bluuebunny/crossref_metadata_2025 huggingface dataset:
Live-cell single-molecule tracking highlights requirements for stable Smc5/6 chromatin associationin vivo
Authors: Etheridge Thomas J. , Villahermosa Desiree , Campillo-Funollet Eduard , Herbert Alex , Irmisch Anja , Watson Adam T. , Dang Hung Q. , Osborne Mark A. , Oliver Antony W. , Carr Antony M. , Murray Johanne M.
Published: June 2020

The essential Smc5/6 complex is required in response to replication stress and is best known for ensuring the fidelity of homologous recombination. Using single-molecule tracking in live fission yeast to investigate Smc5/6 chromatin association, we show that Smc5/6 is chromatin associated in unchallenged cells and this depends on the non-SMC protein Nse6. We define a minimum of two Nse6-dependent sub-pathways, one of which requires the BRCT-domain protein Brc1. Using defined mutants in genes encoding the core Smc5/6 complex subunits we show that the Nse3 double-stranded DNA binding activity and the arginine fingers of the two Smc5/6 ATPase binding sites are critical for chromatin association. Interestingly, disrupting the ssDNA binding activity at the hinge region does not prevent chromatin association but leads to elevated levels of gross chromosomal rearrangements during replication restart. This is consistent with a downstream function for ssDNA binding in regulating homologous recombination.
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes
Authors: Robertson C.C. , Inshaw J.R.J. , Onengut-Gumuscu S. , Chen W.M. , Flores Santa Cruz D. , Yang H. , Cutler A.J. , Crouch D.J.M. , Farber E. , Bridges S.L. , Edberg J.C. , Kimberly R.P. , Buckner J.H. , Deloukas P. , Divers J. , Dabelea D. , Lawrence J.M. , Marcovina S. , Shah A.S. , Greenbaum C.J. , Atkinson M.A. , Gregersen P.K. , Oksenberg J.R. , Pociot F. , Rewers M.J. , Steck A.K. , Dunger D.B. ,   Type 1 Diabetes Genetics Consortium, Wicker L.S. , Concannon P. , Todd J.A. , Rich S.S.
Published: June 2020

We report the largest and most ancestrally diverse genetic study of type 1 diabetes (T1D) to date (61,427 participants), yielding 152 regions associated to false discovery rate < 0.01, including 36 regions associated to genome-wide significance for the first time. Credible sets of disease-associated variants are specifically enriched in immune cell accessible chromatin, particularly in CD4+effector T cells. Colocalization with chromatin accessibility quantitative trait loci (QTL) in CD4+T cells identified five regions where differences in T1D risk and chromatin accessibility are potentially driven by the same causal variant. Allele-specific chromatin accessibility further refined the set of putative causal variants with functional relevance in CD4+T cells and integration of whole blood expression QTLs identified candidate T1D genes, providing high-yield targets for mechanistic follow-up. We highlight rs72938038 inBACH2as a candidate causal T1D variant, where the T1D risk allele leads to decreased enhancer accessibility andBACH2expression in T cells. Finally, we prioritise potential drug targets by integrating genetic evidence, functional genomic maps, and immune protein-protein interactions, identifying 12 genes implicated in T1D that have been targeted in clinical trials for autoimmune diseases. These findings provide an expanded genomic landscape for T1D, including proposed genetic regulatory mechanisms of T1D-associated variants and genetic support for therapeutic targets for immune intervention.
FastPG: Fast clustering of millions of single cells
Authors: Bodenheimer Tom , Halappanavar Mahantesh , Jefferys Stuart , Gibson Ryan , Liu Siyao , Mucha Peter J. , Stanley Natalie , Parker Joel S. , Selitsky Sara R.
Published: June 2020

Current single-cell experiments can produce datasets with millions of cells. Unsupervised clustering can be used to identify cell populations in single-cell analysis but often leads to interminable computation time at this scale. This problem has previously been mitigated by subsampling cells, which greatly reduces accuracy. We built on the graph-based algorithm PhenoGraph and developed FastPG which has the same cell assignment accuracy but is on average 27x faster in our tests. FastPG also has higher cell assignment accuracy than two other fast clustering methods, FlowSOM and PARC.

Availability

FastPG is available here:https://github.com/sararselitsky/FastPG
Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches
Authors: Goletic Teufik , Konjhodzic Rijad , Fejzic Nihad , Goletic Sejla , Eterovic Toni , Softic Adis , Kustura Aida , Salihefendic Lana , Ostojic Maja , Travar Maja , Mrdjen Visnja , Tihic Nijaz , Jazic Sead , Musa Sanjin , Marjanovic Damir , Hukic Mirsada
Published: June 2020

Whole Genome Sequence of four samples from COVID-19 outbreaks was done in two laboratories in Bosnia and Herzegovina (Veterinary Faculty Sarajevo and Alea Genetic Center). All four BiH sequences cluster mainly with European ones (Italy, Austria, France, Sweden, Cyprus, England). The constructed phylogenetic tree indicates probable multiple independent introduction events. The success of future containment measures concernig new introductions will be highly challenging for country due to the significant proportion of BH population living abroad.
Postponing production exponentially enhances the molecular memory of a stochastic switch
Authors: Bokes Pavol
Published: June 2020

