bluuebunny/crossref_metadata_2025 huggingface dataset:
Population differentiation and phylogeography inLycianthes moziniana(Solanaceae: Capsiceae), a perennial herb endemic to the Mexican Transition Zone
Authors: Anguiano-Constante Marco Antonio , Zamora-Tavares Pilar , Ruiz-Sanchez Eduardo , Dean Ellen , Rodríguez Aarón , Munguía-Lino Guadalupe
Published: November 2020

Lycianthes moziniana (Solanaceae: Capsiceae) is a perennial herb with edible fruits that is endemic to Mexico. Three varieties are recognized, all known in the Mexican Transition Zone. Lycianthes moziniana var. margaretiana grows in the Sierra Madre Oriental, whereas L. moziniana var. moziniana is common along the Trans-Mexican Volcanic Belt and in the Sierra Madre Occidental. Lycianthes moziniana var. oaxacana is found exclusively in the Sierra Madre del Sur. The Mexican Transition Zone is a complex geological, climatic and biogeographical area, the result of tectonic and volcanic activity that has promoted genetic divergence and speciation. We determined the genetic variation and structure of L. moziniana. Using phylogeographical approaches, we described the demographic history and evolutionary processes leading its divergence. The intergenic spacers rpl32-trnL and ycf1 were sequenced for 133 individuals pertaining to 15 populations. The genealogical relationships were analysed using haplotype networks. Finally, based on ecological niche models, we inferred the palaeodistribution of L. moziniana during the Pleistocene. The genetic differences and the haplogroups matched the three described varieties. Geological and climatic events of the Mexican Transition Zone facilitated these results. The Trans-Mexican Volcanic Belt isolated the populations of the Sierra Madre Oriental and the Sierra Madre del Sur, while allowing the migration to the Sierra Madre Occidental, during the middle Holocene.
Geographical and environmental contributions to genomic divergence in mangrove forests
Authors: Da Silva Michele Fernandes , Cruz Mariana Vargas , Vidal Júnior João De Deus , Zucchi Maria Imaculada , Mori Gustavo Maruyama , De Souza Anete Pereira
Published: November 2020

Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.
Stepwise crosstalk between aberrant Nf1, Tp53 and Rb signalling pathways induces gliomagenesis in zebrafish
Authors: Luo Juanjuan , Liu Pei , Lu Chunjiao , Bian Wanping , Su Dongsheng , Zhu Chenchen , Xie Shaolin , Pan Yihang , Li Ningning , Cui Wei , Pei De-Sheng , Yang Xiaojun
Published: November 2020

The molecular pathogenesis of glioblastoma indicates that RTK/Ras/PI3K, RB and TP53 pathways are critical for human gliomagenesis. Here, several transgenic zebrafish lines with single or multiple deletions of nf1, tp53 and rb1 in astrocytes, were established to genetically induce gliomagenesis in zebrafish. In the mutant with a single deletion, we found only the nf1 mutation low-efficiently induced tumour incidence, suggesting that the Nf1 pathway is critical for the initiation of gliomagenesis in zebrafish. Combination of mutations, nf1;tp53 and rb1;tp53 combined knockout fish, showed much higher tumour incidences, high-grade histology, increased invasiveness, and shortened survival time. Further bioinformatics analyses demonstrated the alterations in RTK/Ras/PI3K, cell cycle, and focal adhesion pathways, induced by abrogated nf1, tp53, or rb1, were probably the critical stepwise biological events for the initiation and development of gliomagenesis in zebrafish. Gene expression profiling and histological analyses showed the tumours derived from zebrafish have significant similarities to the subgroups of human gliomas. Furthermore, temozolomide treatment effectively suppressed gliomagenesis in these glioma zebrafish models, and the histological responses in temozolomide-treated zebrafish were similar to those observed in clinically treated glioma patients. Thus, our findings will offer a potential tool for genetically investigating gliomagenesis and screening potential targeted anti-tumour compounds for glioma treatment.
Cortical connectivity of the nucleus basalis of Meynert in Parkinson’s disease and Lewy body dementias
Authors: Oswal Ashwini , Gratwicke James , Akram Harith , Jahanshahi Marjan , Zaborszky Laszlo , Brown Peter , Hariz Marwan , Zrinzo Ludvic , Foltynie Tom , Litvak Vladimir
Published: November 2020

Parkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB) are related conditions that are associated with cholinergic system dysfunction. Dysfunction of the nucleus basalis of Meynert (NBM), a basal forebrain structure that provides the dominant source of cortical cholinergic innervation, has been implicated in the pathogenesis of both PDD and DLB. Here we leverage the temporal resolution of magnetoencephalography with the spatial resolution of MRI tractography to explore the intersection of functional and structural connectivity of the NBM in a unique cohort of PDD and DLB patients undergoing deep brain stimulation of this structure. We observe that NBM-cortical structural and functional connectivity correlate within spatially and spectrally segregated networks including: (i) a beta band network to supplementary motor area, where activity in this region was found to drive activity in the NBM; (ii) a delta/theta band network to medial temporal lobe structures encompassing the parahippocampal gyrus; and (iii) a delta/theta band network to visual areas including lingual gyrus. These findings reveal functional networks of the NBM that are likely to subserve important roles in motor control, memory and visual function, respectively. Furthermore, they motivate future studies aimed at disentangling network contribution to disease phenotype.
Psychosis in neurodegenerative disease: differential patterns of hallucination and delusion symptoms
Authors: Naasan Georges , Shdo Suzanne M , Rodriguez Estrella Morenas , Spina Salvatore , Grinberg Lea , Lopez Lucia , Karydas Anna , Seeley William W , Miller Bruce L , Rankin Katherine P
Published: November 2020

Although psychosis is a defining feature of Lewy body disease, psychotic symptoms occur in a subset of patients with every major neurodegenerative disease. Few studies, however, have compared disease-related rates of psychosis prevalence in a large autopsy-based cohort, and it remains unclear how diseases differ with respect to the nature or content of the psychosis. We conducted a retrospective chart review of 372 patients with autopsy-confirmed neurodegenerative pathology: 111 with Alzheimer’s disease, 59 with Lewy body disease and concomitant Alzheimer’s disease, 133 with frontotemporal lobar degeneration (FTLD) with tau inclusions (including progressive supranuclear palsy, corticobasal degeneration or Pick’s disease), and 69 with FTLD and TDP inclusions (FTLD-TDP, including types A–C). Psychosis content was classified by subtype, and the frequency of each subtype was compared among pathological diagnoses using logistic regression. A total of 111 of 372 patients had psychosis. Compared to other groups, patients with Lewy body disease/Alzheimer’s disease pathology were significantly more likely to have hallucinations and were more likely to have more than one subtype of hallucination. Patients with Braak Parkinson stage 5–6 Lewy body disease were significantly more likely than those with no Lewy body disease to have visual hallucinations of misperception, peripheral hallucinations, hallucinations that moved, hallucinations of people/animals/objects, as well as delusions regarding a place and delusions of misidentification. The feeling of a presence occurred significantly more frequently in patients with Lewy body disease/Alzheimer’s disease than all other pathologies. Patients with FTLD-TDP were significantly more likely to have delusions, and for the delusions to occur in the first 3 years of the disease, when compared to patients with Alzheimer’s disease and FTLD-tau, though rates were not significantly greater than patients with Lewy body disease/Alzheimer’s disease. Paranoia occurred more frequently in the FTLD-TDP and Lewy body disease/Alzheimer’s disease categories compared to patients with Alzheimer’s disease or FTLD-tau. Patients with FTLD-TDP pathology had delusions of misidentification as frequently as patients with Lewy body disease/Alzheimer’s disease, and were significantly more likely to have self-elevating delusions such as grandiosity and erotomania compared to patients with other pathologies including FTLD-tau. These data show that the nature and content of psychosis can provide meaningful information about the underlying neurodegenerative pathology, emphasizing the importance of characterizing patients’ psychoses for prediction of the neuropathological diagnosis, regardless of a patient’s clinical syndrome.
Genomic profiling of multifocal intrahepatic cholangiocarcinoma reveals intraindividual concordance of genetic alterations
Authors: Lee Sung Hwan , Simoneau Eve B , Karpinets Tatiana , Futreal P Andrew , Zhang Jianjun , Javle Milind , Zhang Jianhua , Vauthey Jean-Nicolas , Lee Ju-Seog , Estrella Jeannelyn S , Chun Yun Shin
Published: November 2020

