluded from the cell in a voltage-dependent manner, which can be followed by means of fluorescence microscopy, flow cytometry, or fluorometry. Since the cell’s ability to maintain transmembrane potential relies upon low membrane ion conductivity, voltage-sensitive dyes are also highly sensitive reporters for the activity of membrane-targeting antibacterials. However, the presence of an additional membrane layer in Gram-negative (diderm) bacteria significantly complicates their use. In this manuscript, we provide guidance on how membrane potential and its changes can be reliably monitored in Gram-negatives using the voltage-sensitive dye DiSC3(5). We also discuss the confounding effects caused by the presence of the outer membrane, or by measurements performed in buffers rather than growth medium. We hope that the discussed methods and protocols provide an easily accessible basis for the use of voltage-sensitive dyes in Gram-negative organisms, and raise awareness of potential experimental pitfalls associated with their use.
Drug-like small molecules that inhibit expression of the oncogenic microRNA-21
Authors: Shortridge Matthew D. , Chaubey Bhawna , Zhang Huanyu J. , Pavelitz Thomas , Olsen Gregory L. , Calin George A. , Varani Gabriele
Published: May 2022

We report the discovery of a series of drug-like small molecules which bind specifically to the precursor of the oncogenic and pro-fibrotic microRNA-21 with mid-nanomolar affinity. These molecules are highly ligand-efficient (MW<330) and display specific biochemical and cellular activity by suppressing maturation of miR-21, thereby providing an avenue towards therapeutic intervention in multiple diseases where miR-21 is abnormally expressed. The small molecules target a local structure at the Dicer cleavage site and induce distinctive structural changes in the RNA which correlate with specific inhibition of miRNA processing. Structurally conservative single nucleotide substitutions eliminate the conformational change, which is not observed in other miRNA precursors. The most potent ofthesecompounds reduces cellular proliferation and miR-21 levels in cancer cell lines without inhibiting kinases or classical receptors, while closely related compounds without this specific binding activity are inactive in cells.
Asynchronous excitatory neuron development in an isogenic cortical spheroid model of Down syndrome
Authors: Li Zhen , Klein Jenny A. , Rampam Sanjeev , Kurzion Ronni , Patel Yesha , Haydar Tarik F , Zeldich Ella
Published: May 2022

The intellectual disability (ID) in Down syndrome (DS) is thought to result from a variety of developmental deficits such as alterations in neural progenitor division, neurogenesis, gliogenesis, cortical architecture, and reduced cortical volume. However, the molecular processes underlying these neurodevelopmental changes are still elusive, preventing an understanding of the mechanistic basis of ID in DS. In this study, we used a pair of isogenic (trisomic and euploid) induced pluripotent stem cell (iPSC) lines to generate cortical spheroids (CS) that model the impact of trisomy 21 on brain development. CS contain neurons, astrocytes, and oligodendrocytes and they are widely used to approximate early neurodevelopment. Using single cell RNA sequencing (scRNA-seq), we uncovered cell type-specific transcriptomic changes in the trisomic CS. In particular, we found that excitatory neuron populations were most affected and that a specific population of cells with a transcriptomic profile resembling layer IV cortical neurons displayed the most profound divergence in developmental trajectory between trisomic and euploid genotypes. We also identified candidate genes potentially driving the developmental asynchrony between trisomic and euploid excitatory neurons. Direct comparison between the current isogenic CS scRNA-seq data and previously published datasets revealed several recurring differentially expressed genes between DS and control samples. Altogether, our study highlights the power and importance of cell type-specific analyses within a defined genetic background, coupled with broader examination of mixed samples, to comprehensively evaluate cellular phenotypes in the context of DS.
Passive surveillance of human-biting ticks correlates with town-level disease rates in Massachusetts
Authors: Lavoie Nathalie , Xu Guang , Brown Catherine , Ledizet Michel , Rich Stephen M.
Published: May 2022

