ATP-Driven Separation of Liquid Phase Condensates in Bacteria.

Liquid-liquid phase-separated (LLPS) states are key to compartmentalizing components in the absence of membranes; however, it is unclear whether LLPS condensates are actively and specifically organized in the subcellular space and by which mechanisms. Here, we address this question by focusing on the ParABS DNA segregation system, composed of a centromeric-like sequence (parS), a DNA-binding protein (ParB), and a motor (ParA). We show that parS and ParB associate to form nanometer-sized, round condensates. ParB molecules diffuse rapidly within the nucleoid volume but display confined motions when trapped inside ParB condensates. Single ParB molecules are able to rapidly diffuse between different condensates, and nucleation is strongly favored by parS. Notably, the ParA motor is required to prevent the fusion of ParB condensates. These results describe a novel active mechanism that splits, segregates, and localizes non-canonical LLPS condensates in the subcellular space.

When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae).

Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.

Levels of leucaena hay associated with cactus pear in diets for crossbred steers.

Our hypothesis is that the total replacement of ground corn grain (GCG) by cactus pear (CP) in association with 70% of leucaena hay (LH) increases dry matter (DM) intake and digestibility and nitrogen metabolism and maintains the feeding behavior of cattle. The objective was to evaluate the effects of inclusion of these feeds on the nutritional parameters and nitrogen metabolism of cattle. Eight steers, average age of 12 months, weight of 267.5 ± 15 kg, were distributed into two simultaneous 4 × 4 Latin squares according to a 2 × 2 factorial scheme, in which the first factor evaluated was different proportions of inclusion of LH (50 or 70% DM basis), and the second factor was the total replacement of GCG with CP. There was lower DM intake in animals fed with 70% LH. There was an interaction between the factors for DM digestibility, in which the animals fed CP did not differ regardless of the inclusion of LH, but for animals without CP, the greater inclusion of LH decreases DM digestibility. The inclusion of CP decreased free water intake. There was an interaction for total water intake (WI), in which the animals fed without CP presented similarity for this, while in the inclusion of CP, the animals fed 70% of LH presented higher WI. Also, lower values of chewing were observed for animals fed with CP. The replacement of GCG with CP improves the efficiency of nitrogen utilization in the rumen. The inclusion of 70% LH depresses intake.

Inclusion of calcium oxide in sugarcane silage under different particle sizes on performance of dairy cows.

Our objective was to evaluate voluntary intake, apparent digestibility, performance, and nitrogen balance of dairy cows fed sugarcane silage under different particle sizes treated or not with calcium oxide (CaO). Eight F1 Holstein/Zebu cows, with body weight of 521.5 ± 55.17 kg, and 60 ± 10 days in milk were used, distributed into two simultaneous 4 × 4 Latin squares. The treatments were composed of sugarcane into two particle sizes (15 and 30 mm) with and without the addition of CaO (10 g/kg of natural matter), being the treatments compared according to a 2 × 2 factorial arrangement. Data were analyzed by the MIXED procedure of SAS. The intake of dry matter (13.05 kg/day), crude protein, non-fibrous carbohydrates, and neutral detergent fiber was not modified (P > 0.05) by the inclusion of the calcium oxide, nor by particles size and interaction among both. However, there was interaction between CaO and particle size on dry matter digestibility (P = 0.002), being that the CaO was effective in promoting greater DM digestibility in silages with larger particle size. The milk yield and composition were also not affected by the diets (P > 0.05), similarly for nitrogen balance (P > 0.05). The addition of CaO to sugarcane silage with different particle sizes (15 and 30 mm) does not affect the milk yield and composition of dairy cows, nor the nitrogen balance. However, when CaO is added to the sugarcane silage under larger particle sizes, there are benefits in DM digestibility.

Effects of different banana crop wastes on nutrient intake and digestibility, microbial protein synthesis, feeding behavior, and animal performance of ¾ Holstein × Zebu heifers in a semiarid rangeland.

