bluuebunny/crossref_metadata_2025 huggingface dataset:
Anastomotic Technique and Preoperative Imaging in Microsurgical Lower-Extremity Reconstruction
Authors: Carney Martin J. , Samra Fares , Momeni Arash , Bauder Andrew R. , Weissler Jason M. , Kovach Stephen J.
Published: January 2020

Background

The need for preoperative imaging as well as anastomotic technique (ie, end-to-side [ETS] vs end-to-end [ETE]) are areas of controversy in microsurgical lower-extremity reconstruction. The objective of this study was to (1) investigate whether preoperative imaging is mandatory and (2) to elicit if the type of anastomosis impacts clinical outcomes.

Methods

A retrospective review of all patients who underwent microvascular lower-extremity reconstruction between 2007 and 2015 by a single surgeon was performed. Patients were categorized into groups based on anastomotic technique, that is, ETE versus ETS anastomosis. Patients in the ETE group were further subclassified into those who had preoperative imaging (computed tomography angiography [CTA]+) versus those who did not (CTA−). Parameters of interest included flap type, thrombosis rate, flap loss, length of stay (LOS), return to ambulation, and rate of secondary amputation. Two-sided statistical analysis was performed using Kruskal-Wallis rank-sum test and Fisher exact test.

Results

One hundred twenty-eight patients were analyzed: ETE (n = 40) and ETS (n = 88). Mean follow-up for both groups was 20 ± 19 months. Anterolateral thigh flaps were most commonly performed (71%). Overall flap loss rate was 3.1% without any significant differences noted with respect to thrombosis (arterial, P = 0.09; venous, P = 0.56), flap loss (P = 0.33), LOS (P = 0.28), amputation (P = 1.00), or return to ambulation (P = 0.77). Furthermore, the availability of preoperative imaging (CTA+: N = 11 vs CTA−: N = 29) did not impact rates of thrombosis (arterial, P = 0.29; venous, P = 0.31), flap loss (P = 1.00), LOS (P = 0.26), or return to mobility (P = 0.62).

Conclusions

In light of similar reconstructive outcomes, we prefer to preserve distal extremity perfusion via ETS anastomoses whenever possible. Furthermore, preoperative vascular imaging angiography might not be necessary in patients with palpable pedal pulses on preoperative examination. An actionable algorithm for determining ETS versus ETE anastomosis in lower-extremity reconstruction is presented.
Turnover modulates the need for a cost of resistance in adaptive therapy
Authors: Strobl Maximilian , West Jeffrey , Viossat Yannick , Damaghi Mehdi , Robertson-Tessi Mark , Brown Joel , Gatenby Robert , Maini Philip , Anderson Alexander
Published: January 2020

“Control and conquer” - this is the philosophy behind adaptive therapy, which seeks to exploit intra-tumoural competition to avoid, or at least, delay the emergence of therapy resistance in cancer. Motivated by promising results from theoretical, experimental and, most recently, a clinical study in prostate cancer, there is an increasing interest in extending this approach to other cancers. As such, it is urgent to understand the characteristics of a cancer which determine whether it will respond well to adaptive therapy, or not. A plausible candidate for such a selection criterion is the fitness cost of resistance. In this paper, we study a simple competition model between sensitive & resistant cell populations to investigate whether the presence of a cost is a necessary condition for adaptive therapy to extend the time to progression beyond that of a standard-of-care continuous therapy. We find that for tumours close to their environmental carrying capacity such a cost of resistance is not required. However, for tumours growing far from carrying capacity, a cost may be required to see meaningful gains. Notably, we show that in such cases it is important to consider the cell turnover in the tumour and we discuss its role in modulating the impact of a cost of resistance. Overall, our work helps to clarify under which circumstances adaptive therapy may be beneficial, and suggests that turnover may play an unexpectedly important role in the decision making process.
Spatial and epidemiological drivers of P. falciparum malaria among adults in the Democratic Republic of the Congo
Authors: Deutsch-Feldman Molly , Brazeau Nicholas F. , Parr Jonathan B. , Thwai Kyaw L. , Muwonga Jérémie , Kashamuka Melchior , Tshefu Antoinette K. , Aydemir Ozkan , Bailey Jeffrey A. , Edwards Jessie K. , Verity Robert , Emch Michael , Gower Emily W. , Juliano Jonathan J. , Meshnick Steven R.
Published: January 2020

Background

Malaria remains a significant public health problem in sub-Saharan Africa. Adults are frequently infected and may serve as a reservoir for further transmission, yet we know relatively little about risk factors for adult infections. In this study, we assessed malaria risk factors amongst adults using samples from the nationally representative, cross-sectional 2013-2014 Demographic and Health Survey (DHS) conducted in the Democratic Republic of Congo (DRC). We further explored differences in risk factors by urbanicity.

Methods

Plasmodium falciparum infection was determined by polymerase chain reaction (PCR). Covariates were drawn from the DHS to model individual, community, and environmental level risk factors for infection. Additionally, we used deep sequencing data to estimate the community-level proportions of drug resistant infections and included these estimates as potential risk factors. All identified factors were assessed for differences in associations by urbanicity.

