bluuebunny/crossref_metadata_2025 huggingface dataset:
Resist or perish: fate of a microbial population subjected to a periodic presence of antimicrobial
Authors: Marrec Loïc , Bitbol Anne-Florence
Published: November 2019

The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, using a stochastic model that includes variations of both population composition and size, and fully incorporates stochastic population extinctions. We show that fast alternations of presence and absence of antimicrobial are inefficient to eradicate the microbial population and strongly favor the establishment of resistance, unless the antimicrobial increases enough the death rate. We further demonstrate that if the period of alternations is longer than a threshold value, the microbial population goes extinct upon the first addition of antimicrobial, if it is not rescued by resistance. We express the probability that the population is eradicated upon the first addition of antimicrobial, assuming rare mutations. Rescue by resistance can happen either if resistant mutants preexist, or if they appear after antimicrobial is added to the environment. Importantly, the latter case is fully prevented by perfect biostatic antimicrobials that completely stop division of sensitive microorganisms. By contrast, we show that the parameter regime where treatment is efficient is larger for biocidal drugs than for biostatic drugs. This sheds light on the respective merits of different antimicrobial modes of action.

Author summary

Antimicrobials select for resistance, which threatens to make antimicrobials useless. Understanding the evolution of antimicrobial resistance is therefore of crucial importance. Under what circumstances are microbial populations eradicated by antimicrobials? Conversely, when are they rescued by resistance? We address these questions employing a stochastic model that incorporates variations of both population composition and size. We consider periodic alternations of absence and presence of antimicrobial, which may model a treatment. We find a threshold period above which the first phase with antimicrobial fully determines the fate of the population. Faster alternations strongly select for resistance, and are inefficient to eradicate the microbial population, unless the death rate induced by the treatment is large enough. For longer alternation periods, we calculate the probability that the microbial population gets eradicated. We further demonstrate the different merits of biostatic antimicrobials, which prevent sensitive microbes from dividing, and of biocidal ones, which kill sensitive microbes.
Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework
Authors: Wasimuddin  , Schlaeppi Klaus , Ronchi Francesca , Leib Stephen L , Erb Matthias , Ramette Alban
Published: November 2019

The “One Health” framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently lacking. To address this methodological gap, we evaluated the performance of DNA extractions kits and commonly recommended primer pairs targeting different hypervariable regions (V3-V4, V4, V5-V6, V5-V6-V7) of the 16S rRNA gene, on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. We also included faeces from gnotobiotic mice colonized with defined bacterial taxa and mock communities to confirm the robustness of our molecular and bioinformatic approaches on these defined low microbial diversity samples. Based on Amplicon Sequence Variants, the primer pair 515F-806R led to the highest estimates of species richness and diversity in all sample types and offered maximum diversity coverage of reference databases in in silico primer analysis. The influence of the DNA extraction kits was negligible compared to the influence of the choice of primer pairs. Comparing microbiomes using 515F-806R revealed that soil and root samples have the highest estimates of species richness and inter-sample variation. Species richness decreased gradually along the food chain, with the lowest richness observed in human faeces. Primer pair choice directly influenced the estimation of community changes (beta diversity) within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains in the context of the One Health framework.
Narrative and Gaming Experience Interact to Affect Presence and Cybersickness in Virtual Reality
Authors: Weech Séamas , Kenny Sophie , Lenizky Markus , Barnett-Cowan Michael
Published: November 2019

Research has established a link between presence and cybersickness in virtual environments, but there is significant disagreement regarding the directionality of the relationship (positive or negative) between the two factors, and if the relationship is modulated by other top-down influences. Several studies have revealed a negative association between the factors, highlighting the prospect that manipulating one factor might affect the other. Here we examined if a top-down factor (narrative context) enhances presence, and whether this effect is associated with a decrease in cybersickness. We analyzed the association between responses to questionnaire measures of cybersickness and presence, as well as the degree to which their relationship was affected by the administration of an ‘enriched’ or ‘minimal’ verbal narrative context. The results of the first experiment, conducted in a controlled laboratory environment, revealed that enriched narrative was associated with increased presence, but that the reductive effect of narrative on cybersickness depended on video gaming experience. We also observed the expected negative association between presence and cybersickness, but only in the enriched narrative group. In a second experiment, conducted with a diverse sample at a public museum, we confirmed our previous finding that presence and cybersickness are negatively correlated, specifically when participants experienced an enriched narrative. We also confirmed the interaction between narrative and gaming experience with respect to cybersickness. These results highlight the complexity of the presence-cybersickness relationship, and confirm that both factors can be modulated in a beneficial manner for virtual reality users by means of top-down interventions.
Distinct roles for the Charcot-Marie-Tooth disease-causing endosomal regulators Mtmr5 and Mtmr13 in axon radial sorting and Schwann cell myelination
Authors: Mammel Anna E. , Delgado Katherine C. , Chin Andrea L. , Condon Alec F. , Hill Jo Q. , Aicher Sue A. , Wang Yingming , Fedorov Lev M. , Robinson Fred L.
Published: November 2019

