bluuebunny/crossref_metadata_2025 huggingface dataset:
Suppression of aggregate and amyloid formation by a novel intrinsically disordered region in metazoan Hsp110 chaperones
Authors: Yakubu Unekwu M. , Morano Kevin A.
Published: January 2021

Molecular chaperones maintain protein homeostasis (proteostasis) by ensuring the proper folding of polypeptides. Loss of proteostasis has been linked to the onset of numerous neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease. Hsp110 is related to the canonical Hsp70 class of protein folding molecular chaperones and interacts with Hsp70 as a nucleotide exchange factor (NEF), promoting rapid cycling of ADP for ATP. In addition to its NEF activity, Hsp110 possesses an Hsp70-like substrate binding domain (SBD) whose biological roles remain undefined. Previous work inDrosophila melanogasterhas shown that loss of the sole Hsp110 gene (Hsc70cb) accelerates the aggregation of polyglutamine (polyQ)-expanded human Huntingtin, while its overexpression protects against polyQ-mediated neuronal cell death. We hypothesize that in addition to its role as an Hsp70 NEF,DrosophilaHsp110 may function in the fly as a protective protein “holdase”, preventing the aggregation of unfolded polypeptides via the SBD-β subdomain. Using anin vitroprotein aggregation assay we demonstrate for the first time thatDrosophilaHsp110 effectively prevents aggregation of the model substrate citrate synthase. We also report the discovery of a redundant and heretofore unknown potent holdase capacity in a 138 amino-acid region of Hsp110 carboxyl-terminal to both SBD-β and SBD-α (henceforth called the C-terminal extension). This sequence is highly conserved in metazoan Hsp110 genes, completely absent from fungal representatives, includingSaccharomyces cerevisiae SSE1, and is computationally predicted to contain an intrinsically disordered region (IDR). We demonstrate that this IDR sequence within the human Hsp110s, Apg-1 and Hsp105α, inhibits the formation of amyloid Aβ-42 and α-synuclein fibrilsin vitrobut cannot mediate fibril disassembly. Together these findings demonstrate the existence of a second independent, passive holdase property of metazoan Hsp110 chaperones capable of suppressing both general protein aggregation and amyloidogenesis and raise the possibility of exploitation of this IDR for therapeutic benefit in combating neurodegenerative disease.
Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium
Authors: Trotter Valentine V. , Shatsky Maxim , Price Morgan N. , Juba Thomas R. , Zane Grant M. , De León Kara B. , Majumder Erica L. , Gui Qin , Ali Rida , Wetmore Kelly M. , Kuehl Jennifer V. , Arkin Adam P. , Wall Judy D. , Deutschbauer Adam M. , Chandonia John-Marc , Butland Gareth P.
Published: January 2021

Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRBDesulfovibrio vulgarisHildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.
Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein
Authors: Hodge Curtis D. , Rosenberg Daniel J. , Wilamowski Mateusz , Joachimiak Andrzej , Hura Greg L. , Hammel Michal
Published: January 2021

Monoclonal antibodies (mAbs) are the basis of treatments and diagnostics for pathogens and other biological phenomena. We conducted a structural characterization of mAbs against the N-terminal domain of nucleocapsid protein (NPNTD) from SARS-CoV-2 using small angle X-ray scattering (SAXS). Our solution-based results distinguished the mAbs’ flexibility and how this flexibility impacts the assembly of multiple mAbs on an antigen. By pairing two mAbs that bind different epitopes on the NPNTD, we show that flexible mAbs form a closed sandwich-like complex. With rigid mAbs, a juxtaposition of the Fabs is prevented, enforcing a linear arrangement of the mAb pair, which facilitates further mAb polymerization. In a modified sandwich ELISA, we show the rigid mAb-pairings with linear polymerization led to increased NPNTDdetection sensitivity. These enhancements can expedite the development of more sensitive and selective antigen-detecting point-of-care lateral flow devices (LFA), key for early diagnosis and epidemiological studies of SARS-CoV-2 and other pathogens.
A fragment-based protein interface design algorithm for symmetric assemblies
Authors: Laniado Joshua , Meador Kyle , Yeates Todd O.
Published: January 2021

Theoretical and experimental advances in protein engineering have led to the creation of precisely defined, novel protein assemblies of great size and complexity, with diverse applications. One powerful approach involves designing a new attachment or binding interface between two simpler symmetric oligomeric protein components. The required methods of design, which present both similarities and key differences compared to problems in protein docking, remain challenging, and are not yet routine. With the aim of more fully enabling this emerging area of protein material engineering, we developed a computer program, Nanohedra, to introduce two key advances. First, we encoded in the program the construction rules (i.e. the search space parameters) that underlie all possible symmetric material constructions. Second, we developed algorithms for rapidly identifying favorable docking/interface arrangements based on tabulations of empirical patterns of known protein fragment-pair associations. As a result, the candidate poses that Nanohedra generates for subsequent amino acid interface design appear highly native-like (at the protein backbone level), while simultaneously conforming to the exacting requirements for symmetry-based assembly. A retrospective computational analysis of successful vs failed experimental studies supports the expectation that this should improve the success rate for this challenging area of protein engineering.
Essential Role of Placenta Derived Interferon Stimulated Gene 20 Against ZIKA Virus Infection
Authors: Ding Jiahui , Aldo Paulomi , Roberts Cai M. , Stabach Paul , Liu Hong , You Yuan , Qiu Xuemin , Jeong Jiwon , Maxwell Anthony , Lindenbach Brett , Braddock Demetrios , Liao Aihua , Mor Gil
Published: January 2021

