Phase-specific Changes Research Articles

Comparative analysis of biomechanical patterns in sprinting: A machine learning approach to optimize running performance in track athletes

Athletes’ success in field and track competitions has been reported to be determined by their sprinting skills. Therefore, it is crucial to understand what biomechanical and physiological factors contribute to the most effective sprinting attributes. The scientific research on sprint evaluation has predominantly dealt with discrete metrics simultaneously, avoiding the interplay between multiple factors as the sprint progresses. Incorporating all the factors that could potentially influence the impact of excellent sprint ability is the primary objective of the present study. This research investigates the biomechanics of sprinting using a Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM) hybrid approach, focusing mainly on factors like stride length, ground reaction forces, joint angles, and muscle activation patterns. The hybrid Machine Learning (ML) model accurately identifies between the two groups, and the results indicate that sprinters performing at the national level have more extended movements, higher reaction time to ground forces, and improved joint angles. The research project set up a 20-meter track for the race, and 30 participants, divided 50-50 between two distinct groups that included comparable college-level and national-level performers, participated. With a 92.4% accuracy, 90.2% precision, and 90.9% F1 score, the hybrid approach performed better than standard models in predicting optimum sprinting patterns. The higher efficiency is caused by phase-specific changes that the model unattended, such as enhanced knee angles and joint accelerated motion in the swing phase. In comparison, the SVM model, though respectable, lags behind with an accuracy of 85.7% and a lower precision and recall (82.4% and 80.9%, respectively). The RF model performed better than SVM with an accuracy of 88.1% and a balanced F1-score of 86.8% but still fell short of the CNN-LSTM hybrid. The standalone LSTM model performed relatively well, with an accuracy of 89.3% and an F1 score of 88.1%, showing its capability but still not matching the hybrid model’s performance.

The coincidence of climate extremes with sensitive crop growth phases: Projected impact on sustainable crop water use and crop yield in the IGB river basins

Increased climate variability and extremes are unequivocal with unprecedented impacts on water resources and agriculture production systems. However, little is known about the impacts of climate extremes at the intra-seasonal level which remained largely unexplored. We investigated the coincidence of climate extremes with sensitive crop growth phases of wheat and rice in the Indus, Ganges and Brahmaputra (IGB) river basins of South Asia. We also quantified the related impacts on irrigation water demand (IWD), gross primary production (GPP) and crop yields (CY) simulated by a hydrological-vegetation model (LPJmL) during 1981–2100 using RCP4.5-SSP1 and RCP8.5-SSP3 framework. The climate extremes revealed a higher frequency and intensity during crop growth phases with significant increasing trends in future. Diverse changes in IWD, GPP and CY are projected in future under the influence of crop phase-specific extremes. The crop phase-specific changes in the IWD of wheat and rice will intensify in the future. More than 50 % of the change in future wheat irrigation is caused by warm and dry extremes during the ripening phase. Whereas, increase in IWD for rice is mainly associated with warm extremes only. The crop phase-specific GPP shows a decreasing trend in future for both wheat and rice in the Western part of IGB with the largest decrease during the reproductive phase of wheat (up to 36 %) and vegetative phase of rice (>20 %). This decrease is clearly reflected in seasonal yields i.e., both wheat (20 %) and rice (12 %) showed a decrease in future linked with warm and dry extremes. However, in the Eastern part of IGB, the GPP will mostly increase in future during the three crop phases of wheat and rice. These results can be used to help develop efficient adaptation strategies considering seasonal changes and sensitive crop phases for sustained food and water security in South Asia.

