Large Family Research Articles

On the Number of Linear Regions of Convolutional Neural Networks With Piecewise Linear Activations.

One fundamental problem in deep learning is understanding the excellent performance of deep Neural Networks (NNs) in practice. An explanation for the superiority of NNs is that they can realize a large family of complicated functions, i.e., they have powerful expressivity. The expressivity of a Neural Network with Piecewise Linear activations (PLNN) can be quantified by the maximal number of linear regions it can separate its input space into. In this paper, we provide several mathematical results needed for studying the linear regions of Convolutional Neural Networks with Piecewise Linear activations (PLCNNs), and use them to derive the maximal and average numbers of linear regions for one-layer PLCNNs. Furthermore, we obtain upper and lower bounds for the number of linear regions of multi-layer PLCNNs. Our results suggest that deeper PLCNNs have more powerful expressivity than shallow PLCNNs, while PLCNNs have more expressivity than fully-connected PLNNs per parameter, in terms of the number of linear regions.

Risk Factors of Wasting-Based Malnutrition in the Flood-Affected Areas of Pakistan: A Cross-Sectional Study

ABSTRACT The current study aimed to find the risk factors of wasting in flood-affected areas of Khyber Pakhtunkhwa, Pakistan. Sociodemographic and anthropometric data was collected. Children living in large family are 2.59 times more likely to be wasted (AOR = 2.59, 95% confidence interval (CI): 1.10, 6.10; p value = .029) and children living in medium size family are 2.23 times more likely to be wasted (AOR = 2.23, 95% CI: 1.03, 4.80; p value = .04) as compared to children in small family size. The study underscores the need for targeted interventions to address the identified risk factors and mitigate the impact of flooding on child nutrition.

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish.

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine-freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene 'cassettes'. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

Penyuluhan Dan Pelatihan Masyarakat Ibu Dan Anak RT 004, Kel Pulogadung, Kec Pulogadung, Jakarta Timur Mengenai Kesehatan Gigi Dan Mulut Serta Penggunaan Obat Kumur

The COVID-19 pandemic is a valuable lesson and experience for the world community in facing challenges to maintain health and daily life. The psychological and emotional impact of the COVID-19 pandemic on family behavior and society in general. Dental and oral health education for children other than mothers is one of the health efforts that can be carried out to increase the knowledge, willingness and skills of children and mothers as a large family in maintaining dental and oral health and hygiene. Explanations need to be given to children and mothers about why and how to maintain healthy teeth and mouth properly. Dental and oral health education delivered in the form of stories through audiovisual media and simulations will be able to create a pleasant learning atmosphere so that it is more effective in attracting attention and facilitating the process of absorbing information by parents, especially children.

Copy number variation and population-specific immune genes in the model vertebrate zebrafish.

Copy number variation in large gene families is well characterized for plant resistance genes, but similar studies are rare in animals. The zebrafish (Danio rerio) has hundreds of NLR immune genes, making this species ideal for studying this phenomenon. By sequencing 93 zebrafish from multiple wild and laboratory populations, we identified a total of 1513 NLRs, many more than the previously known 400. Approximately half of those are present in all wild populations, but only 4% were found in 80% or more of the individual fish. Wild fish have up to two times as many NLRs per individual and up to four times as many NLRs per population than laboratory strains. In contrast to the massive variability of gene copies, nucleotide diversity in zebrafish NLR genes is very low: around half of the copies are monomorphic and the remaining ones have very few polymorphisms, likely a signature of purifying selection.

Carboxyl-group compounds activate voltage-gated potassium channels via a distinct mechanism.

Voltage-gated ion channels are responsible for the electrical excitability of neurons and cardiomyocytes. Thus, they are obvious targets for pharmaceuticals aimed to modulate excitability. Compounds activating voltage-gated potassium (KV) channels are expected to reduce excitability. To search for new KV-channel activators, we performed a high-throughput screen of 10,000 compounds on a specially designed Shaker KV channel. Here, we report on a large family of channel-activating compounds with a carboxyl (COOH) group as the common motif. The most potent COOH activators are lipophilic (4 < LogP <7) and are suggested to bind at the interface between the lipid bilayer and the channel's positively charged voltage sensor. The negatively charged form of the COOH-group compounds is suggested to open the channel by electrostatically pulling the voltage sensor to an activated state. Several of the COOH-group compounds also activate the therapeutically important KV7.2/7.3 channel and can thus potentially be developed into antiseizure drugs. The COOH-group compounds identified in this study are suggested to act via the same site and mechanism of action as previously studied COOH-group compounds, such as polyunsaturated fatty acids and resin acids, but distinct from sites for several other types of potassium channel-activating compounds.