Zika virus is a positive-sense single-stranded RNA virus, which can be transmitted across the placenta and leads to adverse effects on fetal development during pregnancy. The severity of these complications highlights the importance of prevention and treatment. However, no vaccines or drugs are currently available. In this study, we characterized the IFNβ-mediated antiviral response in trophoblast cells in order to identify critical components that are necessary for the successful control of viral replication; and determined whether we could use the components of the IFN-induced response as a replacement therapy for ZIKA viral infection during pregnancy. We identified and characterized interferon stimulated gene 20 (ISG20), playing a central role in controlling Zika infection in trophoblast cells, and successfully established a recombinant ISG20-Fc protein that effectively decrease viral titers in vitro and in vivo by maintaining its exonuclease activity and displaying immune modulatory functions. Therefore, rISG20-Fc is a promising anti-viral/immune modulatory approach for the control and prevention of RNA viral infections such as ZIKA virus.
CwlQ is required for swarming motility but not flagellar assembly inBacillus subtilis
Authors: Sanchez Sandra , Dunn Caroline M , Kearns Daniel B.
Published: January 2021

Hydrolytic enzymes play an essential role in the remodeling of bacterial peptidoglycan (PG), an extracellular mesh-like structure that retains the membrane in the context of high internal osmotic pressure. Peptidoglycan (PG) integrity must be unfailingly stable to preserve cell integrity but must also be dynamically remodeled for the cell grow, divide and insert macromolecular machines. The flagellum is one such macromolecular machine that transits the PG and the insertion of which is aided by localized activity of a dedicated PG hydrolase in Gram-negative bacteria. To date, there is no known dedicated hydrolase in Gram-positive bacteria for insertion of flagella and here we take a reverse-genetic candidate-gene approach to find that cells mutated for the lytic transglycosylase CwlQ exhibited a severe defect in flagellar dependent swarming motility. We show that CwlQ required its active site to promote swarming, was expressed by the motility sigma factor SigD, and was secreted by the type III secretion system housed inside the flagellum. Nonetheless, cells mutated for CwlQ remained proficient for flagellar biosynthesis even when mutated in combination with four other hydrolases related to motility (LytC, LytD, LytF, and CwlO). The PG hydrolase essential for flagellar synthesis inB. subtilis, if any, remains unknown.
Immunogenicity and protective efficacy of a highly thermotolerant, trimeric SARS-CoV-2 receptor binding domain derivative
Authors: Malladi Sameer Kumar , Patel Unnatiben Rajeshbhai , Rajmani Raju S , Singh Randhir , Pandey Suman , Kumar Sahil , Khaleeq Sara , van Vuren Petrus Jansen , Riddell Shane , Goldie Sarah , Gayathri Savitha , Chakraborty Debajyoti , Kalita Parismita , Pramanick Ishika , Agarwal Nupur , Reddy Poorvi , Girish Nidhi , Upadhyaya Aditya , Khan Mohammad Suhail , Kanjo Kawkab , Bhat Madhuraj , Mani Shailendra , Bhattacharyya Sankar , Siddiqui Samreen , Tyagi Akansha , Jha Sujeet , Pandey Rajesh , Tripathi Shashank , Dutta Somnath , McAuley Alexander J. , Singanallur Nagendrakumar Balasubramanian , Vasan Seshadri S. , Ringe Rajesh P. , Varadarajan Raghavan
Published: January 2021

The Receptor Binding Domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of ∼80-100 mg/liter in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of upto 100 °C and were stable to long term storage of over 4 weeks at 37 °C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation, elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were ∼ three-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1 and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.
Epidemiological Investigation of New SARS-CoV-2 Variant of Concern 202012/01 in England
Authors: Gravagnuolo Alfredo Maria , Faqih Layla , Cronshaw Cara , Wynn Jackie , Burglin Lewis , Klapper Paul , Wigglesworth Mark
Published: January 2021

Lighthouse Labs network tests for the presence of RNA of SARS-CoV-2, the causative agent of COVID-19. The Thermofisher TaqPath assay targets three regions of SARS-CoV-2; ORF1ab, N and S-genes. The assay identified a drop in S-gene target detection among positive samples due to the circulation of a new SARS-CoV-2 Variant of Concern (VOC) designated as 202012/01. By end of December 2020, 60% of daily positive test results at Alderley Park Lighthouse Labs, were linked to the new Variant of Concern. This timeline view identifies the rapid spread of the variant across the country.
Comparison and analysis of various complementary diagnosis methods for the current situation and problems of COVID-19 diagnosis
Authors: Huh Hee Jin , Chae Seok Lae , Kim Dong-Min
Published: January 2021

