bluuebunny/crossref_metadata_2025 huggingface dataset:
Fibroblast growth factor receptor 2 (FGFR2) fusions in Japanese patients with intrahepatic cholangiocarcinoma
Authors: Tsujie Masanori , Iwai Tomohisa , Kubo Shoji , Ura Takashi , Hatano Etsuro , Sakai Daisuke , Takeda Yutaka , Kaibori Masaki , Kobayashi Tomoe , Katanuma Akio , Katayose Yu , Fukase Koji , Sakurai Naoki , Ito Yukiko , Sato Fumiya , Maeda Atsuyuki , Asada Masanori , Morizane Chigusa
Published: February 2021

Objective

Fibroblast growth factor receptor gene alterations have emerged as promising drug targets for intrahepatic cholangiocarcinoma, a rare cancer that has a poor prognosis. This study evaluated the frequency of fibroblast growth factor receptor 2 fusions in clinical specimens from Japanese patients with iCCA.

Methods

This study enrolled 116 patients who had histologically or cytologically confirmed adenocarcinoma and been diagnosed as relapsing after resection or with unresectable intrahepatic cholangiocarcinoma. We evaluated the frequency of fibroblast growth factor receptor 2 fusions-positive cells in their specimens using break-apart fluorescent in situ hybridization ‘for 114 patients who met the study protocol’.

Results

Of a total of 114 cases, six (5.3%) were identified as fibroblast growth factor receptor 2 fusions-positive with a high frequency (87% or more) of fibroblast growth factor receptor 2 fusions-positive tumour cells whereas the remainder, with the exception of three cases with indeterminate results, were identified as fibroblast growth factor receptor 2 fusions-negative. The patients’ baseline characteristics as well as their objective response rates, disease control rates, times to progression, and times to treatment failure with previous or ongoing first-line chemotherapy did not have any obvious relationship to the proportion of fibroblast growth factor receptor 2 fusions-positive case.

Conclusions

Further detailed elucidation of fibroblast growth factor receptor 2 fusion status is expected to contribute to the development of promising therapeutic options for patients suffering from recurrent or unresectable intrahepatic cholangiocarcinoma.
Evaluation of Polarized Light and Fluorescence Microscopy of Congo Red Stain in the Diagnosis of Renal Amyloidosis
Authors: Lee Adrian Y S , Bayly Angela , Lin Ming-Wei
Published: February 2021

Background

Amyloidosis is a devastating multisystemic disease resulting from organ deposition of misfolded proteins and subsequent organ dysfunction. An accurate diagnosis relies frequently on biopsies and microscopy techniques to detect amyloid deposition. We evaluated the diagnostic performance of Congo red staining using polarized light (PM) and fluorescence microscopy (FM) techniques in renal amyloidosis.

Methods

We performed a retrospective and prospective analysis of all renal biopsies submitted at a large quarternary hospital in Sydney, Australia, that had undergone PM and FM evaluation using Congo red staining. Identification of amyloid fibrils on electron microscopy was considered the reference method.

Results

PM and FM displayed very high sensitivity and specificity in correctly identifying amyloid deposits in renal biopsies that tested positive via Congo red staining. Comparison of the diagnostic statistics revealed that they are diagnostically equivalent.

Conclusion

In the diagnosis of renal amyloidosis on biopsy, evaluation of Congo red staining may be reliably performed via PM or FM.
Magnetic fields in late-stage proto-neutron stars
Authors: Lander S K , Haensel P , Haskell B , Zdunik J L , Fortin M
Published: February 2021

We explore the thermal and magnetic field structure of a late-stage proto-neutron star (proto-NS). We find the dominant contribution to the entropy in different regions of the star, from which we build a simplified equation of state (EOS) for the hot neutron star (NS). With this, we numerically solve the stellar equilibrium equations to find a range of models, including magnetic fields and rotation up to Keplerian velocity. We approximate the EOS as a barotrope, and discuss the validity of this assumption. For fixed magnetic field strength, the induced ellipticity increases with temperature; we give quantitative formulae for this. The Keplerian velocity is considerably lower for hotter stars, which may set a de facto maximum rotation rate for non-recycled NSs well below 1 kHz. Magnetic fields stronger than around 1014 G have qualitatively similar equilibrium states in both hot and cold NSs, with large-scale simple structure and the poloidal field component dominating over the toroidal one; we argue this result may be universal. We show that truncating magnetic field solutions at low multipoles leads to serious inaccuracies, especially for models with rapid rotation or a strong toroidal-field component.
SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis
Authors: Tian Wenwen , Wang Ruyi , Bo Cunpei , Yu Yingjun , Zhang Yuanyuan , Shin Gyeong-Im , Kim Woe-Yeon , Wang Lei
Published: February 2021

Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
Efficacy and safety of combination therapy with sodium–glucose cotransporter 2 inhibitors and renin–angiotensin system blockers in patients with type 2 diabetes: a systematic review and meta-analysis
Authors: Tian Beichen , Deng Yuanjun , Cai Yang , Han Min , Xu Gang
Published: February 2021

Background

This study was designed to evaluate the efficiency and safety of combination therapy with sodium–glucose cotransporter 2 (SGLT2) inhibitors and renin–angiotensin system blockers such as angiotensin-converting enzyme inhibitor (ACEI) and angiotensin receptor blocker (ARB) in patients with type 2 diabetes mellitus (T2DM).

