bluuebunny/crossref_metadata_2025_split huggingface dataset:
The integrin-mediated adhesome complex, essential to multicellularity, is present in the most recent common ancestor of animals, fungi, and amoebae
Authors: Kang Seungho , Tice Alexander K. , Stairs Courtney W. , Lahr Daniel J. G. , Jones Robert E. , Brown Matthew W. 
Published: May 2020

AbstractIntegrins are transmembrane receptor proteins that activate signal transduction pathways upon extracellular matrix binding. The Integrin Mediated Adhesion Complex (IMAC), mediates various cell physiological process. The IMAC was thought to be an animal specific machinery until over the last decade these complexes were discovered in Obazoa, the group containing animals, fungi, and several microbial eukaryote lineages. Amoebozoa is the eukaryotic supergroup sister to Obazoa. Even though Amoebozoa represents the closest outgroup to Obazoa, little genomic-level data and attention to gene inventories has been given to the supergroup. To examine the evolutionary history of the IMAC, we examine gene inventories of deeply sampled set of 100+ Amoebozoa taxa, including new data from several taxa. From these robust data sampled from the entire breadth of known amoebozoan clades, we show the presence of an ancestral complex of integrin adhesion proteins that predate the evolution of the Amoebozoa. Our results highlight that many of these proteins appear to have evolved earlier in eukaryote evolution than previously thought. Co-option of an ancient protein complex was key to the emergence of animal type multicellularity. The role of the IMAC in a unicellular context is unknown but must also play a critical role for at least some unicellular organisms.
Possible Anti-viral effects of Neem (Azadirachta indica) on Dengue virus
Authors: Rao Vikas B , Yeturu Kalidas 
Published: May 2020

Dengue virus (DENV) has become a major health threat worldwide accounting for 50-100 million infections every year and keeping 2.5 billion people at a risk of the infection. Seriousness of the viral infection can be attributed to its lethality when not treated in time and potential to cause health complications post infection. Currently there are only preventive strategies and development of vaccination is still in its infancy of research. It is therefore highly necessary to discover newer drugs and therapies for this deadly virus. In this paper we report important insights we have obtained through a computational analysis of small molecules of Neem (Azadirachta indica) against dengue viral proteins and its required proteins in human. Our study involves identification of the effect of specific small molecules of Neem on proteins of human and virus corresponding to different pathways using simulated molecular binding analyses. We report here Gedunin and Pongamol contained in naturally occurring Neem as potential drugs against the Dengue virus.Significance StatementWe report important ligands in Neem that have potential antiviral activity against Dengue. Our selection of Neem for testing for antiviral properties has been inspired from Ayurveda. Due to unhygienic living conditions that facilitate mosquito breeding, Dengue is a major threat in developing countries causing millions of deaths. Despite the severity of the infection, no specific antiviral drug is available. The results obtained, in terms of newer potential ligands against Dengue are significant as this provides a basis for experimentally verifying and extending the same to develop a cure.We hope that this study would would spur scientific curiosity and undertaking of further elaborate experimental studies.
Susceptibility of tree shrew to SARS-CoV-2 infection
Authors: Zhao Yuan , Wang Junbin , Kuang Dexuan , Xu Jingwen , Yang Mengli , Ma Chunxia , Zhao Siwen , Li Jingmei , Long Haiting , Ding Kaiyun , Gao Jiahong , Liu Jiansheng , Wang Haixuan , Li Haiyan , Yang Yun , Yu Wenhai , Yang Jing , Zheng Yinqiu , Wu Daoju , Lu Shuaiyao , Liu Hongqi , Peng Xiaozhong 
Published: May 2020

