bluuebunny/crossref_metadata_2025 huggingface dataset:
Biophysical network models of phase-synchronization in MEG resting-state
Authors: Williams N , Toselli B , Siebenhühner F , Palva S , Arnulfo G , Kaski S , Palva JM
Published: August 2021

Magnetoencephalography (MEG) is used extensively to study functional connectivity (FC) networks of phase-synchronization, but the relationship of these networks to their biophysical substrates is poorly understood. Biophysical Network Models (BNMs) have been used to produce networks corresponding to MEG-derived networks of phase-synchronization, but the roles of inter-regional conduction delays, the structural connectome and dynamics of model of individual brain regions, in obtaining this correspondence remain unknown. In this study, we investigated the roles of conduction delays, the structural connectome, and dynamics of models of individual regions, in obtaining a correspondence between model-generated and MEG-derived networks between left-hemispheric regions. To do this, we compared three BNMs, respectively comprising Wilson-Cowan oscillators interacting with diffusion Magnetic Resonance Imaging (MRI)-based patterns of structural connections through zero delays, constant delays and distance-dependent delays respectively. For the BNM whose networks corresponded most closely to the MEG-derived network, we used comparisons against null models to identify specific features of each model component, e.g. the pattern of connections in the structure connectome, that contributed to the observed correspondence. The Wilson-Cowan zero delays model produced networks with a closer correspondence to the MEG-derived network than those produced by the constant delays model, and the same as those produced by the distance-dependent delays model. Hence, there is no evidence that including conduction delays improves the correspondence between model-generated and MEG-derived networks. Given this, we chose the Wilson-Cowan zero delays model for further investigation. Comparing the Wilson-Cowan zero delays model against null models revealed that both the pattern of structural connections and Wilson-Cowan oscillatory dynamics contribute to the correspondence between model-generated and MEG-derived networks. Our investigations yield insight into the roles of conduction delays, the structural connectome and dynamics of models of individual brain regions, in obtaining a correspondence between model-generated and MEG-derived networks. These findings result in a parsimonious BNM that produces networks corresponding closely to MEG-derived networks of phase-synchronization.

Highlights

Simple biophysical model produces close match (ρ=0.49) between model and MEG networks

No evidence for conduction delays improving match between model and MEG networks

Pattern of structural connections contributes to match between model and MEG networks

Wilson-Cowan oscillatory dynamics contribute to match between model and MEG networks
Membrane remodeling and matrix dispersal intermediates during mammalian acrosomal exocytosis
Authors: Leung Miguel Ricardo , Ravi Ravi Teja , Gadella Bart M. , Zeev-Ben-Mordehai Tzviya
Published: August 2021

To become fertilization-competent, mammalian sperm must undergo a complex series of biochemical and morphological changes in the female reproductive tract. These changes, collectively called capacitation, culminate in the exocytosis of the acrosome, a large vesicle overlying the nucleus. Acrosomal exocytosis is not an all-or-nothing event, but rather a regulated process in which vesicle cargo disperses gradually. However, the structural mechanisms underlying this controlled release remain undefined. In addition, unlike other exocytotic events, fusing membranes are shed as vesicles; the cell thus loses the entire anterior two-thirds of its plasma membrane and yet remains intact while the remaining non-vesiculated plasma membrane becomes fusogenic. Precisely how cell integrity is maintained through-out this drastic vesiculation process is unclear, as is how it ultimately leads to the acquisition of fusion competence. Here, we use cryo-electron tomography to visualize these processes in unfixed, unstained, fully-hydrated sperm. We show that crystalline structures within the acrosome disassemble during capacitation and acrosomal exocytosis, representing a plausible mechanism for gradual dispersal of the acrosomal matrix. We find that the architecture of the sperm head supports an atypical membrane fission-fusion pathway that maintains cell integrity. Finally, we detail how the acrosome reaction transforms both the micron-scale topography and the nano-scale protein landscape of the sperm surface, thus priming the sperm for fertilization.

Significance

Mammalian sperm must undergo a complex series of biochemical and morphological changes in the female reproductive tract in order to become fertilization-competent. These changes culminate in acrosomal exocytosis, during which multiple membrane fusions destabilize the acrosomal vesicle and liberate its contents, which include proteins implicated in penetrating and binding to the egg vestments. Here, we use cryo-electron tomography to visualize acrosomal exocytosis intermediates in unfixed, unstained sperm. Our results suggest structural bases for how gradual dispersal of acrosome contents is regulated, as well as for how the cell remains intact after losing much of its plasma membrane, We also show that acrosomal exocytosis transforms both the micron-scale topography and the nano-scale molecular landscape of the sperm surface, thus priming it for interaction and fusion with the egg. These findings yield important insights into sperm physiology and contribute to our understanding of the fundamental yet enigmatic process of mammalian fertilization.
ComF is a key mediator in single-stranded DNA transport and handling during natural transformation
Authors: Damke Prashant P. , Celma Louisa , Kondekar Sumedha , Guilmi Anne Marie Di , Marsin Stéphanie , Dépagne Jordane , Veaute Xavier , Legrand Pierre , Walbott Hélène , Vercruyssen Julien , Guérois Raphaël , Quevillon-Cheruel Sophie , Radicella J. Pablo
Published: August 2021