The form of Charcot-Marie-Tooth type 4B (CMT4B) disease caused by mutations in myotubularin-related 5 (MTMR5; also calledSET Binding Factor 1; SBF1) shows a spectrum of axonal and demyelinating nerve phenotypes. This contrasts with the CMT4B subtypes caused byMTMR2orMTMR13(SBF2) mutations, which are characterized by myelin outfoldings and classic demyelination. Thus, it is unclear whether MTMR5 plays an analogous or distinct role from that of its homolog, MTMR13, in the peripheral nervous system (PNS). MTMR5 and MTMR13 are pseudophosphatases predicted to regulate endosomal trafficking by activating Rab GTPases and binding to the phosphoinositide 3-phosphatase MTMR2. In the mouse PNS, Mtmr2 was required to maintain wild type levels of Mtmr5 and Mtmr13, suggesting that these factors function in discrete protein complexes. Genetic elimination of both Mtmr5 and Mtmr13 in mice led to perinatal lethality, indicating that the two proteins have partially redundant functions during embryogenesis. Loss of Mtmr5 in mice did not cause CMT4B-like myelin outfoldings. However, adultMtmr5-/-mouse nerves contained fewer myelinated axons than control nerves, likely as a result of axon radial sorting defects. Mtmr5 levels were highest during axon radial sorting, whereas Mtmr13 levels rose as myelin formed, and remained high through adulthood. Our findings suggest that Mtmr5 and Mtmr13 ensure proper axon radial sorting and Schwann cell myelination, respectively, perhaps through their direct interactions with Mtmr2. This study enhances our understanding of the non-redundant roles of the endosomal regulators MTMR5 and MTMR13 during normal peripheral nerve development and disease.
Functional Organization of Mouse Primary Auditory Cortex in adult C57BL/6 and F1 (CBAxC57) mice
Authors: Bowen Zac , Winkowski Daniel E. , Kanold Patrick O.
Published: November 2019

The primary auditory cortex (A1) plays a key role for sound perception since it represents one of the first cortical processing stations for sounds. Recent studies have shown that on the cellular level the frequency organization of A1 is more heterogeneous than previously appreciated. However, many of these studies were performed in mice on the C57BL/6 background which develop high frequency hearing loss with age making them a less optimal choice for auditory research. In contrast, mice on the CBA background retain better hearing sensitivity in old age. Since potential strain differences could exist in A1 organization between strains, we performed comparative analysis of neuronal populations in A1 of adult (~10 weeks) C57BL/6 mice and CBAxC57 F1 mice. We used in vivo 2-photon imaging of pyramidal neurons in cortical layers L4 and L2/3 of awake mouse primary auditory cortex (A1) to characterize the populations of neurons that were active to tonal stimuli. Pure tones recruited neurons of widely ranging frequency preference in both layers and strains with neurons in CBA mice exhibiting a wider range of frequency preference particularly to higher frequencies. Frequency selectivity was slightly higher in C57BL/6 mice while neurons in CBA mice showed a greater sound-level sensitivity. The spatial heterogeneity of frequency preference was present in both strains with CBA mice exhibiting higher tuning diversity across all measured length scales. Our results demonstrate that the tone evoked responses and frequency representation in A1 of adult C57BL/6 and CBAxC57 F1 mice is largely similar.
Integrated Genomic Analysis Reveals Key Features of Long Undecoded Transcript Isoform (LUTI)-based Gene Repression
Authors: Tresenrider Amy , Jorgensen Victoria , Chia Minghao , Liao Hanna , van Werven Folkert J. , Ünal Elçin
Published: November 2019

Long Undecoded Transcript Isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed some important aspects of LUTI-based repression, how these features impact gene regulation at a global scale is unknown. By using transcript leader and direct RNA sequencing, here we identify 74 LUTI candidates that are expressed specifically during meiotic prophase. Translational repression of these candidates is ubiquitous and dependent on upstream open reading frames. However, LUTI-based transcriptional repression is highly variable. In only 50% of the cases, LUTI transcription causes downregulation of the protein-coding transcript isoform. Higher LUTI expression, enrichment of histone 3 lysine 36 trimethylation, and changes in nucleosome position are the strongest predictors of LUTI-based transcriptional repression. We conclude that LUTIs downregulate gene expression in a manner that integrates translational repression, chromatin state changes, and the magnitude of LUTI expression.
RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids
Authors: Di Lin , Fu Yusi , Sun Yue , Li Jie , Liu Lu , Yao Jiacheng , Wang Guanbo , Wu Yalei , Lao Kaiqin. , Lee Raymond W. , Zheng Genhua , Xu Jun , Oh Juntaek , Wang Dong , Xie X. Sunney , Huang Yanyi , Wang Jianbin
Published: November 2019

