Molecular Segmentation of the Spinal Trigeminal Nucleus in the Adult Mouse Brain

The trigeminal column is a hindbrain structure formed by second order sensory neurons that receive afferences from trigeminal primary (ganglionic) nerve fibers. Classical studies subdivide it into the principal sensory trigeminal nucleus located next to the pontine nerve root, and the spinal trigeminal nucleus which in turn consists of oral, interpolar and caudal subnuclei. On the other hand, according to the prosomeric model, this column would be subdivided into segmental units derived from respective rhombomeres. Experimental studies have mapped the principal sensory trigeminal nucleus to pontine rhombomeres (r) r2-r3 in the mouse. The spinal trigeminal nucleus emerges as a plurisegmental formation covering several rhombomeres (r4 to r11 in mice) across pontine, retropontine and medullary hindbrain regions. In the present work we reexamined the issue of rhombomeric vs. classical subdivisions of this column. To this end, we analyzed its subdivisions in an AZIN2-lacZ transgenic mouse, known as a reference model for hindbrain topography, together with transgenic reporter lines for trigeminal fibers. We screened as well for genes differentially expressed along the axial dimension of this structure in the adult and juvenile mouse brain. This analysis yielded genes from multiple functional families that display transverse domains fitting the mentioned rhombomeric map. The spinal trigeminal nucleus thus represents a plurisegmental structure with a series of distinct neuromeric units having unique combinatorial molecular profiles.

Searching sequence databases for functional homologs using profile HMMs: how to set bit score thresholds?

UniProt and BFD databases together have 2.5 billion protein sequences. A large majority of these proteins have been electronically annotated. Automated annotation pipelines, vis-á-vis manual curation, have the advantage of scale and speed but are fraught with relatively higher error rates. This is because sequence homology does not necessarily translate to functional homology, molecular function specification is hierarchic and not all functional families have the same amount of experimental data that one can exploit for annotation. Consequently, customization of annotation workflow is inevitable to minimize annotation errors. In this study, we illustrate possible ways of customizing the search of sequence databases for functional homologs using profile HMMs. Choosing an optimal bit score threshold is a critical step in the application of HMMs. We illustrate ways in which an optimal bit score can be arrived at using four Case Studies. These are the single domain nucleotide sugar 6-dehydrogenase and lysozyme-C families, and SH3 and GT-A domains which are typically found as a part of multi-domain proteins. We also discuss the limitations of using profile HMMs for functional annotation and suggests some possible ways to partially overcome such limitations.

ПОРІВНЯЛЬНИЙ АНАЛІЗ РЕЗУЛЬТАТІВ ЛОНГІТЮДНОГО ДОСЛІДЖЕННЯ ОСОБЛИВОСТЕЙ УЯВЛЕНЬ ДІТЕЙ ІЗ ПОВНИХ ФУНКЦІОНАЛЬНИХ РОДИН ТА РОДИН ТРУДОВИХ МІГРАНТІВ