In multifocal intrahepatic cholangiocarcinoma (IHC), intrahepatic metastases (IM) represent a contraindication to surgical resection, whereas satellite nodules (SN) do not. However, no consensus criteria exist to distinguish IM from SN. The purpose of this study was to determine genetic alterations and clonal relationships in surgically resected multifocal IHC. Next-generation sequencing of 34 spatially separated IHC tumors was performed using a targeted panel of 201 cancer-associated genes. Proposed definitions in the literature were applied of SN located in the same liver segment and ≤2 cm from the primary tumor; and IM located in a different liver segment and/or >2 cm from the primary tumor. Somatic point mutations concordant across tumors from individual patients included BAP1, SMARCA4 and IDH1. Small insertions and deletions (indels) present at the same genome positions among all tumors from individuals included indels in DNA repair genes, CHEK1, ERCC5, ATR and MSH6. Copy number alterations were also similar between all tumors in each patient. In this cohort of multifocal IHC, genomic profiles were concordant across all tumors in each patient, suggesting a common progenitor cell origin, regardless of the location of tumors in the liver. The decision to perform surgery should not be based upon a perceived distinction between IM and SN.
Divergence in Photoperiod Responses of a Classical Biological Control Agent, Galerucella calmariensis (Coleoptera: Chrysomelidae), Across a Climatic and Latitudinal Gradient
Authors: Wepprich Tyson , Grevstad Fritzi S
Published: November 2020

A key knowledge gap in classical biological control is to what extent insect agents evolve to novel environments. The introduction of biological control agents to new photoperiod regimes and climates may disrupt the coordination of diapause timing that evolved to the growing season length in the native range. We tested whether populations of Galerucella calmariensis L. have evolved in response to the potential mismatch of their diapause timing since their intentional introduction to the United States from Germany in the 1990s. Populations collected from 39.4° to 48.8° latitude in the western United States were reared in growth chambers to isolate the effects of photoperiod on diapause induction and development time. For all populations, shorter day lengths increased the proportion of beetles that entered diapause instead of reproducing. The critical photoperiods, or the day length at which half of a population diapauses, differed significantly among the sampled populations, generally decreasing at lower latitudes. The latitudinal trend reflects changes in growing season length, which determines the number of generations possible, and in local day lengths, at the time when beetles are sensitive to this cue. Development times were similar across populations, with one exception, and did not vary with photoperiod. These results show that there was sufficient genetic variation from the two German source populations to evolve different photoperiod responses across a range of environmental conditions. This study adds to the examples of rapid evolution of seasonal adaptations in introduced insects.
Politics and Diplomacy: Lessons from Donald Tusk’s Time as President of the European Council
Authors: Hagemann Sara
Published: November 2020

The 2020 COVID pandemic has posed an unprecedented challenge to Europe’s economies, societies and political institutions. Finding solutions for the immediate and longer-term impact of the pandemic requires collaboration between the European Union’s (EU) member states and leadership from their governments at both national and European levels. The President of the European Council is central to this process, as he leads and facilitates the collaboration between the heads of states and governments. Looking back at the lessons from Donald Tusk’s time as President of the European Council from 2014 to 2019, this article argues that Tusk made an immensely important political contribution to the EU as he set the tone for a liberal and progressive agenda at a time of significant threat from populist and pro-Russian voices in Europe. However, with the recent political and institutional developments in the EU, and based on the insights from Mr Tusk’s successes and challenges, the article also argues that the role of the European Council President today requires strong brokering skills and leadership behind the scenes more than an openly political and public figure.
Stability of maxillary anterior teeth after 2 years of retention in adolescents: a randomized controlled trial comparing two bonded and a vacuum-formed retainer
Authors: Naraghi Sasan , Ganzer Niels , Bondemark Lars , Sonesson Mikael
Published: November 2020

Background

Retention of the maxillary anterior teeth is commonly recommended to maintain the teeth in their corrected positions. Both fixed and removable retention methods are used, but the certainty of evidence is low.

Objective

To evaluate post-treatment changes in irregularity of the maxillary six anterior teeth and single tooth contact point discrepancy (CPD) of three different retention methods.

Trial design

Three-arm parallel group single-centre randomized controlled trial.

Materials and methods

Ninety patients, 54 girls and 36 boys, were recruited to the study. The inclusion criteria were adolescent patients treated with fixed appliances at least in the maxilla. After gaining informed consent from the patient and their custodians, the patients were randomized to one of three groups: bonded retainer 13–23, bonded retainer 12–22, and removable vacuum-formed retainer (VFR) covering the maxillary teeth including the second molars. The randomization, prepared by an independent person, used blocks of 30. The primary outcomes were changes in single CPD and Little’s irregularity index (LII) measured on digitalized three-dimensional study casts before and after 2-year retention. The study casts were anonymized before assessment and the changes were blinded for the assessor. Data were evaluated on an intention-to-treat basis. Thus, all randomized patients were incorporated into the final analysis.

Results

The LII and CPDs increased slightly in all three groups without any statistically significant differences between the groups. The VFR group showed a small intercanine width increase and some more changes of canine rotations than in the other groups.

