Improved motif-scaffolding with SE(3) flow matching

Protein design often begins with the knowledge of a desired function from a motif which motif-scaffolding aims to construct a functional protein around. Recently, generative models have achieved breakthrough success in designing scaffolds for a range of motifs. However, generated scaffolds tend to lack structural diversity, which can hinder success in wet-lab validation. In this work, we extend FrameFlow, an SE(3) flow matching model for protein backbone generation, to perform motif-scaffolding with two complementary approaches. The first is motif amortization, in which FrameFlow is trained with the motif as input using a data augmentation strategy. The second is motif guidance, which performs scaffolding using an estimate of the conditional score from FrameFlow without additional training. On a benchmark of 24 biologically meaningful motifs, we show our method achieves 2.5 times more designable and unique motif-scaffolds compared to state-of-the-art. Code: https://github.com/microsoft/protein-frame-flow.

De novo design of protein structure and function with RFdiffusion

There has been considerable recent progress in designing new proteins using deep-learning methods1-9. Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence-structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.

A dynamic simulation model to support reduction in illegal trade within legal wildlife markets

Sustainable wildlife trade is critical for biodiversity conservation, livelihoods, and food security. Regulatory frameworks are needed to secure these diverse benefits of sustainable wildlife trade. However, regulations limiting trade can backfire, sparking illegal trade if demand is not met by legal trade alone. Assessing how regulations affect wildlife market participants' incentives is key to controlling illegal trade. Although much research has assessed how incentives at both the harvester and consumer ends of markets are affected by regulations, little has been done to understand the incentives of traders (i.e., intermediaries). We built a dynamic simulation model to support reduction in illegal wildlife trade within legal markets by focusing on incentives traders face to trade legal or illegal products. We used an Approximate Bayesian Computation approach to infer illegal trading dynamics and parameters that might be unknown (e.g., price of illegal products). We showcased the utility of the approach with a small-scale fishery case study in Chile, where we disentangled within-year dynamics of legal and illegal trading and found that the majority (∼77%) of traded fish is illegal. We utilized the model to assess the effect of policy interventions to improve the fishery's sustainability and explore the trade-offs between ecological, economic, and social goals. Scenario simulations showed that even significant increases (over 200%) in parameters proxying for policy interventions enabled only moderate improvements in ecological and social sustainability of the fishery at substantial economic cost. These results expose how unbalanced trader incentives are toward trading illegal over legal products in this fishery. Our model provides a novel tool for promoting sustainable wildlife trade in data-limited settings, which explicitly considers traders as critical players in wildlife markets. Sustainable wildlife trade requires incentivizing legal over illegal wildlife trade and consideration of the social, ecological, and economic impacts of interventions.

Enriching a cellulose hydrogel with a biologically active marine exopolysaccharide for cell-based cartilage engineering

The development of biologically and mechanically competent hydrogels is a prerequisite in cartilage engineering. We recently demonstrated that a marine exopolysaccharide, GY785, stimulates the in vitro chondrogenesis of adipose stromal cells. In the present study, we thus hypothesized that enriching our silated hydroxypropyl methylcellulose hydrogel (Si-HPMC) with GY785 might offer new prospects in the development of scaffolds for cartilage regeneration. The interaction properties of GY785 with growth factors was tested by surface plasmon resonance (SPR). The biocompatibility of Si-HPMC/GY785 towards rabbit articular chondrocytes (RACs) and its ability to maintain and recover a chondrocytic phenotype were then evaluated in vitro by MTS assay, cell counting and qRT-PCR. Finally, we evaluated the potential of Si-HPMC/GY785 associated with RACs to form cartilaginous tissue in vivo by transplantation into the subcutis of nude mice for 3 weeks. Our SPR data indicated that GY785 was able to physically interact with BMP-2 and TGFβ. Our analyses also showed that three-dimensionally (3D)-cultured RACs into Si-HPMC/GY785 strongly expressed type II collagen (COL2) and aggrecan transcripts when compared to Si-HPMC alone. In addition, RACs also produced large amounts of extracellular matrix (ECM) containing glycosaminoglycans (GAG) and COL2. When dedifferentiated RACs were replaced in 3D in Si-HPMC/GY785, the expressions of COL2 and aggrecan transcripts were recovered and that of type I collagen decreased. Immunohistological analyses of Si-HPMC/GY785 constructs transplanted into nude mice revealed the production of a cartilage-like extracellular matrix (ECM) containing high amounts of GAG and COL2. These results indicate that GY785-enriched Si-HPMC appears to be a promising hydrogel for cartilage tissue engineering. Copyright © 2015 John Wiley & Sons, Ltd.