We assessed the temporal and spatial distribution of Borrelia burgdorferi, Borrelia miyamotoi, Babesia microti, and Anaplasma phagocytophilum among human-biting Ixodes scapularis ticks in Massachusetts using ticks submitted to the TickReport pathogen passive surveillance program. From January 2015 to December 2017, Ixodes scapularis was the most frequently submitted tick species (n=7462). B. burgdorferi prevalence increased in ticks during the study period in adults and nymphs (37.1-39.1% in adults, 19.0%-23.9% in nymphs). The proportion of B. microti infected ticks increased from 5.7% to 8.1% in adult ticks but remained constant in nymphs (5.4-5.6%). Stable or decreasing annual prevalence of B. miyamotoi (2.2 – 2.2% in adults, 1.0-1.9% in nymphs) and A.phagocytophilum (7.6-7.2% in adults, 5.0-4.0% in nymphs) were detected. Coinfections were observed and included all pathogen combinations.

Ticks were submitted year-round and had stable infection rates. The temporal pattern of B. burgdorferi- positive nymphs aligned with reported cases of Lyme disease, as did positive B. microti nymphs and babesiosis. A similar situation is seen with B. miyamotoi with an insignificant fall peak in cases. Anaplasmosis demonstrated a significant bimodal distribution with reported cases peaking in the spring and fall. This pattern is similar to that of A. phagocytophilum-infected adult ticks.

B. microti infected nymphs were significantly predictive of town-level babesiosis incidence and A. phagocytophilum infected adults were significantly predictive of town-level anaplasmosis incidence in a spatially adjusted negative binomial model. Unlike field collection studies, the high number of ticks submitted provides a high-resolution picture of pathogen prevalence and provides data relevant to human health at the town level. Through temporal and geographic analyses we demonstrate concordance between our passive surveillance tick pathogen data and state reports of tickborne disease.
Adherence to the HIV early infant diagnosis testing protocol among HIV exposed infants in a hard-to-reach fishing community in Uganda
Authors: Remegio Ndyanabo , Nalugya Aisha , Ssekamatte Tonny , Nakafero Mary , Kisakye Angela , Mukose Aggrey David
Published: May 2022

Background

Infants born to HIV-infected mothers are at a high risk of acquiring the infection. The World Health Organization (WHO) recommends early diagnosis of HIV-exposed infants (HEIs) through deoxyribonucleic acid polymerase chain reaction (DNA PCR) and rapid HIV testing. Early detection of paediatric HIV is critical for access to antiretroviral therapy treatment (ART) and child survival. There’s, however, limited evidence of the adherence to early infant diagnosis (EID) of HIV testing protocol among HEIs in fishing communities in Uganda. This study assessed adherence to EID of HIV testing protocol among HIV-exposed infants in a hard-to-reach fishing community in Uganda.

Methods

We conducted a cross-sectional study employing quantitative data collection methods among HEIs in selected healthcare facilities in Buvuma islands, Buvuma district. We obtained secondary data from mother-infant pair files enrolled on the EID program using a data extraction tool. Data were analysed using STATA Version 14. Modified poisson regression analysis was used to determine the factors associated with non-adherence to the 1st DNA PCR test among HIV-exposed infants enrolled into care.

Results

None of the HIV-exposed infants had done all the EID tests prescribed by the HIV testing protocol within the recommended time frame for the period of January 2014-December 2016. Adherence to the 1st and 2nd DNA PCR, and rapid HIV tests was 39.5%, 6.1% and 81.0% respectively. Being under the care of single mothers (PR=1.11, 95% CI: 1.01-1.23, p=0.023) and cessation of breast feeding (PR=0.90, 95% CI: 0.83-0.98, p=0.025) were significantly associated with non-adherence to the 1st DNA PCR.