ABSTRACTSince SARS-CoV-2 became a pandemic event in the world, it has not only caused huge economic losses, but also a serious threat to global public health. Many scientific questions about SARS-CoV-2 and COVID-19 were raised and urgently need to be answered, including the susceptibility of animals to SARS-CoV-2 infection. Here we tested whether tree shrew, an emerging experimental animal domesticated from wild animal, is susceptible to SARS-CoV-2 infection. No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39° C) particular in female animals during infection. Low levels of virus shedding and replication in tissues occurred in all three age groups, each of which showed his own characteristics. Histopathological examine revealed that pulmonary abnormalities were mild but the main changes although slight lesions were also observed in other tissues. In summary, tree shrew is not susceptible to SARS-CoV-2 infection and may not be a suitable animal for COVID-19 related researches.
Cell-type specificin vitrogene expression profiling of stem-cell derived neural models
Authors: Gregory James A. , Hoelzli Emily , Abdelaal Rawan , Braine Catherine , Cuevas Miguel , Halpern Madeline , Barretto Natalie , Schrode Nadine , Akbalik Güney , Kang Kristy , Cheng Esther , Bowles Kathryn , Lotz Steven , Goderie Susan , Karch Celeste M. , Temple Sally , Goate Alison , Brennand Kristen J. , Phatnani Hemali 
Published: May 2020

AbstractGenetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease, but also challenge our ability to resolve cell-type specific perturbations. Here we report an extension of the RiboTag system, first developed to achieve cell-type restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety ofin vitroapplications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables efficient depletion of off-target RNA in mixed species primary co-cultures and in hiPSC-derived neural progenitor cells, motor neurons, and GABAergic neurons. Nonetheless, depletion efficiency varies across independent experimental replicates. The challenges and potential of implementing RiboTags in complexin vitrocultures are discussed.
SARM1 depletion rescues NMNAT1 dependent photoreceptor cell death and retinal degeneration
Authors: Sasaki Yo , Kakita Hiroki , Kubota Shunsuke , Sene Abdoulaye , Lee Tae Jun , Ban Norimitsu , Dong Zhenyu , Lin Joseph B. , Boye Sanford L. , DiAntonio Aaron , Boye Shannon E. , Apte Rajendra S. , Milbrandt Jeffrey 
Published: May 2020

AbstractLeber congenital amaurosis type 9 is an autosomal recessive retinopathy caused by mutations of the NAD+synthesis enzyme NMNAT1. Despite the ubiquitous expression of NMNAT1, patients do not manifest pathologies other than retinal degeneration. Here we demonstrate that widespread NMNAT1 depletion in adult mice mirrors the human pathology, with selective loss of photoreceptors highlighting the exquisite vulnerability of these cells to NMNAT1 loss. Conditional deletion demonstrates that NMNAT1 is required within the photoreceptor. Mechanistically, loss of NMNAT1 activates the NADase SARM1, the central executioner of axon degeneration, to trigger photoreceptor death and vision loss. Hence, the essential function of NMNAT1 in photoreceptors is to inhibit SARM1, highlighting an unexpected shared mechanism between axonal degeneration and photoreceptor neurodegeneration. These results define a novel SARM1-dependent photoreceptor cell death pathway and identifies SARM1 as a therapeutic candidate for retinopathies.
Polyamine-controlled proliferation and protein biosynthesis are independent determinants of hair follicle stem cell fate
Authors: Allmeroth Kira , Kim Christine S. , Annibal Andrea , Pouikli Andromachi , Chacón-Martínez Carlos Andrés , Latza Christian , Antebi Adam , Tessarz Peter , Wickström Sara A. , Denzel Martin S. 
Published: May 2020

AbstractStem cell differentiation is accompanied by an increase in mRNA translation. The rate of protein biosynthesis is influenced by the polyamines putrescine, spermidine, and spermine that are essential for cell growth and stem cell maintenance. However, the role of polyamines as endogenous effectors of stem cell fate and whether they act through translational control remains obscure. Here, we investigated the function of polyamines in stem cell fate decisions using hair follicle stem cell (HFSC) organoids. HFSCs showed lower translation rates than progenitor cells, and a forced suppression of translation by direct targeting of the ribosome or through specific depletion of natural polyamines elevated stemness. In addition, we identified N1-acetylspermidine as a novel parallel regulator of cell fate decisions, increasing proliferation without reducing translation. Overall, this study delineates the diverse routes of polyamine metabolism-mediated regulation of stem cell fate decisions.Key PointsLow mRNA translation rates characterize hair follicle stem cell (HFSC) stateDepletion of natural polyamines enriches HFSCs via reduced translationN1-acetylspermidine promotes HFSC state without reducing translationN1-acetylspermidine expands the stem cell pool through elevated proliferation
Experimental study of tissue-engineered urethra with collagen / chitosan composite as scaffolds
Authors: Hongfeng Zhai , Changhong Qiu , Jun Jin , Xin Shao 
Published: May 2020