Results

A total of 16,126 adults were included. Overall prevalence of malaria was 30.3% (SE = 1.1) by PCR; province-level prevalence ranged from 6.7-58.3%. Only 17% of individuals lived in households with at least one bednet for every two people, as recommended by the World Health Organization. Protective factors included increasing within-household bednet coverage (PR = 0.85, 95% CI = 0.76 - 0.95) and modern housing (PR = 0.58, 95% CI = 0.49 - 0.69). Community level protective factors included: increased average education and wealth (PR = 0.77, 95% CI = 0.65-0.91; PR - 0.84, 95% CI = 0.80 - 0.89). Education, wealth, and modern housing showed protective associations in cities but not in rural areas.

Conclusions

The DRC continues to suffer from a high burden of malaria; interventions that target high-risk groups and sustained investment in malaria control are sorely needed. Differences in risk factors by urbanicity may be due to differences in transmission intensity or access to resources.
Quantifying the Dynamics of Migration after a Disaster: Impact of Hurricane Maria in Puerto Rico
Authors: Acosta Rolando J. , Kishore Nishant , Irizarry Rafael A. , Buckee Caroline
Published: January 2020

Population displacement may occur after natural disasters, permanently altering the demographic composition of the affected regions. Measuring this displacement is vital for both optimal post-disaster resource allocation and calculation of measures of public health interest such as mortality estimates. Here, we analyzed data generated by mobile phones and social media to estimate the weekly island-wide population at risk and within-island geographic heterogeneity of migration in Puerto Rico after Hurricane Maria. We compared these two data sources to population estimates derived from air travel records and census data. We observed a loss of population across all data sources throughout the study period, however, the magnitude and dynamics differ by data source. Census data predict a population loss of just over 129,000 from July 17 to July 2018, a 4% decrease; air travel data predicts a population loss of 168,295 for the same period of time, a 5% decrease; mobile phone based estimates predicts a loss of 235,375 form July 2017 to May 2018, an 8% decrease; and social media based estimates predict a loss of 476,779 from August 2017 to August 2018; a 17% decrease. On average, municipalities with smaller population size lost a bigger proportion of their population. Moreover, we infer that these municipalities experienced greater infrastructure damage as measured by the proportion of unknown locations stemming from these regions. Finally, our analysis measures a general shift of population from rural to urban centers within the island.
Detecting substrate glycans of fucosyltransferases on glycoproteins with fluorescent fucose
Authors: Wu Zhengliang L , Whitaker Mark , Person Anthony D , Kalabokis Vassili
Published: January 2020

Like sialylation, fucose usually locates at the non-reducing ends of various glycans on glycoproteins and constitutes important glycan epitopes. Detecting the substrate glycans of fucosyltransferases is important for understanding how these glycan epitopes are regulated in response to different growth conditions and external stimuli. Here we report the detection of these glycans via enzymatic incorporation of fluorescent tagged fucose using fucosyltransferases including FUT2, FUT6, FUT7, and FUT8 and FUT9. More specifically, we describe the detection of substrate glycans of FUT8 and FUT9 on therapeutic antibodies and the detection of high mannose glycans on glycoproteins by enzymatic conversion of high mannose glycans to the substrate glycans of FUT8. By establishing a series of precursor glycans, we also demonstrate the substrate specificities of FUT8. Furthermore, using simultaneous enzymatic incorporation of both fluorescent sialic acids and fluorescent fucoses, we demonstrate the interplay between fucosylation and sialylation.
Composition of the North American wood frog (Rana sylvatica) skin microbiome and seasonal variation in community structure
Authors: Douglas Alexander J. , Hug Laura. A. , Katzenback Barbara A.
Published: January 2020

While a number of amphibian microbiomes have been characterized, it is unclear how microbial communities might vary in response to seasonal changes in the environment and the behaviors which many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defenses against pathogens, investigating how changes in the environment impact the microbial species present, and thus their potential contribution to skin host defense, will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the microbial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether the microbial composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity, however, this may be due to our limited female sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs’ respective pond water. Across seasons, diversity analyses suggest there are significant differences between the skin microbiome of frogs from spring and summer/fall groups while the average α-diversity per frog remained consistent. Bacterial genera known to have antifungal properties such asPseudomonasspp. andRhizobiumspp. were prevalent, and several were considered core microbiota during at least one season. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.
KALRNMutations Promote Anti-tumor Immunity and Immunotherapy Response in Cancer
Authors: Li Mengyuan , Ma Yuxiang , Zhong You , Qiang Lei , Wang Xiaosheng
Published: January 2020

Background

KALRN(kalirin RhoGEF kinase) is mutated in a wide range of cancers. Nevertheless, the association betweenKALRNmutations and the pathogenesis of cancer remains unexplored. The identification of biomarkers for cancer immunotherapy response is important considering that immunotherapies show beneficial effects only in a subset of cancer patients.

Methods

We explored the correlation betweenKALRNmutations and anti-tumor immunity in 10 cancer cohorts from The Cancer Genome Atlas (TCGA) program by the bioinformatics approach. Moreover, we verified the findings from bioinformatics analysis by in vitro experiments. Furthermore, we explored the correlation betweenKALRNmutations and immunotherapy response in four cancer cohorts receiving immune checkpoint blockade therapy.