The objective of this study was to evaluate the use of banana crop wastes in diets of ¾ Holstein × » Zebu heifers on the intake and digestibility of nutrients, microbial protein synthesis, feeding behavior, and animal performance. Eight ¾ Holstein × » Zebu heifers were utilized with an average age of 18 ± 1.0 months and an average body weight (BW) of 298 ± 3.06 kg. The experiment was distributed in two simultaneous 4 × 4 Latin squares. The treatments were as follows: Diet 1 (SS)-sorghum silage as exclusive dietary roughage; diet 2 (SSL)-sorghum silage (50%) associated with 50% leaf hay of banana trees (on a DM basis); diet 3 (SSBP)-sorghum silage (50%) associated with 50% banana peel hay; and diet 4 (SSPS)-sorghum silage (50%) associated with 50% pseudostem hay of banana trees. The roughage:concentrate ratio was 75:25. The greatest dry matter intake (DMI; p < 0.01) was found in heifers that received the SS and SSBP diet, mean of 10.19 kg/day. The SS diet showed greatest dry matter digestibility (DMD; p < 0.01) and crude protein digestibility (CPD; p < 0.01). The concentration of total purines (p < 0.01) and absorbed purines (p < 0.01), microbial protein synthesis (p < 0.01), and microbial efficiency (p < 0.01) was higher in the SSBP diet in comparison with SS and SSL diets. The longest eating time was observed in animals that received the SSL diet, being 17.79% higher (p = 0.01) than the SSBP diet. The final BW (p = 0.39) and BW gain (p = 0.39) were similar, with averages of 319.84 kg and 1.08 kg/day, respectively. Biometric measurements were not altered as a function of bedtime (p > 0.05). Banana wastes can be used to feed ¾ Holstein × » Zebu heifers in partial replacement for sorghum silage as they do not alter the animals' weight gain and body development.

Supplemental Trichomonas vaginalis testing is required to maintain control following a transition from Pap smear to HPV DNA testing for cervical screening: a mathematical modelling study.

OBJECTIVES: Using mathematical modelling, we have previously shown that the prevalence of infection with Trichomonas vaginalis (TV) is likely to increase in the general population in Australia with the transition from Pap smear-based cervical screening to human papillomavirus (HPV) DNA testing. Here we use the existing model to estimate the level of supplemental testing required to maintain TV control. METHODS: A compartmental mathematical model describing the transmission of TV in the general heterosexual population in Australia was used to evaluate the impact of a range of screening scenarios on TV prevalence over time following the transition to HPV DNA testing for cervical screening. Scenarios considered were the inclusion of a TV test with the HPV test and the addition of TV testing to routine chlamydia testing conducted in primary care. RESULTS: Our modelling suggests that with sufficient coverage, inclusion of TV testing with routine chlamydia screening in general practice, TV prevalence can be reduced over time, but at the current reported coverage will gradually increase following the transition to HPV testing. Inclusion of TV testing with HPV testing in the cervical screening programme is preferable to no supplemental testing but is considerably less effective in controlling TV. CONCLUSIONS: These findings support the inclusion of TV testing with routine chlamydia testing of young people.

Revising the PLAC8 gene family: from a central role in differentiation, proliferation, and apoptosis in mammals to a multifunctional role in plants.

PLAC8 is a cysteine-rich protein described as a central mediator of tumor evolution in mammals; as such, it represents a promising candidate for diagnostic and therapeutic targeting. The human PLAC8 gene is also involved in contact hypersensitivity response and presents a role in psoriatic skin. In plants, PLAC8 motif-containing proteins are involved in the determination of organ size and growth, response to infection, Ca2+ influx, Cd resistance, and zinc detoxification. In general, PLAC8 motif-containing proteins present the conserved CCXXXXCPC or CLXXXXCPC region. However, there is no devised nomenclature for the PLAC8 motif-containing proteins. Here, through the analysis of 445 sequences, we show that PLAC8 motif-containing proteins constitute a unique gene family, and we propose a unified nomenclature. This is the first report indicating the existence of different groups of PLAC8 proteins, which we have called types I, II, and III. Type I genes are found in mammals, fungi, plants, and algae, and types II and III are exclusive to plants. Our study describes for the first time PLAC8 type III proteins. Whether these sequences maintain their known functional role or possess distinct functions of types I and II genes remains unclear.

Anatomical distribution analysis reveals lack of Langerin+ dermal dendritic cells in footpads and tail of C57BL/6 mice.

Epidermal Langerhans cells (LCs) and dermal dendritic cells (dDCs) capture cutaneous antigens and present them to T-cells in lymph nodes (LNs). The function of LCs and Langerin+ dDCs was extensively studied in the mouse, but their anatomical repartition is unknown. Here, we found LCs in back skin, footpads and tail skin of C57BL/6, BALB/c, 129/Sv and CBA/J mice. Langerin+ dDCs were readily observed in back skin of all strains, but only in footpads and tail of BALB/c and CBA/J mice. Similarly, while LCs were equally present in all LNs and strains, Langerin+ dDCs were found in popliteal LNs (draining footpads) only in BALB/c and CBA/J mice. The sciatic LNs, which we identified as the major tail-draining lymphoid organ, were devoid of Langerin+ dDCs in all strains. Thus, functionally different DCs reside in different skin areas, with variations among mouse strains, implying a potential impact on the cutaneous immune reaction.