Delayed production can substantially alter the qualitative behaviour of feedback systems. Motivated by stochastic mechanisms in gene expression, we consider a protein molecule which is produced in randomly timed bursts, requires an exponentially distributed time to activate, and then partakes in positive regulation of its burst frequency. Asymptotically analysing the underlying master equation in the large-delay regime, we provide tractable approximations to time-dependent probability distributions of molecular copy numbers. Importantly, the presented analysis demonstrates that positive feedback systems with large production delays can constitute a stable toggle switch even if they operate with low copy numbers of active molecules.
SON and SRRM2 form nuclear speckles in human cells
Authors: Ilık İbrahim Avşar , Malszycki Michal , Lübke Anna Katharina , Schade Claudia , Meierhofer David , Aktaş Tuğçe
Published: June 2020

The nucleus of higher eukaryotes is a highly compartmentalized and dynamic organelle consisting of several biomolecular condensates that regulate gene expression at multiple levels (1, 2). First reported more than 100 years ago by Ramon y Cajal, nuclear speckles (NS) are among the most prominent of such condensates (3). Despite their prevalence, research on the function of NS is virtually restricted to colocalization analyses, since an organizing core, without which NS cannot form, remains unidentified (4, 5). The monoclonal antibody SC35, which was raised against a spliceosomal extract, is a frequently used reagent to mark NS since its debut in 1990 (6). Unexpectedly, we found that this antibody has been misidentified and the main target of SC35 mAb is SRRM2, a large (∼300 kDa), spliceosomeassociated (7) protein with prominent intrinsically disordered regions (IDRs) that sharply localizes to NS (8). Here we show that, the elusive core of NS is formed by SON and SRRM2, since depletion of SON leads only to a partial disassembly of NS, while combined depletion of SON together with SRRM2, but not other NS associated factors, or depletion of SON in a cell line where IDRs of SRRM2 are genetically deleted, leads to a near-complete dissolution of NS. This work, therefore, paves the way to study the role of NS under diverse physiological and stress conditions.
Human Prostate Cancer-Associated Macrophage Subtypes with Prognostic Potential Revealed by Single-cell Transcriptomics
Authors: Siefert Joseph C , Cioni Bianca , Muraro Mauro J , Alshalalfa Mohammed , Vivié Judith , van der Poel Henk , Feng Felix Y , Wessels Lodewyk , Zwart Wilbert , Bergman Andries M
Published: June 2020

Macrophages in the tumor microenvironment are causally linked with prostate cancer development and progression, yet little is known about their composition in neoplastic human tissue. By performing single cell transcriptomic analysis of human prostate cancer resident macrophages, three distinct populations were identified in the diseased prostate. Unexpectedly, macrophages isolated from the tumor-adjacent site of the prostatectomy specimen were identical to those from the tumorous site. Markers associated with canonical M1 and M2 macrophage phenotypes were identifiable, however these were not the main factors defining unique subtypes. The genes selectively associated with each macrophage cluster were used to develop a gene signature which was highly associated with both recurrence-free and metastasis-free survival. These results highlight the relevance of tissue-specific macrophage subtypes in the tumour microenvironment for prostate cancer progression and demonstrates the utility of profiling single-cell transcriptomics in human tumor samples as a strategy to design gene classifiers for patient prognostication.
Colors everywhere: enhanced chromatic processing across the first visual synapse in the zebrafish central brain
Authors: Guggiana Nilo Drago A. , Riegler Clemens , Hübener Mark , Engert Florian
Published: June 2020

Larval zebrafish (Danio rerio) are an ideal organism to study color vision, as their eye possesses four types of cone photoreceptors, covering most of the visible range and into the UV [1,2]. Additionally, their entire eye and nervous system are accessible to imaging, given they are naturally transparent [3–5]. Relying on this advantage, recent research has found that, through a set of color specific horizontal, bipolar and retinal ganglion cells (RGCs) [6–8], the eye then relays tetrachromatic information to several retino-recipient areas (RAs) [9,10]. The main RA is the optic tectum, receiving 97% of the RGC axons via the neuropil mass termed Arborization Field 10 (AF10) [11,12]. In this work, we aim to understand the processing of color signals at the interface between RGCs and their targets in the brain. We used 2-photon calcium imaging to separately measure the responses of RGCs and neurons in the dorsal brain to stimulation with four different colors in awake animals. We find that color information is widespread throughout the larval brain, with a large variety of color responses among RGCs, and an even greater diversity in their targets. Specific combinations of response types are localized to specific nuclei, but we observe no single color processing structure. In the main interface in this pathway, the connection between Arborization Field 10 and the tectum, we observe key elements of color processing such as enhanced signal decorrelation and improved decoding [13,14]. Finally, when presenting a richer set of stimuli, we identify parallel processing of color, motion and luminance information in the same cells/terminals, evidence of a rich color vision machinery in this small vertebrate brain.
DNA damage inhibits root growth by enhancing cytokinin biosynthesis inArabidopsis thaliana
Authors: Takahashi Naoki , Inagaki Soichi , Nishimura Kohei , Sakakibara Hitoshi , Antoniadi Ioanna , Karady Michal , Ljung Karin , Umeda Masaaki
Published: June 2020