Conclusion

None of the HIV-exposed infants adhered to all the EID tests of HIV testing protocol. Adherence to the 1st DNA PCR was positively associated with being a single mother and exclusive breast feeding. Therefore, single mothers and those who stop breastfeeding should be supported to ensure timely EID.
A 5-year Review of Incidence, Presentation and Management of Bartholin Gland Cysts and Abscesses in a Tertiary Hospital, Yenagoa, South-South Nigeria
Authors: Oriji PC , Allagoa DO , Ubom AE , Oriji VK
Published: May 2022

Background

Bartholin gland cysts and abscesses are common in women of reproductive age and declines after menopause. Organisms implicated in Bartholin abscess include, Neisseria gonorrhoeae, Chlamydia trachomatis, Escherichia coli, Staphylococcus aureus and Bacterioides spp.

Aim

To determine the incidence, presentation and management of Bartholin gland cysts and abscesses at the Federal Medical Centre, Yenagoa, Bayelsa State, South-South Nigeria, over a five-year period.

Settings and Design

This retrospective study was conducted in the Gynaecological Unit of the Federal Medical Centre, Yenagoa, Bayelsa State, South-South, Nigeria, between January 1, 2016 and December 31, 2020.

Materials and Methods

Relevant data were retrieved, entered into a pre-designed proforma, and analysed.

Statistical Analysis

Statistical Package for the Social Sciences version 25.0 was used for data analysis. Results were presented in frequencies and percentages for categorical variables.

Results

There were 2,478 gynaecological cases managed in our Centre; out of which there were 26 cases of Bartholin cyst and abscess, giving an incidence of 1.05%. Most of the women were ≤ 30 years (14, 53.8%), single (17, 65.4%), nulliparous (13, 50.0%), traders (11, 42.3%), with only primary/secondary education (18, 69.2%). The left Bartholin gland was the most frequently affected (17, 65.4%). A positive microbial culture was obtained in 84% of cases, with Staphylococcus aureus and Escherichia coli being the isolated organisms. Marsupialisation was the treatment modality in all the patients.

Conclusion

Women of reproductive age-group should be counselled on this condition and encouraged to keep good perineal hygiene and better sexual conduct so as to reduce the risk of Bartholin cysts and abscesses.
A Simulator for Somatic Evolution Study Design
Authors: Srivatsa Arjun , Lei Haoyun , Schwartz Russell
Published: May 2022

Motivation

Somatic evolution plays a key role in development, cell differentiation, and normal aging, but also diseases such as cancer, which is now mainly thought of as a disease of genetic and epigenetic modification. Understanding mechanisms of somatic mutability — variant types and frequencies, phylogenetic structure, mutational signatures, and clonal heterogeneity — and how they can vary between cell lineages will likely play a crucial role in biological discovery and medical applications. This need has led to a proliferation of new technologies for profiling single-cell variation, each with distinctive capabilities and limitations that can be leveraged alone or in combination with other technologies. The enormous space of options for assaying somatic variation, however, presents unsolved informatics problems with regards to selecting optimal combinations of technologies for designing appropriate studies for any particular scientific questions. Versatile simulation tools are needed to make it possible to explore and optimize potential study designs if researchers are to deploy multiomic technologies effectively.

Results

In this paper, we present a simulator allowing for the generation of synthetic data from a wide range of clonal lineages, variant classes, and sequencing technology choices, intended to provide a platform for effective study design in somatic lineage analysis. Our simulation framework allows for the assessment of study design setups and their statistical validity in determining different ground-truth cancer mechanisms. The user is able to input various properties of the somatic evolutionary system, mutation classes (e.g., single nucleotide polymorphisms, copy number changes, and classes of structural variation), and biotechnology options (e.g., coverage, bulk vs single cell, whole genome vs exome, error rate, number of samples) and can then generate samples of synthetic sequence reads and their corresponding ground-truth parameters for a given study design. We demonstrate the utility of the simulator for testing and optimizing study designs for various experimental queries.