The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA.

Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded regions, and comprising BRCT, Myb and RCT well-structured domains. Here, we present the architectures of Rap1 and a Rap1/DNA complex, built through a step-by-step integration of small angle X-ray scattering, X-ray crystallography and nuclear magnetic resonance data. Our results reveal Rap1 structural adjustment upon DNA binding that involves a specific orientation of the C-terminal (RCT) domain with regard to the DNA binding domain (DBD). Crystal structure of DBD in complex with a long DNA identifies an essential wrapping loop, which constrains the orientation of the RCT and affects Rap1 affinity to DNA. Based on our structural information, we propose a model for Rap1 assembly at telomere.

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.

Long-distance dispersal in the short-distance dispersing house sparrow (Passer domesticus).

The house sparrow (Passer domesticus) is a small passerine known to be highly sedentary. Throughout a 30-year capture-mark-recapture study, we have obtained occasional reports of recoveries far outside our main metapopulation study system, documenting unusually long dispersal distances. Our records constitute the highest occurrence of long-distance dispersal events recorded for this species in Scandinavia. Such long-distance dispersals radically change the predicted distribution of dispersal distances and connectedness for our study metapopulation. Moreover, it reveals a much greater potential for colonization than formerly recorded for the house sparrow, which is an invasive species across four continents. These rare and occasional long-distance dispersal events are challenging to document but may have important implications for the genetic composition of small and isolated populations and for our understanding of dispersal ecology and evolution.

Periparturient Changes in Voluntary Intake, Digestibility, and Performance of Grazing Zebu Beef Cows with or without Protein Supplementation.

We aimed to understand the changes in nutritional parameters and performance of beef cows during the peripartum, whether receiving or not receiving protein supplements. Forty cows were used, divided into two treatments: CON-mineral mix and SUP-protein supplementation. Digestibility trial was performed at 45, 30, and 15 days (d) before the parturition and at 20 and 40 d of lactation. The ADG of cows pre- and postpartum was recorded along with the BCS in gestational (GT) and maternal (MT) tissues in the prepartum. There was an effect of treatment and period (p ≤ 0.044) for intakes of DM and CP. The forage intake was similar (p > 0.90) but varied with the effect of days related to parturition (p < 0.001). There was a 14.37% decrease in DM intake from d -30 to d -15 of prepartum. In the postpartum, at 20 d of lactation, there was an increase of 72.7% in relation to d -15 of prepartum. No differences were observed in postpartum ADG or BCS at parturition and postpartum (p ≥ 0.12). However, higher total and MT ADG (p ≤ 0.02) were observed in animals receiving supplementation, while ADG in GT remained similar (p > 0.14). In conclusion, there is a decrease in intake for pregnant cows close to parturition and greater performance of animals supplemented in prepartum.

Neuro-regenerative behavior of adipose-derived stem cells in aligned collagen I hydrogels.

Peripheral nerve injuries persist as a major clinical issue facing the US population and can be caused by stretch, laceration, or crush injuries. Small nerve gaps are simple to treat, and the nerve stumps can be reattached with sutures. In longer nerve gaps, traditional treatment options consist of autografts, hollow nerve guidance conduits, and, more recently, manufactured fibrous scaffolds. These manufactured scaffolds often incorporate stem cells, growth factors, and/or extracellular matrix (ECM) proteins to better mimic the native environment but can have issues with homogenous cell distribution or uniformly oriented neurite outgrowth in scaffolds without fibrous alignment. Here, we utilize a custom device to fabricate collagen I hydrogels with aligned fibers and encapsulated adipose-derived mesenchymal stem cells (ASCs) for potential use as a peripheral nerve repair graft. Initial results of our scaffold system revealed significantly less cell viability in higher collagen gel concentrations; 3 mg/mL gels showed 84.8 ± 7.3% viable cells, compared to 6 mg/mL gels viability of 76.7 ± 9.5%. Mechanical testing of the 3 mg/mL gels showed a Young's modulus of 6.5 ± 0.8 kPa nearly matching 7.45 kPa known to support Schwann cell migration. Further analysis of scaffolds coupled with stretching in vitro revealed heightened angiogenic and factor secretion, ECM deposition, fiber alignment, and dorsal root ganglia (DRG) neurite outgrowth along the axis of fiber alignment. Our platform serves as an in vitro testbed to assess neuro-regenerative potential of ASCs in aligned collagen fiber scaffolds and may provide guidance on next-generation nerve repair scaffold design.