Plant root growth is influenced by external factors to adapt to changing environmental conditions. However, the mechanisms by which environmental stresses affect root growth remain elusive. Here we found that DNA double-strand breaks (DSBs) induce the expression of genes for the synthesis of cytokinin hormones and enhance the accumulation of cytokinins in theArabidopsisroot tip. This is a programmed response to DSBs through the DNA damage signaling pathway. Our data showed that activation of cytokinin signalling suppresses the expression ofPIN-FORMEDgenes that encode efflux carriers of another plant hormone, auxin, thereby disturbing downward auxin flow and causing cell cycle retardation in the G2 phase. Elevated cytokinin signalling also promotes an early transition from cell division to endoreplication, resulting in a reduction of the root meristem size. We propose that in response to DNA stress, plants inhibit root growth by orchestrating hormone biosynthesis and signalling.
Using cost-effective surveys from platforms of opportunity to assess cetacean occurrence patterns for marine park management in the heart of the Coral Triangle
Authors: Sahri Achmad , Mustika Putu Liza Kusuma , Purwanto  , Murk Albertinka J. , Scheidat Meike
Published: June 2020

The Wakatobi National Park (WNP) at the heart of Coral Triangle is an important area for cetaceans in Indonesia. Currently there is insufficient information on spatio-temporal occurrence patterns of cetaceans to inform effective conservation strategies. This study used platforms of opportunity from May 2004 to May 2012 as a cost-effective way to address this knowledge gap. A database was created of cetacean sightings per surveyed days at sea, allowing for an analysis of species diversity and habitat use around the islands. A total of 11 cetacean species were identified. Spinner and bottlenose dolphins were sighted most often, followed by melon-headed and sperm whales. Spinner dolphin showed a wide distribution in the area, whilst bottlenose dolphin and melon-headed whale occupied the waters between the main islands and south atolls. Sperm whales occurred mostly in waters to the north of the main islands and as melon-headed whales were mostly found in deep waters. Most cetacean sightings occurred in the zones designated for human use, indicating where potential conflicts might occur. No sightings were found in the Park core zone, indicating a mismatch between WNP design and the ecological needs of the cetaceans. A sub-sample of the data from dedicated fishing monitoring trips was used to derive a sighting frequency. Occurrence of both small and large cetaceans was highest during inter-monsoonal seasons, possibly related to an increase of prey availability due to seasonal upwelling and increase in survey activity. Inter-annual occurrence of cetaceans was variable, with no large cetaceans being sighted in 2010-2012, likely due to reduced survey efforts. In areas with limited resources for designated surveys, the use of platforms of opportunity can be a cost-effective tool to provide valuable data on cetacean occurrence. It helps identify potentially important areas as well as highlight where to direct designated research efforts. We discuss the implications of our findings for the conservation management of these cetaceans and give suggestions for improved marine park management.
Maintaining structural and functional homeostasis of theDrosophilarespiratory epithelia requires stress-modulated JAK/STAT activity
Authors: Niu Xiao , Fink Christine , Kallsen Kimberley , Shi Leizhi , Mincheva Viktoria , Franzenburg Sören , Prange Ruben , Bruchhaus Iris , Bossen Judith , Heine Holger , Roeder Thomas
Published: June 2020

Signaling mediated by the Janus kinase (JAK)/Signal Transducer and Activator of Transcription (STAT) pathway is critical for maintaining cellular and functional homeostasis in the lung. Thus, chronically activated JAK/STAT signaling is causally associated with lung diseases such as lung cancer, asthma, and chronic obstructive pulmonary disease. To elucidate the molecular processes that transform increased JAK/STAT signaling in airway epithelial cells into the known pathological states, we used a highly simplified model system, the fruit flyDrosophila melanogaster. Here, the JAK/STAT pathway is permanently active in almost all airway cells and responds to airborne stressors with increased activity. Silencing of this signaling pathway in epithelial cells resulted in apoptosis. Since the above-mentioned lung diseases are commonly associated with increased JAK/STAT signaling, we assessed this by its ectopic activation in the respiratory epithelium ofDrosophila. This intervention triggered cell-autonomous structural changes in epithelial cells. These structural changes included phenotypes associated with asthma, namely, thickening of the epithelium, substantial narrowing of the air-conducting space, and impairment of the secretory epicuticular structure of the tracheae. Pharmacological manipulation of JAK/STAT signaling reversed this pathological phenotype. Transcriptomic analyses revealed that several biological processes were affected, which is consistent with the impairment of junction protein trafficking also observed in this study. These results indicate that balanced JAK/STAT signaling is essential for the functionality of the respiratory epithelium and, by extension, the entire organ. In contrast, chronic overactivation of this signaling leads to massive structural changes that are closely associated with pathologies typical of chronic inflammatory lung diseases.