Contact

russells@andrew.cmu.edu

Availability

https://github.com/CMUSchwartzLab/MosaicSim
Angiotensin II regulates the neural expression of subjective fear in humans - precision pharmaco-neuroimaging approach
Authors: Zhang Ran , Zhao Weihua , Qi Ziyu , Xu Ting , Zhou Feng , Becker Benjamin
Published: May 2022

Background

Rodent models and pharmacological neuroimaging studies in humans have been employed to test novel pharmacological agents to reduce fear. However, these strategies are limited with respect to determining process-specific effects on the actual subjective experience of fear which represents the key symptom why patients seek treatment. We here employed a novel precision pharmacological fMRI approach that is based on process-specific neuroaffective signatures to determine effects of the selective angiotensin II type 1 receptor (ATR1) antagonist losartan on the subjective experience of fear.

Methods

In a double-blind, placebo-controlled randomized pharmacological fMRI design n = 87 healthy participants were administered 50mg losartan or placebo before they underwent an oddball paradigm which included neutral, novel and fear oddballs. Losartan effects on brain activity and connectivity as well as on process-specific multivariate neural signatures were examined.

Results

AT1R blockade selectively reduces the neurofunctional reactivity to fear-inducing visual oddballs in terms of attenuating dorsolateral prefrontal activity and amygdala-ventral anterior cingulate (vACC) communication. Neurofunctional decoding further demonstrates fear-specific effects given that ATR1 blockade (1) reduces the neural expression of subjective fear, but not threat or non-specific negative expressions, and (2) does not affect reactivity to novel oddballs.

Conclusions

These results show a specific role of the AT1R in regulating subjective fear experience and demonstrate the feasibility of a precision pharmacological fMRI approach to the affective characterization of novel receptor targets for fear in humans.
Distinct Mechanisms of Innate and Adaptive Immune Regulation Underlie Poor Oncologic Outcomes Associated with KRAS-TP53 Co-Alteration in Pancreatic Cancer
Authors: Datta Jashodeep , Bianchi Anna , De Castro Silva Iago , Deshpande Nilesh U. , Cao Long Long , Mehra Siddharth , Singh Samara , Rafie Christine , Sun Xiaodian , Chen Xi , Dai Xizi , Colaprico Antonio , Sharma Prateek , Dosch Austin R. , Pillai Asha , Hosein Peter J. , Nagathihalli Nagaraj S. , Komanduri Krishna V. , Wilson Julie M. , Ban Yuguang , Merchant Nipun B.
Published: May 2022

Co-occurrent KRAS and TP53 mutations define a majority of patients with pancreatic ductal adenocarcinoma (PDAC) and define its pro-metastatic proclivity. Here, we demonstrate that KRAS-TP53 co-alteration is associated with worse survival compared with either KRAS-alone or TP53-alone altered PDAC in 245 patients with metastatic disease treated at a tertiary referral cancer center, and validate this observation in two independent molecularly annotated datasets. Compared with non-TP53 mutated KRAS-altered tumors, KRAS-TP53 co-alteration engenders disproportionately innate immune-enriched and CD8+ T-cell-excluded immune signatures. Leveraging in silico, in vitro, and in vivo models of human and murine PDAC, we discover a novel intersection between KRAS-TP53 co-altered transcriptomes, TP63-defined squamous trans-differentiation, and myeloid-cell migration into the tumor microenvironment. Comparison of single-cell transcriptomes between KRAS-TP53 co-altered and KRAS-altered/TP53WT tumors revealed cancer cell-autonomous transcriptional programs that orchestrate innate immune trafficking and function. Moreover, we uncover granulocyte-derived inflammasome activation and TNF signaling as putative paracrine mediators of innate immunoregulatory transcriptional programs in KRAS-TP53 co-altered PDAC. Immune subtyping of KRAS-TP53 co-altered PDAC reveals conflation of intratumor heterogeneity with progenitor-like stemness properties. Coalescing these distinct molecular characteristics into a KRAS-TP53 co-altered “immunoregulatory program” predicts chemoresistance in metastatic PDAC patients enrolled in the COMPASS trial, as well as worse overall survival.
Accelerated aging induced by stress in experimental murine ocular hypertension
Authors: Xu Qianlan , Rydz Cezary , Nguyen Huu Viet Anh , Rocha Lorena , Palomino La Torre Claudia , Lee Irene , Cho William , Jabari Mary , Donello John , Weinreb Robert N. , Lyon David C. , Ju Won-Kyu , Foik Andrzej , Skowronska-Krawczyk Dorota
Published: May 2022