[Lymphatic filariasis transmission assessment survey in schools three years after stopping mass drug treatment with albendazole and ivermectin in the 7 endemic districts in Togo]

The aim of this study is to verify the level of transmission of lymphatic filariasis three years after stopping mass drug treatment in the 7 endemic districts in Togo. The survey was conducted in 2012 in Togo's 7 endemic districts grouped into four evaluation units (EU) using the WHO-recommended transmission assessment survey (TAS) protocol. Children aged 6-7 years were screened for Wuchereria bancofti antigen using the immunochromatographic card (ICT) method. A cluster sampling method was used to select eligible children in schools as the net primary-school enrolment ratio is greater than or equal to 75% in each of the four EUs. The number of children and schools to be selected in each EU, the randomization list for the selection of these children and the critical cut-off number of positive cases not to exceed were automatically generated using the Survey Sample Builder (SSB) tool, (NTD Support Center, Atlanta, Ga, USA). For confirmation, positive cases were subsequently tested for microfilaremia using nocturnal thick blood smear and for filarial antigen using Og4C3 antigen ELISA (TropBio ELISA Kit®, Townsville, Queensland, Australia). An EU is considered to have passed the test successfully (it is assumed that transmission can no longer be sustained), when the number of positive cases is below the critical cut-off number set by the SSB, which is roughly equivalent to 2% prevalence. Of the 1 706 children surveyed in Kpendjal-Tone's EU, 1 549 in Binah-Doufelgou's EU, 1 550 in Kozah's EU and the 1 575 in Amou-Haho's EU, 8 (0.46%), 1 (0.08%), 0 (0.00%) and 4 (0.25%) ICT positive cases respectively were detected. The number of positive ICT tests was well below 18, the critical cut number for each of the 4 EUs. All 13 ICT positive cases tested negative for nocturnal microfilaremia and Og4C3 ELISA. We conclude that all four EU passed the TAS with success, and the transmission of Wuchereria bancrofti is no longer likely to be sustained in the 7 endemic districts in Togo 3 years after stopping the MDA. A new TAS will be carried out in 2015, after which, if the results are still good, the country will submit a dossier to WHO for verification of the elimination of lymphatic filariasis.

An optimized device for staining electron microscopy grids

Proper staining of grids is critical for transmission electron microscopy (TEM). Staining must be done as quickly as possible using minimal reagents and with consideration for the environment. We developed a new device for efficient staining of multiple TEM grids. We studied reagent evaporation, rinsing volume, flow rate and re-use of uranyl acetate, and provide here a procedure for efficient staining using the new device. Our device permits TEM grids to be stained with less reagent than alternative staining apparatuses; staining requires a total volume of 260 μl for five grids. Reagent evaporation is less than 6% even if used at 37° C. Moreover, our staining apparatus reduces chemical waste and shortens experiment time by staining several grids simultaneously. Our staining device is a compromise between time-consuming single grid processing and expensive commercial devices that consume large amounts of reagents.

Homozygous and compound heterozygous MMP20 mutations in amelogenesis imperfecta

In this article, we focus on hypomaturation autosomal-recessive-type amelogenesis imperfecta (type IIA2) and describe 2 new causal Matrix metalloproteinase 20 (MMP20) mutations validated in two unrelated families: a missense mutation p.T130I at the expected homozygous state, and a compound heterozygous mutation having the same mutation combined with a nucleotide deletion, leading to a premature stop codon (p.N120fz*2). We characterized the enamel structure of the latter case using scanning electron microscopy analysis and microanalysis (Energy-dispersive X-ray Spectroscopy, EDX) and confirmed the hypomaturation-type amelogenesis imperfecta as identified in the clinical diagnosis. The mineralized content was slightly decreased, with magnesium substituting for calcium in the crystal structure. The anomalies affected enamel with minimal inter-rod enamel present and apatite crystals perpendicular to the enamel prisms, suggesting a possible new role for MMP20 in enamel formation.