Highlights

JAK/STAT signaling is active in the entireDrosophilarespiratory system in all developmental stages.

The signaling pathway is indispensable for the survival of the tracheal cell.

Overactivation of the signaling has significant effects on tracheal development and also displays a human disease-associated phenotype inDrosophilatrachea.

Abstract Figure
Convergence of modality invariance and attention selectivity in the cortical semantic circuit
Authors: Nakai Tomoya , Yamaguchi Hiroto Q. , Nishimoto Shinji
Published: June 2020

The human linguistic system is characterized by modality invariance and attention selectivity. Previous studies have examined these properties independently and reported perisylvian region involvement for both; however, their relationship and the linguistic information they harbor remain unknown. Participants were assessed by functional MRI, while spoken narratives (auditory) and written texts (visual) were presented, either separately or simultaneously. Participants were asked to attend to one stimulus when both were presented. We extracted phonemic and semantic features from these auditory and visual modalities, to train multiple, voxel-wise encoding models. Cross-modal examinations of the trained models revealed that perisylvian regions were associated with modality-invariant semantic representations. Attentional modulation was quantified by examining the modeling performance for attended and unattended conditions. We have determined that perisylvian regions exhibited attention selectivity. Both modality invariance and attention selectivity are both prominent in models that use semantic but not phonemic features. Modality invariance was significantly correlated with attention selectivity in some brain regions; however, we also identified cortical regions associated with only modality invariance or only attention selectivity. Thus, paying selective attention to a specific sensory input modality may regulate the semantic information that is partly processed in brain networks that are shared across modalities.
Unravelling the genetic basis for the rapid diversification of male genitalia betweenDrosophilaspecies
Authors: Hagen Joanna F. D. , Mendes Cláudia C. , Booth Shamma R. , Jimenez Javier Figueras , Tanaka Kentaro M. , Franke Franziska A. , Baudouin-Gonzalez Luis. , Ridgway Amber M. , Arif Saad , Nunes Maria D. S. , McGregor Alistair P.
Published: June 2020

In the last 240,000 years, males of theDrosophila simulansspecies clade have evolved striking differences in the morphology of their epandrial posterior lobes and claspers (surstyli). These changes have most likely been driven by sexual selection and mapping studies indicate a highly polygenic and generally additive genetic basis. However, we have limited understanding of the gene regulatory networks that control the development of genital structures and how they evolved to result in this rapid phenotypic diversification. Here, we used newD. simulans / D. mauritianaintrogression lines on chromosome 3L to generate higher resolution maps of posterior lobe and clasper differences between these species. We then carried out RNA-seq on the developing genitalia of both species to identify the genes expressed during this process and those that are differentially expressed between the two species. This allowed us to test the function of expressed positional candidates during genital development inD. melanogaster. We identified several new genes involved in the development and possibly the evolution of these genital structures, including the transcription factors Hairy and Grunge. Furthermore, we discovered that during clasper development Hairy negatively regulatestartan, a gene known to contribute to divergence in clasper morphology. Taken together our results provide new insights into the regulation of genital development and how this evolves between species.
Transgene codon usage drives viral fitness and therapeutic efficacy in oncolytic adenoviruses
Authors: Núñez-Manchón Estela , Farrera-Sal Martí , Castellano Giancarlo , Medel David , Alemany Ramon , Villanueva Eneko , Fillat Cristina
Published: June 2020

Arming oncolytic adenoviruses with therapeutic transgenes is a well-established strategy for multimodal tumour attack. However, this strategy sometimes leads to unexpected attenuated viral replication and a loss of oncolytic effects, preventing these viruses from reaching the clinic. Previous work has shown that altering codon usage in viral genes can hamper viral fitness. Here, we have analysed how transgene codon usage impacts viral replication and oncolytic activity. We observe that, although transgenes with optimised codons show high expression levels at a first round of infection, they impair viral fitness and are therefore not expressed in a sustained manner. Conversely, transgenes encoded by suboptimal codons do not compromise viral replication and are thus stably expressed over time allowing a greater oncolytic activity bothin vitroandin vivo. Altogether, our work shows that fine-tuning codon usage leads to a concerted optimisation of transgene expression and viral replication paving the way for the rational design of more efficacious oncolytic therapies.
Experimental manipulation of body size alters senescence in hydra
Authors: Ngo Kha Sach , Almási Berta , Barta Zoltán , Tökölyi Jácint
Published: June 2020