Results

We found that anti-tumor immune signatures were stronger inKALRN-mutated than inKALRN-wildtype cancers. Moreover,KALRNmutations correlated with increased tumor mutation burden and the microsatellite instability or DNA damage repair deficiency genomic properties which may explain the elevated anti-tumor immunity inKALRN-mutated cancers. Furthermore, we found that PD-L1 expression was significantly upregulated inKALRN-mutated versusKALRN-wildtype cancers. The enhanced anti-tumor immune signatures and PD-L1 expression inKALRN-mutated cancers may favor the response to immune checkpoint blockade therapy in this cancer subtype, as evidenced in four cancer cohorts receiving anti-PD-1/PD-L1/CTLA-4 immunotherapy. We further revealed that the significant association betweenKALRNmutations and increased anti-tumor immunity was attributed to thatKALRNmutations compromised the function of KALRN target Rho GTPases on regulating DNA damage repair pathways.

Conclusions

TheKALRNmutation is a useful biomarker for predicting the response to immunotherapy in cancer patients.
Pharmaceutical-grade Rigosertib is a Microtubule-destabilizing Agent
Authors: Jost Marco , Chen Yuwen , Gilbert Luke A. , Horlbeck Max A. , Krenning Lenno , Menchon Grégory , Rai Ankit , Cho Min Y. , Stern Jacob J. , Prota Andrea E. , Kampmann Martin , Akhmanova Anna , Steinmetz Michel O. , Tanenbaum Marvin E. , Weissman Jonathan S.
Published: January 2020

We recently used CRISPRi/a-based chemical-genetic screens and targeted cell biological, biochemical, and structural assays to determine that rigosertib, an anti-cancer agent in phase III clinical trials, kills cancer cells by destabilizing microtubules. In a recent manuscript, Reddy and co-workers suggest that this microtubule-destabilizing activity of rigosertib is mediated not by rigosertib itself but by a contaminating degradation product of rigosertib, ON01500, present in formulations obtained from commercial vendors (Baker et al., 2019). Here, we demonstrate that treatment of cells with pharmaceutical-grade rigosertib (>99.9% purity) results in qualitatively indistinguishable phenotypes as treatment with commercially obtained rigosertib across multiple assays. The two compounds have indistinguishable chemical-genetic interactions with genes involved in modulating the microtubule network (KIF2CandTACC3), both destabilize microtubules in cells andin vitro, and both show substantially reduced toxicity in cell lines expressing a rationally-designed mutant of tubulin (L240FTUBBmutant), in which the rigosertib binding site in tubulin is mutated. Importantly, the specificity of the L240FTUBBmutant for microtubule-destabilizing agents, which is disputed by Reddy and co-workers, was recently confirmed by an independent research group (Patterson et al., 2019). We conclude that rigosertib kills cancer cells by destabilizing microtubules, in agreement with our original findings.
Horizontal gene transfer in the human and skin commensalMalassezia: a bacterially-derived flavohemoglobin is required for NO resistance and host interaction
Authors: Ianiri Giuseppe , Coelho Marco A. , Ruchti Fiorella , Sparber Florian , McMahon Timothy J. , Fu Ci , Bolejack Madison , Donovan Olivia , Smutney Hayden , Myler Peter , Dietrich Fred , Fox David , LeibundGut-Landmann Salomé , Heitman Joseph
Published: January 2020

The skin of humans and animals is colonized by commensal and pathogenic fungi and bacteria that share this ecological niche and have established microbial interactions.Malasseziaare the most abundant fungal skin inhabitant of warm-blooded animals, and have been implicated in skin diseases and systemic disorders, including Crohn’s disease and pancreatic cancer. Flavohemoglobin is a key enzyme involved in microbial nitrosative stress resistance and nitric oxide degradation. Comparative genomics and phylogenetic analyses within theMalasseziagenus revealed that flavohemoglobin-encoding genes were acquired through independent horizontal gene transfer events from different donor bacteria that are part of the mammalian microbiome. Through targeted gene deletion and functional complementation inM. sympodialis, we demonstrated that bacterially-derived flavohemoglobins are cytoplasmic proteins required for nitric oxide detoxification and nitrosative stress resistance under aerobic conditions. RNAseq analysis revealed that endogenous accumulation of nitric oxide resulted in upregulation of genes involved in stress response, and downregulation of the MalaS7 allergen-encoding genes. Solution of the high-resolution X-ray crystal structure ofMalasseziaflavohemoglobin revealed features conserved with both bacterial and fungal flavohemoglobins.In vivopathogenesis is independent ofMalasseziaflavohemoglobin. Lastly, we identified additional 30 genus- and species-specific horizontal gene transfer candidates that might have contributed to the evolution of this genus as the most common inhabitants of animal skin.