We evaluated and compared the diagnostic performance of fluorescence immunoassay (FIA) and two types of serological diagnostic tests: enzyme-linked immunosorbent assay (ELISA) and immunochromatographic assay (ICA) for detection of SARS-CoV-2 antigen and antibody to diagnose COVID-19 infections. This study is aimed to analyze and compare the current status and problems of COVID-19 diagnosis and various alternative diagnostic methods that are viable. The enrolled subjects in our study population were tested with real-time polymerase chain reaction (RT-PCR). ELISA and immunochromatographic diagnostic kit were used to diagnose 362 positive and 3010 negative SARS-CoV-2 specimens, and antigen fluorescence immunoassay kit was used on 62 positive and 70 negative SARS-CoV-2 RT-PCR confirmed samples for diagnosis. As a result, categorizing by the patient symptom onset days, PCL COVID19 Total Ab EIA (ELISA) showed the sensitivity of 93.4% from 15 to 21 days, 94.2% from over 22 days, and the specificity of 99.97%. PCL COVID19 IgG/IgM Rapid Gold (ICA) had a sensitivity of 86.9%, 97.4%, and the specificity of 98.14% respectively. PCL COVID19 Ag Rapid FIA sensitivity was 93.8% from 0 to 7 days, 71.4% from 8 to 12 days and specificity was 98.57%. In conclusion, COVID-19 Ab ELISA and ICA, and COVID-19 Ag FIA are all complementary and applicable diagnostic methods to resolve the current problems of COVID-19 diagnosis.
SARS-CoV-2 infection control implementation based on sources of infection showing directions for three age groups in Japan
Authors: Hata Atsuko , Kurita Junko , Muso Eri , Katayama Toshiro , Hata Takahide , Ohkusa Yasushi
Published: January 2021

Background

Some aspects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in children and adults remain unclear. This report describes different SARS-CoV-2 transmission patterns by age group in Japan.

Methods and findings

This retrospective observational case series study analyzed transmission patterns of real-time polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infections found by local health authorities and commercial laboratories during January 14 through July 31, 2020 in Japan. After ascertaining the infection source for every symptomatic case as clusters at households, daycare facilities, schools, hospitals and workplaces etc., their associated transmission patterns were analyzed. Identified cases were divided into three groups: underage, < 20; adults, 20–59; and elderly people 60 years old and older. The reproductive number (R)s of respective transmission directions found for the respective age groups were compared.

Of 26,986 total cases, 23,746 unknown cases were found, leaving 3,240 ascertained sources of infection (12.0%) comprising 125 (3.9%) underage, 2350 (72.5%) adult, and 765 (23.6%) elderly people. The respective Rs of underage infection sources directed to underage, adult, and elderly people were estimated respectively as 0.0415 (95% CI, 0.0138–0.0691), 1.11 (95% CI, 0.9171–1.3226), and 0.2811 (95% CI, 0.2074–0.3687). The respective Rs of adult infection source directed to underage, adult, and elderly people were estimated respectively as 0.0140 (95% CI, 0.0120–0.0162), 0.5392 (95% CI, 0.5236–0.5550), and 0.1135 (95% CI, 0.1074–0.1197). The respective Rs of elderly infection source directed to underage, adult, and elderly people were estimated as 0.065 (95% CI, 0.0039–0.0091), 0.3264 (95% CI, 0.3059–0.3474), and 0.3991 (95% CI, 0.3757–0.4229).

Conclusions

The main sources of SARS-CoV-2 infection were adults and elderly people. The R of underage people directed to adults was greater than 1 because of close familial contact but they were unlikely to become carriers transmitting SARS-CoV-2 because they accounted for a minority for transmissions. Apparently, SARS-CoV-2 was transmitted among adults and elderly people, suggesting that infection control of SARS-CoV-2 should be managed specifically by generation.
Reference values and validation of the 1-min sit-to-stand test in healthy 5- to 16-year-old youth: a cross-sectional study
Authors: Haile Sarah R , Fühner Thea , Granacher Urs , Stocker Julien , Radtke Thomas , Kriemler Susi
Published: January 2021

Objectives

It is essential to have simple, reliable and valid tests to measure children’s functional capacity in schools or medical practice. The 1-min sit-to-stand test (STS) is a quick fitness test requiring little equipment or space that is increasingly used in both healthy populations and those with chronic disease. We aimed to provide age and sex-specific reference values of STS in healthy children and adolescents and to evaluate its short-term reliability and construct validity.

Design, setting and participants

Cross-sectional random sample from 6 public schools and 1 science fair in central Europe. Overall, 587 healthy participants aged 5-16 years were recruited and divided into age groups of 3 years each.

Outcomes

1-minute STS. To evaluate short-term reliability, some children performed the STS twice. To evaluate construct validity, some children also performed a standing long jump (SLJ) and a maximal incremental exercise test.