Natural transformation plays a major role in the spreading of antibiotic resistances and virulence factors. Whilst bacterial species display specificities in the molecular machineries allowing transforming DNA capture and integration into their genome, the ComF(C) protein is essential for natural transformation in all Gram-positive and - negative species studied. Despite this, its role remains largely unknown. Here, we show that Helicobacter pylori ComF is not only involved in DNA transport through the cell membrane, but it also required for the handling of the ssDNA once it is delivered into the cytoplasm. ComF crystal structure revealed the presence of a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for its in vivo activity. ComF is a membrane-associated protein with affinity for single-stranded DNA. Collectively, our results suggest that ComF provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.
LRET-derived HADDOCK structural models describe the conformational heterogeneity required for processivity of the Mre11-Rad50 DNA damage repair complex
Authors: Canny Marella D. , Latham Michael P.
Published: August 2021

The Mre11-Rad50-Nbs1 protein complex is one of the first responders to DNA double strand breaks. Studies have shown that the catalytic activities of the evolutionarily conserved Mre11-Rad50 (MR) core complex depend on an ATP-dependent global conformational change that takes the macromolecule from an open, extended structure in the absence of ATP to a closed, globular structure when ATP is bound. We have previously identified an additional ‘partially open’ conformation using Luminescence Resonance Energy Transfer (LRET) experiments. Here, a combination of LRET and the molecular docking program HADDOCK was used to further investigate this partially open state and identify three conformations of ATP-bound MR in solution: closed, partially open, and open, which are in addition to the extended, apo conformation. These models are supported with mutagenesis and SAXS data that corroborate the presence of these three states and suggest a mechanism for the processivity of the MR complex along the DNA.
Helical Ordering of Envelope Associated Proteins and Glycoproteins in Respiratory Syncytial Virus Filamentous Virions
Authors: Conley Michaela J. , Short Judith M. , Hutchings Joshua , Burns Andrew M. , Streetley James , Bakker Saskia E. , Jaffery Hussain , Stewart Murray , Power B. Joanne , Zanetti Giulia , Fearns Rachel , Vijayakrishnan Swetha , Bhella David
Published: August 2021

Human respiratory syncytial virus (RSV) causes severe respiratory illness in children and the elderly. Treatments for RSV disease are however limited and efforts to produce an effective vaccine have so far been unsuccessful. Understanding RSV virion structure is an important prerequisite for developing interventions to treat or prevent infection but has been challenging because of the fragility of virions propagated in cell culture. Here we show, using cryogenic electron microscopy (cryoEM) and cryogenic electron tomography (cryoET) of RSV particles cultivated directly on transmission electron microscopy (TEM) grids, that there is extensive helical symmetry in RSV filamentous virions. We have calculated a 16 Å resolution three-dimensional reconstruction of the viral envelope, targeting the matrix protein (M) that forms an endoskeleton below the viral membrane. These data define a helical lattice of M proteins, showing how M is oriented relative to the viral envelope and that helical ordering of viral glycoproteins that stud the viral envelope is coordinated by the M layer. Moreover, the helically ordered viral glycoproteins in RSV filamentous virions cluster in pairs, which may have implications for the conformation of fusion (F) glycoprotein epitopes that are the principal target for vaccine and monoclonal antibody development. We also report the presence, in authentic virus infections, of N-RNA rings packaged within RSV filamentous virions. Overall, the structural data obtained provides molecular insight into the organization of the virion and the mechanism of its assembly.
Role of polycomb repressive complex 2 in regulation of human transcription factor gene expression
Authors: Brown Jay C.
Published: August 2021