Methods

We searched the PubMed, Embase, Web of Science and Cochrane Library databases from their inception to May 2020. Two authors independently performed study selection, risk-of-bias assessment and data extraction. The quality and risk of bias were assessed by the Cochrane Risk of Bias Tool. Statistical heterogeneity was determined by the I2 statistics.

Results

Seven studies including 1757 patients were analysed. Compared with ACEI/ARB alone, combination therapy with SGLT2 inhibitors and ACEIs/ARBs produced a reduction in systolic blood pressure (SBP) [weighted mean difference (WMD) −3.84 mmHg], diastolic blood pressure (DBP; WMD −1.06 mmHg), 24 h ambulatory SBP (WMD −4.59 mmHg), 24-h ambulatory DBP (WMD −2.08 mmHg), urine albumin:creatinine ratio (WMD −29.70%), evaluated glomerular filtration rate (WMD −3.46 mL/min/1.73 m2), haemoglobin A1c [standardized mean difference (SMD) −0.48], fasting plasma glucose (SMD −0.28), uric acid (SMD −0.35) and body weight (SMD −0.29). The risk of hypoglycaemia with combination therapy was higher than in the control group (risk ratio 1.37). As for the risks of total adverse events, genital infection and urinary tract infection, no significant difference was revealed.

Conclusion

Compared with ACEI/ARB alone, the combination therapy with SGLT2 inhibitors and ACEIs/ARBs in T2DM was effective and well-tolerated and could achieve additional effects including better control of blood pressure, improvement of renal outcomes, alleviation of long-term renal function and a decrease in blood glucose and body weight. The combination therapy showed an increased risk of hypoglycaemia.
Organophosphate poisoning in a young child: a case report
Authors: Sharma Namita , Nin-Gonzalez Rosa
Published: February 2021

Unintentional ingestions are a common form of poisoning in children worldwide. Organophosphates are commonly used in households worldwide and are a common cause of childhood poisonings. This case report describes an unintentional ingestion of a child in East Africa. A thorough patient history and a high index of suspicion are needed in recognizing an organophosphate poisoning. Prompt patient stabilization and treatment improve outcomes. Neurologic sequela may occur and thus patient follow-up is recommended.
Unexpected diversity of ferredoxin-dependent thioredoxin reductases in cyanobacteria
Authors: Buey Rubén M , Fernández-Justel David , González-Holgado Gloria , Martínez-Júlvez Marta , González-López Adrián , Velázquez-Campoy Adrián , Medina Milagros , Buchanan Bob B , Balsera Monica
Published: February 2021

Thioredoxin reductases control the redox state of thioredoxins (Trxs)—ubiquitous proteins that regulate a spectrum of enzymes by dithiol–disulfide exchange reactions. In most organisms, Trx is reduced by NADPH via a thioredoxin reductase flavoenzyme (NTR), but in oxygenic photosynthetic organisms, this function can also be performed by an iron-sulfur ferredoxin (Fdx)-dependent thioredoxin reductase (FTR) that links light to metabolic regulation. We have recently found that some cyanobacteria, such as the thylakoid-less Gloeobacter and the ocean-dwelling green oxyphotobacterium Prochlorococcus, lack NTR and FTR but contain a thioredoxin reductase flavoenzyme (formerly tentatively called deeply-rooted thioredoxin reductase or DTR), whose electron donor remained undefined. Here, we demonstrate that Fdx functions in this capacity and report the crystallographic structure of the transient complex between the plant-type Fdx1 and the thioredoxin reductase flavoenzyme from Gloeobacter violaceus. Thereby, our data demonstrate that this cyanobacterial enzyme belongs to the Fdx flavin-thioredoxin reductase (FFTR) family, originally described in the anaerobic bacterium Clostridium pasteurianum. Accordingly, the enzyme hitherto termed DTR is renamed FFTR. Our experiments further show that the redox-sensitive peptide CP12 is modulated in vitro by the FFTR/Trx system, demonstrating that FFTR functionally substitutes for FTR in light-linked enzyme regulation in Gloeobacter. Altogether, we demonstrate the FFTR is spread within the cyanobacteria phylum and propose that, by substituting for FTR, it connects the reduction of target proteins to photosynthesis. Besides, the results indicate that FFTR acquisition constitutes a mechanism of evolutionary adaptation in marine phytoplankton such as Prochlorococcus that live in low-iron environments.
Effects of Dual-Task Gait Treadmill Training on Gait Ability, Dual-Task Interference, and Fall Efficacy in People With Stroke: A Randomized Controlled Trial
Authors: Baek Chang Yoon , Chang Woo Nam , Park Beom Yeol , Lee Kyoung Bo , Kang Kyoung Yee , Choi Myung Ryul
Published: February 2021

Objective

This study aimed to investigate the effects of dual-task gait training using a treadmill on gait ability, dual-task interference, and fall efficacy in people with stroke.