Harms

No harm was observed in any subjects and none of the patients needed retreatment.

Limitations

The trial was a single-centre study and short-term changes were evaluated.

Conclusions

All three retention methods showed equally effective retention capacity and all the changes found in the three groups were small and considered clinically insignificant. Thus, the null hypothesis was confirmed. All three methods can be recommended.

Trial registration

NCT04616755
Living Alone During COVID-19: Social Contact and Emotional Well-being Among Older Adults
Authors: Fingerman Karen L , Ng Yee To , Zhang Shiyang , Britt Katherine , Colera Gianna , Birditt Kira S , Charles Susan T
Published: November 2020

Objective

The COVID-19 outbreak and associated physical distancing measures altered the social world for most older adults, but people who live alone may have been disproportionately affected. The current study examined how living alone was associated with daily social contact and emotional well-being among older adults during the pandemic.

Method

Adults (N = 226) aged 69+ completed a brief survey assessing their living situation, social contact with different social partners (in person, by phone, electronically), and emotions during the morning, afternoon, and evening the prior day.

Results

Older adults who live alone were less likely to see others in person or to receive or provide help. Living alone was associated with more positive emotions concurrent with in-person contact. In contrast, phone contact was associated with higher levels of negative affect among those living alone, but not among those who live with others. Older adults who live alone were more likely to have contact with friends (rather than family).

Discussion

Findings suggest older adults who live alone may be more reactive to social contact during the COVID-19 outbreak than older adults who reside with others. In-person contact may confer distinct benefits not available via telephone contact, suggesting that possible interventions during the pandemic may work best with safe forms of in-person contact, possibly with nonfamily members.
Decreased turnover of the CNS myelin protein Opalin in a mouse model of hereditary spastic paraplegia 35
Authors: Hardt Robert , Jordans Silvia , Winter Dominic , Gieselmann Volkmar , Wang-Eckhardt Lihua , Eckhardt Matthias
Published: November 2020

Spastic paraplegia 35 (SPG35) (OMIM: 612319) or fatty acid hydroxylase-associated neurodegeneration (FAHN) is caused by deficiency of fatty acid 2-hydroxylase (FA2H). This enzyme synthesizes sphingolipids containing 2-hydroxylated fatty acids, which are particularly abundant in myelin. Fa2h-deficient (Fa2h−/−) mice develop symptoms reminiscent of the human disease and therefore serve as animal model of SPG35. In order to understand further the pathogenesis of SPG35, we compared the proteome of purified CNS myelin isolated from wild type and Fa2h−/− mice at different time points of disease progression using tandem mass tag labeling. Data analysis with a focus on myelin membrane proteins revealed a significant increase of the oligodendrocytic myelin paranodal and inner loop protein (Opalin) in Fa2h−/− mice, whereas the concentration of other major myelin proteins was not significantly changed. Western blot analysis revealed an almost 6-fold increase of Opalin in myelin of Fa2h−/− mice aged 21–23 months. A concurrent unaltered Opalin gene expression suggested a decreased turnover of the Opalin protein in Fa2h−/− mice. Supporting this hypothesis, Opalin protein half-life was reduced significantly when expressed in CHO cells synthesizing 2-hydroxylated sulfatide, compared to cells synthesizing only non-hydroxylated sulfatide. Degradation of Opalin was inhibited by inhibitors of lysosomal degradation but unaffected by proteasome inhibitors. Taken together, these results reveal a new function of 2-hydroxylated sphingolipids namely affecting the turnover of a myelin membrane protein. This may play a role in the pathogenesis of SPG35.
Consensus as a Basis for Dynamic Interpretation of the ECHR—A Critical Assessment
Authors: Łącki Paweł
Published: November 2020

This article attempts to analyse the argumentative model of European consensus as a ground for adopting or refusing to adopt a dynamic interpretation of the ECHR’s provisions. The consensus model promises an objective and verifiable method of dynamic interpretation. This aspiration is rooted in the positivistic character of the model—the evolutionary interpretation is thought to reflect the currently dominant societal axiological views, which are established through purely legal reasoning involving comparative legal analysis. Unfortunately, the theoretical promise of the consensus method remains unfulfilled. The professionalisation of the Court’s comparative research will not be able to rescue this method if there are no coherent criteria for evaluating the data resulting from the research. In addition, the majoritarian logic that lies behind the consensus model cannot satisfy the justificatory need invoked from the perspective of a respondent State.
The pandemic economic crisis, precautionary behavior, and mobility constraints: an application of the dynamic disequilibrium model with randomness
Authors: Stiglitz Joseph E , Guzman Martin M
Published: November 2020