Significance statement

Malasseziaspecies are the main fungal components of the mammalian skin microbiome and are associated with a number of skin disorders. Recently,Malasseziahas also been found in association with Crohn’s Disease and with pancreatic cancer. The elucidation of the molecular bases of skin adaptation byMalasseziais critical to understand its role as commensal and pathogen. In this study we employed evolutionary, molecular, biochemical, and structural analyses to demonstrate that the bacterially-derived flavohemoglobins acquired byMalasseziathrough horizontal gene transfer resulted in a gain of function critical for nitric oxide detoxification and resistance to nitrosative stress. Our study underscores horizontal gene transfer as an important force modulatingMalasseziaevolution and niche adaptation.
Complete Reconstitution and Deorphanization of the 3 MDa NOCAP (NOCardiosis-Associated Polyketide) Synthase
Authors: Yuet Kai P. , Liu Corey W. , Lynch Stephen R. , Kuo James , Michaels Wesley , Lee Robert B. , McShane Abigail E. , Zhong Brian L. , Fischer Curt R. , Khosla Chaitan
Published: January 2020

SeveralNocardiastrains associated with nocardiosis, a potentially life-threatening disease, house a nonamodular assembly-line polyketide synthase (PKS) that presumably synthesizes an unknown natural product. Here, we report the discovery and structure elucidation of the NOCAP (NOCardiosis-Associated Polyketide) aglycone by first fully reconstituting the NOCAP synthasein vitrofrom purified protein components followed by heterologous expression inE. coliand spectroscopic analysis of the purified products. The NOCAP aglycone has an unprecedented structure comprised of a substituted resorcylaldehyde headgroup linked to a 15-carbon tail that harbors two conjugated all-transtrienes separated by a stereogenic hydroxyl group. This report is the first example of reconstituting atrans-acyltransferase assembly-line PKS eitherin vitroor inE. coli, and of using these approaches to “deorphanize” a complete assembly-line PKS identified via genomic sequencing. With the NOCAP aglycone in hand, the stage is set for understanding how this PKS and associated tailoring enzymes confer an advantage to their native hosts during humanNocardiainfections.
JAK Inhibitors Suppress Colon Cancer Cachexia-Associated Anorexia and Adipose Wasting in Mice
Authors: Arora Gurpreet , Gupta Arun , Guo Tong , Gandhi Aakash , Laine Aaron , Ahn Chul , Williams Dorothy , Iyengar Puneeth , Infante Rodney
Published: January 2020

Background

Cachexia (CX), a syndrome of muscle atrophy, adipose loss, and anorexia, is associated with reduced survival in cancer patients. The colon adenocarcinoma C26c20 cell line secretes the cytokine leukemia inhibitor factor (LIF) which induces CX. We characterized how LIF promotes CX-associated weight loss and anorexia in mice through JAK-dependent changes in adipose and hypothalamic tissues.

Methods

CX was inducedin vivowith C26c20 colon adenocarcinoma cells or recombinant LIF administration in the absence or presence of JAK inhibitors. Blood, adipose, and hypothalamic tissues were collected and processed for cyto/adipokine ELISAs, immunoblot analysis, and quantitative RT-PCR. CX was inducedin vitroby stimulating differentiated adipocytes with recombinant LIF or IL-6 in the absence or presence of lipase or JAK inhibitors. These activated adipocytes were processed for lipolysis, immunoblot analysis, and RT-PCR.

Results

Tumor-secreted LIF induced changes in adipose tissue expression and serum levels of IL-6 and leptin in a JAK-dependent manner influencing CX-associated adipose wasting and anorexia. We identified two JAK inhibitors that block cytokine-mediated adipocyte lipolysis and IL-6 induction using anin vitroCX lipolysis assay. JAK inhibitors administered toin vivocolon cancer CX mouse models led to 1) a decrease in STAT3 phosphorylation in hypothalamic and adipose tissues, 2) a reverse in the CX serum cyto/adipokine signature, 3) a delay in colon cancer CX-associated anorexia and adipose loss, and 4) an improvement in overall survival.

Conclusions

JAK inhibitors suppress cytokine-associated adipose loss and anorexia in multiplein vitroandin vivomodels of cancer CX.
A peptidergic amygdala microcircuit modulates sexually dimorphic contextual fear
Authors: Rajbhandari AK , Octeau JC , Gonzalez S , Pennington ZT , Trott J , Chavez J , Ngyuen E , Keces N , Hong WZ , Neve RL , Waschek J , Khakh BS , Fanselow MS
Published: January 2020

Trauma can cause dysfunctional fear regulation leading some to develop disorders like post-traumatic stress disorder (PTSD). The amygdala regulates fear, and, PACAP and PAC1 receptors are linked to PTSD symptom severity at genetic/epigenetic levels, with a strong link in females with PTSD. We discovered a PACAPergic projection from the basomedial amygdala (BMA) to the medial intercalated cells (mICCs). In vivo optogenetic stimulation of this pathway increased cfos expression in mICCs, decreased fear retention and increased fear extinction. Selective deletion of PAC1 receptors from the mICCs in females reduced fear acquisition, but enhanced fear generalization and reduced fear extinction in males. Optogenetic stimulation of the BMA-mICCs PACAPergic pathway produced excitatory postsynaptic currents (EPSCs) in mICCs neurons, which was enhanced by PAC1 receptor antagonist, PACAP 6-38. Our findings show that mICCs modulate contextual fear in a dynamic and sex-dependent manner via the microcircuit containing the BMA and mICCs, dependent on behavioral state.
Genome-wide mapping and prediction of plant architecture in a sorghum nested association mapping population
Authors: Olatoye Marcus O. , Hu Zhenbin , Morris Geoffrey P.
Published: January 2020