Body size has a fundamental impact on the ecology and physiology of animals. Large size, for instance, is often associated with increased fecundity and reproductive success. A persistent correlation between body size and individual longevity is also observed across the animal world, although this relationship proved difficult to understand due to the inseparability of body size from growth rate and the widespread collinear relationship between body size with other life history traits. Here, we usedHydra oligactis, a freshwater cnidarian with high tissue plasticity and inducible ageing as an experimental system to understand the causal roles of body size on reproduction and senescence. We first show that large size predicts accelerated sexual development, increased fecundity and reduced survival in a population sample of this species kept under common garden conditions in the laboratory. Next, using phenotypic engineering, we experimentally increased or decreased body size by reciprocally grafting pieces of the body column differing in size between hydra polyps. Experimentally reduced body size was associated with delayed sexual development and reduced fecundity. In parallel, post–reproductive survival was significantly higher in polyps with reduced size. These results suggest that small hydra can physiologically detect their reduced body size and adjust reproductive decisions to achieve a higher post–reproductive survival. Our observations offer a new perspective on why smaller individuals within a species live longer by suggesting a growth–independent link between body size, reproduction and senescence.
Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2
Authors: Dittmar Mark , Lee Jae Seung , Whig Kanupriya , Segrist Elisha , Li Minghua , Jurado Kellie , Samby Kirandeep , Ramage Holly , Schultz David , Cherry Sara
Published: June 2020

There are an urgent need for antivirals to treat the newly emerged SARS-CoV-2. To identify new candidates we screened a repurposing library of ~3,000 drugs. Screening in Vero cells found few antivirals, while screening in human Huh7.5 cells validated 23 diverse antiviral drugs. Extending our studies to lung epithelial cells, we found that there are major differences in drug sensitivity and entry pathways used by SARS-CoV-2 in these cells. Entry in lung epithelial Calu-3 cells is pH-independent and requires TMPRSS2, while entry in Vero and Huh7.5 cells requires low pH and triggering by acid-dependent endosomal proteases. Moreover, we found 9 drugs are antiviral in lung cells, 7 of which have been tested in humans, and 3 are FDA approved including Cyclosporine which we found is targeting Cyclophilin rather than Calcineurin for its antiviral activity. These antivirals reveal essential host targets and have the potential for rapid clinical implementation.
A nanobody suite for yeast scaffold nucleoporins provides details of the Nuclear Pore Complex structure
Authors: Nordeen Sarah A , Andersen Kasper , Knockenhauer Kevin E , Ingram Jessica R , Ploegh Hidde , Schwartz Thomas U
Published: June 2020

Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working inS. cerevisiae, and to study the assembly of these two essential subcomplexes, we developed a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite inS. cerevisiaerevealed accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.
Enhancing mitochondrial activity in neurons protects against neurodegeneration in CNS inflammation
Authors: Rosenkranz Sina C. , Shaposhnykov Artem A. , Träger Simone , Engler Jan Broder , Witte Maarten E. , Roth Vanessa , Vieira Vanessa , Paauw Nanne , Bauer Simone , Schwencke-Westphal Celina , Bal Lukas , Schattling Benjamin , Pless Ole , van Horssen Jack , Freichel Marc , Friese Manuel A.
Published: June 2020

Central nervous system (CNS) inflammation in multiple sclerosis (MS) drives neuro-axonal loss resulting in irreversible disability. While transcripts of mitochondrial genes are strongly suppressed in neurons during CNS inflammation, it is unknown whether this results in mitochondrial dysfunction and whether interventions that increase mitochondrial function can rescue neurodegeneration. Here we show that suppression of mitochondrial gene transcripts in inflamed neurons was predominantly affecting genes of the electron transport chain resulting in impaired mitochondrial complex IV activity. This was associated with posttranslational inactivation of the transcriptional co-regulator peroxisome proliferator-activated receptor gamma co-activator 1-α (PGC-1α). Neuronal overexpression ofPgc-1αled to increased numbers of mitochondria, complex IV activity and elevated maximum respiratory capacity. Moreover,Pgc-1α-overexpressing neurons showed a higher mitochondrial membrane potential that related to an improved calcium buffering capacity. Accordingly, neuronal deletion ofPgc-1αaggravated neurodegeneration during experimental autoimmune encephalomyelitis (EAE), while neuronal overexpression ofPgc-1αameliorated EAE disease course and preserved neurons. Our study provides systemic insights into mitochondrial dysfunction in neurons during inflammation and commends elevation of mitochondrial activity as a promising neuroprotective strategy.
Anti-Bacterial Activity of Substances Produced from Lactic Acid Bacteria in Metata Ayib (Traditional Ethiopian Spiced Fermented Cottage)
Authors: Essayas Alazar , Pandit Sujata , Verma Deepak Kumar
Published: June 2020