Transcriptome profiling by RNA sequencing (RNA-seq) has been widely used to characterize cellular status but it relies on second strand cDNA synthesis to generate initial material for library preparation. Here we use bacterial transposase Tn5, which has been increasingly used in various high-throughput DNA analyses, to construct RNA-seq libraries without second strand synthesis. We show that Tn5 transposome can randomly bind RNA/DNA heteroduplexes and add sequencing adapters onto RNA directly after reverse transcription. This method, Sequencing HEteRo RNA-DNA-hYbrid (SHERRY), is versatile and scalable. SHERRY accepts a wide range of starting materials, from bulk RNA to single cells. SHERRY offers a greatly simplified protocol, and produces results with higher reproducibility and GC uniformity compared with prevailing RNA-seq methods.

Significance Statement

RNA sequencing is widely used to measure gene expression in biomedical research; therefore, improvements in the simplicity and accuracy of the technology are desirable. All existing RNA sequencing methods rely on the conversion of RNA into double-stranded DNA through reverse transcription followed by second strand synthesis. The latter step requires additional enzymes and purification, and introduces sequence-dependent bias. Here, we show that Tn5 transposase, which randomly binds and cuts double-stranded DNA, can directly fragment and prime the RNA/DNA heteroduplexes generated by reverse transcription. The primed fragments are then subject to PCR amplification. This provides a new approach for simple and accurate RNA characterization and quantification.
Dynamic Brain-Body Coupling of Breath-by-Breath O2-CO2Exchange Ratio with Resting State Cerebral Hemodynamic Fluctuations
Authors: Chan Suk-tak , Evans Karleyton C. , Song Tian-yue , Selb Juliette , van der Kouwe Andre , Rosen Bruce R. , Zheng Yong-ping , Ahn Andrew C. , Kwong Kenneth
Published: November 2019

The origin of low frequency cerebral hemodynamic fluctuations (CHF) in resting state remains unknown. Here we studied the contribution of respiratory gas exchange (RGE) metrics to CHF during spontaneous breathing. RGE metrics include the breath-by-breath changes of partial pressure of oxygen (ΔPO2) and carbon dioxide (ΔPCO2) between end inspiration and end expiration, and their ratio breath-by-breath O2-CO2exchange ratio (bER). We used transcranial Doppler sonography to evaluate CHF changes during spontaneous breathing by measuring the cerebral blood flow velocity (CBFv) in the middle cerebral arteries. The regional CHF changes during spontaneous breathing were mapped with blood oxygenation level dependent (BOLD) signal changes using functional magnetic resonance imaging (fMRI) technique. We found that prominent oscillations with periods of 0.5 to 2 minutes characterized ΔPO2, ΔPCO2and bER. The oscillations of bER were coherent with CHF during spontaneous breathing at the frequency range of 0.008-0.03Hz which is consistent with the low frequency resting state CHF. CHF had strong correlation with bER, followed by ΔPO2and then by ΔPCO2. Brain regions with the strongest bER-CHF coupling overlapped with many areas of default mode network. Although the physiological mechanisms underlying the strong correlation between bER and CHF are not completely understood, our findings suggest the contribution of bER to low frequency resting state CHF. It also provides a novel insight of brain-body interaction via CHF and oscillations of RGE metrics.
Synergistic and Antagonistic Drug Interactions in the Treatment of Systemic Fungal Infections
Authors: Wambaugh Morgan A. , Denham Steven T. , Brammer Brianna , Stonhill Miekan , Brown Jessica C. S.
Published: November 2019

Invasive fungal infections cause 1.6 million deaths annually, primarily in immunocompromised individuals. Mortality rates are as high as 90% due to limited number of efficacious drugs and poor drug availability. The azole class antifungal, fluconazole, is widely available and has multi-species activity but only inhibits fungal cell growth instead of killing fungal cells, necessitating long treatments. To improve fluconazole treatments, we used our novel high-throughput method, the overlap2method (O2M), to identify drugs that interact with fluconazole, either increasing or decreasing efficacy. Although serendipitous identification of these interactions is rare, O2M allows us to screen molecules five times faster than testing combinations individually and greatly enriches for interactors. We identified 40 molecules that act synergistically (amplify activity) and 19 molecules that act antagonistically (decrease efficacy) when combined with fluconazole. We found that critical frontline beta-lactam antibiotics antagonize fluconazole activity. A promising fluconazole-synergizing anticholinergic drug, dicyclomine, increases fungal cell permeability and inhibits nutrient intake when combined with fluconazole.In vivo, this combination doubled the time-to-endpoint of mice with disseminatedCryptococcus neoformansinfections. Thus, our ability to rapidly identify synergistic and antagonistic drug interactions can potentially alter the patient outcomes.
Proteolytic Cleavage by Matriptase Exacerbating Kidney Injury: a Novel Therapeutic Target
Authors: Ozawa Shota , Matsubayashi Masaya , Nanaura Hitoki , Yanagita Motoko , Mori Kiyoshi , Asanuma Katsuhiko , Kajiwara Nobuyuki , Hayashi Kazuyuki , Ohashi Hiroshi , Kasahara Masato , Yokoi Hideki , Kataoka Hiroaki , Mori Eiichiro , Nakagawa Takahiko
Published: November 2019