The purpose of the article is to highlight the results of the empirical longitudinal research on the development of family ideas among middle and high school-age children. The article highlights the importance of the young generation’s ideas about their future family life in the context of the peculiarities, which labor migrants’ children have. Changes in the adolescents’ attitude to their future marriage in longitude are considered. The sample included children from labor migrants’ families aged 12–14 (88 respondents), who were surveyed in 2014 and a part of this sample’s respondents (49 students), who were surveyed in 2017, and, at that time, they were 15–17 full years respectively. Also, in 2014 it was carried out the psycho-diagnostic examination of children from complete families (63 respondents) and 23 of them were surveyed in 2017. Methods. To diagnose the peculiarities of family ideas in longitude, S.V. Kovalev’s questionnaire “Preventive Marriage Satisfaction” was chosen (to identify the level of positive attitude to the future marriage) and the author’s drawing method “My future family” (to identify emotional attitude to the future family and possible problematic family ideas, which can have a destructive effect on marital and child-parent relationships). Hypothesis. There is a possibility that negative tendencies during the formation of family ideas among labor migrants’ children remain constant throughout the adolescent period. Results. Statistical analysis. It is carried out the comparative analysis of family ideas, which adolescents from complete functional families have. The descriptive statistics are used to determine the average, minimum, maximum indicators in the group, the indicators of standard deviation; the Student’s t-criterion. As a result of the longitudinal study of family ideas, it has been revealed that children from labor migrants’ families have negative dynamics in the formation of ideas about the future family, that is, the representations are predictably more and more unfavorable in comparison with children from complete functional families. Conclusions. It has been proved a decrease in the level of preventive satisfaction with marriage and desirability of interaction between family members that will affect the development of marital and family relations in the future, namely the strength of the future marriage, spouses’ compatibility and success of parenthood, etc. Research limitation concerns the number of the same participants in the longitude, as some respondents did not continue their education in high school.Key words: image of the future family, labor migration, labor migrants’ children, preventive satisfaction with marriage, longitudinal research. Метою статті є висвітлення результатів емпіричного подовжнього дослідження розвитку сімейних уявлень дітей середнього та старшого шкільного віку. Висвітлено питання важливості уявлень молодого покоління про своє майбутнє сімейне життя в контексті їх особливостей у дітей трудових мігрантів. Розглянуто зміни ставлення підлітків до свого майбутнього шлюбу у лонгітюді. До вибірки увійшли діти з родин заробітчан 12–14 років (88 респондентів), яких було обстежено у 2014 році, частина респондентів цієї вибірки (49 школярів), яких було обстежено у 2017 році, що на той час мали 15–17 років повних років. Окрім того, у 2014 році проведено психодігностичне обстеження дітей з повних родин (63 респонденти), з них 23 респонденти обстежено у 2017 році.Методи. Для діагностики особливостей сімейних уявлень у лонгітюді вибрано опитувальник С. Ковальова «Превентивна задоволеність шлюбом» (для виявлення рівня позитивного ставлення до майбутнього шлюбу) та авторська малюнкова методика «Моя майбутня родина» (для виявлення емоцій-ного ставлення до майбутньої родини та можливих проблемних сімейних уявлень, які можуть впливати деструктивно на подружні та дитячо-батьківські стосунки). Наявна така гіпотеза:існує вірогідність того, що негативні тенденції під час формування сімейних уявлень дітей трудових мігрантів залишаються сталими протягом усього підліткового періоду.Результати. Застосовано порівняльний аналіз сімейних уявлень з підлітками з повних функціо-нальних сімей. Використаноописову статистику для визначення середніх, мінімальних, максимальних показників у групі, показників стандартного відхилення; t-критерій Стьюдента. В результаті подовжнього дослідження сімейних уявлень виявлено негативну динаміку у формуванні уявлень про майбутню родину у дітей з родин трудових мігрантів, тобто уявлення є все більш прогностично неблагополучними порівняно з дітьми з повних функціональних родин.Висновки. Доведено зменшення рівня превентивної задоволеності шлюбом та бажаності взаємодії між членами родини, а це в майбутньому впливатиме на розвиток шлюбно-сімейних відносин, а саме міцність майбутнього шлюбу, сумісність подружжя та успішність батьківства. Обмеження дослідження стосується кількості тих самих учасників у лонгітюді, оскільки деякі респонденти не продовжили навчання у старшій школі.Ключові слова: образ майбутньої сім’ї, трудова міграція, діти трудових мігрантів, превентивна задоволеність шлюбом, лонгітюдне дослідження.

Clustering FunFams using sequence embeddings improves EC purity

MotivationClassifying proteins into functional families can improve our understanding of a protein’s function and can allow transferring annotations within the same family. Toward this end, functional families need to be “pure”, i.e., contain only proteins with identical function. Functional Families (FunFams) cluster proteins within CATH superfamilies into such groups of proteins sharing function, based on differentially conserved residues. 11% of all FunFams (22,830 of 203,639) also contain EC annotations and of those, 7% (1,526 of 22,830) have at least two different EC annotations, i.e., inconsistent functional annotations.ResultsWe propose an approach to further cluster FunFams into smaller and functionally more consistent sub-families by encoding their sequences through embeddings. These embeddings originate from deep learned language models (LMs) transferring the knowledge gained from predicting missing amino acids in a sequence (ProtBERT) and have been further optimized to distinguish between proteins belonging to the same or a different CATH superfamily (PB-Tucker). Using distances between sequences in embedding space and DBSCAN to cluster FunFams, as well as identify outlier sequences, resulted in twice as many more pure clusters per FunFam than for a random clustering. 52% of the impure FunFams were split into pure clusters, four times more than for random. While functional consistency was mainly measured using EC annotations, we observed similar results for binding annotations. Thus, we expect an increased purity also for other definitions of function. Our results can help generating FunFams; the resulting clusters with improved functional consistency can be used to infer annotations more reliably. We expect this approach to succeed equally for any other grouping of proteins by their phenotypes.AvailabilityThe source code and PB-Tucker embeddings are available via GitHub: https://github.com/Rostlab/FunFamsClustering