This article analyzes the economic impact of the pandemic, providing insights into the consequences of alternative policies. Our framework focuses on three key features: (i) COVID-19 is a sectoral shock of unknown depth and duration affecting some sectors and technologies more than others; (ii) there are constraints in shifting resources across sectors; and (iii) there is a high level of uncertainty about the disease and its economic aftermath, inducing a high level of precautionary behavior by some agents and leading to others facing more severe credit constraints. Because of macroeconomic externalities, precautionary behavior exacerbates the downturn, and even sectors where COVID-19 does not directly affect consumption or production may face unemployment. Multipliers associated with different government expenditure programs differ markedly. The article describes policies that can mitigate precautionary behavior, leading to reduced unemployment. Greater wage flexibility may lead to increased unemployment. The precautionary behavior is the antithesis of equilibrium behavior, suggesting that standard equilibrium approaches may not provide the appropriate framework for analyzing the pandemic: individuals know that they don’t know the future, that existing and newly made contracts and plans may be broken, and that they need to be able to respond to these unknowable contingencies.
Public policies and the art of catching up: matching the historical evidence with a multicountry agent-based model
Authors: Dosi Giovanni , Roventini Andrea , Russo Emanuele
Published: November 2020

In this article, we study the effects of industrial policies on international convergence using a multicountry agent-based model which builds upon Dosi et al. (2019b, J. Econ. Dyn. Control, 101, 101–129). The model features a group of microfounded economies, with evolving industries, populated by heterogeneous firms that compete in international markets. In each country, technological change is driven by firms’ activities of search and innovation, while aggregate demand formation and distribution follow Keynesian dynamics. Interactions among countries take place via trade flows and international technological imitation. We employ the model to assess the different strategies that laggard countries can adopt to catch up with leaders: market-friendly policies; industrial policies targeting the development of firms’ capabilities and R&D investments, as well as trade restrictions for infant industry protection; protectionist policies focusing on tariffs only. We find that markets cannot do the magic: in absence of government interventions, laggards will continue to fall behind. On the contrary, industrial policies can successfully drive international convergence among leaders and laggards, while protectionism alone is not sufficient to support catching up and countries get stuck in a sort of middle-income trap. Finally, in a global trade war, where developed economies impose retaliatory tariffs, both laggards and leaders are worse off and world productivity growth slows down.
Understanding economic and cultural underpinnings of anti-immigrant attitudes: multilevel evidence from the Asian Barometer Survey Wave IV (2014–2016)
Authors: Kim Harris Hyun-Soo , Kim Hyun Jin
Published: November 2020

A large body of research exists concerning determinants of public opinion on immigration and immigrants, primarily based on Western countries. Given that South–South migratory flows have increased dramatically in recent decades, we contribute to the literature by analyzing cross-national probability data in the Asian context. Using multilevel modeling, we derive and test economic and cultural hypotheses concerning natives’ support for restrictive immigration policy. Results show that at the individual level, along with xenophobic tendency, personal financial insecurity, unequal material distribution in society, and sociotropic economic concern all significantly predict the outcome. As a theoretical contribution, contextual effects are also reported: living in a subnational region with more national pride and with higher parochialism is positively associated with it.
‘No more routine outpatient appointments in the NHS’: it is time to shift to data-driven appointment
Authors: Chowdhury Tasnia , Nilforooshan Ramin
Published: November 2020

Currently, outpatient care in the UK is expensive and needs improvement, with traditional systems having been identified as no longer fit for purpose. Making sustainable changes to outpatient appointment systems is vital in order to meet increasing demands and cost. Shifting to data and technology-driven outpatient care may be one way to tackle these demands. As technology becomes more diverse and accessible, its implementation into healthcare systems can make services more efficient and help with transitioning from outdated practices to more effective protocols. Patient Recorded Outcome Measures (PROMs) and home-monitoring devices could be the key step in identifying which patients require input and help shift to more data-driven appointment scheduling based on clinical need, rather than at regular intervals of time. Virtual care and technology-driven service provision could also revolutionise outpatient systems, maintaining high quality care while improving accessibility to patients. Patient involvement and empowerment while making these changes will assist shared decision making surrounding their care and allow them to be champions of their own health, helping clinicians to provide a patient-centred service. Understanding how these may be implemented will help clinicians take an active role in the development of these practices.
Comprehensive Treatment of Single Finger Frostbite: A Case Study
Authors: Zhang Yonghu , Song Jintong , Huang Guobao
Published: November 2020