“The burden is upon your shoulders to feed and take care of your children, not religion or culture”: qualitative evaluation of participatory community dialogues to promote family planning’s holistic benefits and reshape community norms on family success in rural Uganda

BackgroundFamily planning has significant health and social benefits, but in settings like Uganda, is underutilized due to prevalent community and religious norms promoting large family size and gender inequity. Family Health = Family Wealth (FH = FW) is a multi-level, community-based intervention that used community dialogues grounded in Campbell and Cornish’s social psychological theory of transformative communication to reshape individual endorsement of community norms that negatively affect gender equitable reproductive decision-making among couples in rural Uganda.MethodsThis study aimed to qualitatively evaluate the effect of FH = FW’s community dialogue approach on participants’ personal endorsement of community norms counter to family planning acceptance and gender equity. A pilot quasi-experimental controlled trial was implemented in 2021. This paper uses qualitative, post-intervention data collected from intervention arm participants (N = 70) at two time points: 3 weeks post-intervention (in-depth interviews, n = 64) and after 10-months follow-up (focus group discussions [n = 39] or semi-structured interviews [n = 27]). Data were analyzed through thematic analysis.ResultsThe community dialogue approach helped couples to reassess community beliefs that reinforce gender inequity and disapproval of family planning. FH = FW’s inclusion of economic and relationship content served as key entry points for couples to discuss family planning. Results are presented in five central themes: (1) Community family size expectations were reconsidered through discussions on economic factors; (2) Showcasing how relationship health and gender equity are central to economic health influenced men’s acceptance of gender equity; (3) Linking relationship health and family planning helped increase positive attitudes towards family planning and the perceived importance of shared household decision-making to family wellness; (4) Program elements to strengthen relationship skills helped to translate gender equitable attitudes into changes in relationship dynamics and to facilitate equitable family planning communication; (5) FH = FW participation increased couples’ collective family planning (and overall health) decision-making and uptake of contraceptive methods.ConclusionCommunity dialogues may be an effective intervention approach to change individual endorsement of widespread community norms that reduce family planning acceptance. Future work should continue to explore innovative ways to use this approach to increase gender equitable reproductive decision-making among couples in settings where gender, religious, and community norms limit reproductive autonomy. Future evaluations of this work should aim to examine change in norms at the community-level.Trial registrationClinicaltrials.gov (NCT04262882).

Zeolite and Neurodegenerative Diseases.

Neurodegenerative diseases (NDs), characterized by progressive degeneration and death of neurons, are strongly related to aging, and the number of people with NDs will continue to rise. Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common NDs, and the current treatments offer no cure. A growing body of research shows that AD and especially PD are intricately related to intestinal health and the gut microbiome and that both diseases can spread retrogradely from the gut to the brain. Zeolites are a large family of minerals built by [SiO4]4- and [AlO4]5- tetrahedrons joined by shared oxygen atoms and forming a three-dimensional microporous structure holding water molecules and ions. The most widespread and used zeolite is clinoptilolite, and additionally, mechanically activated clinoptilolites offer further improved beneficial effects. The current review describes and discusses the numerous positive effects of clinoptilolite and its forms on gut health and the gut microbiome, as well as their detoxifying, antioxidative, immunostimulatory, and anti-inflammatory effects, relevant to the treatment of NDs and especially AD and PD. The direct effects of clinoptilolite and its activated forms on AD pathology in vitro and in vivo are also reviewed, as well as the use of zeolites as biosensors and delivery systems related to PD.

ERNEST COST action overview on the (patho)physiology of GPCRs and orphan GPCRs in the nervous system.

G protein-coupled receptors (GPCRs) are a large family of cell surface receptors that play a critical role in nervous system function by transmitting signals between cells and their environment. They are involved in many, if not all, nervous system processes, and their dysfunction has been linked to various neurological disorders representing important drug targets. This overview emphasises the GPCRs of the nervous system, which are the research focus of the members of ERNEST COST action (CA18133) working group 'Biological roles of signal transduction'. First, the (patho)physiological role of the nervous system GPCRs in the modulation of synapse function is discussed. We then debate the (patho)physiology and pharmacology of opioid, acetylcholine, chemokine, melatonin and adhesion GPCRs in the nervous system. Finally, we address the orphan GPCRs, their implication in the nervous system function and disease, and the challenges that need to be addressed to deorphanize them.