Abstract 6002: Characterizing dynamic landscape of DNA methylation in ovarian high-grade serous carcinoma

Abstract Dysregulated DNA methylation (DNAm) is a hallmark of all cancer types, though the precise role of these aberrations in tumor progression and treatment response remains elusive. Advances in whole-genome bisulfite sequencing (WGBS) have enabled profiling methylomes at full resolution and stimulated interest to explore dynamics of DNAm across tumor sites and cancer treatment. A major challenge in the analysis of patient data is that a surgically removed tumor sample represents a mixture of cancer cells and microenvironment, and that the insights on DNAm changes are intertwined due to mixed effects from patient epigenomic background, tissue context, and treatment pressure. By using a computational approach, these effects can be decomposed into patient background, tissue site, and treatment phase specific changes, and controlled for natural microenvironment variation. retion, and action, as well as in several oncogenic signaling cascades. The analysis of the tissue profiles indicated that the progression of HGSC from the tissues-of-origin to the metastatic deposits is accompanied by drastic changes in DNAm profiles. Thus, when comparing ovaries and peritoneum, intra-abdominal tissues mesentery and omentum featured prominent change of promoter DNAm: loss in 10% and gain in 20% of genes. Interestingly, the genes with aberrant DNAm included ABC transporters implicated in pumping drugs across the cell membrane, as well as the members of MAPK and PI3K signaling cascades. The joint analysis of both treatment and tissue contributions suggests that the overall modest effect of NACT is further reduced in metastases, mediated via DNAm changes in genes involved in multidrug resistance. Citation Format: Alexandra Lahtinen, Giovanni Marchi, Daria Afenteva, Susanna Holmström, Kaisa Huhtinen, Anni Virtanen, Johanna Hynninen, Antti Häkkinen, Sampsa Hautaniemi. Characterizing dynamic landscape of DNA methylation in ovarian high-grade serous carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6002.

Changes in subjective stress experiences and self-efficacy beliefs of preschool teachers in Germany: A longitudinal study during 12 months of the COVID-19 pandemic

This study collected monthly data between September 2020 and August 2021 to document the consequences of the COVID-19 pandemic for German preschool teachers during different pandemic phases. This longitudinal study investigated how subjective stress experiences and self-efficacy beliefs of preschool teachers (N = 279) change over time and explored associations on the inter- and intraindividual level. We observed phase-specific changes in subjective stress experiences and interindividual differences in change rates, but no systematic increase across the entire study period. Results also highlight self-efficacy beliefs as a resource for preschool teachers, which should be strengthened to better face stress experiences.

Changes in Metabotropic Glutamate Receptor Gene Expression in Rat Brain in a Lithium-Pilocarpine Model of Temporal Lobe Epilepsy.

Preventing epileptogenesis in people at risk is an unmet medical need. Metabotropic glutamate receptors (mGluRs) are promising targets for such therapy. However, drugs acting on mGluRs are not used in the clinic due to limited knowledge of the involvement of mGluRs in epileptogenesis. This study aimed to analyze the changes in gene expression of mGluR subtypes (1–5, 7, 8) in various rat brain regions in the latent and chronic phases of a lithium–pilocarpine model of epilepsy. For this study, multiplex test systems were selected and optimized to analyze mGluR gene expression using RT-qPCR. Region- and phase-specific changes in expression were revealed. During the latent phase, mGluR5 mRNA levels were increased in the dorsal and ventral hippocampus, and expression of group III genes was decreased in the hippocampus and temporal cortex, which could contribute to epileptogenesis. Most of the changes in expression detected in the latent stage were absent in the chronic stage, but mGluR8 mRNA production remained reduced in the hippocampus. Moreover, we found that gene expression of group II mGluRs was altered only in the chronic phase. The study deepened our understanding of the mechanisms of epileptogenesis and suggested that agonists of group III mGluRs are the most promising targets for preventing epilepsy.

Single-cell transcriptomics following ischemic injury identifies a role for B2M in cardiac repair

The efficiency of the repair process following ischemic cardiac injury is a crucial determinant for the progression into heart failure and is controlled by both intra- and intercellular signaling within the heart. An enhanced understanding of this complex interplay will enable better exploitation of these mechanisms for therapeutic use. We used single-cell transcriptomics to collect gene expression data of all main cardiac cell types at different time-points after ischemic injury. These data unveiled cellular and transcriptional heterogeneity and changes in cellular function during cardiac remodeling. Furthermore, we established potential intercellular communication networks after ischemic injury. Follow up experiments confirmed that cardiomyocytes express and secrete elevated levels of beta-2 microglobulin in response to ischemic damage, which can activate fibroblasts in a paracrine manner. Collectively, our data indicate phase-specific changes in cellular heterogeneity during different stages of cardiac remodeling and allow for the identification of therapeutic targets relevant for cardiac repair.