BRCA2-HSF2BP oligomeric ring disassembly by BRME1 promotes homologous recombination.

In meiotic homologous recombination (HR), BRCA2 facilitates loading of the recombinases RAD51 and DMC1 at the sites of double-strand breaks (DSBs). The HSF2BP-BRME1 complex interacts with BRCA2. Its absence causes a severe reduction in recombinase loading at meiotic DSB. We previously showed that, in somatic cancer cells ectopically producing HSF2BP, DNA damage can trigger HSF2BP-dependent degradation of BRCA2, which prevents HR. Here, we report that, upon binding to BRCA2, HSF2BP forms octameric rings that are able to interlock into a large ring-shaped 24-mer. Addition of BRME1 leads to dissociation of both of these ring structures and cancels the disruptive effect of HSF2BP on cancer cell resistance to DNA damage. It also prevents BRCA2 degradation during interstrand DNA crosslink repair in Xenopus egg extracts. We propose that, during meiosis, the control of HSF2BPBRCA2 oligomerization by BRME1 ensures timely assembly of the ring complex that concentrates BRCA2 and controls its turnover, thus promoting HR.

Application of the ARIMA Model to Predict Under-Reporting of New Cases of Hansen's Disease during the COVID-19 Pandemic in a Municipality of the Amazon Region.

This work aimed to apply the ARIMA model to predict the under-reporting of new Hansen's disease cases during the COVID-19 pandemic in Palmas, Tocantins, Brazil. This is an ecological time series study of Hansen's disease indicators in the city of Palmas between 2001 and 2020 using the autoregressive integrated moving averages method. Data from the Notifiable Injuries Information System and population estimates from the Brazilian Institute of Geography and Statistics were collected. A total of 7035 new reported cases of Hansen's disease were analyzed. The ARIMA model (4,0,3) presented the lowest values for the two tested information criteria and was the one that best fit the data, as AIC = 431.30 and BIC = 462.28, using a statistical significance level of 0.05 and showing the differences between the predicted values and those recorded in the notifications, indicating a large number of under-reporting of Hansen's disease new cases during the period from April to December 2020. The ARIMA model reported that 177% of new cases of Hansen's disease were not reported in Palmas during the period of the COVID-19 pandemic in 2020. This study shows the need for the municipal control program to undertake immediate actions in terms of actively searching for cases and reducing their hidden prevalence.

A new highly sensitive point of care screen for spontaneous bacterial peritonitis using the leukocyte esterase method.

BACKGROUND & AIMS: Urine reagent strips measuring leukocyte esterase activity have been studied to screen spontaneous bacterial peritonitis (SBP) but are insensitive. We calibrated a strip specifically for ascitic fluid to achieve high sensitivity in this diagnosis. METHODS: Experiments were conducted on ascitic fluid from patients with cirrhosis. Samples with SBP were diluted with native acellular ascitic fluid to achieve PMN counts below, above, and close to the diagnostic threshold of 250 PMN/microl. A model of SBP was created by spiking negative ascitic fluid samples (<250 PMN/microl) with activated PMN from blood of patients with sepsis, and diluted to achieve a range of PMN. Aliquots were tested at 2, 3, 4, and 10 min with the Periscreen leukocyte esterase strip. PMN/microl was correlated to timings and color scales: white defined negative (PMN <250/microl); and shades of brown, purple, and pink defined positive. Ascitic fluid samples were obtained from 58 patients. Negative ascitic fluid was used from 32 to generate the model SBP. RESULTS: One thousand three hundred and four experiments were performed with a median PMN count of 492/microl (0-7510). After exclusion of uninterpretable colorimetric results, 1089 experiments were analyzed [PMN of 444/microl (0-7510)]. The best result was obtained at 3 min (n=299), with Se: 100%, Sp: 57.9%; NPV: 100%, PPV: 76.5%. The test was not interpretable in bloody, chylous or bilious ascitic fluid, or concurrent imipenem treatment. CONCLUSIONS: This new leukocyte esterase strip calibrated to an ascitic fluid PMN count 250/microl is a robust screening tool when the strip turns any hue of tan/brown at 3 min.

Time-resolved SAXS measurements facilitated by online HPLC buffer exchange.