Results

Data from 547 5-16 year old youth were finally included in the analyses. The median number of repetitions in 1 minute in males (females) ranged from 55 [95% CI 38 to 72] (53 [35 to 76]) in 14-16 year-olds to 59 [41 to 77] (60 [38 to 77]) in 8-10 year-olds. Children who repeated STS showed a learning effect of on average 4.8 repetitions more than the first test (95% limits of agreement −6.7 to 16.4). Moderate correlations were observed between the STS and the SLJ (r= 0.48) and the maximal exercise test (r= 0.43).

Conclusions

The reported STS reference values can be used to interpret STS test performance in children and adolescents. The STS appears to have good test-retest reliability, but a learning effect of about 10%. The association of STS with other measures of physical fitness should be further explored in a larger study and technical standards for its conduct are needed.

Strengths and Limitations of this Study

Large sample size (N = 547)

Reference values according to sex and age group (5-7, 8-10, 11-13 and 14-16)

Evaluation of test-retest reliability and construct validity

Convenience not population-based sample

Not all outcomes have been measured on each participant
Importance of patient bed pathways and length of stay differences in predicting COVID-19 bed occupancy in England
Authors: Leclerc Quentin J. , Fuller Naomi M. , Keogh Ruth H. , Diaz-Ordaz Karla , Sekula Richard , Semple Malcolm G ,   ISARIC4C Investigators,   CMMID COVID-19 Working Group, Atkins Katherine E. , Procter Simon R. , Knight Gwenan M.
Published: January 2021

Objectives

Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient’s “bed pathway” - the sequence of transfers between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy.

Design

We obtained data from University College Hospital (UCH) and the ISARIC4C COVID-19 Clinical Information Network (CO-CIN) on hospitalised patients with COVID-19 who required care in general ward or critical care (CC) beds to determine possible bed pathways and LoS. We developed a discrete-time model to examine the implications of using either bed pathways or only average LoS by bed type to forecast bed occupancy. We compared model-predicted bed occupancy to publicly available bed occupancy data on COVID-19 in England between March and August 2020.

Results

In both the UCH and CO-CIN datasets, 82% of hospitalised patients with COVID-19 only received care in general ward beds. We identified four other bed pathways, present in both datasets: “Ward, CC, Ward”, “Ward, CC”, “CC” and “CC, Ward”. Mean LoS varied by bed type, pathway, and dataset, between 1.78 and 13.53 days.

For UCH, we found that using bed pathways improved the accuracy of bed occupancy predictions, while only using an average LoS for each bed type underestimated true bed occupancy. However, using the CO-CIN LoS dataset we were not able to replicate past data on bed occupancy in England, suggesting regional LoS heterogeneities.

Conclusions

We identified five bed pathways, with substantial variation in LoS by bed type, pathway, and geography. This might be caused by local differences in patient characteristics, clinical care strategies, or resource availability, and suggests that national LoS averages may not be appropriate for local forecasts of bed occupancy for COVID-19.
U-shaped effect of blood pressure on structural OCT metrics and retinal blood flow autoregulation in ophthalmologically healthy subjects
Authors: Pappelis Konstantinos , Jansonius Nomdo M.
Published: January 2021

Objective

1) To investigate the effect of low blood pressure (BP), treated arterial hypertension (AHT), and untreated AHT on the ganglion cell-inner plexiform layer (GCIPL) and the retinal nerve fiber layer (RNFL) thickness of non-glaucomatous eyes and 2) to elucidate whether this effect is related to crossing the lower limit of retinal blood flow (RBF) autoregulation.

Design

Cross-sectional, case-control.

Subjects

We included 96 eyes of 96 ophthalmologically healthy subjects (age 50-65). Participants were prospectively recruited from a large-scale cohort study in the northern Netherlands (n=167,000; Lifelines Biobank). They were allocated to four groups (low BP, normal BP [controls], treated AHT, untreated AHT), based on information from previous visits and strict distribution criteria.

Methods

Inner retinal layer thicknesses were obtained with optical coherence tomography (OCT). Fractal dimension of the superficial microvasculature was quantified with OCT-angiography and customized software. Central retinal vessel diameters were obtained from fundus images. BP and intraocular pressure measurements were also acquired. Measurements were combined with a validated physiological model to estimate vascular outcome measures. Structural and vascular metrics were compared across groups and mediation analysis was performed.

Main outcome measures

Structural: macular GCIPL and RNFL (mRNFL), peripapillary RNFL (pRNFL) thickness. Vascular: RBF, retinal vascular resistance (RVR), autoregulatory reserve (AR).

Results

Compared to controls, GCIPL was thinner in the low BP group (P=0.013), treated hypertensives (P=0.007), and untreated hypertensives (P=0.007). Treated hypertensives exhibited the thinnest mRNFL (P=0.001), temporal pRNFL (P=0.045), and inferior pRNFL (P=0.034). In multivariable analysis, RBF was mediating the association of GCIPL thickness with BP within the combined low BP group and controls (P=0.003), RVR together with AR were mediating the same association within the combined treated hypertensives and controls (P=0.001 and P=0.032), and RVR was mediating the association within the combined untreated antihypertensives and controls (P=0.022).