The study described here was pursued with the idea that information about control of human gene expression might result from comparing the promoter regions of a highly expressed gene population with that of a related population that is weakly expressed. Systematic differences in the two promoter populations would be candidates for a role in causing the distinct expression levels observed. The results reported here were obtained with human genes encoding transcription factors (TF). Among TF genes, those with wide tissue transcription are strongly expressed while those expressed in one or only a few tissues are weakly transcribed in most cases. The promoter regions of the two populations were compared using the results of ChIP-seq experiments. Results demonstrated that the promoter region of broadly expressed TF genes is enriched in binding sites for POLR2A, a component of RNA polymerase II while promoters of tissue targeted genes are enriched in EZH2, a subunit of polycomb repressive complex 2 (PRC2). It was rare to observe promoters with binding sites for both POLR2A and EZH2 or for neither one. The findings are interpreted to indicate that strong expression of broadly expressed TF genes is due to the presence of RNA polymerase II at the promoter while weak expression of tissue targeted promoters results from the presence of PRC2. Finally, transcription factor families were compared in the proportion of broadly expressed and tissue targeted genes. The results demonstrated that most families possess both broadly expressed and tissue targeted members. For instance, this was the case with 16 of 20 TF families. The results are interpreted to indicate that while individual TFs such as EZH2 may be specific for broadly expressed or tissue targeted genes, this is not a property of most TF families. Most have both broadly expressed and tissue targeted members.
Regulators of male and female sexual development critical for transmission of a malaria parasite
Authors: Russell Andrew J C , Sanderson Theo , Bushell Ellen , Talman Arthur M , Anar Burcu , Girling Gareth , Hunziker Mirjam , Kent Robyn S , Metcalf Tom , Montandon Ruddy , Pandey Vikash , Brett Roberts A , Sayers Claire , Schwach Frank , Rayner Julian C , Voet Thierry , Modrzynska Katarzyna K , Waters Andrew P. , Lawniczak Mara K N , Billker Oliver
Published: August 2021

The transmission of malaria parasites from vertebrate host to mosquito vector requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei the transcription factor AP2-G is required and sufficient for this switch, but how a particular sex is determined in a haploid parasite remains unknown. Using a global screen of barcoded mutants, we here identify ten genes essential for the formation of either male or female sexual forms and validate their importance for transmission. High-resolution single-cell transcriptomics of wild-type and mutant parasites portrays the developmental bifurcation and reveals a regulatory cascade of putative gene functions in determination and subsequent differentiation of each sex. A male-determining gene with a LOTUS/OST-HTH domain points towards unexpected conservation of molecular mechanisms of gametogenesis in animals and a distantly related eukaryotic parasite.
Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam
Authors: Higgins Janet , Santos Bruno , Khanh Tran Dang , Trung Khuat Huu , Duong Tran Duy , Phuong Doai Nguyen Thi , Hall Anthony , Dyer Sarah , Ham Le Huy , Caccamo Mario , De Vega Jose
Published: August 2021

Background and aims

Vietnam harnesses a rich diversity of rice landraces adapted to a broad range of conditions, which constitute a largely untapped source of genetic diversity for the continuous improvement of rice cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica-5 group. Here, we leveraged on that strong differentiation, and the 672 rice genomes generated, to identify genes within genomic regions putatively selected during domestication and breeding of rice in Vietnam.

Methodology

We identified significant distorted patterns in allele frequency (XP-CLR method) and population differentiation scores (FST), resulting from differential selective pressures between native subpopulations, and compared them with QTLs previously identified by GWAS in the same panel. We particularly focused on the outlying Indica-5 subpopulation because of its likely novelty and differential evolution.

Results

We identified selection signatures in each of the Vietnamese subpopulations and carried out a comprehensive annotation of the 52 regions selected in Indica-5, which represented 8.1% of the rice genome. We annotated the 4,576 genes in these regions, verified the overlap with QTLs identified in the same diversity panel and the comparison with a FST analysis between subpopulations, to select sixty-five candidate genes as promising breeding targets, several of which harboured alleles with non-synonymous substitutions.

Conclusions

Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

Key Message

We localised regions in the rice genome selected during breeding by comparing allele frequency patterns among Vietnamese rice subpopulations. We characterised candidate genes in the Indica-5 subpopulation with breeding potential.
Transcranial Ultrasound Stimulation in Anterior Cingulate Cortex Impairs Information Sampling and Learning in Loss Contexts
Authors: Boroujeni Kianoush Banaie , Sigona Michelle K , Treuting Robert Louie , Manuel Thomas J. , Caskey Charles F. , Womelsdorf Thilo
Published: August 2021

Neuronal subgroups in anterior cingulate cortex (ACC) and the anterior striatum (STR) encode the reward structure of a given environment. But whether or how this reward information is used to guide information sampling, optimize decision making, or motivate behavior in cognitively challenging situations has remained elusive. Here, we causally tested these scenarios by transiently disrupting ACC and STR of rhesus monkeys with transcranial ultrasound with a learning task that independently varied cognitive and motivational demands. We found that disrupting the ACC, but not the STR, prolonged information sampling and reduced learning efficiency whenever the motivational payoff was low. These impairments were most pronounced at high cognitive demands and based on an inability to use loss experiences to improve performance. These results provide causal evidence that the ACC is necessary for motivation, to overcome anticipated costs from negative (loss) outcomes, and for cognition, to enhance visual information sampling during adaptive behavior.

HIGHLIGHTS

Transcranial ultrasound stimulation of the anterior cingulate cortex disrupts learning after loss experience.

The ultrasound-induced learning deficit is exacerbated at high cognitive load.

The ultrasound-induced learning deficit is accompanied by inefficient fixational information sampling.