Phase specific changes in the countermovement jump occur without change in peak metrics following training

The countermovement jump (CMJ) is routinely used to assess changes in strength-power qualities. Common measures derived from this test include jump height, peak power and peak velocity. However, valuable information on training induced changes in CMJ performance may be missed if phase and subphase variables are not included in the analysis also. The objective of this investigation was to determine whether significant performance changes can occur in the CMJ in the absence of changes in jump height or peak-form metrics. Sixteen recreationally trained males undertook 10-weeks of resistance training consisting of weightlifting, ballistic and plyometric actions with heavy and light loads. The CMJ was performed pre- and post-test with both peak-form metrics and mean phase/subphase metrics analysed. Mean velocity (p < 0.01) and mean power (p < 0.01) significantly improved following training while peak velocity (p = 0.18), peak power (p = 0.29), and jump height (p = 0.24) did not. Work, countermovement depth, eccentric duration and total movement duration significantly improved too (p < 0.01 to 0.03). Practitioners should consider using CMJ variables beyond jump height and instantaneous metrics to more thoroughly diagnose performance changes of the leg extensors following training.

The proteome of human Fallopian tube lavages during the phase of embryo transit reveals candidate proteins for the optimization of preimplantation embryo culture.

Are there phase-specific changes in the early secretory (ES) phase human tubal lavage proteome that can inform and potentially optimize IVF culture media? The human tubal lavage proteome during the ES phase relative to the menstrual phase reveals substantial differential protein abundance in pathways such as glycolysis, redox homeostasis and activation of 14-3-3 zeta-mediated signaling. The Fallopian tube is uniquely suited to the development of the preimplantation embryo as it transits the tube during the ES phase of the menstrual cycle. Euploid cleavage-stage embryo arrest may reflect incomplete recapitulation of in-vivo conditions by current media formulations. Proteome-wide analysis of distal tubal lavage specimens collected from 26 healthy women undergoing open microtubal anastomosis surgery from January 2013 to January 2018 was performed. Specimens were grouped by menstrual cycle phase in order to analyze phase-specific differences in protein abundance. For the murine embryo assay, single-cell embryos (N = 482) were collected from superovulated wild type C57BL/6 female mice and cultured in microdrops over 5 days for the assessment of blastocyst development. Human tubal lavage specimens were processed for label-free mass spectrometry. Reported menstrual cycle day was confirmed by measuring serum hormones. Key protein targets in the ES phase were validated via immunoblot. The ES phase-specific increase in 14-3-3 zeta protein was confirmed via ELISA of conditioned media obtained from primary human Fallopian tube epithelial cell culture. A murine embryo assay was performed to investigate the impact of graduated concentrations of 14-3-3 zeta on the blastocyst development rate. Comparison of the ES and menstrual phase human tubal lavage proteomes revealed 74 differentially expressed proteins with enrichment of pathways and biological processes involved in the regulation of carbohydrate metabolism, oxidative stress and cell survival. The adapter-regulator protein 14-3-3 zeta was among the most significantly increased in the ES phase. Supplementation of embryo culture media with 14-3-3 zeta at concentrations tested did not significantly improve the murine blastocyst development. Although select associations were recapitulated in the conditioned media from sex steroid exposed primary human tubal epithelial cells, cell culture represents an in-vitro approximation. Changes to embryo culture media, such as protein supplementation, must undergo rigorous preclinical safety testing prior to adoption for human use. This study represents the first description of the human Fallopian tube lavage proteome across the menstrual cycle, revealing a unique proteomic signature during the ES phase. Although supplementation of culture media with 14-3-3 zeta at appropriate concentrations showed no significant impact on the murine blastocyst development rate, other biologically plausible candidate proteins for individual or high throughput testing strategies are identified. This work was funded in part by an Army Medical Department Advanced Medical Technology Initiative grant from the United States Army Medical Research and Materiel Command's Telemedicine and Advanced Technology Research Center. There are no competing interests. N/A.

Promoters for lipogenesis-specific downregulation in Yarrowia lipolytica.