Conclusions

We uncovered GCIPL and RNFL thinning related to both tails of the BP distribution. GCIPL thinning was associated with reduced RBF autoregulatory capacity. This predisposition to glaucomatous damage could explain the frequent epidemiological finding of increased glaucoma risk in certain subgroups, such as subjects with nocturnal BP dipping or aggressively treated AHT. Longitudinal studies could confirm this postulation.
Heart rate and heart rate variability in patients with chronic inflammatory joint disease: The role of pain duration and the insular cortex
Authors: Buschmann Leona Katharin , Spindler Melanie , Sörös Peter , Bantel Carsten
Published: January 2021

Chronic inflammatory joint diseases (CIJD) have been linked to increased cardiovascular morbidity and mortality. A decisive reason could be a dysregulation of the autonomic nervous system (ANS), which is responsible for the control of cardio-vascular function. So far, the cause of changes in ANS functions remains elusive. In this study, we investigate the role of chronic pain and the insular cortex in autonomic control of cardiac functioning in patients with CIJD. We studied the sympathetic and parasympathetic branch of the ANS through the assessment of heart rate and heart rate variability (HRV) at rest and under cognitive stimulation. Furthermore, we investigated insular cortex volume by performing surface-based brain morphometry with FreeSurfer. For this study, 22 individual age- and sex-matched pairs for the magnetic resonance imaging analyses and 14 for the HRV analyses were recruited. Pain duration was negatively correlated with the resting heart rate in patients with chronic inflammatory joint diseases (n = 19). In a multiple linear regression model including only CIJD patients with HR at rest as a dependent variable, we found a significant positive relationship between HR at rest and the volume of the left insular cortex and a significant negative relationship between HR at rest and the volume of the right insular cortex. However, we found no significant differences in HRV parameters or insular cortex volumes between both groups. In this study we provide evidence to suggest insular cortex involvement in the process of ANS changes due to chronic pain in CIJD patients.
Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection
Authors: Silverstein Noah J. , Wang Yetao , Manickas-Hill Zachary , Carbone Claudia , Dauphin Ann , Boribong Brittany P. , Loiselle Maggie , Davis Jameson , Leonard Maureen M. , Kuri-Cervantes Leticia ,   MGH COVID-19 Collection & Processing Team, Meyer Nuala J. , Betts Michael R. , Li Jonathan Z. , Walker Bruce , Yu Xu G. , Yonker Lael M. , Luban Jeremy
Published: January 2021

Risk of severe COVID-19 increases with age, is greater in males, and is associated with lymphopenia, but not with higher burden of SARS-CoV-2. It is unknown whether effects of age and sex on abundance of specific lymphoid subsets explain these correlations. This study found that the abundance of innate lymphoid cells (ILCs) decreases more than 7-fold over the human lifespan — T cell subsets decrease less than 2-fold — and is lower in males than in females. After accounting for effects of age and sex, ILCs, but not T cells, were lower in adults hospitalized with COVID-19, independent of lymphopenia. Among SARS-CoV-2-infected adults, the abundance of ILCs, but not of T cells, correlated inversely with odds and duration of hospitalization, and with severity of inflammation. ILCs were also uniquely decreased in pediatric COVID-19 and the numbers of these cells did not recover during follow-up. In contrast, children with MIS-C had depletion of both ILCs and T cells, and both cell types increased during follow-up. In both pediatric COVID-19 and MIS-C, ILC abundance correlated inversely with inflammation. Blood ILC mRNA and phenotype tracked closely with ILCs from lung. Importantly, blood ILCs produced amphiregulin, a protein implicated in disease tolerance and tissue homeostasis, and the percentage of amphiregulin-producing ILCs was higher in females than in males. These results suggest that, by promoting disease tolerance, homeostatic ILCs decrease morbidity and mortality associated with SARS-CoV-2 infection, and that lower ILC abundance accounts for increased COVID-19 severity with age and in males.
Understanding COVID-19 dynamics and the effects of interventions in the Philippines: A mathematical modelling study
Authors: Caldwell Jaime M. , Lara-Tuprio Elvira de , Teng Timothy Robin , Estuar Maria Regina Justina E. , Sarmiento Raymond Francis R. , Abayawardana Milinda , Leong Robert Neil F. , Gray Richard T. , Wood James G. , McBryde Emma S. , Ragonnet Romain , Trauer James M.
Published: January 2021

Objective

COVID-19 appears to have caused less severe outbreaks in many low- and middle-income countries (LMIC) compared with high-income countries, possibly because of differing demographics, socio-economics, surveillance, and policy responses. Here, we investigate the role of multiple factors on COVID-19 dynamics in the Philippines, a LMIC that has had a relatively severe COVID-19 outbreak.