Anterior cingulate cortex causally supports credit assignment of aversive outcomes to visual features.
Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA
Authors: Rapala Jackson , Miller Brenda , Garcia Maximiliano , Dolan Megan , Bockman Matthew , Hansson Mats , Russell Daniel A. , Garlena Rebecca A. , Cresawn Steven G. , Westbye Alexander B. , Beatty J. Thomas , Alvey Richard M. , Bollivar David W.
Published: August 2021

The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.
Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules
Authors: Zamuner Stefano , Seno Flavio , Trovato Antonio
Published: August 2021

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference state associated to the null interaction case. Despite their significant effectiveness, the physical interpretation of knowledge-based potentials has been repeatedly questioned, with no consensus on the choice of the reference state. Here we use the fact that the Flory theorem, originally derived for chains in a dense polymer melt, holds also for chain fragments within the core of globular proteins, if the average over buried fragments collected from different non-redundant native structures is considered. After verifying that the ensuing Gaussian statistics, a hallmark of effectively non-interacting polymer chains, holds for a wide range of fragment lengths, we use it to define a ‘bona fide’ reference state. Notably, despite the latter does depend on fragment length, deviations from it do not. This allows to estimate an effective interaction potential which is not biased by the presence of correlations due to the connectivity of the protein chain. We show how different sequence-independent effective statistical potentials can be derived using this approach by coarse-graining the protein representation at varying levels. The possibility of defining sequence-dependent potentials is explored.
Retinoic acid treatment recruits macrophages and increases axonal regeneration after optic nerve injury in the frog Rana pipiens
Authors: De La Rosa-Reyes Valeria , Duprey-Díaz Mildred V. , Blagburn Jonathan M. , Blanco Rosa E.
Published: August 2021

Retinoic acid (RA) plays major roles during nervous system development, and during regeneration of the adult nervous system. We have previously shown that components of the RA signaling pathway are upregulated after optic nerve injury, and that exogenous application of all-trans retinoic acid (ATRA) greatly increases the survival of axotomized retinal ganglion cells (RGCs). The objective of the present study is to investigate the effects of ATRA application on the macrophages in the optic nerve after injury, and to determine whether this affects axonal regeneration. The optic nerve was crushed and treated with PBS, ATRA and/or clodronate-loaded liposomes. Nerves were examined at one and two weeks after axotomy with light microscopy, immunocytochemistry and electron microscopy. ATRA application to the optic nerve caused transient increases in the number of macrophages and microglia one week after injury. The macrophages are consistently labeled with M2-type markers, and have considerable phagocytic activity. ATRA increased ultrastructural features of ongoing phagocytic activity in macrophages at one and two weeks. ATRA treatment also significantly increased the numbers of regenerating GAP-43-labeled axons. Clodronate liposome treatment depleted macrophage numbers by 80%, completely eliminated the ATRA-mediated increase in axonal regeneration, and clodronate treatment alone decreased axonal numbers by 30%. These results suggest that the success of axon regeneration is partially dependent on the presence of debris-phagocytosing macrophages, and that the increases in regeneration caused by ATRA are in part due to their increased numbers. Further studies will examine whether macrophage depletion affects RGC survival.
Change in the bladder function of rats with focal cerebral infarction induced by photochemically-induced thrombosis
Authors: Ota Yuya , Kubota Yasue , Hotta Yuji , Matsumoto Mami , Matsuyama Nayuka , Kato Taiki , Hamakawa Takashi , Kataoka Tomoya , Kimura Kazunori , Sawamoto Kazunobu , Yasui Takahiro
Published: August 2021

The photochemically-induced thrombosis(photothrombosis) method can create focal cerebral infarcts anywhere in the relatively superficial layers of the cerebrum; it is easy to implement and minimally invasive. Taking advantage of this versatility, we aimed to establish a new rat model of urinary frequency with focal cerebral infarction, which was characterized by its simplicity, nonlethal nature, and high reproducibility. The prefrontal cortex and the anterior cingulate cortex, which are urinary centers, were targeted for focal cerebral infarction, and urinary parameters were measured by cystometrogram. Cystometric analysis indicated that micturition intervals significantly shortened in photothrombosis-treated rats compared with those in the sham operative group on Days 1 and 7 (P < 0.01), but prolonged after 14 days, with no difference between the two groups. Immunopathological evaluation showed an accumulation of activated microglia, followed by an increase in reactive astrocytes at the peri-infarct zone after photothrombotic stroke. Throughout this study, all postphotothrombosis rats showed cerebral infarction in the prefrontal cortex and anterior cingulate cortex; there were no cases of rats with fatal cerebral infarction. This model corresponded to the clinical presentation, in that the micturition status changed after stroke. In conclusion, this novel model combining nonlethality and high reproducibility may be a suitable model of urinary frequency after focal cerebral infarction.
The creation of functioning gastrojejunostomy following magnetic compression
Authors: Qiao Wei , Lv Yi , Du Zhaoqing , Li Hui , Du Lixue , Hu Haitian , Li Dichen
Published: August 2021

Background

Magnetic compression for creating gastrojejunostomy has many advantages according to previous studies. However, following mechanical device release after healing, the anastomotic stenosis becomes the pivotal point.