Methods

Patients with chronic stroke (N = 34) were recruited and randomly allocated to the experimental or control group. Both groups underwent gait training on a treadmill and a cognitive task. In the experimental group, gait training was conducted in conjunction with the cognitive task, whereas in the control group, the training and the cognitive task were conducted separately. Each intervention was provided for 60 minutes, twice a week, for a period of 6 weeks for both groups. The primary outcomes were as follows: gait parameters (speed, stride, variability, and cadence) under single-task and dual-task conditions, correct response rate (CRR) under single-task and dual-task conditions, and dual-task cost (DTC) in gait parameters and CRR. The secondary outcome was the Fall Efficacy Scale.

Results

Dual-task gait training using a treadmill improved all gait parameters in the dual-task condition, speed, stride, and variability in the single-task condition, and CRR in both conditions. A difference between the groups was observed in speed, stride, and variability in the dual-task condition. Furthermore, dual-task gait training on a treadmill improved DTC in speed, variability, and cadence along with that in CRR, indicating true improvement of DTC, which led to significant improvement in DTC in speed and variability compared with single-task training.

Conclusions

Dual-task gait treadmill training was more effective in improving gait ability in dual-task training and dual-task interference than single-task training involving gait and cognitive task separately in people with chronic stroke.
Adapting to the culture of ‘new normal’: an emerging response to COVID-19
Authors: Corpuz Jeff Clyde G
Published: February 2021

A year after COVID-19 pandemic has emerged, we have suddenly been forced to adapt to the ‘new normal’: work-from-home setting, parents home-schooling their children in a new blended learning setting, lockdown and quarantine, and the mandatory wearing of face mask and face shields in public. For many, 2020 has already been earmarked as ‘the worst’ year in the 21st century. Ripples from the current situation have spread into the personal, social, economic and spiritual spheres. Is this new normal really new or is it a reiteration of the old? A recent correspondence published in this journal rightly pointed out the involvement of a ‘supportive’ government, ‘creative’ church and an ‘adaptive’ public in the so-called culture. However, I argue that adapting to the ‘new normal’ can greatly affect the future. I would carefully suggest that we examine the context and the location of culture in which adaptations are needed.
Epigenetic Element-Based Transcriptome-Wide Association Study Identifies Novel Genes for Bipolar Disorder
Authors: Yao Shi , Wu Hao , Liu Tong-Tong , Wang Jia-Hao , Ding Jing-Miao , Guo Jing , Rong Yu , Ke Xin , Hao Ruo-Han , Dong Shan-Shan , Yang Tie-Lin , Guo Yan
Published: February 2021

Since the bipolar disorder (BD) signals identified by genome-wide association study (GWAS) often reside in the non-coding regions, understanding the biological relevance of these genetic loci has proven to be complicated. Transcriptome-wide association studies (TWAS) providing a powerful approach to identify novel disease risk genes and uncover possible causal genes at loci identified previously by GWAS. However, these methods did not consider the importance of epigenetic regulation in gene expression. Here, we developed a novel epigenetic element-based transcriptome-wide association study (ETWAS) that tested the effects of genetic variants on gene expression levels with the epigenetic features as prior and further mediated the association between predicted expression and BD. We conducted an ETWAS consisting of 20 352 cases and 31 358 controls and identified 44 transcriptome-wide significant hits. We found 14 conditionally independent genes, and 10 genes that did not previously implicate with BD were regarded as novel candidate genes, such as ASB16 in the cerebellar hemisphere (P = 9.29 × 10–8). We demonstrated that several genome-wide significant signals from the BD GWAS driven by genetically regulated expression, and NEK4 explained 90.1% of the GWAS signal. Additionally, ETWAS identified genes could explain heritability beyond that explained by GWAS-associated SNPs (P = 5.60 × 10–66). By querying the SNPs in the final models of identified genes in phenome databases, we identified several phenotypes previously associated with BD, such as schizophrenia and depression. In conclusion, ETWAS is a powerful method, and we identified several novel candidate genes associated with BD.
Use of the precision-fed cecectomized rooster assay to determine standardized amino acid digestibility, true metabolizable energy content, and digestible indispensable amino acid scores of plant-based protein by-products used in canine and feline diets
Authors: Reilly Lauren M , von Schaumburg Patrick C , Hoke Jolene M , Davenport Gary M , Utterback Pamela L , Parsons Carl M , de Godoy Maria R C
Published: February 2021