Modifying plant architecture is often necessary for yield improvement and climate adaptation, but we lack understanding of the genotype-phenotype map for plant morphology in sorghum. Here, we use a nested association mapping (NAM) population that captures global allelic diversity of sorghum to characterize the genetics of leaf erectness, leaf width (at two stages), and stem diameter. Recombinant inbred lines (n = 2200) were phenotyped in multiple environments (35,200 observations) and joint linkage mapping was performed with ∼93,000 markers. Fifty-four QTL of small to large effect were identified for trait BLUPs (9–16 per trait) each explaining 0.4–4% of variation across the NAM population. While some of these QTL colocalize with sorghum homologs of grass genes [e.g. involved in hormone synthesis (maizespi1), floral transition (SbCN8), and transcriptional regulation of development (riceIdeal plant architecture1)], most QTL did not colocalize with ana prioricandidate gene (82%). Genomic prediction accuracy was generally high in five-fold cross-validation (0.65–0.83), and varied from low to high in leave-one-family-out cross-validation (0.04–0.61). The findings provide a foundation to identify the molecular basis of architecture variation in sorghum and establish genomic-enabled breeding for improved plant architecture.

Core ideas

Understanding the genetics of plant architecture could facilitate the development of crop ideotypes for yield and adaptation

The genetics of plant architecture traits was characterized in sorghum using multi-environment phenotyping in a global nested association mapping population

Fifty-five quantitative trait loci were identified; some colocalize with homologs of known developmental regulators but most do not

Genomic prediction accuracy was consistently high in five-fold cross-validation, but accuracy varied considerably in leave-one-family-out predictions
Off-target glycans encountered along the synthetic biology route towards humanized N-glycans inPichia pastoris
Authors: Laukens Bram , Jacobs Pieter P. , Geysens Katelijne , Martins Jose , De Wachter Charlot , Ameloot Paul , Morelle Willy , Haustraete Jurgen , Renauld Jean-Christophe , Samyn Bart , Contreras Roland , Devos Simon , Callewaert Nico
Published: January 2020

Background

The glycosylation pathways of several eukaryotic protein expression hosts are being engineered to enable the production of therapeutic glycoproteins with humanized application-customized glycan structures. In several expression hosts, this has been quite successful, but one caveat is that the new N-glycan structures inadvertently might be substrates for one or more of the multitude of endogenous glycosyltransferases in such heterologous background. This then results in the formation of novel, undesired glycan structures, which often remain insufficiently characterized.

Results

When expressing mouse interleukin-22 (mIL-22) in aPichia pastoris(syn.Komagataella phaffi) GlycoSwitchM5 strain which had been optimized to produce Man5GlcNAc2N-glycans, glycan profiling revealed two major species: Man5GlcNAc2and an unexpected, partially α-mannosidase-resistant structure. A detailed structural analysis using exoglycosidase sequencing, mass spectrometry, linkage analysis and NMR, revealed that this novel glycan was Man5GlcNAc2modified with a Glcα-1,2-Manβ-1,2-Manβ-1,3-Glcα-1,3-R tetra-saccharide. Also the biosynthetic intermediates of this off-target modification were detected. Expression of a Golgi-targeted GlcNAc Transferase-I strongly inhibited the formation of this novel modification, resulting in more homogeneous modification with the targeted GlcNAcMan5GlcNAc2structure. We have also observed the off-target glycan on other glycoproteins produced in the GlycoSwitchM5 strain. This illustrates the intricacies of Golgi glycosylation pathways and cautions that the use of glyco-engineered expression host cells should always be accompanied by detailed glycan analysis of the particular therapeutic proteins being produced.

Conclusions

Our findings reinforce accumulating evidence that robustly customizing the N-glycosylation pathway inPichia pastoristo produce particular human-type structures is still an incompletely solved synthetic biology challenge, which will require further innovation to enable safe glycoprotein pharmaceutical production.
Diverse cell stimulation kinetics identify predictive signal transduction models
Authors: Jashnsaz Hossein , Fox Zachary R , Hughes Jason , Li Guoliang , Munsky Brian , Neuert Gregor
Published: January 2020

The drive to understand cell signaling responses to environmental, chemical and genetic perturbations has produced outstanding fits of computational models to increasingly intricate experiments, yet predicting quantitative responses for new biological conditions remains challenging. Overcoming this challenge depends not only on good models and detailed experimental data but perhaps more so on how well the two are integrated. Our quantitative, live single-cell fluorescence imaging datasets and computational framework to model generic signaling networks show how different changing environments (hereafter ‘kinetic stimulations’) probe and result in distinct pathway activation dynamics. Utilizing multiple diverse kinetic stimulations better constrains model parameters and enables predictions of signaling dynamics that would be impossible using traditional step-change stimulations. To demonstrate our approach’s generality, we use identified models to predict signaling dynamics in normal, mutated, and drug-treated conditions upon multitudes of kinetic stimulations and quantify which proteins and reaction rates are most sensitive to which extracellular stimulations.
Chloe: Flexible, Efficient Data Provenance and Management
Authors: Kazic Toni
Published: January 2020