Third- and fourth-degree frostbites usually result in loss of skin and tissue requiring amputation, and scarring. The 3- to 6-week waiting period is often necessary to determine the severity of the lesion. This period is also a critical time for the rescue of frostbitten tissue. This patient was a 30-year-old man who developed frostbite of his right index finger. He presented to our hospital 4 hours after injury with loss of sensation on the whole index finger and early signs of necrosis. The patient received a series of comprehensive treatments, including fasciotomy, injection of papaverine hydrochloride, baking lamp irradiation, and negative pressure treatment. At the time of discharge, he had re-epithelialization of the index finger by 21 days after injury. The conclusion of this paper is that the comprehensive treatments combined with negative pressure wound treatment has certain clinical application value for the rescue of deep frostbite tissues.
First mass spectrometric report of cryptocyanin, a moulting protein from the mud crab Scylla serrata (Forskål, 1775) (Decapoda: Brachyura: Portunidae) in India
Authors: Asthana Manu , Ahamed Maqusood , Shanthi Chittibabu
Published: November 2020

The mud crab Scylla serrata (Forskål, 1775) is a highly abundant and economically important species throughout coastal India. Cryptocyanin plays an important role during the moult cycle of brachyuran crabs, and the presence of cryptocyanin and haemocyanin in oocytes, embryos, and zoeas of various species suggests that cryptocyanin is available from the very early stage of cuticle formation in development. Cryptocyanin is highly similar to haemocyanin in structure, but it is a copper-free enzyme that lacks an oxygen-binding capacity. Cryptocyanin has furthermore been reported as an important factor in immunity in crustaceans. The precise molecular weight of the cryptocyanin protein from gill tissues of S. serrata (79.11 kDa) is reported with the help of the matrix-assisted laser desorption/ionization mass spectrophotometry (MALDI-MS) technique.
Yield Response of Determinate Chipping Potato to Artificial Defoliation
Authors: Hoback W Wyatt , Hayashida Rafael , Ziems Jesse , Zechmann Ben , de Freitas Bueno Adeney , Higley Leon G
Published: November 2020

The relationship between canopy defoliation by insects and yield loss in potato (Solanum tuberosum L.) has been extensively researched. However, detailed analysis of varieties with different properties and examination of methods of defoliation are still lacking. Absence of research results has led many producers to use a very conservative economic threshold (ET) of 10% defoliation in the management of insect defoliators. A series of leaf removal experiments was conducted on a determinate chipping variety of potato at different plant stages. In 2002, the highest levels of defoliation induced upon the plant canopy were 50, 30, and 75% for tuber initiation, full bloom, and plant maturity stages, respectively. In 2003, defoliation levels were increased to 70, 80, and 90% for tuber initiation, full bloom, and plant maturity, respectively. Total yield was unaffected, and no significant changes in market sized yield, or number of marketable tubers were observed at any growth stage in either year. Because the determinate variety showed remarkable ability to recover from substantial defoliation, two different methods of defoliation: hand cut (cutting the edge of leaves with scissors while avoiding the midrib) and hole punching (hole-punching leaf tissue [15.08-mm diameter] while avoiding midrib) were tested. Although total yield was unaffected, marketable yield and small potato yield were reduced, Thus, although defoliation methods must be considered, a 10% defoliation ET is exceedingly conservative and an ET of 60% for all stages of determinate chipping potato could be adopted by growers.
Surface Movement of Billbugs (Coleoptera: Curculionidae) in Harvested and Nonharvested Sod
Authors: Gireesh Midhula , Joseph Shimat V
Published: November 2020

The billbug complex, Sphenophorus spp. (Coleoptera: Curculionidae), is an important pest on the sod farms of Georgia. The feeding damage of larvae within stolons and on roots delays the sod harvest and makes it difficult to conduct machine harvests. To develop an effective management strategy, the timing of insecticide applications is critical. The activity of billbugs, especially soon after sod harvest, has not been documented, as newly emerging adults could reinfest the harvested area or adjacent nonharvested sod fields. In 2019 and 2020, adult billbugs were sampled from harvested and nonharvested areas of sod farms by using linear pitfall traps. Although a significantly greater number of billbug adults were captured from the nonharvested sod, the data showed that adults were present in the harvested sod area. To understand the direction of billbug movement in harvested and nonharvested sod, a square area was selected, and the sod inside the square was removed. Linear pitfall traps were deployed along the perimeter of square areas to collect adults from outside and inside the square. In 2020, a significantly greater number of billbug adults were collected in the traps from the nonharvested areas outside the square than from harvested area inside the square, whereas in 2019, adult captures were similar from both areas. The data documented the activity of billbugs in the areas where sod was harvested, posing a risk of infestation for both strips of nonharvested grass in the harvested area and the adjacent, nonharvested sod fields that were near harvest.
Update From the Advisory Committee on Immunization Practices
Authors: O′Leary Sean T , Maldonado Yvonne A , Kimberlin David W
Published: November 2020