Feasibility of short message service to document bleeding episodes in children with haemophilia

The increasing emphasis on home-based treatment for the management of children with haemophilia has meant that many of these children no longer regularly report to a medical facility. Consequently, it is difficult to monitor incidence of bleeding episodes. The aim of this study was to assess the feasibility of using a short message service (SMS) to monitor incidence of bleeding episodes in children with haemophilia. One hundred and four children with moderate and severe haemophilia A or B took part in a 1-year prospective study between 2008 and 2010. Children or their parents were asked to maintain a bleeds diary. They received a weekly SMS asking whether there had been a bleeding episode in the preceding week. Response rates were calculated. Children were followed for a total of 4839 person-weeks. SMS replies were received for 4201 weeks. Thus, the rate of follow-up was 86.8%. Median responses rates were 94.2% (IQR: 86.1-100%). Weekly SMS is a feasible reporting tool for documenting bleeding episodes in children with haemophilia. It is associated with high response rates and minimal expense and intrusion. The use of SMS could be extended to encourage compliance to prophylactic treatment, particularly in adolescents with haemophilia.

Nationwide integrated mapping of three neglected tropical diseases in Togo: countrywide implementation of a novel approach

OBJECTIVE

To conduct a nationwide integrated neglected tropical disease (NTD) prevalence survey to define the need for public health interventions using an innovative mapping protocol.

METHODS

Two villages were selected in every peripheral health unit in endemic districts: 29 districts for schistosomiasis and STH, 15 of them for trachoma. In each village, 15 children aged 6-9 years at a randomly selected school were tested. An additional convenience sample of 35 children aged 1-5 years underwent an eye examination for trachoma. This integrated mapping was followed by a 20-cluster trachoma survey in each district that surpassed the WHO-defined threshold of 10% prevalence of trachomatous inflammation-follicular (TF).

RESULTS

A total of 1096 villages were surveyed in <6 weeks. The district prevalence of schistosomiasis ranged from 2 to 49% and of STH from 5 to 70%, with prevalence at the village level ranging from 0 to 100% for both diseases. Two districts passed the threshold of 10% for active trachoma, but the cluster survey indicated this was because of misclassification bias and that the real prevalence was <1%.

CONCLUSION

Results of this mapping were used by the MoH and partners to plan integrated mass drug administration (MDA). Mass drug administration for trachoma was not implemented as no district passed the threshold requiring public health intervention.

Mapping, monitoring, and surveillance of neglected tropical diseases: towards a policy framework

As national programmes respond to the new opportunities presented for scaling up preventive chemotherapy programmes for the coadministration of drugs to target lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminthiasis, and trachoma, possible synergies between existing disease-specific policies and protocols need to be examined. In this report we compare present policies for mapping, monitoring, and surveillance for these diseases, drawing attention to both the challenges and opportunities for integration. Although full integration of all elements of mapping, monitoring, and surveillance strategies might not be feasible for the diseases targeted through the preventive chemotherapy approach, there are opportunities for integration, and we present examples of integrated strategies. Finally, if advantage is to be taken of scaled up interventions to address neglected tropical diseases, efforts to develop rapid, inexpensive, and easy-to-use methods, whether disease-specific or integrated, should be increased. We present a framework for development of an integrated monitoring and evaluation system that combines both integrated and disease-specific strategies.

[What do we know about trachoma in the economically weakest infantile population of Kara in Togo?]

PURPOSE

To describe the distribution of the trachoma in the infantile population of Kara region.

MATERIALS AND METHODS

A descriptive cross sectional investigation has been achieved in 6 sanitary districts of Kara's region in November 2009. In each of the 2 villages of the sanitary area of every peripheral health unit (PHU), 15 schoolchildren aged of 6 to 9 years then 35 children of the community aged of 1 to 5 years have been examined to search signs of trachoma with the help of a lamp wipes coupled of a binocular loupe (2.5X magnification).

RESULTS

To the total 10,100 children have been examined in 202 villages of the sanitary areas of 101 PHU. Among the 7070 children aged of 1-5 years, 289 presented trachomatous inflammation follicular (TF) and 131 trachomatous inflammation intense (TI), corresponding to a prevalence rate of 5.94%. Among the 3030 schoolchildren, 68 presented TF and 62 TI corresponding to 4.29% prevalence rate. The prevalence rate of the active trachoma was of 5.44% in the infantile population of this region.