1

Reproducible and sharable research requires robust data provenance during and after the experimental process. Each laboratory and experiment has its own goals and methods, and these change frequently. Planning, managing, and collecting data from research crops are particularly labor-intensive tasks, given the tightly compressed time schedule and the operating environments. Moving from a lab’s present record-keeping approach to an electronic ecosystem that improves provenance is an additional burden for groups without dedicated, consistent computational support to make that transition and then to adapt the system as needed. This high barrier to entry and the press of field work makes it easy to postpone “computerizing”.

I have developedChloeto reduce manual effort during experiments and maintain data provenance. A flexible, modular system,Chloeintegrates simple equipment, data collection strategies, and software into workflows. The design lets one use parts without deploying the whole. This reduces the barriers to entry while still improving workflow efficiency and makingChloeaccessible to a wide range of users. I offer guidance on ways to adaptChloeto one’s own experimental situation.Chloehas been tested and refined with many changes of students, hardware, and experimental goals over the last fourteen years. Though originally designed for maize genetics and computational experiments,Chloecan accommodate other types of experiments, wetbench work, and other crops.
Peripheral Myelin Protein 22 Preferentially Partitions into Ordered Phase Membrane Domains
Authors: Marinko Justin T. , Li Geoffrey C. , Kenworthy Anne K. , Sanders Charles R.
Published: January 2020

The ordered environment of membrane rafts is thought to exclude many transmembrane proteins. Nevertheless, some multi-pass transmembrane proteins have been proposed to partition into ordered domains. Here, giant plasma membrane vesicles (GPMVs) were employed to quantitatively show that the tetraspan peripheral myelin protein 22 (PMP22) exhibits a pronounced preference for, promotes the formation of, and stabilizes ordered membrane domains. Neither S-palmitoylation of PMP22 nor its putative cholesterol binding motifs are required for partitioning to ordered domains. In contrast, disruption of its unusual first transmembrane helix (TM1) reduced ordered phase preference. Charcot-Marie-Tooth disease-causing mutations that destabilize PMP22 also reduced or eliminated this preference in favor of the disordered phase. These studies demonstrate PMP22’s ordered phase preference derives both from the distinctive properties of TM1 and global structural features associated with its transmembrane domain, providing a first glimpse at the structural factors that promote raft partitioning for multi-pass proteins.

Significance Statement

The preferential partitioning of single span membrane proteins for the ordered phase of ordered/disordered phase-separated membranes is now reasonably well understood, but little is known about this phase preferences of multi-pass membrane proteins. Here, it is shown that the disease-linked tetraspan integral membrane protein, PMP22, displays a pronounced preference to partition into the ordered phase, a preference that is reversed by disease mutations. This phase preference may be related to the role of PMP22 in cholesterol homeostasis in myelinating Schwann cells, a role that is also known to be disrupted under conditions of CMTD peripheral neuropathy caused bypmp22mutations.
Predictive Patterns of Antidepressant Response from Pre-Treatment Reward Processing using Functional MRI and Deep Learning: Key Results from the EMBARC Randomized Clinical Trial
Authors: Nguyen Kevin P , Chin Fatt Cherise , Treacher Alex , Mellema Cooper , Cooper Crystal , Jha Manish , Kurian Benji , Fava Maurizio , McGrath Patrick J , Weissman Myrna , Phillips Mary L , Trivedi Madhukar H , Montillo Albert
Published: January 2020

Uncertainty in selecting the appropriate antidepressant for each patient is a major challenge in treatment of major depressive disorder (MDD). No biologically driven markers are currently available to improve precision in treatment selection, thus leading to a trial-and-error process and prolonged morbidity for most patients. This study developed deep learning models that accurately predict treatment outcomes for sertraline, bupropion and placebo. Models were trained on data from the EMBARC study, in which 223 un-medicated subjects with MDD underwent pre-treatment reward task fMRI and received 8 weeks of treatment with sertraline, bupropion, or placebo. These models integrate fMRI and clinical measures and they explain up to 37% of the variance in ΔHAMD, classify remitters with NNT of 2.3-4.3, and classify responders with NNT of 3.2-4.9. Findings reveal new regions predictive of treatment outcome such as the hippocampus and paracentral lobule, while additional regions implicated in existing research are corroborated. Distinct models were identified for each treatment and provide substantial evidence of their potential to improve precision in treatment selection for MDD.
Neural Circuit Dynamics for Sensory Detection
Authors: Mallik Sruti , Nizampatnam Srinath , Nandi Anirban , Saha Debajit , Raman Baranidharan , Ching ShiNung
Published: January 2020