Yarrowia lipolytica is a non-conventional yeast with potential applications in the biofuel and biochemical industries. It is an oleaginous yeast that accumulates lipids when it encounters nutrient limitation in the presence of excess carbon. Its molecular toolbox includes promoters for robust constitutive expression, regulated expression through the addition of media components and inducible expression during lipid accumulation. To date, no promoters have been identified that lead to downregulation at the transition from growth to lipid accumulation. We identified four native Y. lipolytica promoters that downregulate the expression of genes at this natural transition. Using the fatty acid desaturase genes FAD2 and OLE1 as reporter genes for these promoters, we correlated repression of desaturase transcript levels with a reduction of desaturated fatty acids at the transition to lipid accumulation. These promoters can restrict to the growth phase an essential or favorable activity that is undesirable during lipid accumulation under traditional fermentation conditions without media additions. This expression pattern results in lipogenesis phase-specific changes that could be useful in applications relating to optimizing lipid yield and composition.

A Pilot Daily Diary Study of Changes in Stress and Cannabis Use Quantity Across the Menstrual Cycle

Menstrual cycle (MC) phase appears to influence changes in females’ addictive behaviours (e.g., drinking,cigarette smoking). Few studies have examined cannabis use across the MC. We examined phase-specific changes in stress and cannabis use quantity across the MC in daily cannabis users. We hypothesized there would be an increase in self-reported stress and cannabis quantity premenstrually and menstrually versus other MC phases. Data were obtained prospectively, using a 32-day daily diary, from 14 normally- cycling, community-recruited, female cannabis users (Age: M = 29.3 years old, SD = 4.9). Participants completed measures pertaining to their daily stress levels (the General Stress Scale) and the quantity of cannabis used daily. A priori planned comparison t-tests and non-parametric Wilcoxon rank tests revealed MC phase effects on stress levels and cannabis quantity, respectively. In partial support of stress-response dampening (SRD) model and self-medication theory (SMT) predictions, stress levels were higher in the premenstrual versus the ovulatory phase, and a higher quantity of cannabis was used premenstrually versus the follicular and ovulatory phases. Findings suggest stress levels and cannabis use quantity are MC phase-sensitive. Results are consistent with SRD model and SMT predictions, where females learn to increase the quantity of cannabis used premenstrually to dampen their heightened stress response and negative affect. Female cannabis users of reproductive age could be trained to employ alternative strategies to cope with elevated stress during the premenstrual phase to prevent increased cannabis use.

Phase-Specific Changes in Rate of Force Development and Muscle Morphology Throughout a Block Periodized Training Cycle in Weightlifters.

The purpose of this study was to investigate the kinetic and morphological adaptations that occur during distinct phases of a block periodized training cycle in weightlifters. Athlete monitoring data from nine experienced collegiate weightlifters was used. Isometric mid-thigh pull (IMTP) and ultrasonography (US) results were compared to examine the effects of three specific phases of a training cycle leading up to a competition. During the high volume strength-endurance phase (SE) small depressions in rate of force development (RFD) but statistically significant (p ≤ 0.05) increases in vastus lateralis cross-sectional area (CSA), and body mass (BM) were observed. The lower volume higher intensity strength-power phase (SP) caused RFD to rebound above pre-training cycle values despite statistically significant reductions in CSA. Small to moderate increases only in the earlier RFD time bands (<150 ms) occurred during the peak/taper phase (PT) while CSA and BM were maintained. Changes in IMTP RFD and CSA from US reflected the expected adaptations of block periodized training phases. Changes in early (<100 ms) and late (≥150 ms) RFD time bands may not occur proportionally throughout different training phases. Small increases in RFD and CSA can be expected in well-trained weightlifters throughout a single block periodized training cycle.