The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.

A large family of enzymes with the function of hydrolyzing peptide bonds, called peptidases or cysteine proteases (CPs), are divided into three categories according to the peptide chain involved. CPs catalyze the hydrolysis of amide, ester, thiol ester, and thioester peptide bonds. They can be divided into several groups, such as papain-like (CA), viral chymotrypsin-like CPs (CB), papain-like endopeptidases of RNA viruses (CC), legumain-type caspases (CD), and showing active residues of His, Glu/Asp, Gln, Cys (CE). The catalytic mechanism of CPs is the essential cysteine residue present in the active site. These mechanisms are often studied through computational methods that provide new information about the catalytic mechanism and identify inhibitors. The role of computational methods during drug design and development stages is increasing. Methods in Computer-Aided Drug Design (CADD) accelerate the discovery process, increase the chances of selecting more promising molecules for experimental studies, and can identify critical mechanisms involved in the pathophysiology and molecular pathways of action. Molecular dynamics (MD) simulations are essential in any drug discovery program due to their high capacity for simulating a physiological environment capable of unveiling significant inhibition mechanisms of new compounds against target proteins, especially CPs. Here, a brief approach will be shown on MD simulations and how the studies were applied to identify inhibitors or critical information against cysteine protease from several microorganisms, such as Trypanosoma cruzi (cruzain), Trypanosoma brucei (rhodesain), Plasmodium spp. (falcipain), and SARS-CoV-2 (Mpro). We hope the readers will gain new insights and use our study as a guide for potential compound identifications using MD simulations.

Compact spaces homeomorphic to their respective squares

We deal with topological spaces homeomorphic to their respective squares. Primarily, we investigate the existence of large families of such spaces in some subclasses of compact metrizable spaces. As our main result we show that there is a family of size continuum of pairwise non-homeomorphic compact metrizable zero-dimensional spaces homeomorphic to their respective squares. This answers a question of Włodzimierz J. Charatonik. We also discuss the situation in the classes of continua, Peano continua and absolute retracts.

Guidelines for Conducting Worship During Epidemic Transmission According to Islamic and Scientific Perspectives

The Coronavirus is a large family of viruses that cause illnesses ranging from the common cold to more severe diseases. COVID-19 is an infectious disease caused by the novel coronavirus (SARS-CoV-2). The government has issued guidelines to control the spread of the virus, including matters involving activities in mosques such as the implementation of prayer rituals. Some laws and practices in the prayer rituals, issued by the mufti and religious departments, initially caused confusion among the Muslim community because such matters had never occurred in Malaysia and there was a lack of explanation by religious experts. Thus, this study is conducted to obtain views from a panel of experts on matters that can be improved and enhanced in these guidelines. This study employs the method of focus group discussions (FGD) involving 6 expert panelists from the fields of religion, science, and medicine. All expert panelists agree that the development of these guidelines is very beneficial for the community to refer to in the event of airborne virus transmission such as COVID-19 in the future. These guidelines provide justification from both Islamic and scientific perspectives to make the community more confident and comfortable in practicing them.

Prediction of viral families and hosts of single-stranded RNA viruses based on K-Mer coding from phylogenetic gene sequences

There are billions of virus species worldwide, and viruses, the smallest parasitic entities, pose a serious threat. Therefore, fighting associated disorders requires an understanding of the genetic structure of viruses. Considering the wide diversity and rapid evolution of viruses, there is a critical need to quickly and accurately classify viral species and their potential hosts to better understand transmission dynamics, facilitating the development of targeted therapies. Recognizing this, this study has investigated the classes of RNA viruses based on their genomic sequences using Machine Learning (ML) and Deep Learning (DL) models. The PhyVirus dataset, consisting of pathogenic Single-stranded RNA viruses of Baltimore group four (+ssRNA) and five (-ssRNA) with different hosts and species, was analyzed. The dataset containing viral gene sequences was analyzed using the K-Mer coding technique, which is based on base words of various lengths. The study used classical ML algorithms (Random Forest, Gradient Boosting and Extra Trees) and the Fully Connected Deep Neural Network, a Deep Learning algorithm, to predict viral families and hosts. Detailed analyses were performed on the classifier performance in scenarios with different train-test ratios and different word lengths (k-values) for K-Mer. The observed results show that Fully Connected Deep Neural Network has a high success rate of 99.60 % in predicting virus families. In predicting virus hosts, the Extra Trees classifier achieved the highest success rate of 81.53 %. This study is considered to be the first classification study in the literature on this dataset, which has a very large family and host diversity consisting of gene sequences of Single-stranded RNA viruses. Our detailed investigations on how varying word lengths based on K-Mer coding in gene sequences affect the classification into viral families and hosts make this study particularly valuable. This study shows that ML and DL methods have the potential to produce valuable results in phylogenetic studies. In addition, the results and high-performance values show that these methods can be successfully used in regenerative applications of gene sequences or in studies such as the elimination of losses in gene sequences.