Traditionally, protein by-products from oil seeds and cereal grains have been used in pet foods as sustainable, inexpensive, and protein-rich ingredients. However, the on-going demonization of soy- and corn-based ingredients continue to hinder their use in pet food and treat formulations. Ideally, the further demonstration of their protein quality and nutrient composition may encourage their favorable return as acceptable ingredients in pet foods and treats. Therefore, the objectives of this study were to determine the macronutrient composition, indispensable amino acid profile, standardized amino acid digestibility, true metabolizable energy content corrected for nitrogen (TMEn), and digestible indispensable amino acid scores (DIAAS-like) of soy flakes (SF), peanut flour (PF), soybean meal (SBM), and corn gluten meal (CGM). Standardized amino acid digestibility was assessed using the precision-fed cecectomized rooster assay. All test ingredients demonstrated a profile of highly digestible indispensable amino acids except for lysine in PF, which was lowest (P < 0.05) at 45.5%. The SBM and CGM had the highest (P > 0.05) digestibilities of indispensable amino acids. A DIAAS-like value was calculated for each ingredient using either AAFCO (2020) recommended values or NRC (2006) recommended allowances as the reference protein pattern. For adult dogs compared to AAFCO recommended values, the first-limiting amino acid was lysine for PF and CGM but it was methionine for SF and SBM. For adult cats compared to AAFCO recommended values, the first-limiting amino acid was lysine for PF and CGM but it was threonine for SF. There was no first-limiting amino acid in SBM for cats as DIAAS-like values were over 100% for all indispensable amino acids. The TMEn values were highest (P < 0.05) for PF and CGM (4.58 and 4.31 kcal/g [dry matter basis], respectively). The protein quality of these plant-based protein by-products reflects their value as nutritional ingredients for canine and feline diets. However, the prior processing of these by-products must be considered before exposing them to additional processing methods, such as extrusion. Additionally, the inclusion of complementary proteins or supplemental amino acids will be needed to meet all indispensable amino acid requirements for a portion of nutritionally complete and balanced pet food.
Cork cells in cork oak periderms undergo programmed cell death and proanthocyanidin deposition
Authors: Inácio Vera , Lobato Carolina , Graça José , Morais-Cecílio Leonor
Published: February 2021

Vascular plants with secondary growth develop a periderm mostly composed of dead suberized cork cells to face environmental hostile conditions. Cork oak has a highly active and long-living phellogen forming a remarkably thick periderm that is periodically debarked for industrial purposes. This wounding originates the quick formation of a new traumatic periderm, making cork oak an exceptional model to study the first periderm differentiation during normal development in young sprigs and traumatic (wound) periderm formation after debarking. Here, we studied the poorly known first periderm differentiation steps that involve cell wall suberization, polyphenolic accumulation and programmed cell death (PCD) by combining transmission electron microscopy, histochemical and molecular methods in periderms from young sprigs. These processes were further compared with traumatic periderms formed after wounding using molecular and histochemical techniques, such as the polyphenolic accumulation. In the first periderms from young sprigs, four distinct differentiation stages were defined according to the presence of PCD morphological features. First young and traumatic periderms showed an upregulation of genes related to suberin biosynthesis, proanthocyanidins biosynthesis and transport, autophagy, and PCD. Traumatic periderms revealed an overall upregulation of these genes, likely resulting from ontogeny differences and distinct phellogen origin associated with a faster metabolism, highlighting the impact of wounding on phellogen activity after debarking. First periderms from young sprigs showed gradual accumulation of proanthocyanidins in the vacuoles throughout PCD stages until total filled lumens, whereas in traumatic periderms, these compounds were found cell wall linked in already empty cells. This work enabled a comprehensive overview of the cork cells differentiation processes contributing to deepening the knowledge of the fundamental ontogenic program of this protective tissue, which is also a unique forest product, constituting the basis of a sustainable and profitable industry.
The Begomovirus Species Melon Chlorotic Leaf Curl Virus is Composed of Two Highly Divergent Strains that Differ in Their Genetic and Biological Properties
Authors: Maliano Minor R. , Melgarejo Tomas A. , Rojas Maria R. , Barboza Natalia , Gilbertson Robert L.
Published: February 2021

Since the early 1990s, squash production in Costa Rica has been affected by a whitefly-transmitted disease characterized by stunting and yellow mottling of leaves. The squash yellow mottle disease (SYMoD) was shown to be associated with a bipartite begomovirus, originally named squash yellow mild mottle virus (SYMMoV). It was subsequently established that SYMMoV is a strain of melon chlorotic leaf curl virus (MCLCuV), a bipartite begomovirus that causes a chlorotic leaf curl disease of melons in Guatemala. In the present study, the complete sequences of the DNA-A and DNA-B components of a new isolate of the strain MCLCuV-Costa Rica (MCLCuV-CR) were determined. Comparisons of full-length DNA-A sequences revealed 97% identity with a previously characterized isolate of MCLCuV-CR and identities of 90 to 91% with those of isolates of the strain MCLCuV-Guatemala (MCLCuV-GT), which is below or at the current begomovirus species demarcation threshold of 91%. A more extensive analysis of the MCLCuV-CR and -GT sequences revealed substantial divergence in both components and different histories of recombination for the DNA-A components. The cloned full-length DNA-A and DNA-B components of this new MCLCuV-CR isolate were infectious and induced SYMoD in a range of squashes and in pumpkin, thereby fulfilling Koch’s postulates for this disease. However, in contrast to MCLCuV-GT, MCLCuV-CR induced mild symptoms in watermelon and no symptoms in melon and cucumber. Taken together, our results indicate that MCLCuV-CR and -GT have substantially diverged, genetically and biologically, and have evolved to cause distinct diseases of different cucurbit crops. Taxonomically, these viruses are at the strain/species boundary, but retain the designation as strains of Melon chlorotic leaf curl virus under current International Committee on Taxonomy guidelines.
Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Authors: Gerth Michael , Martinez-Montoya Humberto , Ramirez Paulino , Masson Florent , Griffin Joanne S. , Aramayo Rodolfo , Siozios Stefanos , Lemaitre Bruno , Mateos Mariana , Hurst Gregory D. D.
Published: February 2021