Methods

Rectangle-shaped magnets were used for magnetic compression in rabbits. Both paclitaxel-loaded magnets and a strategy of pyloric ligation were chosen to improve the gastrojejunostomy. Based on these choices, the half-capsule was applied to occlude the pylorus after anastomotic formation. The size and patency of the anastomoses were analyzed to evaluate the efficacy of these approaches. A histological examination was also performed.

Results

The positive effect of ligating the pylorus on gastrojejunostomy was significantly greater than that achieved using paclitaxel-loaded magnets during either short- or long-term follow-up. There were fewer scar tissue and collagen fibers at the anastomotic site in the treatment group than in the control group. The anastomotic aperture was of great interest at 9 months after the ligation of the pylorus following magnetic compression. In the view of the jejunum, although the aperture was barely visible, gastric juice was continuously spilling through it like a spring, and the aperture was clearly visible from the stomach side. All half-capsules failed to block the pylorus.

Conclusion

The effect of paclitaxel on maintaining gastrojejunostomy patency was temporary. The ligation of the pylorus ensured the long-term patency of gastrojejunostomy, and the aperture was comparable to the pylorus which could play an anti-reflux role. Further studies for the sort of gastrointestinal aperture are being planned.
Evaluation of freshness and physicochemical characteristics of blankets of pirarucu (Arapaima gigas) bred in captivity at different ages in relation to the seasons
Authors: de Rosa Krishna R. , da Silva Alessandra A. , de Barros Wander M. , Pedroso Anaqueli L. , Ferreira Maria Fernanda E. , Savay-da-Silva Luciana K. , de F. Mateus Lucia Aparecida , Kubota Ernesto H.
Published: August 2021

This study aimed to evaluate the freshness and physicochemical characterization of pirarucu blankets at different ages bred in captivity in excavated tanks in northern Mato Grosso State, Brazil, in different seasons (rain and dry seasons). Four harvests were performed in two different tanks and five specimens obtained in each evaluated period, with animals aged 18 and 24 months, respectively, at the beginning of the experiment. The animals were slaughtered in a local establishment that had an inspection service following humane standards, and the blankets were later sent to analysis. The samples were analyzed for freshness via total volatile nitrogenous bases and physicochemical characteristics (pH in 24 h, water activity, water retention capacity, dripping loss, cooking loss, and shear force). There was a statistical difference for total nitrogenous volatile bases and shear force with higher values in the rainy season (24 month-of-old animals). Additionally, pH and water activity differed statistically at 24 h in the same period, albeit for 18-month-of-old animals. It was possible to conclude that climate variation affected the freshness and physicochemical characteristics of the pirarucu blankets while age did not.
Preliminary analysis of a neotropical plant extract antiviral potential against Chikungunya and Mayaro viruses
Authors: Feitoza Pires Ellen Caroline , da Silva Francini Pereira , Schallenberger Karoline , Hermann Bruna Saraiva , Mallmann Larissa , dos Santos Alini Godinho , Moura Wellington S. , de Oliveira Eugênio E. , Smagghe Guy , Ascêncio Sergio Donizeti , Santos Barbosa Robson dos , Mendes Ilsamar , Fleck Juliane Deise , Ribeiro Bergmann Morais , de Souza Aguiar Raimundo Wagner
Published: August 2021

Chikungunya and Mayaro fevers are viral infectious diseases, without vaccine or treatment, that causes fever and arthralgia. Establishing novel antiviral tools capable of preventing or treating Chikungunya virus (CHIKV), and Mayaro virus (MAYV) infections are needed. The use of plant-based compounds that affect the replication cycles of these viruses has been proposed as a promising strategy. Chiococca alba (L.) Hitchc. is a neotropical plant used by Yucatec Mayas traditional healers, mainly, as antipyretic and antirheumatic. To evaluate the potential of C. alba methanolic extracts against CHIKV and MAYV through preliminary analysis in vitro and in silico. The cytotoxicity profile of two C. alba roots methanolic extracts in Vero cells was performed by lysosomal viability using the neutral red assay, and the antiviral potential was determined by plaque assay. We further assessed, through in silico computational predictions, the possible interactions between the active site of the nsP2 proteases of these viruses with some secondary metabolites present in C. alba extracts, identified by High-Performance Liquid Chromatography (HPLC). Our partial phytochemical analysis revealed the presence of flavonoids, and phenolic acids in the C. alba extracts. Our in vitro assays showed that both C. alba extracts inhibited more than 70% of CHIKV and MAYV activities at 60 µg/mL concentration. Based on our in silico computational predictions, the flavonoids naringin and vitexin showed the greatest affinity energies with the CHIKV and MAYV nsP2 proteases, revealing the great potential of these compounds as viral inhibitors. The findings described here indicates that C. alba extracts, or their secondary metabolites, as a potential source of novel antiviral compounds.
Exploring of bacterial blight resistance in landraces, mining of resistant gene(s) and genetic divergence of resistant germplasm through molecular markers and quantitative traits
Authors: Anik Touhidur Rahman , Nihad Sheikh Arafat Islam , Hasan Md. Al-Imran , Hossain Mohammad Ahasan , Rashid Md. Mamunur , Iqbal Khan Mohammad Ashik , Latif Mohammad Abdul
Published: August 2021