State Policy of Far East Development: How to Ensure Accelerated Progress?

Against the backdrop of the authorities’ efforts to accelerate the development of the Far East, dissatisfaction remains, an indicator of which is the trend of population decline. The article argues that the growing financial flow, with the same approach, without a precise formula of the goal, without the definition of priorities, will not give the desired result. It is proposed to accelerate the transition from a resource-export model of the economy to a new industrialization. The justification of priorities is based on combining the efforts of the subjects of the federation of the macroregion, involving the potential of the country’s entrepreneurs focused on Asian markets, and integration cooperation with the countries of the AsiaPacific region.The widest field for cooperation is seen in the field of exploration of the World Ocean, space exploration and in the field of Culture. Such a turn increases the attractiveness of the Far East and increases the demand for labor. It will be necessary to see a different solution to demographic problems. If the State is the main beneficiary of population growth, it is obliged to recognize the birth and upbringing of children in the family as productive work, which is remunerated, counted in the length of service, and provided with a pension.The stability of a young family is determined by the availability of housing, and the key to having many children is a house “on the ground”. But the house is not financial bondage, not a mortgage, but an incentive for expanded reproduction. The course towards industrialization provides an opportunity for a decent income for the head of the family, the work of women is paid, and a roof over their heads is a guarantee of a stable and large family. And the Far East is a testing ground where a model is created, control mechanisms are polished, and efficiency is demonstrated.

Bradycardia in a long QT type 2 family: coinciding KCNH2 and HCN4 variants

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): the Dutch Research Council: NWO Talent Scheme Background A large multigenerational family harboring a pathogenic KCNH2 variant (L69P) was identified. This gene encodes the hERG channel, responsible for the cardiac rapid delayed rectifier K+ current (IKr). Pathogenic variants in KCNH2 can cause Long QT syndrome type 2 (LQTS2). Interestingly, in addition to LQTS2 we observed a high incidence of bradycardia in this family. Bradycardia is a known feature of some types of LQTS. However, evidence of bradycardia in LQTS2 is limited to a few sporadic cases. Purpose This study aims to identify the genetic variants and biophysiological changes in ion channel function, explanatory of the phenotypes LQTS2 and bradycardia. Methods An overview of the phenotype and genetic information of the index and family members was generated , including symptoms and electrocardiogram (ECG) parameters. QTc was calculated using Bazetts’ correction. Segregation of the identified genetic variants with LQTS and bradycardia were determined by LOD score. Biophysiological properties of the encoded ion channels was measured by manual whole-cell patch-clamp experiments. Results On the basis of linkage analysis, the pathogenic variant KCNH2-p.L69P was found to be unrelated to the bradycardia. Therefore, Sanger sequencing of HCN4, encoding the channel responsible for the hyperpolarization-activated current (If), an important current for sinoatrial node automaticity, was performed. We identified the HCN4-p.R666W variant in multiple family members, which co-segregated with bradycardia (LOD-score 3.2). Patients carrying both variants had more severe phenotypes than carriers of a single variant. Patch-clamp experiments in HEK293A-cells expressing wild type, or KCNH2-p.L69P show a reduced current density, and an altered time component of the fast deactivation, explaining the observed LQTS2. Functional assays of HCN4-p.R666W will elucidate the biophysiological changes possibly underlying the bradycardia. Conclusion we present a large multigenerational family that harbors a likely pathogenic variant in HCN4 in conjunction with a pathogenic variant of KCNH2. Double carriers were more affected than single carriers, arguing for continued alertness and deep phenotyping even in families with known pathogenic variants. Furthermore, we identified functional changes in the kinetics of the hERG channel encoded by KCNH2-p.L69P, elucidating the molecular mechanism underlying LQTS2 in this family.