Chronic kidney disease (CKD) is a progressive disease, and podocyte injury is a potential mechanism. We found that Matriptase was activated at podocytes in CKD patients and mice while a Matriptase inhibitor slowed the progression of mouse kidney disease. The mechanism could be accounted for by an imbalance favoring Matriptase over its cognate inhibitor, hepatocyte growth factor activator inhibitor type 1 (HAI-1), as conditional depletion of HAI-1 in podocytes accelerates podocyte injury. Intriguingly, the N-terminal of Podocin (Podocin-N), as a consequence of Matriptase cleavage of Podocin, translocates to nucleoli. These results suggest that aberrant activation of Matriptase would cause podocyte injury, and a targeting Matriptase could be a novel therapeutic strategy for CKD patients.

Significant statement

Chronic kidney disease (CKD) is a progressive disease. If podocytes, which are specialized cells of the kidney glomerulus that wrap around capillaries, are injured, kidney injury is exacerbated. Thus, a therapeutic strategy to addressing CKD would be to block podocyte injury. The present study provides evidence that Matriptase cleaves Podocin, a component of podocyte slit membrane, and the N-terminal of podocin translocates to nucleoli, causing kidney injury. Our findings show that the N-terminal of Podocin plays an efficient role for cell fate in podocytes. In addition, the inhibition of Matriptase would be a potential therapeutic target for CKD.
Structural basis of peptidoglycan endopeptidase regulation
Authors: Shin Jung-Ho , Sulpizio Alan G. , Kelley Aaron , Alvarez Laura , Murphy Shannon G. , Cava Felipe , Mao Yuxin , Saper Mark A. , Dörr Tobias
Published: November 2019

Most bacteria surround themselves with a cell wall, a strong meshwork consisting primarily of the polymerized aminosugar peptidoglycan (PG). PG is essential for structural maintenance of bacterial cells, and thus for viability. PG is also constantly synthesized and turned over, the latter process is mediated by PG cleavage enzymes, for example the endopeptidases (EPs). EPs themselves are essential for growth, but also promote lethal cell wall degradation after exposure to antibiotics that inhibit PG synthases (e.g., β-lactams). Thus, EPs are attractive targets for novel antibiotics and their adjuvants. However, we have a poor understanding of how these enzymes are regulatedin vivo, depriving us of novel pathways for the development of such antibiotics. Here, we have solved crystal structures of the LysM/M23 family peptidase ShyA, the primary EP of the cholera pathogenVibrio cholerae.Our data suggest that ShyA assumes two drastically different conformations; a more open form that allows for substrate binding, and a closed form, which we predicted to be catalytically inactive. Mutations expected to promote the open conformation caused enhanced activityin vitroandin vivo, and these results were recapitulated in EPs from the divergent pathogensNeisseria gonorrheaeandEscherichia coli. Our results suggest that LysM/M23 EPs are regulated via release of the inhibitory Domain1 from the M23 active site, likely through conformational re-arrangementin vivo.

Significance

Bacteria digest their cell wall following exposure to antibiotics like penicillin. The endopeptidases (EPs) are among the proteins that catalyze cell wall digestion processes after antibiotic exposure, but we do not understand how these enzymes are regulated during normal growth. Herein, we present the structure of the major EP from the diarrheal pathogenVibrio cholerae.Surprisingly, we find that EPs from this and other pathogens appear to be produced as a largely inactive precursor that undergoes a conformational shift exposing the active site to engage in cell wall digestion. These results enhance our understanding of how EPs are regulated and could open the door for the development of novel antibiotics that overactivate cell wall digestion processes.
Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes
Authors: Suresh Pooja , Long Alexandra F. , Dumont Sophie
Published: November 2019