Spiroplasma

is a genus of

Mollicutes

whose members include plant pathogens, insect pathogens and endosymbionts of animals.

Spiroplasma

phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in

Spiroplasma

symbionts and plant pathogens. These observations suggest that

Spiroplasma

evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of

Spiroplasma poulsonii

, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that

S. poulsonii

substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across

Spiroplasma

, and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse

Spiroplasma

lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several

Spiroplasma

lineages and other endosymbionts. Overall, our results highlight the peculiar nature of

Spiroplasma

genome evolution, which may explain unusual features of its evolutionary ecology.
Home stay reflects symptoms severity in major depressive disorder: A multicenter observational study using geolocation data from smartphones
Authors: Laiou Petroula , Kaliukhovich Dzmitry A. , Folarin Amos , Ranjan Yatharth , Rashid Zulqarnain , Conde Pauline , Stewart Callum , Sun Shaoxiong , Zhang Yuezhou , Matcham Faith , Ivan Alina , Lavelle Grace , Siddi Sara , Lamers Femke , Penninx Brenda W.J.H. , Haro Josep Maria , Annas Peter , Cummins Nicholas , Vairavan Srinivasan , Manyakov Nikolay V. , Narayan Vaibhav A. , Dobson Richard , Hotopf Matthew
Published: February 2021

Most smartphones and wearables are nowadays equipped with location sensing (using Global Positioning System and mobile network information) that enable continuous location tracking of their users. Several studies have reported that the amount of time an individual experiencing symptoms of Major Depressive Disorder (MDD) spends at home a day (i.e., home stay), as well as various mobility related metrics, are associated with symptom severity in MDD. Due to the use of small and homogeneous cohorts of participants, it is uncertain whether the findings reported in those studies generalize to a broader population of individuals with the MDD symptoms. In the present study, we examined the relationship between overall severity of the depressive symptoms, as assessed by the eight-item Patient Health Questionnaire (PHQ-8), and median daily home stay over the two weeks preceding the completion of a questionnaire in individuals with MDD. We used questionnaire and geolocation data of 164 participants collected in the observational Remote Assessment of Disease and Relapse – Major Depressive Disorder (RADAR-MDD) study. Participant age and severity of the MDD symptoms were found to be significantly related to home stay, with older and more severely affected individuals spending more time at home. The association between home stay and symptom severity appeared to be stronger on weekdays than on weekends. Furthermore, we found a significant modulation of home stay by occupational status, with employment reducing home stay. Our findings suggest that home stay is associated with symptom severity in MDD and demonstrate the importance of accounting for confounding factors in future MDD studies.
Potential of fungicides, botanicals and biocontrol agents to induce physio-biochemical tolerance onCurcuma longaimpaired byColletotrichum gloeosporioides
Authors: Musheer Nasreen , Ashraf Shabbir , Jamil Arshi
Published: February 2021

Necrotic leaf spot ofCurcuma longa(turmeric) limits the chief physio-biochemical activity for maintaining the plant health and productivity. In the present study, polyhouse and open field trials were conducted to estimate the pathogenicity ofC. gloeosporioideson turmeric and to evaluate the foliar efficiency of propiconazole @ RD and copper oxychloride, extracts ofA. indica, A. sativumandO. sanctum@ 40%, and culture filtrates ofT. viride, T. harzianumandT. virens @4×106cfu/ml in inducing physio-biochemical tolerance of pathogen inoculated and non-inoculated plants. In both the trials, these three agents yielded the highest efficiency to enhance the physio-biochemical traits. The induced physio-biochemical tolerance in treated turmeric plants showed variation in the elevation of plant health and immunity in response to pathogen aggressiveness or disease severity. However, phytophenol content was quite higher in infected plants than non-infected plants due to initiation of defense reaction in response of pathogenic elicitors. Thus, the present study demonstrated the novelty of physio-biochemical tolerance induction on turmeric plants by using fungicides, biocontrol agents and phytoextracts.

Highlights

Foliar treatments improve desirable plant physio-biochemical traits against pathogen.

Physio-biochemical variation induces the innate plant defense system.

High phytophenol accumulation counteracts the pathogenic stress.