Modelling of a RYR2-associated left ventricular non-compaction and sudden cardiac death overlap syndrome in hiPSC-EHTs

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – EU funding. Main funding source(s): ESC training grant; DZHK Background Genetic cardiomyopathies contribute to a significant proportion of morbidity and mortality among young people. Over the past decades, a wide range of underlying molecular mechanisms has been discovered. The current project arose from the clinical observation of a left ventricular non-compaction and sudden cardiac death overlap syndrome in a large family in northern Italy. Whole exome sequencing performed on family members of different generations revealed a single nucleotide polymorphism in the RYR2 gene (RYR2 c.5654G&amp;gt;A homozygous – RyR2 p.G1885E - exon37:missense) with an autosomal-recessive inheritance pattern. The mutation is localized in the DR3 region of the RyR2 protein, adjacent to the FKBP12.6 binding site, a protein that is known to stabilize RyR2, preventing aberrant activation of the channel. Methods and Results Patient-derived, human induced pluripotent stem cells (hiPSCs), carrying the variant homo- and heterozygously, were generated by reprogramming patient-derived peripheral blood mononuclear cells using a non-integrative Sendai virus protocol. The lines were fully characterized and expressed high levels of pluripotency markers at the RNA and protein level. Patient lines were all able to efficiently differentiate into cardiomyocytes. Subsequently, 3D strip-format, force-generating Engineered Heart Tissues (EHTs) were cast and structurally and functionally characterized. Contraction analysis over 60 days showed differences in force development of the patient-derived lines. In particular, the EHTs carrying the homozygous pathogenic variant showed progressive reduction in both beating rate and force over time, increased spontaneous arrhythmogenicity and reduced inotropic response after exposure to isoprenaline, compared to the heterozygous line and unrelated healthy controls. Starting from day 30 after casting, patient-derived EHTs developed morphological changes with areas of marked cellular overgrowth and reduced troponin expression. Transcriptomic and proteomic analysis at 30 and 60 days after EHTs generation, as well as in 2D cardiomyocytes, complement the phenotyping and provide molecular insights into the underlying pathophysiology. To directly evaluate pathogenicity of the genetic variant identified, we generated isogenic homo- and heterozygously corrected hiPSCs, using CRISPR/ Cas9 technology, starting from the homozygous patient-line. The characterization of these corrected clones is currently ongoing. The genetically corrected 3D tissue models will be critical not only in defining the role of the novel RyR2 variant in the familial phenotype described, but also to unveil mechanistic roles of ryanodine receptor in cardiac disease. Conclusion We describe a novel recessive RYR2 variant associated with a left ventricular non- compaction and sudden cardiac death overlap syndrome. 3D cardiac tissue modelling based on patient-derived hiPSCs uncovered a proarrhythmic and structural phenotype of the mutated lines.

Phenotypic and Genotypic Features of the FAN1 Mutation-Related Disease in a Large Hungarian Family.

Pathogenic variants in the FAN1 gene lead to a systemic disease with karyomegalic interstitial nephritis (KIN) at the forefront clinically. The phenotypic-genotypic features of a FAN1 mutation-related disease involving five members of a Hungarian Caucasian family are presented. Each had adult-onset chronic kidney disease of unknown cause treated with renal replacement therapy and elevated liver enzymes. Short stature, emaciation, latte-colored skin, freckles, and a hawk-like nose in four patients, a limited intellect in two patients, and chronic restrictive lung disease in one patient completed the phenotype. Severe infections occurred in four patients. All five patients had ceased. Four patients underwent autopsy. KIN and extrarenal karyomegaly were observed histologically; the livers showed no specific abnormality. The genotyping using formalin-fixed tissue samples detected a hitherto undescribed homozygous FAN1 mutation (c.1673_1674insT/p.Met558lfs*4; exon 5) in three of these patients and a heterozygous FAN1 mutation in one patient. The reason for the heterozygosity is discussed. In addition, 56 family members consented to the screening for FAN1 mutation from which 17 individuals proved to be heterozygous carriers; a blood chemistry evaluation of their kidney and liver function did not find any abnormality. The clinical presentation of FAN1-related disease was multifaceted, and not yet described manifestations were observed besides kidney and liver disease. Mutation in this gene should be suspected in adults with small kidneys of unknown cause, elevated liver enzymes, and recurrent infections, even without a family history.

Nano-achiral complex composites for extreme polarization optics.