There have been incerases in antibiotic resistant strains of human pathogens and causing treatment of microbial infections difficult. These days more attention is given to seraching new antimicrobial drugs to combat pathogenic microbes. Traditional fermented cottage of Metata Ayib which is naturally enriched with lactic acid bacteria (LAB) and used to preserve cheese for long time in Northern Ethiopia, may have antimicrobial activity against various human pathogens. However, there was no scientific report on the antimicrobial activity of lactic acid bacteria isolated from Metata Ayib. The objective of this study is to evaluate antibacterial activity of lactic acid bacteria fromMetata Ayibagainst clinical and standard human pathogens. The study was laboratory based experiment. Antibiotic production by the LAB was performed by inoculating the LAB isolates into 6.0 ml MRS medium and incubating at 30 °C. Cell free supernatants (CFS) were collected by centrifugation (10,000 rpm for 15 min at 4 °C) of the six day fermented broth cultures. The pH of the CFS was adjusted to 6.5 with 4 N NaOH to eliminate the effect of organic acids.The susceptibility of produced antibiotic against test organisms was done by growing on Muller Hinton agar in triplicate using well diffusion method and the inhibition zone was recorded. Preceddingly, MIC and MBC was determined using standard methods. The antibiotic substance exhibited antimicrobial activity towards standard and drug resistant bacteral strains with the inhibition zone ranges upto 25.33±3.21 mm. The result of MIC against tested ornaisnms showed a considerable antimicrobial activity of the antibiotic substance withn the range values 6.25% to12.5%. In addition, the result of this study showed that LAB obtained from Metata Ayib exhibits antimicrobial activity against standard and pathogenic pathogenic test bacterial species ranged from 12.5-25% of MBC value. This might be due to the production of organic acids, but also other compounds, such as ethanol, hydrogen peroxide, diacetyl, reuterin and bacteriocins. The results of this investigation can also provide baseline for information for future studies about the application of antibacterial substances produced by LAB from fermented Metata ayib.
Lymph node swelling combined with temporary effector T cell retention aids T cell response in a model of adaptive immunity
Authors: Johnson Sarah C , Frattolin Jennifer , Edgar Lowell T. , Jafarnejad Mohammad , Moore James E.
Published: June 2020

Swelling of lymph nodes is commonly observed during the adaptive immune response, yet the impact on T cell trafficking and subsequent immune response is not well known. To better understand the effect of macro-scale alterations, we developed an agent-based model of the lymph node para-cortex, describing T cell trafficking and response to antigen-presenting dendritic cells alongside swelling-induced changes in T cell recruitment and egress, and regulation of expression of egress-modulating T cell receptor Sphingosine-1-phosphate receptor-1. Analysis of effector T cell response under varying swelling conditions showed that swelling consistently aided T cell activation. However, subsequent effector CD8+T cell production could be reduced if swelling occurred too early in the T cell proliferative phase or if T cell cognate frequency was low due to increased opportunity for T cell exit. Temporarily extending retention of newly differentiated effector T cells, mediated by Sphingosine-1-phosphate receptor-1 expression, mitigated any negative effects of swelling by allowing facilitation of activation to outweigh increased access to exit areas. These results suggest targeting temporary effector T cell retention and egress associated with swelling may offer new ways to modulate effector TC responses in, for example, immuno-suppressed patients and optimisation of vaccine design.
Structural analysis of different LINC complexes reveals distinct binding modes
Authors: Cruz Victor E. , Demircioglu F. Esra , Schwartz Thomas U.
Published: June 2020

Linker of nucleoskeleton and cytoskeleton (LINC) complexes are molecular tethers that span the nuclear envelope (NE) and physically connect the nucleus to the cytoskeleton. They transmit mechanical force across the NE in processes such as nuclear anchorage, nuclear migration, and homologous chromosome pairing during meiosis. LINC complexes are composed of KASH proteins traversing the outer nuclear membrane, and SUN proteins crossing the inner nuclear membrane. Humans have several SUN- and KASH-containing proteins, yet what governs their proper engagement is poorly understood. To investigate this question, we solved high resolution crystal structures of human SUN2 in complex with the KASH-peptides of Nesprin3, Nesprin4, and KASH5. In comparison to the published structures of SUN2-KASH1/2 we observe alternative binding modes for these KASH peptides. While the core interactions between SUN and the C-terminal residues of the KASH peptide are similar in all five complexes, the extended KASH-peptide adopts at least two different conformations. The much-improved resolution allows for a more detailed analysis of other elements critical for KASH interaction, including the KASH-lid and the cation loop, and a possible self-locked state for unbound SUN. In summary, we observe distinct differences between the examined SUN-KASH complexes. These differences may have an important role in regulating the SUN-KASH network.
Role of livestock parameters on cattle vulnerability to drought in the coastal semi-arid areas, Kenya
Authors: Omolo Jack Owiti , Mathew Muturi , Owiny Maurice , Ngugi Jeremiah N , Ganda Joseph Ogola , Malenga Cornel K , Musimba Stephen Kioko
Published: June 2020