We consider the question of how sensory networks enable the detection of sensory stimuli in a combinatorial coding space. We are specifically interested in the olfactory system, wherein recent experimental studies have reported the existence of rich, enigmatic response patterns associated with stimulus onset and offset. This study aims to identify the functional relevance of such response patterns, i.e., what benefits does such neural activity provide in the context of detecting stimuli in a natural environment. We study this problem through the lens of normative, optimization-based modeling. Here, we define the notion of a low dimensional latent representation of stimulus identity, which is generated through action of the sensory network. The objective of our optimization framework is to ensure high fidelity tracking of a nominal representation in this latent space in an energy efficient manner. It turns out that the optimal motifs emerging from this framework possess morphological similarity with prototypical onset and offset responses observedin vivo. Furthermore, this objective can be exactly achieved by a network with reciprocal excitatory-inhibitory competitive dynamics, similar to interactions between principal neurons (PNs) and local neurons (LNs) in the early olfactory system of insects. The derived model also makes several predictions regarding maintenance of robust latent representations in the presence of confounding background information and tradeoffs between the energy of sensory activity and resultant behavioral measures such as speed and accuracy of stimulus detection.

Significance Statement

A key area of study in olfactory coding involves understanding the transformation from high-dimensional sensory stimulus to low-dimensional decoded representation. Here, we treat not only the dimensionality reduction of this mapping but also its temporal dynamics, with specific focus on stimuli that are temporally continuous. We examine through optimization-based synthesis how sensory networks can track representations without prior assumption of discrete trial structure. We show that such tracking can be achieved by canonical network architectures and dynamics, and that the resulting responses resemble observations from neurons in the insect olfactory system. Thus, our results provide hypotheses regarding the functional role of olfactory circuit activity at both single neuronal and population scales.
Purkinje cell neurotransmission patterns cerebellar basket cells into zonal modules that are defined by distinct pinceau sizes
Authors: Zhou Joy , Brown Amanda M. , Lackey Elizabeth P. , Arancillo Marife , Lin Tao , Sillitoe Roy V.
Published: January 2020

Ramón y Cajal proclaimed the neuron doctrine based on circuit features he exemplified using cerebellar basket cell projections. Basket cells form dense inhibitory plexuses that wrap Purkinje cell somata and terminate as pinceaux at the initial segment of axons. Here, we demonstrate that HCN1, Kv1.1, PSD95 and GAD67 unexpectedly mark patterns of basket cell pinceaux that map onto Purkinje cell functional zones. Using cell-specific genetic tracing with anAscl1CreERT2mouse conditional allele, we reveal that basket cell zones comprise different sizes of pinceaux. We tested whether Purkinje cells instruct the assembly of inhibitory projections into zones, as they do for excitatory afferents. Genetically silencing Purkinje cell neurotransmission blocks the formation of sharp Purkinje cell zones and disrupts excitatory axon patterning. The distribution of pinceaux into size-specific zones is eliminated without Purkinje cell output. Our data uncover the cellular and molecular diversity of a foundational synapse that revolutionized neuroscience.
Hilbert space filling curves for interpretable point mutation effects on peptide conformational dynamics
Authors: Rath Siddharth S. , Hennig Tatum G. , Jorgenson Tyler D. , Fischer-Marques Pedro , Kumar Nitya Krishna , Starkebaum David , Ustundag Burak Berk , Sarikaya Mehmet
Published: January 2020

Spontaneous self-organization of solid-binding peptides on single-layer atomic materials offers enormous potential in employing these systems for practical technological and medical applications. Molecular self-organization of peptides depends highly on their sequences which, in turn, affect their conformational behavior under aqueous conditions. Traditional ways of computationally studying the effect of mutations on the conformation states involves dimension reduction on cosine and sine transformed torsion angles, often represented as Ramachandran plots. Although these studies successfully cluster conformation states, they fail to intuitively characterize the effect of the point mutation(s) directly, necessitating further data analysis. Here, we apply Hilbert Space-Filling-Curve (HSFC) on the torsion angles and demonstrate intuitive visualization for the effect of point mutations on conformation states and secondary structure dynamics along a reaction coordinate. We perform molecular dynamics (MD) simulation on wild-type graphene binding peptide (WT-GrBP5). The 12-amino acid long peptide was selected by directed evolution and known to self-organize on atomically flat surface of graphene only under low-neutral pH at room temperature. A charge neutral mutant, M9-GrBP5, on the other hand, assembles at a broader range of pH’s at room temperature, as expected. The HSFC shows clearly that the mutated amino acids in M9 do not correlate with the reaction coordinate of pH change, unlike that of WT, confirming heuristic knowledge. Understanding the effect of specific amino acid φ-ψ pairs that contribute most to the changes in the conformational space of the peptide with changing conditions, will help in analyzing effects of point mutations in peptide sequences. The knowledge of the conformational behavior of solid binding peptides, in general, and its effect on their self-organization propensities on solid surfaces would lead to the rational design of sequences that form soft bio/nano hybrid interfaces in the future towards robust strategies for surface biofunctionalization, in general, and bioelectronics and biosensors, in particular.
CD44 regulates blood-brain barrier integrity in response to fluid shear stress
Authors: DeOre Brandon J. , Partyka Paul P. , Fan Fan , Galie Peter A.
Published: January 2020