Composites from 2D nanomaterials show uniquely high electrical, thermal and mechanical properties1,2. Pairing their robustness with polarization rotation is needed for hyperspectral optics in extreme conditions3,4. However, the rigid nanoplatelets have randomized achiral shapes, which scramble the circular polarization of photons with comparable wavelengths. Here we show that multilayer nanocomposites from 2D nanomaterials with complex textured surfaces strongly and controllably rotate light polarization, despite being nano-achiral and partially disordered. The intense circular dichroism (CD) in nanocomposite films originates from the diagonal patterns of wrinkles, grooves or ridges, leading to an angular offset between axes of linear birefringence (LB) and linear dichroism (LD). Stratification of the layer-by-layer (LBL) assemblednanocomposites affords precise engineering of the polarization-active materials from imprecise nanoplatelets with an optical asymmetry g-factor of 1.0, exceeding those of typical nanomaterials by about 500 times. High thermal resilience of the composite optics enables operating temperature as high as 250 °C and imaging of hot emitters in the near-infrared (NIR) part of the spectrum. Combining LBL engineered nanocomposites with achiral dyes results in anisotropic factors for circularly polarized emission approaching the theoretical limit. The generality of the observed phenomena is demonstrated by nanocomposite polarizers from molybdenum sulfide (MoS2), MXene and graphene oxide (GO) and by two manufacturing methods. A large family of LBL optical nanocomponents can be computationally designed and additively engineered for ruggedized optics.

Genome-wide identification, characterization, and expression analysis of the small auxin-up RNA gene family during zygotic and somatic embryo maturation of the cacao tree (Theobroma cacao)

Small auxin-up RNA (SAUR) proteins were known as a large family that supposedly participated in various biological processes in higher plant species. However, the SAUR family has been still not explored in cacao (Theobroma cacao L.), one of the most important industrial trees. The present work, as an in silico study, revealed comprehensive aspects of the structure, phylogeny, and expression of TcSAUR gene family in cacao. A total of 90 members of the TcSAUR gene family have been identified and annotated in the cacao genome. According to the physic-chemical features analysis, all TcSAUR proteins exhibited slightly similar characteristics. Phylogenetic analysis showed that these TcSAUR proteins could be categorized into seven distinct groups, with 10 sub-groups. Our results suggested that tandemly duplication events, segmental duplication events, and whole genome duplication events might be important in the growth of the TcSAUR gene family in cacao. By re-analyzing the available transcriptome databases, we found that a number of TcSAUR genes were exclusively expressed during the zygotic embryogenesis and somatic embryogenesis. Taken together, our study will be valuable to further functional characterizations of candidate TcSAUR genes for the genetic engineering of cacao.

New insights into the domain of unknown function (DUF) of EccC5, the pivotal ATPase providing the secretion driving force to the ESX-5 secretion system.

Type VII secretion (T7S) systems, also referred to as ESAT-6 secretion (ESX) systems, are molecular machines that have gained great attention due to their implications in cell homeostasis and in host-pathogen interactions in mycobacteria. The latter include important human pathogens such as Mycobacterium tuberculosis (Mtb), the etiological cause of human tuberculosis, which constitutes a pandemic accounting for more than one million deaths every year. The ESX-5 system is exclusively found in slow-growing pathogenic mycobacteria, where it mediates the secretion of a large family of virulence factors: the PE and PPE proteins. The secretion driving force is provided by EccC5, a multidomain ATPase that operates using four globular cytosolic domains: an N-terminal domain of unknown function (EccC5DUF) and three FtsK/SpoIIIE ATPase domains. Recent structural and functional studies of ESX-3 and ESX-5 systems have revealed EccCDUF to be an ATPase-like fold domain with potential ATPase activity, the functionality of which is essential for secretion. Here, the crystal structure of the MtbEccC5DUF domain is reported at 2.05 Å resolution, which reveals a nucleotide-free structure with degenerated cis-acting and trans-acting elements involved in ATP binding and hydrolysis. This crystallographic study, together with a biophysical assessment of the interaction of MtbEccC5DUF with ATP/Mg2+, supports the absence of ATPase activity proposed for this domain. It is shown that this degeneration is also present in DUF domains from other ESX and ESX-like systems, which are likely to exhibit poor or null ATPase activity. Moreover, based on an in silico model of the N-terminal region of MtbEccC5DUF, it is hypothesized that MtbEccC5DUF is a degenerated ATPase domain that may have retained the ability to hexamerize. These observations draw attention to DUF domains as structural elements with potential implications in the opening and closure of the membrane pore during the secretion process via their involvement in inter-protomer interactions.