AbstractIn this article we investigated the preparation of tissue-engineered urethra by using the urethral epithelial subculture cells of male New Zealand young rabbits. We inoculated the epithelial cells of urinary mucosa of male New Zealand young rabbits on collagen, chitosan and collagen chitosan composite as scaffolds to prepare tissue-engineered urethra. The results of inverted phase contrast microscope, HE staining and scanning electron microscope of three kinds of tissue-engineered urethra were compared. What’s more, we reported a new method for quantitative and rapid detection of epithelial cell activity of urinary mucosa in situ by Interactive Laser Cytometer. The collagen chitosan composite was more similar to the extracellular matrix of mammalian. Its three-dimensional porous structure had a high area volume ratio, which was conducive to cell adhesion, growth and metabolism. In vitro, the urethral epithelial cells had been cultured on collagen chitosan composite, and the tissue-engineered urethra was successfully prepared, which laid a solid foundation for further in vivo experiments.
Characterizing the body morphology of the first metacarpal in the Homininae using 3D geometric morphometrics
Authors: Morley Jonathan , Bucchi Ana , Lorenzo Carlos , Püschel Thomas A. 
Published: May 2020

AbstractObjectivesThe morphological characteristics of the thumb are of particular interest due to its fundamental role in enhanced manipulation. Despite its possible importance regarding this issue, the body of the first metacarcapal (MC1) has not been fully characterized using morphometrics. This could provide further insights into its anatomy, as well as its relationship with manipulative capabilities. Hence, this study quantifies the shape of the MC1’s body in the extant Homininae and some fossil hominins to provide a better characterization of its morphology.Materials and methodsThe sample includes MC1s of modern humans (n=42), gorillas (n=27) and chimpanzees (n=30), as well asHomo neanderthalensis, Homo nalediandAustralopithecus sediba. 3D geometric morphometrics were used to quantify the shape of MC1’s body.ResultsThe results show a clear distinction among the three extant genera.H. neanderthalensismostly falls within the modern human range of variation.H. naledivaries slightly from modern humans, although also showing some unique trait combination, whereasA. sedibavaries to an even greater extent. When classified using a discriminant analysis, the three fossils are categorized within theHomogroup. Conclusion: The modern human MC1 is characterized by a distinct suite of traits, not present to the same extent in the great apes, that are consistent with an ability to use forceful precision grip. This morphology was also found to align very closely with that ofH. neanderthalensis. H. naledishows a number of human-like adaptations, whilstA. sedibapresents a mix of both derived and more primitive traits.
Salt transport by the gill Na+-K+-2Cl-symporter in palaemonid shrimps: exploring physiological, molecular and evolutionary landscapes
Authors: Maraschi Anieli Cristina , Faria Samuel Coelho , McNamara John Campbell 
Published: May 2020

ABSTRACTPalaemonid shrimps include species from distinct osmotic niches that hyper-regulate hemolymph osmolality and ionic concentrations in dilute media but hypo-regulate in saline media. Their gill epithelia express ion transporters like the Na+-K+-2Cl-symporter (NKCC) thought to play a role in salt secretion. Using a palaemonid series from niches including marine tide pools through estuaries (Palaemon) to coastal and continental fresh waters (Macrobrachium), we established their critical upper salinity limits (UL50) and examined their short-(24 h) and long-term (120 h) hypo-regulatory abilities at salinities corresponding to 80% of the UL50’s (80%UL50). We tested for phylogenetic correlations between gill NKCC gene and protein expression and hemolymph Cl-hypo-regulatory capability, and evaluated whether niche salinity might have driven gill NKCC expression. ThePalaemonspecies from saline habitats showed the highest UL50’s and greatest hypo-regulatory capabilities compared to theMacrobrachiumspecies among which UL50’s were higher in the diadromous than in the hololimnetic species. While basal gill NKCC mRNA transcription rates differed among species, expressions were unaffected by exposure time or salinity, suggesting post-transcriptional regulation of protein synthesis. Unexpectedly, hemolymph Cl-hyper-regulatory capability correlated with gill NKCC gene expression, while gill NKCC protein synthesis was associated withhyper-regulation of hemolymph osmolality at the 80%UL50’s of almost allMacrobrachiumspecies, suggesting a role for the gill NKCC symporter in salt uptake. The evolutionary history of osmoregulation in these palaemonid shrimps suggests that, while some molecular and systemic mechanisms have accompanied cladogenetic events during radiation into different osmotic niches, others may be driven by salinity.
Australian rodents reveal conserved Cranial Evolutionary Allometry across 10 million years of murid evolution
Authors: Marcy Ariel E. , Guillerme Thomas , Sherratt Emma , Rowe Kevin C. , Phillips Matthew J. , Weisbecker Vera 
Published: May 2020