The Advisory Committee on Immunization Practices (ACIP), a group of medical and public health experts, normally meets 3 times per year to develop recommendations for vaccine use in the United States. Because of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) pandemic, there are several SARS-CoV-2 vaccines currently in late-stage clinical trials, so the ACIP is now meeting monthly for single day meetings, with plans to continue standard 2- to 3-day meetings as per usual (February, June, and October). Emergency meetings of ACIP may occur if a vaccine candidate receives an Emergency Use Authorization from the food and drug administration (FDA). This Update provides a combined summary of the August 26 and September 22, 2020, meetings, both of which focused completely on Coronavirus disease 2019 (COVID-19) vaccines. The representatives from the American Academy of Pediatrics (Y. A. M. and D. W. K.) and the Pediatric Infectious Diseases Society (S. T. O.) are present as liaisons to the ACIP.
β-Catenin/Lin28/let-7 regulatory network determines type II alveolar epithelial stem cell differentiation phenotypes following thoracic irradiation
Authors: Liu Xiaozhuan , Zhang Tingting , Zhou Jianwei , Xiao Ziting , Li Yanjun , Zhang Yuwei , Yue Haodi , Li Zhitao , Tian Jian
Published: November 2020

The contribution of type II alveolar epithelial stem cells (AEC II) to radiation-induced lung fibrosis (RILF) is largely unknown. Cell differentiation phenotypes are determined by the balance between Lin28 and lethal-7 microRNA (let-7 miRNA). Lin28 is activated by β-catenin. The aim of this study was to track AEC II phenotypes at different phases of injury following thoracic irradiation and examine the expression of β-catenin, Lin28 and let-7 to identify their role in AEC II differentiation. Results showed that coexpression of prosurfactant protein C (proSP-C, an AEC II biomarker) and HOPX (homeobox only protein X, an AEC I biomarker) or vimentin (a differentiation marker) was detected in AEC II post-irradiation. The protein expression levels of HOPX and proSP-C were significantly downregulated, but vimentin was significantly upregulated following irradiation. The expression of E-cadherin, which prevents β-catenin from translocating to the nucleus, was downregulated, and the expression of β-catenin and Lin28 was upregulated after irradiation (P < 0.05 to P < 0.001). Four let-7 miRNA members (a, b, c and d) were upregulated in irradiated lungs (P < 0.05 to P < 0.001), but let-7d was significantly downregulated at 5 and 6 months (P < 0.001). The ratios of Lin28 to four let-7 members were low during the early phase of injury and were slightly higher after 2 months. Intriguingly, the Lin28/let-7d ratio was strikingly increased after 4 months. We concluded that β-catenin contributed to RILF by promoting Lin28 expression, which increased the number of AEC II and the transcription of profibrotic molecules. In this study, the downregulation of let-7d miRNA by Lin28 resulted in the inability of AEC II to differentiate into type I alveolar epithelial cells (AEC I).
Every cloud has a silver lining: how abiotic stresses affect gene expression in plant-pathogen interactions
Authors: Zarattini Marco , Farjad Mahsa , Launay Alban , Cannella David , Soulié Marie-Christine , Bernacchia Giovanni , Fagard Mathilde
Published: November 2020

Current environmental and climate changes are having a pronounced influence on the outcome of plant–pathogen interactions, further highlighting the fact that abiotic stresses strongly affect biotic interactions at various levels. For instance, physiological parameters such as plant architecture and tissue organization together with primary and specialized metabolism are affected by environmental constraints, and these combine to make an individual plant either a more or less suitable host for a given pathogen. In addition, abiotic stresses can affect the timely expression of plant defense and pathogen virulence. Indeed, several studies have shown that variations in temperature, and in water and mineral nutrient availability affect the expression of plant defense genes. The expression of virulence genes, known to be crucial for disease outbreak, is also affected by environmental conditions, potentially modifying existing pathosystems and paving the way for emerging pathogens. In this review, we summarize our current knowledge on the impact of abiotic stress on biotic interactions at the transcriptional level in both the plant and the pathogen side of the interaction. We also perform a metadata analysis of four different combinations of abiotic and biotic stresses, which identifies 197 common modulated genes with strong enrichment in Gene Ontology terms related to defense . We also describe the multistress-specific responses of selected defense-related genes.
TGA class II transcription factors are essential to restrict oxidative stress in response to UV-B stress in Arabidopsis
Authors: Herrera-Vásquez Ariel , Fonseca Alejandro , Ugalde José Manuel , Lamig Liliana , Seguel Aldo , Moyano Tomás C , Gutiérrez Rodrigo A , Salinas Paula , Vidal Elena A , Holuigue Loreto
Published: November 2020

Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription–PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure.
Strategies for Sustainability of University-Based Medical Laboratory Sciences Programs
Authors: Behan Kristina Jackson
Published: November 2020

The COVID-19 pandemic has taken a major toll on the economy and funding for public education. For that reason, the pandemic has a worrisome effect on the sustainability of university/college based Medical Laboratory Sciences MLS training programs. Stakeholders of university-based MLS programs include university administrators, students, clinical affiliates and faculty. Each group has specific goals and challenges that affect the sustainability of the program. This report details strategies that can be used to satisfy the goals specific to key stakeholders that lead to sustainability. These strategies apply in pandemic times and in the back-to-normal future.
Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes
Authors: Tennessen Jacob A , Duraisingh Manoj T
Published: November 2020

Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host–parasite coevolutionary dynamics.
Human GTPBP5 is involved in the late stage of mitoribosome large subunit assembly
Authors: Cipullo Miriam , Pearce Sarah F , Lopez Sanchez Isabel G , Gopalakrishna Shreekara , Krüger Annika , Rosenberger Florian A , Busch Jakob D , Li Xinping , Wredenberg Anna , Atanassov Ilian , Rorbach Joanna
Published: November 2020

Human mitoribosomes are macromolecular complexes essential for translation of 11 mitochondrial mRNAs. The large and the small mitoribosomal subunits undergo a multistep maturation process that requires the involvement of several factors. Among these factors, GTP-binding proteins (GTPBPs) play an important role as GTP hydrolysis can provide energy throughout the assembly stages. In bacteria, many GTPBPs are needed for the maturation of ribosome subunits and, of particular interest for this study, ObgE has been shown to assist in the 50S subunit assembly. Here, we characterize the role of a related human Obg-family member, GTPBP5. We show that GTPBP5 interacts specifically with the large mitoribosomal subunit (mt-LSU) proteins and several late-stage mitoribosome assembly factors, including MTERF4:NSUN4 complex, MRM2 methyltransferase, MALSU1 and MTG1. Interestingly, we find that interaction of GTPBP5 with the mt-LSU is compromised in the presence of a non-hydrolysable analogue of GTP, implying a different mechanism of action of this protein in contrast to that of other Obg-family GTPBPs. GTPBP5 ablation leads to severe impairment in the oxidative phosphorylation system, concurrent with a decrease in mitochondrial translation and reduced monosome formation. Overall, our data indicate an important role of GTPBP5 in mitochondrial function and suggest its involvement in the late-stage of mt-LSU maturation.
Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems
Authors: Mestre Mario Rodríguez , González-Delgado Alejandro , Gutiérrez-Rus Luis I , Martínez-Abarca Francisco , Toro Nicolás
Published: November 2020

Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.
Genome-wide integration site detection using Cas9 enriched amplification-free long-range sequencing
Authors: van Haasteren Joost , Munis Altar M , Gill Deborah R , Hyde Stephen C
Published: November 2020

The gene and cell therapy fields are advancing rapidly, with a potential to treat and cure a wide range of diseases, and lentivirus-based gene transfer agents are the vector of choice for many investigators. Early cases of insertional mutagenesis caused by gammaretroviral vectors highlighted that integration site (IS) analysis was a major safety and quality control checkpoint for lentiviral applications. The methods established to detect lentiviral integrations using next-generation sequencing (NGS) are limited by short read length, inadvertent PCR bias, low yield, or lengthy protocols. Here, we describe a new method to sequence IS using Amplification-free Integration Site sequencing (AFIS-Seq). AFIS-Seq is based on amplification-free, Cas9-mediated enrichment of high-molecular-weight chromosomal DNA suitable for long-range Nanopore MinION sequencing. This accessible and low-cost approach generates long reads enabling IS mapping with high certainty within a single day. We demonstrate proof-of-concept by mapping IS of lentiviral vectors in a variety of cell models and report up to 1600-fold enrichment of the signal. This method can be further extended to sequencing of Cas9-mediated integration of genes and to in vivo analysis of IS. AFIS-Seq uses long-read sequencing to facilitate safety evaluation of preclinical lentiviral vector gene therapies by providing IS analysis with improved confidence.