Methods

We applied an age-structured compartmental model that incorporated time-varying mobility, testing, and personal protective behaviors (through a “Minimum Health Standards” policy, MHS) to represent the Philippines COVID-19 epidemic nationally and for three highly affected regions (Calabarzon, Central Visayas, and the National Capital Region). We estimated effects of control measures, key epidemiological parameters, and interventions.

Findings

Population age structure, contact rates, mobility, testing, and MHS were sufficient to explain the Philippines epidemic based on the good fit between modelled and reported cases, hospitalisations, and deaths. Several of the fitted epidemiological parameters were consistent with those reported in high-income settings. The model indicated that MHS reduced the probability of transmission per contact by 15-26%. The February 2021 case detection rate was estimated at ∼9%, population recovered at ∼12%, and scenario projections indicated high sensitivity to MHS adherence.

Conclusions

COVID-19 dynamics in the Philippines are driven by age, contact structure, mobility, and MHS adherence, and the epidemic can be understood within a similar framework as for high-income settings. Continued compliance with low-cost MHS should allow the Philippines to maintain epidemic control until vaccines are widely distributed, but disease resurgence could occur due to low population immunity and detection rates.
An Estimation of Reproduction Number of SARS-CoV-2 by Age Class for Age Classes in Japan
Authors: Kurita Junko , Hata Takahide , Sugawara Tamie , Ohkusa Yasushi , Hata Atsuko
Published: January 2021

Background

Infectiousness of COVID-19 by age class inferred from the infection source and by infected people might be different. However, studies of such infectiousness have not been reported.

Object

The object of this study was estimation of reproduction numbers by age class of the source of infection and the infected persons. To do so, after examining a new procedure for reproduction number estimation, we checked infected places by age class of the source of infection and the infected persons.

Method

We ignore patients who infected no one because their reliability might be lower than that of patients who infected more than one person. We estimated the reproduction number from the histogram of the number of the infected people by the same patient, assuming that the histogram follows an exponential distribution.

Discussion and Conclusion

The obtained results demonstrated that the effective reproduction numbers for infection from children were very low. They were higher among adult and elderly people than among the same age class. Moreover, although the highest and second-highest infected places were ‘other’ and ‘at home’ with some exceptions, the data for infection at hospitals were remarkable among adults and elderly people. Among elderly people, infection at facilities for elderly was also high. Infections at nursing schools, schools, restaurants, and entertainment venues at night were negligible.
Gene expression profiling of lymph node sub-capsular sinus macrophages in cancer
Authors: Pellin Danilo , Claudio Natalie , Pucci Ferdinando
Published: January 2021

Lymph nodes are key lymphoid organs collecting lymph fluid and migratory cells from the tissue area they survey. When cancerous cells arise within a tissue, the sentinel lymph node is the first immunological organ to mount an immune response. Sub-capsular sinus macrophages (SSMs) are specialized macrophages residing in the lymph nodes that play important roles as gatekeepers against particulate antigenic material. In the context of cancer, SSMs capture tumor-derived extracellular vesicles (tEVs), a form of particulate antigen released in high amounts by tumor cells. We have recently demonstrated that SSMs possess anti-tumor activity because in their absence tumors grow faster. A comprehensive profiling of SSMs represents an important first step to identify the cellular and molecular mechanisms responsible for SSM anti-tumor activity. Unfortunately, the isolation of SSMs for molecular analyses is very challenging. Here, we combined an optimized dissociation protocol, careful marker selection and stringent gating strategies to highly purify SSMs. We provide evidence of decreased T and B cell contamination, which allowed us to reveal the gene expression profile of this elusive macrophage subset. Squamous cell carcinomas induced an increase in the expression of Fc receptors, lysosomal and proteasomal enzymes in SSMs. These results suggest that SSMs may be able to capture immune complexes for antigen processing and presentation to B and T cells on both MHC class I and II.
A convergent structure-function substrate of cognitive imbalances in autism
Authors: Hong Seok-Jun , Mottron Laurent , Park Bo-yong , Benkarim Oualid , Valk Sofie L. , Paquola Casey , Larivière Sara , Vos de Wael Reinder , Degré-Pelletier Janie , Soulieres Isabelle , Ramphal Bruce , Margolis Amy , Milham Michael , Di Martino Adriana , Bernhardt Boris C.
Published: January 2021