Small-angle X-ray scattering (SAXS) is a powerful technique to structurally characterize biological macromolecules in solution. Heterogeneous solutions are inherently challenging to study. However, since SAXS data from ideal solutions are additive, with careful computational analysis it may be possible to separate contributions from individual species present in solution. Hence, time-resolved SAXS (TR-SAXS) data of processes in development can be analyzed. Many reported TR-SAXS results are initialized by a sudden change in buffer conditions facilitated by rapid mixing combined with either continuous or stopped flow. In this paper a method for obtaining TR-SAXS data from systems where the reaction is triggered by removal of a species is presented. This method is based on fast buffer exchange over a short desalting column facilitated by an online HPLC (high-performance liquid chromatography) connected to the SAXS sample cell. The sample is stopped in the sample cell and the evolving reaction is followed. In this specific system the removal of phenol initiates a self-association process of long-acting insulin analogues. For this experiment, data were collected in time series while varying concentrations. The method can be generally applied to other systems where removal of a species or other changes in experimental conditions trigger a process.

The biology and engineered modeling strategies of cancer-nerve crosstalk.

A recent finding critical to cancer aggravation is the interaction between cancer cells and nerves. There exist two main modes of cancer-nerve interaction: perineural invasion (PNI) and tumor innervation. PNI occurs when cancer cells infiltrate the adjacent nerves, and its relative opposite, tumor innervation, occurs when axons extend into tumor bodies. Like most cancer studies, these crosstalk interactions have mostly been observed in patient samples and animal models at this point, making it difficult to understand the mechanisms in a controlled manner. As such, in recent years in vitro studies have emerged that have helped identify various microenvironmental factors responsible for cancer-nerve crosstalk, including but not limited to neurotrophic factors, neurotransmitters, chemokines, cancer-derived exosomes, and Schwann cells. The versatility of in vitro systems warrants continuous development to increase physiological relevance to study PNI and tumor innervation, for example by utilizing biomimetic three-dimensional (3D) culture systems. Despite the wealth of 3D in vitro cancer models, comparatively there exists a lack of 3D in vitro models of nerve, PNI, and tumor innervation. Native-like 3D in vitro models of cancer-nerve interactions may further help develop therapeutic strategies to curb nerve-mediated cancer aggravation. As such, we provide an overview of the key players of cancer-nerve crosstalk and current in vitro models of the crosstalk, as well as cancer and nerve models. We also discuss a few future directions in cancer-nerve crosstalk research.

Spontaneous Pneumomediastinum and Diffuse Subcutaneous Emphysema after Methamphetamine Inhalation.

Methamphetamines are commonly abused drugs for their stimulant and euphoric effects. Inhaled and intravenous use may cause damage to the respiratory system. Spontaneous pneumomediastinum is a condition where changes in intrathoracic pressure leads to alveolar rupture and dissection of air along the tracheobronchial tree. Massive subcutaneous emphysema may result from pneumomediastinum which may compromise the central airway. In this case report, we present an unusual case of spontaneous pneumomediastinum and severe subcutaneous emphysema following inhalation of methamphetamine. This case emphasizes the rising concern on the acute respiratory complications of methamphetamine use.

Elevational divergence in the great tit complex revealed by major hemoglobin genes.

Gene flow and demographic history can play important roles in the adaptive genetic differentiation of species, which is rarely understood in the high-altitude adaptive evolution of birds. To elucidate genetic divergence of populations in the great tit complex (Parus major, P. minor and P. cinereus) at different elevations, we compared the genetic structure and gene flow in hemoglobin genes with neutral loci. Our results revealed the elevationally divergent structure of α A -globin gene, distinctive from that of the ß A -globin gene and neutral loci. We further investigated gene flow patterns among the populations in the central-northern (> 1,000 m a.s.l.), south-eastern (< 1,000 m a.s.l.) regions and the Southwest Mountains (> 2,000 m a.s.l.) in China. The high-altitude (> 1,000 m a.s.l.) diverged α A -globin genetic structure coincided with higher α A -globin gene flow between highland populations, in contrast to restricted neutral gene flow concordant with the phylogeny. The higher α A -globin gene flow suggests the possibility of adaptive evolution during population divergence, contrary to the lower α A -globin gene flow homogenized by neutral loci during population expansion. In concordance with patterns of historical gene flow, genotypic and allelic profiles provide distinctive patterns of fixation in different high-altitude populations. The fixation of alleles at contrasting elevations may primarily due to highland standing variants α A 49Asn/72Asn/108Ala originating from the south-western population. Our findings demonstrate a pattern of genetic divergence with gene flow in major hemoglobin genes depending on population demographic history.