Growth phase-specific changes in the composition of E. coli transcription complexes

In E. coli, a single oligomeric enzyme transcribes the genomic DNA, while multiple auxiliary proteins and regulatory RNA interact with the core RNA polymerase (RP) during different stages of the transcription cycle to influence its function. In this work, using fast protein isolation techniques combined with mass spectrometry (MS) and immuno-analyses, we studied growth phase-specific changes in the composition of E. coli transcription complexes. We show that RP isolated from actively growing cells is represented by prevalent double copy assemblies and single copy RP–RNA and RP–RNA–RapA complexes. We demonstrate that RpoD/σ70 obtained in fast purification protocols carries tightly associated RNA and show evidence pointing to a role of sigma-associated RNA in the formation of native RP–(RNA)–RpoD/σ70 (holoenzyme) complexes. We report that enzymes linked functionally to the metabolism of lipopolysaccharides co-purify with RP–RNA complexes and describe two classes of RP-associated molecules (phospholipids and putative phospholipid–rNT species). We hypothesize that these modifications could enable anchoring of RP–RNA and RNA in cell membranes. We also report that proteins loosely associated with ribosomes and degradosomes (S1, Hfq) co-purify with RP–RNA complexes isolated from actively growing cells – a result consistent with their proposed roles as adaptor-proteins. In contrast, GroEL, SecB, and SecA co-purified with RP obtained from cells harvested in early stationary phase. Our results demonstrate that fast, affinity chromatography-based isolation of large multi-protein assemblies in combination with MS can be used as a tool for analysis of their composition and the profiling of small protein-associated molecules (SPAM).

How leaves of mycoheterotrophic plants evolved - from the view point of a developmental biologist.

How mycoheterotrophs have evolved and how they are sustained are enigmas. Structural analyses of the plastid genome and phylogenetic analyses of mycoheterotrophs have been used to identify mycorrhizal fungi. Molecular genetic studies have also revealed the mechanism for plant-fungi interactions. However, the evolution of the small, scale-like vegetative leaves of mycoheterotrophs is unknown. As almost all genes determining leaf size affect the floral organ sizes, it is highly implausible that loss-of-function mutations in leaf size regulators caused the evolution of smaller foliage leaves in mycoheterotrophs. In this Viewpoint, possible evolutionary scenarios of scale-like leaves in mycoheterotrophs are discussed from the perspective of developmental genetics of leaves in model plants, including: vegetative phase-specific changes in expression of leaf size regulator(s); the change from foliage leaves to scale-like lateral organs; and expression of suppressor(s) involved in organ development. These possibilities can be tested in future studies. This approach will provide a new research field in the developmental biology of plants.

Functional analyses of putative PalS (Palindromic Self-recognition) motifs in bacterial Hfq

The bacterial protein Hfq has been linked to nucleic acid metabolism and signaling, however its explicit role has been elusive. Recently it was proposed that the C-termini of Hfq subunits in Hfq6 complexes could be involved in functional interactions with other Hfq hexamers and/or nucleic acids. To test the proposed model of the native Hfq complex experimentally, we genetically engineered chimeric Hfq6 complexes, in which C-termini of bacterial Hfq subunits were substituted with a sequence derived from human histone H2B (hH2B) that includes multiple functionally significant amino acids whose modifications have been linked to carcinogenesis. We demonstrate that this substitution results in an enhanced formation of dodecameric assemblies by the Hfq–hH2B hybrid – a result pointing to the possibility of a (functional) homology between these motifs in proteins from distant kingdoms. We hypothesize that these putative Palindromic Self-recognition (PalS) motifs could act as proteins' ‘cohesive ends’ that could allow the protein complexes carrying such motifs to interact dynamically and dissociate–reassociate in response to stress and/or growth phase-specific changes. We provide experimental support to the latter hypothesis and demonstrate that in E. coli the dodecameric Hfq assemblies are formed in a growth stage-specific manner. We describe a refined system – consisting solely of purified Hfq, polynucleotide phosporylase (PNP) and ADP – that allows reconstitution in vitro of characteristic ‘SDS-insensitive’ Hfq6–Hfq6 assemblies observed in experiments with whole-cell extracts obtained from exponentially-growing cells. We also optimized conditions for the extraction of intact native dodecameric Hfq complexes.

Trait-demography relationships underlying small mammal population fluctuations.