Turmeric plant’s health and yield enhance by the reduction of disease intensity.
Resting EEG spectral slopes are associated with age-related differences in information processing speed
Authors: Pathania A. , Euler M.J. , Clark M. , Cowan R. , Duff K. , Lohse K.R.
Published: February 2021

Background

Previous research has shown the slope of the EEG power spectrum differentiates between older and younger adults in various experimental cognitive tasks. Here, we extend that work, assessing the relation between the EEG power spectrum and performance on the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS), a widely-used neuropsychological instrument that assesses a broad range of cognitive domains.

Methods

Forty-four participants (21 younger adults, 23 older adults) completed the RBANS with EEG data collected at-rest. Using spectral parameterization, we tested the mediating effect of the spectral slope on age-related differences in subsequent cognitive task performance.

Results

Older adults performed reliably worse on the RBANS overall, and on the Attention and Delayed Memory domains. However, evidence of mediation was only found for the Coding subtest, a measure of information processing speed.

Conclusions

We found some evidence that the slope of the resting EEG power spectrum mediated age-related differences in cognition. These effects were evident only in tasks requiring speeded processing, whereas this effect was not statistically significant for delayed memory, even though age-related differences were present.
Jumper Enables Discontinuous Transcript Assembly in Coronaviruses
Authors: Sashittal Palash , Zhang Chuanyi , Peng Jian , El-Kebir Mohammed
Published: February 2021

Genes in SARS-CoV-2 and, more generally, in viruses in the order ofNidoviralesare expressed by a process of discontinuous transcription mediated by the viral RNA-dependent RNA polymerase. This process is distinct from alternative splicing in eukaryotes, rendering current transcript assembly methods unsuitable toNidoviralessequencing samples. Here, we introduce the DiscontinuousTranscriptAssemblyproblem of finding transcriptsand their abundancescgiven an alignmentunder a maximum likelihood model that accounts for varying transcript lengths. Underpinning our approach is the concept of a segment graph, a directed acyclic graph that, distinct from the splice graph used to characterize alternative splicing, has a unique Hamiltonian path. We provide a compact characterization of solutions as subsets of non-overlapping edges in this graph, enabling the formulation of an efficient mixed integer linear program. We show using simulations that our method, Jumper, drastically outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1 and SARS-CoV-2 samples, we find that Jumpernot only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are well supported by direct evidence from long-read data, presence in multiple, independent samples or a conserved core sequence. Jumperenables detailed analyses ofNidoviralestranscriptomes.

Code availability

Software is available athttps://github.com/elkebir-group/Jumper
The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity
Authors: Pezic Dubravka , Weeks Samuel , Varsally Wazeer , Dewari Pooran S. , Pollard Steven , Branco Miguel R. , Hadjur Suzana
Published: February 2021

Several studies have shown a role for Stag proteins in cell identity. Our understanding of how Stag proteins contribute to cell identity have largely been focused on its roles in chromosome topology as part of the cohesin complex and the impact on protein-coding gene expression. Furthermore, several Stag paralogs exist in mammalian cells with non-reciprocal chromosome structure and cohesion functions. Why cells have so many Stag proteins and what specific functions each Stag protein performs to support a given cell state are poorly understood. Here we reveal that Stag1 is the dominant paralog in mouse embryonic stem cells (mESC) and is required for pluripotency. Through the discovery of diverse, naturally occurring Stag1 isoforms in mESCs, we shed new light not only on the unique ends of Stag1 but also the critical role that their levels play in stem cell identity. Furthermore, we revel a new role for Stag1, and specifically its unique N-terminal end, in regulating nucleolar integrity and safeguarding mESCs from totipotency. Stag1 is localised to repressive perinucleolar regions, bound at repeats and interacts with Nucleolin and TRIM28. Loss of the Stag1 N-terminus, leads to decreased LINE-1 and rRNA expression and disruption of nucleolar structure and function which consequently leads to activation of the two-cell-like (2C-LC)-specific transcription factor DUX and conversion of pluripotent mESCs to totipotent 2C-LCs. Our results move beyond protein-coding gene regulation via chromatin loops into a new role for Stag1 in repeat regulation and nucleolar structure, and offer fresh perspectives on how Stag proteins contribute to cell identity and disease.
The Role Of Senescent Cells Removal For Cell Culture Rejuvenation
Authors: Prokhorov Leonid Yu.
Published: February 2021

It is well known that aging reduces the number of healthy, vital cells, increases the number of dead cells, some of which are replaced by connective tissue. Similar processes occur in cell culture. If endlessly dividing transformed, or cancer cells grow in glass flasks and after their death for various reasons detach from the growth surface, lyzed and thus free up space for the growth of “young” cells, the culture lives arbitrarily long. But if in culture the “senescent” cells do not detach from the growth surface and do not make room for “young” cells, the “young” cells do not have the ability to devide and die. Because of this, the entire population of cells dies. Also in the body, “senescent” cells and intercellular tissues occupy a certain place in the body and do not allow “young”, “healthy” cells to divide.
Assessment of the reproducibility and inter-site transferability of the murine direct splenocyte mycobacterial growth inhibition assay (MGIA)
Authors: Tanner Rachel , Zelmer Andrea , Painter Hannah , Stylianou Elena , Pinpathomrat Nawamin , Harrington-Kandt Rachel , Biffar Lucia , Brennan Michael J. , McShane Helen , Fletcher Helen A.
Published: February 2021