Bacterial blight, one of the oldest and severe diseases of rice poses a major threat towards global rice production and food security. Thereafter, sustainable management of this disease has given paramount importance globally. In the current study, we explored 792 landraces to evaluate their disease reaction status against three highly virulent strains (BXo69, BXo87 and BXo93) of Xanthomonas oryzae pv. oryzae (Xoo). Subsequently, we intended to identify the possible candidate resistant (R) genes responsible for the resistant reaction using six STS markers correspond to Xa4, xa5, Xa7, xa13, Xa21 and Xa23 genes and finally, we evaluated morphological and molecular diversity of the potential bacterial blight resistant germplasm using quantitative traits and ISSR markers. Based on pathogenicity test, a single germplasm was found as highly resistant while, 33 germplasm were resistant and 40 were moderately resistant. Further molecular study on these 74 germplasm divulged that 41 germplasm carried Xa4 gene, 15 carried xa5 gene, 62 carried Xa7 gene, 33 carried xa13 gene, and 19 carried Xa23 gene. Only a single germplasm consisted of Xa21 gene. Interestingly, we found a wide range of gene combinations ranged from 2 to 4 genes among the germplasm resistant to bacterial blight and G3 genotype (Acc. No. 4216; highly resistant) having Xa4, Xa7, xa13, Xa21 and G43 genotype (Acc. No. 1523; resistant) having Xa4, xa5, xa13 and Xa23 gene combination being the most effective against all the Xoo strains. Nonetheless, UPGMA dendrogram and heatmap analysis based on quantitative traits identified two important clusters viz. cluster-III and cluster-VIII with multiple desired traits However, genetic similarity based on ISSR marker data pointed out 3 germplasm, namely, G20 (Acc. No. 4004; contained Xa4, Xa7, xa13 genes), G17 (Acc. No. 3981; contained Xa7, xa13 genes) and G6 (Acc. No. 991; contained Xa4, Xa7, xa13, Xa23 genes) having comparatively lower genetic similarity (0.30, 0.37 and 0.38, respectively) with elite variety BRRI dhan28. Notably, Mantle test of molecular and morphological data indicated that there was a positive correlation (r = 0.113) between them. The outcome of this study would enrich and diversify the rice gene pool and would be useful for the development of durable bacterial blight resistant varieties.
Population structure and genetic diversity of chickpea germplasms
Authors: Yadav Garima , Jayaswal Deepanshu , Jayaswall Kuldip , Bhandawat Abhishek , Singh Arvind Nath , Tilgam Jyotsana , Rai Abhishek Kumar , Chaturvedi Rachna , Kumar Ashutosh , Kumar Sanjay
Published: August 2021

In various leguminous crops, chickpea is the fourth most important legume contributing 3.1% to the total legume production. Grains of chickpea are rich source of proteins, minerals and vitamins which makes them suitable for both food and feed. For any crop to be improved, the knowledge of genetic diversity of wild and elite cultivar is very important. Therefore among various available marker systems, molecular markers are more reliable and accurate, therefore are very commonly used for genetic diversity analysis, phylogenetic studies and cultivar identification. Due to several advantages of Inter Simple Sequence Repeat (ISSR) markers in present study we analyzed the genetic diversity, structure, cross-species transferability and allelic richness in 50 chickpea collection using 23 ISSR markers. The observed parameters such as allele number varied from 3 to 16, and PIC varied from 0.15 to 0.4988 respectively. Further, range of allele size varied from 150 to 1600 bp which shows the significance of ISSR markers for chickpea germplasms characterization. On the basis of ISSR marker genotypic data dendrogram were constructed which divides these 50 chickpea in group I and II showing the reliability of ISSR markers. Among 50 chickpea, the accession P 74-1 is in group I and rest are in group II. Further we made mini-core collection of 15 diverse chickpea and subgrouped them. Dendrogram, PCA, Dissimilarity matrix and Bayesian model based genetic clustering of 50 chickpea germplasms revealed that P 74-1,P 1883, P 1260 very diverse chickpea accession. Characterization of these diverse chickpea would help in maintenance breeding, conservation and in future could be used to develop climate resilient elite cultivar of chickpea. Utilization of these novel ISSRs markers in diversity analysis and population structure characterization of 50 chickpea germplasm suggests their wider efficacy in superior scale for molecular breeding studies in chickpea.
Comparison of genetic variation between rare and common congeners ofDipodomyswith estimates of contemporary and historical effective population size
Authors: Halsey Michaela K. , Stuhler John D. , Bayona-Vasquez Natalia , Platt Roy N. , Goetze Jim R. , Martin Robert E. , Matocha Kenneth G. , Bradley Robert D. , Stevens Richard D. , Ray David A.
Published: August 2021