Livestock keeping forms main occupation in arid and semi-arid lands. Increase in drought frequency and intensity globally negatively affect livestock production and livelihood. Cattle are the most drought sensitive livestock due to size, grazing behavior and nutritional requirements. Factors for vulnerability of cattle to droughts are individual cattle parameters, health and husbandry practices. This cross sectional study aimed to those factors in semi-arid Kaloleni sub-county. Data on household (HH) head demographics, cattle and production collected from 194 enrolled HH using structured questionnaires. Cattle ages were grouped into young (<1 year old), growers (1-2 years old) and adults (>2years old). Data was analyzed using STATA 12 software. Univariate, bivariate and multivariate logistic regression analysis conducted and reported in Crude Odds Ratio (cOR), Adjusted Odds Ratio (aOR) and Confidence Interval (CI). We used Pearson product-moment correlation to determine relationship between HH head, cattle herd, individual cattle characteristics and drought characteristics, p = <0.05 being significant. Mean age HH heads was 40.7 ± 12.6 years, 44.3% (86) had basic education, males were 65.3% (n=126). Mixed livestock production was practiced by 69.1% (134), while 86.1% (167) practiced free range communal grazing. Adult cattle were 54.1% (1295). Female cattle were 72.7% (1741). Average body condition score was 3.0 ± 0.6, and calves had 2.6 ± 1.3. About 20.6% had various forms of illness, calves mostly affected at 29.1%. Up to 63.4% HH, spray cattle at home, 93.3% HH reported no vaccination history. Home straying was protective (cOR 0.3, 95% CI 0.14 – 0.53). Herd size (aOR 2.9, 95% CI 1.5 – 5.5) and having no disease control method (aOR 2.8, 95% CI 1.85 – 9.19) were contributing to reporting disease. We report positive correlation between drought outcomes and HH head (r=0.076, p>0.01), cattle herd (r=0.216, p=0.003 and individual cattle characteristics(r=0.139, p>0.01). The findings on cattle conditions exacerbate their vulnerability in presence of stressful conditions like droughts especially in calves and cows. This study demonstrates weak disease control efforts and unorganized husbandry practices. We propose strategic and focused disease control plans to improve cattle resilience and further research on livestock based factors as drought response metrics for the livestock livelihood.
Genome-wide correlation analysis revealsRorcas potential amplitude regulator of circadian transcriptome output
Authors: Littleton Evan S. , Kojima Shihoko
Published: June 2020

Cell-autonomous circadian system, consisting of core clock genes, generates near 24-hour rhythms and regulates the downstream rhythmic gene expression. While it has become clear that the percentage of rhythmic genes varies among mouse tissues, it remains unclear how this variation can be generated, particularly when the clock machinery is nearly identical in all tissues. In this study, we sought to characterize circadian transcriptome datasets that are publicly available and identify the critical component(s) involved in creating this variation. We found that the relative amplitude of 13 genes and the average level of 197 genes correlated with the percentage of cycling genes. Of those, the correlation ofRorcin both relative amplitude and the average level was one of the strongest. In addition, the level ofPer2AS, a novel non-coding transcript that is expressed at thePeriod 2locus, was also linearly correlated, although with a much lesser degree compared toRorc. Overall, our study provides insight into how the variation in the percentage of clock-controlled genes can be generated in mouse tissues and suggests thatRorcand potentiallyPer2ASare involved in regulating the amplitude of circadian transcriptome output.
The genomics of trait combinations and their influence on adaptive divergence
Authors: Calvert McCall B. , Doellman Meredith M. , Feder Jeffrey L. , Hood Glen R. , Meyers Peter , Egan Scott P. , Powell Thomas H.Q. , Glover Mary M. , Tait Cheyenne , Schuler Hannes , Berlocher Stewart H. , Smith James J. , Nosil Patrik , Hahn Daniel A. , Ragland Gregory J.
Published: June 2020

Understanding rapid adaptation requires quantifying natural selection on traits and elucidating the genotype-phenotype relationship for those traits. However, recent studies have often failed to predict the direction of adaptive allelic variation in natural populations from laboratory studies. Here, we test for genomic signatures of genetic correlations to illustrate how multifarious, correlational selection may drive counterintuitive patterns of population divergence in the apple maggot fly,Rhagoletis pomonella(Diptera: Tephritidae). Apple-infesting populations with relatively early emerging adults have recently evolved from hawthorn-infesting populations consisting of relatively later emerging adults. Multiple studies have reported a paradoxical relationship between population differentiation and seasonal timing, as determined by the timing of diapause termination; alleles associated with late termination occur at higher frequencies in the earlier emerging apple-infesting populations compared to hawthorn-infesting populations. We present evidence that historical selection on diapause termination and another trait, initial diapause intensity, over geographic gradients generated genetic correlations between the traits in a direction antagonistic to contemporary selection on apple-infesting populations. Single nucleotide polymorphism in genomic regions of high linkage disequilibrium associated strongly with diapause termination and intensity, population divergence, geography, and evolutionary responses in laboratory selection experiments. These associations were consistent with geographically variable selection and with correlated evolutionary responses driving higher frequencies of late-associated alleles in the early emerging apple race. In contrast, loci associated only with diapause termination showed the expected pattern (more early-associated alleles in the apple race) in half of the population pairs. Our results suggest that selection on loci demonstrating antagonistic pleiotropy may often shape genomic footprints of rapid adaptation.
RUNX1 marks a luminal castration resistant lineage established at the onset of prostate development
Authors: Mevel Renaud , Steiner Ivana , Mason Susan , Galbraith Laura C.A. , Patel Rahima , Fadlullah Muhammad ZH , Ahmad Imran , Leung Hing Y. , Oliveira Pedro , Blyth Karen , Baena Esther , Lacaud Georges
Published: June 2020