Tuberculosis (TB) vaccine candidates must be tested for safety and efficacy using preclinical challenge models prior to advancement to human trials, because of the lack of a validated immune correlate or biomarker of protection. New, unbiased tools are urgently needed to expedite the selection of vaccine candidates at an early stage of development and reduce the number of animals experimentally infected with virulentMycobacterium tuberculosis(M.tb). In recent years, there has been a concerted effort to develop standardised functionalex vivomycobacterial growth inhibition assays (MGIAs) as a potential surrogate read-out of vaccine efficacy. We have previously described a direct MGIA for use with mouse splenocytes. In the current study, we set out to systematically compare co-culture conditions for the murine direct splenocyte MGIA with respect to both intra-assay repeatability and inter-site reproducibility. Common sample sets were shared between laboratory sites and reproducibility and sensitivity to detect a BCG-vaccine induced response were assessed. Co-culturing 5×106splenocytes in 48-well plates resulted in improved reproducibility and superior sensitivity to detect a vaccine response compared with standing or rotating sealed 2ml screw-cap tubes. As the difference between naïve and BCG vaccinated mice was not consistently detected across both sample sets at both sites, we sought to further improve assay sensitivity by altering the multiplicity of infection (MOI). Cell viability at the end of the co-culture period was improved when splenocyte input number was reduced, with the highest viability for the condition of 3×106splenocytes in 48-well plates. This cell input was also associated with the greatest sensitivity to detect a BCG vaccine-mediated MGIA response using anM.tbinoculum. Based on our findings, we recommend optimal co-culture conditions in a move towards aligning direct MGIA protocols and generating a cross-species consensus for early evaluation of TB vaccine candidates and biomarker studies.
Short-term plasticity persists in the absence of PKC phosphorylation of Munc18-1
Authors: Wang Chih-Chieh , Weyrer Christopher , Fioravante Diasynou , Kaeser Pascal S. , Regehr Wade G.
Published: February 2021

Post tetanic potentiation (PTP) is a form of short-term plasticity that lasts for tens of seconds following a burst of presynaptic activity. It has been proposed that PTP arises from protein kinase C (PKC) phosphorylation of Munc18-1, an SM (Sec1/Munc-18 like) family protein that is essential for release. To test this model, we made a knockin mouse in which all Munc18-1 PKC phosphorylation sites were eliminated through serine-to-alanine point mutations (Munc18-1 SA mice). Expression of Munc18-1 was not altered in Munc18-1SA mice, and there were no obvious behavioral phenotypes. At the hippocampal CA3 to CA1 synapse, and the granule cell parallel fiber to Purkinje cell (PF to PC) synapse, basal transmission was largely normal except for small decreases in paired-pulse facilitation that are consistent with a slight elevation in release probability. Phorbol esters that mimic activation of PKC by diacylglycerol still increased synaptic transmission in Munc18-1 SA mice. In Munc18-1 SA mice, 70% of PTP remained at CA3 to CA1 synapses, and the amplitude of PTP was not reduced at PF to PC synapses. These findings indicate that at both CA3 to CA1 and PF to PC synapses, phorbol esters and PTP enhance synaptic transmission primarily by mechanisms that are independent of PKC phosphorylation of Munc18-1.

Significance Statement

A leading mechanism for a prevalent form of short-term plasticity, post-tetanic potentiation (PTP), involves protein kinase C phosphorylation of Munc18-1. This study tests this mechanism by creating a knock in mouse in which Munc18-1 is replaced by a mutated form of Munc18-1 that cannot be phosphorylated. The main finding is that most PTP at hippocampal CA3 to CA1 synapses, or at cerebellar granule cell to Purkinje cell synapses does not rely on PKC phosphorylation of Munc18-1. Thus, mechanisms independent of PKC phosphorylation of Munc18-1 are important mediators of PTP.
Sphingosine kinase 2 is essential for remyelination following cuprizone intoxication
Authors: Song Huitong , McEwen Holly P. , Duncan Thomas , Lee Jun Yup , Teo Jonathan D. , Don Anthony S.
Published: February 2021