The spindle generates force to segregate chromosomes at cell division. In mammalian cells, kinetochore-fibers connect chromosomes to the spindle. The dynamic spindle anchors kinetochore-fibers in space and time to coordinate chromosome movement. Yet, how it does so remains poorly understood as we lack tools to directly challenge this anchorage. Here, we adapt microneedle manipulation to exert local forces on the spindle with spatiotemporal control. Pulling on kinetochore-fibers reveals that the spindle retains local architecture in its center on the seconds timescale. Upon pulling, sister, but not neighbor, kinetochore-fibers remain tightly coupled, restricting chromosome stretching. Further, pulled kinetochore-fibers freely pivot around poles but not around chromosomes, retaining their orientation within 3 µm of chromosomes. This local reinforcement has a 20 s lifetime, and requires the microtubule crosslinker PRC1. Together, these observations indicate short-lived, specialized reinforcement of the kinetochore-fiber in the spindle center. This could help the spindle protect local structure near chromosomes from transient forces while allowing its remodeling over longer timescales, thereby supporting robust chromosome attachments and movements.
Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)
Authors: O’Connell Kyle A. , Oaks Jamie R. , Hamidy Amir , Shaney Kyle J. , Kurniawan Nia , Smith Eric N. , Fujita Matthew K.
Published: November 2019

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (GenusRhacophorus) on Sumatra. We generate target-capture data (∼950 loci and ∼440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (∼80 kya). However, we infer a stronger signal of expansion in southern populations around ∼400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.
Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin
Authors: Vonica Alin , Bhat Neha , Phan Keith , Guo Jinbai , Iancu Lăcrimioara , Weber Jessica A. , Karger Amir , Cain John W. , Wang Etienne C. E. , DeStefano Gina M. , O’Donnell-Luria Anne H. , Christiano Angela M. , Riley Bruce , Butler Samantha J. , Luria Victor
Published: November 2019

Animal development and homeostasis depend on precise temporal and spatial intercellular signaling. Components shared between signaling pathways, generally thought to decrease specificity, paradoxically can also provide a solution to pathway coordination. Here we show that the Bone Morphogenetic Protein (BMP) and Wnt signaling pathways share Apcdd1 as a common inhibitor and that Apcdd1 is a taxon-restricted gene with novel domains and signaling functions. Previously, we showed that Apcdd1 inhibits Wnt signaling, here we find that Apcdd1 potently inhibits BMP signaling in body axis formation and neural differentiation in chicken, frog, zebrafish, and humans. Our results from experiments and modeling suggest that Apcdd1 may coordinate the outputs of two signaling pathways central to animal development and human disease.

Significance Statement

Apcdd1is a taxon-restricted gene that inhibits both BMP and Wnt intercellular signaling pathways in multiple organisms including mice, frog, zebrafish, and chicken. It encodes a bi-functional protein with a novel protein domain that can bind to Wnt and BMP receptors and block downstream signaling.
Phosphate transporter PstSCAB of Campylobacter jejuni is essential for lactate-dependent growth and colonization in chickens
Authors: Sinha Ritam , LeVeque Rhiannon M. , Bowlin Marvin Q. , Gray Michael J. , DiRita Victor J.
Published: November 2019

Campylobacter jejuni causes acute gastroenteritis world-wide and is transmitted primarily through poultry, in which it is often a commensal member of the intestinal microbiota. Previous RNASeq experiments showed that transcripts from an operon encoding a high affinity phosphate transporter (PstSCAB) of C. jejuni were among the most abundant when grown in chickens. Elevated levels of the pstSCAB mRNA were also identified in an RNASeq experiment from human infection studies. In this study, we explore the role of PstSCAB in the biology and colonization potential of C. jejuni. Our experimental results demonstrate that cells lacking PstSCAB survive poorly in stationary phase, nutrient-limiting media, and under osmotic conditions reflective of those in the chicken. Polyphosphate levels in the mutant cells were elevated at stationary phase, consistent with alterations in expression of polyphosphate metabolism genes. C. jejuni were highly attenuated in colonization of newly hatched chicks, recovered at levels several orders of magnitude below wild type. Mutant and wild type grew similarly in complex media but the pstSCAB mutant exhibited a significant growth defect in minimal media supplemented with L-lactate, postulated as a carbon source in vivo. Poor growth in lactate correlated with diminished expression of acetogenesis pathway genes previously demonstrated as important for colonizing chickens. The phosphate transport system is thus essential for diverse aspects of C. jejuni physiology and in vivo fitness and survival.

Importance

C. jejuni causes millions of gastrointestinal infections annually worldwide. Poultry and poultry products are major sources of C. jejuni infection to human as the microbe is a commensal colonizer of the chicken gastrointestinal tract. Due to the emergence of multi-drug resistance in C. jejuni, there is need to identify alternative ways to control this pathogen. Genes encoding the high-affinity phosphate transporter PstSCAB were highly expressed during colonization of C. jejuni in chicken and human. In this study, we address the role this high-affinity phosphate transporter PstSCAB of C. jejuni on chicken colonization and for its general physiology. PstSCAB is required for colonization in chicken, metabolism and survival under different stress responses and during growth on lactate, a potential substrate for growth of C. jejuni in chickens. Our study highlights that PstSCAB may be an effective target to develop mechanisms to control the bacterial burden in both chicken and human.
Zika virus infection during pregnancy and induced brain pathology in beclin1-deficient mouse model
Authors: Muthu Karuppan Mohan Kumar , Ojha Chet Raj , Rodriguez Myosotys , Lapierre Jessica , Javad Aman M. , Kashanchi Fatah , Toborek Michal , Nair Madhavan , El-Hage Nazira
Published: November 2019