Autism is a common neurodevelopmental condition characterized by substantial phenotypic heterogeneity, which hinders diagnosis, research, and intervention. A leading example can be found in marked imbalances in language and perceptual skills, where deficits in one domain often co-exist with normal or even superior performance in the other domain. The current work capitalized on multiple data analytics including data-driven subtyping and dimensional approaches to quantify cognitive imbalances in multi-site datasets of individuals diagnosed with autism spectrum disorder (ASD) and neurotypical controls, and assessed structural and functional brain network substrates. Studying cognitive dimensions as well as multimodal neuroimaging signatures in 155 ASD and 151 neurotypical individuals, we observed robust evidence for a structure-function substrate of cognitive imbalances in ASD. Specifically, ASD presented with marked imbalances in cognitive profiles relative to neurotypical controls, characterized by verbal to non-verbal intelligence discrepancy. Different analytical approaches including subtyping and dimensional regression methods converged in showing that these imbalances were reflected in atypical cortical thickening and functional integration of language networks, alongside with sensory and higher cognitive networks. Phenotypic findings could be replicated in an independent sample of 325 ASD and 569 neurotypical controls. Although verbal and non-verbal intelligence are currently considered as specifiers unrelated to the categorical diagnosis of autism, our results show that intelligence disparities are accentuated in ASD and relate to a consistent structure-function substrate affecting multiple brain networks. Our findings motivate the incorporation of cognitive imbalances in future autism research, which may help to parse the phenotypic heterogeneity of autism and potentially inform intervention-oriented subtyping.
Improving integrative 3D modeling into low- to medium- resolution EM structures with evolutionary couplings
Authors: McCafferty Caitlyn L. , Taylor David W. , Marcotte Edward M.
Published: January 2021

Electron microscopy (EM) continues to provide near-atomic resolution structures for well-behaved proteins and protein complexes. Unfortunately, structures of some complexes are limited to low- to medium-resolution due to biochemical or conformational heterogeneity. Thus, the application of unbiased systematic methods for fitting individual structures into EM maps is important. A method that employs co-evolutionary information obtained solely from sequence data could prove invaluable for quick, confident localization of subunits within these structures. Here, we incorporate the co-evolution of intermolecular amino acids as a new type of distance restraint in the Integrative Modeling Platform (IMP) in order to build three-dimensional models of atomic structures into EM maps ranging from 10-14 Å in resolution. We validate this method using four complexes of known structure, where we highlight the conservation of intermolecular couplings despite dynamic conformational changes using the BAM complex. Finally, we use this method to assemble the subunits of the bacterial holo-translocon into a model that agrees with previous biochemical data. The use of evolutionary couplings in integrative modeling improves systematic, unbiased fitting of atomic models into medium- to low-resolution EM maps, providing additional information to integrative models lacking in spatial data.
Exonic Disruption Facilitates Antiviral CRISPR-Cas9 Activity for Multistrain HIV-1 Elimination
Authors: Herskovitz Jonathan , Hasan Mahmudul , Patel Milankumar , Blomberg Wilson R. , Cohen Jacob D. , Machhi Jatin , Stein Daniel , Schroder Evan A. , McMillan JoEllyn , Gurumurthy Channabasavaiah B. , Kevadiya Bhavesh D. , Gendelman Howard E.
Published: January 2021

A barrier to HIV-1 cure rests in the persistence of proviral DNA in infected CD4+ leukocytes. The high mutation rate of HIV-1 gives rise to numerous circulating strains with increased capacity for immune evasion and antiretroviral drug resistance. To facilitate viral elimination while accounting for this diversity, we propose genetic inactivation of proviral DNA with CRISPR-spCas9. We designed a library of “mosaic gRNAs” against a HIV-1 consensus sequence constructed from 4004 clinical strains, targeting the viral transcriptional regulator tat. Testing in 7 HIV-1 transmitted founder strains led, on average, to viral reductions of 82% with tandem TatD and TatE (TatDE) treatment. No off-target cleavages were recorded. Lentiviral transduction of TatDE attenuated latency reversal by 94% in HIV-infected, transcriptionally silent ACH2 T cells. In all, TatDE guide RNAs successfully disrupted 5 separate HIV-1 exons (tat1-2/rev1-2/gp41) providing a pathway for CRISPR-directed HIV-1 cure therapies.

Significance Statement

Over 38 million individuals worldwide are infected with HIV-1, which necessitates lifelong dependence on antiretroviral therapy (ART) to prevent viral replication that leads to AIDS. Efforts to rid hosts of HIV-1 are limited by the virus’ abilities to integrate proviral DNA in nuclei, mutate their genomes, and lay dormant for decades during ART treatment. We developed mosaic guide RNAs, TatD and TatE, for CRISPR-Cas9 that recognize the majority of known HIV-1 strains and inactivate 94% of proviral DNA in latently infected cells. Tandem TatDE-CRISPR inactivation of 5 viral exons (tat1-2,rev1-2, andgp41), which blocked HIV-1 replication for 28 days in CD4+ T cells without unwanted editing to the host genome, may serve as a viable strategy for HIV cure.
Crosstalk between H2A variant-specific modifications impacts vital cell functions
Authors: Schmücker Anna , Lei Bingkun , Lorković Zdravko J. , Capella Matías , Braun Sigurd , Bourguet Pierre , Mathieu Olivier , Mechtler Karl , Berger Frédéric
Published: January 2021