Large-scale fluctuations in abundance are a common feature of small mammal populations and have been the subject of extensive research. These demographic fluctuations are often associated with concurrent changes in the average body mass of individuals, sometimes referred to as the 'Chitty effect'. Despite the long-standing recognition of this phenomenon, an empirical investigation of the underlying coupled dynamics of body mass and population growth has been lacking. Using long-term life-history data combined with a trait-based demographic approach, we examined the relationship between body mass and demography in a small mammal population that exhibits non-cyclic, large-scale fluctuations in abundance. We used data from the male segment of a 25-year study of the monogamous prairie vole, Microtus ochrogaster, in Illinois, USA. Specifically, we investigated how trait-demography relationships and trait distributions changed between different phases of population fluctuations, and the consequences of these changes for both trait and population dynamics. We observed phase-specific changes in male adult body mass distribution in this population of prairie voles. Our analyses revealed that these changes were driven by variation in ontogenetic growth, rather than selection acting on the trait. The resulting changes in body mass influenced most life-history processes, and these effects varied among phases of population fluctuation. However, these changes did not propagate to affect the population growth rate due to the small effect of body mass on vital rates, compared to the overall differences in vital rates between phases. The increase phase of the fluctuations was initiated by enhanced survival, particularly of juveniles and fecundity, whereas the decline phase was driven by an overall reduction in fecundity, survival and maturation rates. Our study provides empirical support, as well as a potential mechanism, underlying the observed trait changes accompanying population fluctuations. Body size dynamics and population fluctuations resulted from different life-history processes. Therefore, we conclude that body size dynamics in our population do not drive the observed population dynamics. This more in-depth understanding of different components of small mammal population fluctuations will help us to better identify the mechanistic drivers of this interesting phenomenon.

Metabolic Effects of Social Isolation in Adult C57BL/6 Mice.

Obesity and metabolic dysfunction are risk factors for a number of chronic diseases, such as type 2 diabetes, hypertension, heart disease, stroke, and certain forms of cancers. Both animal studies and human population-based and clinical studies have suggested that chronic stress is a risk factor for metabolic disorders. A good social support system is known to exert positive effects on the mental and physical well-being of an individual. On the other hand, long-term deprivation of social contacts may represent a stressful condition that has negative effects on health. In the present study, we investigated the effects of chronic social isolation on metabolic parameters in adult C57BL/6 mice. We found that individually housed mice had increased adipose mass compared to group-housed mice, despite comparable body weight. The mechanism for the expansion of white adipose tissue mass was depot-specific. Notably, food intake was reduced in the social isolated animals, which occurred around the light-dark phase transition periods. Similarly, reductions in heat generated and the respiratory exchange ratio were observed during the light-dark transitions. These phase-specific changes due to long-term social isolation have not been reported previously. Our study shows social isolation contributes to increased adiposity and altered metabolic functions.

D. melanogaster imaginal disk mitotic abnormalities induced by a tumor-suppressor Dlg-silencing construction

Mitosis, cytokinesis and nuclear texture of wing imaginal disk cells silenced by UAS-RNAi-dlg construct activated by a 1096-Gal4 driver were studied. The construct is a P-element genomic insertion with a UAS-promoter driving the silencing element. The latter contains a coding region of the dlg gene and complementary region. They produce an RNA hairpin processed by the endogenous protein Dicer (Dietzl et al., 2007). The resulting RNA fragments silence dlg mRNA. The complex is cleaved with the genomic Dicer, and dlg mRNA disintegrates. The tumor suppressor gene dlg encodes 21 transcripts. The construct UAS-RNAi-dlg inactivates 14 transcripts (RE, RH, RQ, RS, RG, RD, RL, RB, RK, RR, RT, RN, RA, RP) and does not silence 7 others (RO, RF, RI, RU, RJ, RC, RM). This permits one to study the function of proteins containing guanilate-kinase domain IPR008145 at the protein C-end. The most important consequences of the silencing are the abnormal mitoses exit and binuclear cells formation. Quantitative fluorescence measurements of anti-H3-p histone and DAPI signals showed phase-specific changes in nuclear texture. The most probable dlg target is inactivation of cellular cortex polarization in mitosis.