Aby bolo menej sirôt žijúcich otcov

Orphans of Living Fathers Summary In the course of the last decades, the phenomenon of orphans with living fathers has occured in the Euro-American civilisation as we are witnessing a rising number of children growing up without the presence of the father. In some cases it is the result of mother’s deliberate choice (single mothers), in other cases no direct intention is involved as with the divorced mothers, The above situation occurs also in the seemingly functional families, where fathers only have a small share in the upbringing of the children. It seems that the problem begins with the birth of the child who consumes 80% of the mother’s emotional resources. As a result, the woman is not able to give her partner as much affection as she used to, which makes him feel pushed away. In many cases this challenging situation makes the man start perceiving and living the sex life in a sort of materialistic way, which is followed by the wife’s natural reaction i.e. sexual life becomes a burden to her. Fortunately, this is not an unavoidable scenario as there exists an alternative – the possibility to keep developing the tenderness within the marital relationship. On the man’s side this alternative type of tenderness takes on the form of empathy, a concrete attention and care for his wife and child. In order to develop in a healthy way, every child needs to experience the motherly and fatherly love in equal measure and the mutual love between the parents that guarantees a stable and secure home for them. If parents start to perceive God as a loving Father who shows them His tenderness and love, it is the response to His generous offer and the invitation to personal conversion at the same time. God’s tenderness is clearly attested in both Old and New Testament. It is evident from His actions through which He proves to be a caring and tender Father who shows gratuitous love to His children. In the image of such God the humans have been created as male and female. Biblical texts provide numerous examples of these divine traits that can be transformed in everyday life behaviour and attitudes by the spouses in the same way as Jewish families have linked these two realms during the Passover meal and in their everyday life. To sum up, tenderness is a chance to ensure the stability of Catholic families and save their children from becoming the orphans of living fathers.

Termini restraining of small membrane proteins enables structure determination at near-atomic resolution

Small membrane proteins are difficult targets for structural characterization. Here, we stabilize their folding by restraining their amino and carboxyl termini with associable protein entities, exemplified by the two halves of a superfolder GFP. The termini-restrained proteins are functional and show improved stability during overexpression and purification. The reassembled GFP provides a versatile scaffold for membrane protein crystallization, enables diffraction to atomic resolution, and facilitates crystal identification, phase determination, and density modification. This strategy gives rise to 14 new structures of five vertebrate proteins from distinct functional families, bringing a substantial expansion to the structural database of small membrane proteins. Moreover, a high-resolution structure of bacterial DsbB reveals that this thiol oxidoreductase is activated through a catalytic triad, similar to cysteine proteases. Overall, termini restraining proves exceptionally effective for stabilization and structure determination of small membrane proteins.

CATH: increased structural coverage of functional space

CATH (https://www.cathdb.info) identifies domains in protein structures from wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and functional annotations. There are two levels: CATH-B, a daily snapshot of the latest domain structures and superfamily assignments, and CATH+, with additional derived data, such as predicted sequence domains, and functionally coherent sequence subsets (Functional Families or FunFams). The latest CATH+ release, version 4.3, significantly increases coverage of structural and sequence data, with an addition of 65,351 fully-classified domains structures (+15%), providing 500 238 structural domains, and 151 million predicted sequence domains (+59%) assigned to 5481 superfamilies. The FunFam generation pipeline has been re-engineered to cope with the increased influx of data. Three times more sequences are captured in FunFams, with a concomitant increase in functional purity, information content and structural coverage. FunFam expansion increases the structural annotations provided for experimental GO terms (+59%). We also present CATH-FunVar web-pages displaying variations in protein sequences and their proximity to known or predicted functional sites. We present two case studies (1) putative cancer drivers and (2) SARS-CoV-2 proteins. Finally, we have improved links to and from CATH including SCOP, InterPro, Aquaria and 2DProt.