Organisms with low effective population sizes are at greater risk of extinction because of reduced genetic diversity.Dipodomys elatoris a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespreadD. ordiiis thought to exhibit relative geographic and demographic stability. Genetic variation betweenD. elatorandD. ordiisamples was assessed using 3RAD, a modified restriction site associated sequencing approach. It was hypothesized thatD. elatorwould show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared toD. ordii. Also of interest was identifying population structure within contemporary samples ofD. elatorand detecting genetic variation between temporal samples that could indicate demographic dynamics. Up to 61,000 single nucleotide polymorphisms were analyzed. It was determined that genetic variability and effective population size in contemporaryD. elatorpopulations were lower than that ofD. ordii, that there is only slight, if any, structure within contemporaryD. elatorpopulations, and there is little genetic differentiation between spatial or temporal historical samples suggesting little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity ofD. elatorhas remained stable despite claims of reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract any immediate decrease in fitness.
Temperate tree seedlings have similar drought vulnerability despite having different hydraulic drought responses in adults
Authors: Lee Benjamin R. , Ibáñez Inés
Published: August 2021

Climate change is projected result in higher frequencies of drought events across the world and lead to reduced performance in many temperate tree species. However, many studies in this area focus specifically on adult tree drought responses and overlook how trees in other age classes might differ in their vulnerability. Evidence shows that seedling drought response can differ from that of adults and furthermore that demographic performance in the seedling age class will have disproportionately strong effects on the assembly dynamics of future forests, together suggesting that understanding seedling drought responses will be critical to our ability to predict how forests will respond to climate change. In this study, we measured four indices of hydraulic response to drought (leaf water potential, photosynthetic capacity, non-structural carbohydrate concentration, and hydraulic conductivity), as well as interaction effects with shade treatments, for seedlings of two temperate tree species that differ in their adult drought response: isohydric Acer saccharum and anisohydric Quercus rubra. We found a strong isohydric response in A. saccharum seedlings that included conservation of leaf water potentials (>-1.8 MPa) and reductions in non-structural carbohydrate concentrations consistent with reduction of stomatal conductance. Quercus rubra seedlings were able to survive to more negative water potentials, but only rarely, and they showed a similar reduction in photosynthetic capacity as was found for A. saccharum. Our results suggest that, although Q. rubra seedlings display some anisohydric responses to drought, they are more isohydric than adults. Both species seem to be relatively similar in their vulnerability to drought despite the differences predicted from adult drought response, and our results suggest that seedlings of both species will be similarly vulnerable to future drought events.
11β-HSD1 inhibition does not affect murine tumour angiogenesis but may exert a selective effect on tumour growth by modulating inflammation and fibrosis
Authors: Davidson Callam T , Miller Eileen , Muir Morwenna , Dawson John C. , Lee Martin , Aitken Stuart , Serrels Alan , Webster Scott P , Homer Natalie Z. M. , Andrew Ruth , Brunton Valerie G. , Hadoke Patrick W. F. , Walker Brian R.
Published: August 2021

Glucocorticoids inhibit angiogenesis by activating the glucocorticoid receptor. Inhibition of the glucocorticoid-activating enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) reduces tissue-specific glucocorticoid action and promotes angiogenesis in murine models of myocardial infarction. Angiogenesis is important in the growth of some solid tumours. This study used murine models of squamous cell carcinoma (SCC) and pancreatic ductal adenocarcinoma (PDAC) to test the hypothesis that 11β-HSD1 inhibition promotes angiogenesis and subsequent tumour growth. SCC or PDAC cells were injected into female FVB/N or C57BL6/J mice fed either standard diet, or diet containing the 11β-HSD1 inhibitor UE2316. SCC tumours grew more rapidly in UE2316-treated mice, reaching a larger (P<0.01) final volume (0.158 ± 0.037 cm3) than in control mice (0.051 ± 0.007 cm3). However, PDAC tumour growth was unaffected. Immunofluorescent analysis of SCC tumours did not show differences in vessel density (CD31/alpha-smooth muscle actin) or cell proliferation (Ki67) after 11β-HSD1 inhibition, and immunohistochemistry of SCC tumours did not show changes in inflammatory cell (CD3- or F4/80-positive) infiltration. In culture, the growth/viability (assessed by live cell imaging) of SCC cells was not affected by UE2316 or corticosterone. Second Harmonic Generation microscopy showed that UE2316 reduced Type I collagen (P<0.001), whilst RNA-sequencing revealed that multiple factors involved in the innate immune/inflammatory response were reduced in UE2316-treated SCC tumours.