Fluid shear stress is an important mediator of vascular permeability, yet the molecular mechanisms underlying the response of the blood-brain barrier to shear have yet to be studied in cerebral vasculature despite its importance for brain homeostasis. The goal of this study is to probe components of shear mechanotransduction within the blood-brain barrier to gain a better understanding of pathologies associated with changes in cerebral blood flow including ischemic stroke. Interrogating the effects of shear stress in vivo is complicated by the complexity of factors in the brain parenchyma and the difficulty associated with modulating blood flow regimes. Recent advances in the ability to mimic the in vivo microenvironment using three-dimensional in vitro models provide a controlled setting to study the response of the blood-brain barrier to shear stress. The in vitro model used in this study is compatible with real-time measurement of barrier function using transendothelial electrical resistance as well as immunocytochemistry and dextran permeability assays. These experiments reveal that there is a threshold level of shear stress required for barrier formation and that the composition of the extracellular matrix, specifically the presence of hyaluronan, dictates the flow response. Gene editing to modulate the expression of CD44, a receptor for hyaluronan that previous studies have identified to be mechanosensitive, demonstrates that the receptor is required for the endothelial response to shear stress. Manipulation of small GTPase activity reveals CD44 activates Rac1 while inhibiting RhoA activation. Additionally, adducin-γ localizes to tight junctions in response to shear stress and RhoA inhibition and is required to maintain the barrier. This study identifies specific components of the mechanosensing complex associated with the blood-brain barrier response to fluid shear stress, and therefore illuminates potential targets for barrier manipulation in vivo.
Identifying spawning activity in aquatic species based on environmental DNA spikes
Authors: Tsuji Satsuki , Shibata Naoki
Published: January 2020

An understanding of the reproductive biology of aquatic organisms is crucial for the efficient conservation and management of species and/or populations. Nevertheless, conventional spawning surveys such as visual- and capture-based monitoring generally require laborious, time-consuming work and are subject to monitoring biases such as observer bias, as well as miscounts due to false spawning. In addition, direct capture often damages eggs or individuals. Thus, an efficient non-invasive approach for monitoring spawning activity on aquatic species would be a valuable tool to understand their reproductive biology and conserving biodiversity. Here, we proposed an environmental DNA (eDNA)-based approach for monitoring and understanding spawning activity by observing spikes in eDNA concentration after spawning activity. We found in cross experiments using two medaka species (Oryzias latipesandO. sakaizumii, 1:1 individual per tank) that an eDNA spike occurred in only male species after spawning activity. In addition, the magnitude of the eDNA spike was dependent on the number of spawning activities with egg and sperm release. In the field survey during the reproductive season, eDNA concentration after spawning were 3–25 times higher than before spawning. On the other hand, there was no increase in eDNA concentration during the non-reproductive season. Therefore, our results demonstrated that spikes in the eDNA concentration are mainly caused by the release of sperm during spawning activity, and it can be used as evidence of spawning in field survey. The presented approach could be a practical tool for studying reproductive biology and provides an opportunity to design effective conservation and environmental management actions.
Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without STI-associated Urethritis
Authors: Council Olivia D. , Zhou Shuntai , McCann Chase D. , Hoffman Irving , Tegha Gerald , Kamwendo Deborah , Matoga Mitch , Kosakovsky Pond Sergei L. , Cohen Myron S. , Swanstrom Ronald
Published: January 2020

Concurrent sexually transmitted infections (STI) can increase the probability of HIV-1 transmission primarily by increasing the viral load present in semen. In this study, we explored the relationship of HIV-1 in blood and seminal plasma in the presence and absence of urethritis and after treatment of the concurrent STI. Primer ID deep sequencing of the V1/V3 region of the HIV-1envgene was done for paired blood and semen samples from ART-naïve men living in Malawi with (n = 19) and without (n = 5) STI-associated urethritis; for a subset of samples full lengthenvgenes were generated for sequence analysis and to test entry phenotype. Cytokine concentrations in the blood and semen were also measured, and a reduction in the levels of pro-inflammatory cytokines was observed following STI treatment. We observed no difference in the prevalence of diverse compartmentalized semen-derived lineages in men with or without STI-associated urethritis, and these viral populations were largely stable during STI treatment. Clonal amplification of one or a few viral sequences accounted for nearly 50% of the viral population indicating a recent bottleneck followed by limited viral replication. We documented a case of superinfection where the new strain was restricted to the genital tract. We conclude that the male genital tract is a site where virus can be brought in from the blood, where localized sustained replication can occur, where a superinfecting strain can persist, and where specific genotypes can be amplified perhaps initially by cellular proliferation but further by limited viral replication.

Importance

HIV-1 is a sexually transmitted infection that co-exists with other STIs. Here we examine the impact of a concurrent STI resulting in urethritis on the HIV-1 population within the male genital tract. We found that viral populations remain largely stable even with treatment of the STI. These results show that viral populations within the male genital tract are defined by factors beyond transient inflammation associated with a concurrent STI.