Histone variants are distinguished by specific substitutions and motifs that might be subject to post-translational modifications (PTMs). Compared with the high conservation of H3 variants, the N- and C-terminal tails of H2A variants are more divergent and are potential substrates for a more complex array of PTMs, which have remained largely unexplored. We used mass spectrometry to inventory the PTMs of the two heterochromatin-enriched variants H2A.W.6 and H2A.W.7 ofArabidopsis, which harbor the C-terminal motif KSPK. This motif is also found in macroH2A variants in animals and confers specific properties to the nucleosome. We showed that H2A.W.6 is phosphorylated by the cell cycle-dependent kinase CDKA specifically at KSPK. In contrast, this modification is absent on H2A.W.7, which also harbors the SQ motif associated with the variant H2A.X. Phosphorylation of the SQ motif is critical for the DNA damage response but is suppressed in H2A.W.7 by phosphorylation of KSPK. To identify factors involved in this suppression mechanism, we performed a synthetic screen in fission yeast expressing a mimic of theArabidopsisH2A.W.7. Among those factors was the BRCT-domain protein Mdb1. We showed that phosphorylation of KSPK prevents binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and as a result hampers response to DNA damage. Hence, cross-talks between motif-specific PTMs interfere with the vital functions of H2A variants. Such interference could be responsible for the mutual exclusion of specific motifs between distinct H2A variants. We conclude that sequence innovations in H2A variants have potentiated the acquisition of many specific PTMs with still unknown functions. These add a layer of complexity to the nucleosome properties and their impact in chromatin regulation.
The Amot/Integrin protein complex transmits mechanical forces required for vascular expansion
Authors: Zhang Yuanyuan , Zhang Yumeng , Kameishi Sumako , Barutello Giuseppina , Zheng Yujuan , Tobin Nicholas P. , Nicosia John , Hennig Katharina , Chiu David Kung-Chun , Balland Martial , Barker Thomas H. , Cavallo Federica , Holmgren Lars
Published: January 2021

Vascular development is a complex multistep process involving the coordination of cellular functions such as migration, proliferation and differentiation. Understanding the underlying mechanisms of these processes is of importance due to involvement of vessel expansion in various pathologies. How mechanical forces generated by cells and transmission of these physical forces control vascular development is poorly understood. Using an endothelial-specific genetic model in mice, we show that deletion of the scaffold protein, Angiomotin (Amot), inhibits migration and expansion of physical and pathological vascular network. We further show that Amot is required for tip cell migration and the extension of cellular filopodia. Exploitingin vivoandin vitromolecular approaches, we show that Amot binds talin and is essential for relaying forces between fibronectin and the cytoskeleton. Finally, we provide evidence that Amot is a novel component of the endothelial integrin adhesome and propose that Amot integrates spatial cues from the extra-cellular matrix in order to form a functional vascular network.
Adiponectin Preserves Metabolic Fitness During Aging
Authors: Li Na , Zhang Zhuzhen , Zhao Shangang , Zhu Yi , Gliniak Christy M. , Vishvanath Lavanya , An Yu A. , Wang May-yun , Deng Yingfeng , Zhu Qingzhang , Onodera Toshiharu , Oz Orhan K , Gordillo Ruth , Gupta Rana K. , Liu Ming , Horvath Tamas L. , Dixit Vishwa Deep , Scherer Philipp E.
Published: January 2021

Adiponectin is essential for the regulation of tissue substrate utilization and systemic insulin sensitivity. Clinical studies have suggested a positive association of circulating adiponectin with healthspan and lifespan. However, the direct effects of adiponectin on promoting healthspan and lifespan remain unexplored. Here, we are using an adiponectin null mouse and a transgenic adiponectin overexpression model. We directly assessed the effects of circulating adiponectin on the aging process and found that adiponectin null mice display exacerbated age-related glucose and lipid metabolism disorders. Moreover, adiponectin null mice have a significantly shortened lifespan on both chow and high-fat diet (HFD). In contrast, a transgenic mouse model with elevated circulating adiponectin levels has a dramatically improved systemic insulin sensitivity, reduced age-related tissue inflammation and fibrosis, and a prolonged healthspan and median lifespan. These results support a role of adiponectin as an essential regulator for healthspan and lifespan.
Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
Authors: Jones Jennifer E. , Sage Valerie Le , Padovani Gabriella H. , Calderon Michael , Wright Erik S. , Lakdawala Seema S.
Published: January 2021

The influenza A virus (IAV) genome consists of eight negative-sense viral RNA (vRNA) segments that are selectively assembled into progeny virus particles through RNA-RNA interactions. To identify relationships between vRNA segments, we examined parallel evolution between vRNA segments of seasonal human IAV, finding that evolutionary relationships between vRNA segments differ between subtypes and antigenically-shifted strains. Intersegmental relationships were distinct between H3N2 and H1N1 viruses, but largely conserved over time in H3N2 viruses. However, parallel evolution of vRNA segments diverged between H1N1 strains isolated before and after the 2009 pandemic. Surprisingly, intersegmental relationships were not driven solely by protein sequence, which is potentially indicative of RNA-RNA driven coevolution. Colocalization of highly coevolved vRNA segments was enriched over other pairs at the nuclear periphery during a productive viral infection. This study illustrates how phylogenetics can be applied to interrogate putative RNA interactions underlying selective assembly of IAV.