The characterization of prostate epithelial hierarchy and lineage heterogeneity is critical to understand its regenerative properties and malignancies. Here, we report that the transcription factor RUNX1 marks a specific subpopulation of proximal luminal cells (PLCs), enriched in the periurethral region of the developing and adult mouse prostate, and distinct from the previously identified NKX3.1+luminal castration resistant cells. Using scRNA-seq profiling and genetic lineage tracing, we show that RUNX1+PLCs are unaffected by androgen deprivation, and do not contribute to the regeneration of the distal luminal compartments. Furthermore, we demonstrate that a transcriptionally similar RUNX1+population emerges at the onset of embryonic prostate specification to populate the proximal region of the ducts. Collectively, our results reveal that RUNX1+PLCs is an intrinsic castration-resistant and self-sustained lineage that emerges early during prostate development and provide new insights into the lineage relationships of the prostate epithelium.
Curvature effect of PE-included membrane on the behavior of cinnamycin on the membrane
Authors: Lee S-R. , Park Y. , Park J-W.
Published: June 2020

The behavior of the cinnamycin on the biomimetic membrane was studied with respect to the curvature of the phosphatidylethanolamine(PE)-included membrane with the adhesion measured by the atomic force microscope(AFM). The membrane was formed through vesicle fusion on the hydrophobic surface of the sphere spheres, which was used to define the curvature of the membrane. The hydrophobicity was generated by the reaction of alkyl-silane and analyzed with the X-ray photoelectron spectrometer. The cinnamycin, immobilized covalently to the AFM tip coated with 1-mercapto-1-undecanol that was observed inert to any adhesion to the membrane, showed that the adhesion became stronger with the increase in the curvature. The correlation between the adhesion and the curvature was linearly proportional. Previously, it was found that the cinnamycin was bound to PE headgroup and the binding was enhanced by the interaction of the hydrophobic area located at one side of the cinnamycin. Therefore, the linear proportionality seems to suggest that the interaction is related to the one dimensional orientation of the binding.

Statement of Significance

The behavior of the cinnamycin was studied on the phosphatidylethanolamine(PE)-included membrane with respect to the curvature of the membrane. The cinnamycin, immobilized covalently to the atomic force microscope, showed that the adhesion became stronger linearly with the increase in the curvature. Previously, it was found that the specific binding between the cinnamycin and PE headgroup was enhanced by the interaction of the hydrophobic area located at one side of the cinnamycin. Therefore, the linear proportionality seems to suggest that the interaction is related to the one dimensional orientation of the binding.
Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction
Authors: Sadykov Mukhtar , Mourier Tobias , Guan Qingtian , Pain Arnab
Published: June 2020

RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. In an attempt to address this we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5'-UCG-3' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins.
An in-silico based clinical insight on the effect of noticeable CD4 conserved residues of SARS-CoV-2 on the CD4-MHC-II interactions
Authors: C Selvaa Kumar , Kumar Senthil Arun , Dasgupta Debjani , Wei Haiyan
Published: June 2020

The study is aimed to unveil the conserved residues of CD4 in the context of its purposeful interaction with MHC-II at the receptor-binding domain (RBD) of SARS-CoV-2 compared with the envelope (Env) glycoprotein (gp) 120 of HIV-1. The paired CD4 conserved residues, including the matched CD4 interacting MHC-II epitopes of the structural viral protein domains, were chosen for the protein modelling using the SWISS-MODEL online server. Energy minimization and structural validation of the modelled viral protein domains, including the CD4 and MHC-II protein were achieved by CHIMERA and PROCHECK-Ramachandran Plot respectively. Protein-protein docking was performed by the HADDOCK online tool. The binding affinity score was measured using the PRODIGY online server.

As per our docking report, the Env gp120 of HIV-1 with three identical and three conserved residues of CD4 exhibited the highest binding affinity (−13.9 kcal/mol) with MHC-II than the second-highest RBD-S1-SARS-CoV-2 (−12.5 kcal/mol) with three identical and a single conserved residue of CD4. With a noticeable single salt bridge formation identified at the interacting residues Lys305 (of Env gp120-HIV-1) and Glu139 (of MHC-II); the Env gp120 interaction with MHC-II occupied the crucial His144 and Glu194 (salt-bridge) interacting residues of CD4 with the measured buried surface area 2554.8±40.8 Å2. Similarly, the RBD-S1-SARS-CoV-2-MHC-II complex showed two salt bridge formations at the residue sites: 1) Arg567 (of SARS-CoV-2)-Glu194 (of MHC-II) 2) 2) Asp568(of SARS-CoV-2)-Arg165 (of MHC-II) with the increased buried surface area of 1910.9±97.1 Å2over the SARS-CoV score 1708.2±50.8 Å2; that camouflaged all crucial CD4 interacting residues of MHC-II. In conclusion, the noticeable conserved residues of CD4 at the RBD-S1 sites of SARS-CoV-2 could interrupt the aspired CD4-MHC-II interactions of adaptive immune activation.