Therapeutics that promote oligodendrocyte survival and remyelination are needed to restore neurological function in demyelinating diseases. Sphingosine 1-phosphate (S1P) is an essential lipid metabolite that signals through five G-protein coupled receptors. S1P receptor agonists such as Fingolimod are valuable immunosuppressants used to treat multiple sclerosis, and promote oligodendrocyte survival. However, the role for endogenous S1P, synthesized by the enzyme sphingosine kinase 2 (SphK2), in oligodendrocyte survival and myelination has not been established. This study investigated the requirement for SphK2 in oligodendrocyte survival and remyelination using the cuprizone mouse model of acute demyelination, followed by spontaneous remyelination. Oligodendrocyte density did not differ between untreated wild- type (WT) and SphK2 knockout (SphK2-/-) mice. However, cuprizone treatment caused significantly greater loss of mature oligodendrocytes in SphK2-/-compared to WT mice. Following cuprizone withdrawal, spontaneous remyelination occurred in WT but not SphK2-/-mice, even though progenitor and mature oligodendrocyte density increased in both genotypes. Levels of cytotoxic sphingosine and ceramide were higher in the corpus callosum of SphK2-/-mice, and in contrast to WT mice, did not decline following cuprizone withdrawal in SphK2-/-mice. We also observed a significant reduction in myelin thickness with ageing in SphK2-/-compared to WT mice. These results provide the first evidence that SphK2, the dominant enzyme catalysing S1P synthesis in the adult brain, is essential for remyelination following a demyelinating insult and myelin maintenance with ageing. We propose that persistently high levels of sphingosine and ceramide, a direct consequence of SphK2 deficiency, may block remyelination.

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Main Points

The lipid kinase sphingosine kinase 2 (SphK2) is essential for remyelination following a demyelinating insult (cuprizone).

SphK2 protects against cuprizone-mediated oligodendrocyte loss.

SphK2 deficiency leads to thinner myelin with ageing.
SARS-CoV-2 antibody immunoassays in serial samples reveal earlier seroconversion in acutely ill COVID-19 patients developing ARDS
Authors: Buchholtz Marie-Luise , Arend Florian M. , Eichhorn Peter , Weigand Michael , Kleinhempel Alisa , Häusler Kurt , Bruegel Mathias , Holdt Lesca M. , Teupser Daniel
Published: February 2021

Objectives

During the COVID-19 pandemic, SARS-CoV-2 antibody testing has been suggested for (1) screening populations for disease prevalence, (2) diagnostics, and (3) guiding therapeutic applications. Here, we conducted a detailed clinical evaluation of four Anti-SARS-CoV-2 immunoassays in samples from acutely ill COVID-19 patients and in two negative cohorts.

Methods

443 serum specimens from serial sampling of 29 COVID-19 patients were used to determine clinical sensitivities. Patients were stratified for the presence of acute respiratory distress syndrome (ARDS). Individual serum specimens from a pre-COVID-19 cohort of 238 healthy subjects and from a PCR-negative clinical cohort of 257 patients were used to determine clinical specificities. All samples were measured side-by-side with the Anti-SARS-CoV-2-ELISA (IgG), Anti-SARS-CoV-2-ELISA (IgA) and Anti-SARS-CoV-2-NCP-ELISA (IgG) (Euroimmun AG, Lübeck, Germany) and the Elecsys Anti-SARS-CoV-2 ECLIA (Roche Diagnostics International, Rotkreuz, Switzerland).

Results

Median seroconversion occurred earlier in ARDS patients (8-9 days) than in non-ARDS patients (11-17 days), except for EUR N-IgG. Rates of positivity and mean signal ratios in the ARDS group were significantly higher than in the non-ARDS group. Sensitivities between the four tested immunoassays were equivalent. In the set of negative samples, the specificity of the Anti-SARS-CoV-2-ELISA (IgA) was lower (93.9 %) compared to all other assays (≥98.8 %) and the specificity of Anti-SARS-CoV-2-NCP-ELISA (IgG) was lower (98.8 %) than that of Elecsys Anti-SARS-CoV-2 (100 %).

Conclusions

Serial sampling in COVID-19 patients revealed earlier seroconversion and higher signal ratios of SARS-CoV-2 antibodies as a potential risk marker for the development of ARDS, suggesting a utility for antibody testing in acutely diseased patients.
Nets-within-nets for modeling emergent patterns in ontogenetic processes
Authors: Bardini Roberta , Benso Alfredo , Politano Gianfranco , Di Carlo Stefano
Published: February 2021

Ontogenesis is the development of an organism from its earliest stage to maturity, including homeostasis maintenance throughout adulthood despite environmental perturbations. Almost all cells of a multicellular organism share the same genomic information. Nevertheless, phenotypic diversity and complex supra-cellular architectures emerge at every level, starting from tissues and organs. This is possible thanks to a robust and dynamic interplay of regulative mechanisms.

To study ontogenesis, it is necessary to consider different levels of regulation, both genetic and epigenetic. Each cell undergoes a specific path across a landscape of possible regulative states affecting both its structure and its functions during development. This paper proposes using the Nets-Within-Nets formalism, which combines Petri Nets’ simplicity with the capability to represent and simulate the interplay between different layers of regulation connected by non-trivial and context-dependent hierarchical relations.

In particular, this work introduces a modeling strategy based on Nets-Within-Nets that can model several critical processes involved in ontogenesis. Moreover, it presents a case study focusing on the first phase of Vulval Precursor Cells specification inC. Elegans. The case study shows that the proposed model can simulate the emergent morphogenetic pattern corresponding to the observed developmental outcome of that phase, in both the physiological case and different mutations. The model presented in the results section is available online athttps://github.com/sysbio-polito/NWN_CElegans_VPC_model/