We investigated the role of the autophagy protein, Beclin1, in the replication and disease of Zika virus (ZIKV) in pregnant dams and their offspring using Beclin1-deficient (Atg6+/−) and wild-type (Atg6+/+) mouse model infected with the Honduran (R103451), Puerto Rican (PRVABC59), and the Uganda (MR766) strains of ZIKV. Pregnant dams infected subcutaneously at embryonic stage (E)9 showed viral RNA in serum harvested at E13 and in various organs removed postmortem at E17. Subcutaneous infections with ZIKV also showed the vertical transmission of ZIKV from the placenta to embryos removed postmortem at E17. From the three isolates, R103451-infected Atg6+/− dams had the lowest mortality rate while 30 % of their offspring containing the hemizygous beclin1 allele (Atg6+/−) were smaller in size and had smaller and underdeveloped brain. Growth impairment in the pups became noticeable after two weeks post-birth. After 21-days, pups were sacrificed and brain tissues removed postmortem showed expression of the envelope (E) and the non-structural (NS)-1 proteins, along with signs of neuronal injury, despite an absence in viral RNA detection. A significant decrease in the mRNA expression levels of the insulin-like growth factor-1 (IGF-1) by 8-fold and a decrease in the mRNA expression levels of several microcephaly related genes along with an increase in the secretion of several inflammatory molecules may have contributed to the observed phenotype. Since autophagy regulates cytokines and chemokines production, a dysregulation in this pathway may have further exacerbated the pathology of ZIKV.

IMPORTANCE

Pups delivered from ZIKV-infected dams showed significant growth impairments in the body and the brain. We believe that the reduction in insulin growth factor together with the increase secretion of inflammatory molecules may have triggered neuronal injury and the downregulation of the microcephalic genes, while reduced expression of the autophagy protein, Beclin1 further exacerbated the pathology. Although the mechanism is still unknown, the autophagy pathway seems to play a key role in ZIKV pathology. It is therefore of great significance to study the role of autophagy during viral infection with the goal to identify potential targets for anti-ZIKV therapeutic intervention.
aCPSF1 controlled archaeal transcription termination: a prototypical eukaryotic model
Authors: Yue Lei , Li Jie , Zhang Bing , Qi Lei , Zhao Fangqing , Li Lingyan , Dong Xiuzhu
Published: November 2019

Transcription termination defines RNA 3′-ends and guarantees programmed transcriptomes, thus is an essential biological process for life. However, transcription termination mechanisms remain almost unknown in Archaea. Here reported the first general transcription termination factor of Archaea, the conserved ribonuclease aCPSF1, and elucidated its 3′-end cleavage dependent termination mechanism. Depletion of Mmp-aCPSF1 in a methanoarchaeon Methanococcus maripaludis caused a genome-wide transcription termination defect and overall transcriptome chaos, and cold-sensitive growth. Transcript-3′end-sequencing (Term-seq) revealed transcriptions mostly terminated downstream of a uridine-rich terminator motif, where Mmp-aCPSF1 performed cleavage. The endoribonuclease activity was determined essential to terminate transcription in vivo as well. Through super-resolution photoactivated localization microscopy imaging, co-immunoprecipitation, and chromatin immunoprecipitation, we demonstrated that Mmp-aCPSF1 localizes within nucleoid and associates with RNAP and chromosomes. aCPSF1 appears to co-evolve with archaeal RNAPs, and two distant orthologs each from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to termination transcription. Thus, aCPSF1 dependent termination mechanism could be universally employed in Archaea, including Lokiarchaeota, one supposed archaeal ancestor of Eukaryotes. Therefore, the reported aCPSF1 cleavage-dependent termination mode not only hints an archetype of Eukaryotic 3′-end processing/cleavage triggered RNAP II termination, but also would shed lights on understanding the complex eukaryotic termination based on the simplified archaeal model.
A comprehensive survey of developmental programs reveals a dearth of tree-like lineage graphs and ubiquitous regeneration
Authors: Mani Somya , Tlusty Tsvi
Published: November 2019