11β-HSD1 inhibition increases SCC tumour growth, likely via suppression of inflammatory/immune cell signalling and extracellular matrix deposition, but does not promote tumour angiogenesis or growth of all solid tumours.
Efficient differentiation of human primordial germ cells through geometric control reveals a key role for NODAL signaling
Authors: Jo Kyoung , Teague Seth , Chen Bohan , Khan Hina Aftab , Freeburne Emily , Li Hunter , Li Bolin , Spence Jason , Heemskerk Idse
Published: August 2021

Human primordial germ cells (hPGCs) form around the time of implantation and are the precursors of eggs and sperm. Many aspects of hPGC specification remain poorly understood. Here we show that micropatterned human pluripotent stem cells (hPSCs) treated with BMP4 give rise to hPGC-like cells (hPGCLC) and use these as a quantitatively reproducible and simple in vitro model to interrogate this important developmental event. We characterize micropatterned hPSCs up to 96h for the first time and show that hPGCLC populations are stable and continue to mature. By perturbing signaling during hPGCLC differentiation, we identify a previously unappreciated role for NODAL signaling and find that the relative timing and duration of BMP and NODAL signaling are critical parameters controlling the number of hPGCLCs. We formulate a mathematical model for a network of cross-repressive fates driven by NODAL and BMP signaling which predicts the measured fate patterns after signaling perturbations. Finally, we show that hPSC colony size dictates the efficiency of hPGCLC specification, which led us to dramatically improve the efficiency of hPGCLC differentiation over current protocols.
An efficient miRNA knockout approach using CRISPR-Cas9 in Xenopus
Authors: Godden Alice M. , Ward Nicole J. , van der Lee Michael , Abu-Daya Anita , Guille Matthew , Wheeler Grant N.
Published: August 2021

In recent years CRISPR-Cas9 knockouts (KO) have become increasingly ultilised to study gene function. MicroRNAs (miRNAs) are short non-coding RNAs, 20-22 nucleotides long, which affect gene expression through post-transcriptional repression. We previously identified miRNAs-196a and −219 as implicated in the development of Xenopus neural crest (NC). The NC is a multipotent stem-cell population, specified during early neurulation. Following EMT NC cells migrate to various points in the developing embryo where they give rise to a number of tissues including parts of the peripheral nervous system and craniofacial skeleton. Dysregulation of NC development results in many diseases grouped under the term neurocristopathies. As miRNAs are so small it is difficult to design CRISPR sgRNAs that reproducibly lead to a KO. We have therefore designed a novel approach using two guide RNAs to effectively ‘drop out’ a miRNA. We have knocked out miR-196a and miR-219 and compared the results to morpholino knockdowns (KD) of the same miRNAs. Validation of efficient CRISPR miRNA KO and phenotype analysis included use of whole-mount in situ hybridization of key NC and neural plate border markers such as Pax3, Xhe2, Sox10 and Snail2, q-RT-PCR and Sanger sequencing. miRNA-219 and miR-196a KO’s both show loss of NC, altered neural plate and hatching gland phenotypes. Tadpoles show gross craniofacial and pigment phenotypes.
Naturalistic paradigm reveals multi-component emotion dynamics in theta and beta bands using DENS dataset
Authors: Mishra Sudhakar , Asif Mohammad , Tiwary Uma Shanker
Published: August 2021

The emotion research with artificial stimuli does not represent the dynamic processing of emotions in real-life situations. The lack of data on emotion with the ecologically valid naturalistic paradigm hinders the knowledge of emotion mechanism in a real-world interaction. To this aim, we collected the emotional multimedia clips, validated them with the university students, recorded the neuro-physiological activities and self-assessment ratings for these stimuli. Participants localized their emotional feelings (in time) and were free to choose the best emotion for describing their feelings with minimum distractions and cognitive load. The obtained electrophysiological and self-assessment responses were analyzed with functional connectivity, machine learning and source localization techniques. We observed that the connectivity patterns in the theta and beta band could differentiate emotions better. Using machine learning, we observed that the classification of affective self-assessment features, namely dominance, familiarity, and self-relevance, involves midline brain regions responsible for mentalization and event construction activity compared to valence and arousal, which were mainly associated with lateral brain regions. This finding advocates the need for more than two dimensions for emotion representation. In addition, the channels with high predictability were source localized to the brain regions in default-mode, sensorimotor and salience networks. Hence, in this naturalistic study, we find that the domain-general systems contribute to emotion construction.