Aging, a universal process that affects all cells in an organism, is a major risk factor for a group of neuropathies called glaucoma, where elevated intraocular pressure is one of the known stresses affecting the tissue. Our understanding of molecular impact of aging on response to stress in retina is very limited, therefore we developed a new mouse model to approach this question experimentally. Here we show that susceptibility to response to stress increases with age and is primed on epigenetic level. We demonstrate that program activated by hypertension is similar to natural aging, and that one of the earliest pathways activated upon stress is senescence. Finally, we show that multiple instances of pressure elevation cause accelerated aging of young retina as measured on transcriptional and epigenetic level. Our work emphasizes the importance of early diagnosis and prevention as well as age-specific management of age-related eye-diseases, including glaucoma.
Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis
Authors: Imoto Yusuke , Nakamura Tomonori , Escolar Emerson G. , Yoshiwaki Michio , Kojima Yoji , Yabuta Yukihiro , Katou Yoshitaka , Yamamoto Takuya , Hiraoka Yasuaki , Saitou Mitinori
Published: May 2022

Single-cell RNA sequencing (scRNA-seq) can determine gene expression in numerous individual cells simultaneously, promoting progress in the biomedical sciences. However, scRNA-seq data are high-dimensional with substantial technical noise, including dropouts. During analysis of scRNA-seq data, such noise engenders a statistical problem known as the curse of dimensionality (COD). Based on high-dimensional statistics, we herein formulate a noise reduction method, RECODE (resolution of the curse of dimensionality), for high-dimensional data with random sampling noise. We show that RECODE consistently eliminates COD in relevant scRNA-seq data with unique molecular identifiers. RECODE does not involve dimension reduction and recovers expression values for all genes, including lowly expressed genes, realizing precise delineation of cell-fate transitions and identification of rare cells with all gene information. Compared to other representative imputation methods, RECODE employs different principles and exhibits superior overall performance in cell-clustering and single-cell level analysis. The RECODE algorithm is parameter-free, data-driven, deterministic, and high-speed, and notably, its applicability can be predicted based on the variance normalization performance. We propose RECODE as a general strategy for preprocessing noisy high-dimensional data.
Mechanical communication-induced cell directional migration and branching connections mediated by calcium channels, integrin β1 and N-cadherin
Authors: Ouyang Mingxing , Zhu Yiming , Wang Jiajia , Zhang Qingyu , Bu Bing , Guo Jia , Deng Linhong
Published: May 2022

Cell-cell mechanical communications at large spatial scale (above hundreds of micrometers) have been increasingly recognized in recent decade, which shows importance in tissue-level assembly and morphodynamics. The involved mechanosensing mechanism and resulted physiological functions are still to be fully understood. Recent work showed that traction force sensation in the matrix induces cell communications for self-assembly. Here, based on the experimental model of cell directional migration on Matrigel hydrogel containing 0.5 mg/ml type I collagen, we studied the mechano-responsive pathways for cell distant communications. Airway smooth muscle (ASM) cells assembled network structure on the hydrogel, whereas stayed isolated individually when cultured on glass without force transmission. Cell directional migration, or network assembly was significantly attenuated by inhibited actomyosin activity, or inhibition of inositol 1,4,5-trisphosphate receptor (IP3R) calcium channel or SERCA pump on endoplasmic reticulum (ER) membrane, or L-type calcium channel on the plasma membrane. Inhibition of integrin β1 with siRNA knockdown reduced cell directional migration and branching assembly, whereas inhibition of cell junctional N-cadherin with siRNA had little effect on distant attractions but blocked branching assembly. Our work demonstrated that the ER calcium channels and integrin are mechanosensing signals for cell mechanical communications regulated by actomyosin activity, while N-cadherin is responsible for traction force-induced cell stable connections in the assembly.