Background: Multicellular organisms are characterized by a wide diversity of forms and complexity despite a restricted set of key molecules and mechanisms at the base of organismal development. Development combines three basic processes --- asymmetric cell division, signaling and gene regulation --- in a multitude of ways to create this overwhelming diversity of multicellular life-forms. Here, we use a generative model to test the limits to which such processes can be combined to generate multiple differentiation paths during development, and attempt to chart the diversity of multicellular organisms generated. Results: We sample millions of biologically feasible developmental schemes, allowing us to comment on the statistical properties of cell-differentiation trajectories they produce. We characterize model-generated `organisms` using the graph topology of their cell-type lineage maps. Remarkably, tree-type lineage differentiation maps are the rarest in our data. Additionally, a majority of the 'organisms' generated by our model appear to be endowed with the ability to regenerate using pluripotent cells. Conclusions: Our results indicate that, in contrast to common views, cell-type lineage graphs are unlikely to be tree-like. Instead, they are more likely to be directed acyclic graphs, with multiple lineages converging on the same terminal cell-type. Furthermore, the high incidence of pluripotent cells in model-generated organisms stands in line with the long-standing hypothesis that whole-body regeneration is an epiphenomenon of development. We discuss experimentally testable predictions of our model, and some ways to adapt the generative framework to test additional hypotheses about general features of development.
Quantifying individual influence in leading-following behavior of Bechstein’s bats
Authors: Mavrodiev Pavlin , Fleischmann Daniela , Kerth Gerald , Schweitzer Frank
Published: November 2019

Leading-following behavior as a way of transferring information about the location of resources is widespread in different animal societies. However, it cannot always be observed directly. Here, we develop a general method to infer leading-following events from observational data if only the discrete appearance of individuals is recorded. Our method further allows to distinguish such events from local enhancement at the resource, such as swarming behavior in case of bats, which is another widespread way of transferring information among animals. To test our methodology, we analyze longitudinal data about the roosting behavior of Bechstein’s bats from two different colonies and different years. The detection of leading-following events allows us, in a second step, to construct social networks in which nodes represent individual bats and directed and weighted links the leading-following events. We analyze the topology of these networks on the level of the colony, to see whether all individuals participate in leading-following behavior. Further, based on the leading-following network we measure the importance of individuals in this leading-following behavior by calculating different centrality measures. We find that individuals can be consistently ranked regarding their influence on others. Moreover, we identify a small set of individuals that play a central role in leading other bats to roosts. Our methodology can be used to understand the leading-following behavior and the individual impact of group members on the spread of information in animal groups in general.
Data-driven modeling of leading-following behavior in Bechstein’s bats
Authors: Mavrodiev Pavlin , Fleischmann Daniela , Kerth Gerald , Schweitzer Frank
Published: November 2019

Leading-following behaviour in Bechstein’s bats transfers information about suitable roost sites from experienced to inexperienced individuals, and thus ensures communal roosting. We analyze 9 empirical data sets about individualized leading-following (L/F) events, to infer rules that likely determine the formation of L/F pairs. To test these rules, we propose five models that differ regarding the empirical information taken into account to form L/F pairs: activity of a bat in exploring possible roosts, tendency to lead and to follow. The comparison with empirical data was done by constructing social networks from the observed L/F events, on which centralities were calculated to quantify the importance of individuals in these L/F networks. The centralities from the empirical network are then compared for statistical differences with the model-generated centralities obtained from 105model realizations. We find that two models perform well in comparison with the empirical data: One model assumes an individual tendency to lead, but chooses followers at random. The other model assumes an individual tendency to follow and chooses leaders according to their overall activity. We note that neither individual preferences for specific individuals, nor other influences such as kinship or reciprocity, are taken into account to reproduce the empirical findings.
CXCR4 intracellular protein regulates drug resistance and tumorigenic potential via modulating the expression of Death Receptor 5
Authors: Nengroo Mushtaq Ahmed , Maheshwari Shrankhla , Singh Akhilesh , Singh Anup Kumar , Arya Rakesh Kumar , Chaturvedi Priyank , Verma Ayushi , Saini Krishan Kumar , Gupta Annapurna , Mishra Anjali , Datta Dipak
Published: November 2019

CXCR4 overexpression in solid tumors has been strongly associated with poor prognosis and adverse clinical outcome. However, CXCR4 signaling inhibitor drug Plerixafor has shown limited clinical success in cancer treatment. Therefore, CXCR4 signaling may not be the exclusive contributor to its pro-tumorigenic functions. In our continuous effort to understand the chemokine receptor signaling inhibition as cancer therapy, here we unexpectedly discovered that instead of its signaling, intracellular CXCR4 protein augments therapy resistance and pro-tumorigenic functions. Unbiased proteome profiler apoptosis array followed by immunoblot, FACS, real-time PCR and ChIP analyses demonstrate that CXCR4 promotes DR5 downregulation via modulating differential recruitment of transcription factors p53 and YY1 to its promoter. Surprisingly, inhibiting CXCR4 mediated signals failed to block the above phenotype. Irrespective of CXCR4 surface expression, its loss compromised colon tumor growthin vivo. Finally, TCGA data mining and human patient sample data analysis showed CXCR4 and DR5 are inversely regulated in human cancers. Together, we showed evidence for the first time that targeting CXCR4 intracellular protein may be critical to dampen the pro-tumorigenic functions of CXCR4.
Characterization of Mollivirus kamchatka, the first modern representative of the proposed Molliviridae family of giant viruses
Authors: Christo-Foroux Eugene , Alempic Jean-Marie , Lartigue Audrey , Santini Sebastien , Labadie Karine , Legendre Matthieu , Abergel Chantal , Claverie Jean-Michel
Published: November 2019

Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing researches in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky river in Kamchatka. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleo-cytoplasmic replication cycle identical to that of M. sibericum. Its spherical particle (0.6-μm in diameter) encloses a 648-kb GC-rich double stranded DNA genome coding for 480 proteins of which 61 % are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92 % identical residues in average) despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to the virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry.

Importance

Virology has long been viewed through the prism of human, cattle or plant diseases leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under light microscopy (i.e., >0.3μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenomes analyses have shown the presence of giant viruses in most terrestrial and aquatic environments including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae. We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year old arctic permafrost.
Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers
Authors: Rodrigues D.R. , Briggs W. , Duff A. , Chasser K. , Murugesan R. , Pender C. , Ramirez S. , Petri D. , Bielke L.R.
Published: November 2019

The potential of probiotics to manipulate the intestinal microbial ecosystem toward commensal bacteria growth offers great hope for enhancing health and performance in poultry. This study aimed to evaluate the efficacy of five probiotic-based formulations in modulating cecal microbiota in broilers at 21 and 42 days of age. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-formingBacillus amyloliquefaciens(SINGLE1),B. subtilis(SINGLE2) andB. licheniformis(SINGLE3). Metagenomics analyses showed that the cecal microbiota of SINGLE, YEAST, and MULTI supplemented birds had low diversity compared to the control diet without probiotics (CON) at 21d. At the same age, birds fed SYNBIO had a high population ofLactobacillus salivarusandLachnospiraceae, which was reflected in a singular microbial community illustrated by beta-diversity analyses. By 42d, there were no differences in alpha or beta-diversity in the microbiota of probiotic-treated broilers compared to CON. Birds treated with SINGLE2 had a lower abundance of lactic acid bacteria, while a higher (p<0.05) population of unidentifiedLachnospiraceaeandRuminococcaceae. Although the investigated probiotic formulations shared similar taxonomy, modulation of microbiota was not a core outcome for all probiotic-treated broilers indicating the success of microbiota-based intervention may ultimately be dependent on probiotic mixture and broiler’s age.
Translational readthrough goes unseen by natural selection
Authors: Kleppe April Snofrid , Bornberg-Bauer Erich
Published: November 2019

Occasionally during protein synthesis, the ribosome bypasses the stop codon and continues translation to the next stop codon in frame. This error is called translational readthrough (TR). Earlier research suggest that TR is a relatively common error, in several taxa, yet the evolutionary relevance of this translational error is still unclear. By analysing ribosome profiling data, we have conducted species comparisons between yeasts to infer conservation of TR between orthologs. Moreover, we infer the evolutionary rate of error prone and canonically translated proteins to deduct differential selective pressure. We find that about 40% of error prone proteins in Schizosaccharomyces pombe do not have any orthologs in Saccharomyces cerevisiae, but that 60% of error prone proteins in S. pombe are undergoing canonical translation in S. cerevisiae. Error prone proteins tend to have a higher GC-content in the 3’-UTR, unlike their canonically translated ortholog. We do not find the same trends for GC-content of the CDS. We discuss the role of 3’-UTR and GC-content regarding translational readthrough. Moreover, we find that there is neither selective pressure against or for TR. We suggest that TR is a near-neutral error that goes unseen by natural selection. We speculate that TR yield neutral protein isoforms that are not being purged. We suggest that isoforms, yielded by TR, increase proteomic diversity in the cell, which is readily available upon sudden environmental shifts and which therefore may become adaptive.

Author Summary

There is an evolutionary balance act between adaptation and selection against change. Any system needs to be able to adapt facing novel environmental conditions. Simultaneously, biological systems are under selection to maintain fitness and thus undergo selection against mutations. Phenotypic mutations - translational errors during protein synthesis - have been suggested to play a role in protein evolvability by enabling quick assessment of viable phenotypes and thus enable quick adaptation. Here we test this hypothesis, by inferring evolutionary rate of proteins prone to a specific case of phenotypic mutations: translational readthrough (TR). By making use of publicly available data of yeasts, we find that TR goes unseen by natural selection and appear as a neutral event. We suggest that TR goes unseen by selection and occurs as “permissive wallflowers”, which may become relevant and yield adaptive benefits. This work highlights that stochastic processes are not necessarily under stringent selection but may prevail. In conclusion, we suggest that TR is a neutral non-adaptive process that can yield adaptive benefits.