The extracellular matrix locally regulates asynchronous concurrent lactation in tammar wallaby (Macropus eugenii)

Asynchronous concurrent lactation (ACL) is an extreme lactation strategy in macropod marsupials including the tammar wallaby, that may hold the key to understanding local control of mammary epithelial cell function. Marsupials have a short gestation and a long lactation consisting of three phases; P2A, P2B and P3, representing early, mid and late lactation respectively and characterised by profound changes in milk composition. A lactating tammar is able to concurrently produce phase 2A and 3 milk from adjacent glands in order to feed a young newborn and an older sibling at heel. Physiological effectors of ACL remain unknown and in this study the extracellular matrix (ECM) is investigated for its role in switching mammary phenotypes between phases of tammar wallaby lactation. Using the level of expression of the genes for the phase specific markers tELP, tWAP, and tLLP-B representing phases 2A, 2B and 3 respectively we show for the first time that tammar wallaby mammary epithelial cells (WallMECs) extracted from P2B acquire P3 phenotype when cultured on P3 ECM. Similarly P2A cells acquire P2B phenotype when cultured on P2B ECM. We further demonstrate that changes in phase phenotype correlate with phase-specific changes in ECM composition. This study shows that progressive changes in ECM composition in individual mammary glands provide a local regulatory mechanism for milk protein gene expression thereby enabling the mammary glands to lactate independently.

Dual Effects of IL-1 Overactivity on the Immune System in a Mouse Model of Arthritis due to Deficiency of IL-1 Receptor Antagonist

Previous studies have revealed the significance of cytokine interleukin 1 (IL-1) in the onset and progression of rheumatoid arthritis (RA). The precise molecular mechanisms related to IL-1 underlying RA is still elusive. We conducted a whole genome-wide transcriptomal comparison of wild-type (WT) and arthritis-prone IL-1 receptor antagonist (IL-1rn) deficient BALB/c mice to address this issue. To refine our search efforts, gene expression profiling was also performed on paired wild-type and arthritis-resistant IL-1rn deficient DBA/1 mice as internal controls when identifying causative arthritis candidate genes. Two hundred and fifteen transcripts were found to be dysregulated greater than or equal to 2-fold in the diseased mice. The altered transcriptome in BALB/c mice revealed increased myeloid cell activities and impaired lymphocyte functionality, suggesting dual regulatory effects of IL-1 hyperactivity on immunological changes associated with arthritis development. Phase-specific gene expression changes were identified, such as early increase and late decrease of heat shock protein coding genes. Moreover, common gene expression changes were also observed, especially the upregulation of paired Ig-like receptor A (Pira) in both early and late phases of arthritis. Real-time PCR was performed to validate the expression of Pira and an intervention experiment with a major histocompatibility complex (MHC) class I inhibitor (brefeldin A) was carried out to investigate the role of suppressing Pira activity. We conclude that global pattern changes of common and distinct gene expressions may represent novel opportunities for better control of RA through early diagnosis and development of alternative therapeutic strategies.

Cell cycle‐specific function of Ikaros in human leukemia

The loss of Ikaros is associated with the development of B and T cell leukemia. Data on Ikaros function, including its role as a tumor suppressor and a regulator of cell cycle progression, come almost exclusively from murine studies; little is known of the mechanisms that regulate human Ikaros function. Our studies are the first to examine the function and regulation of human Ikaros isoforms during the cell cycle in human ALL. Electromobility shift assay (EMSA), confocal microscopy, and phosphopeptide mapping were used to study Ikaros function during different stages of the cell cycle. The DNA-binding activity of human Ikaros complexes undergoes dynamic changes as the cell cycle progresses. In S phase, Ikaros DNA-binding affinity for regulatory regions of its target genes decreases, while its binding to pericentromeric heterochromatin is preserved and correlates with Ikaros pericentromeric localization. These S phase-specific changes in Ikaros function are controlled by phosphorylation via the CK2 kinase pathway. During cell cycle progression, the subcellular pericentromeric localization of the largest human Ikaros isoforms is different from that in mouse cells, suggesting unique functions for human Ikaros. Our results demonstrate that the function of Ikaros is cell cycle-specific and controlled by CK2-mediated phosphorylation during S phase of the cell cycle in human T-cell and B-cell ALL. The differences we observe in murine and human Ikaros function highlight the importance of using human cells in studies of ALL. These data identify the CK2 pathway as a target for therapies in ALL.