CONCLUSION

This investigation could confirm that active trachoma still exists in this region. Another investigation will be carried out to determine the prevalence of trachoma among the adult subjects in order to have a more complete data base in view of further action for trachoma elimination in this region.

Feasibility and limits of bone marrow mononuclear cell expansion following irradiation

PURPOSE

To define the ability of bone marrow mononuclear cells (BMMNC) to expand after irradiation and to determine the amount of apoptosis in irradiated expanded cells.

MATERIALS AND METHODS

Non-human primate BMMNC were irradiated in vitro at doses ranging from 0 to 4 Gy and were cultured during 1 week in the presence of interleukin 3, interleukin 6, stem cell factor, thrombopoietin and fms-like tyrosine kinase-3 ligand. The expansion yield of BMMNC, colony-forming cells and CD34(+) cells were compared with non-irradiated control cultures. Apoptosis in expanded cells was also defined by annexin V/propidium iodine staining.

RESULTS

Irradiation of BMMNC up to 1 Gy did not modify the ability of haematopoietic cells to expand. At higher doses, expansion of haematopoietic cells is reduced as compared with non-irradiated cultures but it remains significant. This reduction in expansion of BMMNC was related to radiation-induced apoptosis.

CONCLUSION

The results suggest that it is possible to expand haematopoietic cells after irradiation doses at least up to 2 Gy. This suggests a possible use of cell therapy for the treatment of radiation accident victims.

Markov Modelling of Immunological and Virological States in HIV-1 Infected Patients

The purpose of this study was to evaluate the evolution of HIV infected patients and to bring out some significant factors associated with this pathology. The main criteria revealing the State of illness is viral load measurement (VL). However the CD4 lymphocytes also represent an important marker as these reflect the State of the immune reservoir. Many studies have been carried out in this field and different models have been proposed with a view to a better understanding of this disease. Multi State Markov models defined in terms of CD4 counts, or in terms of viral load, have proved to be very useful tools for modelling HIV disease progression. The model we have developed in this study is based on both the CD4 lymphocytes counts and VL. Markov models are characterized by transition intensities. In this paper we explored several structures in succession. First, we used a homogeneous continuous time Markov process with four states defined by crossed values of CD4 and VL in a given patient at a given time. Then, the effect of certain covariates on the infection process was introduced into the model via the transition intensity functions, as with a Cox regression model. Since the hypothesis of homogeneity may be unrealistic in certain cases, we also considered piecewise homogeneous Markov models. Finally, the effects of covariates and time were combined in a piecewise homogeneous model with a covariate. We applied these methods to data from 1313 HIV-infected patients included in the NADIS cohort.

Factors associated with participation in a campaign of mass treatment against lymphatic filariasis, in Leogane, Haiti

In October 2000, to interrupt transmission of Wuchereria bancrofti, an intense health-education campaign followed by a mass drug administration (MDA) with diethylcarbamazine and albendazole was undertaken in Leogane, Haiti. Three months after the MDA, which was the first in the study area, a knowledge-attitude-practice (KAP) survey, with a cluster-sample design and probability sampling, was undertaken, to determine the existing knowledge of the local residents, their attitudes toward the MDA, and the possible reasons for non-compliance. Questionnaire-based interviews were used to explore the KAP of 304 subjects (one randomly chosen resident aged > 14 years from each selected household) in 33 communities. Most (93%) of the interviewees were aware of filariasis and 72% knew at least one clinical sign of the disease. Awareness of the MDA was high (91%). The most frequently mentioned sources of information were other people (56%) and radio announcements (33%). More than 80% of the respondents encouraged other people to take the drugs distributed in the MDA and 63% had been treated. The primary reasons given for failing to take the drugs were absenteeism during the distribution (17%), use of contraceptive drugs (12%) and pregnancy (11%). In a multivariate analysis, being male [odds ratio (OR) = 3.3; 95% confidence interval (CI) = 1.5-7.4], knowing that a mosquito transmits the disease (OR = 2.6; CI = 1.2-5.4), and having learned about the MDA through posters and banners (OR = 2.9; CI = 1.2-7.5) were found to be positively associated with taking the drugs. Information from such post-treatment surveys should be useful in developing better health communication for subsequent MDA.