ABSTRACTAmong vertebrates, placental mammals are particularly variable in the covariance between their cranial shapes and body size (allometry), with the notable exception of rodents. Australian murid rodents present an opportunity to assess the cause of this anomaly because they radiated on an ecologically diverse continent unique for lacking other terrestrial placentals. Here we used 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask if ecological opportunity resulted in greater allometric diversity; conversely, we test if intrinsic constraints and/or stabilizing selection conserved allometry. To increase confidence in species-level allometric slopes, we introduce a new phylogeny-based method of bootstrapping and randomly resampling across the whole sample. We found exceedingly conserved allometry across the 10 million year split betweenMusand the clade containing Australian murids. Cranial shapes followed craniofacial evolutionary allometry (CREA) patterns, with larger species having relatively longer snouts and smaller braincases. CREA is consistent with both intrinsic constraints and stabilizing selection hypotheses for conserved allometry. However, large-bodied frugivores evolved faster, while carnivorous specialists showed skull modifications known to conflict with masticatory efficiency. These results suggest a strong role of stabilizing selection on the masticatory apparatus of murid rodents.
Sex estimation in cranial remains: A comparison of machine learning and discriminant analysis in Italian populations
Authors: Pozzi A , Raffone C , Belcastro MG , Camilleri-Carter TL 
Published: May 2020

ABSTRACTObjectivesUsing cranial measurements in two Italian populations, we compare machine learning methods to the more traditional method of linear discriminant analysis in estimating sex. We use crania in sex estimation because it is useful especially when remains are fragmented or displaced, and the cranium may be the only remains found.Materials and MethodsUsing the machine learning methods of decision tree learning, support-vector machines, k-nearest neighbor algorithm, and ensemble methods we estimate the sex of two populations: Samples from Bologna and samples from the island of Sardinia. We used two datasets, one containing 17 cranial measurements, and one measuring the foramen magnum.Results and DiscussionOur results indicate that machine learning models produce similar results to linear discriminant analysis, but in some cases machine learning produces more consistent accuracy between the sexes. Our study shows that sex can be accurately predicted (> 80%) in Italian populations using the cranial measurements we gathered, except for the foramen magnum, which shows a level of accuracy of ∼70% accurate which is on par with previous geometric morphometrics studies using crania in sex estimation. We also find that our trained machine learning models produce population-specific results; we see that Italian crania are sexually dimorphic, but the features that are important to this dimorphism differ between the populations.
The RNA Polymerase II core subunit RPB-9 directs transcriptional elongation at piRNA loci inCaenorhabditis elegans
Authors: Berkyurek Ahmet C. , Furlan Giulia , Lampersberger Lisa , Beltran Toni , Weick Eva-Maria , Nischwitz Emily , Navarro Isabela Cunha , Braukmann Fabian , Akay Alper , Price Jonathan , Butter Falk , Sarkies Peter , Miska Eric A. 
Published: May 2020

ABSTRACTPIWI-interacting RNAs (piRNAs) are genome-encoded small RNAs that regulate germ cell development and maintain germline integrity in many animals. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. piRNA biogenesis mechanisms are diverse and remain poorly understood. Here, we identify the RNA Polymerase II (RNA Pol II) core subunit RPB-9 as required for piRNA-mediated silencing in the nematodeCaenorhabditis elegans. rpb-9mutants fail to initiate heritable piRNA-mediated gene silencing. Furthermore, we show that RPB-9 is required to repress two DNA transposon families and a subset of somatic genes in theC. elegansgermline. We provide genetic and biochemical evidence that RPB-9 is required for piRNA biogenesis. We demonstrate that RPB-9 acts to promote transcriptional elongation/termination at endogenous piRNA loci. We conclude that as a part of its rapid evolution the piRNA pathway has co-opted another ancient machinery, this time for high-fidelity transcription.
Evidences of histologic Thrombotic Microangiopathy and the impact in renal outcomes of patients with IgA nephropathy
Authors: Neves Precil D , Souza Rafael A , Torres Fábio M , Reis Fábio A , Pinheiro Rafaela B , Dias Cristiane B , Yu Luis , Woronik Viktoria , Furukawa Luzia S , Cavalcante Lívia B , Malheiros Denise M , Jorge Lectícia B 
Published: May 2020

ABSTRACTIntroductionIgA nephropathy (IgAN) is the most common primary glomerulopathy worldwide. According to the Oxford Classification, changes in the kidney vascular compartment are not related with worse outcomes. This paper aims to assess the impact of thrombotic microangiopathy (TMA) in the outcomes of Brazilian patients with IgAN.Materials and MethodsAnalysis of clinical data and kidney biopsy findings from patients with IgAN to assess the impact of TMA on renal outcomes.ResultsThe majority of the 118 patients included were females (54.3%); mean age of 33 years (25;43); hypertension and hematuria were observed in 67.8% and 89.8%, respectively. Median creatinine: 1.45mg/dL; eGFR: 48.8ml/min/1.73m2; 24-hour proteinuria: 2.01g; low serum C3: 12.5%. Regarding to Oxford Classification: M1: 76.3%; E1: 35.6%; S1: 70.3%; T1/T2: 38.3%; C1/C2: 28.8%. Average follow-up: 65 months. Histologic evidence of TMA were detected in 21 (17.8%) patients and those ones presented more frequently hypertension (100%vs.61%,p<0.0001), hematuria (100%vs87.6%,p=0.0001), worse creatinine levels (3.8vs. 1.38 mg/dL,p=0.0001), eGFR (18vs.60 ml/min/1.73m2),p=0.0001), low serum C3 (28.5%vs. 10.4%,p=0.003), lower hemoglobin levels (10.6vs.12.7g/dL,p<0.001) and platelet counts (207,000vs. 267,000, p=0.001). Biopsy findings of individuals with TMA revealed only greater proportions of E1 (68%vs.32%,p= 0.002). Individuals with TMA were followed for less time (7vs. 65 months, p<0.0001) since they progressed more frequently to chronic kidney disease (CKD) requiring renal replacement therapy (RRT) (71.4%vs. 21,6%, p<0.0001). Male sex, T1/T2, and TMA were independently associated with progression to CKD-RRT.ConclusionsIn this study patients with TMA had worse clinical manifestations and outcomes. In terms of histologic evidence, E1 distinguished patients with TMA from other patients. These findings indicate that vascular compartment may also be a prognostic marker in IgAN patients.
Does earnings surprise determine the timing of the earnings announcement? Evidence from earnings announcements of Indian companies
Authors: Prasad Krishna , Prabhu Nandan 
Published: May 2020

PurposeThe purpose of this study is to investigate whether the earnings surprise influences decision to make earnings announcements during or after the trading hours is influenced by the earnings surprise resulting from the difference between consensus earnings estimates and the actual reported earnings.Design/methodology/approachEvent study methodology was employed to test the hypotheses relating to earnings surprise and timing of earnings announcements. Twelve quarterly earnings announcements of 30 companies, drawn from BSE SENSEX of India, were studied to test the hypothesized relationships.FindingsThe study has found statistically significant differences in the market responses to the earnings announcements made during and after the trading hours. The market demonstrated a negative response to the earnings announcements made after the trading hours. Further, the results of the logistic regression have shown that the presence of significant earnings surprises is likely to induce firms to make earnings announcements after the trading hours. The results indicate that those firms that intend to reduce the overreaction and underreaction to earnings surprises are likely to make earnings announcements after the trading hours.Originality/valueThis paper highlights the market response to the earnings announcement made during and after the regular trading hour. Further, the paper examines if the earnings surprise influences the decision to announce the results.